From ae98ee0d962d64f15171966cb18b66a56d874992 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Fri, 2 Aug 2019 15:31:50 +1000 Subject: [PATCH 001/111] Set CICE output compression with history_deflate_level = 1; see https://github.com/COSIMA/cice5/issues/33 --- ice/cice_in.nml | 1 + 1 file changed, 1 insertion(+) diff --git a/ice/cice_in.nml b/ice/cice_in.nml index d7042c90..d62f7666 100644 --- a/ice/cice_in.nml +++ b/ice/cice_in.nml @@ -33,6 +33,7 @@ , hist_avg = .true. , history_dir = './OUTPUT/' , history_file = 'iceh' + , history_deflate_level = 1 , write_ic = .false. , incond_dir = './OUTPUT/' , incond_file = 'iceh_ic' From 23335e585457fbaa9c8d246d4597412519b6e45c Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Tue, 6 Aug 2019 15:50:42 +1000 Subject: [PATCH 002/111] use frazil_3d_int_z in diag_table - see https://github.com/COSIMA/access-om2/issues/139 --- ocean/diag_table | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/ocean/diag_table b/ocean/diag_table index ffbf720f..deb95ea7 100644 --- a/ocean/diag_table +++ b/ocean/diag_table @@ -7,7 +7,7 @@ ACCESS-OM2 # https://raw.githubusercontent.com/COSIMA/access-om2/master/MOM_diags.txt # https://github.com/COSIMA/access-om2/wiki/Technical-documentation#MOM5-diagnostics-list -#output files +# output files "ocean_month", 1, "months", 1, "days", "time", "ocean", 1, "months", 1, "days", "time", "ocean_grid", -1, "months", 1, "days", "time", @@ -69,6 +69,7 @@ ACCESS-OM2 "ocean_model","sfc_salt_flux_ice","sfc_salt_flux_ice","ocean_month","all",.true.,"none",2 "ocean_model","sfc_salt_flux_coupler","sfc_salt_flux_coupler","ocean_month","all",.true.,"none",2 "ocean_model","net_sfc_heating","net_sfc_heating", "ocean_month","all",.true.,"none",2 +"ocean_model","frazil_3d_int_z","frazil_3d_int_z", "ocean_month","all",.true.,"none",2 "ocean_model","tau_x","tau_x", "ocean_month","all",.true.,"none",2 "ocean_model","tau_y","tau_y", "ocean_month","all",.true.,"none",2 "ocean_model","bmf_u","bmf_u", "ocean_month","all",.true.,"none",2 From 8681ca954ec0e203fd456fbbe03aefa70fa16512 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Tue, 6 Aug 2019 16:14:32 +1000 Subject: [PATCH 003/111] disable net_sfc_heating and total_net_sfc_heating in diag_table - see https://github.com/COSIMA/access-om2/issues/139 --- ocean/diag_table | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/ocean/diag_table b/ocean/diag_table index deb95ea7..dc2fb7ce 100644 --- a/ocean/diag_table +++ b/ocean/diag_table @@ -68,7 +68,8 @@ ACCESS-OM2 "ocean_model","sfc_salt_flux_restore","sfc_salt_flux_restore","ocean_month","all",.true.,"none",2 "ocean_model","sfc_salt_flux_ice","sfc_salt_flux_ice","ocean_month","all",.true.,"none",2 "ocean_model","sfc_salt_flux_coupler","sfc_salt_flux_coupler","ocean_month","all",.true.,"none",2 -"ocean_model","net_sfc_heating","net_sfc_heating", "ocean_month","all",.true.,"none",2 +# see https://github.com/COSIMA/access-om2/issues/139 +# "ocean_model","net_sfc_heating","net_sfc_heating", "ocean_month","all",.true.,"none",2 "ocean_model","frazil_3d_int_z","frazil_3d_int_z", "ocean_month","all",.true.,"none",2 "ocean_model","tau_x","tau_x", "ocean_month","all",.true.,"none",2 "ocean_model","tau_y","tau_y", "ocean_month","all",.true.,"none",2 @@ -91,7 +92,8 @@ ACCESS-OM2 "ocean_model","total_ocean_heat","total_ocean_heat", "ocean_scalar","all",.true.,"none",1 "ocean_model","eta_global","eta_global", "ocean_scalar","all",.true.,"none",1 "ocean_model","total_ocean_sfc_salt_flux_coupler","total_ocean_sfc_salt_flux_coupler","ocean_scalar","all",.true.,"none",1 -"ocean_model","total_net_sfc_heating","total_net_sfc_heating","ocean_scalar","all",.true.,"none",1 +# see https://github.com/COSIMA/access-om2/issues/139 +# "ocean_model","total_net_sfc_heating","total_net_sfc_heating","ocean_scalar","all",.true.,"none",1 "ocean_model","total_ocean_pme_river","total_ocean_pme_river" ,"ocean_scalar","all",.true.,"none",1 "ocean_model","total_ocean_river","total_ocean_river" ,"ocean_scalar","all",.true.,"none",1 "ocean_model","total_ocean_runoff","total_ocean_runoff" ,"ocean_scalar","all",.true.,"none",1 From fa2b5b9011835122cba54a545c797567d95d47e8 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Wed, 7 Aug 2019 10:04:00 +1000 Subject: [PATCH 004/111] use use relative winds in CICE (highfreq=true) - see https://github.com/COSIMA/access-om2/issues/138 --- ice/cice_in.nml | 1 + 1 file changed, 1 insertion(+) diff --git a/ice/cice_in.nml b/ice/cice_in.nml index d62f7666..124c619b 100644 --- a/ice/cice_in.nml +++ b/ice/cice_in.nml @@ -175,6 +175,7 @@ , restore_ice = .false. , ustar_min = 0.0005 , tfrz_option = 'linear_salt' + , highfreq = .true. / &icefields_nml From b7b7921e443241cf915537d4ebbde49e484a3a84 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Thu, 8 Aug 2019 17:03:06 +1000 Subject: [PATCH 005/111] set zmax_pen = 1.0e6 (the default) in ocean/input.nml --- ocean/input.nml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ocean/input.nml b/ocean/input.nml index 938c11ff..061fd324 100644 --- a/ocean/input.nml +++ b/ocean/input.nml @@ -363,7 +363,7 @@ optics_morel_antoine = .false. read_chl = .true. use_this_module = .true. - zmax_pen = 300.0 + zmax_pen = 1.0e6 / &ocean_shortwave_jerlov_nml use_this_module = .false. From 4b696b69cac3d59ea71abd3a90688b9921bc087c Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Mon, 12 Aug 2019 12:01:06 +1000 Subject: [PATCH 006/111] more harmonisation across default configurations --- README.md | 4 ++++ accessom2.nml | 2 +- atmosphere/forcing.json | 2 +- config.yaml | 3 +-- 4 files changed, 7 insertions(+), 4 deletions(-) create mode 100644 README.md diff --git a/README.md b/README.md new file mode 100644 index 00000000..efe88a42 --- /dev/null +++ b/README.md @@ -0,0 +1,4 @@ +# 1deg_jra55_iaf +Standard configuration for 1 degree [ACCESS-OM2](https://github.com/COSIMA/access-om2) experiment (ACCESS-OM2-025) with JRA55-do interannual forcing (IAF). + +Note that the default timestep for this run is 5400 seconds, but you may need shorter timesteps during the first year of model equilibration. diff --git a/accessom2.nml b/accessom2.nml index 316838b7..5707cca8 100644 --- a/accessom2.nml +++ b/accessom2.nml @@ -9,5 +9,5 @@ ! Runtime for a single segment/job/submit, format is years, months, seconds, ! two of which must be zero. - restart_period = 1, 0, 0 + restart_period = 5, 0, 0 &end diff --git a/atmosphere/forcing.json b/atmosphere/forcing.json index f481505f..7b9f7ae3 100644 --- a/atmosphere/forcing.json +++ b/atmosphere/forcing.json @@ -1,5 +1,5 @@ { - "description": "JRA55-do V1.3 RYF 1990-91 forcing", + "description": "JRA55-do V1.3 IAF forcing", "inputs": [ { "filename": "/g/data1/ua8/JRA55-do/latest/rsds.{{year}}.nc", diff --git a/config.yaml b/config.yaml index 3f18d2c5..ef3377bd 100644 --- a/config.yaml +++ b/config.yaml @@ -50,6 +50,5 @@ qsub_flags: -lother=hyperthread -W umask=027 platform: nodesize: 28 -# DANGER! Do not uncomment this without checking the script is synching -# to the correct location! +# DANGER! Do not uncomment this without checking the script is synching to the correct location! # postscript: sync_output_to_gdata.sh From 3bd5382512c2d0f0baa9e5b2d72b7b58837d07f5 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Mon, 12 Aug 2019 13:31:24 +1000 Subject: [PATCH 007/111] set neutralrho_min=1028.0 and neutralrho_max=1038.0; see https://github.com/COSIMA/access-om2/issues/135 --- ocean/input.nml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ocean/input.nml b/ocean/input.nml index 061fd324..94316de4 100644 --- a/ocean/input.nml +++ b/ocean/input.nml @@ -130,8 +130,8 @@ eos_linear = .false. eos_preteos10 = .true. layer_nk = 80 - neutralrho_max = 1030.0 - neutralrho_min = 1020.0 + neutralrho_min = 1028.0 + neutralrho_max = 1038.0 potrho_max = 1038.0 potrho_min = 1028.0 / From 5cb4ac5a43655fa80adea49299522162c2ff9790 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Tue, 13 Aug 2019 13:37:32 +1000 Subject: [PATCH 008/111] Fix Rayleigh damping - see https://github.com/COSIMA/access-om2/issues/156 --- ocean/field_table | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/ocean/field_table b/ocean/field_table index 30cae142..730d954e 100644 --- a/ocean/field_table +++ b/ocean/field_table @@ -53,11 +53,11 @@ elon = 360.0 "units", "kg/kg" / "rayleigh_damp_table","ocean_mod","rayleigh_damp_table" -"rayleigh","Ombai","itable=44,jtable=111,ktable_1=1,ktable_2=29,rayleigh_damp_table=5400" -"rayleigh","Lombok","itable=36,jtable=112,ktable_1=1,ktable_2=19,rayleigh_damp_table=5400" -"rayleigh","Torres","itable=62,jtable=105,ktable_1=1,ktable_2=50,rayleigh_damp_table=5400" +"rayleigh","Lombok","itable=36,jtable=112,ktable_1=1,ktable_2=50,rayleigh_damp_table=5400" +"rayleigh","Ombai","itable=44,jtable=111,ktable_1=1,ktable_2=50,rayleigh_damp_table=5400" "rayleigh","Torres","itable=62,jtable=106,ktable_1=1,ktable_2=50,rayleigh_damp_table=5400" "rayleigh","Torres","itable=62,jtable=107,ktable_1=1,ktable_2=50,rayleigh_damp_table=5400" -"rayleigh","Torres","itable=62,jtable=108,ktable_1=1,ktable_2=50,rayleigh_damp_table=5400"/ +"rayleigh","Torres","itable=62,jtable=108,ktable_1=1,ktable_2=50,rayleigh_damp_table=5400" +"rayleigh","Torres","itable=62,jtable=109,ktable_1=1,ktable_2=50,rayleigh_damp_table=5400"/ From 3a725f960febfe7dbd7e06d72ca56d63ae61c707 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Wed, 21 Aug 2019 12:06:34 +1000 Subject: [PATCH 009/111] small tweaks --- config.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/config.yaml b/config.yaml index ef3377bd..ab594acd 100644 --- a/config.yaml +++ b/config.yaml @@ -1,7 +1,7 @@ # PBS configuration # If submitting to a different project to your default uncomment line below # and change project code as appropriate -# project: w35 +# project: v45 walltime: 1:00:00 jobname: 1deg_jra55_iaf @@ -42,7 +42,6 @@ stacksize: unlimited collate: exe: /short/public/access-om2/bin/mppnccombine walltime: 1:00:00 - queue: copyq mem: 4GB qsub_flags: -lother=hyperthread -W umask=027 From 937e1dca644b432360c20b7742e42fc67307fdd1 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Wed, 21 Aug 2019 12:48:41 +1000 Subject: [PATCH 010/111] README.md: add recommendation to watch repos --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index efe88a42..c106c9a1 100644 --- a/README.md +++ b/README.md @@ -2,3 +2,5 @@ Standard configuration for 1 degree [ACCESS-OM2](https://github.com/COSIMA/access-om2) experiment (ACCESS-OM2-025) with JRA55-do interannual forcing (IAF). Note that the default timestep for this run is 5400 seconds, but you may need shorter timesteps during the first year of model equilibration. + +**NOTE:** All ACCESS-OM2 model components and configurations are undergoing continual improvement. We strongly recommend that you "watch" this repo (see button at top of screen; ask to be notified of all conversations) and also watch [ACCESS-OM2](https://github.com/COSIMA/access-om2) and all the [component models](https://github.com/COSIMA/access-om2/tree/master/src), to be kept informed of updates, problems and bug fixes as they arise. From 474c510e15076c6ee233d0374115461b2c37f9b2 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Wed, 21 Aug 2019 13:05:00 +1000 Subject: [PATCH 011/111] README tweak --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index c106c9a1..9571e9ea 100644 --- a/README.md +++ b/README.md @@ -3,4 +3,4 @@ Standard configuration for 1 degree [ACCESS-OM2](https://github.com/COSIMA/acces Note that the default timestep for this run is 5400 seconds, but you may need shorter timesteps during the first year of model equilibration. -**NOTE:** All ACCESS-OM2 model components and configurations are undergoing continual improvement. We strongly recommend that you "watch" this repo (see button at top of screen; ask to be notified of all conversations) and also watch [ACCESS-OM2](https://github.com/COSIMA/access-om2) and all the [component models](https://github.com/COSIMA/access-om2/tree/master/src), to be kept informed of updates, problems and bug fixes as they arise. +**NOTE:** All ACCESS-OM2 model components and configurations are undergoing continual improvement. We strongly recommend that you "watch" this repo (see button at top of screen; ask to be notified of all conversations) and also watch [ACCESS-OM2](https://github.com/COSIMA/access-om2), all the [component models](https://github.com/COSIMA/access-om2/tree/master/src), and [payu](https://github.com/payu-org/payu) to be kept informed of updates, problems and bug fixes as they arise. From 04fac56c56b965ae8b0d5b5b6460823dd5d2e40b Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Wed, 21 Aug 2019 16:47:16 +1000 Subject: [PATCH 012/111] Use safer min_thickness = 1.0e-3; see https://github.com/COSIMA/access-om2/issues/161 --- ocean/input.nml | 1 + 1 file changed, 1 insertion(+) diff --git a/ocean/input.nml b/ocean/input.nml index 94316de4..bc653aa0 100644 --- a/ocean/input.nml +++ b/ocean/input.nml @@ -435,6 +435,7 @@ &ocean_time_filter_nml / &ocean_topog_nml + min_thickness = 1.0e-3 / &ocean_tracer_advect_nml debug_this_module = .false. From 55837b7f30b7641acd39b857ddac848d24a2e8d7 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Thu, 3 Oct 2019 15:26:39 +1000 Subject: [PATCH 013/111] Don't compress MOM outputs/restarts until collation - https://github.com/COSIMA/access-om2/issues/168 --- config.yaml | 9 ++++++--- ocean/input.nml | 2 +- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/config.yaml b/config.yaml index e37e185a..ffd779a9 100644 --- a/config.yaml +++ b/config.yaml @@ -40,9 +40,12 @@ submodels: runlog: true stacksize: unlimited collate: - exe: /short/public/access-om2/bin/mppnccombine - walltime: 1:00:00 - mem: 4GB + walltime: 1:00:00 + mem: 30GB + ncpus: 4 + queue: express + restart: True + exe: /short/public/access-om2/bin/mppnccombine qsub_flags: -lother=hyperthread -W umask=027 # Following two lines required for broadwell queues diff --git a/ocean/input.nml b/ocean/input.nml index bc653aa0..582f0b91 100644 --- a/ocean/input.nml +++ b/ocean/input.nml @@ -43,7 +43,7 @@ neutral = .true. / &mpp_io_nml - deflate_level = 5 + deflate_level = -1 shuffle = 1 / &ocean_adv_vel_diag_nml From ebf3623de34a7485f33dd9db02907fca020b01d7 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Thu, 31 Oct 2019 14:15:34 +1100 Subject: [PATCH 014/111] added tidy_restarts.py --- tidy_restarts.py | 71 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100755 tidy_restarts.py diff --git a/tidy_restarts.py b/tidy_restarts.py new file mode 100755 index 00000000..290da3f6 --- /dev/null +++ b/tidy_restarts.py @@ -0,0 +1,71 @@ +#!/usr/bin/env python +""" + +Tidy up restart directories - see argparse desciption below. + +This is best used with restart_freq: 1 in config.yaml. + +Author: Andrew Kiss, ANU + +""" + +from __future__ import print_function +import os +import sys +from glob import glob + +def tidy(yearskip=1, keeplast=6): + yearskip = abs(yearskip) + keeplast = max(1, abs(keeplast)) # always keep the last restart + restarts = glob('archive/restart???') + restarts.sort() + + keptyear = None + for r in restarts[:-keeplast]: # don't touch the most recent |keeplast| restarts + try: + fn = os.path.join(r, 'ocean/ocean_solo.res') + with open(fn, 'r') as f: + lineList = f.readlines() + year = int(lineList[-1].split()[0]) # the year of the final time in the run + if (keptyear is not None) and (year < keptyear+yearskip): + print('Moving ' + r + ' to ' + r.replace('archive', 'archive/CHUCKABLE')) + os.renames(r, r.replace('archive', 'archive/CHUCKABLE')) + else: # always keep the earliest restart, so tidy has a consistent reference point + print('Keeping ' + r + ': ending time is' + lineList[-1], end='') + keptyear = year + except: + print('Error in', fn+':', sys.exc_info()) + + for r in restarts[-keeplast:]: # this just reports dates of the most recent |keeplast| restarts + try: + fn = os.path.join(r, 'ocean/ocean_solo.res') + with open(fn, 'r') as f: + lineList = f.readlines() + print('Keeping ' + r + ': ending time is' + lineList[-1], end='') + except: + print('Error in', fn+':', sys.exc_info()) + + print("Note: it's up to you to delete anything moved to archive/CHUCKABLE") + + +if __name__ == '__main__': + import argparse + parser = argparse.ArgumentParser(description= + 'Tidy up restart directories, keeping only the most recent \ + --keep-last restarts and the first \ + restart each --year-skip years (counting from the earliest forward, \ + keeping the last one written from the previous year, \ + dated 1 Jan 00:00:00, if available), \ + and moving the rest to archive/CHUCKABLE/ \ + from which the user can delete them manually if needed. \ + This is best used with restart_freq: 1 in config.yaml.') + parser.add_argument('-y', '--year-skip', type=int, + metavar='n', default=1, + help="keep one restart every n years") + parser.add_argument('-k', '--keep-last', type=int, + metavar='n', default=6, + help="keep last n restarts") + args = parser.parse_args() + yearskip = vars(args)['year_skip'] + keeplast = vars(args)['keep_last'] + tidy(yearskip=yearskip, keeplast=keeplast) From bbff9d62b253776998dcedb7693cef4e5851473a Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Tue, 10 Dec 2019 10:24:10 +1100 Subject: [PATCH 015/111] remove trailing comma in atmosphere/forcing.json --- atmosphere/forcing.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/atmosphere/forcing.json b/atmosphere/forcing.json index 7b9f7ae3..54519b12 100644 --- a/atmosphere/forcing.json +++ b/atmosphere/forcing.json @@ -50,7 +50,7 @@ "filename": "/g/data1/ua8/JRA55-do/latest/v_10.{{year}}.nc", "fieldname": "vas_10m", "cname": "vwnd_ai" - }, + } ] } From cd05771dd57984d83dd3e0473a498a6e13477cb4 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Mon, 16 Dec 2019 14:46:21 +1100 Subject: [PATCH 016/111] use input_rc for inputs (temporary - for testing) --- config.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/config.yaml b/config.yaml index cee8c61a..18c76620 100644 --- a/config.yaml +++ b/config.yaml @@ -14,13 +14,13 @@ mem: 500GB # Model configuration name: common model: access-om2 -input: /g/data4/ik11/inputs/access-om2/input_236a3011/common_1deg_jra55 +input: /g/data4/ik11/inputs/access-om2/input_rc/common_1deg_jra55 submodels: - name: atmosphere model: yatm exe: /g/data4/ik11/inputs/access-om2/bin/yatm_1bb8904.exe input: - - /g/data4/ik11/inputs/access-om2/input_236a3011/yatm_1deg + - /g/data4/ik11/inputs/access-om2/input_rc/yatm_1deg - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-3/atmos/3hr/rsds/gn/v20180412/rsds - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-3/atmos/3hr/rlds/gn/v20180412/rlds - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-3/atmos/3hr/prra/gn/v20180412/prra @@ -36,13 +36,13 @@ submodels: - name: ocean model: mom exe: /g/data4/ik11/inputs/access-om2/bin/fms_ACCESS-OM_97e3429_libaccessom2_1bb8904.x - input: /g/data4/ik11/inputs/access-om2/input_236a3011/mom_1deg + input: /g/data4/ik11/inputs/access-om2/input_rc/mom_1deg ncpus: 216 - name: ice model: cice5 exe: /g/data4/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_b37ea14_libaccessom2_1bb8904.exe - input: /g/data4/ik11/inputs/access-om2/input_236a3011/cice_1deg + input: /g/data4/ik11/inputs/access-om2/input_rc/cice_1deg ncpus: 24 # Collation From 547eddf6dc5dc24a52eb02d60b7e3d1ad72a82ac Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Tue, 17 Dec 2019 18:51:16 +1100 Subject: [PATCH 017/111] increase memory request for sync_output_to_gdata.sh from 2Gb to 4Gb --- sync_output_to_gdata.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sync_output_to_gdata.sh b/sync_output_to_gdata.sh index bfc53f5f..96e30e0e 100755 --- a/sync_output_to_gdata.sh +++ b/sync_output_to_gdata.sh @@ -2,7 +2,7 @@ #PBS -q copyq #PBS -l ncpus=1 #PBS -l wd -#PBS -l walltime=1:00:00,mem=2GB +#PBS -l walltime=1:00:00,mem=4GB #PBS -P v45 #PBS -N output_to_gdata From c093ff71fd83de7cbf175aeda40e434c71396fa3 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Fri, 20 Dec 2019 16:09:59 +1100 Subject: [PATCH 018/111] revert cice commit https://github.com/COSIMA/cice5/commit/ab473434 - see https://github.com/COSIMA/cice5/issues/38 --- config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config.yaml b/config.yaml index 18c76620..0497b0df 100644 --- a/config.yaml +++ b/config.yaml @@ -41,7 +41,7 @@ submodels: - name: ice model: cice5 - exe: /g/data4/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_b37ea14_libaccessom2_1bb8904.exe + exe: /g/data4/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_d3e8bdf_libaccessom2_1bb8904.exe input: /g/data4/ik11/inputs/access-om2/input_rc/cice_1deg ncpus: 24 From 307e3a290ce21d9675e069a78016ca9e6655edc2 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Mon, 13 Jan 2020 10:13:28 +1100 Subject: [PATCH 019/111] sync_output_to_gdata.sh: set PBS flag for storage on gadi; exit if paths inaccessible --- sync_output_to_gdata.sh | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/sync_output_to_gdata.sh b/sync_output_to_gdata.sh index 96e30e0e..28a084a6 100755 --- a/sync_output_to_gdata.sh +++ b/sync_output_to_gdata.sh @@ -4,6 +4,7 @@ #PBS -l wd #PBS -l walltime=1:00:00,mem=4GB #PBS -P v45 +#PBS -l storage=gdata/hh5+scratch/v45 #PBS -N output_to_gdata # Set this directory to something in /g/data3/hh5/tmp/cosima/ @@ -11,8 +12,8 @@ # DOUBLE-CHECK IT IS UNIQUE SO YOU DON'T OVERWRITE EXISTING OUTPUT! GDATADIR=/ERROR/SET/GDATADIR/IN/sync_output_to_gdata.sh -mkdir -p ${GDATADIR} -cd archive +mkdir -p ${GDATADIR} || exit 1 +cd archive || exit 1 rsync --exclude "*.nc.*" --exclude "ocean_daily_3d_*" --exclude "*ocean_*_3hourly*" --exclude "*iceh_03h*" -vrltoD --safe-links output* ${GDATADIR} rsync -vrltoD --safe-links error_logs ${GDATADIR} rsync -vrltoD --safe-links pbs_logs ${GDATADIR} From 2ea5aa914d1bf225a98ccdc2b469b530c21a9d25 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Wed, 15 Jan 2020 09:30:40 +1100 Subject: [PATCH 020/111] combine sync_output_to_gdata.sh, sync_restarts_to_gdata.sh, RM_SYNCHED_OUTPUT.sh into sync_to_gdata.sh and also copy git history. Closes https://github.com/COSIMA/access-om2/issues/171 --- RM_SYNCHED_OUTPUT.sh | 33 ------------- config.yaml | 2 +- sync_output_to_gdata.sh | 19 ------- sync_restarts_to_gdata.sh | 11 ----- sync_to_gdata.sh | 101 ++++++++++++++++++++++++++++++++++++++ 5 files changed, 102 insertions(+), 64 deletions(-) delete mode 100755 RM_SYNCHED_OUTPUT.sh delete mode 100755 sync_output_to_gdata.sh delete mode 100755 sync_restarts_to_gdata.sh create mode 100755 sync_to_gdata.sh diff --git a/RM_SYNCHED_OUTPUT.sh b/RM_SYNCHED_OUTPUT.sh deleted file mode 100755 index 41a2ebdd..00000000 --- a/RM_SYNCHED_OUTPUT.sh +++ /dev/null @@ -1,33 +0,0 @@ -#!/bin/bash -#PBS -q copyq -#PBS -l ncpus=1 -#PBS -l wd -#PBS -l walltime=1:00:00,mem=2GB -#PBS -P v45 -#PBS -N RM_SYNCHED_OUTPUT - -# This script will sync output to g/data and then remove from archive everything that was successfully synced. -# It should be run interactively. -# It doesn't sync or remove restarts. - -# NB: from -# https://download.samba.org/pub/rsync/rsync.html -# --remove-source-files -# This tells rsync to remove from the sending side the files (meaning non-directories) that are a part of the transfer and have been successfully duplicated on the receiving side. -# Note that you should only use this option on source files that are quiescent. If you are using this to move files that show up in a particular directory over to another host, make sure that the finished files get renamed into the source directory, not directly written into it, so that rsync can't possibly transfer a file that is not yet fully written. If you can't first write the files into a different directory, you should use a naming idiom that lets rsync avoid transferring files that are not yet finished (e.g. name the file "foo.new" when it is written, rename it to "foo" when it is done, and then use the option --exclude='*.new' for the rsync transfer). -# -# Starting with 3.1.0, rsync will skip the sender-side removal (and output an error) if the file's size or modify time has not stayed unchanged. - -# As of 14 Sep 2018, raijin has rsync version 3.0.6 so we don't have this protection! -# So include this little warning. - -echo "WARNING: do not proceed if there are any running jobs or collations underway." -read -p "Proceed? (y/n) " yesno -case $yesno in - [Yy] ) break;; - * ) echo "Cancelled. Wait until all jobs are finished before trying again."; exit 0;; -esac - -source sync_output_to_gdata.sh # to define GDATADIR and cd archive - -rsync --remove-source-files --exclude "*.nc.*" --exclude "ocean_daily_3d_*" --exclude "*ocean_*_3hourly*" --exclude "*iceh_03h*" -vrltoD --safe-links output??? ${GDATADIR} diff --git a/config.yaml b/config.yaml index 0497b0df..20ed78d8 100644 --- a/config.yaml +++ b/config.yaml @@ -62,4 +62,4 @@ platform: nodesize: 48 # DANGER! Do not uncomment this without checking the script is synching to the correct location! -# postscript: sync_output_to_gdata.sh +# postscript: sync_to_gdata.sh diff --git a/sync_output_to_gdata.sh b/sync_output_to_gdata.sh deleted file mode 100755 index 28a084a6..00000000 --- a/sync_output_to_gdata.sh +++ /dev/null @@ -1,19 +0,0 @@ -#!/bin/bash -#PBS -q copyq -#PBS -l ncpus=1 -#PBS -l wd -#PBS -l walltime=1:00:00,mem=4GB -#PBS -P v45 -#PBS -l storage=gdata/hh5+scratch/v45 -#PBS -N output_to_gdata - -# Set this directory to something in /g/data3/hh5/tmp/cosima/ -# Make a unique path for your set of runs. -# DOUBLE-CHECK IT IS UNIQUE SO YOU DON'T OVERWRITE EXISTING OUTPUT! -GDATADIR=/ERROR/SET/GDATADIR/IN/sync_output_to_gdata.sh - -mkdir -p ${GDATADIR} || exit 1 -cd archive || exit 1 -rsync --exclude "*.nc.*" --exclude "ocean_daily_3d_*" --exclude "*ocean_*_3hourly*" --exclude "*iceh_03h*" -vrltoD --safe-links output* ${GDATADIR} -rsync -vrltoD --safe-links error_logs ${GDATADIR} -rsync -vrltoD --safe-links pbs_logs ${GDATADIR} diff --git a/sync_restarts_to_gdata.sh b/sync_restarts_to_gdata.sh deleted file mode 100755 index a735c061..00000000 --- a/sync_restarts_to_gdata.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/bash -#PBS -q copyq -#PBS -l ncpus=1 -#PBS -l wd -#PBS -l walltime=2:00:00,mem=2GB -#PBS -P v45 -#PBS -N restarts_to_gdata - -source sync_output_to_gdata.sh # to define GDATADIR and cd archive - -rsync -av --safe-links --no-g restart* ${GDATADIR} diff --git a/sync_to_gdata.sh b/sync_to_gdata.sh new file mode 100755 index 00000000..3612d88a --- /dev/null +++ b/sync_to_gdata.sh @@ -0,0 +1,101 @@ +#!/bin/bash +#PBS -q copyq +#PBS -l ncpus=1 +#PBS -l wd +#PBS -l walltime=4:00:00,mem=4GB +#PBS -P v45 +#PBS -l storage=gdata/hh5+scratch/v45 +#PBS -N sync + +# Set this directory to something in /g/data3/hh5/tmp/cosima/ +# Make a unique path for your set of runs. Must be an absolute path. +# DOUBLE-CHECK IT IS UNIQUE SO YOU DON'T OVERWRITE EXISTING OUTPUT! +GDATADIR=/ERROR/SET/GDATADIR/IN/sync_to_gdata.sh + +exitcode=0 +help=false +restarts=false +rmlocal=false + +# parse argument list +while [ $# -ge 1 ]; do + case $1 in + -h) + help=true + ;; + -r) + echo "syncing restarts instead of output directories" + restarts=true + ;; + -D) + # --remove-source-files tells rsync to remove from the sending side the files (meaning non-directories) + # that are a part of the transfer and have been successfully duplicated on the receiving side. + # This option should only be used on source files that are quiescent. + # Require interaction here to avoid syncing and removing partially-written files. + echo "DELETING LOCAL COPIES OF SYNCED FILES!" + echo "WARNING: to avoid losing data, do not proceed if there are any running jobs or collations underway." + read -p "Proceed? (y/n) " yesno + case $yesno in + [Yy] ) rmlocal=true;; + * ) echo "Cancelled. Wait until all jobs are finished before trying again."; exit 0;; + esac + ;; + -*) + echo $1": invalid option" + help=true + exitcode=1 + ;; + *) + echo $1": invalid argument" + help=true + exitcode=1 + ;; + esac + shift +done + +if [ $exitcode != "0" -o $help == true ]; then + echo $0": rsync model run outputs (and optionally restarts) to /g/data" + echo " Must be invoked from a control directory." + echo " "$0" should be edited to set GDATADIR." + echo " Default will rsync all output directories, leaving local copies intact." + echo " Also rsyncs error_logs and pbs_logs." + echo " Also updates git-runlog, a git clone of the control directory (whose git history documents all changes in the run)." + echo "usage: "$0" [-h] [-r] [-D]" + echo " -h: show this help message and exit" + echo " -r: sync all restart directories (default syncs output directories)" + echo " -D: delete local copies of synced files in all but the most recent synced directories (outputs or restarts, depending on -r). Must be done interactively. (Default leaves local copies intact.)" + exit $exitcode +fi + +sourcepath="$PWD" +mkdir -p ${GDATADIR} || exit 1 +cd archive || exit 1 + +if [ $restarts == true ]; then + # only sync/remove restarts + rsync -vrltoD --safe-links restart* ${GDATADIR} + if [ $rmlocal == true ]; then + # Now do removals. Don't remove final local copy, so we can continue run. + rsync --remove-source-files --exclude `\ls -1d restart[0-9][0-9][0-9] | tail -1` -vrltoD --safe-links restart* ${GDATADIR} + fi +else + # default - only sync/remove outputs + rsync --exclude "*.nc.*" --exclude "ocean_daily_3d_*" --exclude "*ocean_*_3hourly*" --exclude "*iceh_03h*" -vrltoD --safe-links output* ${GDATADIR} + if [ $rmlocal == true ]; then + # Now do removals. Don't remove final local copy, so we can continue run. + rsync --remove-source-files --exclude `\ls -1d output[0-9][0-9][0-9] | tail -1` --exclude "*.nc.*" --exclude "ocean_daily_3d_*" --exclude "*ocean_*_3hourly*" --exclude "*iceh_03h*" -vrltoD --safe-links output* ${GDATADIR} + fi +fi + +# Also sync error and PBS logs +rsync -vrltoD --safe-links error_logs ${GDATADIR} +rsync -vrltoD --safe-links pbs_logs ${GDATADIR} + +# create/update a clone of the run history in ${GDATADIR}/git-runlog +cd ${GDATADIR} || exit 1 +ls git-runlog || git clone $sourcepath git-runlog +cd git-runlog +git pull + +echo $0" completed successfully" \ No newline at end of file From e92b9109e553eee56ce6f123c4f668c801cb092d Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Mon, 24 Feb 2020 16:36:40 +1100 Subject: [PATCH 021/111] fix /g/data paths for gadi - https://github.com/COSIMA/access-om2/issues/188 --- config.yaml | 16 +- manifests/exe.yaml | 18 - manifests/input.yaml | 3249 --------------------------------------- manifests/restart.yaml | 3 - sync_output_to_gdata.sh | 2 +- 5 files changed, 9 insertions(+), 3279 deletions(-) delete mode 100644 manifests/exe.yaml delete mode 100644 manifests/input.yaml delete mode 100644 manifests/restart.yaml diff --git a/config.yaml b/config.yaml index cb700d77..a42a9007 100644 --- a/config.yaml +++ b/config.yaml @@ -14,13 +14,13 @@ mem: 500GB # Model configuration name: common model: access-om2 -input: /g/data4/ik11/inputs/access-om2/input_236a3011/common_1deg_jra55 +input: /g/data/ik11/inputs/access-om2/input_236a3011/common_1deg_jra55 submodels: - name: atmosphere model: yatm - exe: /g/data4/ik11/inputs/access-om2/bin/yatm_575fb04.exe + exe: /g/data/ik11/inputs/access-om2/bin/yatm_575fb04.exe input: - - /g/data4/ik11/inputs/access-om2/input_236a3011/yatm_1deg + - /g/data/ik11/inputs/access-om2/input_236a3011/yatm_1deg - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-3/atmos/3hr/rsds/gn/v20180412/rsds - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-3/atmos/3hr/rlds/gn/v20180412/rlds - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-3/atmos/3hr/prra/gn/v20180412/prra @@ -35,14 +35,14 @@ submodels: - name: ocean model: mom - exe: /g/data4/ik11/inputs/access-om2/bin/fms_ACCESS-OM_4a2f211_libaccessom2_575fb04.x - input: /g/data4/ik11/inputs/access-om2/input_236a3011/mom_1deg + exe: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM_4a2f211_libaccessom2_575fb04.x + input: /g/data/ik11/inputs/access-om2/input_236a3011/mom_1deg ncpus: 216 - name: ice model: cice5 - exe: /g/data4/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_365bdc1_libaccessom2_575fb04.exe - input: /g/data4/ik11/inputs/access-om2/input_236a3011/cice_1deg + exe: /g/data/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_365bdc1_libaccessom2_575fb04.exe + input: /g/data/ik11/inputs/access-om2/input_236a3011/cice_1deg ncpus: 24 # Collation @@ -51,7 +51,7 @@ collate: mem: 30GB ncpus: 4 queue: express - exe: /g/data4/ik11/inputs/access-om2/bin/mppnccombine + exe: /g/data/ik11/inputs/access-om2/bin/mppnccombine # Misc runlog: true diff --git a/manifests/exe.yaml b/manifests/exe.yaml deleted file mode 100644 index fd9a5195..00000000 --- a/manifests/exe.yaml +++ /dev/null @@ -1,18 +0,0 @@ -format: yamanifest -version: 1.0 ---- -work/atmosphere/yatm_17bed6f.exe: - fullpath: /g/data4/ik11/inputs/access-om2/bin/yatm_17bed6f.exe - hashes: - binhash: a7bfde502102b7338d9e2e380cab879d - md5: b33db988be3a98b97d735378655d59d8 -work/ice/cice_auscom_360x300_24p_b37ea14_libaccessom2_17bed6f.exe: - fullpath: /g/data4/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_b37ea14_libaccessom2_17bed6f.exe - hashes: - binhash: 1df4768e6d6b901d98e0c6ee23b621e6 - md5: 5fa2f7b1e0232adf202d41f89a3be67c -work/ocean/fms_ACCESS-OM_66a3e59_libaccessom2_17bed6f.x: - fullpath: /g/data4/ik11/inputs/access-om2/bin/fms_ACCESS-OM_66a3e59_libaccessom2_17bed6f.x - hashes: - binhash: dd16be873a3b757f9f8a5f5b120af7bc - md5: f22ba28134ddc3abb7d9fd3be420b5de diff --git a/manifests/input.yaml b/manifests/input.yaml deleted file mode 100644 index 1f0373f4..00000000 --- a/manifests/input.yaml +++ /dev/null @@ -1,3249 +0,0 @@ -format: yamanifest -version: 1.0 ---- -work/INPUT/rmp_jra55_cice_conserve.nc: - fullpath: /g/data4/ik11/inputs/access-om2/input_236a3011/common_1deg_jra55/rmp_jra55_cice_conserve.nc - hashes: - binhash: 67c1bf5bd80f5b0809560e037dec88b9 - md5: 79885c8149d65a55d093244935f62360 -work/INPUT/rmp_jra55_cice_smooth.nc: - fullpath: /g/data4/ik11/inputs/access-om2/input_236a3011/common_1deg_jra55/rmp_jra55_cice_smooth.nc - hashes: - binhash: f6421cbcbda8b0f664f9bda94ce9c17c - md5: aa91ea2e3cdef04f58ed5db8f8d7de6d -work/atmosphere/INPUT/ncar_precip.0001.nc: - fullpath: /g/data4/ik11/inputs/access-om2/input_236a3011/yatm_1deg/ncar_precip.0001.nc - hashes: - binhash: 7aa17263c4d1b83ace0e6a631272eb7a - md5: 502be1947e13269dedff21d34e34a543 -work/atmosphere/INPUT/ncar_rad.0001.nc: - fullpath: /g/data4/ik11/inputs/access-om2/input_236a3011/yatm_1deg/ncar_rad.0001.nc - hashes: - binhash: 2a40d7b173ae746b1b1d8b67c4cf7e80 - md5: 4d3d3e3d26f9d558411847d4f34579c8 -work/atmosphere/INPUT/q_10.0001.nc: - fullpath: /g/data4/ik11/inputs/access-om2/input_236a3011/yatm_1deg/q_10.0001.nc - hashes: - binhash: 6a695ee13231ff0816ace4fd2609242a - md5: d9f27d865c8e86a5f5bc2576b3805c52 -work/atmosphere/INPUT/q_10.1958.nc: - 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md5: d95d45424492bad16d647c104e78b442 -work/ocean/INPUT/ssw_atten_depth.nc: - fullpath: /g/data4/ik11/inputs/access-om2/input_236a3011/mom_1deg/ssw_atten_depth.nc - hashes: - binhash: 9c2178dc209cfe84dce1b81be793cead - md5: 6142db126b8d2c8d8f4b6fb0e05d60c5 -work/ocean/INPUT/temp_sfc_restore.nc: - fullpath: /g/data4/ik11/inputs/access-om2/input_236a3011/mom_1deg/temp_sfc_restore.nc - hashes: - binhash: 3f65be76fc6b5b3830632e35cc2c1373 - md5: e5f54b9a2392f660f0b3774802f2a84c -work/ocean/INPUT/tideamp.nc: - fullpath: /g/data4/ik11/inputs/access-om2/input_236a3011/mom_1deg/tideamp.nc - hashes: - binhash: 4c3394bb168774fb4362826996c74bcb - md5: b2840af757d9b7b40207f33f1fc84c5c -work/ocean/INPUT/topog.nc: - fullpath: /g/data4/ik11/inputs/access-om2/input_236a3011/mom_1deg/topog.nc - hashes: - binhash: 86a9468fa56d6b3c5612c919618efab3 - md5: f01ddc02cfe21d8db99c2976e9fcc828 diff --git a/manifests/restart.yaml b/manifests/restart.yaml deleted file mode 100644 index f1e1197c..00000000 --- a/manifests/restart.yaml +++ /dev/null @@ -1,3 +0,0 @@ -format: yamanifest -version: 1.0 ---- {} diff --git a/sync_output_to_gdata.sh b/sync_output_to_gdata.sh index 3d6312a5..f7b71fe6 100755 --- a/sync_output_to_gdata.sh +++ b/sync_output_to_gdata.sh @@ -7,7 +7,7 @@ #PBS -l storage=gdata/hh5+scratch/v45 #PBS -N output_to_gdata -# Set this directory to something in /g/data3/hh5/tmp/cosima/ +# Set this directory to something in /g/data/hh5/tmp/cosima/ # Make a unique path for your set of runs. # DOUBLE-CHECK IT IS UNIQUE SO YOU DON'T OVERWRITE EXISTING OUTPUT! GDATADIR=/ERROR/SET/GDATADIR/IN/sync_output_to_gdata.sh From f179a144047e0939cf41e7afd04cfd6ea0e27695 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Mon, 16 Mar 2020 15:15:35 +1100 Subject: [PATCH 022/111] remove references to /g/data3 --- sync_to_gdata.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sync_to_gdata.sh b/sync_to_gdata.sh index 3612d88a..6765a59e 100755 --- a/sync_to_gdata.sh +++ b/sync_to_gdata.sh @@ -7,7 +7,7 @@ #PBS -l storage=gdata/hh5+scratch/v45 #PBS -N sync -# Set this directory to something in /g/data3/hh5/tmp/cosima/ +# Set this directory to something in /g/data/hh5/tmp/cosima/ # Make a unique path for your set of runs. Must be an absolute path. # DOUBLE-CHECK IT IS UNIQUE SO YOU DON'T OVERWRITE EXISTING OUTPUT! GDATADIR=/ERROR/SET/GDATADIR/IN/sync_to_gdata.sh From 58a942462f762053feb89f843fc689232642c776 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Wed, 18 Mar 2020 09:25:32 +1100 Subject: [PATCH 023/111] stop using qsub_flags: -lother=hyperthread - see https://github.com/COSIMA/access-om2/issues/191 --- config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config.yaml b/config.yaml index 3aaeeb1e..c0996e73 100644 --- a/config.yaml +++ b/config.yaml @@ -56,7 +56,7 @@ collate: # Misc runlog: true stacksize: unlimited -qsub_flags: -lother=hyperthread -W umask=027 +qsub_flags: -W umask=027 # set number of cores per node (28 for normalbw, 48 for normal on gadi) platform: nodesize: 48 From b6367451bda1b525eaa2a3d76384e80dacdefab6 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Thu, 19 Mar 2020 21:37:13 +1100 Subject: [PATCH 024/111] rename sync_to_gdata.sh to sync_data.sh and recommend syncing to /g/data/ik11 rather than hh5 --- config.yaml | 2 +- sync_to_gdata.sh => sync_data.sh | 34 +++++++++++++++++--------------- 2 files changed, 19 insertions(+), 17 deletions(-) rename sync_to_gdata.sh => sync_data.sh (77%) diff --git a/config.yaml b/config.yaml index c0996e73..6ac3ef60 100644 --- a/config.yaml +++ b/config.yaml @@ -66,4 +66,4 @@ qsub_flags: -l storage=gdata/hh5+gdata/qv56+gdata/ik11+gdata/ua8 # DANGER! Do not uncomment this without checking the script is synching # to the correct location! -# postscript: sync_to_gdata.sh +# postscript: sync_data.sh diff --git a/sync_to_gdata.sh b/sync_data.sh similarity index 77% rename from sync_to_gdata.sh rename to sync_data.sh index 6765a59e..d4f82481 100755 --- a/sync_to_gdata.sh +++ b/sync_data.sh @@ -4,13 +4,15 @@ #PBS -l wd #PBS -l walltime=4:00:00,mem=4GB #PBS -P v45 -#PBS -l storage=gdata/hh5+scratch/v45 +#PBS -l storage=gdata/hh5+gdata/ik11+scratch/v45 #PBS -N sync -# Set this directory to something in /g/data/hh5/tmp/cosima/ -# Make a unique path for your set of runs. Must be an absolute path. -# DOUBLE-CHECK IT IS UNIQUE SO YOU DON'T OVERWRITE EXISTING OUTPUT! -GDATADIR=/ERROR/SET/GDATADIR/IN/sync_to_gdata.sh +# Set SYNCDIR to the path you want your data copied to. +# This must be a unique absolute path for your set of runs. +# If you want to share your data, use SYNCDIR=/g/data/ik11/outputs/ +# but first add an experiment description - see /g/data/ik11/outputs/README +# DOUBLE-CHECK SYNCDIR PATH IS UNIQUE SO YOU DON'T OVERWRITE EXISTING OUTPUT! +SYNCDIR=/ERROR/SET/SYNCDIR/IN/sync_data.sh exitcode=0 help=false @@ -55,9 +57,9 @@ while [ $# -ge 1 ]; do done if [ $exitcode != "0" -o $help == true ]; then - echo $0": rsync model run outputs (and optionally restarts) to /g/data" + echo $0": rsync model run outputs (and optionally restarts) to another location." echo " Must be invoked from a control directory." - echo " "$0" should be edited to set GDATADIR." + echo " "$0" should be edited to set SYNCDIR." echo " Default will rsync all output directories, leaving local copies intact." echo " Also rsyncs error_logs and pbs_logs." echo " Also updates git-runlog, a git clone of the control directory (whose git history documents all changes in the run)." @@ -69,31 +71,31 @@ if [ $exitcode != "0" -o $help == true ]; then fi sourcepath="$PWD" -mkdir -p ${GDATADIR} || exit 1 +mkdir -p ${SYNCDIR} || exit 1 cd archive || exit 1 if [ $restarts == true ]; then # only sync/remove restarts - rsync -vrltoD --safe-links restart* ${GDATADIR} + rsync -vrltoD --safe-links restart* ${SYNCDIR} if [ $rmlocal == true ]; then # Now do removals. Don't remove final local copy, so we can continue run. - rsync --remove-source-files --exclude `\ls -1d restart[0-9][0-9][0-9] | tail -1` -vrltoD --safe-links restart* ${GDATADIR} + rsync --remove-source-files --exclude `\ls -1d restart[0-9][0-9][0-9] | tail -1` -vrltoD --safe-links restart* ${SYNCDIR} fi else # default - only sync/remove outputs - rsync --exclude "*.nc.*" --exclude "ocean_daily_3d_*" --exclude "*ocean_*_3hourly*" --exclude "*iceh_03h*" -vrltoD --safe-links output* ${GDATADIR} + rsync --exclude "*.nc.*" --exclude "ocean_daily_3d_*" --exclude "*ocean_*_3hourly*" --exclude "*iceh_03h*" -vrltoD --safe-links output* ${SYNCDIR} if [ $rmlocal == true ]; then # Now do removals. Don't remove final local copy, so we can continue run. - rsync --remove-source-files --exclude `\ls -1d output[0-9][0-9][0-9] | tail -1` --exclude "*.nc.*" --exclude "ocean_daily_3d_*" --exclude "*ocean_*_3hourly*" --exclude "*iceh_03h*" -vrltoD --safe-links output* ${GDATADIR} + rsync --remove-source-files --exclude `\ls -1d output[0-9][0-9][0-9] | tail -1` --exclude "*.nc.*" --exclude "ocean_daily_3d_*" --exclude "*ocean_*_3hourly*" --exclude "*iceh_03h*" -vrltoD --safe-links output* ${SYNCDIR} fi fi # Also sync error and PBS logs -rsync -vrltoD --safe-links error_logs ${GDATADIR} -rsync -vrltoD --safe-links pbs_logs ${GDATADIR} +rsync -vrltoD --safe-links error_logs ${SYNCDIR} +rsync -vrltoD --safe-links pbs_logs ${SYNCDIR} -# create/update a clone of the run history in ${GDATADIR}/git-runlog -cd ${GDATADIR} || exit 1 +# create/update a clone of the run history in ${SYNCDIR}/git-runlog +cd ${SYNCDIR} || exit 1 ls git-runlog || git clone $sourcepath git-runlog cd git-runlog git pull From 39152c398fd314db3b9f23de7ad5a974cfd2e1fc Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Fri, 20 Mar 2020 14:12:05 +1100 Subject: [PATCH 025/111] remove payu workaround for gadi storage issue - see https://github.com/payu-org/payu/issues/215 --- config.yaml | 3 --- 1 file changed, 3 deletions(-) diff --git a/config.yaml b/config.yaml index 6ac3ef60..40e539a1 100644 --- a/config.yaml +++ b/config.yaml @@ -61,9 +61,6 @@ qsub_flags: -W umask=027 platform: nodesize: 48 -# payu bug workaround for gadi - see https://github.com/payu-org/payu/issues/215 -qsub_flags: -l storage=gdata/hh5+gdata/qv56+gdata/ik11+gdata/ua8 - # DANGER! Do not uncomment this without checking the script is synching # to the correct location! # postscript: sync_data.sh From 4d879941a5cdd1cdd2efe6354be9502ee7f3ff1b Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Thu, 26 Mar 2020 14:38:37 +1100 Subject: [PATCH 026/111] clarify comment in sync_data.sh --- sync_data.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sync_data.sh b/sync_data.sh index d4f82481..cc391c34 100755 --- a/sync_data.sh +++ b/sync_data.sh @@ -9,7 +9,7 @@ # Set SYNCDIR to the path you want your data copied to. # This must be a unique absolute path for your set of runs. -# If you want to share your data, use SYNCDIR=/g/data/ik11/outputs/ +# To share your data, sync to a subdirectory in /g/data/ik11/outputs/ # but first add an experiment description - see /g/data/ik11/outputs/README # DOUBLE-CHECK SYNCDIR PATH IS UNIQUE SO YOU DON'T OVERWRITE EXISTING OUTPUT! SYNCDIR=/ERROR/SET/SYNCDIR/IN/sync_data.sh From 7fde28b5f72e7f82940c4df6fb9e845f0a4f30ed Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Thu, 26 Mar 2020 15:15:44 +1100 Subject: [PATCH 027/111] use normal queue --- config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config.yaml b/config.yaml index 40e539a1..0f317696 100644 --- a/config.yaml +++ b/config.yaml @@ -2,7 +2,7 @@ # If submitting to a different project to your default uncomment line below # and change project code as appropriate # project: w35 -queue: express +queue: normal walltime: 3:00:00 jobname: 1deg_jra55_iaf ncpus: 252 From cc26e6bc03b73cc739f50ec7124eb91a02cab489 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Tue, 21 Apr 2020 07:25:10 +1000 Subject: [PATCH 028/111] more helpful README --- README.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 9571e9ea..4cf4c995 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,8 @@ # 1deg_jra55_iaf -Standard configuration for 1 degree [ACCESS-OM2](https://github.com/COSIMA/access-om2) experiment (ACCESS-OM2-025) with JRA55-do interannual forcing (IAF). +Standard configuration for 1 degree [ACCESS-OM2](https://github.com/COSIMA/access-om2) experiment (ACCESS-OM2) with JRA55-do interannual forcing (IAF). -Note that the default timestep for this run is 5400 seconds, but you may need shorter timesteps during the first year of model equilibration. +For usage instructions, see the [ACCESS-OM2 wiki](https://github.com/COSIMA/access-om2/wiki). + +Run length and timestep are set in `accessom2.nml`. The timestep is normally set to a factor of the JRA55-do forcing period of 3hr = 10800s, for example one of 100, 108, 120, 135, 144, 150, 180, 200, 216, 225, 240, 270, 300, 360, 400, 432, 450, 540, 600, 675, 720, 900, 1080, 1200, 1350, 1800, 2160, 2700, 3600 or 5400s. The default timestep for this configuration is 5400 seconds, and the model is stable with this timestep right from the start. However if you alter the configuration you may need a shorter timestep during the first year or two of model equilibration. **NOTE:** All ACCESS-OM2 model components and configurations are undergoing continual improvement. We strongly recommend that you "watch" this repo (see button at top of screen; ask to be notified of all conversations) and also watch [ACCESS-OM2](https://github.com/COSIMA/access-om2), all the [component models](https://github.com/COSIMA/access-om2/tree/master/src), and [payu](https://github.com/payu-org/payu) to be kept informed of updates, problems and bug fixes as they arise. From 824c6b0a94ac98115d98544e567bac4b249e5113 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Tue, 28 Apr 2020 11:45:28 +1000 Subject: [PATCH 029/111] Automatically sweep and resubmit on specific errors - https://github.com/payu-org/payu/issues/241 --- config.yaml | 4 ++++ resub.sh | 57 +++++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100755 resub.sh diff --git a/config.yaml b/config.yaml index 0f317696..42884692 100644 --- a/config.yaml +++ b/config.yaml @@ -60,6 +60,10 @@ qsub_flags: -W umask=027 # set number of cores per node (28 for normalbw, 48 for normal on gadi) platform: nodesize: 48 +# sweep and resubmit on specific errors - see https://github.com/payu-org/payu/issues/241#issuecomment-610739771 +userscripts: + error: resub.sh + run: rm -f resubmit.count # DANGER! Do not uncomment this without checking the script is synching # to the correct location! diff --git a/resub.sh b/resub.sh new file mode 100755 index 00000000..a9f09c45 --- /dev/null +++ b/resub.sh @@ -0,0 +1,57 @@ +#!/usr/bin/bash + +logfile='resubmit.log' +counterfile='resubmit.count' +outfile='access-om2.err' + +MAX_RESUBMISSIONS=2 +date >> ${logfile} + +# Define errors from which a resubmit is appropriate +declare -a errors=( + "Segmentation fault: address not mapped to object", + "Transport retry count exceeded" + ) + +resub=false +for error in "${errors[@]}" +do + if grep -q ${error} ${outfile} + then + echo "Error found: ${error}" >> ${logfile} + resub=true + break + else + echo "Error not found: ${error}" >> ${logfile} + fi +done + +if ! ${resub} +then + echo "Error not eligible for resubmission" >> ${logfile} + exit 0 +fi + +if [ -f "${counterfile}" ] +then + PAYU_N_RESUB=$(cat ${counterfile}) +else + echo "Reset resubmission counter" >> ${logfile} + PAYU_N_RESUB=${MAX_RESUBMISSIONS} +fi + +echo "Resubmission counter: ${PAYU_N_RESUB}" >> ${logfile} + +if [[ "${PAYU_N_RESUB}" -gt 0 ]] +then + # Sweep and re-run + ${PAYU_PATH}/payu sweep >> ${logfile} + ${PAYU_PATH}/payu run -n ${PAYU_N_RUNS} >> ${logfile} + # Decrement resub counter and save to counter file + ((PAYU_N_RESUB=PAYU_N_RESUB-1)) + echo "${PAYU_N_RESUB}" > ${counterfile} +else + echo "Resubmit limit reached ... " >> ${logfile} + rm ${counterfile} +fi + From cf2687098d9553c34c4c2817cf922c66242bfac1 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Wed, 29 Apr 2020 15:22:12 +1000 Subject: [PATCH 030/111] compress restarts - see https://github.com/COSIMA/access-om2/issues/168 --- config.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/config.yaml b/config.yaml index 8342d493..dc096864 100644 --- a/config.yaml +++ b/config.yaml @@ -48,6 +48,7 @@ submodels: # Collation collate: + restart: true walltime: 1:00:00 mem: 30GB ncpus: 4 From 94920cc97c5b5338da5e325bc8a37c49e4a88b2d Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Wed, 29 Apr 2020 17:56:45 +1000 Subject: [PATCH 031/111] update manifests --- manifests/input.yaml | 175 ++++++++++++++++++++++------------------- manifests/restart.yaml | 3 + 2 files changed, 98 insertions(+), 80 deletions(-) create mode 100644 manifests/restart.yaml diff --git a/manifests/input.yaml b/manifests/input.yaml index eef9265f..d0d0fbc4 100644 --- a/manifests/input.yaml +++ b/manifests/input.yaml @@ -1,15 +1,30 @@ format: yamanifest version: 1.0 --- -work/INPUT/rmp_jra55_cice_conserve.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/common_1deg_jra55/rmp_jra55_cice_conserve.nc +work/INPUT/JRA55_MOM1_conserve2nd.nc: + fullpath: /g/data/ik11/inputs/access-om2/input_rc/common_1deg_jra55/JRA55_MOM1_conserve2nd.nc hashes: - binhash: 67c1bf5bd80f5b0809560e037dec88b9 + binhash: 1e898bb683160f7eb91e9e49a8e39160 + md5: 00be8ec0f1126055b65dc68178ce4eb5 +work/INPUT/JRA55_MOM1_patch.nc: + fullpath: /g/data/ik11/inputs/access-om2/input_rc/common_1deg_jra55/JRA55_MOM1_patch.nc + hashes: + binhash: b6f946067a63b8944eb1165e17e58196 + md5: 6c345282e51521828f62b842e58dd734 +work/INPUT/rmp_jra55_cice_1st_conserve.nc: + fullpath: /g/data/ik11/inputs/access-om2/input_rc/common_1deg_jra55/rmp_jra55_cice_1st_conserve.nc + hashes: + binhash: c581a8a58b807c6dc1c5304c126c80ee + md5: 6404d936d4898e5ed31e62b585d630cf +work/INPUT/rmp_jra55_cice_2nd_conserve.nc: + fullpath: /g/data/ik11/inputs/access-om2/input_rc/common_1deg_jra55/rmp_jra55_cice_2nd_conserve.nc + hashes: + binhash: b1eae275f3f4f89fd5b6537758563d0b md5: 79885c8149d65a55d093244935f62360 -work/INPUT/rmp_jra55_cice_smooth.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/common_1deg_jra55/rmp_jra55_cice_smooth.nc +work/INPUT/rmp_jra55_cice_patch.nc: + fullpath: /g/data/ik11/inputs/access-om2/input_rc/common_1deg_jra55/rmp_jra55_cice_patch.nc hashes: - binhash: f6421cbcbda8b0f664f9bda94ce9c17c + binhash: 1af1de55ea267ced7c966e2991bee5e8 md5: aa91ea2e3cdef04f58ed5db8f8d7de6d work/atmosphere/INPUT/friver_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_19580101-19581231.nc: fullpath: /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/land/day/friver/gr/v20190429/friver/friver_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_19580101-19581231.nc @@ -942,14 +957,14 @@ work/atmosphere/INPUT/licalvf_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4- binhash: 42373f33e0bfacba3e3584538c14d77f md5: 7d09d06ec59b71f0dffe288f7507b06d work/atmosphere/INPUT/ncar_precip.0001.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/yatm_1deg/ncar_precip.0001.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/yatm_1deg/ncar_precip.0001.nc hashes: - binhash: 7aa17263c4d1b83ace0e6a631272eb7a + binhash: e328c61ff137bcaa07c97a940379519e md5: 502be1947e13269dedff21d34e34a543 work/atmosphere/INPUT/ncar_rad.0001.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/yatm_1deg/ncar_rad.0001.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/yatm_1deg/ncar_rad.0001.nc hashes: - binhash: 2a40d7b173ae746b1b1d8b67c4cf7e80 + binhash: ac51aa16461c18af3e0e31d76d988cc1 md5: 4d3d3e3d26f9d558411847d4f34579c8 work/atmosphere/INPUT/prra_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010130-195812312230.nc: fullpath: /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/prra/gr/v20190429/prra/prra_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010130-195812312230.nc @@ -1882,9 +1897,9 @@ work/atmosphere/INPUT/psl_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr binhash: 7ca04d02a8e25a0bce26412aef7189b3 md5: 9433ee01eeb6b9f1dad59a67cfc63b0f work/atmosphere/INPUT/q_10.0001.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/yatm_1deg/q_10.0001.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/yatm_1deg/q_10.0001.nc hashes: - binhash: 6a695ee13231ff0816ace4fd2609242a + binhash: fc99955a2d7230c4caa6d412c812344d md5: d9f27d865c8e86a5f5bc2576b3805c52 work/atmosphere/INPUT/rlds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010130-195812312230.nc: fullpath: /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/rlds/gr/v20190429/rlds/rlds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010130-195812312230.nc @@ -2197,24 +2212,24 @@ work/atmosphere/INPUT/rlds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_g binhash: 9e80b14cd2ca6208bed4ba7c3f616581 md5: 3d08213bdacd00ba2cfde806cf6d6b6f work/atmosphere/INPUT/rmp_corr_to_cict_CONSERV.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/yatm_1deg/rmp_corr_to_cict_CONSERV.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/yatm_1deg/rmp_corr_to_cict_CONSERV.nc hashes: - binhash: c8f9aeeed7740f65e83213cc4cc94ca9 + binhash: dada4e4ac4029c9c6551fe42fbfefb39 md5: f080a1a3bc639639bcc183d5759bce12 work/atmosphere/INPUT/rmp_daitren_runoff_MOM1_conserve2nd.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/yatm_1deg/rmp_daitren_runoff_MOM1_conserve2nd.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/yatm_1deg/rmp_daitren_runoff_MOM1_conserve2nd.nc hashes: - binhash: 0d7fbb1cd7081de94ada3181e78110b0 + binhash: b35d62bd81d3692945d86969a3959b40 md5: fd63d086dbede3c6e9795c750a3263e2 work/atmosphere/INPUT/rmp_jra55_runoff_cice_conserve.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/yatm_1deg/rmp_jra55_runoff_cice_conserve.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/yatm_1deg/rmp_jra55_runoff_cice_conserve.nc hashes: - binhash: 858a4646b1bdb7dac5fdb6c2bd275e8a + binhash: 9a61f517188c9fbb874f595b388fa95d md5: 4ea275ecdee40694db28c7bfb5d275f0 work/atmosphere/INPUT/rmp_jrar_to_cict_CONSERV.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/yatm_1deg/rmp_jrar_to_cict_CONSERV.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/yatm_1deg/rmp_jrar_to_cict_CONSERV.nc hashes: - binhash: 65e7855288148d5e977badea1e8d0a5c + binhash: 41783dfa9a46d7c1e7a7f3387c6e476e md5: 10f0b5ea6b8102a03ad1140e5163a0f7 work/atmosphere/INPUT/rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010130-195812312230.nc: fullpath: /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/rsds/gr/v20190429/rsds/rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010130-195812312230.nc @@ -2527,19 +2542,19 @@ work/atmosphere/INPUT/rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_g binhash: 5b861eb4a80c6f1ebdd5d094fcdd4c56 md5: ff51b282d75d57fa40bd321e3e715684 work/atmosphere/INPUT/runoff.daitren.clim.10FEB2011.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/yatm_1deg/runoff.daitren.clim.10FEB2011.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/yatm_1deg/runoff.daitren.clim.10FEB2011.nc hashes: - binhash: ba68462c23b7ca7c9f1f418fa59dcfda + binhash: 23e524c55cd8cc9bb75ad5f04275eb30 md5: 2471c5665be8b49f004dada041341817 work/atmosphere/INPUT/slp.0001.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/yatm_1deg/slp.0001.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/yatm_1deg/slp.0001.nc hashes: - binhash: 61c0f5237ec1c22fea6af9b91f047c96 + binhash: 2c8ae97b4f9a97dd272a719e11e7d7bc md5: 743b0941d76feef69d1f12acce8050e7 work/atmosphere/INPUT/t_10.0001.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/yatm_1deg/t_10.0001.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/yatm_1deg/t_10.0001.nc hashes: - binhash: e67a47f108a6269c591c207da5b8f4f1 + binhash: c8030e99600e30fd11214f4e66ae861e md5: cc8a4863da3f6cfb209a607caaf0f085 work/atmosphere/INPUT/tas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010000-195812312100.nc: fullpath: /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hrPt/tas/gr/v20190429/tas/tas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010000-195812312100.nc @@ -2852,9 +2867,9 @@ work/atmosphere/INPUT/tas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr binhash: f299c3152adb7fbeb992816e0f694d0f md5: 837cc3100dccb5252d76eeb62d189cda work/atmosphere/INPUT/u_10.0001.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/yatm_1deg/u_10.0001.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/yatm_1deg/u_10.0001.nc hashes: - binhash: b2d6ad3036fe4cd7142977c222827aaa + binhash: 8dbce9286bcfe18309add08e383aa3f9 md5: e4073e81a24d10352157284d438e4c83 work/atmosphere/INPUT/uas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010000-195812312100.nc: fullpath: /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hrPt/uas/gr/v20190429/uas/uas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010000-195812312100.nc @@ -3167,9 +3182,9 @@ work/atmosphere/INPUT/uas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr binhash: 7b1ba750ed9ea2f847c4c8a7c9382d6c md5: f1cdb45f72e9f95dff0c244f005a9c4c work/atmosphere/INPUT/v_10.0001.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/yatm_1deg/v_10.0001.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/yatm_1deg/v_10.0001.nc hashes: - binhash: a0e341211d26a817ed039bbf3decb063 + binhash: b953ce69b0101e61e820552a30337234 md5: 96914ca8a353bdc40ea0d3cba4350f16 work/atmosphere/INPUT/vas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010000-195812312100.nc: fullpath: /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hrPt/vas/gr/v20190429/vas/vas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010000-195812312100.nc @@ -3483,127 +3498,127 @@ work/atmosphere/INPUT/vas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr md5: b0e514bfac0d9dfbf538d36b8ecd17f9 work/ice/RESTART/grid.nc: copy: true - fullpath: /g/data/ik11/inputs/access-om2/input_20200422/cice_1deg/grid.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/cice_1deg/grid.nc hashes: - binhash: 74620c19f4503d4dae351b24e02b79e7 + binhash: 6b6c08bc458eed00641f8d5cd5b7ccac md5: 1213e346055ee073fe33dc12578d99c6 work/ice/RESTART/i2o.nc: copy: true - fullpath: /g/data/ik11/inputs/access-om2/input_20200422/cice_1deg/i2o.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/cice_1deg/i2o.nc hashes: binhash: 527d494c80b2a3418645b962fd8706d0 md5: c96e06c3c80c0f680545db59ed3349e5 work/ice/RESTART/kmt.nc: copy: true - fullpath: /g/data/ik11/inputs/access-om2/input_20200422/cice_1deg/kmt.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/cice_1deg/kmt.nc hashes: - binhash: 8ae1aa8eadb151db7794c5e6fd9b2e1c + binhash: f04a0c2a4f27bdb8ef32da0ab8ec8a61 md5: a5a7b4be90ec06044588b623d555c4ad work/ice/RESTART/monthly_sstsss.nc: copy: true - fullpath: /g/data/ik11/inputs/access-om2/input_20200422/cice_1deg/monthly_sstsss.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/cice_1deg/monthly_sstsss.nc hashes: - binhash: af12fa116cad37b1208376f98ddaa08c + binhash: c73864b41a23b7c9a7e888d6565cc577 md5: 323d4c605f83f4d7d3126da70153c2ed work/ice/RESTART/o2i.nc: copy: true - fullpath: /g/data/ik11/inputs/access-om2/input_20200422/cice_1deg/o2i.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/cice_1deg/o2i.nc hashes: - binhash: 2e89778bfe92a3b0c41721c3dfe84871 + binhash: 304e0d0a02d5d6a95a7ffbb8f8e6871a md5: 3498246dcd7da40d3b8c6b4a908b260f work/ice/RESTART/u_star.nc: copy: true - fullpath: /g/data/ik11/inputs/access-om2/input_20200422/cice_1deg/u_star.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/cice_1deg/u_star.nc hashes: - binhash: 29bf2f18c57caafb8d499e4a534d2afe + binhash: fb1becadd07fa9cbbc88a7f47e96d9b4 md5: 68cf0ef92576f96ef085cd7f243d0c39 work/ocean/INPUT/basin_mask.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/mom_1deg/basin_mask.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/basin_mask.nc hashes: - binhash: 5a77cae16b1a6c7d5042a1abbdfd8fda + binhash: 0432b240a183f391bac96cd5bdbadafa md5: 20fd8740f24ca95c7c086343077e9c0d work/ocean/INPUT/chl.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/mom_1deg/chl.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/chl.nc hashes: - binhash: c1f8d6d3e4000ac41159f1413a373cf6 + binhash: 0ddec40146ae7f0fbc1a06da8ad94b9d md5: a7aa5bcf4a3b9fa8102edd3b6b67c3a2 work/ocean/INPUT/geothermal_heating.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/mom_1deg/geothermal_heating.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/geothermal_heating.nc hashes: - binhash: 2d04abc82a3df5b9f43d6d0cc495d053 + binhash: 4214c902e835d82643f84cbec1a5a65e md5: 381cb231d8d059576adca0c2bea9c030 work/ocean/INPUT/grid_spec.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/mom_1deg/grid_spec.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/grid_spec.nc hashes: - binhash: afeb8a676f0d829ebe248ee707e5c08b + binhash: f3f3d1eb44108483348881f9e862e2ff md5: 027d2f8fb1eda3ef1cf0a3f520a217f7 work/ocean/INPUT/mask_table.24.16x15: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/mom_1deg/mask_table.24.16x15 + fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/mask_table.24.16x15 hashes: - binhash: 60297e9f316c78a4570201d4c8404a61 + binhash: 397aac7f65a9508f19de85de61646909 md5: 2203b38758fb2b56a145ef16b7872af9 work/ocean/INPUT/ocean_hgrid.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/mom_1deg/ocean_hgrid.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/ocean_hgrid.nc hashes: - binhash: 1f1755cd82099150fa70927585368836 + binhash: bef3659bf2505b3d1e3167579718fabb md5: 51f58be0f4ea6da2cb438a893f95c689 work/ocean/INPUT/ocean_mask.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/mom_1deg/ocean_mask.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/ocean_mask.nc hashes: - binhash: b5422ec543d44e369f3c42ce180638ee + binhash: 4cd2ab42c4890a101295bdb151d59abb md5: 1d9dfb140919f355037f72bc89f15db0 work/ocean/INPUT/ocean_mask_table: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/mom_1deg/ocean_mask_table + fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/ocean_mask_table hashes: - binhash: c0a5f59e52818b729e122afe1f706baf + binhash: 9e95917d763f90bc14e7b470074931f5 md5: 2203b38758fb2b56a145ef16b7872af9 work/ocean/INPUT/ocean_mosaic.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/mom_1deg/ocean_mosaic.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/ocean_mosaic.nc hashes: - binhash: 33713867c5816891b45d936897ef67d3 + binhash: 150ae65ecbe60d7d2357a76909635839 md5: cb42e630ee31d3686156fcbdc2f9d07c work/ocean/INPUT/ocean_temp_salt.res.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/mom_1deg/ocean_temp_salt.res.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/ocean_temp_salt.res.nc hashes: - binhash: 1c88f650aae9ae9fad0bf65ff0f34417 + binhash: b836632dc8139d895992fe8b67954681 md5: c9814c04b393cf73fe3d16daf5d421af work/ocean/INPUT/ocean_vgrid.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/mom_1deg/ocean_vgrid.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/ocean_vgrid.nc hashes: - binhash: aa922e4af9bdf6deedfecb81efcee14d + binhash: af2ce0ec0bfcac448a5b1558dc42254a md5: 6eebf039362b6572eaad5477740236bf work/ocean/INPUT/roughness_amp.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/mom_1deg/roughness_amp.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/roughness_amp.nc hashes: - binhash: 5eea2353c6fe3213aa919ef71a0a92e0 + binhash: 6f092a5efcf2131d21e96ff7d4a5a89b md5: 185dadeb53da2de75b47c53fd7085f89 work/ocean/INPUT/roughness_cdbot.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/mom_1deg/roughness_cdbot.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/roughness_cdbot.nc hashes: - binhash: cb42646c5d09ae4a09abfe89d610e7b9 + binhash: 12a32c9840ab654b5c9bc5ec43929c6f md5: b50f0595f3ebc872cbcf5f3223115643 work/ocean/INPUT/salt_sfc_restore.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/mom_1deg/salt_sfc_restore.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/salt_sfc_restore.nc hashes: - binhash: 1611eb28494b657838c8b5543410e679 - md5: d95d45424492bad16d647c104e78b442 + binhash: bed136991ec6d0fcc103d00bd36fb8e5 + md5: b2bd35c44017597ba99b85fb61ed4d72 work/ocean/INPUT/ssw_atten_depth.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/mom_1deg/ssw_atten_depth.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/ssw_atten_depth.nc hashes: - binhash: 9c2178dc209cfe84dce1b81be793cead - md5: 6142db126b8d2c8d8f4b6fb0e05d60c5 + binhash: 9f3eeeebbd0756bed573cb7a6fb5fba5 + md5: 4aa30be87abb6f0f17484b0dc36ff737 work/ocean/INPUT/temp_sfc_restore.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/mom_1deg/temp_sfc_restore.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/temp_sfc_restore.nc hashes: - binhash: 3f65be76fc6b5b3830632e35cc2c1373 - md5: e5f54b9a2392f660f0b3774802f2a84c + binhash: f7c5a64fe9405e07298f5b991177b53e + md5: 36892b884a6da1db25dcc3016c95c0ca work/ocean/INPUT/tideamp.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/mom_1deg/tideamp.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/tideamp.nc hashes: - binhash: 4c3394bb168774fb4362826996c74bcb + binhash: ec1984c78b79127c907258cf06607ff1 md5: b2840af757d9b7b40207f33f1fc84c5c work/ocean/INPUT/topog.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_236a3011/mom_1deg/topog.nc + fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/topog.nc hashes: - binhash: 86a9468fa56d6b3c5612c919618efab3 + binhash: 022ac4a9232c6f11d977d3337b89d004 md5: f01ddc02cfe21d8db99c2976e9fcc828 diff --git a/manifests/restart.yaml b/manifests/restart.yaml new file mode 100644 index 00000000..f1e1197c --- /dev/null +++ b/manifests/restart.yaml @@ -0,0 +1,3 @@ +format: yamanifest +version: 1.0 +--- {} From 291adb7d634e024438bfed610f47ca85fbefc0e4 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Wed, 29 Apr 2020 19:29:45 +1000 Subject: [PATCH 032/111] fix resub.sh - https://github.com/payu-org/payu/issues/241#issuecomment-621078189 --- resub.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/resub.sh b/resub.sh index a9f09c45..e106fa43 100755 --- a/resub.sh +++ b/resub.sh @@ -9,14 +9,14 @@ date >> ${logfile} # Define errors from which a resubmit is appropriate declare -a errors=( - "Segmentation fault: address not mapped to object", + "Segmentation fault: address not mapped to object" "Transport retry count exceeded" ) resub=false for error in "${errors[@]}" do - if grep -q ${error} ${outfile} + if grep -q "${error}" ${outfile} then echo "Error found: ${error}" >> ${logfile} resub=true From 707d8c5a25264274438f2511cbd8fb8d3a5edb20 Mon Sep 17 00:00:00 2001 From: Nic Hannah Date: Wed, 29 Apr 2020 21:20:32 +1000 Subject: [PATCH 033/111] Simpified/generalised namcouple --- namcouple | 159 ++++++++++++++++++++++++++---------------------------- 1 file changed, 75 insertions(+), 84 deletions(-) diff --git a/namcouple b/namcouple index b7405c48..335153db 100644 --- a/namcouple +++ b/namcouple @@ -1,5 +1,5 @@ # This is a typical input file for OASIS 3.0, using netCDF format -# for restart input files. Oasis reads this file at run-time. +# for restart input files. Oasis reads this file at run-time. # # Any line beginning with # is ignored. Blank lines are not allowed. # @@ -12,7 +12,7 @@ ######################################################################### $NFIELDS -# This is the total number of fields being exchanged. +# This is the total number of fields being exchanged. ### 10 fields atm -> ice ### 15 fields ice -> ocn ### 7 fields ocn -> ice @@ -48,8 +48,8 @@ # $END ########################################################################### # $MODINFO -# Indicates if a header is encapsulated within the field brick -# in binary restart files for all communication techniques, and +# Indicates if a header is encapsulated within the field brick +# in binary restart files for all communication techniques, and # for coupling field exchanges for PIPE, SIPC and GMEM. # (YES or NOT) # NOT @@ -80,7 +80,7 @@ # --- note file cf_name_table.txt does not include all the coupling flds --- # --- listed below. so the fld number (367 for swfld etc) may not point --- # --- to the realistic 'longname' of the variable. (may modify this file --- -# --- to add more fields in the future.) +# --- to add more fields in the future.) ############################################################################ # # ATMOSPHERE --->>> ICE @@ -88,62 +88,57 @@ ########## # Field 01 : swflx down ########## -swfld_ai swfld_i 367 10800 3 a2i.nc EXPORTED +swfld_ai swfld_i -1 -1 2 NA EXPORTED jrat cict LAG=0 SEQ=+1 P 0 P 0 # -LOCTRANS MAPPING SCRIPR +LOCTRANS MAPPING INSTANT -../INPUT/rmp_jra55_cice_conserve.nc dst -CONSERV LR SCALAR LATLON 10 FRACNNEI FIRST +../INPUT/rmp_jra55_cice_1st_conserve.nc dst ######### # Field 02 : lwflx down ########## -lwfld_ai lwfld_i 366 10800 3 a2i.nc EXPORTED +lwfld_ai lwfld_i -1 -1 2 NA EXPORTED jrat cict LAG=0 SEQ=+1 P 0 P 0 # -LOCTRANS MAPPING SCRIPR +LOCTRANS MAPPING INSTANT -../INPUT/rmp_jra55_cice_conserve.nc dst -CONSERV LR SCALAR LATLON 10 FRACNNEI FIRST +../INPUT/rmp_jra55_cice_1st_conserve.nc dst ########## # Field 03 : rainfall ########## -rain_ai rain_i 26 10800 3 a2i.nc EXPORTED +rain_ai rain_i -1 -1 2 NA EXPORTED jrat cict LAG=0 SEQ=+1 P 0 P 0 # -LOCTRANS MAPPING SCRIPR +LOCTRANS MAPPING INSTANT -../INPUT/rmp_jra55_cice_conserve.nc dst -CONSERV LR SCALAR LATLON 10 FRACNNEI FIRST +../INPUT/rmp_jra55_cice_1st_conserve.nc dst ########## # Field 04 : snowfall ########## -snow_ai snow_i 26 10800 3 a2i.nc EXPORTED +snow_ai snow_i -1 -1 2 NA EXPORTED jrat cict LAG=0 SEQ=+1 P 0 P 0 # -LOCTRANS MAPPING SCRIPR +LOCTRANS MAPPING INSTANT -../INPUT/rmp_jra55_cice_conserve.nc dst -CONSERV LR SCALAR LATLON 10 FRACNNEI FIRST +../INPUT/rmp_jra55_cice_1st_conserve.nc dst ########## # Field 05 : surface pressure ########## -press_ai press_i 33 10800 3 a2i.nc EXPORTED +press_ai press_i -1 -1 2 NA EXPORTED jrat cict LAG=0 SEQ=+1 P 0 P 0 # -LOCTRANS MAPPING SCRIPR +LOCTRANS MAPPING INSTANT -../INPUT/rmp_jra55_cice_smooth.nc dst -CONSERV LR SCALAR LATLON 10 FRACNNEI FIRST +../INPUT/rmp_jra55_cice_patch.nc dst ########## # Field 06 : runoff. Runoff is passed on the destination grid. ########## -runof_ai runof_i 297 10800 1 a2i.nc EXPORTED +runof_ai runof_i -1 -1 1 NA EXPORTED cict cict LAG=0 SEQ=+1 P 0 P 0 # @@ -152,45 +147,41 @@ INSTANT ########## # Field 07 : near surface (2m) air temp ########## -tair_ai tair_i 110 10800 3 a2i.nc EXPORTED +tair_ai tair_i -1 -1 2 NA EXPORTED jrat cict LAG=0 SEQ=+1 P 0 P 0 # -LOCTRANS MAPPING SCRIPR +LOCTRANS MAPPING INSTANT -../INPUT/rmp_jra55_cice_smooth.nc dst -CONSERV LR SCALAR LATLON 10 FRACNNEI FIRST +../INPUT/rmp_jra55_cice_patch.nc dst ########## # Field 08 : 2m air humidity ########## -qair_ai qair_i 339 10800 3 a2i.nc EXPORTED +qair_ai qair_i -1 -1 2 NA EXPORTED jrat cict LAG=0 SEQ=+1 P 0 P 0 # -LOCTRANS MAPPING SCRIPR +LOCTRANS MAPPING INSTANT -../INPUT/rmp_jra55_cice_smooth.nc dst -CONSERV LR SCALAR LATLON 10 FRACNNEI FIRST +../INPUT/rmp_jra55_cice_patch.nc dst ########## # Field 09 : 10m wind (u) ########## -uwnd_ai uwnd_i 56 10800 2 a2i.nc EXPORTED +uwnd_ai uwnd_i -1 -1 1 NA EXPORTED jrat cict LAG=0 SEQ=+1 P 0 P 0 # -MAPPING SCRIPR -../INPUT/rmp_jra55_cice_smooth.nc dst -DISTWGT LR VECTOR LATLON 10 4 vwnd_ai +MAPPING +../INPUT/rmp_jra55_cice_patch.nc dst ########## # Field 10 : 10m wind (v) ########## -vwnd_ai vwnd_i 56 10800 2 a2i.nc EXPORTED +vwnd_ai vwnd_i -1 -1 1 NA EXPORTED jrat cict LAG=0 SEQ=+1 P 0 P 0 # -MAPPING SCRIPR -../INPUT/rmp_jra55_cice_smooth.nc dst -DISTWGT LR VECTOR LATLON 10 4 uwnd_ai +MAPPING +../INPUT/rmp_jra55_cice_patch.nc dst ############################################################################ # # ICE --->>> OCEAN @@ -198,23 +189,23 @@ DISTWGT LR VECTOR LATLON 10 4 uwnd_ai ########## # Field 11 : ice-ocean interface stress (x-direction) ########## -strsu_io u_flux 170 5400 1 i2o.nc IGNORED +strsu_io u_flux -1 -1 1 i2o.nc IGNORED cict cict LAG=0 SEQ=+1 # LOCTRANS INSTANT -########## +########## # Field 12 : ice-ocean interface stress (y-direction) ########## -strsv_io v_flux 175 5400 1 i2o.nc IGNORED +strsv_io v_flux -1 -1 1 i2o.nc IGNORED cict cict LAG=0 SEQ=+1 # LOCTRANS INSTANT -########## +########## # Field 13 : freshwater flux ########## -rain_io lprec 27 5400 1 i2o.nc IGNORED +rain_io lprec -1 -1 1 i2o.nc IGNORED cict cict LAG=0 SEQ=+1 # LOCTRANS @@ -222,31 +213,31 @@ INSTANT ########## # Field 14 : freshwater flux ########## -snow_io fprec 28 5400 1 i2o.nc IGNORED +snow_io fprec -1 -1 1 i2o.nc IGNORED cict cict LAG=0 SEQ=+1 # LOCTRANS INSTANT -########## +########## # Field 15 : salt flux (no ref no for saltflux yet!) ########## -stflx_io salt_flx 454 5400 1 i2o.nc IGNORED +stflx_io salt_flx -1 -1 1 i2o.nc IGNORED cict cict LAG=0 SEQ=+1 # LOCTRANS INSTANT -########## +########## # Field 16 : next heat flux (heatflux into ocean. '42' not right.) ########## -htflx_io mh_flux 42 5400 1 i2o.nc IGNORED +htflx_io mh_flux -1 -1 1 i2o.nc IGNORED cict cict LAG=0 SEQ=+1 # LOCTRANS INSTANT -########## -# Field 17 : swflux penetrating through ice into ocean +########## +# Field 17 : swflux penetrating through ice into ocean ######### -swflx_io sw_flux 367 5400 1 i2o.nc IGNORED +swflx_io sw_flux -1 -1 1 i2o.nc IGNORED cict cict LAG=0 SEQ=+1 # LOCTRANS @@ -254,7 +245,7 @@ INSTANT ########## # Field 18 : latent heat flux ########## -qflux_io q_flux 452 5400 1 i2o.nc IGNORED +qflux_io q_flux -1 -1 1 i2o.nc IGNORED cict cict LAG=0 SEQ=+1 # LOCTRANS @@ -262,7 +253,7 @@ INSTANT ######### # Field 19 : Sensible heat flux ########## -shflx_io t_flux 362 5400 1 i2o.nc IGNORED +shflx_io t_flux -1 -1 1 i2o.nc IGNORED cict cict LAG=0 SEQ=+1 # LOCTRANS @@ -270,92 +261,92 @@ INSTANT ########## # Field 20 : LW radiation flux down ########## -lwflx_io lw_flux 366 5400 1 i2o.nc IGNORED +lwflx_io lw_flux -1 -1 1 i2o.nc IGNORED cict cict LAG=0 SEQ=+1 # LOCTRANS INSTANT ########## # Field 21 : runoff -########## -runof_io runof 297 5400 1 i2o.nc IGNORED +########## +runof_io runof -1 -1 1 i2o.nc IGNORED cict cict LAG=0 SEQ=+1 # LOCTRANS INSTANT ########## # Field 22 : surface pressure -########## -press_io p 33 5400 1 i2o.nc IGNORED +########## +press_io p -1 -1 1 i2o.nc IGNORED cict cict LAG=0 SEQ=+1 # LOCTRANS INSTANT ########## # Field 23 : ice concentration -########## -aice_io aice 44 5400 1 i2o.nc IGNORED +########## +aice_io aice -1 -1 1 i2o.nc IGNORED cict cict LAG=0 SEQ=+1 # -LOCTRANS +LOCTRANS INSTANT ########## # Field 24 : ice melting waterflux -########## -melt_io wfimelt 36 5400 1 i2o.nc IGNORED +########## +melt_io wfimelt -1 -1 1 i2o.nc IGNORED cict cict LAG=0 SEQ=+1 # LOCTRANS INSTANT ########## # Field 25 : ice forming eaterflux -########## -form_io wfiform 36 5400 1 i2o.nc IGNORED +########## +form_io wfiform -1 -1 1 i2o.nc IGNORED cict cict LAG=0 SEQ=+1 # LOCTRANS INSTANT ############################################################################ -# +# # OCEAN --->>> ICE # ---------------- -########## +########## # Field 26 : Sea surface temperature (Celsius in MOM4, Kelvin in MOM5) ########## -t_surf sst_i 1 5400 1 o2i.nc IGNORED +t_surf sst_i -1 -1 1 o2i.nc IGNORED cict cict LAG=0 SEQ=+1 -# +# LOCTRANS INSTANT -########## +########## # Field 27 : Sea surface salinity (psu) ########## -s_surf sss_i 312 5400 1 o2i.nc IGNORED +s_surf sss_i -1 -1 1 o2i.nc IGNORED cict cict LAG=0 SEQ=+1 -# +# LOCTRANS INSTANT ########## # Field 28 : 'eastward' sea surface water velocity -########## -u_surf ssu_i 181 5400 1 o2i.nc IGNORED +########## +u_surf ssu_i -1 -1 1 o2i.nc IGNORED cict cict LAG=0 SEQ=+1 # LOCTRANS INSTANT -########## +########## # Field 29 : 'northward' sea surface water velocity ########## -v_surf ssv_i 261 5400 1 o2i.nc IGNORED +v_surf ssv_i -1 -1 1 o2i.nc IGNORED cict cict LAG=0 SEQ=+1 # LOCTRANS INSTANT ########## -# Field 30 : frazil ice fromation energy (J/m^2) +# Field 30 : frazil ice fromation energy (J/m^2) # ('441' is "upward_sea_ice_basal_heat_flux' 'W m-2') ########## -frazil pfmice_i 441 5400 1 o2i.nc IGNORED +frazil pfmice_i -1 -1 1 o2i.nc IGNORED cict cict LAG=0 SEQ=+1 # LOCTRANS @@ -364,7 +355,7 @@ INSTANT # Field 31 : sea surface slope _x_ (m/m) # ( '203' is "height" ...) ########## -dssldx sslx_i 203 5400 1 o2i.nc IGNORED +dssldx sslx_i -1 -1 1 o2i.nc IGNORED cict cict LAG=0 SEQ=+1 # LOCTRANS @@ -373,7 +364,7 @@ INSTANT # Field 32 : sea surface slope _y_ (m/m) # ( '310' is "sea_surface_elevation") ########## -dssldy ssly_i 310 5400 1 o2i.nc IGNORED +dssldy ssly_i -1 -1 1 o2i.nc IGNORED cict cict LAG=0 SEQ=+1 # LOCTRANS From 6b2549c673e3494bfdc22364743728297b888d4d Mon Sep 17 00:00:00 2001 From: Nic Hannah Date: Wed, 29 Apr 2020 22:05:32 +1000 Subject: [PATCH 034/111] Further clean-ups to namcouple --- namcouple | 220 +++++++++++++++++------------------------------------- 1 file changed, 70 insertions(+), 150 deletions(-) diff --git a/namcouple b/namcouple index 335153db..39bb5caa 100644 --- a/namcouple +++ b/namcouple @@ -88,87 +88,76 @@ ########## # Field 01 : swflx down ########## -swfld_ai swfld_i -1 -1 2 NA EXPORTED -jrat cict LAG=0 SEQ=+1 +swfld_ai swfld_i -1 -1 1 NA EXPORTED +NA NA P 0 P 0 # -LOCTRANS MAPPING -INSTANT +MAPPING ../INPUT/rmp_jra55_cice_1st_conserve.nc dst ######### # Field 02 : lwflx down ########## -lwfld_ai lwfld_i -1 -1 2 NA EXPORTED -jrat cict LAG=0 SEQ=+1 +lwfld_ai lwfld_i -1 -1 1 NA EXPORTED +NA NA P 0 P 0 # -LOCTRANS MAPPING -INSTANT +MAPPING ../INPUT/rmp_jra55_cice_1st_conserve.nc dst ########## # Field 03 : rainfall ########## -rain_ai rain_i -1 -1 2 NA EXPORTED -jrat cict LAG=0 SEQ=+1 +rain_ai rain_i -1 -1 1 NA EXPORTED +NA NA P 0 P 0 # -LOCTRANS MAPPING -INSTANT +MAPPING ../INPUT/rmp_jra55_cice_1st_conserve.nc dst ########## # Field 04 : snowfall ########## -snow_ai snow_i -1 -1 2 NA EXPORTED -jrat cict LAG=0 SEQ=+1 +snow_ai snow_i -1 -1 1 NA EXPORTED +NA NA P 0 P 0 # -LOCTRANS MAPPING -INSTANT +MAPPING ../INPUT/rmp_jra55_cice_1st_conserve.nc dst ########## # Field 05 : surface pressure ########## -press_ai press_i -1 -1 2 NA EXPORTED -jrat cict LAG=0 SEQ=+1 +press_ai press_i -1 -1 1 NA EXPORTED +NA NA P 0 P 0 # -LOCTRANS MAPPING -INSTANT +MAPPING ../INPUT/rmp_jra55_cice_patch.nc dst ########## # Field 06 : runoff. Runoff is passed on the destination grid. ########## -runof_ai runof_i -1 -1 1 NA EXPORTED -cict cict LAG=0 SEQ=+1 -P 0 P 0 -# -LOCTRANS -INSTANT +runof_ai runof_i -2 -1 0 NA IGNORED +NA NA ########## # Field 07 : near surface (2m) air temp ########## -tair_ai tair_i -1 -1 2 NA EXPORTED -jrat cict LAG=0 SEQ=+1 +tair_ai tair_i -1 -1 1 NA EXPORTED +NA NA P 0 P 0 # -LOCTRANS MAPPING -INSTANT +MAPPING ../INPUT/rmp_jra55_cice_patch.nc dst ########## # Field 08 : 2m air humidity ########## -qair_ai qair_i -1 -1 2 NA EXPORTED -jrat cict LAG=0 SEQ=+1 +qair_ai qair_i -1 -1 1 NA EXPORTED +NA NA P 0 P 0 # -LOCTRANS MAPPING -INSTANT +MAPPING ../INPUT/rmp_jra55_cice_patch.nc dst ########## # Field 09 : 10m wind (u) ########## uwnd_ai uwnd_i -1 -1 1 NA EXPORTED -jrat cict LAG=0 SEQ=+1 +NA NA P 0 P 0 # MAPPING @@ -177,7 +166,7 @@ MAPPING # Field 10 : 10m wind (v) ########## vwnd_ai vwnd_i -1 -1 1 NA EXPORTED -jrat cict LAG=0 SEQ=+1 +NA NA P 0 P 0 # MAPPING @@ -189,123 +178,78 @@ MAPPING ########## # Field 11 : ice-ocean interface stress (x-direction) ########## -strsu_io u_flux -1 -1 1 i2o.nc IGNORED -cict cict LAG=0 SEQ=+1 -# -LOCTRANS -INSTANT +strsu_io u_flux -1 -1 0 i2o.nc IGNORED +NA NA ########## # Field 12 : ice-ocean interface stress (y-direction) ########## -strsv_io v_flux -1 -1 1 i2o.nc IGNORED -cict cict LAG=0 SEQ=+1 -# -LOCTRANS -INSTANT +strsv_io v_flux -1 -1 0 i2o.nc IGNORED +NA NA ########## # Field 13 : freshwater flux ########## -rain_io lprec -1 -1 1 i2o.nc IGNORED -cict cict LAG=0 SEQ=+1 -# -LOCTRANS -INSTANT +rain_io lprec -1 -1 0 i2o.nc IGNORED +NA NA ########## # Field 14 : freshwater flux ########## -snow_io fprec -1 -1 1 i2o.nc IGNORED -cict cict LAG=0 SEQ=+1 -# -LOCTRANS -INSTANT +snow_io fprec -1 -1 0 i2o.nc IGNORED +NA NA ########## # Field 15 : salt flux (no ref no for saltflux yet!) ########## -stflx_io salt_flx -1 -1 1 i2o.nc IGNORED -cict cict LAG=0 SEQ=+1 -# -LOCTRANS -INSTANT +stflx_io salt_flx -1 -1 0 i2o.nc IGNORED +NA NA ########## -# Field 16 : next heat flux (heatflux into ocean. '42' not right.) +# Field 16 : next heat flux (heatflux into ocean) ########## -htflx_io mh_flux -1 -1 1 i2o.nc IGNORED -cict cict LAG=0 SEQ=+1 -# -LOCTRANS -INSTANT +htflx_io mh_flux -1 -1 0 i2o.nc IGNORED +NA NA ########## # Field 17 : swflux penetrating through ice into ocean ######### -swflx_io sw_flux -1 -1 1 i2o.nc IGNORED -cict cict LAG=0 SEQ=+1 -# -LOCTRANS -INSTANT +swflx_io sw_flux -1 -1 0 i2o.nc IGNORED +NA NA ########## # Field 18 : latent heat flux ########## -qflux_io q_flux -1 -1 1 i2o.nc IGNORED -cict cict LAG=0 SEQ=+1 -# -LOCTRANS -INSTANT +qflux_io q_flux -1 -1 0 i2o.nc IGNORED +NA NA ######### # Field 19 : Sensible heat flux ########## -shflx_io t_flux -1 -1 1 i2o.nc IGNORED -cict cict LAG=0 SEQ=+1 -# -LOCTRANS -INSTANT +shflx_io t_flux -1 -1 0 i2o.nc IGNORED +NA NA ########## # Field 20 : LW radiation flux down ########## -lwflx_io lw_flux -1 -1 1 i2o.nc IGNORED -cict cict LAG=0 SEQ=+1 -# -LOCTRANS -INSTANT +lwflx_io lw_flux -1 -1 0 i2o.nc IGNORED +NA NA ########## # Field 21 : runoff ########## -runof_io runof -1 -1 1 i2o.nc IGNORED -cict cict LAG=0 SEQ=+1 -# -LOCTRANS -INSTANT +runof_io runof -1 -1 0 i2o.nc IGNORED +NA NA ########## # Field 22 : surface pressure ########## -press_io p -1 -1 1 i2o.nc IGNORED -cict cict LAG=0 SEQ=+1 -# -LOCTRANS -INSTANT +press_io p -1 -1 0 i2o.nc IGNORED +NA NA ########## # Field 23 : ice concentration ########## -aice_io aice -1 -1 1 i2o.nc IGNORED -cict cict LAG=0 SEQ=+1 -# -LOCTRANS -INSTANT +aice_io aice -1 -1 0 i2o.nc IGNORED +NA NA ########## # Field 24 : ice melting waterflux ########## -melt_io wfimelt -1 -1 1 i2o.nc IGNORED -cict cict LAG=0 SEQ=+1 -# -LOCTRANS -INSTANT +melt_io wfimelt -1 -1 0 i2o.nc IGNORED +NA NA ########## # Field 25 : ice forming eaterflux ########## -form_io wfiform -1 -1 1 i2o.nc IGNORED -cict cict LAG=0 SEQ=+1 -# -LOCTRANS -INSTANT +form_io wfiform -1 -1 0 i2o.nc IGNORED +NA NA ############################################################################ # # OCEAN --->>> ICE @@ -313,60 +257,36 @@ INSTANT ########## # Field 26 : Sea surface temperature (Celsius in MOM4, Kelvin in MOM5) ########## -t_surf sst_i -1 -1 1 o2i.nc IGNORED -cict cict LAG=0 SEQ=+1 -# -LOCTRANS -INSTANT +t_surf sst_i -1 -1 0 o2i.nc IGNORED +NA NA ########## # Field 27 : Sea surface salinity (psu) ########## -s_surf sss_i -1 -1 1 o2i.nc IGNORED -cict cict LAG=0 SEQ=+1 -# -LOCTRANS -INSTANT +s_surf sss_i -1 -1 0 o2i.nc IGNORED +NA NA ########## # Field 28 : 'eastward' sea surface water velocity ########## -u_surf ssu_i -1 -1 1 o2i.nc IGNORED -cict cict LAG=0 SEQ=+1 -# -LOCTRANS -INSTANT +u_surf ssu_i -1 -1 0 o2i.nc IGNORED +NA NA ########## # Field 29 : 'northward' sea surface water velocity ########## -v_surf ssv_i -1 -1 1 o2i.nc IGNORED -cict cict LAG=0 SEQ=+1 -# -LOCTRANS -INSTANT +v_surf ssv_i -1 -1 0 o2i.nc IGNORED +NA NA ########## # Field 30 : frazil ice fromation energy (J/m^2) -# ('441' is "upward_sea_ice_basal_heat_flux' 'W m-2') ########## -frazil pfmice_i -1 -1 1 o2i.nc IGNORED -cict cict LAG=0 SEQ=+1 -# -LOCTRANS -INSTANT +frazil pfmice_i -1 -1 0 o2i.nc IGNORED +NA NA ########## # Field 31 : sea surface slope _x_ (m/m) -# ( '203' is "height" ...) ########## -dssldx sslx_i -1 -1 1 o2i.nc IGNORED -cict cict LAG=0 SEQ=+1 -# -LOCTRANS -INSTANT +dssldx sslx_i -1 -1 0 o2i.nc IGNORED +NA NA ########## # Field 32 : sea surface slope _y_ (m/m) -# ( '310' is "sea_surface_elevation") ########## -dssldy ssly_i -1 -1 1 o2i.nc IGNORED -cict cict LAG=0 SEQ=+1 -# -LOCTRANS -INSTANT +dssldy ssly_i -1 -1 0 o2i.nc IGNORED +NA NA $END From 59e7684fce09ce88b7bfd923e9a0dff5f08ed137 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Tue, 5 May 2020 21:19:40 +1000 Subject: [PATCH 035/111] improve CICE diagnostic consistency across configs --- ice/cice_in.nml | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/ice/cice_in.nml b/ice/cice_in.nml index 4ccbe248..da5b53b1 100644 --- a/ice/cice_in.nml +++ b/ice/cice_in.nml @@ -209,10 +209,10 @@ , f_snow_ai = 'm' , f_rain = 'x' , f_rain_ai = 'm' - , f_sst = 'm' - , f_sss = 'm' - , f_uocn = 'm' - , f_vocn = 'm' + , f_sst = 'x' + , f_sss = 'x' + , f_uocn = 'x' + , f_vocn = 'x' , f_frzmlt = 'm' , f_fswfac = 'm' , f_fswabs = 'x' @@ -245,7 +245,7 @@ , f_meltl = 'm' , f_fresh = 'x' , f_fresh_ai = 'm' - , f_fsalt = 'x' + , f_fsalt = 'm' , f_fsalt_ai = 'm' , f_fhocn = 'x' , f_fhocn_ai = 'm' @@ -253,7 +253,7 @@ , f_fswthru_ai = 'm' , f_fsurf_ai = 'x' , f_fcondtop_ai = 'm' - , f_fmeltt_ai = 'x' + , f_fmeltt_ai = 'm' , f_strairx = 'm' , f_strairy = 'm' , f_strtltx = 'm' @@ -267,8 +267,8 @@ , f_strength = 'm' , f_divu = 'm' , f_shear = 'm' - , f_sig1 = 'x' - , f_sig2 = 'x' + , f_sig1 = 'm' + , f_sig2 = 'm' , f_dvidtt = 'm' , f_dvidtd = 'm' , f_daidtt = 'm' @@ -300,7 +300,7 @@ , f_dardg1dt = 'x' , f_dardg2dt = 'x' , f_dvirdgdt = 'x' - , f_opening = 'x' + , f_opening = 'm' , f_ardgn = 'x' , f_vrdgn = 'x' , f_dardg1ndt = 'x' @@ -318,14 +318,14 @@ f_apondn = 'x' , f_apeffn = 'x' , f_hpondn = 'x' - , f_apond = 'm' - , f_hpond = 'm' - , f_ipond = 'm' - , f_apeff = 'm' - , f_apond_ai = 'm' - , f_hpond_ai = 'm' - , f_ipond_ai = 'm' - , f_apeff_ai = 'm' + , f_apond = 'x' + , f_hpond = 'x' + , f_ipond = 'x' + , f_apeff = 'x' + , f_apond_ai = 'x' + , f_hpond_ai = 'x' + , f_ipond_ai = 'x' + , f_apeff_ai = 'x' / &icefields_bgc_nml From 20d63b15bbfbc35d90d5541460e19ceeba3482fc Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Wed, 6 May 2020 21:57:42 +1000 Subject: [PATCH 036/111] Remove redundant neutral physics namelist entries - see https://github.com/COSIMA/access-om2/issues/197 --- ocean/input.nml | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/ocean/input.nml b/ocean/input.nml index 3c7fa988..f68581a7 100644 --- a/ocean/input.nml +++ b/ocean/input.nml @@ -220,7 +220,6 @@ &ocean_nphysics_util_new_nml / &ocean_nphysics_util_nml - agm = 600.0 agm_closure = .true. agm_closure_baroclinic = .true. agm_closure_buoy_freq = 0.004 @@ -228,31 +227,17 @@ agm_closure_eady_cap = .true. agm_closure_eady_smooth_horz = .true. agm_closure_eady_smooth_vert = .true. - agm_closure_eden_gamma = 0.0 - agm_closure_eden_greatbatch = .false. agm_closure_grid_scaling = .true. agm_closure_length = 50000.0 - agm_closure_length_bczone = .false. - agm_closure_length_fixed = .false. - agm_closure_length_rossby = .false. agm_closure_lower_depth = 2000.0 agm_closure_max = 600.0 agm_closure_min = 50.0 agm_closure_scaling = 0.07 agm_closure_upper_depth = 100.0 - agm_damping_time = 45.0 - agm_smooth_space = .false. - agm_smooth_time = .false. aredi = 600.0 aredi_equal_agm = .false. drhodz_mom4p1 = .true. - drhodz_smooth_horz = .false. - drhodz_smooth_vert = .false. nphysics_util_zero_init = .true. - rossby_radius_max = 100000.0 - rossby_radius_min = 15000.0 - tracer_mix_micom = .false. - vel_micom = 0.0 / &ocean_nphysicsa_nml use_this_module = .false. From f9bd1e0ebe81b2e093d771ea05d265204b393081 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Thu, 14 May 2020 15:44:34 +1000 Subject: [PATCH 037/111] put namelists in a consistent format with nmltab.py --tidy_overwrite - should work identically to before --- atmosphere/atm.nml | 4 +- ice/cice_in.nml | 675 ++++++++++++++++++++-------------------- ice/input_ice.nml | 40 ++- ice/input_ice_gfdl.nml | 45 +-- ice/input_ice_monin.nml | 4 +- ocean/input.nml | 111 ++++++- 6 files changed, 487 insertions(+), 392 deletions(-) diff --git a/atmosphere/atm.nml b/atmosphere/atm.nml index 3936149c..1b8a20f3 100644 --- a/atmosphere/atm.nml +++ b/atmosphere/atm.nml @@ -1,6 +1,6 @@ &atm_nml -&end +/ &runoff_nml remap_weights_file = 'INPUT/rmp_jrar_to_cict_CONSERV.nc' -&end +/ diff --git a/ice/cice_in.nml b/ice/cice_in.nml index da5b53b1..4244f4f2 100644 --- a/ice/cice_in.nml +++ b/ice/cice_in.nml @@ -1,368 +1,365 @@ -&setup_nml - days_per_year = 365 - , use_leap_years = .false. - , year_init = 0001 - , istep0 = 0 - , dt = 3600 - , npt = 35040 - , ndtd = 1 - , runtype = 'initial' - , ice_ic = 'default' - , restart = .false. - , restart_ext = .false. - , use_restart_time = .true. - , restart_format = 'nc' - , restart_dir = './RESTART/' - , restart_file = 'iced' - , pointer_file = './RESTART/ice.restart_file' - , dumpfreq = 'y' - , dumpfreq_n = 1 - , dump_last = .true. - , diagfreq = 960 - , diag_type = 'file' - , diag_file = 'ice_diag.d' - , print_global = .false. - , print_points = .false. - , latpnt(1) = 90. - , lonpnt(1) = 0. - , latpnt(2) = -65. - , lonpnt(2) = -45. - , dbug = .false. - , histfreq = 'd','m','x','x','x' - , histfreq_n = 1, 1, 1, 1, 1 - , hist_avg = .true. - , history_deflate_level = 1 - , history_dir = './OUTPUT/' - , history_file = 'iceh' - , history_deflate_level = 1 - , write_ic = .false. - , incond_dir = './OUTPUT/' - , incond_file = 'iceh_ic' +&domain_nml + distribution_type = 'cartesian' + distribution_wght = 'latitude' + ew_boundary_type = 'cyclic' + maskhalo_bound = .true. + maskhalo_dyn = .true. + maskhalo_remap = .true. + nprocs = 24 + ns_boundary_type = 'tripole' + processor_shape = 'slenderX1' / -&grid_nml - grid_format = 'nc' - , grid_type = 'tripole' - , grid_file = 'RESTART/grid.nc' - , kmt_file = 'RESTART/kmt.nc' - , kcatbound = 0 +&dynamics_nml + advection = 'remap' + cosw = 1.0 + dragio = 0.00536 + iceruf = 0.0005 + kdyn = 1 + krdg_partic = 1 + krdg_redist = 1 + kstrength = 1 + mu_rdg = 3 + ndte = 120 + revised_evp = .false. + sinw = 0.0 / -&domain_nml - nprocs = 24 - , processor_shape = 'slenderX1' - , distribution_type = 'cartesian' - , distribution_wght = 'latitude' - , ew_boundary_type = 'cyclic' - , ns_boundary_type = 'tripole' - , maskhalo_dyn = .true. - , maskhalo_remap = .true. - , maskhalo_bound = .true. +&forcing_nml + atm_data_dir = 'unknown_atm_data_dir' + atm_data_format = 'nc' + atm_data_type = 'default' + atmbndy = 'default' + calc_strair = .true. + calc_tsfc = .true. + formdrag = .false. + fyear_init = 1 + highfreq = .true. + oceanmixed_file = 'unknown_oceanmixed_file' + oceanmixed_ice = .false. + ocn_data_dir = 'unknown_ocn_data_dir' + ocn_data_format = 'nc' + precip_units = 'mks' + restore_ice = .false. + restore_sst = .false. + sss_data_type = 'default' + sst_data_type = 'default' + tfrz_option = 'linear_salt' + trestore = 0 + update_ocn_f = .true. + ustar_min = 0.0005 + ycycle = 1 / -&tracer_nml - tr_iage = .false. - , restart_age = .false. - , tr_FY = .false. - , restart_FY = .false. - , tr_lvl = .false. - , restart_lvl = .false. - , tr_pond_cesm = .false. - , restart_pond_cesm = .false. - , tr_pond_topo = .false. - , restart_pond_topo = .false. - , tr_pond_lvl = .false. - , restart_pond_lvl = .false. - , tr_aero = .false. - , restart_aero = .false. +&grid_nml + grid_file = 'RESTART/grid.nc' + grid_format = 'nc' + grid_type = 'tripole' + kcatbound = 0 + kmt_file = 'RESTART/kmt.nc' / -&thermo_nml - kitd = 1 - , ktherm = 1 - , conduct = 'bubbly' - , a_rapid_mode = 0.5e-3 - , Rac_rapid_mode = 10.0 - , aspect_rapid_mode = 1.0 - , dSdt_slow_mode = -5.0e-8 - , phi_c_slow_mode = 0.05 - , phi_i_mushy = 0.85 - , chio = 0.004 +&icefields_bgc_nml + f_aero = 'x' + f_bgc_am_ml = 'x' + f_bgc_am_sk = 'x' + f_bgc_c_sk = 'x' + f_bgc_chl_sk = 'x' + f_bgc_dms_sk = 'x' + f_bgc_dmsp_ml = 'x' + f_bgc_dmspd_sk = 'x' + f_bgc_dmspp_sk = 'x' + f_bgc_n_sk = 'x' + f_bgc_nit_ml = 'x' + f_bgc_nit_sk = 'x' + f_bgc_sil_ml = 'x' + f_bgc_sil_sk = 'x' + f_bphi = 'x' + f_btin = 'x' + f_faero_atm = 'x' + f_faero_ocn = 'x' + f_fbri = 'm' + f_fn = 'x' + f_fn_ai = 'x' + f_fnh = 'x' + f_fnh_ai = 'x' + f_fno = 'x' + f_fno_ai = 'x' + f_fsil = 'x' + f_fsil_ai = 'x' + f_grownet = 'x' + f_hbri = 'm' + f_ppnet = 'x' / -&dynamics_nml - kdyn = 1 - , ndte = 120 - , revised_evp = .false. - , advection = 'remap' - , kstrength = 1 - , krdg_partic = 1 - , krdg_redist = 1 - , mu_rdg = 3 - , cosw = 1.0 - , sinw = 0.0 - , dragio = 0.00536 - , iceruf = 0.0005 +&icefields_drag_nml + f_cdn_atm = 'x' + f_cdn_ocn = 'x' + f_drag = 'x' / -&shortwave_nml - shortwave = 'default' - , albedo_type = 'default' - , albicev = 0.86 - , albicei = 0.44 - , albsnowv = 0.98 - , albsnowi = 0.70 - , ahmax = 0.1 - , R_ice = 0.0 - , R_pnd = 0.0 - , R_snw = 0.0 - , dT_mlt = 1.0 - , rsnw_mlt = 1500. - , dalb_mlt = -0.02 - , Tocnfrz = -1.8 +&icefields_mechred_nml + f_alvl = 'm' + f_aparticn = 'x' + f_araftn = 'x' + f_ardg = 'm' + f_ardgn = 'x' + f_aredistn = 'x' + f_dardg1dt = 'x' + f_dardg1ndt = 'x' + f_dardg2dt = 'x' + f_dardg2ndt = 'x' + f_dvirdgdt = 'x' + f_dvirdgndt = 'x' + f_krdgn = 'x' + f_opening = 'm' + f_vlvl = 'm' + f_vraftn = 'x' + f_vrdg = 'm' + f_vrdgn = 'x' + f_vredistn = 'x' / -&ponds_nml - hp1 = 0.01 - , hs0 = 0. - , hs1 = 0.03 - , dpscale = 1.e-3 - , frzpnd = 'hlid' - , rfracmin = 0.15 - , rfracmax = 1. - , pndaspect = 0.8 +&icefields_nml + f_aice = 'm' + f_aicen = 'm' + f_aisnap = 'x' + f_albice = 'm' + f_albpnd = 'x' + f_albsni = 'm' + f_albsno = 'm' + f_alidr = 'x' + f_alvdr = 'x' + f_angle = .true. + f_anglet = .true. + f_bounds = .false. + f_congel = 'm' + f_coszen = 'x' + f_daidtd = 'm' + f_daidtt = 'm' + f_divu = 'm' + f_dsnow = 'x' + f_dvidtd = 'm' + f_dvidtt = 'm' + f_dxt = .true. + f_dxu = .true. + f_dyt = .true. + f_dyu = .true. + f_evap = 'x' + f_evap_ai = 'm' + f_fcondtop_ai = 'm' + f_fcondtopn_ai = 'm' + f_fhocn = 'x' + f_fhocn_ai = 'm' + f_flat = 'x' + f_flat_ai = 'm' + f_flatn_ai = 'm' + f_flwdn = 'm' + f_flwup = 'x' + f_flwup_ai = 'm' + f_fmeltt_ai = 'm' + f_fmelttn_ai = 'm' + f_frazil = 'm' + f_fresh = 'x' + f_fresh_ai = 'm' + f_frz_onset = 'm' + f_frzmlt = 'm' + f_fsalt = 'm' + f_fsalt_ai = 'm' + f_fsens = 'x' + f_fsens_ai = 'm' + f_fsurf_ai = 'x' + f_fsurfn_ai = 'm' + f_fswabs = 'x' + f_fswabs_ai = 'm' + f_fswdn = 'm' + f_fswfac = 'm' + f_fswthru = 'x' + f_fswthru_ai = 'm' + f_fy = 'x' + f_hi = 'm' + f_hisnap = 'x' + f_hs = 'm' + f_hte = .true. + f_htn = .true. + f_iage = 'm' + f_icepresent = 'm' + f_meltb = 'm' + f_meltl = 'm' + f_melts = 'm' + f_meltt = 'm' + f_mlt_onset = 'm' + f_ncat = .true. + f_qref = 'x' + f_rain = 'x' + f_rain_ai = 'm' + f_shear = 'm' + f_sice = 'm' + f_sig1 = 'm' + f_sig2 = 'm' + f_sinz = 'x' + f_snoice = 'm' + f_snow = 'x' + f_snow_ai = 'm' + f_sss = 'x' + f_sst = 'x' + f_strairx = 'm' + f_strairy = 'm' + f_strcorx = 'm' + f_strcory = 'm' + f_strength = 'm' + f_strintx = 'm' + f_strinty = 'm' + f_strocnx = 'm' + f_strocny = 'm' + f_strtltx = 'm' + f_strtlty = 'm' + f_tair = 'm' + f_tarea = .true. + f_tinz = 'x' + f_tmask = .true. + f_tref = 'x' + f_trsig = 'm' + f_tsfc = 'm' + f_tsnz = 'x' + f_uarea = .true. + f_uocn = 'x' + f_uvel = 'm' + f_vgrdb = .false. + f_vgrdi = .false. + f_vgrds = .false. + f_vicen = 'm' + f_vocn = 'x' + f_vvel = 'm' / -&zbgc_nml - tr_brine = .false. - , restart_hbrine = .false. - , skl_bgc = .false. - , bgc_flux_type = 'Jin2006' - , restart_bgc = .false. - , restore_bgc = .false. - , bgc_data_dir = 'unknown_bgc_data_dir' - , sil_data_type = 'default' - , nit_data_type = 'default' - , tr_bgc_C_sk = .false. - , tr_bgc_chl_sk = .false. - , tr_bgc_Am_sk = .false. - , tr_bgc_Sil_sk = .false. - , tr_bgc_DMSPp_sk = .false. - , tr_bgc_DMSPd_sk = .false. - , tr_bgc_DMS_sk = .false. - , phi_snow = 0.5 +&icefields_pond_nml + f_apeff = 'x' + f_apeff_ai = 'x' + f_apeffn = 'x' + f_apond = 'x' + f_apond_ai = 'x' + f_apondn = 'x' + f_hpond = 'x' + f_hpond_ai = 'x' + f_hpondn = 'x' + f_ipond = 'x' + f_ipond_ai = 'x' / -&forcing_nml - formdrag = .false. - , atmbndy = 'default' - , fyear_init = 0001 - , ycycle = 1 - , atm_data_format = 'nc' - , atm_data_type = 'default' - , atm_data_dir = 'unknown_atm_data_dir' - , calc_strair = .true. - , calc_Tsfc = .true. - , precip_units = 'mks' - , update_ocn_f = .true. - , oceanmixed_ice = .false. - , ocn_data_format = 'nc' - , sss_data_type = 'default' - , sst_data_type = 'default' - , ocn_data_dir = 'unknown_ocn_data_dir' - , oceanmixed_file = 'unknown_oceanmixed_file' - , restore_sst = .false. - , trestore = 0 - , restore_ice = .false. - , ustar_min = 0.0005 - , tfrz_option = 'linear_salt' - , highfreq = .true. +&ponds_nml + dpscale = 0.001 + frzpnd = 'hlid' + hp1 = 0.01 + hs0 = 0.0 + hs1 = 0.03 + pndaspect = 0.8 + rfracmax = 1.0 + rfracmin = 0.15 / -&icefields_nml - f_tmask = .true. - , f_tarea = .true. - , f_uarea = .true. - , f_dxt = .true. - , f_dyt = .true. - , f_dxu = .true. - , f_dyu = .true. - , f_HTN = .true. - , f_HTE = .true. - , f_ANGLE = .true. - , f_ANGLET = .true. - , f_NCAT = .true. - , f_VGRDi = .false. - , f_VGRDs = .false. - , f_VGRDb = .false. - , f_bounds = .false. - , f_sice = 'm' - , f_hi = 'm' - , f_hs = 'm' - , f_Tsfc = 'm' - , f_aice = 'm' - , f_uvel = 'm' - , f_vvel = 'm' - , f_fswdn = 'm' - , f_flwdn = 'm' - , f_snow = 'x' - , f_snow_ai = 'm' - , f_rain = 'x' - , f_rain_ai = 'm' - , f_sst = 'x' - , f_sss = 'x' - , f_uocn = 'x' - , f_vocn = 'x' - , f_frzmlt = 'm' - , f_fswfac = 'm' - , f_fswabs = 'x' - , f_fswabs_ai = 'm' - , f_albsni = 'm' - , f_alvdr = 'x' - , f_alidr = 'x' - , f_albice = 'm' - , f_albsno = 'm' - , f_albpnd = 'x' - , f_coszen = 'x' - , f_flat = 'x' - , f_flat_ai = 'm' - , f_fsens = 'x' - , f_fsens_ai = 'm' - , f_flwup = 'x' - , f_flwup_ai = 'm' - , f_evap = 'x' - , f_evap_ai = 'm' - , f_Tair = 'm' - , f_Tref = 'x' - , f_Qref = 'x' - , f_congel = 'm' - , f_frazil = 'm' - , f_snoice = 'm' - , f_dsnow = 'x' - , f_melts = 'm' - , f_meltt = 'm' - , f_meltb = 'm' - , f_meltl = 'm' - , f_fresh = 'x' - , f_fresh_ai = 'm' - , f_fsalt = 'm' - , f_fsalt_ai = 'm' - , f_fhocn = 'x' - , f_fhocn_ai = 'm' - , f_fswthru = 'x' - , f_fswthru_ai = 'm' - , f_fsurf_ai = 'x' - , f_fcondtop_ai = 'm' - , f_fmeltt_ai = 'm' - , f_strairx = 'm' - , f_strairy = 'm' - , f_strtltx = 'm' - , f_strtlty = 'm' - , f_strcorx = 'm' - , f_strcory = 'm' - , f_strocnx = 'm' - , f_strocny = 'm' - , f_strintx = 'm' - , f_strinty = 'm' - , f_strength = 'm' - , f_divu = 'm' - , f_shear = 'm' - , f_sig1 = 'm' - , f_sig2 = 'm' - , f_dvidtt = 'm' - , f_dvidtd = 'm' - , f_daidtt = 'm' - , f_daidtd = 'm' - , f_mlt_onset = 'm' - , f_frz_onset = 'm' - , f_hisnap = 'x' - , f_aisnap = 'x' - , f_trsig = 'm' - , f_icepresent = 'm' - , f_iage = 'm' - , f_FY = 'x' - , f_aicen = 'm' - , f_vicen = 'm' - , f_Tinz = 'x' - , f_Sinz = 'x' - , f_Tsnz = 'x' - , f_fsurfn_ai = 'm' - , f_fcondtopn_ai = 'm' - , f_fmelttn_ai = 'm' - , f_flatn_ai = 'm' +&setup_nml + days_per_year = 365 + dbug = .false. + diag_file = 'ice_diag.d' + diag_type = 'file' + diagfreq = 960 + dt = 3600 + dump_last = .true. + dumpfreq = 'y' + dumpfreq_n = 1 + hist_avg = .true. + histfreq = 'd', 'm', 'x', 'x', 'x' + histfreq_n = 1, 1, 1, 1, 1 + history_deflate_level = 1 + history_dir = './OUTPUT/' + history_file = 'iceh' + ice_ic = 'default' + incond_dir = './OUTPUT/' + incond_file = 'iceh_ic' + istep0 = 0 + latpnt = 90.0, -65.0 + lonpnt = 0.0, -45.0 + ndtd = 1 + npt = 35040 + pointer_file = './RESTART/ice.restart_file' + print_global = .false. + print_points = .false. + restart = .false. + restart_dir = './RESTART/' + restart_ext = .false. + restart_file = 'iced' + restart_format = 'nc' + runtype = 'initial' + use_leap_years = .false. + use_restart_time = .true. + write_ic = .false. + year_init = 1 / -&icefields_mechred_nml - f_alvl = 'm' - , f_vlvl = 'm' - , f_ardg = 'm' - , f_vrdg = 'm' - , f_dardg1dt = 'x' - , f_dardg2dt = 'x' - , f_dvirdgdt = 'x' - , f_opening = 'm' - , f_ardgn = 'x' - , f_vrdgn = 'x' - , f_dardg1ndt = 'x' - , f_dardg2ndt = 'x' - , f_dvirdgndt = 'x' - , f_krdgn = 'x' - , f_aparticn = 'x' - , f_aredistn = 'x' - , f_vredistn = 'x' - , f_araftn = 'x' - , f_vraftn = 'x' +&shortwave_nml + ahmax = 0.1 + albedo_type = 'default' + albicei = 0.44 + albicev = 0.86 + albsnowi = 0.7 + albsnowv = 0.98 + dalb_mlt = -0.02 + dt_mlt = 1.0 + r_ice = 0.0 + r_pnd = 0.0 + r_snw = 0.0 + rsnw_mlt = 1500.0 + shortwave = 'default' + tocnfrz = -1.8 / -&icefields_pond_nml - f_apondn = 'x' - , f_apeffn = 'x' - , f_hpondn = 'x' - , f_apond = 'x' - , f_hpond = 'x' - , f_ipond = 'x' - , f_apeff = 'x' - , f_apond_ai = 'x' - , f_hpond_ai = 'x' - , f_ipond_ai = 'x' - , f_apeff_ai = 'x' +&thermo_nml + a_rapid_mode = 0.0005 + aspect_rapid_mode = 1.0 + chio = 0.004 + conduct = 'bubbly' + dsdt_slow_mode = -5e-08 + kitd = 1 + ktherm = 1 + phi_c_slow_mode = 0.05 + phi_i_mushy = 0.85 + rac_rapid_mode = 10.0 / -&icefields_bgc_nml - f_faero_atm = 'x' - , f_faero_ocn = 'x' - , f_aero = 'x' - , f_fNO = 'x' - , f_fNO_ai = 'x' - , f_fNH = 'x' - , f_fNH_ai = 'x' - , f_fN = 'x' - , f_fN_ai = 'x' - , f_fSil = 'x' - , f_fSil_ai = 'x' - , f_bgc_N_sk = 'x' - , f_bgc_C_sk = 'x' - , f_bgc_chl_sk = 'x' - , f_bgc_Nit_sk = 'x' - , f_bgc_Am_sk = 'x' - , f_bgc_Sil_sk = 'x' - , f_bgc_DMSPp_sk = 'x' - , f_bgc_DMSPd_sk = 'x' - , f_bgc_DMS_sk = 'x' - , f_bgc_Nit_ml = 'x' - , f_bgc_Am_ml = 'x' - , f_bgc_Sil_ml = 'x' - , f_bgc_DMSP_ml = 'x' - , f_bTin = 'x' - , f_bphi = 'x' - , f_fbri = 'm' - , f_hbri = 'm' - , f_grownet = 'x' - , f_PPnet = 'x' +&tracer_nml + restart_aero = .false. + restart_age = .false. + restart_fy = .false. + restart_lvl = .false. + restart_pond_cesm = .false. + restart_pond_lvl = .false. + restart_pond_topo = .false. + tr_aero = .false. + tr_fy = .false. + tr_iage = .false. + tr_lvl = .false. + tr_pond_cesm = .false. + tr_pond_lvl = .false. + tr_pond_topo = .false. / -&icefields_drag_nml - f_drag = 'x' - , f_Cdn_atm = 'x' - , f_Cdn_ocn = 'x' +&zbgc_nml + bgc_data_dir = 'unknown_bgc_data_dir' + bgc_flux_type = 'Jin2006' + nit_data_type = 'default' + phi_snow = 0.5 + restart_bgc = .false. + restart_hbrine = .false. + restore_bgc = .false. + sil_data_type = 'default' + skl_bgc = .false. + tr_bgc_am_sk = .false. + tr_bgc_c_sk = .false. + tr_bgc_chl_sk = .false. + tr_bgc_dms_sk = .false. + tr_bgc_dmspd_sk = .false. + tr_bgc_dmspp_sk = .false. + tr_bgc_sil_sk = .false. + tr_brine = .false. / diff --git a/ice/input_ice.nml b/ice/input_ice.nml index 52b03bf0..fa770b1d 100644 --- a/ice/input_ice.nml +++ b/ice/input_ice.nml @@ -1,23 +1,29 @@ &coupling_nml - pop_icediag = .true. - ice_pressure_on = .true. + chk_a2i_fields = .false. + chk_frzmlt_sst = .false. + chk_gfdl_roughness = .false. + chk_i2a_fields = .false. + chk_i2o_fields = .false. + chk_o2i_fields = .false. + cst_ocn_albedo = .true. + fields_from_atm = 'swfld_i', 'lwfld_i', 'rain_i', 'snow_i', 'press_i', + 'runof_i', 'tair_i', 'qair_i', 'uwnd_i', 'vwnd_i', + 'licalvf_i' + fields_from_ocn = 'sst_i', 'sss_i', 'ssu_i', 'ssv_i', 'sslx_i', 'ssly_i', + 'pfmice_i' + fields_to_ocn = 'strsu_io', 'strsv_io', 'rain_io', 'snow_io', 'stflx_io', + 'htflx_io', 'swflx_io', 'qflux_io', 'shflx_io', 'lwflx_io', + 'runof_io', 'press_io', 'aice_io', 'melt_io', 'form_io', + 'licefw_io', 'licefh_io' + gfdl_surface_flux = .true. ice_fwflux = .true. - use_ocnslope = .false. - use_umask = .false. - rotate_winds = .true. + ice_pressure_on = .true. limit_icemelt = .false. meltlimit = -200.0 - precip_factor = 1.0 - cst_ocn_albedo = .true. ocn_albedo = 0.1 - gfdl_surface_flux = .true. - chk_gfdl_roughness = .false. - chk_frzmlt_sst = .false. - chk_i2o_fields = .false. - chk_o2i_fields = .false. - chk_i2a_fields = .false. - chk_a2i_fields = .false. - fields_from_atm = 'swfld_i', 'lwfld_i', 'rain_i', 'snow_i', 'press_i', 'runof_i', 'tair_i', 'qair_i', 'uwnd_i', 'vwnd_i', 'licalvf_i' - fields_to_ocn = 'strsu_io', 'strsv_io', 'rain_io', 'snow_io', 'stflx_io', 'htflx_io', 'swflx_io', 'qflux_io', 'shflx_io', 'lwflx_io', 'runof_io', 'press_io', 'aice_io', 'melt_io', 'form_io', 'licefw_io', 'licefh_io' - fields_from_ocn = 'sst_i', 'sss_i', 'ssu_i', 'ssv_i', 'sslx_i', 'ssly_i', 'pfmice_i' + pop_icediag = .true. + precip_factor = 1.0 + rotate_winds = .true. + use_ocnslope = .false. + use_umask = .false. / diff --git a/ice/input_ice_gfdl.nml b/ice/input_ice_gfdl.nml index bf902749..4a8cdaff 100644 --- a/ice/input_ice_gfdl.nml +++ b/ice/input_ice_gfdl.nml @@ -1,24 +1,25 @@ -&surface_flux_nml -no_neg_q = .false. -use_virtual_temp = .true. -alt_gustiness = .false. -old_dtaudv = .false. -use_mixing_ratio = .false. -gust_const = 1.0 -gust_min = 0.0 -ncar_ocean_flux = .true. -ncar_ocean_flux_orig = .false. -raoult_sat_vap = .false. -/ &ocean_rough_nml -roughness_mom = 5.8e-5 -roughness_heat = 5.8e-5 -roughness_moist = 5.8e-5 -roughness_min = 1.0e-6 -charnock = 0.032 -rough_scheme = 'beljaars' -do_highwind = .false. -do_cap40 = .false. -zcoh1 = 0.0 -zcoq1 = 0.0 + charnock = 0.032 + do_cap40 = .false. + do_highwind = .false. + rough_scheme = 'beljaars' + roughness_heat = 5.8e-05 + roughness_min = 1e-06 + roughness_moist = 5.8e-05 + roughness_mom = 5.8e-05 + zcoh1 = 0.0 + zcoq1 = 0.0 +/ + +&surface_flux_nml + alt_gustiness = .false. + gust_const = 1.0 + gust_min = 0.0 + ncar_ocean_flux = .true. + ncar_ocean_flux_orig = .false. + no_neg_q = .false. + old_dtaudv = .false. + raoult_sat_vap = .false. + use_mixing_ratio = .false. + use_virtual_temp = .true. / diff --git a/ice/input_ice_monin.nml b/ice/input_ice_monin.nml index 321d7d73..e3456c97 100644 --- a/ice/input_ice_monin.nml +++ b/ice/input_ice_monin.nml @@ -1,3 +1,3 @@ &monin_obukhov_nml -neutral=.true. -&end + neutral = .true. +/ diff --git a/ocean/input.nml b/ocean/input.nml index f68581a7..23c07ea4 100644 --- a/ocean/input.nml +++ b/ocean/input.nml @@ -14,50 +14,62 @@ tmelt = -0.216 use_ioaice = .true. / + &data_override_nml / + &diag_manager_nml debug_diag_manager = .false. issue_oor_warnings = .true. / + &fms_io_nml fileset_write = 'single' threading_read = 'multi' threading_write = 'single' / + &fms_nml clock_grain = 'LOOP' domains_stack_size = 115200 / + &mom_oasis3_interface_nml - fields_in = 'u_flux', 'v_flux', 'lprec', 'fprec', 'salt_flx', 'mh_flux', 'sw_flux', - 'q_flux', 't_flux', 'lw_flux', 'runof', 'p', 'aice', 'wfimelt', - 'wfiform', 'licefw', 'liceht' - fields_out = 't_surf', 's_surf', 'u_surf', 'v_surf', 'dssldx', 'dssldy', 'frazil', + fields_in = 'u_flux', 'v_flux', 'lprec', 'fprec', 'salt_flx', 'mh_flux', + 'sw_flux', 'q_flux', 't_flux', 'lw_flux', 'runof', 'p', + 'aice', 'wfimelt', 'wfiform', 'licefw', 'liceht' + fields_out = 't_surf', 's_surf', 'u_surf', 'v_surf', 'dssldx', 'dssldy', + 'frazil' num_fields_in = 17 num_fields_out = 7 send_after_ocean_update = .true. send_before_ocean_update = .false. / + &monin_obukhov_nml neutral = .true. / + &mpp_io_nml deflate_level = -1 shuffle = 1 / + &ocean_adv_vel_diag_nml diag_step = 4320 large_cfl_value = 10.0 max_cfl_value = 100.0 verbose_cfl = .true. / + &ocean_advection_velocity_nml max_advection_velocity = 0.5 / + &ocean_albedo_nml ocean_albedo_option = 2 / + &ocean_barotropic_nml barotropic_halo = 10 barotropic_time_stepping_a = .true. @@ -80,6 +92,7 @@ verbose_truncate = .true. zero_tendency = .false. / + &ocean_bbc_nml bmf_implicit = .true. cdbot = 0.001 @@ -89,15 +102,19 @@ uresidual = 0.05 use_geothermal_heating = .false. / + &ocean_bih_friction_nml bih_friction_scheme = 'general' / + &ocean_bih_tracer_nml use_this_module = .false. / + &ocean_bihcst_friction_nml use_this_module = .false. / + &ocean_bihgen_friction_nml bottom_5point = .true. eq_lat_micom = 0.0 @@ -117,15 +134,19 @@ vel_micom_iso = 0.04 visc_crit_scale = 0.25 / + &ocean_blob_nml / + &ocean_convect_nml use_this_module = .false. / + &ocean_coriolis_nml acor = 0.5 use_this_module = .true. / + &ocean_density_nml eos_linear = .false. eos_preteos10 = .true. @@ -135,14 +156,18 @@ potrho_max = 1038.0 potrho_min = 1028.0 / + &ocean_domains_nml max_tracers = 5 / + &ocean_drifters_nml / + &ocean_form_drag_nml use_this_module = .false. / + &ocean_frazil_nml debug_this_module = .false. frazil_only_in_surface = .false. @@ -150,27 +175,35 @@ freezing_temp_simple = .false. use_this_module = .true. / + &ocean_grids_nml debug_this_module = .false. / + &ocean_increment_eta_nml use_this_module = .false. / + &ocean_increment_tracer_nml use_this_module = .false. / + &ocean_increment_velocity_nml use_this_module = .false. / + &ocean_lap_friction_nml lap_friction_scheme = 'general' / + &ocean_lap_tracer_nml use_this_module = .false. / + &ocean_lapcst_friction_nml use_this_module = .false. / + &ocean_lapgen_friction_nml bottom_5point = .true. k_smag_aniso = 0.0 @@ -185,6 +218,7 @@ viscosity_scale_by_rossby = .true. viscosity_scale_by_rossby_power = 4.0 / + &ocean_mixdownslope_nml debug_this_module = .false. mixdownslope_mask_gfdl = .false. @@ -192,6 +226,7 @@ read_mixdownslope_mask = .false. use_this_module = .true. / + &ocean_model_nml baroclinic_split = 1 barotropic_split = 80 @@ -203,13 +238,16 @@ time_tendency = 'twolevel' vertical_coordinate = 'zstar' / + &ocean_momentum_source_nml rayleigh_damp_exp_from_bottom = .false. use_rayleigh_damp_table = .true. use_this_module = .true. / + &ocean_nphysics_new_nml / + &ocean_nphysics_nml debug_this_module = .false. use_nphysicsa = .false. @@ -217,8 +255,10 @@ use_nphysicsc = .true. use_this_module = .true. / + &ocean_nphysics_util_new_nml / + &ocean_nphysics_util_nml agm_closure = .true. agm_closure_baroclinic = .true. @@ -239,12 +279,15 @@ drhodz_mom4p1 = .true. nphysics_util_zero_init = .true. / + &ocean_nphysicsa_nml use_this_module = .false. / + &ocean_nphysicsb_nml use_this_module = .false. / + &ocean_nphysicsc_nml bv_freq_smooth_vert = .true. bvp_bc_mode = 2 @@ -266,13 +309,17 @@ turb_blayer_min = 50.0 use_this_module = .true. / + &ocean_obc_nml / + &ocean_obs_nml / + &ocean_operators_nml use_legacy_div_ud = .false. / + &ocean_overexchange_nml debug_this_module = .false. overexch_npts = 4 @@ -280,20 +327,26 @@ overflow_umax = 5.0 use_this_module = .false. / + &ocean_overflow_nml use_this_module = .false. / + &ocean_overflow_ofp_nml use_this_module = .false. / + &ocean_passive_nml / + &ocean_polar_filter_nml use_this_module = .false. / + &ocean_pressure_nml zero_pressure_force = .false. / + &ocean_rivermix_nml debug_this_module = .false. river_diffuse_salt = .true. @@ -303,12 +356,15 @@ river_insertion_thickness = 40.0 use_this_module = .true. / + &ocean_riverspread_nml use_this_module = .false. / + &ocean_rough_nml rough_scheme = 'beljaars' / + &ocean_sbc_nml avg_sfc_temp_salt_eta = .true. avg_sfc_velocity = .true. @@ -338,9 +394,11 @@ zero_surface_stress = .false. zero_water_fluxes = .false. / + &ocean_shortwave_csiro_nml use_this_module = .false. / + &ocean_shortwave_gfdl_nml debug_this_module = .false. enforce_sw_frac = .true. @@ -348,31 +406,39 @@ optics_morel_antoine = .false. read_chl = .true. use_this_module = .true. - zmax_pen = 1.0e6 + zmax_pen = 1000000.0 / + &ocean_shortwave_jerlov_nml use_this_module = .false. / + &ocean_shortwave_nml use_shortwave_csiro = .false. use_shortwave_gfdl = .true. use_shortwave_jerlov = .false. use_this_module = .true. / + &ocean_sigma_transport_nml use_this_module = .true. / + &ocean_solo_nml / + &ocean_sponges_eta_nml use_this_module = .false. / + &ocean_sponges_tracer_nml use_this_module = .false. / + &ocean_sponges_velocity_nml use_this_module = .false. / + &ocean_submesoscale_nml coefficient_ce = 0.05 debug_this_module = .false. @@ -398,6 +464,7 @@ use_psi_legacy = .false. use_this_module = .true. / + &ocean_tempsalt_nml debug_this_module = .false. pottemp_2nd_iteration = .true. @@ -411,26 +478,32 @@ t_min_limit = -5.0 temperature_variable = 'conservative_temp' / + &ocean_thickness_nml debug_this_module = .false. debug_this_module_detail = .false. rescale_mass_to_get_ht_mod = .false. thickness_method = 'energetic' / + &ocean_time_filter_nml / + &ocean_topog_nml - min_thickness = 1.0e-3 + min_thickness = 0.001 / + &ocean_tracer_advect_nml debug_this_module = .false. read_basin_mask = .false. / + &ocean_tracer_diag_nml diag_step = 4320 do_bitwise_exact_sum = .false. tracer_conserve_days = 30.0 / + &ocean_tracer_nml age_tracer_max_init = 0.0 debug_this_module = .false. @@ -442,8 +515,10 @@ zero_tendency = .false. zero_tracer_source = .false. / + &ocean_velocity_advect_nml / + &ocean_velocity_diag_nml debug_this_module = .false. diag_step = 4320 @@ -451,6 +526,7 @@ large_cfl_value = 10.0 max_cfl_value = 100.0 / + &ocean_velocity_nml adams_bashforth_third = .true. max_cgint = 1.0 @@ -462,17 +538,23 @@ zero_tendency_explicit_b = .false. zero_tendency_implicit = .false. / + &ocean_vert_chen_nml / + &ocean_vert_const_nml / + &ocean_vert_gotm_nml / + &ocean_vert_kpp_iow_nml use_this_module = .false. / + &ocean_vert_kpp_mom4p0_nml / + &ocean_vert_kpp_mom4p1_nml diff_cbt_iw = 0.0 double_diffusion = .true. @@ -483,6 +565,7 @@ use_this_module = .true. visc_cbu_iw = 0.0 / + &ocean_vert_mix_nml aidif = 1.0 bryan_lewis_diffusivity = .false. @@ -490,16 +573,18 @@ hwf_diffusivity = .false. hwf_min_diffusivity = 2e-06 hwf_n0_2omega = 20.0 + j09_bgmax = 5e-06 + j09_bgmin = 1e-06 + j09_diffusivity = .true. + j09_lat = 20.0 use_diff_cbt_table = .false. vert_diff_back_via_max = .true. vert_mix_scheme = 'kpp_mom4p1' - j09_diffusivity = .true. - j09_bgmin = 1.0e-6 - j09_bgmax = 0.5e-5 - j09_lat = 20.0 / + &ocean_vert_pp_nml / + &ocean_vert_tidal_nml background_diffusivity = 0.0 background_viscosity = 0.0001 @@ -523,18 +608,24 @@ use_wave_dissipation = .true. wave_energy_flux_max = 0.1 / + &ocean_xlandinsert_nml use_this_module = .false. / + &ocean_xlandmix_nml use_this_module = .false. / + &oda_core_nml / + &oda_nml / + &surface_flux_nml / + &xgrid_nml interp_method = 'second_order' make_exchange_reproduce = .false. From b27a0b6eef1253d65c8ea530b1e48deaf3ebe80e Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Thu, 14 May 2020 15:50:51 +1000 Subject: [PATCH 038/111] remove repeated history_deflate_level in cice_in.nml --- ice/cice_in.nml | 1 - 1 file changed, 1 deletion(-) diff --git a/ice/cice_in.nml b/ice/cice_in.nml index da5b53b1..645aa0e6 100644 --- a/ice/cice_in.nml +++ b/ice/cice_in.nml @@ -31,7 +31,6 @@ , histfreq = 'd','m','x','x','x' , histfreq_n = 1, 1, 1, 1, 1 , hist_avg = .true. - , history_deflate_level = 1 , history_dir = './OUTPUT/' , history_file = 'iceh' , history_deflate_level = 1 From aa3dc13a6d0bfae0d9f0edb3dd978a8b8b64789f Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Thu, 14 May 2020 19:51:30 +1000 Subject: [PATCH 039/111] Add pot_temp to diag_table since we're using conservative temperature as the prognostic variable https://github.com/OceansAus/access-om2/issues/97 --- ocean/diag_table | 1 + 1 file changed, 1 insertion(+) diff --git a/ocean/diag_table b/ocean/diag_table index e5c11547..a9eeacd3 100644 --- a/ocean/diag_table +++ b/ocean/diag_table @@ -35,6 +35,7 @@ ACCESS-OM2 # Prognostic fields: # 3d fields "ocean_model","temp","temp", "ocean","all",.true.,"none",2 +"ocean_model","pot_temp","pot_temp", "ocean","all",.true.,"none",2 "ocean_model","salt","salt", "ocean","all",.true.,"none",2 "ocean_model","age_global","age_global","ocean","all",.true.,"none",2 "ocean_model","u","u", "ocean","all",.true.,"none",2 From af8fec734f83538075abacd5310e853009e423ce Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Fri, 15 May 2020 16:56:52 +1000 Subject: [PATCH 040/111] remove unused cdbot and default cdbot_roughness_length and use_geothermal_heating in input.nml - see https://github.com/COSIMA/access-om2/issues/200 --- ocean/input.nml | 3 --- 1 file changed, 3 deletions(-) diff --git a/ocean/input.nml b/ocean/input.nml index 23c07ea4..18cde0ad 100644 --- a/ocean/input.nml +++ b/ocean/input.nml @@ -95,12 +95,9 @@ &ocean_bbc_nml bmf_implicit = .true. - cdbot = 0.001 cdbot_hi = 0.007 - cdbot_roughness_length = .false. cdbot_roughness_uamp = .true. uresidual = 0.05 - use_geothermal_heating = .false. / &ocean_bih_friction_nml From 5b504a8a76b181c2349cce06d9ac1eed97e07072 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Fri, 15 May 2020 19:54:03 +1000 Subject: [PATCH 041/111] remove empty namelist groups from ocean/input.nml --- ocean/input.nml | 57 ------------------------------------------------- 1 file changed, 57 deletions(-) diff --git a/ocean/input.nml b/ocean/input.nml index 18cde0ad..d0a2376d 100644 --- a/ocean/input.nml +++ b/ocean/input.nml @@ -15,9 +15,6 @@ use_ioaice = .true. / -&data_override_nml -/ - &diag_manager_nml debug_diag_manager = .false. issue_oor_warnings = .true. @@ -132,9 +129,6 @@ visc_crit_scale = 0.25 / -&ocean_blob_nml -/ - &ocean_convect_nml use_this_module = .false. / @@ -158,9 +152,6 @@ max_tracers = 5 / -&ocean_drifters_nml -/ - &ocean_form_drag_nml use_this_module = .false. / @@ -242,9 +233,6 @@ use_this_module = .true. / -&ocean_nphysics_new_nml -/ - &ocean_nphysics_nml debug_this_module = .false. use_nphysicsa = .false. @@ -253,9 +241,6 @@ use_this_module = .true. / -&ocean_nphysics_util_new_nml -/ - &ocean_nphysics_util_nml agm_closure = .true. agm_closure_baroclinic = .true. @@ -307,12 +292,6 @@ use_this_module = .true. / -&ocean_obc_nml -/ - -&ocean_obs_nml -/ - &ocean_operators_nml use_legacy_div_ud = .false. / @@ -333,9 +312,6 @@ use_this_module = .false. / -&ocean_passive_nml -/ - &ocean_polar_filter_nml use_this_module = .false. / @@ -421,9 +397,6 @@ use_this_module = .true. / -&ocean_solo_nml -/ - &ocean_sponges_eta_nml use_this_module = .false. / @@ -483,9 +456,6 @@ thickness_method = 'energetic' / -&ocean_time_filter_nml -/ - &ocean_topog_nml min_thickness = 0.001 / @@ -513,9 +483,6 @@ zero_tracer_source = .false. / -&ocean_velocity_advect_nml -/ - &ocean_velocity_diag_nml debug_this_module = .false. diag_step = 4320 @@ -536,22 +503,10 @@ zero_tendency_implicit = .false. / -&ocean_vert_chen_nml -/ - -&ocean_vert_const_nml -/ - -&ocean_vert_gotm_nml -/ - &ocean_vert_kpp_iow_nml use_this_module = .false. / -&ocean_vert_kpp_mom4p0_nml -/ - &ocean_vert_kpp_mom4p1_nml diff_cbt_iw = 0.0 double_diffusion = .true. @@ -579,9 +534,6 @@ vert_mix_scheme = 'kpp_mom4p1' / -&ocean_vert_pp_nml -/ - &ocean_vert_tidal_nml background_diffusivity = 0.0 background_viscosity = 0.0001 @@ -614,15 +566,6 @@ use_this_module = .false. / -&oda_core_nml -/ - -&oda_nml -/ - -&surface_flux_nml -/ - &xgrid_nml interp_method = 'second_order' make_exchange_reproduce = .false. From f32846d586ac7979d0290295fe139dbc3282f022 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Fri, 15 May 2020 20:53:28 +1000 Subject: [PATCH 042/111] delete any cice log files that only have a 105-character header and nothing else --- sync_data.sh | 3 +++ 1 file changed, 3 insertions(+) diff --git a/sync_data.sh b/sync_data.sh index cc391c34..c13d38cb 100755 --- a/sync_data.sh +++ b/sync_data.sh @@ -74,6 +74,9 @@ sourcepath="$PWD" mkdir -p ${SYNCDIR} || exit 1 cd archive || exit 1 +# first delete any cice log files that only have a 105-character header and nothing else +find output* -size 105c -iname "ice.log.task_*" -delete + if [ $restarts == true ]; then # only sync/remove restarts rsync -vrltoD --safe-links restart* ${SYNCDIR} From e609d07a21ddc517c49b976cadbf2910caa3e748 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Sun, 17 May 2020 17:20:07 +1000 Subject: [PATCH 043/111] improve alignment of namelists, using ./nmltab.py --tidy_overwrite with https://github.com/aekiss/nmltab/commit/cb35a12cca3ab04060e1c28c9de80f5ed05fdc3b --- ice/cice_in.nml | 630 ++++++++++++++++++++-------------------- ice/input_ice.nml | 50 ++-- ice/input_ice_gfdl.nml | 38 +-- ice/input_ice_monin.nml | 2 +- ocean/input.nml | 391 ++++++++++++------------- 5 files changed, 556 insertions(+), 555 deletions(-) diff --git a/ice/cice_in.nml b/ice/cice_in.nml index 4244f4f2..ce42ad66 100644 --- a/ice/cice_in.nml +++ b/ice/cice_in.nml @@ -1,365 +1,365 @@ &domain_nml distribution_type = 'cartesian' distribution_wght = 'latitude' - ew_boundary_type = 'cyclic' - maskhalo_bound = .true. - maskhalo_dyn = .true. - maskhalo_remap = .true. - nprocs = 24 - ns_boundary_type = 'tripole' - processor_shape = 'slenderX1' + ew_boundary_type = 'cyclic' + maskhalo_bound = .true. + maskhalo_dyn = .true. + maskhalo_remap = .true. + nprocs = 24 + ns_boundary_type = 'tripole' + processor_shape = 'slenderX1' / &dynamics_nml - advection = 'remap' - cosw = 1.0 - dragio = 0.00536 - iceruf = 0.0005 - kdyn = 1 - krdg_partic = 1 - krdg_redist = 1 - kstrength = 1 - mu_rdg = 3 - ndte = 120 - revised_evp = .false. - sinw = 0.0 + advection = 'remap' + cosw = 1.0 + dragio = 0.00536 + iceruf = 0.0005 + kdyn = 1 + krdg_partic = 1 + krdg_redist = 1 + kstrength = 1 + mu_rdg = 3 + ndte = 120 + revised_evp = .false. + sinw = 0.0 / &forcing_nml - atm_data_dir = 'unknown_atm_data_dir' - atm_data_format = 'nc' - atm_data_type = 'default' - atmbndy = 'default' - calc_strair = .true. - calc_tsfc = .true. - formdrag = .false. - fyear_init = 1 - highfreq = .true. - oceanmixed_file = 'unknown_oceanmixed_file' - oceanmixed_ice = .false. - ocn_data_dir = 'unknown_ocn_data_dir' - ocn_data_format = 'nc' - precip_units = 'mks' - restore_ice = .false. - restore_sst = .false. - sss_data_type = 'default' - sst_data_type = 'default' - tfrz_option = 'linear_salt' - trestore = 0 - update_ocn_f = .true. - ustar_min = 0.0005 - ycycle = 1 + atm_data_dir = 'unknown_atm_data_dir' + atm_data_format = 'nc' + atm_data_type = 'default' + atmbndy = 'default' + calc_strair = .true. + calc_tsfc = .true. + formdrag = .false. + fyear_init = 1 + highfreq = .true. + oceanmixed_file = 'unknown_oceanmixed_file' + oceanmixed_ice = .false. + ocn_data_dir = 'unknown_ocn_data_dir' + ocn_data_format = 'nc' + precip_units = 'mks' + restore_ice = .false. + restore_sst = .false. + sss_data_type = 'default' + sst_data_type = 'default' + tfrz_option = 'linear_salt' + trestore = 0 + update_ocn_f = .true. + ustar_min = 0.0005 + ycycle = 1 / &grid_nml - grid_file = 'RESTART/grid.nc' - grid_format = 'nc' - grid_type = 'tripole' - kcatbound = 0 - kmt_file = 'RESTART/kmt.nc' + grid_file = 'RESTART/grid.nc' + grid_format = 'nc' + grid_type = 'tripole' + kcatbound = 0 + kmt_file = 'RESTART/kmt.nc' / &icefields_bgc_nml - f_aero = 'x' - f_bgc_am_ml = 'x' - f_bgc_am_sk = 'x' - f_bgc_c_sk = 'x' - f_bgc_chl_sk = 'x' - f_bgc_dms_sk = 'x' - f_bgc_dmsp_ml = 'x' - f_bgc_dmspd_sk = 'x' - f_bgc_dmspp_sk = 'x' - f_bgc_n_sk = 'x' - f_bgc_nit_ml = 'x' - f_bgc_nit_sk = 'x' - f_bgc_sil_ml = 'x' - f_bgc_sil_sk = 'x' - f_bphi = 'x' - f_btin = 'x' - f_faero_atm = 'x' - f_faero_ocn = 'x' - f_fbri = 'm' - f_fn = 'x' - f_fn_ai = 'x' - f_fnh = 'x' - f_fnh_ai = 'x' - f_fno = 'x' - f_fno_ai = 'x' - f_fsil = 'x' - f_fsil_ai = 'x' - f_grownet = 'x' - f_hbri = 'm' - f_ppnet = 'x' + f_aero = 'x' + f_bgc_am_ml = 'x' + f_bgc_am_sk = 'x' + f_bgc_c_sk = 'x' + f_bgc_chl_sk = 'x' + f_bgc_dms_sk = 'x' + f_bgc_dmsp_ml = 'x' + f_bgc_dmspd_sk = 'x' + f_bgc_dmspp_sk = 'x' + f_bgc_n_sk = 'x' + f_bgc_nit_ml = 'x' + f_bgc_nit_sk = 'x' + f_bgc_sil_ml = 'x' + f_bgc_sil_sk = 'x' + f_bphi = 'x' + f_btin = 'x' + f_faero_atm = 'x' + f_faero_ocn = 'x' + f_fbri = 'm' + f_fn = 'x' + f_fn_ai = 'x' + f_fnh = 'x' + f_fnh_ai = 'x' + f_fno = 'x' + f_fno_ai = 'x' + f_fsil = 'x' + f_fsil_ai = 'x' + f_grownet = 'x' + f_hbri = 'm' + f_ppnet = 'x' / &icefields_drag_nml - f_cdn_atm = 'x' - f_cdn_ocn = 'x' - f_drag = 'x' + f_cdn_atm = 'x' + f_cdn_ocn = 'x' + f_drag = 'x' / &icefields_mechred_nml - f_alvl = 'm' - f_aparticn = 'x' - f_araftn = 'x' - f_ardg = 'm' - f_ardgn = 'x' - f_aredistn = 'x' - f_dardg1dt = 'x' - f_dardg1ndt = 'x' - f_dardg2dt = 'x' - f_dardg2ndt = 'x' - f_dvirdgdt = 'x' - f_dvirdgndt = 'x' - f_krdgn = 'x' - f_opening = 'm' - f_vlvl = 'm' - f_vraftn = 'x' - f_vrdg = 'm' - f_vrdgn = 'x' - f_vredistn = 'x' + f_alvl = 'm' + f_aparticn = 'x' + f_araftn = 'x' + f_ardg = 'm' + f_ardgn = 'x' + f_aredistn = 'x' + f_dardg1dt = 'x' + f_dardg1ndt = 'x' + f_dardg2dt = 'x' + f_dardg2ndt = 'x' + f_dvirdgdt = 'x' + f_dvirdgndt = 'x' + f_krdgn = 'x' + f_opening = 'm' + f_vlvl = 'm' + f_vraftn = 'x' + f_vrdg = 'm' + f_vrdgn = 'x' + f_vredistn = 'x' / &icefields_nml - f_aice = 'm' - f_aicen = 'm' - f_aisnap = 'x' - f_albice = 'm' - f_albpnd = 'x' - f_albsni = 'm' - f_albsno = 'm' - f_alidr = 'x' - f_alvdr = 'x' - f_angle = .true. - f_anglet = .true. - f_bounds = .false. - f_congel = 'm' - f_coszen = 'x' - f_daidtd = 'm' - f_daidtt = 'm' - f_divu = 'm' - f_dsnow = 'x' - f_dvidtd = 'm' - f_dvidtt = 'm' - f_dxt = .true. - f_dxu = .true. - f_dyt = .true. - f_dyu = .true. - f_evap = 'x' - f_evap_ai = 'm' - f_fcondtop_ai = 'm' - f_fcondtopn_ai = 'm' - f_fhocn = 'x' - f_fhocn_ai = 'm' - f_flat = 'x' - f_flat_ai = 'm' - f_flatn_ai = 'm' - f_flwdn = 'm' - f_flwup = 'x' - f_flwup_ai = 'm' - f_fmeltt_ai = 'm' - f_fmelttn_ai = 'm' - f_frazil = 'm' - f_fresh = 'x' - f_fresh_ai = 'm' - f_frz_onset = 'm' - f_frzmlt = 'm' - f_fsalt = 'm' - f_fsalt_ai = 'm' - f_fsens = 'x' - f_fsens_ai = 'm' - f_fsurf_ai = 'x' - f_fsurfn_ai = 'm' - f_fswabs = 'x' - f_fswabs_ai = 'm' - f_fswdn = 'm' - f_fswfac = 'm' - f_fswthru = 'x' - f_fswthru_ai = 'm' - f_fy = 'x' - f_hi = 'm' - f_hisnap = 'x' - f_hs = 'm' - f_hte = .true. - f_htn = .true. - f_iage = 'm' - f_icepresent = 'm' - f_meltb = 'm' - f_meltl = 'm' - f_melts = 'm' - f_meltt = 'm' - f_mlt_onset = 'm' - f_ncat = .true. - f_qref = 'x' - f_rain = 'x' - f_rain_ai = 'm' - f_shear = 'm' - f_sice = 'm' - f_sig1 = 'm' - f_sig2 = 'm' - f_sinz = 'x' - f_snoice = 'm' - f_snow = 'x' - f_snow_ai = 'm' - f_sss = 'x' - f_sst = 'x' - f_strairx = 'm' - f_strairy = 'm' - f_strcorx = 'm' - f_strcory = 'm' - f_strength = 'm' - f_strintx = 'm' - f_strinty = 'm' - f_strocnx = 'm' - f_strocny = 'm' - f_strtltx = 'm' - f_strtlty = 'm' - f_tair = 'm' - f_tarea = .true. - f_tinz = 'x' - f_tmask = .true. - f_tref = 'x' - f_trsig = 'm' - f_tsfc = 'm' - f_tsnz = 'x' - f_uarea = .true. - f_uocn = 'x' - f_uvel = 'm' - f_vgrdb = .false. - f_vgrdi = .false. - f_vgrds = .false. - f_vicen = 'm' - f_vocn = 'x' - f_vvel = 'm' + f_aice = 'm' + f_aicen = 'm' + f_aisnap = 'x' + f_albice = 'm' + f_albpnd = 'x' + f_albsni = 'm' + f_albsno = 'm' + f_alidr = 'x' + f_alvdr = 'x' + f_angle = .true. + f_anglet = .true. + f_bounds = .false. + f_congel = 'm' + f_coszen = 'x' + f_daidtd = 'm' + f_daidtt = 'm' + f_divu = 'm' + f_dsnow = 'x' + f_dvidtd = 'm' + f_dvidtt = 'm' + f_dxt = .true. + f_dxu = .true. + f_dyt = .true. + f_dyu = .true. + f_evap = 'x' + f_evap_ai = 'm' + f_fcondtop_ai = 'm' + f_fcondtopn_ai = 'm' + f_fhocn = 'x' + f_fhocn_ai = 'm' + f_flat = 'x' + f_flat_ai = 'm' + f_flatn_ai = 'm' + f_flwdn = 'm' + f_flwup = 'x' + f_flwup_ai = 'm' + f_fmeltt_ai = 'm' + f_fmelttn_ai = 'm' + f_frazil = 'm' + f_fresh = 'x' + f_fresh_ai = 'm' + f_frz_onset = 'm' + f_frzmlt = 'm' + f_fsalt = 'm' + f_fsalt_ai = 'm' + f_fsens = 'x' + f_fsens_ai = 'm' + f_fsurf_ai = 'x' + f_fsurfn_ai = 'm' + f_fswabs = 'x' + f_fswabs_ai = 'm' + f_fswdn = 'm' + f_fswfac = 'm' + f_fswthru = 'x' + f_fswthru_ai = 'm' + f_fy = 'x' + f_hi = 'm' + f_hisnap = 'x' + f_hs = 'm' + f_hte = .true. + f_htn = .true. + f_iage = 'm' + f_icepresent = 'm' + f_meltb = 'm' + f_meltl = 'm' + f_melts = 'm' + f_meltt = 'm' + f_mlt_onset = 'm' + f_ncat = .true. + f_qref = 'x' + f_rain = 'x' + f_rain_ai = 'm' + f_shear = 'm' + f_sice = 'm' + f_sig1 = 'm' + f_sig2 = 'm' + f_sinz = 'x' + f_snoice = 'm' + f_snow = 'x' + f_snow_ai = 'm' + f_sss = 'x' + f_sst = 'x' + f_strairx = 'm' + f_strairy = 'm' + f_strcorx = 'm' + f_strcory = 'm' + f_strength = 'm' + f_strintx = 'm' + f_strinty = 'm' + f_strocnx = 'm' + f_strocny = 'm' + f_strtltx = 'm' + f_strtlty = 'm' + f_tair = 'm' + f_tarea = .true. + f_tinz = 'x' + f_tmask = .true. + f_tref = 'x' + f_trsig = 'm' + f_tsfc = 'm' + f_tsnz = 'x' + f_uarea = .true. + f_uocn = 'x' + f_uvel = 'm' + f_vgrdb = .false. + f_vgrdi = .false. + f_vgrds = .false. + f_vicen = 'm' + f_vocn = 'x' + f_vvel = 'm' / &icefields_pond_nml - f_apeff = 'x' - f_apeff_ai = 'x' - f_apeffn = 'x' - f_apond = 'x' - f_apond_ai = 'x' - f_apondn = 'x' - f_hpond = 'x' - f_hpond_ai = 'x' - f_hpondn = 'x' - f_ipond = 'x' - f_ipond_ai = 'x' + f_apeff = 'x' + f_apeff_ai = 'x' + f_apeffn = 'x' + f_apond = 'x' + f_apond_ai = 'x' + f_apondn = 'x' + f_hpond = 'x' + f_hpond_ai = 'x' + f_hpondn = 'x' + f_ipond = 'x' + f_ipond_ai = 'x' / &ponds_nml - dpscale = 0.001 - frzpnd = 'hlid' - hp1 = 0.01 - hs0 = 0.0 - hs1 = 0.03 - pndaspect = 0.8 - rfracmax = 1.0 - rfracmin = 0.15 + dpscale = 0.001 + frzpnd = 'hlid' + hp1 = 0.01 + hs0 = 0.0 + hs1 = 0.03 + pndaspect = 0.8 + rfracmax = 1.0 + rfracmin = 0.15 / &setup_nml - days_per_year = 365 - dbug = .false. - diag_file = 'ice_diag.d' - diag_type = 'file' - diagfreq = 960 - dt = 3600 - dump_last = .true. - dumpfreq = 'y' - dumpfreq_n = 1 - hist_avg = .true. - histfreq = 'd', 'm', 'x', 'x', 'x' - histfreq_n = 1, 1, 1, 1, 1 + days_per_year = 365 + dbug = .false. + diag_file = 'ice_diag.d' + diag_type = 'file' + diagfreq = 960 + dt = 3600 + dump_last = .true. + dumpfreq = 'y' + dumpfreq_n = 1 + hist_avg = .true. + histfreq = 'd', 'm', 'x', 'x', 'x' + histfreq_n = 1, 1, 1, 1, 1 history_deflate_level = 1 - history_dir = './OUTPUT/' - history_file = 'iceh' - ice_ic = 'default' - incond_dir = './OUTPUT/' - incond_file = 'iceh_ic' - istep0 = 0 - latpnt = 90.0, -65.0 - lonpnt = 0.0, -45.0 - ndtd = 1 - npt = 35040 - pointer_file = './RESTART/ice.restart_file' - print_global = .false. - print_points = .false. - restart = .false. - restart_dir = './RESTART/' - restart_ext = .false. - restart_file = 'iced' - restart_format = 'nc' - runtype = 'initial' - use_leap_years = .false. - use_restart_time = .true. - write_ic = .false. - year_init = 1 + history_dir = './OUTPUT/' + history_file = 'iceh' + ice_ic = 'default' + incond_dir = './OUTPUT/' + incond_file = 'iceh_ic' + istep0 = 0 + latpnt = 90.0, -65.0 + lonpnt = 0.0, -45.0 + ndtd = 1 + npt = 35040 + pointer_file = './RESTART/ice.restart_file' + print_global = .false. + print_points = .false. + restart = .false. + restart_dir = './RESTART/' + restart_ext = .false. + restart_file = 'iced' + restart_format = 'nc' + runtype = 'initial' + use_leap_years = .false. + use_restart_time = .true. + write_ic = .false. + year_init = 1 / &shortwave_nml - ahmax = 0.1 - albedo_type = 'default' - albicei = 0.44 - albicev = 0.86 - albsnowi = 0.7 - albsnowv = 0.98 - dalb_mlt = -0.02 - dt_mlt = 1.0 - r_ice = 0.0 - r_pnd = 0.0 - r_snw = 0.0 - rsnw_mlt = 1500.0 - shortwave = 'default' - tocnfrz = -1.8 + ahmax = 0.1 + albedo_type = 'default' + albicei = 0.44 + albicev = 0.86 + albsnowi = 0.7 + albsnowv = 0.98 + dalb_mlt = -0.02 + dt_mlt = 1.0 + r_ice = 0.0 + r_pnd = 0.0 + r_snw = 0.0 + rsnw_mlt = 1500.0 + shortwave = 'default' + tocnfrz = -1.8 / &thermo_nml - a_rapid_mode = 0.0005 + a_rapid_mode = 0.0005 aspect_rapid_mode = 1.0 - chio = 0.004 - conduct = 'bubbly' - dsdt_slow_mode = -5e-08 - kitd = 1 - ktherm = 1 - phi_c_slow_mode = 0.05 - phi_i_mushy = 0.85 - rac_rapid_mode = 10.0 + chio = 0.004 + conduct = 'bubbly' + dsdt_slow_mode = -5e-08 + kitd = 1 + ktherm = 1 + phi_c_slow_mode = 0.05 + phi_i_mushy = 0.85 + rac_rapid_mode = 10.0 / &tracer_nml - restart_aero = .false. - restart_age = .false. - restart_fy = .false. - restart_lvl = .false. + restart_aero = .false. + restart_age = .false. + restart_fy = .false. + restart_lvl = .false. restart_pond_cesm = .false. - restart_pond_lvl = .false. + restart_pond_lvl = .false. restart_pond_topo = .false. - tr_aero = .false. - tr_fy = .false. - tr_iage = .false. - tr_lvl = .false. - tr_pond_cesm = .false. - tr_pond_lvl = .false. - tr_pond_topo = .false. + tr_aero = .false. + tr_fy = .false. + tr_iage = .false. + tr_lvl = .false. + tr_pond_cesm = .false. + tr_pond_lvl = .false. + tr_pond_topo = .false. / &zbgc_nml - bgc_data_dir = 'unknown_bgc_data_dir' - bgc_flux_type = 'Jin2006' - nit_data_type = 'default' - phi_snow = 0.5 - restart_bgc = .false. - restart_hbrine = .false. - restore_bgc = .false. - sil_data_type = 'default' - skl_bgc = .false. - tr_bgc_am_sk = .false. - tr_bgc_c_sk = .false. - tr_bgc_chl_sk = .false. - tr_bgc_dms_sk = .false. - tr_bgc_dmspd_sk = .false. - tr_bgc_dmspp_sk = .false. - tr_bgc_sil_sk = .false. - tr_brine = .false. + bgc_data_dir = 'unknown_bgc_data_dir' + bgc_flux_type = 'Jin2006' + nit_data_type = 'default' + phi_snow = 0.5 + restart_bgc = .false. + restart_hbrine = .false. + restore_bgc = .false. + sil_data_type = 'default' + skl_bgc = .false. + tr_bgc_am_sk = .false. + tr_bgc_c_sk = .false. + tr_bgc_chl_sk = .false. + tr_bgc_dms_sk = .false. + tr_bgc_dmspd_sk = .false. + tr_bgc_dmspp_sk = .false. + tr_bgc_sil_sk = .false. + tr_brine = .false. / diff --git a/ice/input_ice.nml b/ice/input_ice.nml index fa770b1d..ae194750 100644 --- a/ice/input_ice.nml +++ b/ice/input_ice.nml @@ -1,29 +1,29 @@ &coupling_nml - chk_a2i_fields = .false. - chk_frzmlt_sst = .false. + chk_a2i_fields = .false. + chk_frzmlt_sst = .false. chk_gfdl_roughness = .false. - chk_i2a_fields = .false. - chk_i2o_fields = .false. - chk_o2i_fields = .false. - cst_ocn_albedo = .true. - fields_from_atm = 'swfld_i', 'lwfld_i', 'rain_i', 'snow_i', 'press_i', - 'runof_i', 'tair_i', 'qair_i', 'uwnd_i', 'vwnd_i', - 'licalvf_i' - fields_from_ocn = 'sst_i', 'sss_i', 'ssu_i', 'ssv_i', 'sslx_i', 'ssly_i', - 'pfmice_i' - fields_to_ocn = 'strsu_io', 'strsv_io', 'rain_io', 'snow_io', 'stflx_io', - 'htflx_io', 'swflx_io', 'qflux_io', 'shflx_io', 'lwflx_io', - 'runof_io', 'press_io', 'aice_io', 'melt_io', 'form_io', - 'licefw_io', 'licefh_io' + chk_i2a_fields = .false. + chk_i2o_fields = .false. + chk_o2i_fields = .false. + cst_ocn_albedo = .true. + fields_from_atm = 'swfld_i', 'lwfld_i', 'rain_i', 'snow_i', 'press_i', + 'runof_i', 'tair_i', 'qair_i', 'uwnd_i', 'vwnd_i', + 'licalvf_i' + fields_from_ocn = 'sst_i', 'sss_i', 'ssu_i', 'ssv_i', 'sslx_i', 'ssly_i', + 'pfmice_i' + fields_to_ocn = 'strsu_io', 'strsv_io', 'rain_io', 'snow_io', 'stflx_io', + 'htflx_io', 'swflx_io', 'qflux_io', 'shflx_io', + 'lwflx_io', 'runof_io', 'press_io', 'aice_io', 'melt_io', + 'form_io', 'licefw_io', 'licefh_io' gfdl_surface_flux = .true. - ice_fwflux = .true. - ice_pressure_on = .true. - limit_icemelt = .false. - meltlimit = -200.0 - ocn_albedo = 0.1 - pop_icediag = .true. - precip_factor = 1.0 - rotate_winds = .true. - use_ocnslope = .false. - use_umask = .false. + ice_fwflux = .true. + ice_pressure_on = .true. + limit_icemelt = .false. + meltlimit = -200.0 + ocn_albedo = 0.1 + pop_icediag = .true. + precip_factor = 1.0 + rotate_winds = .true. + use_ocnslope = .false. + use_umask = .false. / diff --git a/ice/input_ice_gfdl.nml b/ice/input_ice_gfdl.nml index 4a8cdaff..10395c48 100644 --- a/ice/input_ice_gfdl.nml +++ b/ice/input_ice_gfdl.nml @@ -1,25 +1,25 @@ &ocean_rough_nml - charnock = 0.032 - do_cap40 = .false. - do_highwind = .false. - rough_scheme = 'beljaars' - roughness_heat = 5.8e-05 - roughness_min = 1e-06 - roughness_moist = 5.8e-05 - roughness_mom = 5.8e-05 - zcoh1 = 0.0 - zcoq1 = 0.0 + charnock = 0.032 + do_cap40 = .false. + do_highwind = .false. + rough_scheme = 'beljaars' + roughness_heat = 5.8e-05 + roughness_min = 1e-06 + roughness_moist = 5.8e-05 + roughness_mom = 5.8e-05 + zcoh1 = 0.0 + zcoq1 = 0.0 / &surface_flux_nml - alt_gustiness = .false. - gust_const = 1.0 - gust_min = 0.0 - ncar_ocean_flux = .true. + alt_gustiness = .false. + gust_const = 1.0 + gust_min = 0.0 + ncar_ocean_flux = .true. ncar_ocean_flux_orig = .false. - no_neg_q = .false. - old_dtaudv = .false. - raoult_sat_vap = .false. - use_mixing_ratio = .false. - use_virtual_temp = .true. + no_neg_q = .false. + old_dtaudv = .false. + raoult_sat_vap = .false. + use_mixing_ratio = .false. + use_virtual_temp = .true. / diff --git a/ice/input_ice_monin.nml b/ice/input_ice_monin.nml index e3456c97..edc9c2df 100644 --- a/ice/input_ice_monin.nml +++ b/ice/input_ice_monin.nml @@ -1,3 +1,3 @@ &monin_obukhov_nml - neutral = .true. + neutral = .true. / diff --git a/ocean/input.nml b/ocean/input.nml index d0a2376d..076607c0 100644 --- a/ocean/input.nml +++ b/ocean/input.nml @@ -1,18 +1,18 @@ &auscom_ice_nml - aice_cutoff = 0.15 - chk_i2o_fields = .false. - chk_o2i_fields = .false. - do_ice_once = .false. - fixmeltt = .false. - frazil_factor = 1.0 - iceform_adj_salt = .false. - icemlt_factor = 1.0 - kmxice = 5 - pop_icediag = .true. + aice_cutoff = 0.15 + chk_i2o_fields = .false. + chk_o2i_fields = .false. + do_ice_once = .false. + fixmeltt = .false. + frazil_factor = 1.0 + iceform_adj_salt = .false. + icemlt_factor = 1.0 + kmxice = 5 + pop_icediag = .true. redsea_gulfbay_sfix = .false. - sign_stflx = 1.0 - tmelt = -0.216 - use_ioaice = .true. + sign_stflx = 1.0 + tmelt = -0.216 + use_ioaice = .true. / &diag_manager_nml @@ -21,42 +21,43 @@ / &fms_io_nml - fileset_write = 'single' - threading_read = 'multi' - threading_write = 'single' + fileset_write = 'single' + threading_read = 'multi' + threading_write = 'single' / &fms_nml - clock_grain = 'LOOP' + clock_grain = 'LOOP' domains_stack_size = 115200 / &mom_oasis3_interface_nml - fields_in = 'u_flux', 'v_flux', 'lprec', 'fprec', 'salt_flx', 'mh_flux', - 'sw_flux', 'q_flux', 't_flux', 'lw_flux', 'runof', 'p', - 'aice', 'wfimelt', 'wfiform', 'licefw', 'liceht' - fields_out = 't_surf', 's_surf', 'u_surf', 'v_surf', 'dssldx', 'dssldy', - 'frazil' - num_fields_in = 17 - num_fields_out = 7 + fields_in = 'u_flux', 'v_flux', 'lprec', 'fprec', 'salt_flx', + 'mh_flux', 'sw_flux', 'q_flux', 't_flux', 'lw_flux', + 'runof', 'p', 'aice', 'wfimelt', 'wfiform', 'licefw', + 'liceht' + fields_out = 't_surf', 's_surf', 'u_surf', 'v_surf', 'dssldx', + 'dssldy', 'frazil' + num_fields_in = 17 + num_fields_out = 7 send_after_ocean_update = .true. send_before_ocean_update = .false. / &monin_obukhov_nml - neutral = .true. + neutral = .true. / &mpp_io_nml - deflate_level = -1 - shuffle = 1 + deflate_level = -1 + shuffle = 1 / &ocean_adv_vel_diag_nml - diag_step = 4320 - large_cfl_value = 10.0 - max_cfl_value = 100.0 - verbose_cfl = .true. + diag_step = 4320 + large_cfl_value = 10.0 + max_cfl_value = 100.0 + verbose_cfl = .true. / &ocean_advection_velocity_nml @@ -68,33 +69,33 @@ / &ocean_barotropic_nml - barotropic_halo = 10 + barotropic_halo = 10 barotropic_time_stepping_a = .true. barotropic_time_stepping_b = .false. debug_this_module = .false. - diag_step = 4320 - eta_max = 8.0 + diag_step = 4320 + eta_max = 8.0 frac_crit_cell_height = 0.2 - pred_corr_gamma = 0.2 + pred_corr_gamma = 0.2 smooth_eta_diag_laplacian = .true. smooth_eta_t_biharmonic = .false. smooth_eta_t_laplacian = .true. smooth_pbot_t_biharmonic = .false. smooth_pbot_t_laplacian = .true. - truncate_eta = .false. + truncate_eta = .false. use_legacy_barotropic_halos = .false. - vel_micom_bih = 0.01 - vel_micom_lap = 0.05 + vel_micom_bih = 0.01 + vel_micom_lap = 0.05 vel_micom_lap_diag = 0.2 - verbose_truncate = .true. - zero_tendency = .false. + verbose_truncate = .true. + zero_tendency = .false. / &ocean_bbc_nml - bmf_implicit = .true. - cdbot_hi = 0.007 + bmf_implicit = .true. + cdbot_hi = 0.007 cdbot_roughness_uamp = .true. - uresidual = 0.05 + uresidual = 0.05 / &ocean_bih_friction_nml @@ -102,58 +103,58 @@ / &ocean_bih_tracer_nml - use_this_module = .false. + use_this_module = .false. / &ocean_bihcst_friction_nml - use_this_module = .false. + use_this_module = .false. / &ocean_bihgen_friction_nml - bottom_5point = .true. - eq_lat_micom = 0.0 + bottom_5point = .true. + eq_lat_micom = 0.0 eq_vel_micom_aniso = 0.0 - eq_vel_micom_iso = 0.0 - equatorial_zonal = .false. - k_smag_aniso = 0.0 - k_smag_iso = 2.0 + eq_vel_micom_iso = 0.0 + equatorial_zonal = .false. + k_smag_aniso = 0.0 + k_smag_iso = 2.0 ncar_boundary_scaling = .true. ncar_boundary_scaling_read = .false. ncar_rescale_power = 2 - ncar_vconst_4 = 2e-08 - ncar_vconst_5 = 5 - use_this_module = .true. - vel_micom_aniso = 0.0 - vel_micom_bottom = 0.01 - vel_micom_iso = 0.04 - visc_crit_scale = 0.25 + ncar_vconst_4 = 2e-08 + ncar_vconst_5 = 5 + use_this_module = .true. + vel_micom_aniso = 0.0 + vel_micom_bottom = 0.01 + vel_micom_iso = 0.04 + visc_crit_scale = 0.25 / &ocean_convect_nml - use_this_module = .false. + use_this_module = .false. / &ocean_coriolis_nml - acor = 0.5 - use_this_module = .true. + acor = 0.5 + use_this_module = .true. / &ocean_density_nml - eos_linear = .false. - eos_preteos10 = .true. - layer_nk = 80 - neutralrho_max = 1038.0 - neutralrho_min = 1028.0 - potrho_max = 1038.0 - potrho_min = 1028.0 + eos_linear = .false. + eos_preteos10 = .true. + layer_nk = 80 + neutralrho_max = 1038.0 + neutralrho_min = 1028.0 + potrho_max = 1038.0 + potrho_min = 1028.0 / &ocean_domains_nml - max_tracers = 5 + max_tracers = 5 / &ocean_form_drag_nml - use_this_module = .false. + use_this_module = .false. / &ocean_frazil_nml @@ -161,7 +162,7 @@ frazil_only_in_surface = .false. freezing_temp_preteos10 = .true. freezing_temp_simple = .false. - use_this_module = .true. + use_this_module = .true. / &ocean_grids_nml @@ -169,15 +170,15 @@ / &ocean_increment_eta_nml - use_this_module = .false. + use_this_module = .false. / &ocean_increment_tracer_nml - use_this_module = .false. + use_this_module = .false. / &ocean_increment_velocity_nml - use_this_module = .false. + use_this_module = .false. / &ocean_lap_friction_nml @@ -185,23 +186,23 @@ / &ocean_lap_tracer_nml - use_this_module = .false. + use_this_module = .false. / &ocean_lapcst_friction_nml - use_this_module = .false. + use_this_module = .false. / &ocean_lapgen_friction_nml - bottom_5point = .true. - k_smag_aniso = 0.0 - k_smag_iso = 0.0 + bottom_5point = .true. + k_smag_aniso = 0.0 + k_smag_iso = 0.0 restrict_polar_visc = .true. restrict_polar_visc_lat = 60.0 restrict_polar_visc_ratio = 0.35 - use_this_module = .true. - vel_micom_iso = 0.1 - viscosity_ncar = .false. + use_this_module = .true. + vel_micom_iso = 0.1 + viscosity_ncar = .false. viscosity_ncar_2007 = .false. viscosity_scale_by_rossby = .true. viscosity_scale_by_rossby_power = 4.0 @@ -212,37 +213,37 @@ mixdownslope_mask_gfdl = .false. mixdownslope_npts = 4 read_mixdownslope_mask = .false. - use_this_module = .true. + use_this_module = .true. / &ocean_model_nml - baroclinic_split = 1 - barotropic_split = 80 - cmip_units = .true. - debug = .false. - io_layout = 4, 3 - layout = 16, 15 + baroclinic_split = 1 + barotropic_split = 80 + cmip_units = .true. + debug = .false. + io_layout = 4, 3 + layout = 16, 15 surface_height_split = 1 - time_tendency = 'twolevel' + time_tendency = 'twolevel' vertical_coordinate = 'zstar' / &ocean_momentum_source_nml rayleigh_damp_exp_from_bottom = .false. use_rayleigh_damp_table = .true. - use_this_module = .true. + use_this_module = .true. / &ocean_nphysics_nml debug_this_module = .false. - use_nphysicsa = .false. - use_nphysicsb = .false. - use_nphysicsc = .true. - use_this_module = .true. + use_nphysicsa = .false. + use_nphysicsb = .false. + use_nphysicsc = .true. + use_this_module = .true. / &ocean_nphysics_util_nml - agm_closure = .true. + agm_closure = .true. agm_closure_baroclinic = .true. agm_closure_buoy_freq = 0.004 agm_closure_eady_ave_mixed = .true. @@ -252,44 +253,44 @@ agm_closure_grid_scaling = .true. agm_closure_length = 50000.0 agm_closure_lower_depth = 2000.0 - agm_closure_max = 600.0 - agm_closure_min = 50.0 + agm_closure_max = 600.0 + agm_closure_min = 50.0 agm_closure_scaling = 0.07 agm_closure_upper_depth = 100.0 - aredi = 600.0 - aredi_equal_agm = .false. - drhodz_mom4p1 = .true. + aredi = 600.0 + aredi_equal_agm = .false. + drhodz_mom4p1 = .true. nphysics_util_zero_init = .true. / &ocean_nphysicsa_nml - use_this_module = .false. + use_this_module = .false. / &ocean_nphysicsb_nml - use_this_module = .false. + use_this_module = .false. / &ocean_nphysicsc_nml bv_freq_smooth_vert = .true. - bvp_bc_mode = 2 - bvp_min_speed = 0.1 - bvp_speed = 0.0 + bvp_bc_mode = 2 + bvp_min_speed = 0.1 + bvp_speed = 0.0 debug_this_module = .false. - do_gm_skewsion = .true. + do_gm_skewsion = .true. do_neutral_diffusion = .true. - epsln_bv_freq = 1e-12 + epsln_bv_freq = 1e-12 gm_skewsion_bvproblem = .true. gm_skewsion_modes = .false. neutral_eddy_depth = .true. neutral_physics_limit = .true. - number_bc_modes = 2 - regularize_psi = .false. - smax_psi = 0.01 - smooth_psi = .true. - tmask_neutral_on = .true. - turb_blayer_min = 50.0 - use_this_module = .true. + number_bc_modes = 2 + regularize_psi = .false. + smax_psi = 0.01 + smooth_psi = .true. + tmask_neutral_on = .true. + turb_blayer_min = 50.0 + use_this_module = .true. / &ocean_operators_nml @@ -298,22 +299,22 @@ &ocean_overexchange_nml debug_this_module = .false. - overexch_npts = 4 + overexch_npts = 4 overexch_weight_far = .false. - overflow_umax = 5.0 - use_this_module = .false. + overflow_umax = 5.0 + use_this_module = .false. / &ocean_overflow_nml - use_this_module = .false. + use_this_module = .false. / &ocean_overflow_ofp_nml - use_this_module = .false. + use_this_module = .false. / &ocean_polar_filter_nml - use_this_module = .false. + use_this_module = .false. / &ocean_pressure_nml @@ -327,21 +328,21 @@ river_diffusion_thickness = 0.0 river_diffusivity = 0.0 river_insertion_thickness = 40.0 - use_this_module = .true. + use_this_module = .true. / &ocean_riverspread_nml - use_this_module = .false. + use_this_module = .false. / &ocean_rough_nml - rough_scheme = 'beljaars' + rough_scheme = 'beljaars' / &ocean_sbc_nml avg_sfc_temp_salt_eta = .true. - avg_sfc_velocity = .true. - calvingspread = .false. + avg_sfc_velocity = .true. + calvingspread = .false. do_bitwise_exact_sum = .true. do_flux_correction = .false. land_model_heat_fluxes = .false. @@ -349,15 +350,15 @@ max_ice_thickness = 0.0 read_restore_mask = .false. restore_mask_gfdl = .false. - runoff_salinity = 0.0 + runoff_salinity = 0.0 salt_correction_scale = 0.0 salt_restore_as_salt_flux = .true. salt_restore_tscale = 21.28 salt_restore_under_ice = .true. temp_restore_tscale = -10.0 use_full_patm_for_sea_level = .false. - use_waterflux = .true. - zero_heat_fluxes = .false. + use_waterflux = .true. + zero_heat_fluxes = .false. zero_net_salt_correction = .false. zero_net_salt_restore = .true. zero_net_water_correction = .false. @@ -369,59 +370,59 @@ / &ocean_shortwave_csiro_nml - use_this_module = .false. + use_this_module = .false. / &ocean_shortwave_gfdl_nml debug_this_module = .false. - enforce_sw_frac = .true. - optics_manizza = .true. + enforce_sw_frac = .true. + optics_manizza = .true. optics_morel_antoine = .false. - read_chl = .true. - use_this_module = .true. - zmax_pen = 1000000.0 + read_chl = .true. + use_this_module = .true. + zmax_pen = 1000000.0 / &ocean_shortwave_jerlov_nml - use_this_module = .false. + use_this_module = .false. / &ocean_shortwave_nml use_shortwave_csiro = .false. use_shortwave_gfdl = .true. use_shortwave_jerlov = .false. - use_this_module = .true. + use_this_module = .true. / &ocean_sigma_transport_nml - use_this_module = .true. + use_this_module = .true. / &ocean_sponges_eta_nml - use_this_module = .false. + use_this_module = .false. / &ocean_sponges_tracer_nml - use_this_module = .false. + use_this_module = .false. / &ocean_sponges_velocity_nml - use_this_module = .false. + use_this_module = .false. / &ocean_submesoscale_nml - coefficient_ce = 0.05 + coefficient_ce = 0.05 debug_this_module = .false. front_length_const = 5000.0 front_length_deform_radius = .true. - limit_psi = .true. + limit_psi = .true. limit_psi_velocity_scale = 0.5 - min_kblt = 4 + min_kblt = 4 smooth_advect_transport = .true. smooth_advect_transport_num = 2 - smooth_hblt = .false. - smooth_psi = .true. - smooth_psi_num = 2 + smooth_hblt = .false. + smooth_psi = .true. + smooth_psi_num = 2 submeso_advect_flux = .false. submeso_advect_limit = .true. submeso_advect_upwind = .true. @@ -431,21 +432,21 @@ submeso_diffusion_scale = 10.0 submeso_skew_flux = .true. use_hblt_equal_mld = .true. - use_psi_legacy = .false. - use_this_module = .true. + use_psi_legacy = .false. + use_this_module = .true. / &ocean_tempsalt_nml debug_this_module = .false. pottemp_2nd_iteration = .true. - s_max = 70.0 - s_max_limit = 42.0 - s_min = 0.0 - s_min_limit = 2.0 - t_max = 55.0 - t_max_limit = 32.0 - t_min = -20.0 - t_min_limit = -5.0 + s_max = 70.0 + s_max_limit = 42.0 + s_min = 0.0 + s_min_limit = 2.0 + t_max = 55.0 + t_max_limit = 32.0 + t_min = -20.0 + t_min_limit = -5.0 temperature_variable = 'conservative_temp' / @@ -453,20 +454,20 @@ debug_this_module = .false. debug_this_module_detail = .false. rescale_mass_to_get_ht_mod = .false. - thickness_method = 'energetic' + thickness_method = 'energetic' / &ocean_topog_nml - min_thickness = 0.001 + min_thickness = 0.001 / &ocean_tracer_advect_nml debug_this_module = .false. - read_basin_mask = .false. + read_basin_mask = .false. / &ocean_tracer_diag_nml - diag_step = 4320 + diag_step = 4320 do_bitwise_exact_sum = .false. tracer_conserve_days = 30.0 / @@ -476,98 +477,98 @@ debug_this_module = .false. frazil_heating_after_vphysics = .true. frazil_heating_before_vphysics = .false. - limit_age_tracer = .true. + limit_age_tracer = .true. remap_depth_to_s_init = .false. use_tempsalt_check_range = .true. - zero_tendency = .false. + zero_tendency = .false. zero_tracer_source = .false. / &ocean_velocity_diag_nml debug_this_module = .false. - diag_step = 4320 - energy_diag_step = 4320 - large_cfl_value = 10.0 - max_cfl_value = 100.0 + diag_step = 4320 + energy_diag_step = 4320 + large_cfl_value = 10.0 + max_cfl_value = 100.0 / &ocean_velocity_nml adams_bashforth_third = .true. - max_cgint = 1.0 + max_cgint = 1.0 truncate_velocity = .false. truncate_velocity_value = 2.0 - truncate_verbose = .true. - zero_tendency = .false. + truncate_verbose = .true. + zero_tendency = .false. zero_tendency_explicit_a = .false. zero_tendency_explicit_b = .false. zero_tendency_implicit = .false. / &ocean_vert_kpp_iow_nml - use_this_module = .false. + use_this_module = .false. / &ocean_vert_kpp_mom4p1_nml - diff_cbt_iw = 0.0 - double_diffusion = .true. + diff_cbt_iw = 0.0 + double_diffusion = .true. kbl_standard_method = .false. - ricr = 0.3 - smooth_blmc = .false. + ricr = 0.3 + smooth_blmc = .false. smooth_ri_kmax_eq_kmu = .true. - use_this_module = .true. - visc_cbu_iw = 0.0 + use_this_module = .true. + visc_cbu_iw = 0.0 / &ocean_vert_mix_nml - aidif = 1.0 + aidif = 1.0 bryan_lewis_diffusivity = .false. bryan_lewis_lat_depend = .false. - hwf_diffusivity = .false. + hwf_diffusivity = .false. hwf_min_diffusivity = 2e-06 - hwf_n0_2omega = 20.0 - j09_bgmax = 5e-06 - j09_bgmin = 1e-06 - j09_diffusivity = .true. - j09_lat = 20.0 + hwf_n0_2omega = 20.0 + j09_bgmax = 5e-06 + j09_bgmin = 1e-06 + j09_diffusivity = .true. + j09_lat = 20.0 use_diff_cbt_table = .false. vert_diff_back_via_max = .true. - vert_mix_scheme = 'kpp_mom4p1' + vert_mix_scheme = 'kpp_mom4p1' / &ocean_vert_tidal_nml background_diffusivity = 0.0 background_viscosity = 0.0001 - decay_scale = 500.0 + decay_scale = 500.0 drag_dissipation_use_cdbot = .true. - drhodz_min = 1e-10 + drhodz_min = 1e-10 fixed_wave_dissipation = .false. max_wave_diffusivity = 0.01 mixing_efficiency_n2depend = .true. - read_roughness = .true. - read_tide_speed = .true. + read_roughness = .true. + read_tide_speed = .true. read_wave_dissipation = .false. reading_roughness_amp = .true. reading_roughness_length = .false. - roughness_scale = 12000.0 + roughness_scale = 12000.0 shelf_depth_cutoff = -1000.0 tide_speed_data_on_t_grid = .true. use_drag_dissipation = .true. use_legacy_methods = .false. - use_this_module = .true. + use_this_module = .true. use_wave_dissipation = .true. wave_energy_flux_max = 0.1 / &ocean_xlandinsert_nml - use_this_module = .false. + use_this_module = .false. / &ocean_xlandmix_nml - use_this_module = .false. + use_this_module = .false. / &xgrid_nml - interp_method = 'second_order' + interp_method = 'second_order' make_exchange_reproduce = .false. - nsubset = 16 + nsubset = 16 / From b95f0e98369682948c0b7a38727cc99090e5f4fd Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Sun, 17 May 2020 21:48:04 +1000 Subject: [PATCH 044/111] remove redundant clutter in input.nml; no change in results expected --- ocean/input.nml | 125 ------------------------------------------------ 1 file changed, 125 deletions(-) diff --git a/ocean/input.nml b/ocean/input.nml index 076607c0..d7ca8348 100644 --- a/ocean/input.nml +++ b/ocean/input.nml @@ -72,7 +72,6 @@ barotropic_halo = 10 barotropic_time_stepping_a = .true. barotropic_time_stepping_b = .false. - debug_this_module = .false. diag_step = 4320 eta_max = 8.0 frac_crit_cell_height = 0.2 @@ -102,14 +101,6 @@ bih_friction_scheme = 'general' / -&ocean_bih_tracer_nml - use_this_module = .false. -/ - -&ocean_bihcst_friction_nml - use_this_module = .false. -/ - &ocean_bihgen_friction_nml bottom_5point = .true. eq_lat_micom = 0.0 @@ -130,10 +121,6 @@ visc_crit_scale = 0.25 / -&ocean_convect_nml - use_this_module = .false. -/ - &ocean_coriolis_nml acor = 0.5 use_this_module = .true. @@ -153,46 +140,17 @@ max_tracers = 5 / -&ocean_form_drag_nml - use_this_module = .false. -/ - &ocean_frazil_nml - debug_this_module = .false. frazil_only_in_surface = .false. freezing_temp_preteos10 = .true. freezing_temp_simple = .false. use_this_module = .true. / -&ocean_grids_nml - debug_this_module = .false. -/ - -&ocean_increment_eta_nml - use_this_module = .false. -/ - -&ocean_increment_tracer_nml - use_this_module = .false. -/ - -&ocean_increment_velocity_nml - use_this_module = .false. -/ - &ocean_lap_friction_nml lap_friction_scheme = 'general' / -&ocean_lap_tracer_nml - use_this_module = .false. -/ - -&ocean_lapcst_friction_nml - use_this_module = .false. -/ - &ocean_lapgen_friction_nml bottom_5point = .true. k_smag_aniso = 0.0 @@ -209,7 +167,6 @@ / &ocean_mixdownslope_nml - debug_this_module = .false. mixdownslope_mask_gfdl = .false. mixdownslope_npts = 4 read_mixdownslope_mask = .false. @@ -235,7 +192,6 @@ / &ocean_nphysics_nml - debug_this_module = .false. use_nphysicsa = .false. use_nphysicsb = .false. use_nphysicsc = .true. @@ -263,20 +219,11 @@ nphysics_util_zero_init = .true. / -&ocean_nphysicsa_nml - use_this_module = .false. -/ - -&ocean_nphysicsb_nml - use_this_module = .false. -/ - &ocean_nphysicsc_nml bv_freq_smooth_vert = .true. bvp_bc_mode = 2 bvp_min_speed = 0.1 bvp_speed = 0.0 - debug_this_module = .false. do_gm_skewsion = .true. do_neutral_diffusion = .true. epsln_bv_freq = 1e-12 @@ -293,36 +240,7 @@ use_this_module = .true. / -&ocean_operators_nml - use_legacy_div_ud = .false. -/ - -&ocean_overexchange_nml - debug_this_module = .false. - overexch_npts = 4 - overexch_weight_far = .false. - overflow_umax = 5.0 - use_this_module = .false. -/ - -&ocean_overflow_nml - use_this_module = .false. -/ - -&ocean_overflow_ofp_nml - use_this_module = .false. -/ - -&ocean_polar_filter_nml - use_this_module = .false. -/ - -&ocean_pressure_nml - zero_pressure_force = .false. -/ - &ocean_rivermix_nml - debug_this_module = .false. river_diffuse_salt = .true. river_diffuse_temp = .true. river_diffusion_thickness = 0.0 @@ -331,10 +249,6 @@ use_this_module = .true. / -&ocean_riverspread_nml - use_this_module = .false. -/ - &ocean_rough_nml rough_scheme = 'beljaars' / @@ -369,12 +283,7 @@ zero_water_fluxes = .false. / -&ocean_shortwave_csiro_nml - use_this_module = .false. -/ - &ocean_shortwave_gfdl_nml - debug_this_module = .false. enforce_sw_frac = .true. optics_manizza = .true. optics_morel_antoine = .false. @@ -383,10 +292,6 @@ zmax_pen = 1000000.0 / -&ocean_shortwave_jerlov_nml - use_this_module = .false. -/ - &ocean_shortwave_nml use_shortwave_csiro = .false. use_shortwave_gfdl = .true. @@ -398,21 +303,8 @@ use_this_module = .true. / -&ocean_sponges_eta_nml - use_this_module = .false. -/ - -&ocean_sponges_tracer_nml - use_this_module = .false. -/ - -&ocean_sponges_velocity_nml - use_this_module = .false. -/ - &ocean_submesoscale_nml coefficient_ce = 0.05 - debug_this_module = .false. front_length_const = 5000.0 front_length_deform_radius = .true. limit_psi = .true. @@ -437,7 +329,6 @@ / &ocean_tempsalt_nml - debug_this_module = .false. pottemp_2nd_iteration = .true. s_max = 70.0 s_max_limit = 42.0 @@ -451,7 +342,6 @@ / &ocean_thickness_nml - debug_this_module = .false. debug_this_module_detail = .false. rescale_mass_to_get_ht_mod = .false. thickness_method = 'energetic' @@ -462,7 +352,6 @@ / &ocean_tracer_advect_nml - debug_this_module = .false. read_basin_mask = .false. / @@ -474,7 +363,6 @@ &ocean_tracer_nml age_tracer_max_init = 0.0 - debug_this_module = .false. frazil_heating_after_vphysics = .true. frazil_heating_before_vphysics = .false. limit_age_tracer = .true. @@ -485,7 +373,6 @@ / &ocean_velocity_diag_nml - debug_this_module = .false. diag_step = 4320 energy_diag_step = 4320 large_cfl_value = 10.0 @@ -504,10 +391,6 @@ zero_tendency_implicit = .false. / -&ocean_vert_kpp_iow_nml - use_this_module = .false. -/ - &ocean_vert_kpp_mom4p1_nml diff_cbt_iw = 0.0 double_diffusion = .true. @@ -559,14 +442,6 @@ wave_energy_flux_max = 0.1 / -&ocean_xlandinsert_nml - use_this_module = .false. -/ - -&ocean_xlandmix_nml - use_this_module = .false. -/ - &xgrid_nml interp_method = 'second_order' make_exchange_reproduce = .false. From 2ba6c7f3f4f8befbdea27d7374561f72e0786646 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Mon, 18 May 2020 10:54:57 +1000 Subject: [PATCH 045/111] remove redundant ocean_albedo_nml in input.nml --- ocean/input.nml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/ocean/input.nml b/ocean/input.nml index d7ca8348..eefcf68e 100644 --- a/ocean/input.nml +++ b/ocean/input.nml @@ -64,10 +64,6 @@ max_advection_velocity = 0.5 / -&ocean_albedo_nml - ocean_albedo_option = 2 -/ - &ocean_barotropic_nml barotropic_halo = 10 barotropic_time_stepping_a = .true. From 78f70729cb39da1744ccbbc369acd6733088a330 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Mon, 18 May 2020 11:44:32 +1000 Subject: [PATCH 046/111] remove redundant monin_obukhov_nml in input.nml --- ocean/input.nml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/ocean/input.nml b/ocean/input.nml index eefcf68e..41fae256 100644 --- a/ocean/input.nml +++ b/ocean/input.nml @@ -44,10 +44,6 @@ send_before_ocean_update = .false. / -&monin_obukhov_nml - neutral = .true. -/ - &mpp_io_nml deflate_level = -1 shuffle = 1 From ea3eeeb5fd4621244fc24b8c493d1ef7d5228cc9 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Wed, 20 May 2020 07:13:16 +1000 Subject: [PATCH 047/111] reinstate unused namelist groups in input.nml --- ocean/input.nml | 161 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 161 insertions(+) diff --git a/ocean/input.nml b/ocean/input.nml index 41fae256..3326c317 100644 --- a/ocean/input.nml +++ b/ocean/input.nml @@ -15,6 +15,9 @@ use_ioaice = .true. / +&data_override_nml +/ + &diag_manager_nml debug_diag_manager = .false. issue_oor_warnings = .true. @@ -44,6 +47,9 @@ send_before_ocean_update = .false. / +&monin_obukhov_nml +/ + &mpp_io_nml deflate_level = -1 shuffle = 1 @@ -60,6 +66,9 @@ max_advection_velocity = 0.5 / +&ocean_albedo_nml +/ + &ocean_barotropic_nml barotropic_halo = 10 barotropic_time_stepping_a = .true. @@ -93,6 +102,14 @@ bih_friction_scheme = 'general' / +&ocean_bih_tracer_nml + use_this_module = .false. +/ + +&ocean_bihcst_friction_nml + use_this_module = .false. +/ + &ocean_bihgen_friction_nml bottom_5point = .true. eq_lat_micom = 0.0 @@ -113,6 +130,13 @@ visc_crit_scale = 0.25 / +&ocean_blob_nml +/ + +&ocean_convect_nml + use_this_module = .false. +/ + &ocean_coriolis_nml acor = 0.5 use_this_module = .true. @@ -132,6 +156,13 @@ max_tracers = 5 / +&ocean_drifters_nml +/ + +&ocean_form_drag_nml + use_this_module = .false. +/ + &ocean_frazil_nml frazil_only_in_surface = .false. freezing_temp_preteos10 = .true. @@ -139,10 +170,33 @@ use_this_module = .true. / +&ocean_grids_nml +/ + +&ocean_increment_eta_nml + use_this_module = .false. +/ + +&ocean_increment_tracer_nml + use_this_module = .false. +/ + +&ocean_increment_velocity_nml + use_this_module = .false. +/ + &ocean_lap_friction_nml lap_friction_scheme = 'general' / +&ocean_lap_tracer_nml + use_this_module = .false. +/ + +&ocean_lapcst_friction_nml + use_this_module = .false. +/ + &ocean_lapgen_friction_nml bottom_5point = .true. k_smag_aniso = 0.0 @@ -183,6 +237,9 @@ use_this_module = .true. / +&ocean_nphysics_new_nml +/ + &ocean_nphysics_nml use_nphysicsa = .false. use_nphysicsb = .false. @@ -190,6 +247,9 @@ use_this_module = .true. / +&ocean_nphysics_util_new_nml +/ + &ocean_nphysics_util_nml agm_closure = .true. agm_closure_baroclinic = .true. @@ -211,6 +271,14 @@ nphysics_util_zero_init = .true. / +&ocean_nphysicsa_nml + use_this_module = .false. +/ + +&ocean_nphysicsb_nml + use_this_module = .false. +/ + &ocean_nphysicsc_nml bv_freq_smooth_vert = .true. bvp_bc_mode = 2 @@ -232,6 +300,34 @@ use_this_module = .true. / +&ocean_obc_nml +/ + +&ocean_obs_nml +/ + +&ocean_operators_nml +/ + +&ocean_overexchange_nml + use_this_module = .false. +/ + +&ocean_overflow_nml + use_this_module = .false. +/ + +&ocean_overflow_ofp_nml + use_this_module = .false. +/ + +&ocean_passive_nml +/ + +&ocean_pressure_nml + zero_pressure_force = .false. +/ + &ocean_rivermix_nml river_diffuse_salt = .true. river_diffuse_temp = .true. @@ -241,6 +337,10 @@ use_this_module = .true. / +&ocean_riverspread_nml + use_this_module = .false. +/ + &ocean_rough_nml rough_scheme = 'beljaars' / @@ -275,6 +375,10 @@ zero_water_fluxes = .false. / +&ocean_shortwave_csiro_nml + use_this_module = .false. +/ + &ocean_shortwave_gfdl_nml enforce_sw_frac = .true. optics_manizza = .true. @@ -284,6 +388,10 @@ zmax_pen = 1000000.0 / +&ocean_shortwave_jerlov_nml + use_this_module = .false. +/ + &ocean_shortwave_nml use_shortwave_csiro = .false. use_shortwave_gfdl = .true. @@ -295,6 +403,21 @@ use_this_module = .true. / +&ocean_solo_nml +/ + +&ocean_sponges_eta_nml + use_this_module = .false. +/ + +&ocean_sponges_tracer_nml + use_this_module = .false. +/ + +&ocean_sponges_velocity_nml + use_this_module = .false. +/ + &ocean_submesoscale_nml coefficient_ce = 0.05 front_length_const = 5000.0 @@ -339,6 +462,9 @@ thickness_method = 'energetic' / +&ocean_time_filter_nml +/ + &ocean_topog_nml min_thickness = 0.001 / @@ -364,6 +490,9 @@ zero_tracer_source = .false. / +&ocean_velocity_advect_nml +/ + &ocean_velocity_diag_nml diag_step = 4320 energy_diag_step = 4320 @@ -383,6 +512,18 @@ zero_tendency_implicit = .false. / +&ocean_vert_chen_nml +/ + +&ocean_vert_const_nml +/ + +&ocean_vert_gotm_nml +/ + +&ocean_vert_kpp_mom4p0_nml +/ + &ocean_vert_kpp_mom4p1_nml diff_cbt_iw = 0.0 double_diffusion = .true. @@ -410,6 +551,9 @@ vert_mix_scheme = 'kpp_mom4p1' / +&ocean_vert_pp_nml +/ + &ocean_vert_tidal_nml background_diffusivity = 0.0 background_viscosity = 0.0001 @@ -434,6 +578,23 @@ wave_energy_flux_max = 0.1 / +&ocean_xlandinsert_nml + use_this_module = .false. +/ + +&ocean_xlandmix_nml + use_this_module = .false. +/ + +&oda_core_nml +/ + +&oda_nml +/ + +&surface_flux_nml +/ + &xgrid_nml interp_method = 'second_order' make_exchange_reproduce = .false. From e59d76ec5d2fd3c46ff7cfe0e8b7e657449cbb15 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Wed, 20 May 2020 08:50:12 +1000 Subject: [PATCH 048/111] remove redundant zero_pressure_force = .false. in input.nml --- ocean/input.nml | 1 - 1 file changed, 1 deletion(-) diff --git a/ocean/input.nml b/ocean/input.nml index 3326c317..cd20904f 100644 --- a/ocean/input.nml +++ b/ocean/input.nml @@ -325,7 +325,6 @@ / &ocean_pressure_nml - zero_pressure_force = .false. / &ocean_rivermix_nml From cf5ff4d19b20fe01381ca091d6bf61d93c7aad94 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Wed, 20 May 2020 14:23:42 +1000 Subject: [PATCH 049/111] undo sorting of namelist groups in cice_in.nml --- ice/cice_in.nml | 364 ++++++++++++++++++++++++------------------------ 1 file changed, 182 insertions(+), 182 deletions(-) diff --git a/ice/cice_in.nml b/ice/cice_in.nml index ce42ad66..0b72da43 100644 --- a/ice/cice_in.nml +++ b/ice/cice_in.nml @@ -1,3 +1,50 @@ +&setup_nml + days_per_year = 365 + dbug = .false. + diag_file = 'ice_diag.d' + diag_type = 'file' + diagfreq = 960 + dt = 3600 + dump_last = .true. + dumpfreq = 'y' + dumpfreq_n = 1 + hist_avg = .true. + histfreq = 'd', 'm', 'x', 'x', 'x' + histfreq_n = 1, 1, 1, 1, 1 + history_deflate_level = 1 + history_dir = './OUTPUT/' + history_file = 'iceh' + ice_ic = 'default' + incond_dir = './OUTPUT/' + incond_file = 'iceh_ic' + istep0 = 0 + latpnt = 90.0, -65.0 + lonpnt = 0.0, -45.0 + ndtd = 1 + npt = 35040 + pointer_file = './RESTART/ice.restart_file' + print_global = .false. + print_points = .false. + restart = .false. + restart_dir = './RESTART/' + restart_ext = .false. + restart_file = 'iced' + restart_format = 'nc' + runtype = 'initial' + use_leap_years = .false. + use_restart_time = .true. + write_ic = .false. + year_init = 1 +/ + +&grid_nml + grid_file = 'RESTART/grid.nc' + grid_format = 'nc' + grid_type = 'tripole' + kcatbound = 0 + kmt_file = 'RESTART/kmt.nc' +/ + &domain_nml distribution_type = 'cartesian' distribution_wght = 'latitude' @@ -10,6 +57,36 @@ processor_shape = 'slenderX1' / +&tracer_nml + restart_aero = .false. + restart_age = .false. + restart_fy = .false. + restart_lvl = .false. + restart_pond_cesm = .false. + restart_pond_lvl = .false. + restart_pond_topo = .false. + tr_aero = .false. + tr_fy = .false. + tr_iage = .false. + tr_lvl = .false. + tr_pond_cesm = .false. + tr_pond_lvl = .false. + tr_pond_topo = .false. +/ + +&thermo_nml + a_rapid_mode = 0.0005 + aspect_rapid_mode = 1.0 + chio = 0.004 + conduct = 'bubbly' + dsdt_slow_mode = -5e-08 + kitd = 1 + ktherm = 1 + phi_c_slow_mode = 0.05 + phi_i_mushy = 0.85 + rac_rapid_mode = 10.0 +/ + &dynamics_nml advection = 'remap' cosw = 1.0 @@ -25,6 +102,54 @@ sinw = 0.0 / +&shortwave_nml + ahmax = 0.1 + albedo_type = 'default' + albicei = 0.44 + albicev = 0.86 + albsnowi = 0.7 + albsnowv = 0.98 + dalb_mlt = -0.02 + dt_mlt = 1.0 + r_ice = 0.0 + r_pnd = 0.0 + r_snw = 0.0 + rsnw_mlt = 1500.0 + shortwave = 'default' + tocnfrz = -1.8 +/ + +&ponds_nml + dpscale = 0.001 + frzpnd = 'hlid' + hp1 = 0.01 + hs0 = 0.0 + hs1 = 0.03 + pndaspect = 0.8 + rfracmax = 1.0 + rfracmin = 0.15 +/ + +&zbgc_nml + bgc_data_dir = 'unknown_bgc_data_dir' + bgc_flux_type = 'Jin2006' + nit_data_type = 'default' + phi_snow = 0.5 + restart_bgc = .false. + restart_hbrine = .false. + restore_bgc = .false. + sil_data_type = 'default' + skl_bgc = .false. + tr_bgc_am_sk = .false. + tr_bgc_c_sk = .false. + tr_bgc_chl_sk = .false. + tr_bgc_dms_sk = .false. + tr_bgc_dmspd_sk = .false. + tr_bgc_dmspp_sk = .false. + tr_bgc_sil_sk = .false. + tr_brine = .false. +/ + &forcing_nml atm_data_dir = 'unknown_atm_data_dir' atm_data_format = 'nc' @@ -51,75 +176,6 @@ ycycle = 1 / -&grid_nml - grid_file = 'RESTART/grid.nc' - grid_format = 'nc' - grid_type = 'tripole' - kcatbound = 0 - kmt_file = 'RESTART/kmt.nc' -/ - -&icefields_bgc_nml - f_aero = 'x' - f_bgc_am_ml = 'x' - f_bgc_am_sk = 'x' - f_bgc_c_sk = 'x' - f_bgc_chl_sk = 'x' - f_bgc_dms_sk = 'x' - f_bgc_dmsp_ml = 'x' - f_bgc_dmspd_sk = 'x' - f_bgc_dmspp_sk = 'x' - f_bgc_n_sk = 'x' - f_bgc_nit_ml = 'x' - f_bgc_nit_sk = 'x' - f_bgc_sil_ml = 'x' - f_bgc_sil_sk = 'x' - f_bphi = 'x' - f_btin = 'x' - f_faero_atm = 'x' - f_faero_ocn = 'x' - f_fbri = 'm' - f_fn = 'x' - f_fn_ai = 'x' - f_fnh = 'x' - f_fnh_ai = 'x' - f_fno = 'x' - f_fno_ai = 'x' - f_fsil = 'x' - f_fsil_ai = 'x' - f_grownet = 'x' - f_hbri = 'm' - f_ppnet = 'x' -/ - -&icefields_drag_nml - f_cdn_atm = 'x' - f_cdn_ocn = 'x' - f_drag = 'x' -/ - -&icefields_mechred_nml - f_alvl = 'm' - f_aparticn = 'x' - f_araftn = 'x' - f_ardg = 'm' - f_ardgn = 'x' - f_aredistn = 'x' - f_dardg1dt = 'x' - f_dardg1ndt = 'x' - f_dardg2dt = 'x' - f_dardg2ndt = 'x' - f_dvirdgdt = 'x' - f_dvirdgndt = 'x' - f_krdgn = 'x' - f_opening = 'm' - f_vlvl = 'm' - f_vraftn = 'x' - f_vrdg = 'm' - f_vrdgn = 'x' - f_vredistn = 'x' -/ - &icefields_nml f_aice = 'm' f_aicen = 'm' @@ -233,6 +289,28 @@ f_vvel = 'm' / +&icefields_mechred_nml + f_alvl = 'm' + f_aparticn = 'x' + f_araftn = 'x' + f_ardg = 'm' + f_ardgn = 'x' + f_aredistn = 'x' + f_dardg1dt = 'x' + f_dardg1ndt = 'x' + f_dardg2dt = 'x' + f_dardg2ndt = 'x' + f_dvirdgdt = 'x' + f_dvirdgndt = 'x' + f_krdgn = 'x' + f_opening = 'm' + f_vlvl = 'm' + f_vraftn = 'x' + f_vrdg = 'm' + f_vrdgn = 'x' + f_vredistn = 'x' +/ + &icefields_pond_nml f_apeff = 'x' f_apeff_ai = 'x' @@ -247,119 +325,41 @@ f_ipond_ai = 'x' / -&ponds_nml - dpscale = 0.001 - frzpnd = 'hlid' - hp1 = 0.01 - hs0 = 0.0 - hs1 = 0.03 - pndaspect = 0.8 - rfracmax = 1.0 - rfracmin = 0.15 -/ - -&setup_nml - days_per_year = 365 - dbug = .false. - diag_file = 'ice_diag.d' - diag_type = 'file' - diagfreq = 960 - dt = 3600 - dump_last = .true. - dumpfreq = 'y' - dumpfreq_n = 1 - hist_avg = .true. - histfreq = 'd', 'm', 'x', 'x', 'x' - histfreq_n = 1, 1, 1, 1, 1 - history_deflate_level = 1 - history_dir = './OUTPUT/' - history_file = 'iceh' - ice_ic = 'default' - incond_dir = './OUTPUT/' - incond_file = 'iceh_ic' - istep0 = 0 - latpnt = 90.0, -65.0 - lonpnt = 0.0, -45.0 - ndtd = 1 - npt = 35040 - pointer_file = './RESTART/ice.restart_file' - print_global = .false. - print_points = .false. - restart = .false. - restart_dir = './RESTART/' - restart_ext = .false. - restart_file = 'iced' - restart_format = 'nc' - runtype = 'initial' - use_leap_years = .false. - use_restart_time = .true. - write_ic = .false. - year_init = 1 -/ - -&shortwave_nml - ahmax = 0.1 - albedo_type = 'default' - albicei = 0.44 - albicev = 0.86 - albsnowi = 0.7 - albsnowv = 0.98 - dalb_mlt = -0.02 - dt_mlt = 1.0 - r_ice = 0.0 - r_pnd = 0.0 - r_snw = 0.0 - rsnw_mlt = 1500.0 - shortwave = 'default' - tocnfrz = -1.8 -/ - -&thermo_nml - a_rapid_mode = 0.0005 - aspect_rapid_mode = 1.0 - chio = 0.004 - conduct = 'bubbly' - dsdt_slow_mode = -5e-08 - kitd = 1 - ktherm = 1 - phi_c_slow_mode = 0.05 - phi_i_mushy = 0.85 - rac_rapid_mode = 10.0 -/ - -&tracer_nml - restart_aero = .false. - restart_age = .false. - restart_fy = .false. - restart_lvl = .false. - restart_pond_cesm = .false. - restart_pond_lvl = .false. - restart_pond_topo = .false. - tr_aero = .false. - tr_fy = .false. - tr_iage = .false. - tr_lvl = .false. - tr_pond_cesm = .false. - tr_pond_lvl = .false. - tr_pond_topo = .false. +&icefields_bgc_nml + f_aero = 'x' + f_bgc_am_ml = 'x' + f_bgc_am_sk = 'x' + f_bgc_c_sk = 'x' + f_bgc_chl_sk = 'x' + f_bgc_dms_sk = 'x' + f_bgc_dmsp_ml = 'x' + f_bgc_dmspd_sk = 'x' + f_bgc_dmspp_sk = 'x' + f_bgc_n_sk = 'x' + f_bgc_nit_ml = 'x' + f_bgc_nit_sk = 'x' + f_bgc_sil_ml = 'x' + f_bgc_sil_sk = 'x' + f_bphi = 'x' + f_btin = 'x' + f_faero_atm = 'x' + f_faero_ocn = 'x' + f_fbri = 'm' + f_fn = 'x' + f_fn_ai = 'x' + f_fnh = 'x' + f_fnh_ai = 'x' + f_fno = 'x' + f_fno_ai = 'x' + f_fsil = 'x' + f_fsil_ai = 'x' + f_grownet = 'x' + f_hbri = 'm' + f_ppnet = 'x' / -&zbgc_nml - bgc_data_dir = 'unknown_bgc_data_dir' - bgc_flux_type = 'Jin2006' - nit_data_type = 'default' - phi_snow = 0.5 - restart_bgc = .false. - restart_hbrine = .false. - restore_bgc = .false. - sil_data_type = 'default' - skl_bgc = .false. - tr_bgc_am_sk = .false. - tr_bgc_c_sk = .false. - tr_bgc_chl_sk = .false. - tr_bgc_dms_sk = .false. - tr_bgc_dmspd_sk = .false. - tr_bgc_dmspp_sk = .false. - tr_bgc_sil_sk = .false. - tr_brine = .false. +&icefields_drag_nml + f_cdn_atm = 'x' + f_cdn_ocn = 'x' + f_drag = 'x' / From b32d9390453c3b6ef1d5fb330def1e22ccef3b8b Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Wed, 20 May 2020 15:14:09 +1000 Subject: [PATCH 050/111] let payu determine the total ncpus - see https://github.com/payu-org/payu/issues/97 --- config.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/config.yaml b/config.yaml index dc096864..9bc508b2 100644 --- a/config.yaml +++ b/config.yaml @@ -5,7 +5,6 @@ queue: normal walltime: 3:00:00 jobname: 1deg_jra55_iaf -ncpus: 252 mem: 500GB # Force payu to always find, and save, files in this scratch project directory From 9910bbfa0d20658dc53ade0f6fced5d4d113db8e Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Fri, 22 May 2020 21:26:41 +1000 Subject: [PATCH 051/111] Raise limits on number of MOM output files --- ocean/input.nml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/ocean/input.nml b/ocean/input.nml index cd20904f..cc8ecdeb 100644 --- a/ocean/input.nml +++ b/ocean/input.nml @@ -21,6 +21,9 @@ &diag_manager_nml debug_diag_manager = .false. issue_oor_warnings = .true. + max_axes = 200 + max_files = 200 + max_num_axis_sets = 200 / &fms_io_nml From c0057f85c3aa786318a4a836908da2bf12a7e62b Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Tue, 26 May 2020 15:10:01 +1000 Subject: [PATCH 052/111] new diag_table generated from diag_table_source.yaml with make_diag_table.py --- ocean/diag_table | 474 ++++++++++++++++++++++++++--------- ocean/diag_table_source.yaml | 341 +++++++++++++++++++++++++ ocean/make_diag_table.py | 143 +++++++++++ 3 files changed, 843 insertions(+), 115 deletions(-) create mode 100755 ocean/diag_table_source.yaml create mode 100755 ocean/make_diag_table.py diff --git a/ocean/diag_table b/ocean/diag_table index a9eeacd3..b3e66792 100644 --- a/ocean/diag_table +++ b/ocean/diag_table @@ -1,119 +1,363 @@ ACCESS-OM2 1900 1 1 0 0 0 -# The MOM diag_table format is defined here: -# https://github.com/mom-ocean/MOM5/blob/master/src/shared/diag_manager/diag_table.F90 -# and some of the available diagnostics are listed here: -# https://raw.githubusercontent.com/COSIMA/access-om2/master/MOM_diags.txt -# https://github.com/COSIMA/access-om2/wiki/Technical-documentation#MOM5-diagnostics-list - -# output files -"ocean_month", 1, "months", 1, "days", "time", -"ocean", 12, "months", 1, "days", "time", -"ocean_grid", -1, "months", 1, "days", "time", -"ocean_scalar", 1, "months", 1, "days", "time", - - -# Save ocean grid data once and for all -"ocean_model","geolon_t","geolon_t", "ocean_grid","all",.false.,"none",2 -"ocean_model","geolat_t","geolat_t", "ocean_grid","all",.false.,"none",2 -"ocean_model","geolon_c","geolon_c", "ocean_grid","all",.false.,"none",2 -"ocean_model","geolat_c","geolat_c", "ocean_grid","all",.false.,"none",2 -"ocean_model","ht","ht", "ocean_grid","all",.false.,"none",2 -"ocean_model","hu","hu", "ocean_grid","all",.false.,"none",2 -"ocean_model","dxt","dxt", "ocean_grid","all",.false.,"none",2 -"ocean_model","dyt","dyt", "ocean_grid","all",.false.,"none",2 -"ocean_model","dxu","dxu", "ocean_grid","all",.false.,"none",2 -"ocean_model","dyu","dyu", "ocean_grid","all",.false.,"none",2 -"ocean_model","area_t","area_t", "ocean_grid","all",.false.,"none",2 -"ocean_model","area_u","area_u", "ocean_grid","all",.false.,"none",2 -"ocean_model","kmt","kmt", "ocean_grid","all",.false.,"none",2 -"ocean_model","kmu","kmu", "ocean_grid","all",.false.,"none",2 -"ocean_model","drag_coeff","drag_coeff","ocean_grid","all",.false.,"none",2 -#========================================================================== - -# Prognostic fields: -# 3d fields -"ocean_model","temp","temp", "ocean","all",.true.,"none",2 -"ocean_model","pot_temp","pot_temp", "ocean","all",.true.,"none",2 -"ocean_model","salt","salt", "ocean","all",.true.,"none",2 -"ocean_model","age_global","age_global","ocean","all",.true.,"none",2 -"ocean_model","u","u", "ocean","all",.true.,"none",2 -"ocean_model","v","v", "ocean","all",.true.,"none",2 -"ocean_model","wt","wt", "ocean","all",.true.,"none",2 -"ocean_model","dzt","dzt", "ocean","all",.true.,"none",2 -"ocean_model","pot_rho_0","pot_rho_0", "ocean","all",.true.,"none",2 -"ocean_model","pot_rho_2","pot_rho_2", "ocean","all",.true.,"none",2 -"ocean_model","tx_trans","tx_trans", "ocean","all",.true.,"none",2 -"ocean_model","ty_trans","ty_trans", "ocean","all",.true.,"none",2 -#"ocean_model","ty_trans_gm","ty_trans_gm", "ocean","all",.true.,"none",2 -"ocean_model","tx_trans_rho","tx_trans_rho","ocean","all",.true.,"none",2 -"ocean_model","ty_trans_rho","ty_trans_rho","ocean","all",.true.,"none",2 -"ocean_model","ty_trans_rho_gm","ty_trans_rho_gm","ocean","all",.true.,"none",2 -"ocean_model","temp_xflux_adv","temp_xflux_adv","ocean","all",.true.,"none",2 -"ocean_model","temp_yflux_adv","temp_yflux_adv","ocean","all",.true.,"none",2 -"ocean_model","diff_cbt_t","diff_cbt_t", "ocean","all",.true.,"none",2 - - -# 2d fields - monthly output -"ocean_model","sea_level","sea_level", "ocean_month","all",.true.,"none",2 -"ocean_model","eta_t","eta_t", "ocean_month","all",.true.,"none",2 -"ocean_model","sea_level_sq","sea_levelsq", "ocean_month","all",.true.,"none",2 -"ocean_model","mld","mld", "ocean_month","all",.true.,"none",2 -"ocean_model","pme_river","pme_river", "ocean_month","all",.true.,"none",2 -"ocean_model","river","river", "ocean_month","all",.true.,"none",2 -"ocean_model","runoff","runoff", "ocean_month","all",.true.,"none",2 -"ocean_model","ice_calving","ice_calving", "ocean_month","all",.true.,"none",2 -"ocean_model","evap","evap", "ocean_month","all",.true.,"none",2 -"ocean_model","melt","melt", "ocean_month","all",.true.,"none",2 -"ocean_model","sfc_salt_flux_restore","sfc_salt_flux_restore","ocean_month","all",.true.,"none",2 -"ocean_model","sfc_salt_flux_ice","sfc_salt_flux_ice","ocean_month","all",.true.,"none",2 -"ocean_model","sfc_salt_flux_coupler","sfc_salt_flux_coupler","ocean_month","all",.true.,"none",2 -# see https://github.com/COSIMA/access-om2/issues/139 -# "ocean_model","net_sfc_heating","net_sfc_heating", "ocean_month","all",.true.,"none",2 -"ocean_model","frazil_3d_int_z","frazil_3d_int_z", "ocean_month","all",.true.,"none",2 -"ocean_model","tau_x","tau_x", "ocean_month","all",.true.,"none",2 -"ocean_model","tau_y","tau_y", "ocean_month","all",.true.,"none",2 -"ocean_model","bmf_u","bmf_u", "ocean_month","all",.true.,"none",2 -"ocean_model","bmf_v","bmf_v", "ocean_month","all",.true.,"none",2 -"ocean_model","tx_trans_int_z","tx_trans_int_z", "ocean_month","all",.true.,"none",2 -"ocean_model","ty_trans_int_z","ty_trans_int_z", "ocean_month","all",.true.,"none",2 -"ocean_model","pbot_t","pbot_t", "ocean_month","all",.true.,"none",2 - - -# timeseries - 1D scalar variables -"ocean_model","ke_tot","ke_tot", "ocean_scalar","all",.true.,"none",1 -"ocean_model","pe_tot","pe_tot", "ocean_scalar","all",.true.,"none",1 -"ocean_model","temp_global_ave","temp_global_ave", "ocean_scalar","all",.true.,"none",1 -"ocean_model","salt_global_ave","salt_global_ave", "ocean_scalar","all",.true.,"none",1 -"ocean_model","rhoave","rhoave", "ocean_scalar","all",.true.,"none",1 -"ocean_model","temp_surface_ave","temp_surface_ave", "ocean_scalar","all",.true.,"none",1 -"ocean_model","salt_surface_ave","salt_surface_ave", "ocean_scalar","all",.true.,"none",1 -"ocean_model","total_ocean_salt","total_ocean_salt", "ocean_scalar","all",.true.,"none",1 -"ocean_model","total_ocean_heat","total_ocean_heat", "ocean_scalar","all",.true.,"none",1 -"ocean_model","eta_global","eta_global", "ocean_scalar","all",.true.,"none",1 -"ocean_model","total_ocean_sfc_salt_flux_coupler","total_ocean_sfc_salt_flux_coupler","ocean_scalar","all",.true.,"none",1 -# see https://github.com/COSIMA/access-om2/issues/139 -# "ocean_model","total_net_sfc_heating","total_net_sfc_heating","ocean_scalar","all",.true.,"none",1 -"ocean_model","total_ocean_pme_river","total_ocean_pme_river" ,"ocean_scalar","all",.true.,"none",1 -"ocean_model","total_ocean_river","total_ocean_river" ,"ocean_scalar","all",.true.,"none",1 -"ocean_model","total_ocean_runoff","total_ocean_runoff" ,"ocean_scalar","all",.true.,"none",1 -"ocean_model","total_ocean_calving","total_ocean_calving" ,"ocean_scalar","all",.true.,"none",1 -"ocean_model","total_ocean_melt","total_ocean_melt" ,"ocean_scalar","all",.true.,"none",1 -"ocean_model","total_ocean_evap","total_ocean_evap" ,"ocean_scalar","all",.true.,"none",1 -"ocean_model","total_ocean_lprec","total_ocean_lprec" ,"ocean_scalar","all",.true.,"none",1 -"ocean_model","total_ocean_fprec","total_ocean_fprec" ,"ocean_scalar","all",.true.,"none",1 -"ocean_model","total_ocean_runoff_heat","total_ocean_runoff_heat" ,"ocean_scalar","all",.true.,"none",1 -"ocean_model","total_ocean_calving_heat","total_ocean_calving_heat" ,"ocean_scalar","all",.true.,"none",1 -"ocean_model","total_ocean_river_heat","total_ocean_river_heat" ,"ocean_scalar","all",.true.,"none",1 -"ocean_model","total_ocean_hflux_prec","total_ocean_hflux_prec" ,"ocean_scalar","all",.true.,"none",1 -"ocean_model","total_ocean_hflux_evap","total_ocean_hflux_evap" ,"ocean_scalar","all",.true.,"none",1 -"ocean_model","total_ocean_hflux_coupler","total_ocean_hflux_coupler" ,"ocean_scalar","all",.true.,"none",1 -"ocean_model","total_ocean_swflx","total_ocean_swflx" ,"ocean_scalar","all",.true.,"none",1 -"ocean_model","total_ocean_swflx_vis","total_ocean_swflx_vis" ,"ocean_scalar","all",.true.,"none",1 -"ocean_model","total_ocean_lw_heat","total_ocean_lw_heat" ,"ocean_scalar","all",.true.,"none",1 -"ocean_model","total_ocean_evap_heat","total_ocean_evap_heat" ,"ocean_scalar","all",.true.,"none",1 -"ocean_model","total_ocean_fprec_melt_heat","total_ocean_fprec_melt_heat" ,"ocean_scalar","all",.true.,"none",1 -"ocean_model","total_ocean_calving_melt_heat","total_ocean_calving_melt_heat","ocean_scalar","all",.true.,"none",1 -"ocean_model","total_ocean_sens_heat","total_ocean_sens_heat" ,"ocean_scalar","all",.true.,"none",1 +######################################################################################################### +# # +# DO NOT EDIT! Instead, edit diag_table_source.yaml and run make_diag_table.py to re-generate this file # +# # +######################################################################################################### + +# static 2d grid data + +"ocean-2d-area_t", -1, "months", 1, "days", "time" +"ocean_model", "area_t", "area_t", "ocean-2d-area_t", "all", "none", "none", 2 + +"ocean-2d-area_u", -1, "months", 1, "days", "time" +"ocean_model", "area_u", "area_u", "ocean-2d-area_u", "all", "none", "none", 2 + +"ocean-2d-drag_coeff", -1, "months", 1, "days", "time" +"ocean_model", "drag_coeff", "drag_coeff", "ocean-2d-drag_coeff", "all", "none", "none", 2 + +"ocean-2d-dxt", -1, "months", 1, "days", "time" +"ocean_model", "dxt", "dxt", "ocean-2d-dxt", "all", "none", "none", 2 + +"ocean-2d-dxu", -1, "months", 1, "days", "time" +"ocean_model", "dxu", "dxu", "ocean-2d-dxu", "all", "none", "none", 2 + +"ocean-2d-dyt", -1, "months", 1, "days", "time" +"ocean_model", "dyt", "dyt", "ocean-2d-dyt", "all", "none", "none", 2 + +"ocean-2d-dyu", -1, "months", 1, "days", "time" +"ocean_model", "dyu", "dyu", "ocean-2d-dyu", "all", "none", "none", 2 + +"ocean-2d-geolat_c", -1, "months", 1, "days", "time" +"ocean_model", "geolat_c", "geolat_c", "ocean-2d-geolat_c", "all", "none", "none", 2 + +"ocean-2d-geolat_t", -1, "months", 1, "days", "time" +"ocean_model", "geolat_t", "geolat_t", "ocean-2d-geolat_t", "all", "none", "none", 2 + +"ocean-2d-geolon_c", -1, "months", 1, "days", "time" +"ocean_model", "geolon_c", "geolon_c", "ocean-2d-geolon_c", "all", "none", "none", 2 + +"ocean-2d-geolon_t", -1, "months", 1, "days", "time" +"ocean_model", "geolon_t", "geolon_t", "ocean-2d-geolon_t", "all", "none", "none", 2 + +"ocean-2d-ht", -1, "months", 1, "days", "time" +"ocean_model", "ht", "ht", "ocean-2d-ht", "all", "none", "none", 2 + +"ocean-2d-hu", -1, "months", 1, "days", "time" +"ocean_model", "hu", "hu", "ocean-2d-hu", "all", "none", "none", 2 + +"ocean-2d-kmt", -1, "months", 1, "days", "time" +"ocean_model", "kmt", "kmt", "ocean-2d-kmt", "all", "none", "none", 2 + +"ocean-2d-kmu", -1, "months", 1, "days", "time" +"ocean_model", "kmu", "kmu", "ocean-2d-kmu", "all", "none", "none", 2 + + +# yearly 3d fields + +"ocean-3d-age_global-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" +"ocean_model", "age_global", "age_global", "ocean-3d-age_global-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-3d-aiso_bih-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" +"ocean_model", "aiso_bih", "aiso_bih", "ocean-3d-aiso_bih-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-3d-buoyfreq2_wt-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" +"ocean_model", "buoyfreq2_wt", "buoyfreq2_wt", "ocean-3d-buoyfreq2_wt-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-3d-diff_cbt_t-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" +"ocean_model", "diff_cbt_t", "diff_cbt_t", "ocean-3d-diff_cbt_t-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-3d-pot_rho_0-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" +"ocean_model", "pot_rho_0", "pot_rho_0", "ocean-3d-pot_rho_0-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-3d-pot_rho_2-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" +"ocean_model", "pot_rho_2", "pot_rho_2", "ocean-3d-pot_rho_2-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-3d-pot_temp-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" +"ocean_model", "pot_temp", "pot_temp", "ocean-3d-pot_temp-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-3d-salt-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" +"ocean_model", "salt", "salt", "ocean-3d-salt-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-3d-temp_xflux_adv-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" +"ocean_model", "temp_xflux_adv", "temp_xflux_adv", "ocean-3d-temp_xflux_adv-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-3d-temp_yflux_adv-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" +"ocean_model", "temp_yflux_adv", "temp_yflux_adv", "ocean-3d-temp_yflux_adv-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-3d-temp-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" +"ocean_model", "temp", "temp", "ocean-3d-temp-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-3d-tx_trans_rho-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" +"ocean_model", "tx_trans_rho", "tx_trans_rho", "ocean-3d-tx_trans_rho-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-3d-tx_trans-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" +"ocean_model", "tx_trans", "tx_trans", "ocean-3d-tx_trans-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-3d-ty_trans_nrho_submeso-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" +"ocean_model", "ty_trans_nrho_submeso", "ty_trans_nrho_submeso", "ocean-3d-ty_trans_nrho_submeso-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-3d-ty_trans_rho_gm-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" +"ocean_model", "ty_trans_rho_gm", "ty_trans_rho_gm", "ocean-3d-ty_trans_rho_gm-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-3d-ty_trans_rho-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" +"ocean_model", "ty_trans_rho", "ty_trans_rho", "ocean-3d-ty_trans_rho-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-3d-ty_trans_submeso-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" +"ocean_model", "ty_trans_submeso", "ty_trans_submeso", "ocean-3d-ty_trans_submeso-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-3d-ty_trans-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" +"ocean_model", "ty_trans", "ty_trans", "ocean-3d-ty_trans-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-3d-u-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" +"ocean_model", "u", "u", "ocean-3d-u-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-3d-v-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" +"ocean_model", "v", "v", "ocean-3d-v-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-3d-vert_pv-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" +"ocean_model", "vert_pv", "vert_pv", "ocean-3d-vert_pv-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-3d-wt-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" +"ocean_model", "wt", "wt", "ocean-3d-wt-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 + + +# yearly 3d squared fields + +"ocean-3d-u-1-yearly-pow02-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" +"ocean_model", "u", "u", "ocean-3d-u-1-yearly-pow02-ym%4yr%2mo", "all", "pow02", "none", 2 + +"ocean-3d-v-1-yearly-pow02-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" +"ocean_model", "v", "v", "ocean-3d-v-1-yearly-pow02-ym%4yr%2mo", "all", "pow02", "none", 2 + + +# monthly 3d fields + +"ocean-3d-dzt-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "dzt", "dzt", "ocean-3d-dzt-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + + +# monthly 2d fields + +"ocean-2d-agm-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "agm", "agm", "ocean-2d-agm-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-aredi-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "aredi", "aredi", "ocean-2d-aredi-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-bmf_u-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "bmf_u", "bmf_u", "ocean-2d-bmf_u-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-bmf_v-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "bmf_v", "bmf_v", "ocean-2d-bmf_v-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-eta_t-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "eta_t", "eta_t", "ocean-2d-eta_t-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-evap_heat-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "evap_heat", "evap_heat", "ocean-2d-evap_heat-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-evap-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "evap", "evap", "ocean-2d-evap-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-fprec_melt_heat-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "fprec_melt_heat", "fprec_melt_heat", "ocean-2d-fprec_melt_heat-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-fprec-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "fprec", "fprec", "ocean-2d-fprec-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-frazil_3d_int_z-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "frazil_3d_int_z", "frazil_3d_int_z", "ocean-2d-frazil_3d_int_z-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-lprec-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "lprec", "lprec", "ocean-2d-lprec-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-lw_heat-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "lw_heat", "lw_heat", "ocean-2d-lw_heat-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-melt-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "melt", "melt", "ocean-2d-melt-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-mld-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "mld", "mld", "ocean-2d-mld-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-pbot_t-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "pbot_t", "pbot_t", "ocean-2d-pbot_t-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-pme_net-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "pme_net", "pme_net", "ocean-2d-pme_net-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-pme_river-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "pme_river", "pme_river", "ocean-2d-pme_river-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-river-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "river", "river", "ocean-2d-river-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-runoff-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "runoff", "runoff", "ocean-2d-runoff-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-sea_level_sq-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "sea_level_sq", "sea_level_sq", "ocean-2d-sea_level_sq-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-sea_level-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "sea_level", "sea_level", "ocean-2d-sea_level-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-sens_heat-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "sens_heat", "sens_heat", "ocean-2d-sens_heat-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-sfc_hflux_coupler-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "sfc_hflux_coupler", "sfc_hflux_coupler", "ocean-2d-sfc_hflux_coupler-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-sfc_hflux_from_runoff-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "sfc_hflux_from_runoff", "sfc_hflux_from_runoff", "ocean-2d-sfc_hflux_from_runoff-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-sfc_hflux_pme-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "sfc_hflux_pme", "sfc_hflux_pme", "ocean-2d-sfc_hflux_pme-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-sfc_salt_flux_coupler-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "sfc_salt_flux_coupler", "sfc_salt_flux_coupler", "ocean-2d-sfc_salt_flux_coupler-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-sfc_salt_flux_ice-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "sfc_salt_flux_ice", "sfc_salt_flux_ice", "ocean-2d-sfc_salt_flux_ice-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-sfc_salt_flux_restore-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "sfc_salt_flux_restore", "sfc_salt_flux_restore", "ocean-2d-sfc_salt_flux_restore-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-surface_salt-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "surface_salt", "surface_salt", "ocean-2d-surface_salt-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-surface_temp-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "surface_temp", "surface_temp", "ocean-2d-surface_temp-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-sw_heat-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "sw_heat", "sw_heat", "ocean-2d-sw_heat-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-swflx-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "swflx", "swflx", "ocean-2d-swflx-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-tau_x-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "tau_x", "tau_x", "ocean-2d-tau_x-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-tau_y-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "tau_y", "tau_y", "ocean-2d-tau_y-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-temp_int_rhodz-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "temp_int_rhodz", "temp_int_rhodz", "ocean-2d-temp_int_rhodz-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-temp_xflux_adv_int_z-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "temp_xflux_adv_int_z", "temp_xflux_adv_int_z", "ocean-2d-temp_xflux_adv_int_z-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-temp_xflux_submeso_int_z-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "temp_xflux_submeso_int_z", "temp_xflux_submeso_int_z", "ocean-2d-temp_xflux_submeso_int_z-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-temp_yflux_adv_int_z-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "temp_yflux_adv_int_z", "temp_yflux_adv_int_z", "ocean-2d-temp_yflux_adv_int_z-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-temp_yflux_submeso_int_z-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "temp_yflux_submeso_int_z", "temp_yflux_submeso_int_z", "ocean-2d-temp_yflux_submeso_int_z-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-tx_trans_int_z-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "tx_trans_int_z", "tx_trans_int_z", "ocean-2d-tx_trans_int_z-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-ty_trans_int_z-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "ty_trans_int_z", "ty_trans_int_z", "ocean-2d-ty_trans_int_z-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-wfiform-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "wfiform", "wfiform", "ocean-2d-wfiform-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-wfimelt-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "wfimelt", "wfimelt", "ocean-2d-wfimelt-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + + +# monthly 2d fields with different reduction methods + +"ocean-2d-eta_t-1-monthly-pow02-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "eta_t", "eta_t", "ocean-2d-eta_t-1-monthly-pow02-ym%4yr%2mo", "all", "pow02", "none", 2 + +"ocean-2d-mld-1-monthly-max-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "mld", "mld", "ocean-2d-mld-1-monthly-max-ym%4yr%2mo", "all", "max", "none", 2 + +"ocean-2d-surface_temp-1-monthly-min-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "surface_temp", "surface_temp", "ocean-2d-surface_temp-1-monthly-min-ym%4yr%2mo", "all", "min", "none", 2 + + +# daily 2d fields + +"ocean-2d-eta_t-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "eta_t", "eta_t", "ocean-2d-eta_t-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-frazil_3d_int_z-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "frazil_3d_int_z", "frazil_3d_int_z", "ocean-2d-frazil_3d_int_z-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-mld-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "mld", "mld", "ocean-2d-mld-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-pme_river-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "pme_river", "pme_river", "ocean-2d-pme_river-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-sfc_hflux_coupler-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "sfc_hflux_coupler", "sfc_hflux_coupler", "ocean-2d-sfc_hflux_coupler-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-sfc_hflux_from_runoff-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "sfc_hflux_from_runoff", "sfc_hflux_from_runoff", "ocean-2d-sfc_hflux_from_runoff-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-sfc_hflux_pme-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "sfc_hflux_pme", "sfc_hflux_pme", "ocean-2d-sfc_hflux_pme-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-surface_salt-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "surface_salt", "surface_salt", "ocean-2d-surface_salt-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-surface_temp-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "surface_temp", "surface_temp", "ocean-2d-surface_temp-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-u_surf-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "u_surf", "u_surf", "ocean-2d-u_surf-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-v_surf-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "v_surf", "v_surf", "ocean-2d-v_surf-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 + + +# monthly scalar timeseries + +"ocean-scalar-1-monthly-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "eta_global", "eta_global", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "ke_tot", "ke_tot", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "pe_tot", "pe_tot", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "rhoave", "rhoave", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "salt_global_ave", "salt_global_ave", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "salt_surface_ave", "salt_surface_ave", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "temp_global_ave", "temp_global_ave", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "temp_surface_ave", "temp_surface_ave", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "total_ocean_calving_heat", "total_ocean_calving_heat", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "total_ocean_calving_melt_heat", "total_ocean_calving_melt_heat", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "total_ocean_calving", "total_ocean_calving", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "total_ocean_evap_heat", "total_ocean_evap_heat", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "total_ocean_evap", "total_ocean_evap", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "total_ocean_fprec_melt_heat", "total_ocean_fprec_melt_heat", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "total_ocean_fprec", "total_ocean_fprec", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "total_ocean_heat", "total_ocean_heat", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "total_ocean_hflux_coupler", "total_ocean_hflux_coupler", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "total_ocean_hflux_evap", "total_ocean_hflux_evap", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "total_ocean_hflux_prec", "total_ocean_hflux_prec", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "total_ocean_lprec", "total_ocean_lprec", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "total_ocean_lw_heat", "total_ocean_lw_heat", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "total_ocean_melt", "total_ocean_melt", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "total_ocean_pme_river", "total_ocean_pme_river", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "total_ocean_river_heat", "total_ocean_river_heat", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "total_ocean_river", "total_ocean_river", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "total_ocean_runoff_heat", "total_ocean_runoff_heat", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "total_ocean_runoff", "total_ocean_runoff", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "total_ocean_salt", "total_ocean_salt", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "total_ocean_sens_heat", "total_ocean_sens_heat", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "total_ocean_sfc_salt_flux_coupler", "total_ocean_sfc_salt_flux_coupler", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "total_ocean_swflx_vis", "total_ocean_swflx_vis", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "total_ocean_swflx", "total_ocean_swflx", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 + + +# monthly 2d snapshots + + +# monthly 3d snapshots diff --git a/ocean/diag_table_source.yaml b/ocean/diag_table_source.yaml new file mode 100755 index 00000000..63e2922c --- /dev/null +++ b/ocean/diag_table_source.yaml @@ -0,0 +1,341 @@ +####################################################################################################### +# This yaml file is used by make_diag_table.py to create a diag_table file specifying MOM5 diagnostics. +# Latest version: https://github.com/COSIMA/make_diag_table +# +# Define the diagnostics you want in the diag_table section below. +# +# The MOM diag_table format is defined here: +# https://github.com/mom-ocean/MOM5/blob/master/src/shared/diag_manager/diag_table.F90 +####################################################################################################### + + +# Define global default settings which will be applied to all diagnostics, +# unless overridden in diag_table section below, either in defaults or individual fields. +# You're unlikely to need to change any of the global_defaults. +global_defaults: +# global_section: + title: ACCESS-OM2 # any string + base_date: [ 1900, 1, 1, 0, 0, 0 ] # reference time used for the time units. six integers: year, month, day, hour, minute, second +# file section: + file_name: # file name (without trailing ".nc") is constructed from these components, + # separated by file_name_separator, as per https://github.com/COSIMA/access-om2/issues/185 + # All these components (other than field_name) must be names that exist in global_defaults. + # If file_name_date or file_name_date_section are used, it must be the last item. + - file_name_prefix + - file_name_dimension + - field_name # substituted by field name in diag_table section below + - output_freq + - output_freq_units + - reduction_method + - file_name_date + # - file_name_date_section + output_freq: 1 # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run) + output_freq_units: months # time units for output: years, months, days, hours, minutes, or seconds + file_format: 1 # integer, must be 1, specifying NetCDF (the only format currently supported) + time_axis_units: days # time units for the output file time axis: years, months, days, hours, minutes, or seconds + time_axis_name: time # must be "time" (case-insensitive) + new_file_freq: 1 # optional integer: frequency (in new_file_freq_units) for closing the existing file, and creating a new file + new_file_freq_units: years # time units for new_file_freq: years, months, days, hours, minutes, or seconds (optional; required if and only if new_file_freq specified) + start_time: # Time to start the file for the first time. The format of this string is the same as base_date (optional; requires new_file_freq, new_file_freq_units) + file_duration: # integer: How long file should receive data after start time (optional; requires new_file_freq, new_file_freq_units, start_time) + file_duration_units: # units for file_duration: years, months, days, hours, minutes, or seconds (optional; required if and only if file_duration specified) +# field section: + module_name: ocean_model + field_name: # set via keys in the fields section of the diag_table section below + output_name: # same as field_name unless overridden + # file_name: # same as file_name in file_section above unless overridden in diag_table section below + time_sampling: all # Currently not used. Please use the string "all". + reduction_method: mean # mean, snap, rms, pow##, min, max, or diurnal## + # reduction_method options: + # mean or average or true: Average from the last time written to the current time. Becomes "average" in diag_table. + # snap or none or false: No reduction. Write snapshot of current time step value only. Becomes "none" in diag_table. + # rms: Calculate the root mean square from the last time written to the current time. + # pow##: Calculate the mean of the power ## from the last time written to the current time. + # min: Minimum value from last write to current time. + # max: Maximum value from last write to current time. + # diurnal##: ## diurnal averages + regional_section: none # string: bounds of the regional section to capture ("none" indicates a global region). String format: lat_min, lat_max, lon_min, lon_max, vert_min, vert_max. Use vert_min = -1 and vert_max = -1 to get the entire vertical axis. + packing: 2 + # packing is the Fortran number KIND of the data written: + # 1: double precision + # 2: float (single precision) + # 4: packed 16-bit integers + # 8: packed 1-byte (not tested) +# extra things for constructing filename: + file_name_dimension: 3d # descriptor for filename, e.g. 3d, 2d, scalar + file_name_prefix: ocean + file_name_date: "ym%4yr%2mo" # run date/time of file opening; format: %, 1 digit (#digits), one of (yr, mo, dy, hr, mi, sc); date/time components will be separated by _ in filename. + file_name_separator: "-" # used to separate filename components; best not to use "_" to avoid confusion with fields and dates + file_name_omit_empty: true # whether to omit empty filename components to avoid duplicate file_name_separator + file_name_substitutions: # string replacements for filename components + years: yearly + months: monthly + days: daily + hours: hourly + none: snap # careful! will apply to both reduction_method and regional_section + 'False': snap + average: mean + 'True': mean + None: "" # for empty items + file_name_date_section: # These are separated by "_". If file_name_date is used, it must be the last item. + - output_freq + - output_freq_units + - reduction_method + - file_name_date + + +####################################################################################################### +# diag_table section - this defines the diagnostics that will appear in diag_table. +# +# Top-level categories in diag_table have arbitrary names (they're just used for +# comments in the output diag_table). Make as many of these as you like to group +# similar diagnostics with shared defaults. Note that each of the top-level +# categories can have only have one instance of each field name, so if you need +# multiple outputs of the same field (e.g. as both averages and snapshots), you’ll +# need to make additional categories. +# +# Within each top-level category there's an optional defaults section and a +# fields section. The defaults section overrides items in global_defaults for +# all fields in the category. The field section specifies diagnostic field +# names. To add a new diagnostic, all you need to do is add its name to the +# field section in the appropriate category. Each field name can be followed by +# a dictionary overriding the category and global defaults for that field only. +# +# Some of the available diagnostics are listed here: +# https://raw.githubusercontent.com/COSIMA/access-om2/master/MOM_diags.txt +# https://github.com/COSIMA/access-om2/wiki/Technical-documentation#MOM5-diagnostics-list +diag_table: + 'static 2d grid data': + defaults: # these can be overridden for individual fields below + file_name_dimension: 2d # descriptor for filename, e.g. 3d, 2d, scalar + file_name: # file name (without trailing ".nc") is constructed from these components, + # separated by file_name_separator, as per https://github.com/COSIMA/access-om2/issues/185 + # All these components (other than field_name) must be names that exist in global_defaults. + - file_name_prefix + - file_name_dimension + - field_name # substituted by field name in fields section below + reduction_method: snap # mean, snap, rms, pow##, min, max, or diurnal## + output_freq: -1 # Output frequency in output_freq_units (0: every timestep; -1: only at end of run) + new_file_freq: # optional integer: frequency (in new_file_freq_units) for closing the existing file, and creating a new file + fields: + area_t: + area_u: + drag_coeff: + dxt: + dxu: + dyt: + dyu: + geolat_c: + geolat_t: + geolon_c: + geolon_t: + ht: + hu: + kmt: + kmu: + 'yearly 3d fields': + defaults: # these can be overridden for individual fields below + file_name_dimension: 3d # descriptor for filename, e.g. 3d, 2d, scalar + output_freq: 1 # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run) + output_freq_units: years # time units for output: years, months, days, hours, minutes, or seconds + fields: + age_global: + aiso_bih: + buoyfreq2_wt: + diff_cbt_t: + pot_rho_0: + pot_rho_2: + pot_temp: + salt: + temp_xflux_adv: + temp_yflux_adv: + temp: + tx_trans_rho: + tx_trans: + ty_trans_nrho_submeso: + ty_trans_rho_gm: + ty_trans_rho: + ty_trans_submeso: + ty_trans: + u: + v: + vert_pv: + wt: + 'yearly 3d squared fields': # for calculating EKE etc + defaults: # these can be overridden for individual fields below + file_name_dimension: 3d # descriptor for filename, e.g. 3d, 2d, scalar + output_freq: 1 # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run) + output_freq_units: years # time units for output: years, months, days, hours, minutes, or seconds + reduction_method: pow02 # mean, snap, rms, pow##, min, max, or diurnal## + fields: + u: + v: + 'monthly 3d fields': + defaults: # these can be overridden for individual fields below + file_name_dimension: 3d # descriptor for filename, e.g. 3d, 2d, scalar + output_freq: 1 # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run) + output_freq_units: months # time units for output: years, months, days, hours, minutes, or seconds + fields: + dzt: + # neutral_diffusion_temp: + # neutral_gm_temp: + # neutral_temp: + # pot_temp: + # salt: + # temp_advection: + # temp_eta_smooth: + # temp_nonlocal_KPP: + # temp_rivermix: + # temp_sigma_diff: + # temp_submeso: + # temp_tendency_expl: + # temp_tendency: + # temp_vdiffuse_diff_cbt_conv: + # temp_vdiffuse_diff_cbt: + # temp_vdiffuse_impl: + # temp_vdiffuse_k33: + # temp_vdiffuse_sbc: + # temp: + # u: + # v: + 'monthly 2d fields': + defaults: # these can be overridden for individual fields below + file_name_dimension: 2d # descriptor for filename, e.g. 3d, 2d, scalar + output_freq: 1 # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run) + output_freq_units: months # time units for output: years, months, days, hours, minutes, or seconds + fields: + agm: + aredi: + bmf_u: + bmf_v: + eta_t: + evap_heat: + evap: + fprec_melt_heat: + fprec: + frazil_3d_int_z: + lprec: + lw_heat: + melt: + mld: + # net_sfc_heating: # disabled - incorrect - see https://github.com/COSIMA/access-om2/issues/139 + pbot_t: + pme_net: + pme_river: + river: + runoff: + sea_level_sq: + sea_level: + sens_heat: + sfc_hflux_coupler: + sfc_hflux_from_runoff: + sfc_hflux_pme: + sfc_salt_flux_coupler: + sfc_salt_flux_ice: + sfc_salt_flux_restore: + surface_salt: + surface_temp: + sw_heat: + swflx: + tau_x: + tau_y: + temp_int_rhodz: + temp_xflux_adv_int_z: + temp_xflux_submeso_int_z: + temp_yflux_adv_int_z: + temp_yflux_submeso_int_z: + tx_trans_int_z: + ty_trans_int_z: + wfiform: + wfimelt: + 'monthly 2d fields with different reduction methods': + defaults: # these can be overridden for individual fields below + file_name_dimension: 2d # descriptor for filename, e.g. 3d, 2d, scalar + output_freq: 1 # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run) + output_freq_units: months # time units for output: years, months, days, hours, minutes, or seconds + fields: + eta_t: {reduction_method: pow02} # for calculating standard deviation + mld: {reduction_method: max} # max avoids spurious small values due to rainfall + surface_temp: {reduction_method: min} # min for comparison with foundation temperature + 'daily 2d fields': + defaults: # these can be overridden for individual fields below + file_name_dimension: 2d # descriptor for filename, e.g. 3d, 2d, scalar + output_freq: 1 # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run) + output_freq_units: days # time units for output: years, months, days, hours, minutes, or seconds + fields: + eta_t: + frazil_3d_int_z: + mld: + pme_river: + sfc_hflux_coupler: + sfc_hflux_from_runoff: + sfc_hflux_pme: + surface_salt: + surface_temp: + u_surf: + v_surf: + 'monthly scalar timeseries': + defaults: # these can be overridden for individual fields below + file_name_dimension: scalar # descriptor for filename, e.g. 3d, 2d, scalar + file_name: # file name (without trailing ".nc") is constructed from these components, + # separated by file_name_separator, as per https://github.com/COSIMA/access-om2/issues/185 + # All these components (other than field_name) must be names that exist in global_defaults. + - file_name_prefix + - file_name_dimension + - output_freq + - output_freq_units + - file_name_date + output_freq: 1 # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run) + output_freq_units: months # time units for output: years, months, days, hours, minutes, or seconds + packing: 1 # double precision + fields: + eta_global: + ke_tot: + pe_tot: + rhoave: + salt_global_ave: + salt_surface_ave: + temp_global_ave: + temp_surface_ave: + # total_net_sfc_heating: # disabled - incorrect - see https://github.com/COSIMA/access-om2/issues/139 + total_ocean_calving_heat: + total_ocean_calving_melt_heat: + total_ocean_calving: + total_ocean_evap_heat: + total_ocean_evap: + total_ocean_fprec_melt_heat: + total_ocean_fprec: + total_ocean_heat: + total_ocean_hflux_coupler: + total_ocean_hflux_evap: + total_ocean_hflux_prec: + total_ocean_lprec: + total_ocean_lw_heat: + total_ocean_melt: + total_ocean_pme_river: + total_ocean_river_heat: + total_ocean_river: + total_ocean_runoff_heat: + total_ocean_runoff: + total_ocean_salt: + total_ocean_sens_heat: + total_ocean_sfc_salt_flux_coupler: + total_ocean_swflx_vis: + total_ocean_swflx: + 'monthly 2d snapshots': + defaults: # these can be overridden for individual fields below + file_name_dimension: 2d # descriptor for filename, e.g. 3d, 2d, scalar + output_freq: 1 # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run) + output_freq_units: months # time units for output: years, months, days, hours, minutes, or seconds + reduction_method: snap # mean, snap, rms, pow##, min, max, or diurnal## + fields: + # eta_t: + 'monthly 3d snapshots': + defaults: # these can be overridden for individual fields below + file_name_dimension: 3d # descriptor for filename, e.g. 3d, 2d, scalar + output_freq: 1 # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run) + output_freq_units: months # time units for output: years, months, days, hours, minutes, or seconds + reduction_method: snap # mean, snap, rms, pow##, min, max, or diurnal## + fields: + # u: + # v: diff --git a/ocean/make_diag_table.py b/ocean/make_diag_table.py new file mode 100755 index 00000000..2eff913e --- /dev/null +++ b/ocean/make_diag_table.py @@ -0,0 +1,143 @@ +#!/usr/bin/env python +""" + +Generate MOM5 diag_table file from diag_table_source.yaml +Latest version: https://github.com/COSIMA/make_diag_table + +The MOM diag_table format is defined here: +https://github.com/mom-ocean/MOM5/blob/master/src/shared/diag_manager/diag_table.F90 +and some of the available diagnostics are listed here: +https://raw.githubusercontent.com/COSIMA/access-om2/master/MOM_diags.txt +https://github.com/COSIMA/access-om2/wiki/Technical-documentation#MOM5-diagnostics-list + +""" + +from __future__ import print_function +import sys + +try: + assert sys.version_info >= (3, 5) # need python >= 3.5 for combining defaults +except AssertionError: + print('\nFatal error: Python version must be >=3.5') + print('On NCI, do the following and try again:') + print(' module use /g/data/hh5/public/modules; module load conda/analysis3\n') + raise + +try: + import yaml +except ModuleNotFoundError: + print('\nFatal error: pyyaml package not found.') + print('On NCI, do the following and try again:') + print(' module use /g/data/hh5/public/modules; module load conda/analysis3\n') + raise + + +def set_filename(indict): + """ + Create standardised filename as defined in 'file_name' entry. + """ + fn = indict['file_name'] + if isinstance(fn, list): + fnd = indict['file_name_date_section'] + if isinstance(fnd, list): + fnd = [str(indict[k]) for k in fnd] + fnd = [indict['file_name_substitutions'].get(v, v) for v in fnd] + if indict['file_name_omit_empty']: + fnd = [v for v in fnd if v != ''] + if fnd[-1][0] == '%': + # omit _ since date specification already supplies leading _ + indict['file_name_date_section'] = '_'.join(fnd[0:-1]) + fnd[-1] + else: + indict['file_name_date_section'] = '_'.join(fnd) + fn = [str(indict[k]) for k in fn] +# TODO: make substitutions specific to particular components of indict['file_name']? + fn = [indict['file_name_substitutions'].get(v, v) for v in fn] + if indict['file_name_omit_empty']: + fn = [v for v in fn if v != ''] + return indict['file_name_separator'].join(fn) + else: + return fn + + +def strout(v): + """Return string representation, with double quotes around strings.""" + if isinstance(v, str): + return '"' + v + '"' + else: + return str(v) + + +indata = yaml.load(open('diag_table_source.yaml', 'r'), Loader=yaml.SafeLoader) +outstrings = [] # strings to write to diag_table +filenames = {} # diagnostic output filenames + +# global section +d = indata['global_defaults'] +outstrings.append(d['title']) +outstrings.append(' '.join([str(x) for x in d['base_date']])) +outstrings.append(''' +######################################################################################################### +# # +# DO NOT EDIT! Instead, edit diag_table_source.yaml and run make_diag_table.py to re-generate this file # +# # +#########################################################################################################''') + +# interleaved file and field sections +for k, grp in indata['diag_table'].items(): + # ensure expected entries are present in group + if grp is None: + grp = dict() + grp['defaults'] = grp.get('defaults', dict()) + if grp['defaults'] is None: + grp['defaults'] = dict() + grp['fields'] = grp.get('fields', dict()) + if grp['fields'] is None: + grp['fields'] = dict() + + outstrings.append('\n\n# '+ k) # use group name as a comment + + for field_name, field_dict in grp['fields'].items(): + + if field_dict is None: + field_dict = {} + + # combine field_dict with defaults into one dict f + f = {**indata['global_defaults'], + **grp['defaults'], + **field_dict, + 'field_name': field_name} + + if f['output_name'] is None: + f['output_name'] = f['field_name'] + + fname = set_filename(f) + if fname not in filenames: # to ensure that each filename is specified once only + fnameline = [fname, f['output_freq'], f['output_freq_units'], + f['file_format'], f['time_axis_units'], f['time_axis_name']] + if 'new_file_freq' in f: + if f['new_file_freq'] is not None: + fnameline.extend([f['new_file_freq'], f['new_file_freq_units']]) + if 'start_time' in f: + if f['start_time'] is not None: + fnameline.append(' '.join([str(x) for x in f['start_time']])) + if 'file_duration' in f: + if f['file_duration'] is not None: + fnameline.extend([f['file_duration'], f['file_duration_units']]) + outstrings.append('') + outstrings.append(', '.join([strout(v) for v in fnameline])) + filenames[fname] = None + + if f['reduction_method'] in ['snap', False]: + f['reduction_method'] = 'none' + if f['reduction_method'] in ['mean', True]: + f['reduction_method'] = 'average' + + fieldline = [f['module_name'], f['field_name'], f['output_name'], + fname, f['time_sampling'], f['reduction_method'], + f['regional_section'], f['packing']] + outstrings.append(', '.join([strout(v) for v in fieldline])) + +# output outstrings +with open('diag_table', 'w') as f: + for line in outstrings: + f.write('%s\n' % line) From c93239cf7bacc779c444a79dfb98faab781be95e Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Wed, 27 May 2020 13:18:03 +1000 Subject: [PATCH 053/111] diag_table tweaks - see https://github.com/COSIMA/access-om2/issues/203 --- ocean/diag_table | 132 ++++++++++++++++++----------------- ocean/diag_table_source.yaml | 50 ++++--------- 2 files changed, 83 insertions(+), 99 deletions(-) diff --git a/ocean/diag_table b/ocean/diag_table index b3e66792..40317807 100644 --- a/ocean/diag_table +++ b/ocean/diag_table @@ -56,88 +56,85 @@ ACCESS-OM2 "ocean_model", "kmu", "kmu", "ocean-2d-kmu", "all", "none", "none", 2 -# yearly 3d fields - -"ocean-3d-age_global-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" -"ocean_model", "age_global", "age_global", "ocean-3d-age_global-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 - -"ocean-3d-aiso_bih-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" -"ocean_model", "aiso_bih", "aiso_bih", "ocean-3d-aiso_bih-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 +# monthly 3d fields -"ocean-3d-buoyfreq2_wt-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" -"ocean_model", "buoyfreq2_wt", "buoyfreq2_wt", "ocean-3d-buoyfreq2_wt-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-3d-age_global-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "age_global", "age_global", "ocean-3d-age_global-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-3d-diff_cbt_t-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" -"ocean_model", "diff_cbt_t", "diff_cbt_t", "ocean-3d-diff_cbt_t-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-3d-aiso_bih-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "aiso_bih", "aiso_bih", "ocean-3d-aiso_bih-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-3d-pot_rho_0-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" -"ocean_model", "pot_rho_0", "pot_rho_0", "ocean-3d-pot_rho_0-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-3d-buoyfreq2_wt-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "buoyfreq2_wt", "buoyfreq2_wt", "ocean-3d-buoyfreq2_wt-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-3d-pot_rho_2-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" -"ocean_model", "pot_rho_2", "pot_rho_2", "ocean-3d-pot_rho_2-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-3d-diff_cbt_t-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "diff_cbt_t", "diff_cbt_t", "ocean-3d-diff_cbt_t-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-3d-pot_temp-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" -"ocean_model", "pot_temp", "pot_temp", "ocean-3d-pot_temp-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-3d-dzt-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "dzt", "dzt", "ocean-3d-dzt-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-3d-salt-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" -"ocean_model", "salt", "salt", "ocean-3d-salt-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-3d-pot_rho_0-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "pot_rho_0", "pot_rho_0", "ocean-3d-pot_rho_0-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-3d-temp_xflux_adv-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" -"ocean_model", "temp_xflux_adv", "temp_xflux_adv", "ocean-3d-temp_xflux_adv-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-3d-pot_rho_2-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "pot_rho_2", "pot_rho_2", "ocean-3d-pot_rho_2-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-3d-temp_yflux_adv-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" -"ocean_model", "temp_yflux_adv", "temp_yflux_adv", "ocean-3d-temp_yflux_adv-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-3d-pot_temp-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "pot_temp", "pot_temp", "ocean-3d-pot_temp-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-3d-temp-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" -"ocean_model", "temp", "temp", "ocean-3d-temp-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-3d-salt-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "salt", "salt", "ocean-3d-salt-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-3d-tx_trans_rho-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" -"ocean_model", "tx_trans_rho", "tx_trans_rho", "ocean-3d-tx_trans_rho-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-3d-temp_xflux_adv-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "temp_xflux_adv", "temp_xflux_adv", "ocean-3d-temp_xflux_adv-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-3d-tx_trans-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" -"ocean_model", "tx_trans", "tx_trans", "ocean-3d-tx_trans-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-3d-temp_yflux_adv-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "temp_yflux_adv", "temp_yflux_adv", "ocean-3d-temp_yflux_adv-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-3d-ty_trans_nrho_submeso-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" -"ocean_model", "ty_trans_nrho_submeso", "ty_trans_nrho_submeso", "ocean-3d-ty_trans_nrho_submeso-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-3d-temp-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "temp", "temp", "ocean-3d-temp-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-3d-ty_trans_rho_gm-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" -"ocean_model", "ty_trans_rho_gm", "ty_trans_rho_gm", "ocean-3d-ty_trans_rho_gm-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-3d-tx_trans_rho-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "tx_trans_rho", "tx_trans_rho", "ocean-3d-tx_trans_rho-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-3d-ty_trans_rho-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" -"ocean_model", "ty_trans_rho", "ty_trans_rho", "ocean-3d-ty_trans_rho-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-3d-tx_trans-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "tx_trans", "tx_trans", "ocean-3d-tx_trans-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-3d-ty_trans_submeso-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" -"ocean_model", "ty_trans_submeso", "ty_trans_submeso", "ocean-3d-ty_trans_submeso-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-3d-ty_trans_nrho_submeso-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "ty_trans_nrho_submeso", "ty_trans_nrho_submeso", "ocean-3d-ty_trans_nrho_submeso-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-3d-ty_trans-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" -"ocean_model", "ty_trans", "ty_trans", "ocean-3d-ty_trans-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-3d-ty_trans_rho_gm-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "ty_trans_rho_gm", "ty_trans_rho_gm", "ocean-3d-ty_trans_rho_gm-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-3d-u-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" -"ocean_model", "u", "u", "ocean-3d-u-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-3d-ty_trans_rho-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "ty_trans_rho", "ty_trans_rho", "ocean-3d-ty_trans_rho-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-3d-v-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" -"ocean_model", "v", "v", "ocean-3d-v-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-3d-ty_trans_submeso-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "ty_trans_submeso", "ty_trans_submeso", "ocean-3d-ty_trans_submeso-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-3d-vert_pv-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" -"ocean_model", "vert_pv", "vert_pv", "ocean-3d-vert_pv-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-3d-ty_trans-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "ty_trans", "ty_trans", "ocean-3d-ty_trans-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-3d-wt-1-yearly-mean-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" -"ocean_model", "wt", "wt", "ocean-3d-wt-1-yearly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-3d-u-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "u", "u", "ocean-3d-u-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-3d-v-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "v", "v", "ocean-3d-v-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -# yearly 3d squared fields +"ocean-3d-vert_pv-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "vert_pv", "vert_pv", "ocean-3d-vert_pv-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-3d-u-1-yearly-pow02-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" -"ocean_model", "u", "u", "ocean-3d-u-1-yearly-pow02-ym%4yr%2mo", "all", "pow02", "none", 2 +"ocean-3d-wt-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "wt", "wt", "ocean-3d-wt-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-3d-v-1-yearly-pow02-ym%4yr%2mo", 1, "years", 1, "days", "time", 1, "years" -"ocean_model", "v", "v", "ocean-3d-v-1-yearly-pow02-ym%4yr%2mo", "all", "pow02", "none", 2 +# monthly 3d squared fields -# monthly 3d fields +"ocean-3d-u-1-monthly-pow02-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "u", "u", "ocean-3d-u-1-monthly-pow02-ym%4yr%2mo", "all", "pow02", "none", 2 -"ocean-3d-dzt-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" -"ocean_model", "dzt", "dzt", "ocean-3d-dzt-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-3d-v-1-monthly-pow02-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "v", "v", "ocean-3d-v-1-monthly-pow02-ym%4yr%2mo", "all", "pow02", "none", 2 # monthly 2d fields @@ -154,9 +151,6 @@ ACCESS-OM2 "ocean-2d-bmf_v-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "bmf_v", "bmf_v", "ocean-2d-bmf_v-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-2d-eta_t-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" -"ocean_model", "eta_t", "eta_t", "ocean-2d-eta_t-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 - "ocean-2d-evap_heat-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "evap_heat", "evap_heat", "ocean-2d-evap_heat-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 @@ -274,9 +268,6 @@ ACCESS-OM2 # monthly 2d fields with different reduction methods -"ocean-2d-eta_t-1-monthly-pow02-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" -"ocean_model", "eta_t", "eta_t", "ocean-2d-eta_t-1-monthly-pow02-ym%4yr%2mo", "all", "pow02", "none", 2 - "ocean-2d-mld-1-monthly-max-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "mld", "mld", "ocean-2d-mld-1-monthly-max-ym%4yr%2mo", "all", "max", "none", 2 @@ -286,8 +277,11 @@ ACCESS-OM2 # daily 2d fields -"ocean-2d-eta_t-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" -"ocean_model", "eta_t", "eta_t", "ocean-2d-eta_t-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-2d-bottom_temp_max-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "bottom_temp_max", "bottom_temp_max", "ocean-2d-bottom_temp_max-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-bottom_temp-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "bottom_temp", "bottom_temp", "ocean-2d-bottom_temp-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 "ocean-2d-frazil_3d_int_z-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" "ocean_model", "frazil_3d_int_z", "frazil_3d_int_z", "ocean-2d-frazil_3d_int_z-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 @@ -298,6 +292,12 @@ ACCESS-OM2 "ocean-2d-pme_river-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" "ocean_model", "pme_river", "pme_river", "ocean-2d-pme_river-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-2d-sea_level_max-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "sea_level_max", "sea_level_max", "ocean-2d-sea_level_max-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 + +"ocean-2d-sea_level-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "sea_level", "sea_level", "ocean-2d-sea_level-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 + "ocean-2d-sfc_hflux_coupler-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" "ocean_model", "sfc_hflux_coupler", "sfc_hflux_coupler", "ocean-2d-sfc_hflux_coupler-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 @@ -310,6 +310,9 @@ ACCESS-OM2 "ocean-2d-surface_salt-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" "ocean_model", "surface_salt", "surface_salt", "ocean-2d-surface_salt-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-2d-surface_temp_max-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "surface_temp_max", "surface_temp_max", "ocean-2d-surface_temp_max-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 + "ocean-2d-surface_temp-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" "ocean_model", "surface_temp", "surface_temp", "ocean-2d-surface_temp-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 @@ -319,6 +322,9 @@ ACCESS-OM2 "ocean-2d-v_surf-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" "ocean_model", "v_surf", "v_surf", "ocean-2d-v_surf-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-2d-vorticity_z_surf-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "vorticity_z_surf", "vorticity_z_surf", "ocean-2d-vorticity_z_surf-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 + # monthly scalar timeseries diff --git a/ocean/diag_table_source.yaml b/ocean/diag_table_source.yaml index 63e2922c..6e4694fa 100755 --- a/ocean/diag_table_source.yaml +++ b/ocean/diag_table_source.yaml @@ -133,16 +133,17 @@ diag_table: hu: kmt: kmu: - 'yearly 3d fields': + 'monthly 3d fields': defaults: # these can be overridden for individual fields below file_name_dimension: 3d # descriptor for filename, e.g. 3d, 2d, scalar output_freq: 1 # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run) - output_freq_units: years # time units for output: years, months, days, hours, minutes, or seconds + output_freq_units: months # time units for output: years, months, days, hours, minutes, or seconds fields: age_global: aiso_bih: buoyfreq2_wt: diff_cbt_t: + dzt: pot_rho_0: pot_rho_2: pot_temp: @@ -161,43 +162,15 @@ diag_table: v: vert_pv: wt: - 'yearly 3d squared fields': # for calculating EKE etc + 'monthly 3d squared fields': # for calculating EKE etc defaults: # these can be overridden for individual fields below file_name_dimension: 3d # descriptor for filename, e.g. 3d, 2d, scalar output_freq: 1 # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run) - output_freq_units: years # time units for output: years, months, days, hours, minutes, or seconds + output_freq_units: months # time units for output: years, months, days, hours, minutes, or seconds reduction_method: pow02 # mean, snap, rms, pow##, min, max, or diurnal## fields: u: v: - 'monthly 3d fields': - defaults: # these can be overridden for individual fields below - file_name_dimension: 3d # descriptor for filename, e.g. 3d, 2d, scalar - output_freq: 1 # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run) - output_freq_units: months # time units for output: years, months, days, hours, minutes, or seconds - fields: - dzt: - # neutral_diffusion_temp: - # neutral_gm_temp: - # neutral_temp: - # pot_temp: - # salt: - # temp_advection: - # temp_eta_smooth: - # temp_nonlocal_KPP: - # temp_rivermix: - # temp_sigma_diff: - # temp_submeso: - # temp_tendency_expl: - # temp_tendency: - # temp_vdiffuse_diff_cbt_conv: - # temp_vdiffuse_diff_cbt: - # temp_vdiffuse_impl: - # temp_vdiffuse_k33: - # temp_vdiffuse_sbc: - # temp: - # u: - # v: 'monthly 2d fields': defaults: # these can be overridden for individual fields below file_name_dimension: 2d # descriptor for filename, e.g. 3d, 2d, scalar @@ -208,7 +181,6 @@ diag_table: aredi: bmf_u: bmf_v: - eta_t: evap_heat: evap: fprec_melt_heat: @@ -254,7 +226,6 @@ diag_table: output_freq: 1 # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run) output_freq_units: months # time units for output: years, months, days, hours, minutes, or seconds fields: - eta_t: {reduction_method: pow02} # for calculating standard deviation mld: {reduction_method: max} # max avoids spurious small values due to rainfall surface_temp: {reduction_method: min} # min for comparison with foundation temperature 'daily 2d fields': @@ -263,17 +234,22 @@ diag_table: output_freq: 1 # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run) output_freq_units: days # time units for output: years, months, days, hours, minutes, or seconds fields: - eta_t: + bottom_temp_max: + bottom_temp: frazil_3d_int_z: mld: pme_river: + sea_level_max: + sea_level: sfc_hflux_coupler: sfc_hflux_from_runoff: sfc_hflux_pme: surface_salt: + surface_temp_max: surface_temp: u_surf: v_surf: + vorticity_z_surf: 'monthly scalar timeseries': defaults: # these can be overridden for individual fields below file_name_dimension: scalar # descriptor for filename, e.g. 3d, 2d, scalar @@ -329,7 +305,7 @@ diag_table: output_freq_units: months # time units for output: years, months, days, hours, minutes, or seconds reduction_method: snap # mean, snap, rms, pow##, min, max, or diurnal## fields: - # eta_t: + # sea_level: 'monthly 3d snapshots': defaults: # these can be overridden for individual fields below file_name_dimension: 3d # descriptor for filename, e.g. 3d, 2d, scalar @@ -337,5 +313,7 @@ diag_table: output_freq_units: months # time units for output: years, months, days, hours, minutes, or seconds reduction_method: snap # mean, snap, rms, pow##, min, max, or diurnal## fields: + # temp: # u: # v: + # vorticity_z: From 0e26f0bcaae5d86402a4fceb62c51a30ea775751 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Wed, 27 May 2020 15:05:22 +1000 Subject: [PATCH 054/111] increase max_axes to 400 in input.nml --- ocean/input.nml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ocean/input.nml b/ocean/input.nml index cc8ecdeb..a06d7e53 100644 --- a/ocean/input.nml +++ b/ocean/input.nml @@ -21,7 +21,7 @@ &diag_manager_nml debug_diag_manager = .false. issue_oor_warnings = .true. - max_axes = 200 + max_axes = 400 max_files = 200 max_num_axis_sets = 200 / From 26e49070243c9a9298b9d9c15ba3d7a382808779 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Fri, 29 May 2020 11:44:18 +1000 Subject: [PATCH 055/111] more diag_table tweaks --- ocean/diag_table_source.yaml | 25 +++++++++++++++++-------- 1 file changed, 17 insertions(+), 8 deletions(-) diff --git a/ocean/diag_table_source.yaml b/ocean/diag_table_source.yaml index 6e4694fa..b30cfec4 100755 --- a/ocean/diag_table_source.yaml +++ b/ocean/diag_table_source.yaml @@ -140,7 +140,7 @@ diag_table: output_freq_units: months # time units for output: years, months, days, hours, minutes, or seconds fields: age_global: - aiso_bih: + # aiso_bih: buoyfreq2_wt: diff_cbt_t: dzt: @@ -151,16 +151,22 @@ diag_table: temp_xflux_adv: temp_yflux_adv: temp: - tx_trans_rho: - tx_trans: + # tx_trans_gm: + # tx_trans_nrho_submeso: + # tx_trans_rho_gm: + # tx_trans_rho: + # tx_trans_submeso: + # tx_trans: + # ty_trans_gm: ty_trans_nrho_submeso: ty_trans_rho_gm: ty_trans_rho: - ty_trans_submeso: - ty_trans: + # ty_trans_submeso: + # ty_trans: u: v: vert_pv: + # vorticity_z: wt: 'monthly 3d squared fields': # for calculating EKE etc defaults: # these can be overridden for individual fields below @@ -207,15 +213,18 @@ diag_table: sfc_salt_flux_restore: surface_salt: surface_temp: - sw_heat: swflx: tau_x: tau_y: temp_int_rhodz: temp_xflux_adv_int_z: - temp_xflux_submeso_int_z: + # temp_xflux_gm_int_z: + temp_xflux_ndiffuse_int_z: + # temp_xflux_submeso_int_z: temp_yflux_adv_int_z: - temp_yflux_submeso_int_z: + # temp_yflux_gm_int_z: + temp_yflux_ndiffuse_int_z: + # temp_yflux_submeso_int_z: tx_trans_int_z: ty_trans_int_z: wfiform: From c88a53b4b0bc1f62c1bd2aa0ecd140d839ff0425 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Fri, 29 May 2020 12:23:12 +1000 Subject: [PATCH 056/111] yet more diag_table tweaks --- ocean/diag_table_source.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/ocean/diag_table_source.yaml b/ocean/diag_table_source.yaml index b30cfec4..bcc620db 100755 --- a/ocean/diag_table_source.yaml +++ b/ocean/diag_table_source.yaml @@ -143,7 +143,7 @@ diag_table: # aiso_bih: buoyfreq2_wt: diff_cbt_t: - dzt: + # dzt: pot_rho_0: pot_rho_2: pot_temp: @@ -157,12 +157,12 @@ diag_table: # tx_trans_rho: # tx_trans_submeso: # tx_trans: - # ty_trans_gm: + ty_trans_gm: ty_trans_nrho_submeso: ty_trans_rho_gm: ty_trans_rho: - # ty_trans_submeso: - # ty_trans: + ty_trans_submeso: + ty_trans: u: v: vert_pv: From 537b157b4dd2f805aa353a9fadc7051291175453 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Fri, 29 May 2020 15:35:44 +1000 Subject: [PATCH 057/111] even more diag_table tweaks --- ocean/diag_table_source.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ocean/diag_table_source.yaml b/ocean/diag_table_source.yaml index bcc620db..5617acde 100755 --- a/ocean/diag_table_source.yaml +++ b/ocean/diag_table_source.yaml @@ -143,7 +143,7 @@ diag_table: # aiso_bih: buoyfreq2_wt: diff_cbt_t: - # dzt: + dzt: # potentially calculable from other fields - https://github.com/COSIMA/access-om2/issues/203#issuecomment-635752170 pot_rho_0: pot_rho_2: pot_temp: From c02424bfc15789af6eabf3cac4059d8eb186c409 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Fri, 29 May 2020 21:55:53 +1000 Subject: [PATCH 058/111] another diag_table update - see https://github.com/COSIMA/access-om2/issues/203 --- ocean/diag_table | 21 ++++++--------------- 1 file changed, 6 insertions(+), 15 deletions(-) diff --git a/ocean/diag_table b/ocean/diag_table index 40317807..e16ac6f7 100644 --- a/ocean/diag_table +++ b/ocean/diag_table @@ -61,9 +61,6 @@ ACCESS-OM2 "ocean-3d-age_global-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "age_global", "age_global", "ocean-3d-age_global-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-3d-aiso_bih-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" -"ocean_model", "aiso_bih", "aiso_bih", "ocean-3d-aiso_bih-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 - "ocean-3d-buoyfreq2_wt-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "buoyfreq2_wt", "buoyfreq2_wt", "ocean-3d-buoyfreq2_wt-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 @@ -94,11 +91,8 @@ ACCESS-OM2 "ocean-3d-temp-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "temp", "temp", "ocean-3d-temp-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-3d-tx_trans_rho-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" -"ocean_model", "tx_trans_rho", "tx_trans_rho", "ocean-3d-tx_trans_rho-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 - -"ocean-3d-tx_trans-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" -"ocean_model", "tx_trans", "tx_trans", "ocean-3d-tx_trans-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-3d-ty_trans_gm-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "ty_trans_gm", "ty_trans_gm", "ocean-3d-ty_trans_gm-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 "ocean-3d-ty_trans_nrho_submeso-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "ty_trans_nrho_submeso", "ty_trans_nrho_submeso", "ocean-3d-ty_trans_nrho_submeso-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 @@ -226,9 +220,6 @@ ACCESS-OM2 "ocean-2d-surface_temp-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "surface_temp", "surface_temp", "ocean-2d-surface_temp-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-2d-sw_heat-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" -"ocean_model", "sw_heat", "sw_heat", "ocean-2d-sw_heat-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 - "ocean-2d-swflx-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "swflx", "swflx", "ocean-2d-swflx-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 @@ -244,14 +235,14 @@ ACCESS-OM2 "ocean-2d-temp_xflux_adv_int_z-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "temp_xflux_adv_int_z", "temp_xflux_adv_int_z", "ocean-2d-temp_xflux_adv_int_z-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-2d-temp_xflux_submeso_int_z-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" -"ocean_model", "temp_xflux_submeso_int_z", "temp_xflux_submeso_int_z", "ocean-2d-temp_xflux_submeso_int_z-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-2d-temp_xflux_ndiffuse_int_z-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "temp_xflux_ndiffuse_int_z", "temp_xflux_ndiffuse_int_z", "ocean-2d-temp_xflux_ndiffuse_int_z-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 "ocean-2d-temp_yflux_adv_int_z-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "temp_yflux_adv_int_z", "temp_yflux_adv_int_z", "ocean-2d-temp_yflux_adv_int_z-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-2d-temp_yflux_submeso_int_z-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" -"ocean_model", "temp_yflux_submeso_int_z", "temp_yflux_submeso_int_z", "ocean-2d-temp_yflux_submeso_int_z-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-2d-temp_yflux_ndiffuse_int_z-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "temp_yflux_ndiffuse_int_z", "temp_yflux_ndiffuse_int_z", "ocean-2d-temp_yflux_ndiffuse_int_z-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 "ocean-2d-tx_trans_int_z-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "tx_trans_int_z", "tx_trans_int_z", "ocean-2d-tx_trans_int_z-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 From c0b4811bdaf66680c388aca0c68aba9bec72279e Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Sat, 30 May 2020 11:53:06 +1000 Subject: [PATCH 059/111] add tx_trans to diag_table --- ocean/diag_table | 3 +++ ocean/diag_table_source.yaml | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/ocean/diag_table b/ocean/diag_table index e16ac6f7..5bf83f8a 100644 --- a/ocean/diag_table +++ b/ocean/diag_table @@ -91,6 +91,9 @@ ACCESS-OM2 "ocean-3d-temp-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "temp", "temp", "ocean-3d-temp-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-3d-tx_trans-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "tx_trans", "tx_trans", "ocean-3d-tx_trans-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + "ocean-3d-ty_trans_gm-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "ty_trans_gm", "ty_trans_gm", "ocean-3d-ty_trans_gm-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 diff --git a/ocean/diag_table_source.yaml b/ocean/diag_table_source.yaml index 5617acde..2a29a392 100755 --- a/ocean/diag_table_source.yaml +++ b/ocean/diag_table_source.yaml @@ -156,7 +156,7 @@ diag_table: # tx_trans_rho_gm: # tx_trans_rho: # tx_trans_submeso: - # tx_trans: + tx_trans: ty_trans_gm: ty_trans_nrho_submeso: ty_trans_rho_gm: From a7f61763b6b55849f2bd48b866e7bcd0b464abcc Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Sat, 30 May 2020 20:57:51 +1000 Subject: [PATCH 060/111] use inputs from input_20200530 --- config.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/config.yaml b/config.yaml index 9bc508b2..b9bfc600 100644 --- a/config.yaml +++ b/config.yaml @@ -13,13 +13,13 @@ mem: 500GB # Model configuration name: common model: access-om2 -input: /g/data/ik11/inputs/access-om2/input_rc/common_1deg_jra55 +input: /g/data/ik11/inputs/access-om2/input_20200530/common_1deg_jra55 submodels: - name: atmosphere model: yatm exe: /g/data/ik11/inputs/access-om2/bin/yatm_4198e150.exe input: - - /g/data/ik11/inputs/access-om2/input_rc/yatm_1deg + - /g/data/ik11/inputs/access-om2/input_20200530/yatm_1deg - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/rsds/gr/v20190429/rsds - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/rlds/gr/v20190429/rlds - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/prra/gr/v20190429/prra @@ -36,13 +36,13 @@ submodels: - name: ocean model: mom exe: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM_e837d05d_libaccessom2_4198e150.x - input: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg + input: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg ncpus: 216 - name: ice model: cice5 exe: /g/data/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_597e4561_libaccessom2_4198e150.exe - input: /g/data/ik11/inputs/access-om2/input_rc/cice_1deg + input: /g/data/ik11/inputs/access-om2/input_20200530/cice_1deg ncpus: 24 # Collation From 221dfb4476313b8471462ff690d7ae099a0e2aac Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Sat, 30 May 2020 21:16:10 +1000 Subject: [PATCH 061/111] update input manifests --- manifests/input.yaml | 177 +++++++++++++------------------------------ 1 file changed, 51 insertions(+), 126 deletions(-) diff --git a/manifests/input.yaml b/manifests/input.yaml index d0d0fbc4..9ba0dc63 100644 --- a/manifests/input.yaml +++ b/manifests/input.yaml @@ -2,29 +2,29 @@ format: yamanifest version: 1.0 --- work/INPUT/JRA55_MOM1_conserve2nd.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/common_1deg_jra55/JRA55_MOM1_conserve2nd.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20200530/common_1deg_jra55/JRA55_MOM1_conserve2nd.nc hashes: - binhash: 1e898bb683160f7eb91e9e49a8e39160 + binhash: abe66e4b33cbb75d25c010ea5f96f053 md5: 00be8ec0f1126055b65dc68178ce4eb5 work/INPUT/JRA55_MOM1_patch.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/common_1deg_jra55/JRA55_MOM1_patch.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20200530/common_1deg_jra55/JRA55_MOM1_patch.nc hashes: - binhash: b6f946067a63b8944eb1165e17e58196 + binhash: af316080d1711daa25abadbf0548718c md5: 6c345282e51521828f62b842e58dd734 work/INPUT/rmp_jra55_cice_1st_conserve.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/common_1deg_jra55/rmp_jra55_cice_1st_conserve.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20200530/common_1deg_jra55/rmp_jra55_cice_1st_conserve.nc hashes: - binhash: c581a8a58b807c6dc1c5304c126c80ee + binhash: bee0b815a97dc6eaf8c2417b4579a31f md5: 6404d936d4898e5ed31e62b585d630cf work/INPUT/rmp_jra55_cice_2nd_conserve.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/common_1deg_jra55/rmp_jra55_cice_2nd_conserve.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20200530/common_1deg_jra55/rmp_jra55_cice_2nd_conserve.nc hashes: - binhash: b1eae275f3f4f89fd5b6537758563d0b + binhash: 57da74118e8eb06d0c26255fd0b8e6db md5: 79885c8149d65a55d093244935f62360 work/INPUT/rmp_jra55_cice_patch.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/common_1deg_jra55/rmp_jra55_cice_patch.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20200530/common_1deg_jra55/rmp_jra55_cice_patch.nc hashes: - binhash: 1af1de55ea267ced7c966e2991bee5e8 + binhash: f317a81f25961ba37f27b873b364a8d6 md5: aa91ea2e3cdef04f58ed5db8f8d7de6d work/atmosphere/INPUT/friver_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_19580101-19581231.nc: fullpath: /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/land/day/friver/gr/v20190429/friver/friver_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_19580101-19581231.nc @@ -956,16 +956,6 @@ work/atmosphere/INPUT/licalvf_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4- hashes: binhash: 42373f33e0bfacba3e3584538c14d77f md5: 7d09d06ec59b71f0dffe288f7507b06d -work/atmosphere/INPUT/ncar_precip.0001.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/yatm_1deg/ncar_precip.0001.nc - hashes: - binhash: e328c61ff137bcaa07c97a940379519e - md5: 502be1947e13269dedff21d34e34a543 -work/atmosphere/INPUT/ncar_rad.0001.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/yatm_1deg/ncar_rad.0001.nc - hashes: - binhash: ac51aa16461c18af3e0e31d76d988cc1 - md5: 4d3d3e3d26f9d558411847d4f34579c8 work/atmosphere/INPUT/prra_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010130-195812312230.nc: fullpath: /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/prra/gr/v20190429/prra/prra_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010130-195812312230.nc hashes: @@ -1896,11 +1886,6 @@ work/atmosphere/INPUT/psl_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr hashes: binhash: 7ca04d02a8e25a0bce26412aef7189b3 md5: 9433ee01eeb6b9f1dad59a67cfc63b0f -work/atmosphere/INPUT/q_10.0001.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/yatm_1deg/q_10.0001.nc - hashes: - binhash: fc99955a2d7230c4caa6d412c812344d - md5: d9f27d865c8e86a5f5bc2576b3805c52 work/atmosphere/INPUT/rlds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010130-195812312230.nc: fullpath: /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/rlds/gr/v20190429/rlds/rlds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010130-195812312230.nc hashes: @@ -2211,25 +2196,10 @@ work/atmosphere/INPUT/rlds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_g hashes: binhash: 9e80b14cd2ca6208bed4ba7c3f616581 md5: 3d08213bdacd00ba2cfde806cf6d6b6f -work/atmosphere/INPUT/rmp_corr_to_cict_CONSERV.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/yatm_1deg/rmp_corr_to_cict_CONSERV.nc - hashes: - binhash: dada4e4ac4029c9c6551fe42fbfefb39 - md5: f080a1a3bc639639bcc183d5759bce12 -work/atmosphere/INPUT/rmp_daitren_runoff_MOM1_conserve2nd.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/yatm_1deg/rmp_daitren_runoff_MOM1_conserve2nd.nc - hashes: - binhash: b35d62bd81d3692945d86969a3959b40 - md5: fd63d086dbede3c6e9795c750a3263e2 -work/atmosphere/INPUT/rmp_jra55_runoff_cice_conserve.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/yatm_1deg/rmp_jra55_runoff_cice_conserve.nc - hashes: - binhash: 9a61f517188c9fbb874f595b388fa95d - md5: 4ea275ecdee40694db28c7bfb5d275f0 work/atmosphere/INPUT/rmp_jrar_to_cict_CONSERV.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/yatm_1deg/rmp_jrar_to_cict_CONSERV.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20200530/yatm_1deg/rmp_jrar_to_cict_CONSERV.nc hashes: - binhash: 41783dfa9a46d7c1e7a7f3387c6e476e + binhash: d7b11ae77fba63aecab0892891135a1f md5: 10f0b5ea6b8102a03ad1140e5163a0f7 work/atmosphere/INPUT/rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010130-195812312230.nc: fullpath: /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/rsds/gr/v20190429/rsds/rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010130-195812312230.nc @@ -2541,21 +2511,6 @@ work/atmosphere/INPUT/rsds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_g hashes: binhash: 5b861eb4a80c6f1ebdd5d094fcdd4c56 md5: ff51b282d75d57fa40bd321e3e715684 -work/atmosphere/INPUT/runoff.daitren.clim.10FEB2011.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/yatm_1deg/runoff.daitren.clim.10FEB2011.nc - hashes: - binhash: 23e524c55cd8cc9bb75ad5f04275eb30 - md5: 2471c5665be8b49f004dada041341817 -work/atmosphere/INPUT/slp.0001.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/yatm_1deg/slp.0001.nc - hashes: - binhash: 2c8ae97b4f9a97dd272a719e11e7d7bc - md5: 743b0941d76feef69d1f12acce8050e7 -work/atmosphere/INPUT/t_10.0001.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/yatm_1deg/t_10.0001.nc - hashes: - binhash: c8030e99600e30fd11214f4e66ae861e - md5: cc8a4863da3f6cfb209a607caaf0f085 work/atmosphere/INPUT/tas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010000-195812312100.nc: fullpath: /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hrPt/tas/gr/v20190429/tas/tas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010000-195812312100.nc hashes: @@ -2866,11 +2821,6 @@ work/atmosphere/INPUT/tas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr hashes: binhash: f299c3152adb7fbeb992816e0f694d0f md5: 837cc3100dccb5252d76eeb62d189cda -work/atmosphere/INPUT/u_10.0001.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/yatm_1deg/u_10.0001.nc - hashes: - binhash: 8dbce9286bcfe18309add08e383aa3f9 - md5: e4073e81a24d10352157284d438e4c83 work/atmosphere/INPUT/uas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010000-195812312100.nc: fullpath: /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hrPt/uas/gr/v20190429/uas/uas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010000-195812312100.nc hashes: @@ -3181,11 +3131,6 @@ work/atmosphere/INPUT/uas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr hashes: binhash: 7b1ba750ed9ea2f847c4c8a7c9382d6c md5: f1cdb45f72e9f95dff0c244f005a9c4c -work/atmosphere/INPUT/v_10.0001.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/yatm_1deg/v_10.0001.nc - hashes: - binhash: b953ce69b0101e61e820552a30337234 - md5: 96914ca8a353bdc40ea0d3cba4350f16 work/atmosphere/INPUT/vas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010000-195812312100.nc: fullpath: /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hrPt/vas/gr/v20190429/vas/vas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr_195801010000-195812312100.nc hashes: @@ -3498,127 +3443,107 @@ work/atmosphere/INPUT/vas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr md5: b0e514bfac0d9dfbf538d36b8ecd17f9 work/ice/RESTART/grid.nc: copy: true - fullpath: /g/data/ik11/inputs/access-om2/input_rc/cice_1deg/grid.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20200530/cice_1deg/grid.nc hashes: - binhash: 6b6c08bc458eed00641f8d5cd5b7ccac + binhash: e7108317ae28b1f9ae77711728925cb6 md5: 1213e346055ee073fe33dc12578d99c6 work/ice/RESTART/i2o.nc: copy: true - fullpath: /g/data/ik11/inputs/access-om2/input_rc/cice_1deg/i2o.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20200530/cice_1deg/i2o.nc hashes: binhash: 527d494c80b2a3418645b962fd8706d0 md5: c96e06c3c80c0f680545db59ed3349e5 work/ice/RESTART/kmt.nc: copy: true - fullpath: /g/data/ik11/inputs/access-om2/input_rc/cice_1deg/kmt.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20200530/cice_1deg/kmt.nc hashes: - binhash: f04a0c2a4f27bdb8ef32da0ab8ec8a61 + binhash: 51eda44859a964d0fd5a0210c02a9999 md5: a5a7b4be90ec06044588b623d555c4ad work/ice/RESTART/monthly_sstsss.nc: copy: true - fullpath: /g/data/ik11/inputs/access-om2/input_rc/cice_1deg/monthly_sstsss.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20200530/cice_1deg/monthly_sstsss.nc hashes: - binhash: c73864b41a23b7c9a7e888d6565cc577 + binhash: 66f44d84fada351d4ebf05f196762d8c md5: 323d4c605f83f4d7d3126da70153c2ed work/ice/RESTART/o2i.nc: copy: true - fullpath: /g/data/ik11/inputs/access-om2/input_rc/cice_1deg/o2i.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20200530/cice_1deg/o2i.nc hashes: - binhash: 304e0d0a02d5d6a95a7ffbb8f8e6871a + binhash: 56f258e931a8eda2fc42b3a315d485eb md5: 3498246dcd7da40d3b8c6b4a908b260f work/ice/RESTART/u_star.nc: copy: true - fullpath: /g/data/ik11/inputs/access-om2/input_rc/cice_1deg/u_star.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20200530/cice_1deg/u_star.nc hashes: - binhash: fb1becadd07fa9cbbc88a7f47e96d9b4 + binhash: f93a19930c5c59e03751e70a123ab01f md5: 68cf0ef92576f96ef085cd7f243d0c39 -work/ocean/INPUT/basin_mask.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/basin_mask.nc - hashes: - binhash: 0432b240a183f391bac96cd5bdbadafa - md5: 20fd8740f24ca95c7c086343077e9c0d work/ocean/INPUT/chl.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/chl.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/chl.nc hashes: - binhash: 0ddec40146ae7f0fbc1a06da8ad94b9d + binhash: 05b3313121bbb9825a20f0fb58901b21 md5: a7aa5bcf4a3b9fa8102edd3b6b67c3a2 -work/ocean/INPUT/geothermal_heating.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/geothermal_heating.nc - hashes: - binhash: 4214c902e835d82643f84cbec1a5a65e - md5: 381cb231d8d059576adca0c2bea9c030 work/ocean/INPUT/grid_spec.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/grid_spec.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/grid_spec.nc hashes: - binhash: f3f3d1eb44108483348881f9e862e2ff + binhash: 587ca8eb0cbc978232fe55a7bff054c9 md5: 027d2f8fb1eda3ef1cf0a3f520a217f7 work/ocean/INPUT/mask_table.24.16x15: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/mask_table.24.16x15 + fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/mask_table.24.16x15 hashes: - binhash: 397aac7f65a9508f19de85de61646909 + binhash: 77b929b930cd4fca59f185b3222dde49 md5: 2203b38758fb2b56a145ef16b7872af9 work/ocean/INPUT/ocean_hgrid.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/ocean_hgrid.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/ocean_hgrid.nc hashes: - binhash: bef3659bf2505b3d1e3167579718fabb + binhash: 87d66edc0ef57c97b758a3049bfe8a14 md5: 51f58be0f4ea6da2cb438a893f95c689 work/ocean/INPUT/ocean_mask.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/ocean_mask.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/ocean_mask.nc hashes: - binhash: 4cd2ab42c4890a101295bdb151d59abb + binhash: 85321c4533642d2602df6b0086eca477 md5: 1d9dfb140919f355037f72bc89f15db0 work/ocean/INPUT/ocean_mask_table: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/ocean_mask_table + fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/ocean_mask_table hashes: - binhash: 9e95917d763f90bc14e7b470074931f5 + binhash: dc68931f1bb40bcd75a98d209b47d4c4 md5: 2203b38758fb2b56a145ef16b7872af9 work/ocean/INPUT/ocean_mosaic.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/ocean_mosaic.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/ocean_mosaic.nc hashes: - binhash: 150ae65ecbe60d7d2357a76909635839 + binhash: 6aadd388078defe3f80df6f3de77b4bd md5: cb42e630ee31d3686156fcbdc2f9d07c work/ocean/INPUT/ocean_temp_salt.res.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/ocean_temp_salt.res.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/ocean_temp_salt.res.nc hashes: - binhash: b836632dc8139d895992fe8b67954681 + binhash: c56262c68ab55b0998e32bec98dec07d md5: c9814c04b393cf73fe3d16daf5d421af work/ocean/INPUT/ocean_vgrid.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/ocean_vgrid.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/ocean_vgrid.nc hashes: - binhash: af2ce0ec0bfcac448a5b1558dc42254a + binhash: 115586f18cc20a6ca309194b4d59665b md5: 6eebf039362b6572eaad5477740236bf work/ocean/INPUT/roughness_amp.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/roughness_amp.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/roughness_amp.nc hashes: - binhash: 6f092a5efcf2131d21e96ff7d4a5a89b + binhash: 73a425be9e5cf7a3d349d75a8ebeadd1 md5: 185dadeb53da2de75b47c53fd7085f89 work/ocean/INPUT/roughness_cdbot.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/roughness_cdbot.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/roughness_cdbot.nc hashes: - binhash: 12a32c9840ab654b5c9bc5ec43929c6f + binhash: 4ec236c3874fbd4dc5c2fcdec271f557 md5: b50f0595f3ebc872cbcf5f3223115643 work/ocean/INPUT/salt_sfc_restore.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/salt_sfc_restore.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/salt_sfc_restore.nc hashes: - binhash: bed136991ec6d0fcc103d00bd36fb8e5 + binhash: 13101e8424f559b6c172ef86d85b9a8f md5: b2bd35c44017597ba99b85fb61ed4d72 -work/ocean/INPUT/ssw_atten_depth.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/ssw_atten_depth.nc - hashes: - binhash: 9f3eeeebbd0756bed573cb7a6fb5fba5 - md5: 4aa30be87abb6f0f17484b0dc36ff737 -work/ocean/INPUT/temp_sfc_restore.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/temp_sfc_restore.nc - hashes: - binhash: f7c5a64fe9405e07298f5b991177b53e - md5: 36892b884a6da1db25dcc3016c95c0ca work/ocean/INPUT/tideamp.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/tideamp.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/tideamp.nc hashes: - binhash: ec1984c78b79127c907258cf06607ff1 + binhash: 0226a494f8a03f8fb9845060cb694389 md5: b2840af757d9b7b40207f33f1fc84c5c work/ocean/INPUT/topog.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_rc/mom_1deg/topog.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/topog.nc hashes: - binhash: 022ac4a9232c6f11d977d3337b89d004 + binhash: b03638decf5d3a74da46fb225625f445 md5: f01ddc02cfe21d8db99c2976e9fcc828 From f5d0b89953724abe69c819b8ebb7b5f0396e5083 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Thu, 4 Jun 2020 09:44:31 +1000 Subject: [PATCH 062/111] improve sync_data.sh --- sync_data.sh | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/sync_data.sh b/sync_data.sh index c13d38cb..dcbcb296 100755 --- a/sync_data.sh +++ b/sync_data.sh @@ -3,7 +3,6 @@ #PBS -l ncpus=1 #PBS -l wd #PBS -l walltime=4:00:00,mem=4GB -#PBS -P v45 #PBS -l storage=gdata/hh5+gdata/ik11+scratch/v45 #PBS -N sync @@ -86,10 +85,10 @@ if [ $restarts == true ]; then fi else # default - only sync/remove outputs - rsync --exclude "*.nc.*" --exclude "ocean_daily_3d_*" --exclude "*ocean_*_3hourly*" --exclude "*iceh_03h*" -vrltoD --safe-links output* ${SYNCDIR} + rsync --exclude "*.nc.*" -vrltoD --safe-links output* ${SYNCDIR} if [ $rmlocal == true ]; then # Now do removals. Don't remove final local copy, so we can continue run. - rsync --remove-source-files --exclude `\ls -1d output[0-9][0-9][0-9] | tail -1` --exclude "*.nc.*" --exclude "ocean_daily_3d_*" --exclude "*ocean_*_3hourly*" --exclude "*iceh_03h*" -vrltoD --safe-links output* ${SYNCDIR} + rsync --remove-source-files --exclude `\ls -1d output[0-9][0-9][0-9] | tail -1` --exclude "*.nc.*" -vrltoD --safe-links output* ${SYNCDIR} fi fi From 99f0884c35ae9dd9e223e2e68033ff7b3a25f3a9 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Thu, 4 Jun 2020 21:27:33 +1000 Subject: [PATCH 063/111] more diag_table tweaks --- ocean/diag_table | 11 +++++++++++ ocean/diag_table_source.yaml | 7 +++++-- 2 files changed, 16 insertions(+), 2 deletions(-) diff --git a/ocean/diag_table b/ocean/diag_table index 5bf83f8a..0e35eb58 100644 --- a/ocean/diag_table +++ b/ocean/diag_table @@ -148,6 +148,9 @@ ACCESS-OM2 "ocean-2d-bmf_v-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "bmf_v", "bmf_v", "ocean-2d-bmf_v-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-2d-ekman_we-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "ekman_we", "ekman_we", "ocean-2d-ekman_we-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + "ocean-2d-evap_heat-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "evap_heat", "evap_heat", "ocean-2d-evap_heat-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 @@ -172,9 +175,15 @@ ACCESS-OM2 "ocean-2d-melt-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "melt", "melt", "ocean-2d-melt-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-2d-mh_flux-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "mh_flux", "mh_flux", "ocean-2d-mh_flux-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + "ocean-2d-mld-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "mld", "mld", "ocean-2d-mld-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-2d-net_sfc_heating-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "net_sfc_heating", "net_sfc_heating", "ocean-2d-net_sfc_heating-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + "ocean-2d-pbot_t-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "pbot_t", "pbot_t", "ocean-2d-pbot_t-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 @@ -331,6 +340,7 @@ ACCESS-OM2 "ocean_model", "salt_surface_ave", "salt_surface_ave", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 "ocean_model", "temp_global_ave", "temp_global_ave", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 "ocean_model", "temp_surface_ave", "temp_surface_ave", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "total_net_sfc_heating", "total_net_sfc_heating", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 "ocean_model", "total_ocean_calving_heat", "total_ocean_calving_heat", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 "ocean_model", "total_ocean_calving_melt_heat", "total_ocean_calving_melt_heat", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 "ocean_model", "total_ocean_calving", "total_ocean_calving", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 @@ -345,6 +355,7 @@ ACCESS-OM2 "ocean_model", "total_ocean_lprec", "total_ocean_lprec", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 "ocean_model", "total_ocean_lw_heat", "total_ocean_lw_heat", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 "ocean_model", "total_ocean_melt", "total_ocean_melt", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +"ocean_model", "total_ocean_mh_flux", "total_ocean_mh_flux", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 "ocean_model", "total_ocean_pme_river", "total_ocean_pme_river", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 "ocean_model", "total_ocean_river_heat", "total_ocean_river_heat", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 "ocean_model", "total_ocean_river", "total_ocean_river", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 diff --git a/ocean/diag_table_source.yaml b/ocean/diag_table_source.yaml index 2a29a392..37930fba 100755 --- a/ocean/diag_table_source.yaml +++ b/ocean/diag_table_source.yaml @@ -187,6 +187,7 @@ diag_table: aredi: bmf_u: bmf_v: + ekman_we: evap_heat: evap: fprec_melt_heat: @@ -195,8 +196,9 @@ diag_table: lprec: lw_heat: melt: + mh_flux: mld: - # net_sfc_heating: # disabled - incorrect - see https://github.com/COSIMA/access-om2/issues/139 + net_sfc_heating: pbot_t: pme_net: pme_river: @@ -282,7 +284,7 @@ diag_table: salt_surface_ave: temp_global_ave: temp_surface_ave: - # total_net_sfc_heating: # disabled - incorrect - see https://github.com/COSIMA/access-om2/issues/139 + total_net_sfc_heating: total_ocean_calving_heat: total_ocean_calving_melt_heat: total_ocean_calving: @@ -297,6 +299,7 @@ diag_table: total_ocean_lprec: total_ocean_lw_heat: total_ocean_melt: + total_ocean_mh_flux: total_ocean_pme_river: total_ocean_river_heat: total_ocean_river: From 03c17789b3b38907386e673a66db7a07ca78680f Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Thu, 4 Jun 2020 21:37:07 +1000 Subject: [PATCH 064/111] remove old test data --- ocean/checksums.txt | 0 test/access-om2.out | 3240 ------------------------------------------- 2 files changed, 3240 deletions(-) delete mode 100644 ocean/checksums.txt delete mode 100644 test/access-om2.out diff --git a/ocean/checksums.txt b/ocean/checksums.txt deleted file mode 100644 index e69de29b..00000000 diff --git a/test/access-om2.out b/test/access-om2.out deleted file mode 100644 index 10ebee42..00000000 --- a/test/access-om2.out +++ /dev/null @@ -1,3240 +0,0 @@ -NOTE from PE 0: MPP_DOMAINS_SET_STACK_SIZE: stack size set to 32768. - &MPP_IO_NML - HEADER_BUFFER_VAL = 16384, - GLOBAL_FIELD_ON_ROOT_PE = T, - IO_CLOCKS_ON = F, - SHUFFLE = 1, - DEFLATE_LEVEL = 5 - / -NOTE from PE 0: MPP_IO_SET_STACK_SIZE: stack size set to 131072. -NOTE from PE 0: MPP_DOMAINS_SET_STACK_SIZE: stack size set to 115200. - - - - ======== MODEL BEING DRIVEN BY OCEAN_SOLO_MOD ======== - - &OCEAN_SOLO_NML - N_MASK = 0, - LAYOUT_MASK = 2*0, - MASK_LIST = 4096*0, - RESTART_INTERVAL = 6*0, - DEBUG_THIS_MODULE = F, - ACCESSOM2_CONFIG_DIR = ../ - - - - - - - - / -NOTE from PE 0: diag_manager_mod::diag_manager_init: prepend_date only supported when diag_manager_init is called with time_init present. - Reading setup_nml - Reading grid_nml - Reading tracer_nml - Reading thermo_nml - Reading dynamics_nml - Reading shortwave_nml - Reading ponds_nml - Reading forcing_nml - Diagnostic output will be in file - ice_diag.d - - - - &OCEAN_PARAMETERS_NML - CP_OCEAN = 3992.10322329649 , - CP_LIQUID_RUNOFF = 4218.00000000000 , - CP_SOLID_RUNOFF = 2106.00000000000 , - RHO0 = 1035.00000000000 , - TFREEZE = 273.150000000000 , - OMEGA_EARTH = 7.292100000000000E-005, - GRAV = 9.80000000000000 - / - - ======== STARTING MOM INITIALIZATION ======== - - - ==>NOTE: Using dynamically allocated array option in MOM - - - &OCEAN_MODEL_NML - TIME_TENDENCY = twolevel , - IMPOSE_INIT_FROM_RESTART = F, - REINITIALIZE_THICKNESS = F, - BAROCLINIC_SPLIT = 1, - BAROTROPIC_SPLIT = 80, - SURFACE_HEIGHT_SPLIT = 1, - LAYOUT = 16, 15, - IO_LAYOUT = 4, 3, - DEBUG = F, - VERTICAL_COORDINATE = zstar , - DT_OCEAN = -1, - CMIP_UNITS = T, - HORIZONTAL_GRID = bgrid , - USE_BLOBS = F, - USE_VELOCITY_OVERRIDE = F, - MASK_TABLE = INPUT/ocean_mask_table , - INTRODUCE_BLOBS = F, - BETA_TXTY = 0.000000000000000E+000, - BETA_TF = 0.000000000000000E+000, - BETA_QF = 0.000000000000000E+000, - BETA_LWSW = 0.000000000000000E+000 - / - - ==>Note: Running MOM using 216 computer processors. - - - ==>Note: Running MOM with staggered twotime level scheme to compute time tenden - cies. - This is the default. Mass/volume and tracer are conserved with this sc - heme. - - - ==>Note: Time%Time_init = time stamp at very start of the MOM experiment is given by -yyyy/mm/dd hh:mm:ss = 1958/ 1/ 1 0: 0: 0 - - ==>Note: Time%model_time = time stamp at start of this leg of the MOM experiment is -yyyy/mm/dd hh:mm:ss = 1958/ 1/ 1 0: 0: 0 - - ==>Note: Time%init=.true. =>MOM will start from user specified initial conditions. - - ==> Note: time steps (seconds) used for MOM - dtts (tracer) = 5400.00 - dtuv (baroclinic) = 5400.00 - dteta (surface height or bottom pressure) = 5400.00 - dtbt (barotropic) = 67.50 - - ==> Note: The velocity equations will be split into baroclinic and barotropic pieces. - - - ==> Note: Using MOM with B-grid horizontal layout of variables on a grid. - - ==> Note: Using MOM with zstar vertical coordinate. - - The equations are Boussinesq, and so conserve volume rather than mass. - Use one of the pressure-like coordinates to get non-Boussinesq effects. - - - - &OCEAN_GRIDS_NML - DEBUG_THIS_MODULE = F, - VERBOSE_INIT = T, - READ_RHO0_PROFILE = F, - DO_BITWISE_EXACT_SUM = F, - WRITE_GRID = F - / - ==>Note from ocean_grids_mod(set_ocean_grid_size): read grid from mosaic versio - n grid - Reading zbgc_nml -NOTE from PE 0: ==>Note from ocean_grids_mod(set_ocean_grid_size): x_boundary_type is cyclic -NOTE from PE 0: ==>Note from ocean_grids_mod(set_ocean_grid_size): y_boundary_type is fold_north_edge - - ==> Note: Energy conversion errors are nontrivial when using tripolar=.true. - The cause is related to the need to update redundantly computed information - across the Arctic bipolar fold in a bit-wise exact manner for terms contributing - to the energy conversion analysis. The extra code and mpp calls have not been - implemented. - - - &OCEAN_DOMAINS_NML - HALO = 1, - MAX_TRACERS = 5, - X_CYCLIC_OFFSET = 0, - Y_CYCLIC_OFFSET = 0 - / -==> NOTE from ocean_model_init: reading maskmap information from INPUT/ocean_mask_table - parse_mask_table: Number of domain regions masked in ocean model = 24 - mom_domain domain decomposition -whalo = 1, ehalo = 1, shalo = 1, nhalo = 1 - X-AXIS = 23 23 23 23 22 22 22 22 22 22 22 22 23 23 23 23 - Y-AXIS = 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 -NOTE from PE 0: MPP_DOMAINS_SET_STACK_SIZE: stack size set to 275000. - ocean_super_grid domain decomposition -whalo = 2, ehalo = 2, shalo = 2, nhalo = 2 - X-AXIS = 46 46 46 46 44 44 44 44 44 44 44 44 46 46 46 46 - Y-AXIS = 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 -NOTE from PE 0: ==>Note from ocean_grids_mod (set_ocean_hgrid_arrays): altering U-grid arrays at j=0 -[chksum] xt 5227222155343350591 -[chksum] xu 5223776204015802370 -[chksum] yt 3524025294143080071 -[chksum] yu 3533356873625590408 -[chksum] dxt -3859942835758725761 -[chksum] dxu -3858814366858890342 -[chksum] dyt -4245365089591661262 -[chksum] dyu -4232496668783427450 -[chksum] dat -7061889515055535283 -[chksum] dau -7044880903546758732 -[chksum] dxtn -3858725764265149739 -[chksum] dytn -4245884269268605071 -[chksum] dxte -3860029997118692252 -[chksum] dyte -4231975470790906385 -[chksum] dxun -3857620260571262423 -[chksum] dyun -4230552185666092470 -[chksum] dxue -3858896327844488328 -[chksum] dyue -4224360586904360567 -[chksum] dtn+dts -4245365089591661262 -[chksum] dun+dus -4232496668783427450 -[chksum] dte+dtw -3859942835758725761 -[chksum] due+duw -3858814366858890342 -[chksum] dte -4832765571991274682 -[chksum] dtw -4832675138550231117 -[chksum] due -4831634525894608354 -[chksum] duw -4831549246847226606 -[chksum] sin_rot -5025817628090435318 -[chksum] cos_rot -1010217553039298448 - - - &OCEAN_TOPOG_NML - FLAT_BOTTOM = F, - FLAT_BOTTOM_KMT = 50, - FLAT_BOTTOM_HT = 5500.00000000000 , - WRITE_TOPOG = F, - MIN_THICKNESS = 1.00000000000000 , - KMT_RECOMPUTE = F, - KMT_RECOMPUTE_OFFSET = 0, - DEBUG_THIS_MODULE = T - / -NOTE from PE 0: GLOBAL ATT too long - not reading this metadata - Topography checksums -[chksum] ht -2435776769067813075 - - The shallowest wet ocean model grid cell has depth (meters) 45.11149 - and this occurs at (i,j,k) = ( 40,288, 5) - which has (long,lat,depth) = ( -260.7610, 76.8858, 45.11149) - - Beware that shallow regions (e.g., those shallower than 50m) may be subject - to numerical problems if strong surface forcing is not mixed vertically. - Such problems may occur especially in shallow regions with kmt==2. - Current speeds and/or tracer deviations may become large due to the deposition - of wind and/or buoyancy over just a small upper ocean region. Such problems - can be resolved by adding sufficient vertical mixing in these regions. - Such happens in Nature due to tides and breaking surface waves. -[chksum] hu 6340078932675900470 -[chksum] htr 972271619753254155 -[chksum] kmu 5346 -[chksum] kmt 5749 - - - - &OCEAN_OBC_NML - NOBC = 0, - DIRECTION = , - NAME = test_obc none none none , - IS = 4*-999, - IE = 4*-999, - JS = 4*-999, - JE = 4*-999, - IERS = 4*-999, - IERE = 4*-999, - JERS = 4*-999, - JERE = 4*-999, - ITRS = 4*-999, - ITRE = 4*-999, - JTRS = 4*-999, - JTRE = 4*-999, - OBC_NOR = NOGRAD NOGRAD NOGRAD NOGRAD , - OBC_TAN = NOGRAD NOGRAD NOGRAD NOGRAD , - OBC_ETA = NOTHIN NOTHIN NOTHIN NOTHIN , - OBC_UD = NOGRAD NOGRAD NOGRAD NOGRAD , - OBC_TRA = NOGRAD NOGRAD NOGRAD NOGRAD NOGRAD - NOGRAD NOGRAD NOGRAD NOGRAD NOGRAD - NOGRAD NOGRAD NOGRAD NOGRAD NOGRAD NO - GRAD NOGRAD NOGRAD NOGRAD NOGRAD NOGRAD - NOGRAD NOGRAD NOGRAD NOGRAD NOGRAD - NOGRAD NOGRAD NOGRAD NOGRAD NOGRAD - NOGRAD NOGRAD NOGRAD NOGRAD NOGRAD - NOGRAD NOGRAD NOGRAD NOGRAD , - OBC_MIX = NOGRAD NOGRAD NOGRAD NOGRAD , - REL_COEF_ETA_IN = 4*0.000000000000000E+000 , - REL_COEF_ETA_OUT = 4*0.000000000000000E+000 , - REL_ETA_PNTS = 4*1, - REL_CLIN_PNTS = 40*1, - CTROP_MAX = 4*1.50000000000000 , - CTROP_MIN = 4*0.100000000000000 , - CTROP_INC = 4*0.000000000000000E+000 , - CTROP_SMOOTH = 4*0.700000000000000 , - FILENAME_ETA = obc_eta_t.nc none none - none , - FIELDNAME_ETA = eta_t none none none , - FILENAME_UD = obc_ud.nc none none - none , - FIELDNAME_UD = ud none none none , - OBC_CONSIDER_CONVU = 4*F, - OBC_ADJUST_FORCING_BT = 4*F, - OBC_VERT_ADVEL_T = 4*F, - OBC_VERT_ADVEL_U = 4*F, - OBC_ENHANCE_VISC_BACK = NONE NONE NONE NONE , - OBC_ENHANCE_DIFF_BACK = NONE NONE NONE NONE , - ENH_PNTS = 4*1, - ENH_FAC_V = 4*0.900000000000000 , - ENH_FAC_D = 4*1.00000000000000 , - OBC_RELAX_TRACER = 40*F, - OBC_FLOW_RELAX = 40*1, - OBC_CONSIDER_SOURCES = 40*F, - OBC_TRACER_NO_INFLOW = 40*F, - REL_COEF_TRACER_IN = 40*0.000000000000000E+000 , - REL_COEF_TRACER_OUT = 40*0.000000000000000E+000 , - FILENAME_TRACER = INPUT/obc_tr.nc INPUT/obc_tr.nc INPUT/obc_tr.nc - INPUT/obc_tr.nc INPUT/obc_tr.nc - INPUT/obc_tr.nc INPUT/obc_tr.nc INPUT/obc_tr.nc - none none - none none none - none none none - none none - none none none - none none - none none none - none none - none none none - none none - none none none - none none - none none , - FIELDNAME_TRACER = temp_obc temp_obc temp_obc temp_obc salt_obc salt_obc salt_obc salt_obc none none none none none none none none none none none none - none none none none none none none none none none none none none none none none none none none none - , - DEBUG_PHASE_SPEED = F, - DEBUG_THIS_MODULE = F, - OBC_DAMP_NEWTON = 4*F, - DAMP_FACTOR = 4*1.00000000000000 - / - - Number of wet ocean tracer points = 2665454 - Number of wet ocean velocity points = 2525142 - Number of computed ocean tracer points = 5400000 - - Wet ocean volume with eta_t=0.0 (T-cells) = 1.29156344258260070E+18 m^3 (not bit reproducible) - Ocean surface area (T-cells) = 3.61576164485804500E+14 m^2 (not bit reproducible) - - Wet ocean volume with eta_u=0.0 (U-cells) = 1.18685670521597875E+18 m^3 (not bit reproducible) - Wet ocean surface area (U-cells) = 3.49063144058595875E+14 m^2 (not bit reproducible) - - Wet ocean + masked-out (land) surface area (T-cells) = 4.73557361748878687E+14 m^2 (not bit reproducible) - Wet ocean + masked-out (land) surface area (U-cells) = 4.72945709666937375E+14 m^2 (not bit reproducible) - - - - &OCEAN_TRACER_UTIL_NML - REBIN_ONTO_RHO_ALL_VALUES = T, - DEBUG_DIAGNOSE_MASS_OF_LAYER = F, - EPSLN_DIAGNOSE_MASS_OF_LAYER = 1.000000000000000E-005 - / - -Note: ocean_tracer_util: rebin_onto_rho will include density values outside bounds range. - - - &OCEAN_CORIOLIS_NML - DEBUG_THIS_MODULE = F, - USE_THIS_MODULE = T, - ACOR = 0.500000000000000 - / -==>Note: Coriolis on Bgrid computed semi-implicitly to remove inertial time step constraint. - - ==> Note: 2*pi timesteps/(min inertial period) implies a maximum dtuv for time-explicit Coriolis = 6856. sec. - - - &OCEAN_VELOCITY_NML - DEBUG_THIS_MODULE = F, - WRITE_A_RESTART = T, - MAX_CGINT = 1.00000000000000 , - ZERO_TENDENCY = F, - ZERO_TENDENCY_EXPLICIT_A = F, - ZERO_TENDENCY_EXPLICIT_B = F, - ZERO_TENDENCY_IMPLICIT = F, - TRUNCATE_VELOCITY = F, - TRUNCATE_VERBOSE = T, - TRUNCATE_VELOCITY_LAT = 0.000000000000000E+000, - TRUNCATE_VELOCITY_VALUE = 2.00000000000000 , - ADAMS_BASHFORTH_THIRD = T, - ADAMS_BASHFORTH_EPSILON = 0.600000000000000 , - USE_CONSTANT_VELOCITY = F, - CONSTANT_U = 0.000000000000000E+000, - CONSTANT_V = 0.000000000000000E+000, - UPDATE_VELOCITY_VIA_UPRIME = T - / - -==>Note from ocean_velocity_mod: use of twolevel time_tendency - necessitates an Adams-Bashforth treatment of velocity advection. - - Using 3rd order Adams-Bashforth for velocity advection. - This is the MOM default. - -NOTE from PE 0: ==>update_velocity_via_uprime=.true., so keep udrho from external mode solver. - - Baroclinic time step stability most nearly violated at U-cell (i,j) = ( 198, 246), (lon,lat) = ( -82.00, 65.14). - The number of kmu-levels at this point is 22 - The dxu grid distance (m) at this point is 0.467431E+05 - The dyu grid distance (m) at this point is 0.159462E+05 - Due to a specified maximum baroclinic gravity wave speed of 1.00 m/s. - "dtuv" must be less than 15092. sec. "dtuv" = 5400. sec. -NOTE from PE 0: ==> From ocean_velocity_mod: Initializing velocity to zero since Time%init=.true. and did not find INPUT/ocean_velocity.res.nc. - - ===Initial velocity checksums ==> -yyyy/mm/dd hh:mm:ss = 1958/ 1/ 1 0: 0: 0 - From ocean_velocity_mod: initial velocity chksum (taup1) -[chksum] Zonal velocity -5863015549186965400 -[chksum] Meridional velocity -5863015549186965400 -[chksum] Advection of u 0 -[chksum] Advection of v 0 - - - &OCEAN_BAROTROPIC_NML - WRITE_A_RESTART = T, - ZERO_TENDENCY = F, - ZERO_ETA_IC = F, - ZERO_ETA_T = F, - ZERO_ETA_U = F, - ZERO_CORIOLIS_BT = F, - ZERO_NONLINEAR_FORCING_BT = F, - ZERO_FORCING_BT = F, - ZERO_ETA_TENDENCY = F, - BAROTROPIC_TIME_STEPPING_A = T, - BAROTROPIC_TIME_STEPPING_B = F, - TIDAL_FORCING_M2 = F, - TIDAL_FORCING_8 = F, - TIDAL_FORCING_IDEAL = F, - GEOID_FORCING = F, - ALPHAT = 0.948000000000000 , - PRED_CORR_GAMMA = 0.200000000000000 , - SMOOTH_ETA_T_BT_LAPLACIAN = F, - SMOOTH_ETA_T_BT_BIHARMONIC = F, - SMOOTH_ETA_T_LAPLACIAN = T, - SMOOTH_ETA_T_BIHARMONIC = F, - SMOOTH_ANOMPB_BT_LAPLACIAN = F, - SMOOTH_ANOMPB_BT_BIHARMONIC = F, - SMOOTH_PBOT_T_LAPLACIAN = T, - SMOOTH_PBOT_T_BIHARMONIC = F, - SMOOTH_PBOT_T_BIHARMONIC_LEGACY = F, - SMOOTH_ETA_DIAG_LAPLACIAN = T, - SMOOTH_ETA_DIAG_BIHARMONIC = F, - VEL_MICOM_LAP = 5.000000000000000E-002, - VEL_MICOM_LAP_DIAG = 0.200000000000000 , - VEL_MICOM_BIH = 1.000000000000000E-002, - VEL_MICOM_BIH_DIAG = 0.100000000000000 , - TRUNCATE_ETA = F, - VERBOSE_TRUNCATE = T, - ETA_MAX = 8.00000000000000 , - FRAC_CRIT_CELL_HEIGHT = 0.200000000000000 , - VERBOSE_INIT = T, - DEBUG_THIS_MODULE = F, - DIAG_STEP = 4320, - ETA_OFFSET = 1.000000000000000E-012, - PBOT_OFFSET = 1.000000000000000E-012, - INITSUM_WITH_BAR_MOM4P0 = F, - INITSUM_WITH_BAR_MOM4P1 = T, - IDEAL_INITIAL_ETA = F, - IDEAL_INITIAL_ETA_AMPLITUDE = 5.00000000000000 , - IDEAL_INITIAL_ETA_XWIDTH = 100000.000000000 , - IDEAL_INITIAL_ETA_YWIDTH = 100000.000000000 , - UDRHO_BT_LAP = F, - UDRHO_BT_BIH = F, - UDRHO_LAP = F, - UDRHO_BIH = F, - UDRHO_LAP_VEL_MICOM = 5.000000000000000E-002, - UDRHO_BIH_VEL_MICOM = 1.000000000000000E-002, - BAROTROPIC_HALO = 10, - DO_BITWISE_EXACT_SUM = F, - USE_LEGACY_BAROTROPIC_HALOS = F - / - horz diff flux domain decomposition -whalo = 1, ehalo = 1, shalo = 1, nhalo = 1 - X-AXIS = 23 23 23 23 22 22 22 22 22 22 22 22 23 23 23 23 - Y-AXIS = 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 - barotropic domain domain decomposition -whalo = 10, ehalo = 10, shalo = 10, nhalo = 10 - X-AXIS = 23 23 23 23 22 22 22 22 22 22 22 22 23 23 23 23 - Y-AXIS = 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 -NOTE from PE 0: Using barotropic predictor-corrector for integrating barotropic dynamics. - - Predictor-Corrector time filter on barotropic dynamics has value= 0.20 - - Updating eta_t or pbot_t using a big time step as in MOM4.0. Not recommended for OBC applications. - - Initialise sum of barotropic sea level with eta_t or pbot_t. This is the default. - - ==> Note: The barotropic dynamics integrate 160 timesteps for every one baroclinic timestep. - - ==>Using smooth_eta_t_laplacian to smooth eta_t. -NOTE from PE 0: ==>Note from tidal_forcing_init: tidal_forcing=false, so not adding tidal forcing to external mode. - - Barotropic stability most nearly violated at T-cell (i,j) = ( 78, 300), (lon,lat) = ( -275.42, 87.21). - The number of kmt-levels at this point is 46 - The dxt grid spacing (m) at this point is 0.249344E+05 - The dyt grid spacing (m) at this point is 0.494923E+05 - where the barotropic gravity wave speed is ~242.0 m/s. - "dtbt" must be less than 103.000 sec. dtbt = 67.500 sec. - - - &OCEAN_THICKNESS_NML - DEBUG_THIS_MODULE = F, - DEBUG_THIS_MODULE_DETAIL = F, - WRITE_A_RESTART = T, - FULL_STEP_TOPOGRAPHY = F, - INITIALIZE_ZERO_ETA = F, - ENFORCE_POSITIVE_DZT = F, - DEPTH_MIN_FOR_SIGMA = 1.000000000000000E-002, - THICKNESS_METHOD = energetic , - READ_RHO0_PROFILE = F, - THICKNESS_DZT_MIN = 1.00000000000000 , - THICKNESS_DZT_MIN_INIT = 5.00000000000000 , - RESCALE_MASS_TO_GET_HT_MOD = F, - PBOT0_SIMPLE = F, - EPSILON_INIT_THICKNESS = 1.000000000000000E-005, - READ_RESCALE_RHO0_MASK = F, - RESCALE_RHO0_MASK_GFDL = F, - RESCALE_RHO0_BASIN_LABEL = -1.00000000000000 , - RESCALE_RHO0_VALUE = 1.00000000000000 , - LINEAR_FREE_SURFACE = F, - MAX_NUM_BAD_PRINT = 25, - UPDATE_DZWU_K0 = T - / -==>Note: running ocean_thickness with thickness_method=energetic. - - - &OCEAN_OPERATORS_NML - USE_LEGACY_DIV_UD = F - / - horz diff flux domain decomposition -whalo = 1, ehalo = 1, shalo = 1, nhalo = 1 - X-AXIS = 23 23 23 23 22 22 22 22 22 22 22 22 23 23 23 23 - Y-AXIS = 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 - - - &OCEAN_TRACER_NML - DEBUG_THIS_MODULE = F, - ZERO_TENDENCY = F, - ZERO_TRACER_SOURCE = F, - WRITE_A_RESTART = T, - OCEAN_TPM_DEBUG = F, - TMASK_LIMIT_TS_SAME = T, - REMAP_DEPTH_TO_S_INIT = F, - INFLOW_NBOUNDARY = F, - INTERPOLATE_TPROG_TO_PBOTT = T, - INTERPOLATE_TDIAG_TO_PBOTT = F, - LIMIT_AGE_TRACER = T, - AGE_TRACER_MAX_INIT = 0.000000000000000E+000, - FRAZIL_HEATING_BEFORE_VPHYSICS = F, - FRAZIL_HEATING_AFTER_VPHYSICS = T, - COMPUTE_TMASK_LIMIT_ON = T, - USE_TEMPSALT_CHECK_RANGE = T - / -==>Note: frazil heating called after vertical physics and after boundary fluxes. - This is the recommended method. - -NOTE from PE 0: ==>Note from ocean_tracer_mod(ocean_prog_tracer_init): Synchronous timesteps have been specified (dtts = dtuv). - - ==>Note from ocean_tpm_util_mod(otpm_set_tracer_package)[ocean_tracer_mod(ocean - _prog_tracer_init)]: Processing tracer package required - - - &OCEAN_TEMPSALT_NML - DEBUG_THIS_MODULE = F, - TEMPERATURE_VARIABLE = conservative_temp , - POTTEMP_2ND_ITERATION = T, - POTTEMP_EQUAL_CONTEMP = T, - T_MIN = -20.0000000000000 , - T_MAX = 55.0000000000000 , - S_MIN = 0.000000000000000E+000, - S_MAX = 70.0000000000000 , - T_MIN_LIMIT = -5.00000000000000 , - T_MAX_LIMIT = 32.0000000000000 , - S_MIN_LIMIT = 2.00000000000000 , - S_MAX_LIMIT = 42.0000000000000 , - REINIT_TS_WITH_IDEAL = F, - REINIT_TS_WITH_IDEAL_EFOLD = 1000.00000000000 , - REINIT_TS_WITH_IDEAL_TVALUE = 10.0000000000000 , - REINIT_TS_WITH_IDEAL_SVALUE = 30.0000000000000 , - TEOS10 = F, - DO_FAFMIP_HEAT = F - / -==>Note from ocean_tempsalt_mod: MOM prognostic temp = conservative temperature. - MOM diagnostic temp = potential temperature. - -==>Note from ocean_tempsalt_mod: setting potential temp = conservative temp. - This setting is useful for simulations where the difference is irrelevant. - - ==>Note from ocean_tpm_util_mod(otpm_set_prog_tracer)[ocean_tempsalt_mod/ocean_ - tempsalt_init]: Processing prog tracer temp - - ==>Note from ocean_tpm_util_mod(otpm_set_prog_tracer)[ocean_tempsalt_mod/ocean_ - tempsalt_init]: Processing prog tracer salt - - ==>Note from ocean_tpm_util_mod(otpm_set_diag_tracer)[ocean_tempsalt_mod/ocean_ - tempsalt_init]: Processing diag tracer pot_temp -==>Note from ocean_tempsalt_mod: NOT Initializing FAFMIP temperature fields. - - - &OCEAN_FRAZIL_NML - USE_THIS_MODULE = T, - DEBUG_THIS_MODULE = F, - FREEZING_TEMP_SIMPLE = F, - FREEZING_TEMP_PRETEOS10 = T, - FREEZING_TEMP_TEOS10 = F, - FRAZIL_FACTOR = 1.00000000000000 , - AIR_SATURATED_WATER = T, - FRAZIL_ONLY_IN_SURFACE = F - / -NOTE from PE 0: ==>Note from ocean_frazil_mod: USING frazil heating. -==>Note: Using preTEOS10 equation for seawater freezing temperature. -==>Note: Assuming seawater is saturated w/ air for freezing temperature calculation. -Assuming that frazil can form in any ocean grid cell, including cells beneath surface. - - ==>Note from ocean_tpm_util_mod(otpm_set_diag_tracer)[ocean_frazil_mod/ocean_fr - azil_init]: Processing diag tracer frazil -NOT Initializing frazil_redist heat diagnostic tracer for FAFMIP purposes. - -==>Note from ocean_frazil_mod: using frazil_factor= 1.00 -Check value for freezing temperature(C) at (35psu,200dbar) = -0.2076426227617581E+01 -This value differs from published check value by -0.4440892098500626E-15 - - ==>Note from ocean_tpm_util_mod(otpm_set_tracer_package)[ocean_passive_mod(ocea - n_passive_init)]: Processing tracer package ocean_passive - - ==>Note from ocean_passive_mod(ocean_passive_init): - No instances of passive tracers in field_table. - -==>Note: NOT running with idealized passive tracers. -NOTE from PE 0: ==>Note: ocean_passive_mod: NOT using idealized passive tracer module. - - ==>Note from ocean_tpm_util_mod(otpm_set_tracer_package)[ocean_residency_mod(oc - ean_residency_init)]: Processing tracer package ocean_residency - - ==>Note from ocean_residency_mod(ocean_residency_init): No instances - - ==>Note from ocean_tpm_util_mod(otpm_set_tracer_package)[ocean_age_tracer_mod(o - cean_age_tracer_init)]: Processing tracer package ocean_age_tracer - - ==>Note from ocean_age_tracer_mod(ocean_age_tracer_init): 1 - instances - - ==>Note from ocean_tpm_util_mod(otpm_set_prog_tracer)[ocean_age_tracer_mod(ocea - n_age_tracer_init)]: Processing prog tracer age_global - - ==>Note from fm_util_mod(fm_util_start_namelist)[ocean_age_tracer_mod(ocean_age - _tracer_init)]: Processing namelist ocean_age_tracer/global - - ==>Note from ocean_tpm_util_mod(otpm_set_tracer_package)[transport_matrix_mod(t - ransport_matrix_init)]: Processing tracer package transport_matrix - - ==>Note from transport_matrix_mod(transport_matrix_init): No instances - - Dumping tracer_packages tracer tree -tracer_packages/ - ocean_age_tracer/ - names = 'global' - const_init_tracer = T - horizontal-advection-scheme = 'mdppm' - vertical-advection-scheme = 'mdppm' - ppm_hlimiter = 3 - ppm_vlimiter = 3 - restart_file = 'ocean_age.res.nc' - min_tracer_limit = 0.000000000000000E+000 - units = 'yr' - min_range = 0.000000000000000E+000 - max_range = 1.000000000000000E+020 - flux_units = 'm' - max_tracer_limit = 1.000000000000000E+020 - required/ - names = NULL - ocean_passive/ - names = NULL - units = 'dimensionless' - conversion = 1.00000000000000 - offset = 0.000000000000000E+000 - min_tracer = -1000000.00000000 - max_tracer = 1000000.00000000 - min_range = -10.0000000000000 - max_range = 100.000000000000 - restart_file = 'ocean_passive.res.nc' - psom_limit = T - flux_units = 'dimensionless' - min_flux_range = -1.000000000000000E+016 - max_flux_range = 1.000000000000000E+016 - min_tracer_limit = -0.100000000000000 - max_tracer_limit = 1.00000000000000 - vertical-advection-scheme = 'mdppm' - horizontal-advection-scheme = 'mdppm' - ocean_residency/ - names = NULL - units = 'yr' - restart_file = 'ocean_residency.res.nc' - flux_units = 'm' - min_tracer_limit = 0.000000000000000E+000 - max_tracer_limit = 1.000000000000000E+020 - transport_matrix/ - names = NULL - restart_file = 'transport_matrix.res.nc' - - Dumping prog_tracers tracer tree -prog_tracers/ - temp/ - horizontal-advection-scheme = 'mdppm' - vertical-advection-scheme = 'mdppm' - restart_file = 'ocean_temp_salt.res.nc' - ppm_hlimiter = 3 - ppm_vlimiter = 3 - longname = 'Conservative temperature' - units = 'deg_C' - type = '' - conversion = 3992.10322329649 - offset = 273.150000000000 - min_tracer = -20.0000000000000 - max_tracer = 55.0000000000000 - min_range = -10.0000000000000 - max_range = 500.000000000000 - use_only_advection = F - const_init_tracer = F - const_init_value = 0.000000000000000E+000 - psom_limit = F - mdt_scheme = 1 - flux_units = 'Watts/m^2' - min_flux_range = -1.000000000000000E+016 - max_flux_range = 1.000000000000000E+016 - min_tracer_limit = -5.00000000000000 - max_tracer_limit = 32.0000000000000 - salt/ - horizontal-advection-scheme = 'mdppm' - vertical-advection-scheme = 'mdppm' - restart_file = 'ocean_temp_salt.res.nc' - ppm_hlimiter = 3 - ppm_vlimiter = 3 - longname = 'Practical Salinity' - units = 'psu' - type = '' - conversion = 1.000000000000000E-003 - offset = 0.000000000000000E+000 - min_tracer = 0.000000000000000E+000 - max_tracer = 70.0000000000000 - min_range = -10.0000000000000 - max_range = 100.000000000000 - use_only_advection = F - const_init_tracer = F - const_init_value = 0.000000000000000E+000 - psom_limit = F - mdt_scheme = 1 - flux_units = 'kg/(sec*m^2)' - min_flux_range = -100000.000000000 - max_flux_range = 100000.000000000 - min_tracer_limit = 2.00000000000000 - max_tracer_limit = 42.0000000000000 - age_global/ - longname = 'Age (global)' - units = 'yr' - type = '' - conversion = 1.00000000000000 - offset = 0.000000000000000E+000 - min_tracer = -1.000000000000000E+020 - max_tracer = 1.000000000000000E+020 - min_range = 0.000000000000000E+000 - max_range = 1.000000000000000E+020 - use_only_advection = F - restart_file = 'ocean_age.res.nc' - const_init_tracer = T - const_init_value = 0.000000000000000E+000 - psom_limit = F - ppm_hlimiter = 3 - ppm_vlimiter = 3 - mdt_scheme = 1 - flux_units = 'm' - min_flux_range = 1.00000000000000 - max_flux_range = 0.000000000000000E+000 - min_tracer_limit = 0.000000000000000E+000 - max_tracer_limit = 1.000000000000000E+020 - vertical-advection-scheme = 'mdppm' - horizontal-advection-scheme = 'mdppm' - - Dumping namelists tracer tree -namelists/ - ocean_age_tracer/ - global/ - slat = -90.0000000000000 - nlat = 90.0000000000000 - wlon = 0.000000000000000E+000 - elon = 360.000000000000 - coastal_only = F - t_mask[1] = T - t_mask[2] = T - t_mask[3] = T - t_mask[4] = T - t_mask[5] = T - t_mask[6] = T - t_mask[7] = T - t_mask[8] = T - t_mask[9] = T - t_mask[10] = T - t_mask[11] = T - t_mask[12] = T - age_tracer_type = 'not used' - - ==> Note from ocean_tracer_mod: prognostic temperature = conservative temperature. - diagnostic temperature = potential temperature. - - - ==>Note from ocean_tracer_mod(ocean_prog_tracer_init): - Reading prognostic tracer initial conditions or restarts - - Initializing tracer number 1 - at time level tau. This tracer is called temp - Reading restart for prog tracer temp from file ocean_temp_salt.res.nc - After reading ic, linearly interpolate temp to partial cell bottom. - Completed initialization of tracer temp at time level tau - - Initializing tracer number 2 - at time level tau. This tracer is called salt - Reading restart for prog tracer salt from file ocean_temp_salt.res.nc - After reading ic, linearly interpolate salt to partial cell bottom. - Completed initialization of tracer salt at time level tau - - Initializing tracer number 3 - at time level tau. This tracer is called age_global - Initializing the tracer age_global to the constant 0.000000000000000E+000 - Completed initialization of tracer age_global at time level tau - - ==>Note from ocean_tracer_mod(ocean_prog_tracer_init): - finished reading prognostic tracer restarts. - - ==>Note from ocean_tpm_util_mod(otpm_set_diag_tracer)[ocean_shortwave_mod(ocean - _irradiance_init)]: Processing diag tracer irr - - ==>Note from ocean_tracer_mod(ocean_diag_tracer_init): 3 - diagnostic tracers requested. - - Dumping ocean diag field tree after reading diag tracer tree -diag_tracers/ - pot_temp/ - longname = 'Potential temperature' - units = 'deg_C' - type = '' - conversion = 3992.10322329649 - offset = 273.150000000000 - min_tracer = -20.0000000000000 - max_tracer = 55.0000000000000 - min_range = -10.0000000000000 - max_range = 500.000000000000 - restart_file = 'ocean_pot_temp.res.nc' - const_init_tracer = T - const_init_value = 0.000000000000000E+000 - frazil/ - longname = 'frazil heating' - units = 'J/m^2' - type = '' - conversion = 1.00000000000000 - offset = 0.000000000000000E+000 - min_tracer = 0.000000000000000E+000 - max_tracer = 1.000000000000000E+020 - min_range = -10.0000000000000 - max_range = 100.000000000000 - restart_file = 'ocean_frazil.res.nc' - const_init_tracer = T - const_init_value = 0.000000000000000E+000 - irr/ - longname = 'Irradiance' - units = 'Watts/m^2' - type = '' - conversion = 1.00000000000000 - offset = 0.000000000000000E+000 - min_tracer = -1.000000000000000E+020 - max_tracer = 1.000000000000000E+020 - min_range = 1.00000000000000 - max_range = 0.000000000000000E+000 - restart_file = '' - const_init_tracer = T - const_init_value = 0.000000000000000E+000 - ==>Note from ocean_tracer_mod(ocean_diag_tracer_init): - Reading diagnostic tracer initial conditions and/or restarts - - Initializing tracer number 1 - at time level tau. This tracer is called pot_temp - Initializing diagnostic tracer pot_temp to constant 0.000000000000000E+000 - - Initializing tracer number 2 - at time level tau. This tracer is called frazil - Initializing diagnostic tracer frazil to constant 0.000000000000000E+000 - - Initializing tracer number 3 - at time level tau. This tracer is called irr - Skipping tracer irr - ==>Note from ocean_tracer_mod(ocean_diag_tracer_init): - Finished reading diagnostic tracer restarts. - - - &OCEAN_ADVECTION_VELOCITY_NML - DEBUG_THIS_MODULE = F, - MAX_ADVECTION_VELOCITY = 0.500000000000000 , - INFLOW_NBOUNDARY = F, - READ_ADVECTION_VELOCITY = F, - READ_ADVECTION_TRANSPORT = F, - CONSTANT_ADVECTION_VELOCITY = F - / - - Note: Advection stability most nearly violated at T-cell (i,j) = ( 198, 246), (lon,lat) = ( -82.501, 65.069). - Assuming a maximum advection velocity of 0.50 m/s, - Linear stability requires max(dtuv,dtts) be less than 7709.18 sec. - Model is now using (dtuv,dtts) = ( 5400.00, 5400.00) sec. - - - &OCEAN_DENSITY_NML - S_TEST = 20.0000000000000 , - T_TEST = 20.0000000000000 , - P_TEST = 1000.00000000000 , - PRESS_STANDARD = 0.000000000000000E+000, - SN_TEST = 35.0000000000000 , - TN_TEST = 20.0000000000000 , - EOS_LINEAR = F, - ALPHA_LINEAR_EOS = 0.255000000000000 , - BETA_LINEAR_EOS = 0.000000000000000E+000, - EOS_PRETEOS10 = T, - EOS_TEOS10 = F, - POTRHO_PRESS = 2000.00000000000 , - POTRHO_MIN = 1028.00000000000 , - POTRHO_MAX = 1038.00000000000 , - NEUTRALRHO_MIN = 1020.00000000000 , - NEUTRALRHO_MAX = 1030.00000000000 , - LAYER_NK = 80, - THETA_MIN = -2.00000000000000 , - THETA_MAX = 30.0000000000000 , - DEBUG_THIS_MODULE = F, - WRITE_A_RESTART = T, - RHO0_DENSITY = F, - DENSITY_EQUAL_POTRHO = F, - BUOYFREQ_SMOOTH_VERT = T, - NUM_121_PASSES = 1, - EPSLN_DRHODZ = 1.000000000000000E-010, - MASK_DOMAIN_RESTART = F, - DO_BITWISE_EXACT_SUM = F, - DRHODZ_DIAG_STABLE = T, - EPSLN_DRHODZ_DIAG = 1.000000000000000E-010, - GRAD_NRHO_LRPOTRHO_COMPUTE = F, - GRAD_NRHO_LRPOTRHO_MAX = 10.0000000000000 , - GRAD_NRHO_LRPOTRHO_MIN = 1.00000000000000 , - NEUTRAL_DENSITY_OMEGA = F, - NEUTRAL_DENSITY_POTRHO = T, - NEUTRAL_DENSITY_THETA = F, - SMOOTH_STRATIFICATION_FACTOR = F, - UPDATE_DIAGNOSTIC_FACTORS = F, - SMAX_DIAG = -1.00000000000000 , - SMAX_MIN_IN_COLUMN = F - / - - ==> Note: USING preTEOS10 EOS, as relevant for realistic ocean climate simulations. - Subtracting standard atmosphere of 0.000000 dbar for EOS calculation. - - ==> Note: Computing EOS assuming prognostic temp = conservative temperature. - - ==> Note: Computing EOS assuming prognostic salinity = practical salinity. - ==>Note: The Boussinesq rho0 density has a value of (kg/m^3) - 1035.00000000000 - - ==> Note: Computing diagnostic neutral_rho as potential density referenced to pressure potrho_press. - - ==> Note: Enforcing drhodz_diag < 0, so to use stable stratification for certain diagnostic purposes. - - ==> Note: Diagnostic factors are NOT computed. So if enable watermass diagnostics, they will be corrupted. - -preTEOS10 EQUATION OF STATE TEST VALUES -s_test(psu) = 20.00, t_test(C) = 20.00, p_test(dbar) = 1000.00 -rho ( 20.00, 20.00, 1000.00) = 0.1017842890411976E+04 kg/m^3 -diff from JMFWG = 0.5684341886080801E-12 kg/m^3 -alpha( 20.00, 20.00, 1000.00) = 0.2436057013634663E-03 1/C -diff from JMFWG = 0.1409462824231156E-17 1/C -beta ( 20.00, 20.00, 1000.00) = 0.7314818108935242E-03 1/psu -squared sound speed ( 20.00, 20.00, 1000.00) = 0.2311451354560629E+03 (m/s)^2 -diff from JMFWG = -.6505213034913027E-18 1/psu - -NEUTRAL DENSITY EQUATION TEST VALUES -sn_test(psu) = 35.00, tn_test(C) = 20.00 -rho ( 35.00, 20.00) = 0.1024438639277630E+04 kg/m^3 -diff from Klocker and McDougall test = 0.0000000000000000E+00 kg/m^3 - - Initialising salinity for use in density calculation - - ==>Note: From ocean_density_mod: Boussinesq reference density rho0(kg/m3) = 0.103500000000E+04 - Initial rho_average(kg/m3) = 0.103735682116E+04 - Since rho0 .ne. rho_average, consider changing rho0 in - ocean_parameters.F90 to be equal to rho_average for better accuracy. - - - From ocean_density_mod: density chksums from ocean_density_init -yyyy/mm/dd hh:mm:ss = 1958/ 1/ 1 0: 0: 0 -[chksum] rho(taup1) 6106784929722531668 -[chksum] pressure_at_depth 2833038859972097028 -[chksum] denominator_r -3856329882632806246 -[chksum] drhodT 0 -[chksum] drhodS 0 -[chksum] drhodz_zt 5453892586152658933 - - - &OCEAN_BLOB_NML - BLOB_SMALL_MASS = 1000.00000000000 , - DEBUG_THIS_MODULE = F, - REALLY_DEBUG = F, - DO_BITWISE_EXACT_SUM = F, - BITWISE_REPRODUCTION = F, - MAX_PROP_THICKNESS = 0.700000000000000 - / -==>Note: NOT using the Lagrangian buoyancy blobs scheme. - - - &OCEAN_PRESSURE_NML - DEBUG_THIS_MODULE = F, - ZERO_PRESSURE_FORCE = F, - ZERO_CORRECTION_TERM_GRAD = F, - ZERO_DIAGONAL_PRESS_GRAD = F, - ZERO_ETA_OVER_H_ZSTAR_PRESSURE = F - / - ==>NOTE: Running MOM with finite difference formulation of pressure force. - - - &OCEAN_VERT_MIX_NML - DEBUG_THIS_MODULE = F, - VERT_MIX_SCHEME = kpp_mom4p1, - VERBOSE_INIT = T, - AIDIF = 1.00000000000000 , - VERT_DIFF_BACK_VIA_MAX = T, - USE_EXPLICIT_VERT_DIFFUSE = T, - USE_DIFF_CBT_TABLE = F, - LINEAR_TAPER_DIFF_CBT_TABLE = F, - BRYAN_LEWIS_DIFFUSIVITY = F, - BRYAN_LEWIS_LAT_DEPEND = F, - BRYAN_LEWIS_LAT_TRANSITION = 35.0000000000000 , - AFKPH_90 = 0.550000000000000 , - DFKPH_90 = 1.05000000000000 , - SFKPH_90 = 4.500000000000000E-005, - ZFKPH_90 = 250000.000000000 , - AFKPH_00 = 0.550000000000000 , - DFKPH_00 = 1.05000000000000 , - SFKPH_00 = 4.500000000000000E-005, - ZFKPH_00 = 250000.000000000 , - VERT_VISC_BACK = F, - VISC_CBU_BACK_MAX = 1.000000000000000E-002, - VISC_CBU_BACK_MIN = 1.000000000000000E-003, - VISC_CBU_BACK_ZMID = 50.0000000000000 , - VISC_CBU_BACK_ZWID = 30.0000000000000 , - HWF_DIFFUSIVITY = F, - HWF_DEPTH_TRANSITION = 25000000.0000000 , - HWF_MIN_DIFFUSIVITY = 2.000000000000000E-006, - HWF_30_DIFFUSIVITY = 2.000000000000000E-005, - HWF_N0_2OMEGA = 20.0000000000000 , - HWF_DIFFUSIVITY_3D = F, - DIFF_CBT_TANH = F, - DIFF_CBT_TANH_MAX = 1.000000000000000E-003, - DIFF_CBT_TANH_MIN = 2.000000000000000E-005, - DIFF_CBT_TANH_ZMID = 150.000000000000 , - DIFF_CBT_TANH_ZWID = 30.0000000000000 , - J09_DIFFUSIVITY = F, - J09_BGMIN = 1.000000000000000E-006, - J09_BGMAX = 1.000000000000000E-005, - J09_LAT = 20.0000000000000 , - QUEBEC_2009_10_BUG = F, - VMIX_RESCALE_NONBOUSS = F, - VMIX_SET_MIN_DISSIPATION = F, - VMIX_MIN_DISS_CONST = 1.000000000000000E-007, - VMIX_MIN_DISS_BVFREQ_SCALE = 5.999999999999999E-004, - VMIX_MIN_DISS_FLUX_RI_MAX = 0.200000000000000 , - SMOOTH_RHO_N2 = T, - NUM_121_PASSES = 1 - / - - - &OCEAN_VERT_UTIL_NML - DEBUG_THIS_MODULE = F, - SMOOTH_N2 = T, - SMOOTH_RI_NUMBER = T, - NUM_N2_SMOOTH = 1, - NUM_RI_SMOOTH = 1 - / -NOTE from PE 0: ==>Warning: ocean_vert_mix_init NO table for enhanced diff_cbt. No diffusivities read. - - - &OCEAN_VERT_TIDAL_NML - USE_THIS_MODULE = T, - USE_LEGACY_METHODS = F, - DEBUG_THIS_MODULE = F, - USE_WAVE_DISSIPATION = T, - USE_DRAG_DISSIPATION = T, - READ_ROUGHNESS = T, - READ_TIDE_SPEED = T, - DEFAULT_ROUGHNESS_LENGTH = 25.0000000000000 , - DEFAULT_TIDE_SPEED = 1.000000000000000E-002, - SHELF_DEPTH_CUTOFF = -1000.00000000000 , - DECAY_SCALE = 500.000000000000 , - ROUGHNESS_SCALE = 12000.0000000000 , - TIDAL_DISS_EFFICIENCY = 0.333330000000000 , - MIXING_EFFICIENCY = 0.200000000000000 , - MIXING_EFFICIENCY_N2DEPEND = T, - MUNK_ANDERSON_P = 0.250000000000000 , - MUNK_ANDERSON_SIGMA = 3.00000000000000 , - DRAG_DISSIPATION_EFOLD = T, - DRAG_DISSIPATION_TIDE_PERIOD = 43200.0000000000 , - DRAG_MASK_DEEP = T, - DRAG_MASK_DEEP_RATIO = 0.100000000000000 , - BOTTOM_DRAG_CD = 2.400000000000000E-003, - DRHODZ_MIN = 1.000000000000000E-010, - SPEED_MIN = 5.000000000000000E-003, - BACKGROUND_DIFFUSIVITY = 0.000000000000000E+000, - BACKGROUND_VISCOSITY = 1.000000000000000E-004, - MAX_WAVE_DIFFUSIVITY = 1.000000000000000E-002, - MAX_DRAG_DIFFUSIVITY = 5.000000000000000E-003, - SMOOTH_BVFREQ_BOTTOM = T, - VEL_MICOM_SMOOTH = 0.200000000000000 , - SMOOTH_RHO_N2 = T, - NUM_121_PASSES = 1, - WAVE_DIFFUSIVITY_MONOTONIC = T, - TIDE_SPEED_DATA_ON_T_GRID = T, - READING_ROUGHNESS_AMP = T, - READING_ROUGHNESS_LENGTH = F, - READ_WAVE_DISSIPATION = F, - FIXED_WAVE_DISSIPATION = F, - WAVE_ENERGY_FLUX_MAX = 0.100000000000000 , - USE_LEEWAVE_DISSIPATION = F, - READ_LEEWAVE_DISSIPATION = F, - DRAG_DISSIPATION_USE_CDBOT = T - / -NOTE from PE 0: ==>Note: USING ocean_vert_tidal_mod -Using Simmons etal scheme to compute dia-surface diffusivity and viscosity based on internal wave breaking. -Using Lee etal scheme to compute dia-surface diffusivity and viscosity based on barotropic tide drag on bottom. -NOT using Nikurashin scheme for dia-surface diffusivity and viscosity. - ==>ocean_vert_tidal_mod: Completed read of topographic roughness amplitude on T - -grid. -==>Note: NOT reading wave dissipation for ocean_vert_tidal_mod. -==>Note: NOT reading leewave dissipation for ocean_vert_tidal_mod. - ==>ocean_vert_tidal_mod: Completed read of tide_speed on T-grid. -==>Note from ocean_vert_tidal: using cdbot_array(i,j) for tide drag_dissipation scheme. - -==>Note from ocean_vert_mix: KPP_mom4p1 for vert diffusivity, viscosity, nonlocal, and barotropic tide drag. - - - - &OCEAN_VERT_KPP_MOM4P1_NML - USE_THIS_MODULE = T, - SHEAR_INSTABILITY = T, - DOUBLE_DIFFUSION = T, - DIFF_CBT_IW = 0.000000000000000E+000, - VISC_CBU_IW = 0.000000000000000E+000, - VISC_CBU_LIMIT = 5.000000000000000E-003, - DIFF_CBT_LIMIT = 5.000000000000000E-003, - VISC_CON_LIMIT = 0.100000000000000 , - DIFF_CON_LIMIT = 0.100000000000000 , - CONCV = 1.80000000000000 , - RICR = 0.300000000000000 , - NON_LOCAL_KPP = T, - SMOOTH_BLMC = F, - LGAM = 1.04000000000000 , - CW_0 = 0.150000000000000 , - L_SMYTH = 2.00000000000000 , - LTMAX = 5.00000000000000 , - WSTFAC = 0.600000000000000 , - KL_MIN = 2, - KBL_STANDARD_METHOD = F, - DEBUG_THIS_MODULE = F, - LIMIT_WITH_HEKMAN = T, - LIMIT_GHATS = F, - HBL_WITH_RIT = F, - RADIATION_LARGE = F, - RADIATION_ZERO = F, - RADIATION_IOW = F, - USE_SBL_BOTTOM_FLUX = F, - WSFC_COMBINE_RUNOFF_CALVE = T, - BVF_FROM_BELOW = F, - VARIABLE_VTC = F, - USE_MAX_SHEAR = F, - LINEAR_HBL = T, - CALC_VISC_ON_CGRID = F, - SMOOTH_RI_KMAX_EQ_KMU = T, - DO_LANGMUIR = F, - DO_LANGMUIR_CVMIX = F, - CALCULATE_U10 = F - / - - ==> NOTE: USING KPP vertical mixing scheme. - ==> NOTE: KPP is typically run with penetrative shortwave heating. - ==> NOTE: KPP is typically run with a seasonal and/or diurnal cycle. - - -==>Note from ocean_vert_kpp_mom4p1_mod: using forward time step for vert-frict of (secs) 5400.00 - -==>Note from ocean_vert_kpp_mom4p1_mod: using forward time step for vert-diff of (secs) 5400.00 - ==> NOTE from ocean_vert_kpp_mom4p1_mod: adjust kbl to hbl with the non-standard method. - ==>WARNING from ocean_vert_kpp_mom4p1_mod: change kl_min to 1 to avoid negative mixing coefficients with low wind stress. - ==> NOTE from ocean_vert_kpp_mom4p1_mod: Find BVF from a backward derivatives. - ==> NOTE from ocean_vert_kpp_mom4p1_mod: Diagnose hbl with constant concv. - ==> NOTE from ocean_vert_kpp_mom4p1_mod: Use average shear around a tracer cell for diagnostics of hbl. - ==> NOTE from ocean_vert_kpp_mom4p1_mod: Use linear interpolation to find hbl - ==> NOTE from ocean_vert_kpp_mom4p1_mod: Do not limit ghats*diff_cbt to 1. - ==> NOTE from ocean_vert_kpp_mom4p1_mod: Limit hbl with hekman for stable case. - ==> NOTE from ocean_vert_kpp_mom4p1_mod: Interpolate viscosity to c-grid. - ==> NOTE from ocean_vert_kpp_mom4p1_mod: Leave full sw-radiation in non-local surface flux. -Computing vertical mixing from shear instability in KPP module. - - - &OCEAN_BIH_TRACER_NML - USE_THIS_MODULE = F, - ABIH = 0.000000000000000E+000, - TRACER_MIX_MICOM = F, - VEL_MICOM = 0.000000000000000E+000, - READ_DIFFUSIVITY_MASK = F, - HORZ_Z_DIFFUSE = F, - HORZ_S_DIFFUSE = T - / - ==>Note from ocean_bih_tracer_mod: NOT using this module. - - - &OCEAN_LAP_TRACER_NML - USE_THIS_MODULE = F, - ALAP = 0.000000000000000E+000, - TRACER_MIX_MICOM = F, - VEL_MICOM = 0.000000000000000E+000, - VERBOSE_INIT = T, - READ_DIFFUSIVITY_MASK = F, - HORZ_Z_DIFFUSE = F, - HORZ_S_DIFFUSE = T - / - ==>Note from ocean_lap_tracer_mod: NOT using this module. - - - &OCEAN_SIGMA_TRANSPORT_NML - USE_THIS_MODULE = T, - DEBUG_THIS_MODULE = F, - TMASK_SIGMA_ON = F, - SIGMA_DIFFUSION_ON = T, - SIGMA_ADVECTION_ON = F, - SIGMA_ADVECTION_SGS_ONLY = T, - SIGMA_ADVECTION_CHECK = T, - THICKNESS_SIGMA_LAYER = 50.0000000000000 , - THICKNESS_SIGMA_MAX = 100.000000000000 , - THICKNESS_SIGMA_MIN = 10.0000000000000 , - SIGMA_DIFFUSIVITY = 1000.00000000000 , - SIGMA_DIFFUSIVITY_RATIO = 1.000000000000000E-006, - TRACER_MIX_MICOM = F, - VEL_MICOM = 0.500000000000000 , - VERBOSE_INIT = T, - SIGMA_JUST_IN_BOTTOM_CELL = T, - CAMPINGOOSE_MU = 1.000000000000000E-004, - CAMPINGOOSE_DELTA = 0.333300000000000 , - SIGMA_UMAX = 0.100000000000000 , - WRITE_A_RESTART = T, - SMOOTH_SIGMA_THICKNESS = T, - SMOOTH_SIGMA_VELOCITY = T, - SMOOTH_VELMICOM = 0.200000000000000 - / -NOTE from PE 0: ==>Note from ocean_sigma_transport_mod: USING ocean_sigma_transport_mod. -==>Note: ocean_sigma_transport_mod: using forward time step of (secs) 5400.00 -==>Note: ocean_sigma_transport_mod: sigma_diffusion_on=.true. -==>Note: ocean_sigma_transport_mod: sigma_advection_on=.false. -==>Note from ocean_sigma_transport_mod: using sigma_just_in_bottom=.true., as in mom4p0. - flux dom sigma domain decomposition -whalo = 1, ehalo = 1, shalo = 1, nhalo = 1 - X-AXIS = 23 23 23 23 22 22 22 22 22 22 22 22 23 23 23 23 - Y-AXIS = 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 -==>Note: ocean_sigma_transport_mod: initial thickness of sigma layer (m) = 50.0000 -==>Note: ocean_sigma_transport_mod: smooth_sigma_thickness=.true. => diffuse sigma_thickness. - - - &OCEAN_NPHYSICS_NML - USE_THIS_MODULE = T, - DEBUG_THIS_MODULE = F, - WRITE_A_RESTART = T, - USE_NPHYSICSA = F, - USE_NPHYSICSB = F, - USE_NPHYSICSC = T - / - -[Note] ocean_nphysics.F90: USING ocean_nphysics_mod. - - - &OCEAN_NPHYSICS_UTIL_NML - DEBUG_THIS_MODULE = F, - NPHYSICS_UTIL_ZERO_INIT = T, - SMAX = 1.000000000000000E-002, - SWIDTH = 5.000000000000000E-004, - EPSLN_DRHODZ = 1.000000000000000E-030, - DRHODZ_MOM4P1 = T, - DRHODZ_SMOOTH_HORZ = F, - DRHODZ_SMOOTH_VERT = F, - NUM_121_PASSES = 1, - AREDI = 600.000000000000 , - AGM = 600.000000000000 , - AREDI_EQUAL_AGM = F, - TRACER_MIX_MICOM = F, - VEL_MICOM = 0.000000000000000E+000, - BRYAN_LEWIS_AREDI = F, - AHS = 0.000000000000000E+000, - AHB = 0.000000000000000E+000, - NEUTRAL_HORZ_MIX_BDY = F, - VEL_MICOM_BDY = 0.000000000000000E+000, - AH_BDY = 0.000000000000000E+000, - AGM_LAT_BANDS = F, - AGM_LAT_BANDS_BOUNDARY = -999.000000000000 , - AGM_LAT_BANDS_RATIO = 1.00000000000000 , - ROSSBY_RADIUS_MAX = 100000.000000000 , - ROSSBY_RADIUS_MIN = 15000.0000000000 , - AGM_READ_RESTART = F, - AGM_CLOSURE = T, - AGM_CLOSURE_SCALING = 7.000000000000001E-002, - AGM_CLOSURE_MAX = 600.000000000000 , - AGM_CLOSURE_MIN = 50.0000000000000 , - AGM_CLOSURE_GROWTH_SCALE = 0.500000000000000 , - AGM_CLOSURE_LENGTH_FIXED = F, - AGM_CLOSURE_LENGTH = 50000.0000000000 , - AGM_CLOSURE_LENGTH_ROSSBY = F, - AGM_CLOSURE_LENGTH_BCZONE = F, - BCZONE_MAX_PTS = 10, - AGM_CLOSURE_BCZONE_CRIT_RATE = 1.400000000000000E-006, - AGM_CLOSURE_EDEN_GREATBATCH = F, - AGM_CLOSURE_EDEN_GAMMA = 0.000000000000000E+000, - AGM_CLOSURE_EDEN_LENGTH_CONST = F, - AGM_CLOSURE_EDEN_LENGTH = 10000.0000000000 , - AGM_CLOSURE_EADY_SMOOTH_VERT = T, - AGM_CLOSURE_EADY_SMOOTH_HORZ = T, - AGM_CLOSURE_EADY_AVE_MIXED = T, - AGM_CLOSURE_EADY_CAP = T, - AGM_CLOSURE_BAROCLINIC = T, - AGM_CLOSURE_BUOY_FREQ = 4.000000000000000E-003, - AGM_CLOSURE_UPPER_DEPTH = 100.000000000000 , - AGM_CLOSURE_LOWER_DEPTH = 2000.00000000000 , - AGM_CLOSURE_LENGTH_CAP = F, - AGM_CLOSURE_LENGTH_MAX = 50000.0000000000 , - AGM_SMOOTH_SPACE = F, - VEL_MICOM_SMOOTH = 0.200000000000000 , - AGM_SMOOTH_TIME = F, - AGM_DAMPING_TIME = 45.0000000000000 , - AGM_CLOSURE_GRID_SCALING = T, - AGM_CLOSURE_GRID_SCALING_POWER = 2.00000000000000 , - AREDI_DIFFUSIVITY_GRID_SCALING = F, - AGM_CLOSURE_N2_SCALE = F, - AGM_CLOSURE_N2_SCALE_COEFF = 1000.00000000000 , - AGM_CLOSURE_N2_SCALE_NREF_CST = F, - SMAX_GRAD_GAMMA_SCALAR = 1.000000000000000E-002, - EPSLN_DRHODZ_DIAGNOSTICS = 1.000000000000000E-007, - WDIANEUTRAL_SMOOTH = T, - SMOOTH_ETA_TEND_GM90 = F - / - bczone domain decomposition -whalo = 10, ehalo = 10, shalo = 10, nhalo = 10 - X-AXIS = 23 23 23 23 22 22 22 22 22 22 22 22 23 23 23 23 - Y-AXIS = 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 - -[Note] ocean_nphysics_util.F90: Computing 2d flow-dependent tracer diffusivity with agm_closure_baroclinic. - The maximum allowable diffusivity (m^2/s) is given by .60000E+03 - The minimum allowable diffusivity (m^2/s) is given by .50000E+02 - Depths (m) between which compute eady growth and baroclinicity = .10000E+03 .20000E+04 - -[Note] ocean_nphysics_util.F90: Length and time scales set by vertically averaged baroclinicity |grad(rho)|, - as well as the constant buoyancy freq(sec^-1) = .40000E-02 - and the constant length scale (m) = .50000E+05 - -[Note] ocean_nphysics.F90: USING ocean_nphysicsC. - - - &OCEAN_NPHYSICSC_NML - USE_THIS_MODULE = T, - DEBUG_THIS_MODULE = F, - DO_NEUTRAL_DIFFUSION = T, - DO_GM_SKEWSION = T, - NEUTRAL_PHYSICS_LIMIT = T, - NEUTRAL_EDDY_DEPTH = T, - DM_TAPER = T, - GKW_TAPER = F, - TMASK_NEUTRAL_ON = T, - DIFFUSION_ALL_EXPLICIT = F, - TURB_BLAYER_MIN = 50.0000000000000 , - GM_SKEWSION_MODES = F, - NUMBER_BC_MODES = 2, - GM_SKEWSION_BVPROBLEM = T, - BVP_BC_MODE = 2, - BVP_MIN_SPEED = 0.100000000000000 , - BVP_SPEED = 0.000000000000000E+000, - BVP_CONSTANT_SPEED = F, - BV_FREQ_SMOOTH_VERT = T, - NUM_121_PASSES = 1, - MIN_BC_SPEED = 1.000000000000000E-006, - SMOOTH_PSI = T, - EPSLN_BV_FREQ = 1.000000000000000E-012, - REGULARIZE_PSI = F, - SMAX_PSI = 1.000000000000000E-002, - SMOOTH_BC_MODES = F, - USE_NEUTRAL_SLOPES_POTRHO = F, - NEUTRAL_SLOPES_POTRHO_PRESS = 2000.00000000000 , - SMOOTH_ADVECT_TRANSPORT = T, - SMOOTH_ADVECT_TRANSPORT_NUM = 2 - / - -[Note] ocean_nphysicsC.F90: USING ocean_nphysicsC. - - ==> Note from ocean_nphysicsC_mod: using forward time step of (secs) 5400.00 - -[Note] ocean_nphysicsC.F90: computing neutral diffusion acting on each tracer. - -[Note] ocean_nphysicsC.F90: computing GM skewsion w/ streamfunction computed by boundary value problem. - -[Note] ocean_nphysicsC.F90: neutral_physics_limit=.true. - Will revert to horizontal diffusion for points where tracer is outside specified range. - -[Note] ocean_nphysicsC.F90: dm_taper=.true. Will use the tanh scheme - of Danabasoglu and McWilliams to taper neutral diffusion in steep sloped regions - flux dom neutral domain decomposition -whalo = 1, ehalo = 1, shalo = 1, nhalo = 1 - X-AXIS = 23 23 23 23 22 22 22 22 22 22 22 22 23 23 23 23 - Y-AXIS = 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 - -[Note] ocean_nphysics_util.F90: Starting ocean_nphysics_util fields from raw initialization. - aredi_equal_agm=.false. and agm_read_restart=.false. => aredi_array set to static profiles. - -[Note] ocean_nphysics_util.F90: aredi_equal_agm=.false. allows aredi_array to differ from agm_array - ----Neutral direction slope check I for linear stability of neutral diffusion--- -With a neutral physics time step (secs) of 0.5400000E+04 -the most stringent linear stability constraint was found at the following ocean cell: -long( 201, 246) = -0.7950085E+02 -lat ( 201, 246) = 0.6508043E+02 -thick( 201, 246, 5) = 0.5285632E+01 -aredi( 201, 246, 5) = 0.6000000E+03 -delta_iso = 0.1481765E-01 is the maximum neutral direction slope -available for linear stability of the neutral diffusion scheme. -The namelist parameter smax should conservatively be <= delta_iso. - - ----Neutral direction slope check II for linear stability of neutral diffusion--- -Assuming maximum Redi neutral diffusion slope of 0.1000000E-01 -and neutral physics time step (secs) of 0.5400000E+04 -the most stringent linear stability constraint was found at the following ocean cell: -long( 201, 246) = -0.7950085E+02 -lat ( 201, 246) = 0.6508043E+02 -thick( 201, 246, 5)= 0.5285632E+01 -A_max = 0.8783791E+03 (m^2/sec) is the maximum neutral diffusivity -available for linear stability of the neutral diffusion scheme. -Conservatively, neutral diffusivities used in the model should be less than A_max. --------------------------------------------------------------------------------- - - - - &OCEAN_NPHYSICS_NEW_NML - USE_THIS_MODULE = F, - DRHODZ_SMOOTH_VERT = F, - DRHODZ_SMOOTH_HORZ = F, - SMAX = 1.000000000000000E-002, - VEL_MICOM_SMOOTH = 0.200000000000000 - / - - - &OCEAN_NPHYSICS_UTIL_NEW_NML - NUM_121_PASSES = 1 - / - -[Note] ocean_nphysics_new.F90: NOT using ocean_nphysics_new. - - - &OCEAN_SUBMESOSCALE_NML - USE_THIS_MODULE = T, - DEBUG_THIS_MODULE = F, - DIAG_STEP = 1200, - USE_HBLT_CONSTANT = F, - USE_HBLT_EQUAL_MLD = T, - SMOOTH_HBLT = F, - SMOOTH_HBLT_NUM = 2, - CONSTANT_HBLT = 100.000000000000 , - COEFFICIENT_CE = 5.000000000000000E-002, - TIME_CONSTANT = 86400.0000000000 , - FRONT_LENGTH_CONST = 5000.00000000000 , - MIN_KBLT = 4, - MINIMUM_HBLT = 0.000000000000000E+000, - SMOOTH_PSI = T, - SMOOTH_PSI_NUM = 2, - FRONT_LENGTH_DEFORM_RADIUS = T, - LIMIT_PSI = T, - USE_PSI_LEGACY = F, - LIMIT_PSI_VELOCITY_SCALE = 0.500000000000000 , - SUBMESO_LIMIT_FLUX = T, - SMOOTH_ADVECT_TRANSPORT = T, - SMOOTH_ADVECT_TRANSPORT_NUM = 2, - SUBMESO_SKEW_FLUX = T, - SUBMESO_ADVECT_FLUX = F, - SUBMESO_ADVECT_UPWIND = T, - SUBMESO_ADVECT_SWEBY = F, - SUBMESO_ADVECT_LIMIT = T, - SUBMESO_ADVECT_ZERO_BDY = T, - SUBMESO_DIFFUSION = F, - SUBMESO_DIFFUSION_SCALE = 10.0000000000000 , - SUBMESO_DIFFUSION_BIHARMONIC = T - / -NOTE from PE 0: ==>Note: USING ocean_submesoscale_mod -==>Note: For ocean_submesoscale, setting bldepth equal to diagnosed mld. -==>Note: For ocean_submesoscale, tendency computed as skew flux convergence. - mdfl domain decomposition -whalo = 2, ehalo = 2, shalo = 2, nhalo = 2 - X-AXIS = 23 23 23 23 22 22 22 22 22 22 22 22 23 23 23 23 - Y-AXIS = 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 - flux dom submeso domain decomposition -whalo = 1, ehalo = 1, shalo = 1, nhalo = 1 - X-AXIS = 23 23 23 23 22 22 22 22 22 22 22 22 23 23 23 23 - Y-AXIS = 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 - - - &OCEAN_LAP_FRICTION_NML - LAP_FRICTION_SCHEME = general , - DEBUG_THIS_MODULE = F, - WRITE_A_RESTART = T - / -==>Note from ocean_lap_friction_init: general laplacian friction scheme for B-grid is used. - - - &OCEAN_LAPGEN_FRICTION_NML - USE_THIS_MODULE = T, - DEBUG_THIS_MODULE = F, - BOTTOM_5POINT = T, - K_SMAG_ISO = 0.000000000000000E+000, - K_SMAG_ANISO = 0.000000000000000E+000, - VEL_MICOM_ISO = 0.100000000000000 , - VEL_MICOM_ANISO = 0.000000000000000E+000, - EQ_VEL_MICOM_ISO = 0.000000000000000E+000, - EQ_VEL_MICOM_ANISO = 0.000000000000000E+000, - EQ_LAT_MICOM = 0.000000000000000E+000, - EQUATORIAL_ZONAL = F, - EQUATORIAL_ZONAL_LAT = 0.000000000000000E+000, - EQUATORIAL_NO_SMAG = F, - VISCOSITY_NCAR = F, - VISCOSITY_NCAR_2000 = T, - VISCOSITY_NCAR_2007 = F, - NCAR_ISOTROPIC_OFF_EQUATOR = F, - NCAR_ONLY_EQUATORIAL = F, - VCONST_1 = 10000000.0000000 , - VCONST_2 = 0.000000000000000E+000, - VCONST_3 = 0.160000000000000 , - VCONST_4 = 2.000000000000000E-008, - VCONST_5 = 3, - VCONST_6 = 10000000.0000000 , - VCONST_7 = 100.000000000000 , - VCONST_8 = 45.0000000000000 , - DEBUG_NCAR_A = F, - DEBUG_NCAR_B = F, - VISC_VEL_SCALE_LENGTH = 150000.000000000 , - NEPTUNE = F, - NEPTUNE_LENGTH_EQ = 1200.00000000000 , - NEPTUNE_LENGTH_POLE = 3000.00000000000 , - NEPTUNE_DEPTH_MIN = 100.000000000000 , - NEPTUNE_SMOOTH = T, - NEPTUNE_SMOOTH_NUM = 1, - RESTRICT_POLAR_VISC = T, - RESTRICT_POLAR_VISC_LAT = 60.0000000000000 , - RESTRICT_POLAR_VISC_RATIO = 0.350000000000000 , - NCAR_ISOTROPIC_AT_DEPTH = F, - NCAR_ISOTROPIC_DEPTH = 4000.00000000000 , - NCAR_ISOTROPIC_AT_DEPTH_VISC = 10000.0000000000 , - DIVERGENCE_DAMP = F, - DIVERGENCE_DAMP_VEL_MICOM = 0.000000000000000E+000, - VISCOSITY_SCALE_BY_ROSSBY = T, - VISCOSITY_SCALE_BY_ROSSBY_POWER = 4.00000000000000 , - ASYNC_DOMAIN_UPDATE = F, - BLOCKSIZE = 10, - USE_SIDE_DRAG_FRICTION = F, - SIDE_DRAG_FRICTION_SCALING = 1.00000000000000 , - SIDE_DRAG_FRICTION_UVMAG_MAX = 10.0000000000000 , - SIDE_DRAG_FRICTION_MAX = 1.00000000000000 - / -NOTE from PE 0: ==> NOTE: USING ocean_lapgen_friction_mod. -==>Note: not using asynchronous domain update in the vertical loop. This may be slow. - -==> Note from ocean_lapgen_friction_mod: using forward time step of (secs) 5400.00 - ==> Note: Scaling the laplacian viscosity according to grid scale and Rossby radius. - ==> Note: Will reduce horizontal friction to a 5point Laplacian on the bottom - This helps to alleviate numerical problems with thin bottom partial cells. - ==> NOTE: Setting horz isotropic Smagorinsky viscosity to zero. - ==> NOTE: Setting horz anisotropic Smagorinsky viscosity to zero. - ==> NOTE: NOT using NCAR scheme for computing viscosities. - ==> NOTE: USING background horz isotropic viscosity via MICOM. - ==> NOTE: USING zero background horz anisotropic viscosity. - - Using restrict_polar_visc to lower visc_crit poleward of (deg) 60.00000 - by an amount given by the fraction 0.35000 - This approach is useful when coupling to ice, where effective (ocn+ice) visc > ocn visc. - - - - &OCEAN_BIH_FRICTION_NML - BIH_FRICTION_SCHEME = general , - DEBUG_THIS_MODULE = F, - WRITE_A_RESTART = T - / -==>Note from ocean_bih_friction_init: general biharmonic friction scheme for B-grid is used. - - - &OCEAN_BIHGEN_FRICTION_NML - USE_THIS_MODULE = T, - DEBUG_THIS_MODULE = F, - K_SMAG_ISO = 2.00000000000000 , - K_SMAG_ANISO = 0.000000000000000E+000, - VEL_MICOM_ISO = 4.000000000000000E-002, - VEL_MICOM_ANISO = 0.000000000000000E+000, - EQ_VEL_MICOM_ISO = 0.000000000000000E+000, - EQ_VEL_MICOM_ANISO = 0.000000000000000E+000, - EQ_LAT_MICOM = 0.000000000000000E+000, - VEL_MICOM_BOTTOM = 1.000000000000000E-002, - BOTTOM_5POINT = T, - EQUATORIAL_ZONAL = F, - EQUATORIAL_ZONAL_LAT = 0.000000000000000E+000, - VISC_CRIT_SCALE = 0.250000000000000 , - READ_AISO_BIH_BACK = F, - NCAR_BOUNDARY_SCALING = T, - NCAR_RESCALE_POWER = 2, - NCAR_VCONST_4 = 2.000000000000000E-008, - NCAR_VCONST_5 = 5, - NCAR_BOUNDARY_SCALING_READ = F, - NEPTUNE = F, - NEPTUNE_LENGTH_EQ = 4200.00000000000 , - NEPTUNE_LENGTH_POLE = 17000.0000000000 , - NEPTUNE_DEPTH_MIN = 100.000000000000 , - NEPTUNE_SCALING = 1.00000000000000 , - NEPTUNE_SMOOTH = T, - NEPTUNE_SMOOTH_NUM = 1, - VISC_DIVERGE_SCALING = 0.000000000000000E+000, - USE_SIDE_DRAG_FRICTION = F, - SIDE_DRAG_FRICTION_SCALING = 1.00000000000000 , - SIDE_DRAG_FRICTION_UVMAG_MAX = 10.0000000000000 , - SIDE_DRAG_FRICTION_MAX = 1.00000000000000 - / -NOTE from PE 0: ==> NOTE: USING ocean_bihgen_friction_mod. - - -==> Note from ocean_bihgen_friction_mod: using forward time step of (secs) 5400.00 - - - - ==> NOTE: Will make horizontal friction to a 5point Laplacian on the bottom - This helps alleviate numerical problems with thin bottom partial cells. - Computing horziontal isotropic biharmonic viscosity via Smagorinsky. - Setting horzizontal anisotropic biharmonic Smagorinsky viscosity to zero. - Computing background horzizontal biharmonic isotropic viscosity via MICOM. - Setting background horziontal biharmonic anisotropic viscosity to zero. - Note: rescaling background bih viscosities so they are larger in western boundaries. -From ncar_boundary_scale, minimum ncar_rescale = 0.100000E+01 - - - &OCEAN_MOMENTUM_SOURCE_NML - VERBOSE_INIT = T, - USE_THIS_MODULE = T, - DEBUG_THIS_MODULE = F, - USE_RAYLEIGH_DAMP_TABLE = T, - RAYLEIGH_DAMP_EXP_FROM_BOTTOM = F, - RAYLEIGH_DAMP_EXP_SCALE = 100.000000000000 , - RAYLEIGH_DAMP_EXP_TIME = 864000.000000000 - / -==>Note from ocean_momentum_source_mod: USING this module -NOTE from PE 0: ==>Warning: ocean_momentum_source_init NO table for Rayleigh damp time. Nothing read. - - - &OCEAN_FORM_DRAG_NML - VERBOSE_INIT = T, - USE_THIS_MODULE = F, - DEBUG_THIS_MODULE = F, - USE_FORM_DRAG_AIKI = F, - CPRIME_AIKI = 0.300000000000000 , - FORM_DRAG_AIKI_BOTTOM_LAYER = F, - FORM_DRAG_AIKI_BOTTOM_KLEVELS = 3, - FORM_DRAG_AIKI_SCALE_BY_GRADH = F, - FORM_DRAG_AIKI_GRADH_MAX = 5.000000000000000E-002, - FORM_DRAG_AIKI_GRADH_POWER = 1.00000000000000 , - FORM_DRAG_AIKI_SCALE_BY_GM = F, - USE_FORM_DRAG_GBATCH = F, - VISC_CBU_FORM_DRAG_MAX = 1.00000000000000 , - VEL_FORM_DRAG_MAX = 1.00000000000000 , - N_SQUARED_MIN = 1.000000000000000E-010, - AGM_FORM_DRAG = 600.000000000000 , - FORM_DRAG_GBATCH_SURF_LAYER = F, - KSURF_BLAYER_MIN = 3, - FORM_DRAG_GBATCH_ALPHA_F2 = F, - FORM_DRAG_GBATCH_ALPHA = 300000000.000000 , - FORM_DRAG_GBATCH_F2OVERN2 = F, - FORM_DRAG_GBATCH_F2OVERNB2 = F, - FORM_DRAG_GBATCH_SMOOTH_N2 = F, - NUM_121_PASSES = 1, - FORM_DRAG_GBATCH_F2OVERNO2 = F, - FORM_DRAG_GBATCH_NO = 5.000000000000000E-003 - / -NOTE from PE 0: ==>Note from ocean_form_drag_mod: NOT USING this module - - - &OCEAN_TRACER_ADVECT_NML - DEBUG_THIS_MODULE = F, - LIMIT_WITH_UPWIND = F, - ADVECT_SWEBY_ALL = F, - ZERO_TRACER_ADVECT_HORZ = F, - ZERO_TRACER_ADVECT_VERT = F, - WRITE_A_RESTART = T, - PSOM_LIMIT_PRATHER = F, - READ_BASIN_MASK = F, - ASYNC_DOMAIN_UPDATE = F - / - - From ocean_tracer_advect_init: SUMMARY OF TRACER ADVECTION SCHEMES - temp is using multi-dim piecewise parabolic for horz/vert advection. - salt is using multi-dim piecewise parabolic for horz/vert advection. - age_global is using multi-dim piecewise parabolic for horz/vert advection. - - flux domain decomposition -whalo = 1, ehalo = 1, shalo = 1, nhalo = 1 - X-AXIS = 23 23 23 23 22 22 22 22 22 22 22 22 23 23 23 23 - Y-AXIS = 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 - fourth domain decomposition -whalo = 2, ehalo = 2, shalo = 2, nhalo = 2 - X-AXIS = 23 23 23 23 22 22 22 22 22 22 22 22 23 23 23 23 - Y-AXIS = 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 - sixth domain decomposition -whalo = 3, ehalo = 3, shalo = 3, nhalo = 3 - X-AXIS = 23 23 23 23 22 22 22 22 22 22 22 22 23 23 23 23 - Y-AXIS = 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 - quicker domain decomposition -whalo = 2, ehalo = 2, shalo = 2, nhalo = 2 - X-AXIS = 23 23 23 23 22 22 22 22 22 22 22 22 23 23 23 23 - Y-AXIS = 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 - mdfl domain decomposition -whalo = 2, ehalo = 2, shalo = 2, nhalo = 2 - X-AXIS = 23 23 23 23 22 22 22 22 22 22 22 22 23 23 23 23 - Y-AXIS = 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 - mdppm domain decomposition -whalo = 4, ehalo = 4, shalo = 4, nhalo = 4 - X-AXIS = 23 23 23 23 22 22 22 22 22 22 22 22 23 23 23 23 - Y-AXIS = 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 - mdmdt domain decomposition -whalo = 4, ehalo = 4, shalo = 4, nhalo = 4 - X-AXIS = 23 23 23 23 22 22 22 22 22 22 22 22 23 23 23 23 - Y-AXIS = 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 - - - &OCEAN_VELOCITY_ADVECT_NML - DEBUG_THIS_MODULE = F, - ZERO_VELOCITY_ADVECT_HORZ = F, - ZERO_VELOCITY_ADVECT_VERT = F, - VELOCITY_ADVECT_CENTERED = T, - VELOCITY_ADVECT_UPWIND = F - / - ==>Note: running MOM with traditional second order centred advection of linear - momentum. - - - &OCEAN_CONVECT_NML - USE_THIS_MODULE = F, - CONVECT_NCON = F, - NCON = 7, - CONVECT_FULL_SCALAR = F, - CONVECT_FULL_VECTOR = F - / -==>Note: NOT using convective adjustment in gravitationally unstable water columns. - - - &OCEAN_SBC_NML - TEMP_RESTORE_TSCALE = -10.0000000000000 , - SALT_RESTORE_TSCALE = 60.0000000000000 , - SALT_RESTORE_UNDER_ICE = T, - SALT_RESTORE_AS_SALT_FLUX = T, - ETA_RESTORE_TSCALE = -30.0000000000000 , - ZERO_NET_PME_ETA_RESTORE = F, - ROTATE_WINDS = F, - TAUX_SINX = F, - TAUY_SINY = F, - USE_WATERFLUX = T, - WATERFLUX_TAVG = F, - MAX_ICE_THICKNESS = 0.000000000000000E+000, - RUNOFFSPREAD = F, - CALVINGSPREAD = F, - USE_WATERFLUX_OVERRIDE_CALVING = F, - USE_WATERFLUX_OVERRIDE_EVAP = F, - USE_WATERFLUX_OVERRIDE_FPREC = F, - SALINITY_REF = 35.0000000000000 , - ZERO_NET_SALT_RESTORE = T, - ZERO_NET_WATER_RESTORE = T, - ZERO_NET_WATER_COUPLER = T, - ZERO_NET_WATER_COUPLE_RESTORE = T, - ZERO_NET_SALT_CORRECTION = F, - ZERO_NET_WATER_CORRECTION = F, - DEBUG_WATER_FLUXES = F, - ZERO_WATER_FLUXES = F, - ZERO_CALVING_FLUXES = F, - ZERO_PME_FLUXES = F, - ZERO_RUNOFF_FLUXES = F, - ZERO_RIVER_FLUXES = F, - CONVERT_RIVER_TO_PME = F, - ZERO_HEAT_FLUXES = F, - ZERO_SURFACE_STRESS = F, - AVG_SFC_VELOCITY = T, - AVG_SFC_TEMP_SALT_ETA = T, - ICE_SALT_CONCENTRATION = 5.000000000000000E-003, - OCEAN_ICE_SALT_LIMIT = 0.000000000000000E+000, - RUNOFF_SALINITY = 0.000000000000000E+000, - RUNOFF_TEMP_MIN = 0.000000000000000E+000, - READ_RESTORE_MASK = F, - RESTORE_MASK_GFDL = F, - LAND_MODEL_HEAT_FLUXES = F, - USE_FULL_PATM_FOR_SEA_LEVEL = F, - MAX_DELTA_SALINITY_RESTORE = 0.500000000000000 , - DO_FLUX_CORRECTION = F, - SALINITY_RESTORE_LIMIT_LOWER = 0.000000000000000E+000, - SALINITY_RESTORE_LIMIT_UPPER = 100.000000000000 , - TEMP_CORRECTION_SCALE = 0.000000000000000E+000, - SALT_CORRECTION_SCALE = 0.000000000000000E+000, - TAU_X_CORRECTION_SCALE = 0.000000000000000E+000, - TAU_Y_CORRECTION_SCALE = 0.000000000000000E+000, - DO_BITWISE_EXACT_SUM = T, - SBC_HEAT_FLUXES_CONST = F, - SBC_HEAT_FLUXES_CONST_VALUE = 0.000000000000000E+000, - SBC_HEAT_FLUXES_CONST_SEASONAL = F, - USE_CONSTANT_SSS_FOR_RESTORE = F, - CONSTANT_SSS_FOR_RESTORE = 35.0000000000000 , - USE_CONSTANT_SST_FOR_RESTORE = F, - CONSTANT_SST_FOR_RESTORE = 12.0000000000000 , - USE_IDEAL_CALVING = F, - USE_IDEAL_RUNOFF = F, - CONSTANT_HLF = T, - CONSTANT_HLV = T, - READ_STOKES_DRIFT = F, - DO_LANGMUIR = F - / - - - &OCEAN_SBC_OFAM_NML - RESTORE_MASK_OFAM = F, - RIVER_TEMP_OFAM = F - / - sbc domain decomposition -whalo = 0, ehalo = 0, shalo = 0, nhalo = 0 - X-AXIS = 23 23 23 23 22 22 22 22 22 22 22 22 23 23 23 23 - Y-AXIS = 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - ==>Note from ocean_sbc_mod: applying surface restoring to temp - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - -WARNING from PE 0: set_date_c: Year zero is invalid. Resetting year to 1 - - ==>Note from ocean_sbc_mod: applying surface restoring to salt - -==>Note from ocean_sbc_mod: if inputting river water, enable rivermix_mod to get river tracers into ocean. - - ==>Note from ocean_sbc_mod: temp_restore_tscale < 0. no surface restoring for t - emp - ==>Note from ocean_sbc_mod: salt_restore_under_ice=.true. => sss restore even u - nder ice. - ==>Note from ocean_sbc_mod: zero_net_water_restore=.true.=>zero net restoring w - ater put in ocean. - ==>Note from ocean_sbc_mod: zero_net_water_correction=.false.=>nonzero net corr - ection water put in ocean. - ==>Note from ocean_sbc_mod: zero_net_water_coupler=.true.=>zero water into ocea - n via coupler (sans the sea ice). - ==>ocean_sbc_mod: zero_net_water_couple_restore=.true.=>zero water into ocean f - rom restore + coupler (sans the sea ice). - ==>Note from ocean_sbc_mod: eta_restore_tscale < 0. no surface restoring for et - a - ==>If coupling, then avg_sfc_velocity=.true. means will pass averaged ocean vel - ocity to ice model. - ==>If coupling, then avg_sfc_temp_salt_eta=.true. means will pass averaged sst, - sss, eta to ice model. - ==>Note from ocean_sbc_mod: Using constant latent heat of fusion at ocean surfa - ce. - ==>Note from ocean_sbc_mod: Using constant latent heat of evaporation at ocean - surface. - ==>Note that diagnose_sea_level_forcing==.false., so no "eta_tend_" fields will - be diagnosed. - - - &OCEAN_BBC_NML - BMF_IMPLICIT = T, - CDBOT = 1.000000000000000E-003, - URESIDUAL = 5.000000000000000E-002, - CDBOT_LAW_OF_WALL = F, - LAW_OF_WALL_ROUGH_LENGTH = 1.000000000000000E-002, - CDBOT_ROUGHNESS_LENGTH = F, - USE_GEOTHERMAL_HEATING = F, - CONVERT_GEOTHERMAL = 1.000000000000000E-003, - CDBOT_HI = 7.000000000000000E-003, - CDBOT_LO = 1.000000000000000E-003, - CDBOT_GAMMA = 40.0000000000000 , - UVMAG_MAX = 10.0000000000000 , - BMF_MAX = 1.00000000000000 , - DEBUG_THIS_MODULE = F, - CDBOT_ROUGHNESS_UAMP = T, - CDBOT_HH = 1100.00000000000 , - CDBOT_UU = 1.00000000000000 , - CDBOT_WAVE = F - / - - - &OCEAN_BBC_OFAM_NML - READ_TIDE_SPEED = F, - URESIDUAL2_MAX = 5.000000000000000E-002 - / -==>Note: NOT reading tide_speed for ocean_vert_tidal_mod. -NOTE from PE 0: ==>ocean_vert_tidal_mod: Setting tide_speed to default value. -==>Note from ocean_bbc_mod: Computing bottom drag implicitly in time. - ==>ocean_bbc_mod: read in topographic roughness length, assumed to be on B-grid - velocity point. - ==>ocean_bbc_mod: completed read of tidal velocity amplitude, assumed to be on - B-grid velocity point. - - - &OCEAN_SHORTWAVE_NML - USE_THIS_MODULE = T, - USE_SHORTWAVE_GFDL = T, - USE_SHORTWAVE_CSIRO = F, - USE_SHORTWAVE_JERLOV = F, - USE_SHORTWAVE_EXT = F - / -NOTE from PE 0: ==>Note: USING shortwave_mod. - - - &OCEAN_SHORTWAVE_GFDL_NML - USE_THIS_MODULE = T, - READ_CHL = T, - CHL_DEFAULT = 8.000000000000000E-002, - ZMAX_PEN = 300.000000000000 , - SW_FRAC_TOP = 0.000000000000000E+000, - DEBUG_THIS_MODULE = F, - ENFORCE_SW_FRAC = T, - OVERRIDE_F_VIS = T, - SW_MOREL_FIXED_DEPTHS = F, - OPTICS_FOR_UNIFORM_CHL = F, - OPTICS_MOREL_ANTOINE = F, - OPTICS_MANIZZA = T - / -NOTE from PE 0: ==>Note: USING shortwave_gfdl_mod. -=>Note: Using shortwave penetration with GFDL formulaton & Manizza etal optics. -NOTE from PE 0: ==>Note: Reading in chlorophyll-a from data file for shortwave penetration. -=>Note: computing solar shortwave penetration. Assume stf has sw-radiation field - included. Hence, solar shortwave penetration effects placed in sw_source will - subtract out the effects of shortwave at k=1 to avoid double-counting. - ==>Note: Setting optical model coefficients assuming nonuniform chl distribution. - - - &OCEAN_SPONGES_TRACER_NML - USE_THIS_MODULE = F, - DAMP_COEFF_3D = F - / - - - &OCEAN_SPONGES_TRACER_OFAM_NML - USE_ADAPTIVE_RESTORE = F, - USE_SPONGE_AFTER_INIT = F, - USE_NORMALISING = F, - USE_HARD_THUMP = F, - ATHRESH = 0.500000000000000 , - TAUMIN = 720.000000000000 , - LAMBDA = 8.300000000000000E-003, - NPOWER = 1.00000000000000 , - DAYS_TO_RESTORE = 1, - SECS_TO_RESTORE = 0, - DEFLATE = F, - DEFLATE_FRACTION = 0.600000000000000 , - LIMIT_TEMP = F, - LIMIT_TEMP_MIN = -1.80000000000000 , - LIMIT_TEMP_RESTORE = 10800.0000000000 , - LIMIT_SALT = F, - LIMIT_SALT_MIN = 1.000000000000000E-002, - LIMIT_SALT_RESTORE = 3600.00000000000 - / - ==>Note from ocean_sponges_tracer_mod: NOT using ocean tracer sponges. - - - &OCEAN_SPONGES_VELOCITY_NML - USE_THIS_MODULE = F, - DAMP_COEFF_3D = F - / - - - &OCEAN_SPONGES_VELOCITY_OFAM_NML - USE_ADAPTIVE_RESTORE = F, - USE_SPONGE_AFTER_INIT = F, - USE_NORMALISING = F, - USE_HARD_THUMP = F, - ATHRESH = 0.500000000000000 , - TAUMIN = 720.000000000000 , - LAMBDA = 8.300000000000000E-003, - NPOWER = 1.00000000000000 , - DAYS_TO_RESTORE = 1, - SECS_TO_RESTORE = 0 - / - ==>Note from ocean_sponges_velocity_mod: NOT using this module: no velocity spo - nges. - - - &OCEAN_SPONGES_ETA_NML - USE_THIS_MODULE = F - / - - - &OCEAN_SPONGES_ETA_OFAM_NML - USE_ADAPTIVE_RESTORE = F, - USE_SPONGE_AFTER_INIT = F, - USE_NORMALISING = F, - USE_HARD_THUMP = F, - ATHRESH = 0.500000000000000 , - TAUMIN = 720.000000000000 , - LAMBDA = 8.300000000000000E-003, - NPOWER = 1.00000000000000 , - DAYS_TO_RESTORE = 1, - SECS_TO_RESTORE = 0 - / - ==>Note from ocean_sponges_eta_mod: NOT using this module. - - ==>Warning: ocean_xlandinsert_init found n < 1 for xland_insert table. Will NO - T use ocean_xlandinsert. - - - ==>Warning: ocean_riverspread_init: n<1 for riverspread table. Will NOT use tab - le for ocean_riverspread. - - - &OCEAN_RIVERSPREAD_NML - USE_THIS_MODULE = F, - DEBUG_THIS_MODULE = F, - RIVERSPREAD_DIFFUSION = F, - RIVERSPREAD_DIFFUSION_PASSES = 0, - VEL_MICOM_SMOOTH = 0.200000000000000 - / -NOTE from PE 0: ==>From ocean_riverspread_mod: NOT using riverspread module, yet there are n > 0 riverspread points. - - - &OCEAN_RIVERMIX_NML - USE_THIS_MODULE = T, - DEBUG_THIS_MODULE = F, - DEBUG_ALL_IN_TOP_CELL = F, - DEBUG_THIS_MODULE_HEAT = F, - RIVER_DIFFUSE_TEMP = T, - RIVER_DIFFUSE_SALT = T, - RIVER_DIFFUSION_THICKNESS = 0.000000000000000E+000, - RIVER_DIFFUSIVITY = 0.000000000000000E+000, - DISCHARGE_COMBINE_RUNOFF_CALVE = T, - RIVER_INSERTION_THICKNESS = 40.0000000000000 , - RUNOFF_INSERTION_THICKNESS = 0.000000000000000E+000, - CALVING_INSERTION_THICKNESS = 0.000000000000000E+000, - DO_BITWISE_EXACT_SUM = F - / -NOTE from PE 0: ==>From ocean_rivermix_mod: Using rivermix module to mix liquid and/or solid runoff into the ocean. -==>Note: discharging calving+runoff together. The alternative is to separately discharge. -==>Note: if using waterflux and rivers, then will - discharge river tracer over 4 grid points in vertical -NOTE from PE 0: ==>Note: resetting river_diffusion_thickness=dzt(1) for enhanced diff_cbt of temperature. -NOTE from PE 0: ==>Note: resetting river_diffusion_thickness=dzt(1) for enhanced diff_cbt of salt and passive - - - &OCEAN_OVEREXCHANGE_NML - USE_THIS_MODULE = F, - DEBUG_THIS_MODULE = F, - OVEREXCH_NPTS = 4, - OVEREXCH_WIDTH = 1, - OVEREXCH_WEIGHT_FAR = F, - OVERFLOW_MU = 1.000000000000000E-004, - OVERFLOW_DELTA = 0.333300000000000 , - OVERFLOW_UMAX = 5.00000000000000 , - DO_BITWISE_EXACT_SUM = F, - OVEREXCH_STABILITY = 0.250000000000000 , - OVEREXCH_MIN_THICKNESS = 4.00000000000000 , - OVEREXCH_CHECK_EXTREMA = F - / -NOTE from PE 0: ==>From ocean_overexchange_mod: NOT using overflow exchange scheme. - - - &OCEAN_MIXDOWNSLOPE_NML - USE_THIS_MODULE = T, - DEBUG_THIS_MODULE = F, - MIXDOWNSLOPE_NPTS = 4, - MIXDOWNSLOPE_WIDTH = 1, - MIXDOWNSLOPE_WEIGHT_FAR = F, - MIXDOWNSLOPE_FRAC_CENTRAL = 0.250000000000000 , - DO_BITWISE_EXACT_SUM = F, - READ_MIXDOWNSLOPE_MASK = F, - MIXDOWNSLOPE_MASK_GFDL = F - / -NOTE from PE 0: ==>From ocean_mixdownslope_mod: USING downslope mixing scheme. - In ocean_mixdownslope_mod: mixdownslope_npts = 4 - Be sure this number is smaller than dimensions of computational domain. - mixdownslope domain decomposition -whalo = 4, ehalo = 4, shalo = 4, nhalo = 4 - X-AXIS = 23 23 23 23 22 22 22 22 22 22 22 22 23 23 23 23 - Y-AXIS = 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 - - - &OCEAN_OVERFLOW_NML - USE_THIS_MODULE = F, - DEBUG_THIS_MODULE = F, - OVERFLOW_MU = 1.000000000000000E-004, - OVERFLOW_DELTA = 0.333300000000000 , - OVERFLOW_UMAX = 1.000000000000000E-002, - DO_BITWISE_EXACT_SUM = F, - NO_RETURN_FLOW = F, - TRANSPORT_UNITS = Sv - / -NOTE from PE 0: ==>From ocean_overflow_mod: NOT using Campin and Goosse overflow scheme. - -==>Warning: ocean_overflow_OFP_init found n_src < 1 for overflow_OFP table. Will NOT use ocean_overflow_OFP. - - - ==>Note from fm_util_mod(fm_util_start_namelist)[ocean_age_tracer_mod(ocean_age - _tracer_start)]: Processing namelist ocean_age_tracer/global - ==>Note from ocean_age_tracer_mod(ocean_age_tracer_start): Assigning month - 1 - - ==>Note from ocean_age_tracer_mod(set_array): age_global region: 1 - ==>Note from ocean_age_tracer_mod(ocean_age_tracer_start): Duplicating month - 1 as 2 - ==>Note from ocean_age_tracer_mod(ocean_age_tracer_start): Duplicating month - 1 as 3 - ==>Note from ocean_age_tracer_mod(ocean_age_tracer_start): Duplicating month - 1 as 4 - ==>Note from ocean_age_tracer_mod(ocean_age_tracer_start): Duplicating month - 1 as 5 - ==>Note from ocean_age_tracer_mod(ocean_age_tracer_start): Duplicating month - 1 as 6 - ==>Note from ocean_age_tracer_mod(ocean_age_tracer_start): Duplicating month - 1 as 7 - ==>Note from ocean_age_tracer_mod(ocean_age_tracer_start): Duplicating month - 1 as 8 - ==>Note from ocean_age_tracer_mod(ocean_age_tracer_start): Duplicating month - 1 as 9 - ==>Note from ocean_age_tracer_mod(ocean_age_tracer_start): Duplicating month - 1 as 10 - ==>Note from ocean_age_tracer_mod(ocean_age_tracer_start): Duplicating month - 1 as 11 - ==>Note from ocean_age_tracer_mod(ocean_age_tracer_start): Duplicating month - 1 as 12 - - - &OCEAN_ADV_VEL_DIAG_NML - MAX_CFL_VALUE = 100.000000000000 , - LARGE_CFL_VALUE = 10.0000000000000 , - VERBOSE_CFL = T, - DIAG_STEP = 4320 - / - - -==>Maximum T-->U remapping error = 6.193E-07 m/s at (i,j) = ( 345, 273), (lon,lat) = ( 68.16, 68.66) -==>Note: T-->U remapping error will be small (i.e., order 1e-20) only for spherical grids. - - - &OCEAN_TRACER_DIAG_NML - TRACER_CONSERVE_DAYS = 30.0000000000000 , - DIAG_STEP = 4320, - PSU2PPT = 1.00486700000000 , - DEBUG_DIAGNOSE_MIXINGA = F, - DEBUG_DIAGNOSE_MIXINGB = F, - DEBUG_DIAGNOSE_MIXINGC = F, - DEBUG_DIAGNOSE_MIXINGD = F, - SMOOTH_KAPPA_SORT = 0, - RHO_GRAD_MIN = 1.000000000000000E-005, - RHO_GRAD_MAX = 1.000000000000000E+028, - BUOYANCY_CRIT = 3.000000000000000E-004, - DO_BITWISE_EXACT_SUM = F, - FRAZIL_FACTOR = 1.00000000000000 , - SMOOTH_MLD = F, - SMOOTH_MLD_FOR_SUBDUCTION = T, - DTHETA_CRIT = 2.00000000000000 - / - -Note: tracer and mass/volume conservation tests based on time_tendency==twolevel. - - Note: Set frazil_factor = 1.00 for computation of heat diagnostics. - Be sure this agrees with the value set in nml for ocean_frazil_mod - - - &OCEAN_VELOCITY_DIAG_NML - DIAG_STEP = 4320, - ENERGY_DIAG_STEP = 4320, - DO_BITWISE_EXACT_SUM = F, - DEBUG_THIS_MODULE = F, - MAX_CFL_VALUE = 100.000000000000 , - LARGE_CFL_VALUE = 10.0000000000000 , - VERBOSE_CFL = F, - LAND_CELL_NUM_MAX = 100 - / - - - &OCEAN_INCREMENT_ETA_NML - USE_THIS_MODULE = F, - FRACTION_INCREMENT = 1.00000000000000 , - DAYS_TO_INCREMENT = 1, - SECS_TO_INCREMENT = 0 - / - - - &OCEAN_INCREMENT_TRACER_NML - USE_THIS_MODULE = F, - FRACTION_INCREMENT = 1.00000000000000 , - DAYS_TO_INCREMENT = 1, - SECS_TO_INCREMENT = 0 - / - - - &OCEAN_INCREMENT_VELOCITY_NML - USE_THIS_MODULE = F, - FRACTION_INCREMENT = 1.00000000000000 , - DAYS_TO_INCREMENT = 1, - SECS_TO_INCREMENT = 0 - / - - - &OCEAN_WAVE_NML - WAVEDAMP = -10.0000000000000 , - DAMP_WHERE_ICE = T, - WRITE_A_RESTART = T, - DEBUG_THIS_MODULE = F, - USE_TMA = T, - FILTER_WAVE_MOM = T, - USE_THIS_MODULE = F - / -==>Note: Not using the idealized ocean surface wave module. - auscom_ice_nml= - - - &AUSCOM_ICE_NML - DT_CPL = 0, - TLTHK0 = 10.0000000000000 , - POP_ICEDIAG = T, - DO_ICE_ONCE = F, - KMXICE = 5, - FIXMELTT = F, - TMELT = -0.216000000000000 , - LIMIT_SRFSTRESS = F, - MSTRESS = 2.00000000000000 , - USE_IOAICE = T, - AICE_CUTOFF = 0.150000000000000 , - ICEMLT_FACTOR = 1.00000000000000 , - FRAZIL_FACTOR = 1.00000000000000 , - ICEFORM_ADJ_SALT = F, - SIGN_STFLX = 1.00000000000000 , - REDSEA_GULFBAY_SFIX = T, - IRS1 = 314, - IRE1 = 324, - JRS1 = 169, - JRE1 = 196, - IRS2 = 325, - IRE2 = 331, - JRS2 = 169, - JRE2 = 180, - IGS = 328, - IGE = 345, - JGS = 189, - JGE = 198, - KSMAX = 5, - SFIX_HOURS = 12, - CHK_I2O_FIELDS = F, - CHK_O2I_FIELDS = F, - CHK_FIELDS_PERIOD = 1, - CHK_FIELDS_START_TIME = 0 - / - - - &OCEAN_DRIFTERS_NML - USE_THIS_MODULE = F, - OUTPUT_INTERVAL = 1 - / - - ======== COMPLETED MOM INITIALIZATION ======== - - - - &MOM_OASIS3_INTERFACE_NML - NUM_FIELDS_IN = 15, - NUM_FIELDS_OUT = 7, - FIELDS_IN = u_flux v_flux lprec fprec salt_flxmh_flux sw_flux q_flux t_flux lw_flux runof p aice wfimelt wfiform , - FIELDS_OUT = t_surf s_surf u_surf v_surf dssldx dssldy frazil , - SEND_BEFORE_OCEAN_UPDATE = F, - SEND_AFTER_OCEAN_UPDATE = T - / -Calling redsea_gulfbay_hmix_s at runtime = day=714779, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714780, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714780, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714781, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714781, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714782, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714782, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714783, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714783, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714784, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714784, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714785, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714785, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714786, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714786, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714787, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714787, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714788, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714788, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714789, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714789, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714790, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714790, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714791, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714791, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714792, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714792, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714793, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714793, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714794, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714794, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714795, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714795, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714796, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714796, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714797, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714797, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714798, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714798, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714799, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714799, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714800, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714800, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714801, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714801, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714802, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714802, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714803, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714803, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714804, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714804, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714805, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714805, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714806, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714806, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714807, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714807, sec=43200, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714808, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714808, sec=43200, ticks=0 - - Measures of global integrated mass conservation over multiple time steps - - Ocean mass at timestep 3 = 1.33676815379281268E+21 kg. - Ocean mass at timestep 481 = 1.33676491019993770E+21 kg. - Change in ocean mass over time interval = -3.24359287498342400E+15 kg. - Mass input via all contributions over time interval = -3.24359287513339200E+15 kg. - Error in mass content change = 1.49968000000000000E+05 kg. - Error in rate of mass content change = 5.79788138869558461E-02 kg/s. - Mass input via P-E fluxes over time interval = -5.85100971934503000E+15 kg. - Mass input via runoff fluxes over time interval = 2.60741684421163800E+15 kg. - Mass input via ice calving fluxes over time interval = 0.00000000000000000E+00 kg. - Mass input via source fluxes over time interval = -8.20312500000000000E-02 kg. - Mass input via eta_t smoother over time interval = -8.20312500000000000E-02 kg. - Mass input via pbot_t smoother over time interval = 0.00000000000000000E+00 kg. - - - - Measures of global integrated tracer conservation over multiple time steps - - Ocean heat content at timestep 5 = 1.95242966309123083E+25 J. - Ocean heat content at timestep 481 = 1.95266912440977739E+25 J. - Change in ocean heat content = 2.39461318546560542E+21 J. - Total Heat input = 2.39461318550485677E+21 J. - Error in heat content change = -3.92731678720000000E+10 J. - Error in rate of heat content change = -4.19920313666368897E-11 W/m^2. - Heat input by tendency terms = 2.18224640000000000E+07 J. - Heat input by surface fluxes = 2.45936886864850557E+21 J. - Heat input by bottom fluxes = 0.00000000000000000E+00 J. - Heat input by runoff and calving = 1.86972289079574430E+20 J. - Heat input by precip-evap+calving = -3.93756816636247212E+20 J. - Heat input by open boundaries = 0.00000000000000000E+00 J. - Heat input by frazil formation = 1.42028844413024223E+20 J. - Heat input by eta_t smoother = 1.02400000000000000E+03 J. - Heat input by pbot_t smoother = 0.00000000000000000E+00 J. - Heat input by sources = 0.00000000000000000E+00 J. - - - Total salt mass at timestep 5 = 4.64166200943928525E+19 kg - Total salt mass at timestep 481 = 4.64166045261220168E+19 kg - salt change in ocean tracer mass = -1.55682708357120000E+13 kg. - salt error in mass change = -7.83671716308593750E+04 kg. - salt error in rate of mass change = -8.37924951703183937E-17 kg/(m^2 sec). - salt input by tendency terms = 3.56247558593750000E+01 kg. - salt input by surface fluxes = -1.55682707573804531E+13 kg. - salt input by bottom fluxes = 0.00000000000000000E+00 kg*yr. - salt input by runoff and calving = 0.00000000000000000E+00 kg. - salt input by precip-evap+calving = 0.00000000000000000E+00 kg. - salt input by open boundaries = 0.00000000000000000E+00 kg*yr. - salt input by eta_t smoother = 2.44140625000000000E-04 kg. - salt input by pbot_t smoother = 0.00000000000000000E+00 kg. - salt input by sources = 0.00000000000000000E+00 kg. - - - Mass weighted age_global at timestep 5 = 9.11785741025097728E+17 yr*kg. - Mass weighted age_global at timestep 481 = 1.08134542781580149E+20 yr*kg. - age_global total tracer input = 0.00000000000000000E+00 kg*yr. - age_global change in ocean tracer = 1.07222757040555049E+20 kg*yr. - age_global error in tracer change = -1.58156755042079565E+18 kg*yr. - age_global error in rate of tracer change = -5.33657556215036093E+04 kg/(m^2). - age_global input by tendency terms = 2.54500000000000000E+02 kg*yr. - age_global input by surface fluxes = 0.00000000000000000E+00 kg*yr. - age_global input by bottom fluxes = 0.00000000000000000E+00 kg*yr. - age_global input by runoff and calving = 0.00000000000000000E+00 kg*yr. - age_global input by precip-evap+calving = 0.00000000000000000E+00 kg*yr. - age_global input by open boundaries = 0.00000000000000000E+00 kg*yr. - age_global input by eta_t smoother = 0.00000000000000000E+00 kg*yr. - age_global input by pbot_t smoother = 0.00000000000000000E+00 kg*yr. - age_global input by sources = 1.08804324590975844E+20 kg*yr. - - -Calling redsea_gulfbay_hmix_s at runtime = day=714809, sec=0, ticks=0 -Calling redsea_gulfbay_hmix_s at runtime = day=714809, sec=43200, ticks=0 -NOTE from PE 0: MPP_IO_SET_STACK_SIZE: stack size set to 460000. -ncfile created: ./RESTART/i2o.nc -ncfile created: ./RESTART/u_star.nc -ncfile created: ./RESTART/sicemass.nc - - Ending temp chksum (taup1) ==> - - === Prognostic tracer checksum follows === -yyyy/mm/dd hh:mm:ss = 1958/ 2/ 1 0: 0: 0 -[chksum] temp -3183530328807172388 - - Ending salt chksum (taup1) ==> - - === Prognostic tracer checksum follows === -yyyy/mm/dd hh:mm:ss = 1958/ 2/ 1 0: 0: 0 -[chksum] salt 206690554319245094 - - Ending age_global chksum (taup1) ==> - - === Prognostic tracer checksum follows === -yyyy/mm/dd hh:mm:ss = 1958/ 2/ 1 0: 0: 0 -[chksum] age_global 2820061744191982756 - - Ending pot_temp chksum (diag) ==> - === Diagnostic tracer checksum follows === -yyyy/mm/dd hh:mm:ss = 1958/ 2/ 1 0: 0: 0 -[chksum] pot_temp -3183530328807172388 - - Ending frazil chksum (diag) ==> - === Diagnostic tracer checksum follows === -yyyy/mm/dd hh:mm:ss = 1958/ 2/ 1 0: 0: 0 -[chksum] frazil -7986380476917095175 - - From ocean_nphysics_coeff_end: ending chksum -yyyy/mm/dd hh:mm:ss = 1958/ 2/ 1 0: 0: 0 -[chksum] ending agm_array -8973751053372335397 -[chksum] ending aredi_array 5750674511687057408 -[chksum] ending rossby_radius -7164048181657234024 -[chksum] ending rossby_radius_raw 1327457237419365802 -[chksum] ending bczone_radius 0 - - From ocean_bih_friction_end: ending chksum -yyyy/mm/dd hh:mm:ss = 1958/ 2/ 1 0: 0: 0 -[chksum] ending bih_viscosity 3541845222697369559 - - From ocean_lap_friction_end: ending chksum -yyyy/mm/dd hh:mm:ss = 1958/ 2/ 1 0: 0: 0 -[chksum] ending lap_viscosity -301673372938235689 - - From ocean_sigma_transport_mod: ending chksums -yyyy/mm/dd hh:mm:ss = 1958/ 2/ 1 0: 0: 0 -[chksum] thickness_sigma -3820825464576938343 - - From ocean_velocity_mod: ending velocity chksum (taup1) -yyyy/mm/dd hh:mm:ss = 1958/ 2/ 1 0: 0: 0 -[chksum] Zonal velocity 1321889326463449823 -[chksum] Meridional velocity -5835184631554246284 -[chksum] Advection of u 1195690246526377945 -[chksum] Advection of v 8969763010873815707 - - From ocean_barotropic_mod: ending external mode chksums at taup1 -yyyy/mm/dd hh:mm:ss = 1958/ 2/ 1 0: 0: 0 -[chksum] eta_t 4857708699418422289 -[chksum] eta_u 8655837835768958702 -[chksum] deta_dt -6212670054107794935 -[chksum] eta_t_bar 6366444128993900877 -[chksum] pbot_t 1864800495331160117 -[chksum] pbot_u 303235720646413269 -[chksum] dpbot_dt 0 -[chksum] anompb 8531110392261285808 -[chksum] anompb_bar 0 -[chksum] patm_t 0 -[chksum] dpatm_dt 0 -[chksum] ps 4468612462988351412 -[chksum] grad_ps_1 -5850972680894501826 -[chksum] grad_ps_2 -5380922113359656765 -[chksum] grad_anompb_1 0 -[chksum] grad_anompb_2 0 -[chksum] udrho 3483489204195515439 -[chksum] vdrho 1977310147475603108 -[chksum] conv_rho_ud_t -1938749458618683085 -[chksum] source -418899887253057413 -[chksum] eta smoother -418899887253057413 -[chksum] pbot smoother 0 -[chksum] eta_nonbouss 0 -[chksum] forcing_u_bt 717301033293885065 -[chksum] forcing_v_bt -1235870472042373958 - -NOTE from PE 0: MPP_IO_SET_STACK_SIZE: stack size set to 469200. - - From ocean_thickness_mod: ending thickness checksums -yyyy/mm/dd hh:mm:ss = 1958/ 2/ 1 0: 0: 0 -[chksum] Thickness%rho_dzt(taup1) -4155940868267428967 -[chksum] Thickness%rho_dzu(taup1) -4133981278626211550 -[chksum] Thickness%mass_u(taup1) -5717648169720418324 -[chksum] Thickness%rho_dzten(1) -8103951316005837080 -[chksum] Thickness%rho_dzten(2) 409854374194440318 -[chksum] Thickness%rho_dztr 5308024911407704459 -[chksum] Thickness%rho_dzur 4881921568973908437 -[chksum] Thickness%rho_dzt_tendency 3807471274078534953 -[chksum] Thickness%dzt 2375569219308240423 -[chksum] Thickness%dzten(1) -1665361874464443321 -[chksum] Thickness%dzten(2) 6856899001712891418 -[chksum] Thickness%dztlo -2252209241090902823 -[chksum] Thickness%dztup -1530861264264664170 -[chksum] Thickness%dzt_dst 6962520251875338463 -[chksum] Thickness%dzwt(k=0) -8493920962437021780 -[chksum] Thickness%dzwt(k=1:nk) 3089037001948993168 -[chksum] Thickness%dzu 3223998138490668617 -[chksum] Thickness%dzwu(k=0) -5345896440794349391 -[chksum] Thickness%dzwu(k=1:nk) 337107744539578004 -[chksum] Thickness%depth_zt -8989684488027558039 -[chksum] Thickness%geodepth_zt -1466761746316463974 -[chksum] Thickness%depth_zu -4492083038352603458 -[chksum] Thickness%depth_zwt 5215192073834473427 -[chksum] Thickness%depth_zwu -4020989517810571922 -[chksum] Thickness%depth_st -4834016369135903867 -[chksum] Thickness%depth_swt -9093707932936552941 -[chksum] Thickness%dst 6091998697816536916 -[chksum] Thickness%dstlo 1465298839938063736 -[chksum] Thickness%dstup 2173538149074176928 -[chksum] Thickness%dswt(k=0) -8226950619299053568 -[chksum] Thickness%dswt(k=1:nk) 6806721948687210320 -[chksum] Thickness%pbot0 2212446957003815029 -[chksum] Thickness%mass_en(1) -958330410152086765 -[chksum] Thickness%mass_en(2) -533216736455708813 - - - From ocean_density_mod: ending density chksums -yyyy/mm/dd hh:mm:ss = 1958/ 2/ 1 0: 0: 0 -[chksum] rho(taup1) 5987303377033043445 -[chksum] pressure_at_depth 8860816320348643689 -[chksum] denominator_r -5994811966352042937 -[chksum] drhodT 301826773750226286 -[chksum] drhodS -8203044217574076684 -[chksum] drhodz_zt 8835515186958422913 - - - ==================Summary of completed MOM integration======================= - - Some of the basic physical parameters used in the simulation - Reference density for the Boussinesq approximation (kg/m^3) = 0.1035000000E+04 - Gravitational acceleration (m/s^2) = 0.9800000000E+01 - Rotational rate of the earth (radians/sec) = 0.7292100000E-04 - Specific heat capacity of seawater J/(kg*degC) = 0.3992103223E+04 - Specific heat capacity of liquid runoff J/(kg*degC) = 0.4218000000E+04 - Specific heat capacity of solid runoff J/(kg*degC) = 0.4218000000E+04 - Von Karman dimensionless constant for turbulent mixing = 0.4000000000E+00 - - Finished MOM integration using ZSTAR as the vertical coordinate. - B-grid was used for the horizontal layout of discrete variables. - number of time steps = 496 - number of prog-tracers = 3 - number of diag-tracers = 3 - number of i-points(ni) = 360 - number of j-points(nj) = 300 - number of k-points(nk) = 50 - number of computed ocean tracer points(ni*nj*nk) = 5400000 - number of wet ocean tracer points = 2665454 - number of wet ocean velocity points = 2525142 - slow motion time tendency computed using = twolevel - barotropic motion computed using = barotropic_pred_corr - tracer time step dtts (secs) = 5400.000000 - baroclinic velocity time step dtuv (secs) = 5400.000000 - barotropic time step dtbt (secs) = 67.500000 - implicit Coriolis parameter acor = 0.500000 - implicit vertical mixing parameter aidif = 1.000000 - - Did NOT use any open/radiating boundary conditions. - Did NOT use Lagrangian blobs. - Did NOT use velocity override - Computed Coriolis force on Bgrid using semi-implicit time stepping. - Time stepped the baroclinic velocity. - Time stepped the barotropic fields. - Time stepped the prognostic tracer fields. - preTEOS10 equation of state used for density. - Prognostic temperature variable is conservative temperature. - Frazil sea ice anywhere in ocean column with an accurate freezing temp equation. - KPP_mom4p1 used for vertical diffusivities & viscosity & barotropic tide drag. - Did NOT use convective adjustment. - Used tidal wave mixing option for vertical mixing. - Used tidal drag mixing option for vertical mixing. - Did NOT use Bryan-Lewis background vertical diffusivity. - Did NOT use HWF background vertical diffusivity. - Did NOT use tanh background vertical diffusivity. - Did NOT use j09 background vertical diffusivity. - Did NOT use horizontal biharmonic tracer mixing. - Did NOT use horizontal laplacian tracer mixing. - Used general horizontal Laplacian friction. - Used general horizontal biharmonic friction. - Used momentum sources. - Did NOT use parameterized form drag. - Used bottom drag from map of bottom roughness w/ tidal amplitude from law of wall. - Used bottom drag computed implicitly in time. - Did NOT introduce geothermal heating. - Used neutral physics with nphysicsC algorithm. - Did NOT use neutral physics new option. - Used submesoscale closure for surface restratification. - Used ocean sigma transport option. - Did NOT use Campin and Goosse overflow scheme. - Did NOT use overflow exchange scheme. - Used the downslope mixing scheme. This scheme is experimental! - Used GFDL shortwave penetration module with Manizza etal optics. - Did NOT use xlandmix. - Did NOT use xlandinsert. - Used rivermix module to mix liquid and/or solid runoff into ocean. - Did NOT use riverspread module. - Did NOT use the idealized passive tracer module. - Did NOT use ocean eta sponges. - Did NOT use ocean tracer sponges. - Did NOT use ocean velocity sponges. - Did NOT include CMIP6/FAFMIP prognostic temperature tracers. - ==================================================== - - -WARNING from PE 0: diag_util_mod::opening_file: one axis has auxiliary but the corresponding field is NOT found in file ocean_month - -NOTE from PE 0: Potential error in diag_manager_end: temp NOT available, check if output interval > runlength. Netcdf fill_values are written - -WARNING from PE 0: diag_util_mod::opening_file: one axis has auxiliary but the corresponding field is NOT found in file ocean - -NOTE from PE 0: Potential error in diag_manager_end: salt NOT available, check if output interval > runlength. Netcdf fill_values are written -NOTE from PE 0: Potential error in diag_manager_end: age_global NOT available, check if output interval > runlength. Netcdf fill_values are written -NOTE from PE 0: Potential error in diag_manager_end: u NOT available, check if output interval > runlength. Netcdf fill_values are written -NOTE from PE 0: Potential error in diag_manager_end: v NOT available, check if output interval > runlength. Netcdf fill_values are written -NOTE from PE 0: Potential error in diag_manager_end: wt NOT available, check if output interval > runlength. Netcdf fill_values are written -NOTE from PE 0: Potential error in diag_manager_end: dzt NOT available, check if output interval > runlength. Netcdf fill_values are written -NOTE from PE 0: Potential error in diag_manager_end: pot_rho_0 NOT available, check if output interval > runlength. Netcdf fill_values are written -NOTE from PE 0: Potential error in diag_manager_end: pot_rho_2 NOT available, check if output interval > runlength. Netcdf fill_values are written -NOTE from PE 0: Potential error in diag_manager_end: tx_trans NOT available, check if output interval > runlength. Netcdf fill_values are written -NOTE from PE 0: Potential error in diag_manager_end: ty_trans NOT available, check if output interval > runlength. Netcdf fill_values are written -NOTE from PE 0: Potential error in diag_manager_end: tx_trans_rho NOT available, check if output interval > runlength. Netcdf fill_values are written -NOTE from PE 0: MPP_IO_SET_STACK_SIZE: stack size set to 736000. -NOTE from PE 0: Potential error in diag_manager_end: ty_trans_rho NOT available, check if output interval > runlength. Netcdf fill_values are written -NOTE from PE 0: Potential error in diag_manager_end: ty_trans_rho_gm NOT available, check if output interval > runlength. Netcdf fill_values are written -NOTE from PE 0: Potential error in diag_manager_end: temp_xflux_adv NOT available, check if output interval > runlength. Netcdf fill_values are written -NOTE from PE 0: Potential error in diag_manager_end: temp_yflux_adv NOT available, check if output interval > runlength. Netcdf fill_values are written -NOTE from PE 0: Potential error in diag_manager_end: diff_cbt_t NOT available, check if output interval > runlength. Netcdf fill_values are written - ==================*** CICE END ***================= - MPP_DOMAINS_STACK high water mark= 204000 - -Tabulating mpp_clock statistics across 216 PEs... - - tmin tmax tavg tstd tfrac grain pemin pemax -Total runtime 142.689603 142.784137 142.749632 0.020336 1.000 0 0 215 -Ocean 130.342512 132.152756 131.210041 0.398672 0.919 1 0 215 -(Ocean initialization) 2.396334 2.471536 2.434071 0.012135 0.017 11 0 215 -(Ocean ODA) 0.000000 0.000000 0.000000 0.000000 0.000 11 0 215 -(Red Sea/Gulf Bay salinity fix) 37.231897 38.170001 37.926866 0.135359 0.266 31 0 215 -(Ocean advection velocity) 0.807360 1.041410 0.991945 0.031444 0.007 31 0 215 -(Ocean density diag) 0.921795 1.378618 1.077855 0.069977 0.008 31 0 215 -(Ocean update density) 2.070706 2.289089 2.182898 0.043149 0.015 31 0 215 -(Ocean vertical mixing coeff) 5.832384 7.398728 6.520763 0.316352 0.046 31 0 215 -(Ocean neutral physics) 19.132585 21.202745 20.536739 0.525134 0.144 31 0 215 -(Ocean submesoscale restrat) 5.333097 7.485177 6.016325 0.542592 0.042 31 0 215 -(Ocean shortwave) 0.494374 1.562988 1.122916 0.291203 0.008 31 0 215 -(Ocean sponges_eta) 0.000208 0.000788 0.000355 0.000048 0.000 31 0 215 -(Ocean sponges_tracer) 0.000171 0.000515 0.000298 0.000047 0.000 31 0 215 -(Ocean sponges_velocity) 0.000173 0.000440 0.000264 0.000050 0.000 31 0 215 -(Ocean xlandinsert) 0.000224 0.000709 0.000368 0.000057 0.000 31 0 215 -(Ocean xlandmix) 0.000199 0.000674 0.000401 0.000067 0.000 31 0 215 -(Ocean rivermix) 0.114657 0.392733 0.242654 0.052286 0.002 31 0 215 -(Ocean overexchange) 0.000389 0.001373 0.000793 0.000176 0.000 31 0 215 -(Ocean mixdownslope) 1.851516 3.410632 2.544446 0.323035 0.018 31 0 215 -(Ocean blob update) 0.000109 0.000434 0.000191 0.000048 0.000 31 0 215 -(Ocean blob cell update) 0.000000 0.000000 0.000000 0.000000 0.000 31 0 215 -(Ocean blob diagnose depth) 0.000104 0.000258 0.000161 0.000023 0.000 31 0 215 -(Ocean overflow) 0.000926 0.023035 0.002142 0.001669 0.000 31 0 215 -(Ocean overflow_OFP) 0.000344 0.001542 0.000809 0.000192 0.000 31 0 215 -(Ocean sigma transport) 0.802811 1.063952 0.888854 0.044977 0.006 31 0 215 -(Ocean tracer update) 9.998589 11.694307 11.079323 0.356479 0.078 31 0 215 -(Ocean surface flux) 8.759183 10.557796 9.343038 0.426260 0.065 31 0 215 -(Ocean bottom flux) 0.025660 0.046540 0.033628 0.003489 0.000 31 0 215 -(Ocean restoring flux) 3.591129 3.864777 3.693970 0.073569 0.026 31 0 215 -(Ocean TPM source) 0.019807 0.056572 0.033323 0.006836 0.000 31 0 215 -(Ocean TPM bbc) 0.000024 0.000106 0.000048 0.000014 0.000 31 0 215 -(Ocean TPM tracer) 0.003212 0.005170 0.003842 0.000488 0.000 31 0 215 -(Ocean explicit accel_a) 10.058658 10.521820 10.331040 0.139445 0.072 31 0 215 -(Ocean explicit accel_b) 0.168504 0.264012 0.240476 0.010650 0.002 31 0 215 -(Ocean implicit accel) 0.735338 1.245058 1.191489 0.039707 0.008 31 0 215 -(Ocean eta and pbot tendency) 0.002597 0.008715 0.006833 0.000699 0.000 31 0 215 -(Ocean eta and pbot update) 0.034025 0.380287 0.057827 0.030641 0.000 31 0 215 -(Ocean eta and pbot diagnose) 0.250136 2.227039 0.972497 0.419920 0.007 31 0 215 -(Ocean rho_dzt tendency) 0.038226 0.153594 0.144706 0.008863 0.001 31 0 215 -(Ocean dzt_dst update) 0.000000 0.000000 0.000000 0.000000 0.000 31 0 215 -(Ocean surface height smooth) 0.282796 0.724218 0.481428 0.131026 0.003 31 0 215 -(Ocean bottom pressure smooth) 0.000000 0.000000 0.000000 0.000000 0.000 31 0 215 -(Ocean mass forcing) 0.018524 0.050757 0.042404 0.003767 0.000 31 0 215 -(Ocean barotropic forcing) 0.092822 0.404142 0.169704 0.060832 0.001 31 0 215 -(Ocean barotropic dynamics) 3.901889 4.227397 4.026577 0.107871 0.028 31 0 215 -(Ocean velocity update) 0.531337 0.770893 0.702370 0.038088 0.005 31 0 215 -(Ocean diagnostics) 4.993313 6.048906 5.175729 0.102308 0.036 31 0 215 -(Ocean update T-cell thickness) 0.425098 0.759697 0.688768 0.044740 0.005 31 0 215 -(Ocean update Total thickness) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean update L sys. thickness) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean update E sys. thickness) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean update U-cell thickness) 1.053335 1.254295 1.205509 0.032533 0.008 31 0 215 -(Ocean tracer halo updates) 0.134272 0.242219 0.187096 0.026383 0.001 31 0 215 -(Ocean velocity halo update) 0.106292 0.221651 0.195712 0.019588 0.001 31 0 215 -(Ocean sum ocean surface) 0.030474 0.040704 0.037585 0.001841 0.000 31 0 215 -(Ocean average state) 0.001768 0.004488 0.003312 0.000579 0.000 31 0 215 -(Ocean tracer tmask limit) 0.247369 0.887996 0.615921 0.208988 0.004 31 0 215 -(Ocean gotm: advection) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean increment eta) 0.000148 0.000296 0.000206 0.000027 0.000 31 0 215 -(Ocean increment tracer) 0.000151 0.000494 0.000254 0.000039 0.000 31 0 215 -(Ocean increment velocity) 0.000188 0.000539 0.000310 0.000068 0.000 31 0 215 -(Ocean update rho_salinity) 0.018775 0.038378 0.025990 0.004185 0.000 31 0 215 -(Ocean idealized surface waves) 0.000133 0.000424 0.000189 0.000037 0.000 31 0 215 -(Ocean open boundaries) 0.000000 0.000000 0.000000 0.000000 0.000 31 0 215 -(Ocean tracer: bih tracer) 0.000399 0.000858 0.000594 0.000089 0.000 31 0 215 -(Ocean tracer: lap tracer) 0.000355 0.000857 0.000606 0.000096 0.000 31 0 215 -(Ocean tracer: vert diffuse) 0.098711 0.184559 0.130953 0.019745 0.001 31 0 215 -(Ocean tracer: vert diffuse impl 0.692924 0.988883 0.877487 0.059949 0.006 31 0 215 -(Ocean tracer: advection) 8.003811 9.250892 8.829328 0.264346 0.062 31 0 215 -(Ocean tracer: frazil) 0.078462 0.139025 0.094559 0.008873 0.001 31 0 215 -(Ocean tracer: convection) 0.000100 0.000320 0.000155 0.000034 0.000 31 0 215 -(Ocean tracer: Lagrangian blobs) 0.000760 0.001746 0.000993 0.000153 0.000 31 0 215 -(Ocean tracer: implicit blobs) 0.000239 0.000660 0.000343 0.000061 0.000 41 0 215 -(Ocean tracer: adjust the L thic 0.000028 0.000207 0.000061 0.000031 0.000 41 0 215 -(Ocean tracer: adjust the E thic 0.000142 0.000418 0.000216 0.000046 0.000 41 0 215 -(Ocean CT2PT: 1) 0.000000 0.000000 0.000000 0.000000 0.000 31 0 215 -(Ocean CT2PT: 2) 0.000000 0.000000 0.000000 0.000000 0.000 31 0 215 -(Ocean CT2PT: 3) 0.000000 0.000000 0.000000 0.000000 0.000 31 0 215 -(Ocean vmix: constant) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean vmix: PPvmix) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean vmix: KPP_test) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean vmix: KPP_mom4p0) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean vmix: KPP_mom4p1) 2.556791 4.330949 3.385728 0.306981 0.024 41 0 215 -(Ocean vmix: chenvmix) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean vmix: gotmvmix) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean vmix: tidal) 1.919579 3.133729 2.703513 0.209719 0.019 41 0 215 -(Ocean vmix: watermass_diag) 0.000206 0.000474 0.000311 0.000059 0.000 41 0 215 -(Ocean neutral: tracer derivs) 0.658294 1.146296 1.098837 0.045753 0.008 41 0 215 -(Ocean neutral: slopes) 0.300749 0.757018 0.655774 0.057047 0.005 41 0 215 -(Ocean neutral: eady rate) 0.626066 2.033923 1.022607 0.305561 0.007 41 0 215 -(Ocean neutral: baroclinic) 0.001701 0.004894 0.002600 0.000475 0.000 41 0 215 -(Ocean neutral: rossby radius) 0.067911 0.130738 0.088793 0.010591 0.001 41 0 215 -(Ocean neutral: bc zone radius) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean neutral: diffusivity) 0.390924 1.718850 0.627911 0.246809 0.004 41 0 215 -(Ocean neutral: cabbel/thermob) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean neutral: eta_tend_gm90) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean neutral: nrho-trans) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean neutral: rho-trans) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean neutral: theta-trans) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean neutral: diffuse) 4.261838 6.480799 4.841983 0.484192 0.034 41 0 215 -(Ocean neutral: GM stir) 2.377936 4.337258 3.282626 0.425272 0.023 41 0 215 -(Ocean neutral: blayer) 0.215035 1.634450 0.472175 0.233263 0.003 41 0 215 -(Ocean neutral: fz-terms) 1.063489 2.299485 1.284810 0.153986 0.009 41 0 215 -(Ocean ndiffuse: fx-flux) 1.273576 2.083588 1.414856 0.119677 0.010 41 0 215 -(Ocean ndiffuse: fy-flux) 1.284246 1.972697 1.402581 0.107319 0.010 41 0 215 -(Ocean ndiffuse: fz-flux) 0.627449 0.967038 0.788647 0.075569 0.006 41 0 215 -(Ocean gm: fx-flux) 0.514024 0.644973 0.570976 0.029707 0.004 41 0 215 -(Ocean gm: fy-flux) 0.500977 0.606875 0.546058 0.020148 0.004 41 0 215 -(Ocean gm: fz-flux) 0.690329 0.959312 0.776265 0.028154 0.005 41 0 215 -(Ocean gm: bc_modes) 0.152420 1.491820 0.794359 0.315911 0.006 41 0 215 -(Ocean gm: psi_modes) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean gm: psi_bvp) 4.183440 8.191065 6.005115 0.885049 0.042 41 0 215 -(Ocean const lap frict) 0.000000 0.000000 0.000000 0.000000 0.000 31 0 215 -(Ocean general lap frict) 2.732633 3.606330 2.943999 0.093591 0.021 31 0 215 -(Ocean C-grid lap frict) 0.000000 0.000000 0.000000 0.000000 0.000 31 0 215 -(Ocean const bih frict) 0.000000 0.000000 0.000000 0.000000 0.000 31 0 215 -(Ocean general bih frict) 4.903246 5.268783 5.089075 0.105176 0.036 31 0 215 -(Ocean c-grid bih frict) 0.000000 0.000000 0.000000 0.000000 0.000 31 0 215 -(Ocean advect: horz 4th) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean advect: vert 4th) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean advect: horz 6th) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean advect: vert 6th) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean advect: horz quk) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean advect: vert quk) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean advect: horz qukmom3) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean advect: vert qukmom3) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean advect: MDFL-sup-b) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean advect: MDFL-sweby) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean advect: MDFL-sweby-all) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean advect: MDFL-sweby-test) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean advect: DST-linear) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean advect: DST-linear-test) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean advect: MDFL-sweby-mpi) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean advect: MDFL-sweby-cuk) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean advect: MDFL-sweby-cui) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean advect: MDFL-sweby-cuj) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean advect: MDFL-sweby-diag) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean advect: MDPPM) 7.137721 8.269912 7.854404 0.221688 0.055 41 0 215 -(Ocean advect: MDPPM-TEST) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean advect: psom total) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean psom advect: psom_x) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean psom advect: psom_y) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean psom advect: psom_z) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean advect: MDMDT-TEST) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean advect: horz up) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean advect: vert up) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean advect: horz 2nd) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean advect: vert 2nd) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean advect: gyre_overturn) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean advect: advect diss) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean shortwave morel pen) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean shortwave morel pen-mom4p 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean_OFP_init) 0.000000 0.000000 0.000000 0.000000 0.000 31 0 215 -(Ocean_OFP_main) 0.000000 0.000000 0.000000 0.000000 0.000 31 0 215 -(ocean_OFP_update_1) 0.000000 0.000000 0.000000 0.000000 0.000 31 0 215 -(ocean_OFP_update_2) 0.000000 0.000000 0.000000 0.000000 0.000 31 0 215 -(ocean_OFP_update_3) 0.000000 0.000000 0.000000 0.000000 0.000 31 0 215 -(Ocean diagnostics: adv_vel) 2.814867 3.650141 3.076137 0.157993 0.022 31 0 215 -(Ocean diagnostics: tracer) 1.012419 2.862905 1.771321 0.223401 0.012 31 0 215 -(Ocean diagnostics: velocity) 0.296659 0.331405 0.327530 0.002716 0.002 31 0 215 -(Ocean adv_vel_diag: numerics) 0.000079 0.000159 0.000114 0.000016 0.000 41 0 215 -(Ocean adv_vel_diag: s-trans) 0.419264 0.500647 0.456278 0.024219 0.003 41 0 215 -(Ocean adv_vel_diag: rho-trans) 2.360751 3.162637 2.618103 0.152438 0.018 41 0 215 -(Ocean adv_vel_diag: nrho-trans) 0.000407 0.000834 0.000497 0.000077 0.000 41 0 215 -(Ocean adv_vel_diag: theta-trans 0.000127 0.000422 0.000197 0.000052 0.000 41 0 215 -(Ocean tracer_diag: compute_subd 0.000038 0.000162 0.000080 0.000023 0.000 41 0 215 -(Ocean tracer_diag: compute_trac 0.000111 0.000427 0.000225 0.000064 0.000 41 0 215 -(Ocean tracer_diag: mld_dtheta) 0.000029 0.000128 0.000051 0.000012 0.000 41 0 215 -(Ocean tracer_diag: mld) 0.250290 0.480895 0.368349 0.053225 0.003 41 0 215 -(Ocean tracer_diag: rho_mld) 0.000313 0.000825 0.000489 0.000097 0.000 41 0 215 -(Ocean tracer_diag: potrho depth 0.000014 0.000044 0.000025 0.000005 0.000 41 0 215 -(Ocean tracer_diag: theta depth) 0.000014 0.000043 0.000026 0.000006 0.000 41 0 215 -(Ocean tracer_diag: tracer on rh 0.000063 0.000362 0.000173 0.000059 0.000 41 0 215 -(Ocean tracer_diag: tracer_zrho 0.000047 0.000157 0.000091 0.000024 0.000 41 0 215 -(Ocean tracer_diag: numerical) 0.000017 0.000107 0.000048 0.000017 0.000 41 0 215 -(Ocean tracer_diag: diag mixing 0.000064 0.000237 0.000130 0.000030 0.000 41 0 215 -(Ocean tracer_diag: conserve) 0.134145 0.264979 0.192141 0.034858 0.001 41 0 215 -(Ocean tracer_diag: total water 0.000027 0.000154 0.000064 0.000024 0.000 41 0 215 -(Ocean tracer_diag: total water 0.000015 0.000044 0.000026 0.000006 0.000 41 0 215 -(Ocean tracer_diag: total tracer 0.472491 2.454627 1.207544 0.250274 0.008 41 0 215 -(Ocean tracer_diag: integrals) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean tracer_diag: change) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Ocean tracer_diag: land check) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Velocity diag: energy analysis) 0.000000 0.000000 0.000000 0.000000 0.000 31 0 215 -(Velocity diag: press convert) 0.000000 0.000000 0.000000 0.000000 0.000 31 0 215 -(Velocity diag: press energy) 0.000000 0.000000 0.000000 0.000000 0.000 31 0 215 -(Velocity diag: friction energy) 0.000000 0.000000 0.000000 0.000000 0.000 31 0 215 -(Velocity diag: vert dissipation 0.000188 0.000425 0.000274 0.000034 0.000 31 0 215 -(Wave model initialization) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -(Wave diagnostics) 0.000000 0.000000 0.000000 0.000000 0.000 41 0 215 -Override 0.025312 0.058349 0.041812 0.005270 0.000 1 0 215 -OASIS init 1.745689 1.745886 1.745827 0.000030 0.012 1 0 215 -oasis_recv 1.302670 2.467766 2.126505 0.355053 0.015 31 0 215 -oasis_send 0.086235 0.133407 0.094452 0.005811 0.001 31 0 215 -oasis_recv1 0.838041 1.429393 1.198269 0.159289 0.008 31 0 215 -oasis_send1 0.063814 0.109466 0.070395 0.005245 0.000 31 0 215 - MPP_STACK high water mark= 0 - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- - MOM5: --- completed --- From bd697a1d55086956240810097e2c4d37d8110d0b Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Sat, 6 Jun 2020 12:10:17 +1000 Subject: [PATCH 065/111] output MOM scalar diags as daily snapshots --- ocean/diag_table | 74 ++++++++++++++++++------------------ ocean/diag_table_source.yaml | 5 ++- 2 files changed, 40 insertions(+), 39 deletions(-) diff --git a/ocean/diag_table b/ocean/diag_table index 0e35eb58..5a5adc8f 100644 --- a/ocean/diag_table +++ b/ocean/diag_table @@ -329,43 +329,43 @@ ACCESS-OM2 "ocean_model", "vorticity_z_surf", "vorticity_z_surf", "ocean-2d-vorticity_z_surf-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 -# monthly scalar timeseries - -"ocean-scalar-1-monthly-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" -"ocean_model", "eta_global", "eta_global", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "ke_tot", "ke_tot", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "pe_tot", "pe_tot", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "rhoave", "rhoave", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "salt_global_ave", "salt_global_ave", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "salt_surface_ave", "salt_surface_ave", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "temp_global_ave", "temp_global_ave", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "temp_surface_ave", "temp_surface_ave", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "total_net_sfc_heating", "total_net_sfc_heating", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "total_ocean_calving_heat", "total_ocean_calving_heat", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "total_ocean_calving_melt_heat", "total_ocean_calving_melt_heat", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "total_ocean_calving", "total_ocean_calving", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "total_ocean_evap_heat", "total_ocean_evap_heat", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "total_ocean_evap", "total_ocean_evap", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "total_ocean_fprec_melt_heat", "total_ocean_fprec_melt_heat", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "total_ocean_fprec", "total_ocean_fprec", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "total_ocean_heat", "total_ocean_heat", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "total_ocean_hflux_coupler", "total_ocean_hflux_coupler", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "total_ocean_hflux_evap", "total_ocean_hflux_evap", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "total_ocean_hflux_prec", "total_ocean_hflux_prec", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "total_ocean_lprec", "total_ocean_lprec", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "total_ocean_lw_heat", "total_ocean_lw_heat", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "total_ocean_melt", "total_ocean_melt", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "total_ocean_mh_flux", "total_ocean_mh_flux", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "total_ocean_pme_river", "total_ocean_pme_river", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "total_ocean_river_heat", "total_ocean_river_heat", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "total_ocean_river", "total_ocean_river", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "total_ocean_runoff_heat", "total_ocean_runoff_heat", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "total_ocean_runoff", "total_ocean_runoff", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "total_ocean_salt", "total_ocean_salt", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "total_ocean_sens_heat", "total_ocean_sens_heat", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "total_ocean_sfc_salt_flux_coupler", "total_ocean_sfc_salt_flux_coupler", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "total_ocean_swflx_vis", "total_ocean_swflx_vis", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 -"ocean_model", "total_ocean_swflx", "total_ocean_swflx", "ocean-scalar-1-monthly-ym%4yr%2mo", "all", "average", "none", 1 +# daily scalar snapshots + +"ocean-scalar-1-daily-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "eta_global", "eta_global", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "ke_tot", "ke_tot", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "pe_tot", "pe_tot", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "rhoave", "rhoave", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "salt_global_ave", "salt_global_ave", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "salt_surface_ave", "salt_surface_ave", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "temp_global_ave", "temp_global_ave", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "temp_surface_ave", "temp_surface_ave", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "total_net_sfc_heating", "total_net_sfc_heating", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "total_ocean_calving_heat", "total_ocean_calving_heat", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "total_ocean_calving_melt_heat", "total_ocean_calving_melt_heat", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "total_ocean_calving", "total_ocean_calving", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "total_ocean_evap_heat", "total_ocean_evap_heat", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "total_ocean_evap", "total_ocean_evap", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "total_ocean_fprec_melt_heat", "total_ocean_fprec_melt_heat", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "total_ocean_fprec", "total_ocean_fprec", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "total_ocean_heat", "total_ocean_heat", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "total_ocean_hflux_coupler", "total_ocean_hflux_coupler", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "total_ocean_hflux_evap", "total_ocean_hflux_evap", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "total_ocean_hflux_prec", "total_ocean_hflux_prec", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "total_ocean_lprec", "total_ocean_lprec", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "total_ocean_lw_heat", "total_ocean_lw_heat", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "total_ocean_melt", "total_ocean_melt", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "total_ocean_mh_flux", "total_ocean_mh_flux", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "total_ocean_pme_river", "total_ocean_pme_river", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "total_ocean_river_heat", "total_ocean_river_heat", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "total_ocean_river", "total_ocean_river", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "total_ocean_runoff_heat", "total_ocean_runoff_heat", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "total_ocean_runoff", "total_ocean_runoff", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "total_ocean_salt", "total_ocean_salt", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "total_ocean_sens_heat", "total_ocean_sens_heat", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "total_ocean_sfc_salt_flux_coupler", "total_ocean_sfc_salt_flux_coupler", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "total_ocean_swflx_vis", "total_ocean_swflx_vis", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 +"ocean_model", "total_ocean_swflx", "total_ocean_swflx", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 # monthly 2d snapshots diff --git a/ocean/diag_table_source.yaml b/ocean/diag_table_source.yaml index 37930fba..2308882a 100755 --- a/ocean/diag_table_source.yaml +++ b/ocean/diag_table_source.yaml @@ -261,7 +261,7 @@ diag_table: u_surf: v_surf: vorticity_z_surf: - 'monthly scalar timeseries': + 'daily scalar snapshots': # snapshots of global integrals give better parallel performance defaults: # these can be overridden for individual fields below file_name_dimension: scalar # descriptor for filename, e.g. 3d, 2d, scalar file_name: # file name (without trailing ".nc") is constructed from these components, @@ -273,7 +273,8 @@ diag_table: - output_freq_units - file_name_date output_freq: 1 # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run) - output_freq_units: months # time units for output: years, months, days, hours, minutes, or seconds + output_freq_units: days # time units for output: years, months, days, hours, minutes, or seconds + reduction_method: snap # mean, snap, rms, pow##, min, max, or diurnal## packing: 1 # double precision fields: eta_global: From ca057b8066adb3aa3ad4b6c79f346a44b8536ad3 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Sun, 7 Jun 2020 21:10:51 +1000 Subject: [PATCH 066/111] use Large and Yeager (2009) latitude-dependent ocean albedo (cst_ocn_albedo=false) - https://github.com/COSIMA/access-om2/issues/172 --- ice/input_ice.nml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ice/input_ice.nml b/ice/input_ice.nml index ae194750..d77f9187 100644 --- a/ice/input_ice.nml +++ b/ice/input_ice.nml @@ -5,7 +5,7 @@ chk_i2a_fields = .false. chk_i2o_fields = .false. chk_o2i_fields = .false. - cst_ocn_albedo = .true. + cst_ocn_albedo = .false. fields_from_atm = 'swfld_i', 'lwfld_i', 'rain_i', 'snow_i', 'press_i', 'runof_i', 'tair_i', 'qair_i', 'uwnd_i', 'vwnd_i', 'licalvf_i' From 176cdaa68f93f98975ee0461d52bae152045a0ea Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Sun, 7 Jun 2020 22:29:20 +1000 Subject: [PATCH 067/111] update ice diagnostics - see https://github.com/COSIMA/access-om2/issues/207 --- ice/cice_in.nml | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/ice/cice_in.nml b/ice/cice_in.nml index 0b72da43..2bcc3864 100644 --- a/ice/cice_in.nml +++ b/ice/cice_in.nml @@ -177,7 +177,7 @@ / &icefields_nml - f_aice = 'm' + f_aice = 'md' f_aicen = 'm' f_aisnap = 'x' f_albice = 'm' @@ -189,14 +189,14 @@ f_angle = .true. f_anglet = .true. f_bounds = .false. - f_congel = 'm' + f_congel = 'md' f_coszen = 'x' f_daidtd = 'm' f_daidtt = 'm' f_divu = 'm' f_dsnow = 'x' - f_dvidtd = 'm' - f_dvidtt = 'm' + f_dvidtd = 'md' + f_dvidtt = 'md' f_dxt = .true. f_dxu = .true. f_dyt = .true. @@ -215,11 +215,11 @@ f_flwup_ai = 'm' f_fmeltt_ai = 'm' f_fmelttn_ai = 'm' - f_frazil = 'm' + f_frazil = 'md' f_fresh = 'x' f_fresh_ai = 'm' - f_frz_onset = 'm' - f_frzmlt = 'm' + f_frz_onset = 'x' + f_frzmlt = 'md' f_fsalt = 'm' f_fsalt_ai = 'm' f_fsens = 'x' @@ -233,9 +233,9 @@ f_fswthru = 'x' f_fswthru_ai = 'm' f_fy = 'x' - f_hi = 'm' + f_hi = 'md' f_hisnap = 'x' - f_hs = 'm' + f_hs = 'md' f_hte = .true. f_htn = .true. f_iage = 'm' @@ -244,17 +244,17 @@ f_meltl = 'm' f_melts = 'm' f_meltt = 'm' - f_mlt_onset = 'm' + f_mlt_onset = 'x' f_ncat = .true. f_qref = 'x' f_rain = 'x' f_rain_ai = 'm' f_shear = 'm' f_sice = 'm' - f_sig1 = 'm' - f_sig2 = 'm' + f_sig1 = 'x' + f_sig2 = 'x' f_sinz = 'x' - f_snoice = 'm' + f_snoice = 'md' f_snow = 'x' f_snow_ai = 'm' f_sss = 'x' @@ -280,13 +280,13 @@ f_tsnz = 'x' f_uarea = .true. f_uocn = 'x' - f_uvel = 'm' + f_uvel = 'md' f_vgrdb = .false. f_vgrdi = .false. f_vgrds = .false. f_vicen = 'm' f_vocn = 'x' - f_vvel = 'm' + f_vvel = 'md' / &icefields_mechred_nml @@ -344,7 +344,7 @@ f_btin = 'x' f_faero_atm = 'x' f_faero_ocn = 'x' - f_fbri = 'm' + f_fbri = 'x' f_fn = 'x' f_fn_ai = 'x' f_fnh = 'x' @@ -354,7 +354,7 @@ f_fsil = 'x' f_fsil_ai = 'x' f_grownet = 'x' - f_hbri = 'm' + f_hbri = 'x' f_ppnet = 'x' / From e4f2a8151a0ab8850736793d905741be81de3ce8 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Sun, 7 Jun 2020 23:01:42 +1000 Subject: [PATCH 068/111] use latest model executables --- config.yaml | 6 +++--- manifests/exe.yaml | 24 ++++++++++++------------ manifests/input.yaml | 36 ------------------------------------ 3 files changed, 15 insertions(+), 51 deletions(-) diff --git a/config.yaml b/config.yaml index b9bfc600..4d657f8e 100644 --- a/config.yaml +++ b/config.yaml @@ -17,7 +17,7 @@ input: /g/data/ik11/inputs/access-om2/input_20200530/common_1deg_jra55 submodels: - name: atmosphere model: yatm - exe: /g/data/ik11/inputs/access-om2/bin/yatm_4198e150.exe + exe: /g/data/ik11/inputs/access-om2/bin/yatm_d7c3c28.exe input: - /g/data/ik11/inputs/access-om2/input_20200530/yatm_1deg - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/rsds/gr/v20190429/rsds @@ -35,13 +35,13 @@ submodels: - name: ocean model: mom - exe: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM_e837d05d_libaccessom2_4198e150.x + exe: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM_08cf2b5_libaccessom2_d7c3c28.x input: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg ncpus: 216 - name: ice model: cice5 - exe: /g/data/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_597e4561_libaccessom2_4198e150.exe + exe: /g/data/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_26e6159_libaccessom2_d7c3c28.exe input: /g/data/ik11/inputs/access-om2/input_20200530/cice_1deg ncpus: 24 diff --git a/manifests/exe.yaml b/manifests/exe.yaml index 6bbb3149..37d26b32 100644 --- a/manifests/exe.yaml +++ b/manifests/exe.yaml @@ -1,18 +1,18 @@ format: yamanifest version: 1.0 --- -work/atmosphere/yatm_4198e150.exe: - fullpath: /g/data/ik11/inputs/access-om2/bin/yatm_4198e150.exe +work/atmosphere/yatm_d7c3c28.exe: + fullpath: /g/data/ik11/inputs/access-om2/bin/yatm_d7c3c28.exe hashes: - binhash: 6d9aa346608401a4c79df16d21ac3517 - md5: 09508ee51092bee3ba97efd8a604ae29 -work/ice/cice_auscom_360x300_24p_597e4561_libaccessom2_4198e150.exe: - fullpath: /g/data/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_597e4561_libaccessom2_4198e150.exe + binhash: bd49c034de195c97ef35dddd6f0a8cda + md5: e8a6849d153161b8e061f61373b6c0a0 +work/ice/cice_auscom_360x300_24p_26e6159_libaccessom2_d7c3c28.exe: + fullpath: /g/data/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_26e6159_libaccessom2_d7c3c28.exe hashes: - binhash: ea5e60ab19518af2dcc374d454dbda8c - md5: 6af53b6f9fa02930c376f8f81cb455cb -work/ocean/fms_ACCESS-OM_e837d05d_libaccessom2_4198e150.x: - fullpath: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM_e837d05d_libaccessom2_4198e150.x + binhash: 936e345c8b9b6fce3c83be4cce48c800 + md5: 845a1b47f9664b464425916fbd73a309 +work/ocean/fms_ACCESS-OM_08cf2b5_libaccessom2_d7c3c28.x: + fullpath: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM_08cf2b5_libaccessom2_d7c3c28.x hashes: - binhash: 820e6a346026240522708d9c321b84df - md5: b584ee3f239241ca74d549aa68c64e87 + binhash: 9631f63ea58016289f7797c81860c6b4 + md5: b1efe5b4c11d64a33c8af1ad335fc3ac diff --git a/manifests/input.yaml b/manifests/input.yaml index 9ba0dc63..386f56ad 100644 --- a/manifests/input.yaml +++ b/manifests/input.yaml @@ -3441,42 +3441,6 @@ work/atmosphere/INPUT/vas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr hashes: binhash: 024b0814eccc76663b7b43adbcaa4be2 md5: b0e514bfac0d9dfbf538d36b8ecd17f9 -work/ice/RESTART/grid.nc: - copy: true - fullpath: /g/data/ik11/inputs/access-om2/input_20200530/cice_1deg/grid.nc - hashes: - binhash: e7108317ae28b1f9ae77711728925cb6 - md5: 1213e346055ee073fe33dc12578d99c6 -work/ice/RESTART/i2o.nc: - copy: true - fullpath: /g/data/ik11/inputs/access-om2/input_20200530/cice_1deg/i2o.nc - hashes: - binhash: 527d494c80b2a3418645b962fd8706d0 - md5: c96e06c3c80c0f680545db59ed3349e5 -work/ice/RESTART/kmt.nc: - copy: true - fullpath: /g/data/ik11/inputs/access-om2/input_20200530/cice_1deg/kmt.nc - hashes: - binhash: 51eda44859a964d0fd5a0210c02a9999 - md5: a5a7b4be90ec06044588b623d555c4ad -work/ice/RESTART/monthly_sstsss.nc: - copy: true - fullpath: /g/data/ik11/inputs/access-om2/input_20200530/cice_1deg/monthly_sstsss.nc - hashes: - binhash: 66f44d84fada351d4ebf05f196762d8c - md5: 323d4c605f83f4d7d3126da70153c2ed -work/ice/RESTART/o2i.nc: - copy: true - fullpath: /g/data/ik11/inputs/access-om2/input_20200530/cice_1deg/o2i.nc - hashes: - binhash: 56f258e931a8eda2fc42b3a315d485eb - md5: 3498246dcd7da40d3b8c6b4a908b260f -work/ice/RESTART/u_star.nc: - copy: true - fullpath: /g/data/ik11/inputs/access-om2/input_20200530/cice_1deg/u_star.nc - hashes: - binhash: f93a19930c5c59e03751e70a123ab01f - md5: 68cf0ef92576f96ef085cd7f243d0c39 work/ocean/INPUT/chl.nc: fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/chl.nc hashes: From bfbc4f029f797ca8c104b969197ca35e5c13e09a Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Tue, 9 Jun 2020 11:55:30 +1000 Subject: [PATCH 069/111] use latest executables --- config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/config.yaml b/config.yaml index 4d657f8e..ec460aa1 100644 --- a/config.yaml +++ b/config.yaml @@ -17,7 +17,7 @@ input: /g/data/ik11/inputs/access-om2/input_20200530/common_1deg_jra55 submodels: - name: atmosphere model: yatm - exe: /g/data/ik11/inputs/access-om2/bin/yatm_d7c3c28.exe + exe: /g/data/ik11/inputs/access-om2/bin/yatm_a6e5d87.exe input: - /g/data/ik11/inputs/access-om2/input_20200530/yatm_1deg - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/rsds/gr/v20190429/rsds @@ -35,13 +35,13 @@ submodels: - name: ocean model: mom - exe: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM_08cf2b5_libaccessom2_d7c3c28.x + exe: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM_08cf2b5_libaccessom2_a6e5d87.x input: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg ncpus: 216 - name: ice model: cice5 - exe: /g/data/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_26e6159_libaccessom2_d7c3c28.exe + exe: /g/data/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_26e6159_libaccessom2_a6e5d87.exe input: /g/data/ik11/inputs/access-om2/input_20200530/cice_1deg ncpus: 24 From 448f7590713d42044084f37112adba4e40887c1b Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Tue, 9 Jun 2020 12:16:33 +1000 Subject: [PATCH 070/111] update manifests/exe.yaml --- manifests/exe.yaml | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/manifests/exe.yaml b/manifests/exe.yaml index 37d26b32..232d1804 100644 --- a/manifests/exe.yaml +++ b/manifests/exe.yaml @@ -1,18 +1,18 @@ format: yamanifest version: 1.0 --- -work/atmosphere/yatm_d7c3c28.exe: - fullpath: /g/data/ik11/inputs/access-om2/bin/yatm_d7c3c28.exe +work/atmosphere/yatm_a6e5d87.exe: + fullpath: /g/data/ik11/inputs/access-om2/bin/yatm_a6e5d87.exe hashes: - binhash: bd49c034de195c97ef35dddd6f0a8cda - md5: e8a6849d153161b8e061f61373b6c0a0 -work/ice/cice_auscom_360x300_24p_26e6159_libaccessom2_d7c3c28.exe: - fullpath: /g/data/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_26e6159_libaccessom2_d7c3c28.exe + binhash: 6d9d600011995461c261e37d5dd845b7 + md5: f6b6e353080c108a3795127a18485a78 +work/ice/cice_auscom_360x300_24p_26e6159_libaccessom2_a6e5d87.exe: + fullpath: /g/data/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_26e6159_libaccessom2_a6e5d87.exe hashes: - binhash: 936e345c8b9b6fce3c83be4cce48c800 - md5: 845a1b47f9664b464425916fbd73a309 -work/ocean/fms_ACCESS-OM_08cf2b5_libaccessom2_d7c3c28.x: - fullpath: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM_08cf2b5_libaccessom2_d7c3c28.x + binhash: 9ae717a6e1456f8266ed7f5df9b01ce0 + md5: fe1ee3dcbd4e11e8f22e077c40e82e2c +work/ocean/fms_ACCESS-OM_08cf2b5_libaccessom2_a6e5d87.x: + fullpath: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM_08cf2b5_libaccessom2_a6e5d87.x hashes: - binhash: 9631f63ea58016289f7797c81860c6b4 - md5: b1efe5b4c11d64a33c8af1ad335fc3ac + binhash: ff2b4df8f3f96f13953648b4f1b42b2b + md5: d4ff36fcbab1ae4bcfe377c2d56b6680 From 2fe0b86ea45369e717e85497b78a6fa2152b5705 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Tue, 9 Jun 2020 15:27:36 +1000 Subject: [PATCH 071/111] update libaccessom2 again --- config.yaml | 6 +++--- manifests/exe.yaml | 24 ++++++++++++------------ 2 files changed, 15 insertions(+), 15 deletions(-) diff --git a/config.yaml b/config.yaml index ec460aa1..851b4b2e 100644 --- a/config.yaml +++ b/config.yaml @@ -17,7 +17,7 @@ input: /g/data/ik11/inputs/access-om2/input_20200530/common_1deg_jra55 submodels: - name: atmosphere model: yatm - exe: /g/data/ik11/inputs/access-om2/bin/yatm_a6e5d87.exe + exe: /g/data/ik11/inputs/access-om2/bin/yatm_a9d4b67.exe input: - /g/data/ik11/inputs/access-om2/input_20200530/yatm_1deg - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/rsds/gr/v20190429/rsds @@ -35,13 +35,13 @@ submodels: - name: ocean model: mom - exe: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM_08cf2b5_libaccessom2_a6e5d87.x + exe: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM_08cf2b5_libaccessom2_a9d4b67.x input: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg ncpus: 216 - name: ice model: cice5 - exe: /g/data/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_26e6159_libaccessom2_a6e5d87.exe + exe: /g/data/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_26e6159_libaccessom2_a9d4b67.exe input: /g/data/ik11/inputs/access-om2/input_20200530/cice_1deg ncpus: 24 diff --git a/manifests/exe.yaml b/manifests/exe.yaml index 232d1804..a03d8ac5 100644 --- a/manifests/exe.yaml +++ b/manifests/exe.yaml @@ -1,18 +1,18 @@ format: yamanifest version: 1.0 --- -work/atmosphere/yatm_a6e5d87.exe: - fullpath: /g/data/ik11/inputs/access-om2/bin/yatm_a6e5d87.exe +work/atmosphere/yatm_a9d4b67.exe: + fullpath: /g/data/ik11/inputs/access-om2/bin/yatm_a9d4b67.exe hashes: - binhash: 6d9d600011995461c261e37d5dd845b7 - md5: f6b6e353080c108a3795127a18485a78 -work/ice/cice_auscom_360x300_24p_26e6159_libaccessom2_a6e5d87.exe: - fullpath: /g/data/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_26e6159_libaccessom2_a6e5d87.exe + binhash: 75722a5be452b46f55ce2fc0d3cbad44 + md5: 8137dfef69adc41912648e3642f79cc6 +work/ice/cice_auscom_360x300_24p_26e6159_libaccessom2_a9d4b67.exe: + fullpath: /g/data/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_26e6159_libaccessom2_a9d4b67.exe hashes: - binhash: 9ae717a6e1456f8266ed7f5df9b01ce0 - md5: fe1ee3dcbd4e11e8f22e077c40e82e2c -work/ocean/fms_ACCESS-OM_08cf2b5_libaccessom2_a6e5d87.x: - fullpath: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM_08cf2b5_libaccessom2_a6e5d87.x + binhash: 9293e76448d4b655deef829122169429 + md5: f15ee94d35fc3569e06a323ba6a6ef2b +work/ocean/fms_ACCESS-OM_08cf2b5_libaccessom2_a9d4b67.x: + fullpath: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM_08cf2b5_libaccessom2_a9d4b67.x hashes: - binhash: ff2b4df8f3f96f13953648b4f1b42b2b - md5: d4ff36fcbab1ae4bcfe377c2d56b6680 + binhash: 228d9788823a8d6f4ab3f8676006c76e + md5: 69c3a7020be150a02965e935cbab4052 From c1d27f8aae7c1abaab48acd3dc3cfceb076ab307 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Fri, 12 Jun 2020 09:35:54 +1000 Subject: [PATCH 072/111] add run_summary.py --- run_summary.py | 959 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 959 insertions(+) create mode 100755 run_summary.py diff --git a/run_summary.py b/run_summary.py new file mode 100755 index 00000000..62a75a13 --- /dev/null +++ b/run_summary.py @@ -0,0 +1,959 @@ +#!/usr/bin/env python3 +""" + +Tools to summarise access-om2 runs. + +Latest version: https://github.com/aekiss/run_summary +Author: Andrew Kiss https://github.com/aekiss +Apache 2.0 License http://www.apache.org/licenses/LICENSE-2.0.txt +""" + +# TODO: collect data on storage use on hh5 (and short?) with du -bs +# TODO: use starting date/time for determining git commit +# TODO: use PAYU_N_RUNS - does this tell you whether the run is part of a sequence? if so we can determine queue wait for runs in a sequence - but sometimes it is None +# TODO: summary stats: specify list of excel commands e.g. ['sum', 'average', 'min', 'max'] as optional third tuple element in output_format and insert formulas for these. Or just calculate them in python? might as well, as Execel will save formulas as values if formulas aren't displayed... + +from __future__ import print_function +import sys +try: + assert sys.version_info >= (3, 3) # need python >= 3.3 for print flush keyword +except AssertionError: + print('\nFatal error: Python version too old.') + print('On NCI, do the following and try again:') + print(' module use /g/data/hh5/public/modules; module load conda/analysis3\n') + raise + +import os +import glob # BUG: fails if payu module loaded - some sort of module clash with re +import subprocess +import datetime +import dateutil.parser +from collections import OrderedDict +import csv +import copy + +try: + import yaml + import f90nml # from https://f90nml.readthedocs.io/en/latest/ +except ImportError: # BUG: don't get this exception if payu module loaded, even if on python 2.6.6 + print('\nFatal error: modules not available.') + print('On NCI, do the following and try again:') + print(' module use /g/data/hh5/public/modules; module load conda/analysis3\n') + raise +import nmltab # from https://github.com/aekiss/nmltab + + +def num(s): + """ + Return input string as int or float if possible, otherwise return string. + """ + try: + return int(s) + except ValueError: + try: + return float(s) + except ValueError: + return s + + +def get_sync_path(fname): + """ + Return GDATADIR or SYNCDIR path from sync_output_to_gdata.sh or sync_data.sh + + fname: file path to sync_output_to_gdata.sh or sync_data.sh etc + + output: directory string + + """ + dir = None # default return value + searchstrings = ['GDATADIR=', 'SYNCDIR='] + with open(fname, 'r') as infile: + for line in infile: + # NB: subsequent matches will replace earlier ones + for s in searchstrings: + splitline = line.split(s) + if len(splitline) == 2 and splitline[0].strip() == '': + dir_maybe = splitline[1].strip().rstrip('/') + if not(dir_maybe.startswith('/ERROR')): + dir = dir_maybe + return dir + + +def parse_pbs_log(fname): + """ + Return dict of items from parsed PBS log file. + + fname: PBS log file path + + output: dict + + example of PBS log file content to parse: + qsub -q normal -P g40 -l walltime=12600 -l ncpus=2064 -l mem=8256GB -N minimal_01deg_j -l wd -j n -v PAYU_MODULENAME=payu/dev,PYTHONPATH=/projects/access/apps/mnctools/0.1/lib:/projects/access/apps/mnctools/0.1/lib:/projects/access/apps/mnctools/0.1/lib:/projects/v45/apps/payu/dev/lib:/projects/access/apps/mnctools/0.1/lib:/projects/v45/python,PAYU_CURRENT_RUN=137,PAYU_MODULEPATH=/projects/v45/modules,PAYU_N_RUNS=10 -lother=hyperthread -W umask=027 /projects/v45/apps/payu/dev/bin/payu-run + ... + git commit -am "2018-10-08 22:32:26: Run 137" + TODO: Check if commit is unchanged + ====================================================================================== + Resource Usage on 2018-10-08 22:32:36: + Job Id: 949753.r-man2 + Project: x77 + Exit Status: 0 + Service Units: 20440.40 + NCPUs Requested: 5968 NCPUs Used: 5968 + CPU Time Used: 20196:31:07 + Memory Requested: 11.66TB Memory Used: 2.61TB + Walltime requested: 05:00:00 Walltime Used: 03:25:30 + JobFS requested: 36.43GB JobFS used: 1.0KB + ====================================================================================== + + """ + def getproject(l): + return l[1] + + def getpayuversion(l): + return os.path.dirname(os.path.dirname(l[-1])) + # return os.path.dirname([s for s in l[0].split(',')[0].split(':') + # if s.find('payu') > -1][0]) + + def getpayu(l): + return l[0].split(',')[0] + + def getpayuint(l): + return int(l[0].split(',')[0]) + + def getrun(l): + return int(l[4].rstrip('"')) + + def getjob(l): + return int(l[1].split('.')[0]) + + def getint(l): + return int(l[1]) + + def getfloat(l): + return float(l[1]) + + def getsec(l): # convert hh:mm:ss to sec + return sum(x * int(t) for x, t in zip([3600, 60, 1], l[1].split(':'))) + + def getdatetime(l): # BUG: doesn't include time zone (can't tell if we're on daylight savings time) + return l[0]+'T'+l[1].rstrip(':') + + def getbytes(l): # assumes PBS log info uses binary prefixes - TODO: check + s = l[1] + ns = s.strip('BKMGT') # numerical part + units = {'B': 1, + 'KB': 2**10, + 'MB': 2**20, + 'GB': 2**30, + 'TB': 2**40} + return int(round(float(ns)*units[s[len(ns):]])) + + search_items = { # keys are strings to search for; items are functions to apply to whitespace-delimited list of strings following key + 'PAYU_CURRENT_RUN': getpayuversion, # gets path to payu; PAYU_CURRENT_RUN is redundant as this is obtained below from git commit message + # 'PAYU_CURRENT_RUN=': getpayuint, # BUG: misses some runs + 'PAYU_MODULENAME=': getpayu, + 'PAYU_MODULEPATH=': getpayu, + 'PAYU_PATH=': getpayu, + 'LD_LIBRARY_PATH=': getpayu, + 'PAYU_N_RUNS=': getpayuint, + 'PYTHONPATH=': getpayu, +# BUG: git commit will be missing if runlog: False in config.yaml - so we won't get run number! + 'git commit': getrun, # instead of using PAYU_CURRENT_RUN; NB: run with this number might have failed - check Exit Status + 'Resource Usage on': getdatetime, + 'Job Id': getjob, + 'Project': getproject, + 'Exit Status': getint, + 'Service Units': getfloat, + 'NCPUs Requested': getint, + 'NCPUs Used': getint, + 'CPU Time Used': getsec, + 'Memory Requested': getbytes, + 'Memory Used': getbytes, + 'Walltime requested': getsec, + 'Walltime Used': getsec, + 'JobFS requested': getbytes, + 'JobFS used': getbytes} + parsed_items = search_items.fromkeys(search_items, None) # set defaults to None + + with open(fname, 'r') as infile: + for line in infile: + # NB: subsequent matches will replace earlier ones + # NB: processes only the first match of each line + for key, op in search_items.items(): + try: + parsed_items[key] = op(line.split(key)[1].split()) + except IndexError: # key not present in this line + continue + + # change to more self-explanatory keys + rename_keys = {'PAYU_CURRENT_RUN': 'payu version', + # 'PAYU_CURRENT_RUN=': 'Run number', + 'git commit': 'Run number', + 'Memory Requested': 'Memory Requested (bytes)', + 'Memory Used': 'Memory Used (bytes)', + 'Walltime requested': 'Walltime Requested (s)', + 'Walltime Used': 'Walltime Used (s)', + 'Resource Usage on': 'Run completion date'} + for oldkey, newkey in rename_keys.items(): + parsed_items[newkey] = parsed_items.pop(oldkey) + + if parsed_items['Memory Requested (bytes)'] is None: + parsed_items['Memory Requested (Gb)'] = None + else: + parsed_items['Memory Requested (Gb)'] = parsed_items['Memory Requested (bytes)']/2**30 + + if parsed_items['Memory Used (bytes)'] is None: + parsed_items['Memory Used (Gb)'] = None + else: + parsed_items['Memory Used (Gb)'] = parsed_items['Memory Used (bytes)']/2**30 + + if parsed_items['Walltime Requested (s)'] is None: + parsed_items['Walltime Requested (hr)'] = None + else: + parsed_items['Walltime Requested (hr)'] = parsed_items['Walltime Requested (s)']/3600 + + if parsed_items['Walltime Used (s)'] is None: + parsed_items['Walltime Used (hr)'] = None + else: + parsed_items['Walltime Used (hr)'] = parsed_items['Walltime Used (s)']/3600 + + try: + parsed_items['Timeout'] = parsed_items['Walltime Used (s)'] > parsed_items['Walltime Requested (s)'] + except: + parsed_items['Timeout'] = None + + return parsed_items + + +def parse_git_log(basepath, datestr): + """ + Return dict of items from git log from most recent commit before a given date. + + basepath: base directory path string + + datestr: date string + + output: dict + """ + # possible BUG: what time zone flag should be use? local is problematic if run from overseas....? + # use Popen for backwards-compatiblity with Python <2.7 + # pretty format is tab-delimited (%x09) + try: + p = subprocess.Popen('cd ' + basepath + + ' && git log -1 ' + + '--pretty="format:%H%x09%an%x09%ai%x09%B" ' + + '`git rev-list -1 --date=local --before="' + + datestr + '" HEAD`', # TODO: add 1 sec to datestr so we don't rely on the delay between git commit and PBS log? + stdout=subprocess.PIPE, shell=True) + log = p.communicate()[0].decode('ascii').split('\t') + # log = p.communicate()[0].decode('ascii').encode('ascii').split('\t') # for python 2.6 + log[3] = log[3].strip() # strip whitespace from message + except: + log = [None]*4 # default values in case there's no .git, e.g. if runlog: False in config.yaml + parsed_items = dict() + parsed_items['Commit'] = log[0] + parsed_items['Author'] = log[1] + parsed_items['Date'] = log[2] + parsed_items['Message'] = log[3] + return parsed_items + + +def parse_mom_time_stamp(paths): + """ + Return dict of items from parsed MOM time_stamp.out. + + paths: list of base paths + + output: dict parsed from first matching time_stamp.out in paths + + example of MOM time_stamp.out content to parse: + 2001 9 1 0 0 0 Sep + 2001 11 1 0 0 0 Nov + + """ + parsed_items = dict() + keys = ['Model start time', 'Model end time'] + for path in paths: + fname = os.path.join(path, 'ocean/time_stamp.out') + if os.path.isfile(fname): + parsed_items['Time stamp file'] = fname + with open(fname, 'r') as infile: + for key in keys: + line = infile.readline() + parsed_items[key] = datetime.datetime( + *list(map(int, line.split()[0:-1]))).isoformat() + break + try: + d1 = dateutil.parser.parse(parsed_items[keys[0]]) + d2 = dateutil.parser.parse(parsed_items[keys[1]]) + len = d2-d1 # BUG: presumably assumes Gregorian calendar with leap years and time in UTC + parsed_items['Model run length (s)'] = len.total_seconds() + parsed_items['Model run length (days)'] = len.total_seconds()/3600/24 + except KeyError: + pass + return parsed_items + + +def parse_config_yaml(paths): + """ + Return dict of items from parsed config.yaml. + + paths: list of base paths + + output: dict parsed from first matching config.yaml in paths + """ + parsed_items = dict() + for path in paths: + fname = os.path.join(path, 'config.yaml') + if os.path.isfile(fname): + with open(fname, 'r') as infile: + parsed_items = yaml.load(infile, Loader=yaml.FullLoader) + break + return parsed_items + + +def parse_accessom2_out(paths): + """ + Return dict of items from parsed access-om2.out. + + paths: list of base paths + + output: dict of timing names, with dict of statistics + + NB: output may also contain bad data from intermingled CICE output. + """ + parsed_items = dict() + for path in paths: + fname = os.path.join(path, 'access-om2.out') + if os.path.isfile(fname): + with open(fname, 'r') as infile: + for l in infile: + if l.startswith('Tabulating mpp_clock statistics'): + break + for l in infile: + if l.startswith(' tmin'): + break + keys = l.split() + for l in infile: + if l.startswith(' MPP_STACK high water mark='): + break + name = l[0:32].strip() # relies on name being cropped at 32 chars + vals = [num(n) for n in l[32:].split()] + parsed_items[name] = dict(zip(keys, vals)) + break + return parsed_items + + +def parse_ice_diag_d(paths): + """ + Return dict of cice info from ice/ice_diag.d. + + paths: list of base paths + + output: dict + """ + # this is pretty rough-and-ready, e.g. repeated entries end up containing the final value + parsed_items = dict() + for path in paths: + fname = os.path.join(path, 'ice/ice_diag.d') + if os.path.isfile(fname): + with open(fname, 'r') as infile: + for l in infile: + if l.startswith('Timing information:'): + break # handle timing data with parse_cice_timing + try: + key = l.split('=')[0].strip() + val = num(l.split('=')[1].strip()) + parsed_items[key] = val + except: + try: + key = l.split(':')[0].strip() + val = num(l.split(':')[1].strip()) + parsed_items[key] = val + except: + pass + break + + if 'Block size: nx_block' in parsed_items: + parsed_items['nx_block'] = parsed_items['Block size: nx_block'] +# NB: in ice_blocks.F90 +# nx_block = block_size_x + 2*nghost, &! x,y dir including ghost +# ny_block = block_size_y + 2*nghost ! cells + if 'Number of ghost cells' in parsed_items: + if 'nx_block' in parsed_items: + parsed_items['block_size_x'] = parsed_items['nx_block'] - 2*parsed_items['Number of ghost cells'] + if 'ny_block' in parsed_items: + parsed_items['block_size_y'] = parsed_items['ny_block'] - 2*parsed_items['Number of ghost cells'] + parsed_items['timing'] = parse_cice_timing(paths) + return parsed_items + + +def parse_cice_timing(paths): + """ + Return dict of cice timing info from ice/ice_diag.d. + + paths: list of base paths + + output: dict of timing names, with dict of statistics + """ +# sample to parse: +# Timing information: +# +# Timer 1: Total 10894.88 seconds +# Timer stats (node): min = 10894.69 seconds +# max = 10894.88 seconds +# mean= 10894.70 seconds +# Timer stats(block): min = 0.00 seconds +# max = 0.00 seconds +# mean= 0.00 seconds +# Timer 2: TimeLoop 10802.50 seconds +# Timer stats (node): min = 10802.33 seconds +# max = 10802.50 seconds +# mean= 10802.33 seconds +# Timer stats(block): min = 0.00 seconds +# max = 0.00 seconds +# mean= 0.00 seconds + + parsed_items = dict() + for path in paths: + fname = os.path.join(path, 'ice/ice_diag.d') + if os.path.isfile(fname): + with open(fname, 'r') as infile: + for l in infile: + if l.startswith('Timing information:'): + break + for l in infile: + if l.startswith('Timer'): # ignore time is it it node max + timerkey = ' '.join(l[0:21].split()[2:]) + parsed_items[timerkey] = dict() + else: + if l.startswith(' Timer'): + typekey = l.split('(')[-1].split(')')[0] + parsed_items[timerkey][typekey] = dict() + try: + key = l.split('=')[0].split()[-1] + val = num(l.split()[-2]) + parsed_items[timerkey][typekey][key] = val + except: + pass + break + return parsed_items + + +def parse_nml(paths): + """ + Return dict of items from parsed namelists. + + paths: list of base paths to parse for namelists + + output: dict + """ + parsed_items = dict() + parsed_items['accessom2.nml'] = None # default value for non-YATM run + for path in paths: + fnames = [os.path.join(path, 'accessom2.nml')]\ + + glob.glob(os.path.join(path, '*/*.nml')) + for fname in fnames: + if os.path.isfile(fname): # no accessom2.nml for non-YATM run + parsed_items[fname.split(path)[1].strip('/')] \ + = f90nml.read(fname) + return parsed_items + + +def git_diff(basepath, sha1, sha2): + """ + Return dict of git-tracked differences between two commits. + + basepath: base directory path string + + sha1, sha2: strings; sha1 should be earlier than or same as sha2 + """ + try: + p = subprocess.Popen('cd ' + basepath + + ' && git diff --name-only ' + sha1 + ' ' + sha2, + stdout=subprocess.PIPE, shell=True) + c = ', '.join( + p.communicate()[0].decode('ascii').split()) + p = subprocess.Popen('cd ' + basepath + + ' && git log --ancestry-path --pretty="%B\%x09" ' + + sha1 + '..' + sha2, + stdout=subprocess.PIPE, shell=True) + m = [s.strip('\n\\') + for s in p.communicate()[0].decode('ascii').split('\t')][0:-1] + m.reverse() # put in chronological order + if len(m) == 0: + m = None + except: + c = None + m = None + parsed_items = dict() + parsed_items['Changed files'] = c + parsed_items['Messages'] = m # NB: will be None if there's no direct ancestry path from sha1 to sha2) + return parsed_items + + +def dictget(d, l): + """ + Lookup item in nested dict using a list of keys, or None if non-existent + + d: nested dict + l: list of keys, or None + """ + try: + dl0 = d[l[0]] + except (KeyError, TypeError): + return None + if len(l) == 1: + return dl0 + return dictget(dl0, l[1:]) + + +def keylists(d): + """ + Return list of key lists to every leaf node in a nested dict. + Each key list can be used as an argument to dictget. + + d: nested dict + """ + l = [] + for k, v in d.items(): + if isinstance(v, dict): + sublists = keylists(v) + for sli in sublists: + l.append([k]+sli) + else: + l.append([k]) + return l + + +def keylistssuperset(d): + """ + Apply keylists to every value at the top level of input dict d, + and return a list containing one instance of every key list found. + Each key list can be used as an argument to dictget. + + d: nested dict whose values are to be supplied to keylists + """ + all = set() + for v in d.values(): + all.update(['\b'.join(l) for l in keylists(v)]) + return [s.split('\b') for s in all] + + +def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, + dump_all=False, show_fails=False): + """ + Generate run summary + """ + print('Reading run data from ' + basepath, end='') + + # get jobname from config.yaml -- NB: we assume this is the same for all jobs + with open(os.path.join(basepath, 'config.yaml'), 'r') as infile: + configyaml = yaml.load(infile, Loader=yaml.FullLoader) + jobname = configyaml.get('jobname') + sync_script = configyaml.get('postscript') + + if sync_script: + sync_path = get_sync_path(os.path.join(basepath, sync_script)) + else: + sync_path = None + + if outfile is None: + if sync_path: + # outfile = 'run_summary_' + os.path.split(sync_path)[1] + '.csv' + outfile = 'run_summary_' + sync_path.strip(os.sep).replace(os.sep, '_') + '.csv' + else: + outfile = 'run_summary_' + os.path.abspath(basepath).strip(os.sep).replace(os.sep, '_') + '.csv' + # if show_fails: + # outfile = os.path.splitext(outfile)[0]+'_fails.csv' + + + try: + p = subprocess.Popen('cd ' + basepath + + ' && git rev-parse --abbrev-ref HEAD', + stdout=subprocess.PIPE, shell=True) + git_branch = p.communicate()[0].decode('ascii').strip() + except: + git_branch = None + + # get data from all PBS job logs + run_data = dict() + # NB: match jobname[:15] because in some cases the pbs log files use a shortened version of the jobname in config.yaml + # e.g. see /home/157/amh157/payu/025deg_jra55_ryf8485 + # NB: logs in archive may be duplicated in sync_path, in which case the latter is used + logfiles = glob.glob(os.path.join(basepath, 'archive/pbs_logs', jobname[:15] + '*.o*'))\ + + glob.glob(os.path.join(basepath, jobname[:15] + '*.o*')) + if sync_path: + logfiles += glob.glob(os.path.join(sync_path, 'pbs_logs', jobname[:15] + '*.o*')) + logfiles = [f for f in logfiles if '_c.o' not in f] # exclude collation files *_c.o* + for f in logfiles: + print('.', end='', flush=True) + jobid = int(f.split('.o')[1]) + run_data[jobid] = dict() + run_data[jobid]['PBS log'] = parse_pbs_log(f) + run_data[jobid]['PBS log']['PBS log file'] = f + + # get run data for all jobs + for jobid in run_data: + print('.', end='', flush=True) + pbs = run_data[jobid]['PBS log'] + date = pbs['Run completion date'] # BUG: would be better to have time when run began, including time zone + if date is not None: + run_data[jobid]['git log'] = parse_git_log(basepath, date) + # BUG: assumes no commits between run start and end + # BUG: assumes the time zones match - no timezone specified in date - what does git assume? UTC? + if pbs['Exit Status'] == 0: # output dir belongs to this job only if Exit Status = 0 + outdir = 'output' + str(pbs['Run number']).zfill(3) + paths = [] + if sync_path: + paths += [os.path.join(sync_path, outdir)] + paths += [os.path.join(basepath, 'archive', outdir)] + run_data[jobid]['MOM_time_stamp.out'] = parse_mom_time_stamp(paths) + run_data[jobid]['config.yaml'] = parse_config_yaml(paths) + run_data[jobid]['namelists'] = parse_nml(paths) + run_data[jobid]['access-om2.out'] = parse_accessom2_out(paths) + run_data[jobid]['ice_diag.d'] = parse_ice_diag_d(paths) + + all_run_data = copy.deepcopy(run_data) # all_run_data includes failed jobs + + + if show_fails: + # remove all jobs that have no PBS info in log file + for jobid in all_run_data: + if all_run_data[jobid]['PBS log']['Run completion date'] is None: + del run_data[jobid] + # (jobid, run completion date) tuples sorted by run completion date + jobid_run_tuples = sorted([(k, v['PBS log']['Run completion date']) + for (k, v) in run_data.items()], + key=lambda t: t[1]) + if len(jobid_run_tuples) == 0: + print('\nAborting: no jobs?') + return + # jobid keys into run_data sorted by run completion date + sortedjobids = [k[0] for k in jobid_run_tuples] + else: + # remove failed jobs from run_data + for jobid in all_run_data: + print('.', end='', flush=True) + pbs = all_run_data[jobid]['PBS log'] + date = pbs['Run completion date'] + if date is None: # no PBS info in log file + del run_data[jobid] + elif pbs['Run number'] is None: # not a model run log file + del run_data[jobid] + elif pbs['Exit Status'] != 0: # output dir belongs to this job only if Exit Status = 0 + del run_data[jobid] + elif len(run_data[jobid]['config.yaml']) == 0: # output dir missing + del run_data[jobid] + + # (jobid, run number) tuples sorted by run number - re-done below + jobid_run_tuples = sorted([(k, v['PBS log']['Run number']) + for (k, v) in run_data.items()], + key=lambda t: t[1]) + if len(jobid_run_tuples) == 0: + print('\nAborting: no successful jobs?') + return + + # Remove the older jobid if run number is duplicated - assume run was re-done + # (check by date rather than jobid, since jobid sometimes rolls over) + prev_jobid_run = jobid_run_tuples[0] + for jobid_run in jobid_run_tuples[1:]: + if jobid_run[1] == prev_jobid_run[1]: # duplicated run number + if run_data[jobid_run[0]]['PBS log']['Run completion date']\ + > run_data[prev_jobid_run[0]]['PBS log']['Run completion date']: + del run_data[prev_jobid_run[0]] + prev_jobid_run = jobid_run + else: + del run_data[jobid_run[0]] + else: + prev_jobid_run = jobid_run + + # re-do (jobid, run number) tuples sorted by run number + jobid_run_tuples = sorted([(k, v['PBS log']['Run number']) + for (k, v) in run_data.items()], + key=lambda t: t[1]) + if len(jobid_run_tuples) == 0: + print('\nAborting: no successful jobs?') + return + + # jobid keys into run_data sorted by run number + sortedjobids = [k[0] for k in jobid_run_tuples] + + # allow referencing by submodel name as well as list index + for jobid in run_data: + run_data[jobid]['config.yaml']['submodels-by-name'] = dict() + for sm in run_data[jobid]['config.yaml']['submodels']: + run_data[jobid]['config.yaml']['submodels-by-name'][sm['name']] = sm + + # make a 'timing' entry to contain model timestep and run length for both MATM and YATM runs + # run length is [years, months, days, seconds] to accommodate both MATM and YATM + for jobid in run_data: + r = run_data[jobid] + timing = dict() + if r['namelists']['accessom2.nml'] is None: # non-YATM run + timing['Timestep'] = r['config.yaml']['submodels'][1]['timestep'] # MOM timestep + rt = r['config.yaml']['calendar']['runtime'] + timing['Run length'] = [rt['years'], rt['months'], rt['days'], 0] # insert 0 seconds + else: + timing['Timestep'] = r['namelists']['accessom2.nml']['accessom2_nml']['ice_ocean_timestep'] + rp = r['namelists']['accessom2.nml']['date_manager_nml']['restart_period'] + timing['Run length'] = rp[0:2] + [0] + [rp[2]] # insert 0 days + yrs = r['MOM_time_stamp.out']['Model run length (days)']/365.25 # FUDGE: assumes 365.25-day year + timing['SU per model year'] = r['PBS log']['Service Units']/yrs + timing['Walltime (hr) per model year'] = r['PBS log']['Walltime Used (hr)']/yrs + r['timing'] = timing + + # include changes in all git commits since previous run + for i, jobid in enumerate(sortedjobids): + print('.', end='', flush=True) + run_data[jobid]['git diff'] = \ + git_diff(basepath, + run_data[sortedjobids[max(i-1, 0)]]['git log']['Commit'], + run_data[jobid]['git log']['Commit']) + + # count failed jobs prior to each successful run + # BUG: always have zero count between two successful runs straddling a jobid rollover + # BUG: first run also counts all fails after a rollover + prevjobid = -1 + for i, jobid in enumerate(sortedjobids): + c = [e for e in all_run_data.keys() if e > prevjobid and e < jobid + and e not in run_data] + c.sort() + run_data[jobid]['PBS log']['Failed previous jobids'] = c + run_data[jobid]['PBS log']['Failed previous jobs'] = len(c) + prevjobid = jobid + + if list_available: + print('\nInformation which can be tabulated if added to output_format:') + keyliststr = [] + for k in keylistssuperset(run_data): + keyliststr.append("['" + "', '".join(k) + "']") + keyliststr.sort() + for k in keyliststr: + print(k) + + if dump_all: + dumpoutfile = os.path.splitext(outfile)[0]+'.yaml' + print('\nWriting', dumpoutfile) + with open(dumpoutfile, 'w') as outf: + yaml.dump(run_data, outf, default_flow_style=False) + + ########################################################################### + # Specify the output format here. + ########################################################################### + # output_format is a list of (key, value) tuples, one for each column. + # keys are headers (must be unique) + # values are lists of keys into run_data (omitting job id) + # + # run_data dict structure (use list_available for full details): + # + # run_data dict + # L___ job ID dict + # L___ 'PBS log' dict + # L___ 'git log' dict + # L___ 'git diff' dict + # L___ 'MOM_time_stamp.out' dict + # L___ 'config.yaml' dict + # L___ 'access-om2.out' dict + # L___ 'timing' dict + # L___ 'namelists' dict + # L___ 'accessom2.nml' namelist (or None if non-YATM run) + # L___ 'atmosphere/atm.nml' namelist (only if YATM run) + # L___ 'atmosphere/input_atm.nml' namelist (only if MATM run) + # L___ '/ice/cice_in.nml' namelist + # L___ 'ice/input_ice.nml' namelist + # L___ 'ice/input_ice_gfdl.nml' namelist + # L___ 'ice/input_ice_monin.nml' namelist + # L___ 'ocean/input.nml' namelist + # L___ job ID dict + # L___ ... etc + output_format = OrderedDict([ + ('Run number', ['PBS log', 'Run number']), + ('Run start', ['MOM_time_stamp.out', 'Model start time']), + ('Run end', ['MOM_time_stamp.out', 'Model end time']), + ('Run length (years, months, days, seconds)', ['timing', 'Run length']), + ('Run length (days)', ['MOM_time_stamp.out', 'Model run length (days)']), + ('Job Id', ['PBS log', 'Job Id']), + ('Failed previous jobs', ['PBS log', 'Failed previous jobs']), + ('Failed previous jobids', ['PBS log', 'Failed previous jobids']), + ('Run completion date', ['PBS log', 'Run completion date']), + ('Queue', ['config.yaml', 'queue']), + ('Service Units', ['PBS log', 'Service Units']), + ('Walltime Used (hr)', ['PBS log', 'Walltime Used (hr)']), + ('SU per model year', ['timing', 'SU per model year']), + ('Walltime (hr) per model year', ['timing', 'Walltime (hr) per model year']), + ('Memory Used (Gb)', ['PBS log', 'Memory Used (Gb)']), + ('NCPUs Used', ['PBS log', 'NCPUs Used']), + ('MOM NCPUs', ['config.yaml', 'submodels-by-name', 'ocean', 'ncpus']), + ('CICE NCPUs', ['config.yaml', 'submodels-by-name', 'ice', 'ncpus']), + ('Fraction of MOM runtime in oasis_recv', ['access-om2.out', 'oasis_recv', 'tfrac']), + ('Max MOM wait for oasis_recv (s)', ['access-om2.out', 'oasis_recv', 'tmax']), + ('Max CICE wait for coupler (s)', ['ice_diag.d', 'timing', 'waiting_o', 'node', 'max']), + ('Max CICE I/O time (s)', ['ice_diag.d', 'timing', 'ReadWrite', 'node', 'max']), + ('MOM tile layout', ['namelists', 'ocean/input.nml', 'ocean_model_nml', 'layout']), + ('CICE tile distribution', ['namelists', 'ice/cice_in.nml', 'domain_nml', 'distribution_type']), + ('CICE block_size_x', ['ice_diag.d', 'block_size_x']), + ('CICE block_size_y', ['ice_diag.d', 'block_size_y']), + ('Timestep (s)', ['timing', 'Timestep']), + ('MOM barotropic split', ['namelists', 'ocean/input.nml', 'ocean_model_nml', 'barotropic_split']), + ('CICE dynamic split (ndtd)', ['namelists', 'ice/cice_in.nml', 'setup_nml', 'ndtd']), + ('ktherm', ['namelists', 'ice/cice_in.nml', 'thermo_nml', 'ktherm']), + ('Common inputs', ['config.yaml', 'input']), + ('Atmosphere executable', ['config.yaml', 'submodels-by-name', 'atmosphere', 'exe']), + ('Atmosphere inputs', ['config.yaml', 'submodels-by-name', 'atmosphere', 'input']), + ('MOM executable', ['config.yaml', 'submodels-by-name', 'ocean', 'exe']), + ('MOM inputs', ['config.yaml', 'submodels-by-name', 'ocean', 'input']), + ('CICE executable', ['config.yaml', 'submodels-by-name', 'ice', 'exe']), + ('CICE inputs', ['config.yaml', 'submodels-by-name', 'ice', 'input']), + ('Payu version', ['PBS log', 'payu version']), + ('Git hash of run', ['git log', 'Commit']), + ('Commit date', ['git log', 'Date']), + ('Git-tracked file changes since previous run', ['git diff', 'Changed files']), + ('Git log messages since previous run', ['git diff', 'Messages']), + ]) + ########################################################################### + + if show_fails: + # output crash-related info (redefines order of any keys already in output_format) + output_format_prefix = OrderedDict([ + ('Job Id', ['PBS log', 'Job Id']), + ('Run completion date', ['PBS log', 'Run completion date']), + ('Exit Status', ['PBS log', 'Exit Status']), + ('Timeout', ['PBS log', 'Timeout']), + ('Walltime Requested (hr)', ['PBS log', 'Walltime Requested (hr)']), + ('Walltime Used (hr)', ['PBS log', 'Walltime Used (hr)']), + ('qsub_flags', ['config.yaml', 'qsub_flags']), + ]) + output_format_prefix.update(output_format) + output_format = output_format_prefix + else: + # output all namelist changes + output_format_nmls = OrderedDict() + nmls_any_runs = set(run_data[list(run_data.keys())[0]]['namelists'].keys()) + nmls_all_runs = nmls_any_runs + # avoid dict comprehension here to avoid python<2.7 syntax error + nmls_no_runs = dict([(k, True) for k in nmls_any_runs]) # True for namelists that are None for all runs + # nmls_no_runs = {k: True for k in nmls_any_runs} # True for namelists that are None for all runs + for jobid in run_data: + run_nmls = run_data[jobid]['namelists'] + nmls_any_runs = set(run_nmls.keys()) | nmls_any_runs + nmls_all_runs = set(run_nmls.keys()) & nmls_all_runs + for nml in set(nmls_all_runs): + if run_nmls[nml] is None: + nmls_all_runs.remove(nml) + for nml in run_nmls: + newnone = (nml is None) + if nml in nmls_no_runs: + nmls_no_runs[nml] = nmls_no_runs[nml] and newnone + else: + nmls_no_runs.update({nml: newnone}) + for nml in set(nmls_any_runs): + if nmls_no_runs[nml]: + nmls_any_runs.remove(nml) + + # add every changed group/variable in nml files that exist in all runs + for nml in nmls_all_runs: + # avoid dict comprehension here to avoid python<2.7 syntax error + nmllistall = dict([(jobid, + copy.deepcopy(run_data[jobid]['namelists'][nml])) + for jobid in run_data]) + # nmllistall = {jobid: copy.deepcopy(run_data[jobid]['namelists'][nml]) + # for jobid in run_data} + groups = nmltab.superset(nmltab.nmldiff(nmllistall)) + for group in groups: + for var in groups[group]: + ngv = [nml, group, var] + output_format_nmls.update(OrderedDict([ + (' -> '.join(ngv), ['namelists'] + ngv)])) + + # add all group/variables in nml files that exist in only some runs + for nml in nmls_any_runs - nmls_all_runs: + nmllistall = dict() + for jobid in run_data: + if nml in run_data[jobid]['namelists']: + if run_data[jobid]['namelists'][nml] is not None: + nmllistall.update({jobid: + copy.deepcopy(run_data[jobid]['namelists'][nml])}) + groups = nmltab.superset(nmllistall) + for group in groups: + for var in groups[group]: + ngv = [nml, group, var] + output_format_nmls.update(OrderedDict([ + (' -> '.join(ngv), ['namelists'] + ngv)])) + + # alphabetize + output_format_nmls = OrderedDict([(k, output_format_nmls[k]) + for k in sorted(output_format_nmls.keys())]) + + # add output_format entries for every namelist variable that has changed in any run + output_format.update(output_format_nmls) + + # output csv file according to output_format above + print('\nWriting', outfile) + with open(outfile, 'w', newline='') as csvfile: + csvw = csv.writer(csvfile, dialect='excel') + csvw.writerow(['Summary report generated by run_summary.py, https://github.com/aekiss/run_summary']) + csvw.writerow(['report generated:', datetime.datetime.now().replace(microsecond=0).astimezone().isoformat()]) + csvw.writerow(['control directory path:', basepath, 'git branch:', git_branch]) + csvw.writerow(['output path:', sync_path]) + csvw.writerow(output_format.keys()) # header + for jobid in sortedjobids: + csvw.writerow([dictget(run_data, [jobid] + keylist) for keylist in output_format.values()]) + print('Done.') + + return + + +if __name__ == '__main__': + import argparse + parser = argparse.ArgumentParser(description= + 'Summarise ACCESS-OM2 runs.\ + Latest version and help: https://github.com/aekiss/run_summary') + parser.add_argument('-f', '--show_fails', + action='store_true', default=False, + help='include failed runs (disables some output columns)') + parser.add_argument('-l', '--list', + action='store_true', default=False, + help='list all data that could be tabulated by adding it to output_format') + parser.add_argument('-d', '--dump_all', + action='store_true', default=False, + help='also dump all data to .yaml') + parser.add_argument('-o', '--outfile', type=str, + metavar='file', + default=None, + help="output file path; default is 'run_summary_.csv'\ + or 'run_summary_.csv' if sync dir path is invalid;\ + WARNING: will be overwritten") + parser.add_argument('path', metavar='path', type=str, nargs='*', + help='zero or more ACCESS-OM2 control directory paths; default is current working directory') + args = parser.parse_args() + show_fails = vars(args)['show_fails'] + lst = vars(args)['list'] + dump_all = vars(args)['dump_all'] + outfile = vars(args)['outfile'] + basepaths = vars(args)['path'] # a list of length >=0 since nargs='*' + if outfile is None: + if basepaths is None: + run_summary(show_fails=show_fails, list_available=lst, + dump_all=dump_all) + else: + for bp in basepaths: + try: + run_summary(show_fails=show_fails, basepath=bp, + list_available=lst, dump_all=dump_all) + except: + print('\nFailed. Error:', sys.exc_info()) + else: + if basepaths is None: + run_summary(show_fails=show_fails, outfile=outfile, + list_available=lst, dump_all=dump_all) + else: + for bp in basepaths: + try: + run_summary(show_fails=show_fails, basepath=bp, + outfile=outfile, list_available=lst, + dump_all=dump_all) + except: + print('\nFailed. Error:', sys.exc_info()) + +# TODO: run_diff : git diff between 2 runs \ No newline at end of file From 5b95929c5df4e5ca8981e7d8d98663b4c8f5328d Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Fri, 12 Jun 2020 20:04:03 +1000 Subject: [PATCH 073/111] remove calving diagnostics --- ocean/diag_table | 3 --- ocean/diag_table_source.yaml | 3 --- 2 files changed, 6 deletions(-) diff --git a/ocean/diag_table b/ocean/diag_table index 5a5adc8f..09cd16d4 100644 --- a/ocean/diag_table +++ b/ocean/diag_table @@ -341,9 +341,6 @@ ACCESS-OM2 "ocean_model", "temp_global_ave", "temp_global_ave", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 "ocean_model", "temp_surface_ave", "temp_surface_ave", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 "ocean_model", "total_net_sfc_heating", "total_net_sfc_heating", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 -"ocean_model", "total_ocean_calving_heat", "total_ocean_calving_heat", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 -"ocean_model", "total_ocean_calving_melt_heat", "total_ocean_calving_melt_heat", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 -"ocean_model", "total_ocean_calving", "total_ocean_calving", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 "ocean_model", "total_ocean_evap_heat", "total_ocean_evap_heat", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 "ocean_model", "total_ocean_evap", "total_ocean_evap", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 "ocean_model", "total_ocean_fprec_melt_heat", "total_ocean_fprec_melt_heat", "ocean-scalar-1-daily-ym%4yr%2mo", "all", "none", "none", 1 diff --git a/ocean/diag_table_source.yaml b/ocean/diag_table_source.yaml index 2308882a..afbf06c8 100755 --- a/ocean/diag_table_source.yaml +++ b/ocean/diag_table_source.yaml @@ -286,9 +286,6 @@ diag_table: temp_global_ave: temp_surface_ave: total_net_sfc_heating: - total_ocean_calving_heat: - total_ocean_calving_melt_heat: - total_ocean_calving: total_ocean_evap_heat: total_ocean_evap: total_ocean_fprec_melt_heat: From 10f74f0d9fc92c0223c63b4c0714b2077d635d56 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Tue, 16 Jun 2020 16:41:46 +1000 Subject: [PATCH 074/111] add nmltab.py and update run_summary.py --- nmltab.py | 745 +++++++++++++++++++++++++++++++++++++++++++++++++ run_summary.py | 61 ++-- 2 files changed, 773 insertions(+), 33 deletions(-) create mode 100755 nmltab.py diff --git a/nmltab.py b/nmltab.py new file mode 100755 index 00000000..0989eebf --- /dev/null +++ b/nmltab.py @@ -0,0 +1,745 @@ +#!/usr/bin/env python +""" + +General-purpose tools to semantically tabulate, diff and superset Fortran namelist files. +Also includes a command-line interface. + +Latest version: https://github.com/aekiss/nmltab +Author: Andrew Kiss https://github.com/aekiss +Apache 2.0 License http://www.apache.org/licenses/LICENSE-2.0.txt +""" + + +# TODO: handle multiple groups with the same name. tidy should consolidate names, with definitions in later groups taking priority if the same name is defined in two groups of the same name. What happens if a name is repeated in one group? Ask Marshall. + +from __future__ import print_function + +# for testing my modified f90nml +# import sys +# sys.path.insert(0, '/Users/andy/Documents/COSIMA/github/aekiss/f90nml') # BUG: doesn't work with /Users/andy/anaconda/bin/python3 /Users/andy/bin/nmltab.py --fmt latex new/control/025deg_jra55_ryf/ice/input_ice_gfdl.nml + +import f90nml # from http://f90nml.readthedocs.io +import filecmp +import textwrap +import copy +import warnings +import collections +import os +import itertools + +# from IPython.display import display, Markdown + + +def nmldict(nmlfnames): + """ + Return OrderedDict of the groups and variables in Fortran namelist files. + + Parameters + ---------- + nmlfnames : str, tuple or list + string, or tuple or list of any number of namelist file path strings. + Repeated files are silently ignored. + If a file contains repeated groups, only the first instance is used. + + Returns + ------- + OrderedDict + OrderedDict with `key`:`value` pairs where + `key` is filename path string (in supplied order) + `value` is complete Namelist from filename as returned by f90nml.read + + """ + if isinstance(nmlfnames, str): + nmlfnames = [nmlfnames] + + nmlall = collections.OrderedDict() # dict keys are nml paths, values are Namelist dicts + for nml in nmlfnames: + nmlall[nml] = f90nml.read(nml) + if len(nmlall[nml]) == 0: + warnings.warn('{} does not contain any namelist data'.format(nml)) + for nml in nmlall: + for group in nmlall[nml]: + if isinstance(nmlall[nml][group], list): + # A list indicates group is defined more than once in nml file. + # The list contains the groups in order of occurrence. + # For the nth group's values to have any effect in f90, + # the namelist needs to be read n times from the input file, + # without closing the file in between. + # If the same variable name occurs in multiple instances of + # the same group, the last read instance is used. + # Since we don't know how many times the group is read in f90, + # ignoring all but the first seems the safest option. + # TODO: provide an option to consolidate all groups in list? + warnings.warn('&{} occurs {} times in {}. Using only the first instance of this group.'.format(group, str(len(nmlall[nml][group])), nml)) + nmlall[nml][group] = nmlall[nml][group][0] + return nmlall + + +def superset(nmlall): + """ + Return dict of groups and variables present in any of the input Namelists. + + Parameters + ---------- + nmlall : dict or OrderedDict + dict (e.g. returned by nmldict) with `key`:`value` pairs where + `key` is arbitrary (typically a filename string) + `value` is Namelist (typically from filename via f90nml.read) + + Returns + ------- + dict + dict with `key`:`value` pairs where + `key` is group name (including all groups present in any input Namelist) + `value` is Namelist for group (including every variable present in this + group in any input Namelist) + + """ + # if len(nmlall) == 1: # just do a deep copy of the only value + # nmlsuperset = copy.deepcopy(nmlall[list(nmlall.keys())[0]]) + # else: + nmlsuperset = {} + for nml in nmlall: + nmlsuperset.update(nmlall[nml]) + # nmlsuperset now contains all groups that were in any nml + for group in nmlsuperset: + # to avoid the next bit changing the original groups + nmlsuperset[group] = nmlsuperset[group].copy() + # if isinstance(nmlallsuperset[group], list): + # for gr in nmlall[nml][group]: + # nmlsuperset[group].update(gr) + for nml in nmlall: + if group in nmlall[nml]: + nmlsuperset[group].update(nmlall[nml][group]) + # nmlsuperset groups now contain all keys that were in any nml + return nmlsuperset + + +def nmldiff(nmlall, keep=''): + """ + In-place remove every group/variable that's the same in all file Namelists. + + Parameters + ---------- + nmlall : dict or OrderedDict + dict (e.g. returned by nmldict) with `key`:`value` pairs where + `key` is arbitrary (typically a filename path string) + `value` is Namelist (typically from filename via f90nml.read) + keep : variable name + variable name to always keep in diff, unless the group has no differences + + Returns + ------- + dict or OrderedDict + In-place modified input dict with `key`:`value` pairs where + `key` is arbitrary (typically a filename path string) + `value` is Namelist from nmlall, with any variable + common to all other keys (i.e. files) in input removed. + Groups whose contents are identical are also removed. + + """ +# Create diff by removing common groups/variables from nmlall. +# This is complicated by the fact group names / variable names may differ +# or be absent across different nml files. +# +# First make a superset that has all group names and variables that +# appear in any nml file + nmlsuperset = superset(nmlall) + + # now go through nmlall and remove any groups / variables from nmlall that + # are identical to superset in all nmls + # first delete any variables that are common to all nmls, then delete + # any empty groups common to all nmls + for group in nmlsuperset: + # init: whether group is present and identical in all namelist files + deletegroup = True + varkept = False # whether var is kept when it would otherwise be deleted + onlyvarkept = False # whether var is kept and is the only var in this group across all nmls + for nml in nmlall: + deletegroup = deletegroup and (group in nmlall[nml]) + if deletegroup: # group present in all namelist files + for var in nmlsuperset[group]: + # init: whether variable is present and identical + # in all namelist files + deletevar = True + for nml in nmlall: + deletevar = deletevar and (var in nmlall[nml][group]) + if deletevar: # variable is present in all namelist files + for nml in nmlall: + # ... now check if values match in all namelist files + # print("nml={}, group={}, var={}".format(nml, group, var)) + deletevar = deletevar and \ + (nmlall[nml][group][var] == + nmlsuperset[group][var]) + if deletevar: + if var == keep: + varkept = True + else: + for nml in nmlall: + # delete var from this group in all nmls + del nmlall[nml][group][var] + if varkept: + onlyvarkept = True + for nml in nmlall: + onlyvarkept = onlyvarkept and len(nmlall[nml][group]) < 2 + if onlyvarkept and len(nmlall[nml][group]) == 1: + onlyvarkept = list(nmlall[nml][group].keys())[0] == keep + if onlyvarkept: + deletegroup = True + else: + deletegroup = max([len(nmlall[nml][group]) for nml in nmlall]) == 0 + if deletegroup: + # group is common to all nmls and now empty (or only holding keep) so delete + for nml in nmlall: + del nmlall[nml][group] + return nmlall + + +def prunefilelist(fnames): + """ + Remove names of files with identical content to the previous file in list. + + Parameters + ---------- + fnames : List + List of any number of file path strings. + + Returns + ------- + List + New list in same order as fnames but including only names of files with + content that is not identical to that of the previous file in the list. + Non-existent files are ignored and not included in output list. + + Examples + -------- + >>> nmlprune(nmldict(prunefilelist(glob.glob(*.nml)))) + + """ + fntmp = [fn for fn in fnames if os.path.isfile(fn)] + if len(fntmp) <= 1: + outfnames = fntmp + else: + outfnames = [] + outfnames.append(fntmp[0]) + for fn in fntmp[1:]: + if not(filecmp.cmp(outfnames[-1], fn, shallow=False)): + outfnames.append(fn) + return outfnames + + +def nmlprune(nmlall, ignore={}): + """ + In-place remove all Namelists that are the same as the previous one in nmlall. + + Does nothing if nml is not an OrderedDict. + + Parameters + ---------- + nmlall : OrderedDict + OrderedDict (e.g. returned by nmldict) with `key`:`value` pairs where + `key` is arbitrary (typically a filename path string) + `value` is Namelist (typically from filename via f90nml.read) + For efficiency use prunefilelist on file list before passing to nmldict. + + ignore : dict, optional, default={} + dict specifying namelist variables whose differences should be ignored. + key is namelist group + value is a list of variable names within that group + + Returns + ------- + OrderedDict + In-place modified input OrderedDict with `key`:`value` pairs where + `key` is arbitrary (typically a filename path string) + `value` is Namelist from nmlall, with any variable + common to all other keys (i.e. files) in input removed. + Groups whose contents are identical are also removed. + + Examples + -------- + >>> nmlprune(nmldict(prunefilelist(glob.glob(*.nml)))) + """ + if len(nmlall) > 1: + idx = 0 + while True: + # need deepcopy to avoid in-place modification by nmldiff + pair = copy.deepcopy(collections.OrderedDict( + itertools.islice(nmlall.items(), idx, idx+2))) + for group in ignore: + for var in ignore[group]: + for fn in pair: + if group in pair[fn]: + if var in pair[fn][group]: + del pair[fn][group][var] + nmldiff(pair) + if max([len(x) for x in pair.values()]) == 0: + del nmlall[list(pair.keys())[1]] # remove 2nd of pair + else: + idx += 1 # 2nd of pair is different from first, so retain it + if idx > len(nmlall)-2: + break + return nmlall + + +def tidy_overwrite(nmlall): + """ + Overwrite namelist files with parsed namelist data from those files, + sorted alphabetically by group then variable name. + Files with no namelist data are left untouched. + + Parameters + ---------- + nmlall : dict or OrderedDict + dict (e.g. returned by nmldict) with `key`:`value` pairs where + `key` is filename path string to be overwritten + `value` is Namelist (typically from filename via f90nml.read) + + Returns + ------- + None + + """ + for nml in nmlall: + if len(nmlall[nml]) > 0: + nmlout = nml + '-tmp' + try: + f90nml.write(nmlall[nml], nmlout, sort=True) + os.replace(nmlout, nml) + except: # TODO: don't use bare except + warnings.warn("Error {} tidying '{}'; file left untouched. \ +Delete part-converted file '{}' before trying again." + .format(sys.exc_info()[0], nml, nmlout)) + return None + + +def strnmldict(nmlall, fmt='', masterswitch='', hide={}, heading='', url=''): + """ + Return string representation of dict of Namelists. + + Parameters + ---------- + nmlall : dict or OrderedDict + dict (e.g. returned by nmldict) with `key`:`value` pairs where + `key` is arbitrary (typically a filename path string) + `value` is Namelist (typically from filename via f90nml.read) + + fmt : str, optional, case insensitive, default='' + 'md' or 'markdown': markdown string output + 'latex': latex string output (table only, suitable as an input file) + 'latex-complete': latex string, suitable for a complete .tex file + 'text': text output ([*] &group variable [value] file) + 'text-tight': as for 'text', but without aligned columns + anything else: standard string output (different from 'text') + + masterswitch : str, optional, case insensitive, default='' + key with boolean value that disables other variables in group + if present and false, e.g. 'use_this_module' in MOM. + NB: this key might be absent in namelist differences. + Only used for fmt='latex' or 'latex-complete'. + + hide : dict, optional, default={} + dict specifying namelist variables that will not be shown in output. + key is namelist group + value is a list of variable names within that group + Ignored for fmt='md' or 'markdown'. + TODO: implement for all formats + + heading : string, optional, default='' + string to be written above table if fmt='latex-complete' + + url : string, optional, default='' + url prefix for hyperlinked variables and groups if fmt='latex-complete' + url='' (the default) has no hyperlinks + + Returns + ------- + string + String representaion of nmlall. + Default lists alphabetically by group, variable, then dict key, + with undefined namelist variables shown as blank. + + """ + def latexstr(item): + return item.replace('_', '\\_').replace('/', '\\slash ').replace('%', '\%') + + def latexrepr(item): + if isinstance(item, str): + return "'" + latexstr(item) + "'" + elif isinstance(item, float): + return '\\num*{' + repr(item).replace('e+0', 'e+').replace('e-0', 'e-') + '}{}' + elif isinstance(item, list): + s = '' + for i in item: + s += latexrepr(i) + ', ' + return s[:-2] + else: + return repr(item) + + # TODO: fail on unknown fmt + # TODO: put data format in Fortran syntax eg for booleans and arrays - does nf90nml do this? + # - see f90repr in namelist.py: https://github.com/marshallward/f90nml/blob/master/f90nml/namelist.py#L405 + fmt = fmt.lower() + nmlss = superset(nmlall) + nmldss = superset(nmldiff(copy.deepcopy(nmlall))) # avoid in-place modification + fnames = list(nmlall.keys()) + colwidth = max((len(f) for f in fnames), default=0) # default keyword requires Python 3.4 or later + # TODO: test if the following works in python pre- and post-3.4 + # colwidth = max([len(f) for f in fnames] or [0]) # defaults to 0 if fnames is empty list, since empty list evaluates to False + + # TODO: would be faster & more efficient to .append a list of strings + # and then join them: + # http://docs.python-guide.org/en/latest/writing/structure/#mutable-and-immutable-types + st = '' + if fmt in ('md', 'markdown'): + if len(nmlss) > 0: + st += '| ' + 'File'.ljust(colwidth) + ' | ' + nvar = 0 + for group in sorted(nmlss): + for var in sorted(nmlss[group]): + st += '&' + group + '
' + var + ' | ' + nvar += 1 + st += '\n|-' + '-' * colwidth + ':|' + '--:|' * nvar + for fn in fnames: + st += '\n| ' + fn + ' | ' + for group in sorted(nmlss): + for var in sorted(nmlss[group]): + if group in nmlall[fn]: + if var in nmlall[fn][group]: + st += repr(nmlall[fn][group][var]) # TODO: use f90repr + st += ' | ' + st += '\n' + elif fmt.startswith('latex'): + if len(nmlss) > 0: + if fmt == 'latex': + st += textwrap.dedent(r""" + % Latex tabulation of Fortran namelist, auto-generated by nmltab.py + % + % Include this file in a latex document using \import{path/to/this/file}. + % The importing document requires + % \usepackage{ltablex, array, sistyle} + % and possibly (depending on definitions below) + % \usepackage{hyperref, color} + % and also needs to define 'nmldiffer', 'nmllink' and 'ignored' commands, e.g. + % \newcommand{\nmldiffer}[1]{#1} % no special display of differing variables + % \newcommand{\nmldiffer}[1]{\textbf{#1}} % bold display of differing variables + % \definecolor{hilite}{cmyk}{0, 0, 0.9, 0}\newcommand{\nmldiffer}[1]{\colorbox{hilite}{#1}}\setlength{\fboxsep}{0pt} % colour highlight of differing variables (requires color package) + % \newcommand{\nmllink}[2]{#1} % don't link variables + % \newcommand{\nmllink}[2]{\href{https://github.com/mom-ocean/MOM5/search?q=#2}{#1}} % link variables to documentation (requires hyperref package) + % \newcommand{\ignored}[1]{#1} % no special display of ignored variables + % \definecolor{ignore}{gray}{0.7}\newcommand{\ignored}[1]{\textcolor{ignore}{#1}} % gray display of ignored variables (but only in groups where masterswitch key is present and false, so may not work well for differences; requires color package) + % and also define the length 'nmllen' that sets the column width, e.g. + % \newlength{\nmllen}\setlength{\nmllen}{12ex} + + """) + elif fmt == 'latex-complete': + st = textwrap.dedent(r""" % generated by https://github.com/aekiss/nmltab + \documentclass[10pt]{article} + \usepackage[a4paper, truedimen, top=2cm,bottom=2cm,left=2cm,right=2cm]{geometry} + + \usepackage{PTSansNarrow} % narrow sans serif font for urls + \usepackage[scaled=.9]{inconsolata} % for texttt + \renewcommand{\familydefault}{\sfdefault} + + \usepackage[table,dvipsnames]{xcolor} % loads also colortbl + \definecolor{lightblue}{rgb}{0.93,0.95,1.0} % for table rows + \rowcolors{1}{lightblue}{white} + \definecolor{link}{rgb}{0,0,1} + \usepackage[colorlinks, linkcolor={link},citecolor={link},urlcolor={link}, + breaklinks, bookmarks, bookmarksnumbered]{hyperref} + \usepackage{url} + \usepackage{breakurl} + \urlstyle{sf} + + \usepackage{ltablex}\keepXColumns + \usepackage{array, sistyle} + + \usepackage[strings]{underscore} % allows hyphenation at underscores + \usepackage{datetime2}\DTMsetdatestyle{iso} + + \usepackage{makeidx} + \makeindex + + \usepackage{fancyhdr} + \pagestyle{fancy} + \renewcommand{\headrulewidth}{0pt} + \lfoot{{\footnotesize \textsl{Fortran namelist table generated by \url{https://github.com/aekiss/nmltab}}}} + \rfoot{\textsl{\today\ \DTMcurrenttime\ \DTMcurrentzone}} + + \begin{document} + + \definecolor{ignore}{gray}{0.7}\newcommand{\ignored}[1]{\textcolor{ignore}{#1}} % gray display of ignored variables (but only in groups where masterswitch key is present and false, so may not work well for differences; requires color package) + \newlength{\nmllen}\setlength{\nmllen}{12ex} + + """) + st += heading + if url is '': + st += r'\newcommand{\nmllink}[2]{#1\index{#1}}' + else: + st += 'Variables are weblinks to source code searches.\n' + st += r'\newcommand{\nmllink}[2]{\href{' + url + r'#2}{#1}\index{#1}}' + st += '\n' + # TODO: get this use case working: + # % \definecolor{hilite}{cmyk}{0, 0, 0.9, 0}\newcommand{\nmldiffer}[1]{\rowcolor{hilite}#1} % colour highlight of rows with differing variables (requires xcolor package) BUG: DOESN'T WORK! Misplaced \noalign due to leading \hfill (and namelist group name if at start of group) + st += '\\newcolumntype{R}{>{\\raggedleft\\arraybackslash}b{\\nmllen}}\n' + st += '\\begin{tabularx}{\\linewidth}{X' + 'R' * len(fnames) + '}\n' + st += '\\hline\n\\hiderowcolors\n' + st += '\\textbf{Group\\quad\\hfill Variable}' + # for fn in rmcommonprefix(rmcommonsuffix(fnames)): + for fn in fnames: + st += '\t & \t\\textbf{' + latexstr(fn) + '}' + st += ' \\\\\n\\showrowcolors\n\\hline\\endfirsthead\n' + st += '\\hline\n\\hiderowcolors\n' + st += '\\textbf{Group (continued)\\quad\\hfill Variable}' + # for fn in rmcommonprefix(rmcommonsuffix(fnames)): + for fn in fnames: + st += '\t & \t\\textbf{' + latexstr(fn) + '}' + st += ' \\\\\n\\showrowcolors\n\\hline\\endhead\n' + for group in sorted(nmlss): + firstvar = True + for var in sorted(nmlss[group]): + if not ((group in hide) and (var in hide[group])): + if firstvar: # only show group once + gr = '\\&\\nmllink{{{}}}{{{}}}'.format( + latexstr(group), group) + firstvar = False + else: + gr = '' + st1 = '{} \\hfill \\nmllink{{{}}}{{{}}}'.format( + gr, latexstr(var), var) # replaced below if differences + if group in nmldss: + if var in nmldss[group]: # new st1 if differences + st1 = '{} \\hfill \\nmldiffer{{\\nmllink{{{}}}{{{}}}}}'.format( + gr, latexstr(var), var) + st += st1 + for fn in fnames: + st += '\t & \t' + if group in nmlall[fn]: + if var in nmlall[fn][group]: + st1 = latexrepr(nmlall[fn][group][var]) # TODO: use f90repr + if masterswitch in nmlall[fn][group]: + if not nmlall[fn][group][masterswitch] \ + and var != masterswitch: + st1 = '\\ignored{' + st1 + '}' + st += st1 + st += ' \\\\\n' + if not firstvar: + st += '\\hline\n' + st += '\\end{tabularx}\n' + if fmt == 'latex-complete': + st += textwrap.dedent(r""" + \clearpage + \phantomsection % fix hyperrefs to index + \addcontentsline{toc}{part}{\indexname} + \printindex + \end{document} + """) + elif fmt.startswith('text'): + if fmt == 'text': + gwidth = max([len(g) for g in list(nmlss.keys())], default=0) + vwidth = max([max([len(v) for v in list(g.keys())], default=0) + for g in list(nmlss.values())], default=0) + dwidth = max([ + max([max([len(repr(v)) for v in list(g.values())], default=0) + for g in list(nmlall[fn].values())], default=0) + for fn in nmlall.keys()], default=0) + else: # assumes text-tight - TODO: be more stringent + gwidth = 0 + vwidth = 0 + dwidth = 0 + for group in sorted(nmlss): + for var in sorted(nmlss[group]): + if not ((group in hide) and (var in hide[group])): + st1 = ' ' + if group in nmldss: + if var in nmldss[group]: # star if differences + st1 = '* ' + for fn in fnames: + st += st1 + '&' + group.ljust(gwidth) + ' ' + var.ljust(vwidth) + ' ' + dstr = '' + if group in nmlall[fn]: + if var in nmlall[fn][group]: + dstr = repr(nmlall[fn][group][var]) # TODO: use f90repr + st += dstr.ljust(dwidth) + ' ' + fn + '\n' + else: + for group in sorted(nmlss): + for var in sorted(nmlss[group]): + if not ((group in hide) and (var in hide[group])): + st += ' ' * (colwidth + 2) + '&{}\n'.format(group) + st += ' ' * (colwidth + 2) + ' {}\n'.format(var) + for fn in fnames: + st += '{} : '.format(fn.ljust(colwidth)) + if group in nmlall[fn]: + if var in nmlall[fn][group]: + st += repr(nmlall[fn][group][var]) # TODO: use f90repr + st += '\n' + return st + + +def nml_md(nmlfnames, diff=False, prune=False, + ignore={'setup_nml': ['istep0'], + 'coupling': ['inidate', 'truntime0']}): + """ + Display table in a Jupter notebook of groups and variables in Fortran + namelist files. + + Parameters + ---------- + nmlfnames : str, tuple or list + string, or tuple or list of any number of namelist file path strings. + Repeated files are silently ignored. + + diff : boolean, optional, default=False + just display semantic differences + + prune : boolean, optional, default=False + just display the first file in which each variable change occurs + + ignore : dict, optional, + default={'setup_nml': ['istep0'], 'coupling': ['inidate', 'truntime0']} + variable names to ignore differences in if prune=True + + Returns + ------- + None + + """ + from IPython.display import display, Markdown # slow to load so do it here + if prune: + nmld = nmldict(prunefilelist(nmlfnames)) + else: + nmld = nmldict(nmlfnames) + if diff: + nmldiff(nmld) + if prune: + nmlprune(nmld, ignore=ignore) + display(Markdown(strnmldict(nmld, fmt='md'))) + return None + + +# def nmldiff_md(nmlfnames): +# """ +# Display table in a Jupter notebook of semantic differences in groups and +# variables in Fortran namelist files. +# +# Parameters +# ---------- +# nmlfnames : str, tuple or list +# string, or tuple or list of any number of namelist file path strings. +# Repeated files are silently ignored. +# +# Returns +# ------- +# None +# +# """ +# from IPython.display import display, Markdown # slow to load so do it here +# display(Markdown(strnmldict(nmldiff(nmldict(nmlfnames)), fmt='md'))) +# return None + + +if __name__ == '__main__': + import argparse + import sys + parser = argparse.ArgumentParser(description= + 'Semantically tabulate (and optionally diff) multiple Fortran namelist files.\ + Undefined namelist variables are shown as blank.\ + Repeated files are silently ignored.\ + Latest version: https://github.com/aekiss/nmltab') + parser.add_argument('-d', '--diff', + action='store_true', default=False, + help='only show semantic differences (default: show all); \ + exit code 0: no differences; 1: differences') + parser.add_argument('-p', '--prune', + action='store_true', default=False, + help='ignore all but the first in any sequence of files \ + with semantically indentical content') + parser.add_argument('-i', '--ignore_counters', + action='store_true', default=False, + help='when doing --prune, ignore differences in timestep\ + counters etc in CICE and MATM namelists, and also hide\ + them from output (ignored for markdown output)') + parser.add_argument('-k', '--keep', type=str, + metavar='str', default='', + help="variable to always keep in diff, unless it's the\ + only one in a group, e.g. 'use_this_module'") + parser.add_argument('-F', '--format', type=str, + metavar='fmt', default='str', + choices=['markdown', 'latex', 'latex-complete', + 'text', 'text-tight'], + help="optional alternative output format: \ + 'markdown' or 'latex' (table only, suitable as an \ + input file) or 'latex-complete' (a complete .tex file) \ + or 'text' (plain text; with each row row showing \ + [*] &group variable [value] file) \ + or 'text-tight' (like 'text', but without aligned columns)") + parser.add_argument('-u', '--url', type=str, + metavar='url', default='', + help="link all variable and group names to this \ + URL followed by the variable/group name, e.g. \ + https://github.com/COSIMA/libaccessom2/search?q=") + parser.add_argument('--tidy_overwrite', + action='store_true', default=False, + help='OVERWRITE files with only their parsed contents \ + (all comments and non-namelist content are removed), \ + with consistent formatting and sorted alphabetically \ + by group then variable name. \ + This makes standard diff much more useful. \ + Files with no namelist data are left untouched. \ + All other options are ignored. \ + USE WITH CARE!') + parser.add_argument('file', metavar='file', type=str, nargs='+', + help='Fortran namelist file') + args = parser.parse_args() + fmt = vars(args)['format'] + url = vars(args)['url'] + keep = vars(args)['keep'] + diff = vars(args)['diff'] + prune = vars(args)['prune'] + ignore = vars(args)['ignore_counters'] + tidy = vars(args)['tidy_overwrite'] + files = vars(args)['file'] + if prune and ignore: + ignored = {'setup_nml': ['istep0'], #, 'npt', 'restart', 'runtype'], + 'coupling': ['inidate', 'runtime', 'truntime0']} + else: + ignored = {} + if prune and not tidy: + nmld = nmldict(prunefilelist(files)) + else: + nmld = nmldict(files) + if tidy: + tidy_overwrite(nmld) + else: + if diff: + nmldiff(nmld, keep=keep) + if prune: + nmlprune(nmld, ignore=ignored) + nmldss = superset(nmld) + if len(nmldss) == 0: + sys.exit(0) + else: + if fmt == 'latex-complete': + if diff: + heading = textwrap.dedent(r""" + \newcommand{\nmldiffer}[1]{#1} % no special display of differing variables + \noindent Only differences are shown. + \ignored{Greyed values} are ignored. + """) + else: + heading = textwrap.dedent(r""" + \definecolor{hilite}{cmyk}{0, 0, 0.9, 0}\newcommand{\nmldiffer}[1]{\colorbox{hilite}{#1}}\setlength{\fboxsep}{0pt} + \noindent Variables that differ between the namelists are \nmldiffer{\textcolor{link}{highlighted}}. + \ignored{Greyed values} are ignored. + """) + print(strnmldict(nmld, fmt=fmt, masterswitch='use_this_module', + hide=ignored, heading=heading, url=url), + end='', flush=True) + else: + print(strnmldict(nmld, fmt=fmt, masterswitch='use_this_module', + hide=ignored), + end='', flush=True) + if diff: + sys.exit(1) + else: + sys.exit(0) diff --git a/run_summary.py b/run_summary.py index 62a75a13..fa8c76f8 100755 --- a/run_summary.py +++ b/run_summary.py @@ -541,11 +541,12 @@ def keylistssuperset(d): def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, - dump_all=False, show_fails=False): + dump_all=False, show_fails=False, outfile_syncdir=False): """ Generate run summary """ - print('Reading run data from ' + basepath, end='') + basepath = os.path.abspath(basepath) + print('Generating run summary of ' + basepath, end='') # get jobname from config.yaml -- NB: we assume this is the same for all jobs with open(os.path.join(basepath, 'config.yaml'), 'r') as infile: @@ -559,11 +560,10 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, sync_path = None if outfile is None: - if sync_path: - # outfile = 'run_summary_' + os.path.split(sync_path)[1] + '.csv' + if outfile_syncdir and sync_path: outfile = 'run_summary_' + sync_path.strip(os.sep).replace(os.sep, '_') + '.csv' else: - outfile = 'run_summary_' + os.path.abspath(basepath).strip(os.sep).replace(os.sep, '_') + '.csv' + outfile = 'run_summary_' + basepath.strip(os.sep).replace(os.sep, '_') + '.csv' # if show_fails: # outfile = os.path.splitext(outfile)[0]+'_fails.csv' @@ -921,9 +921,18 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, parser.add_argument('-o', '--outfile', type=str, metavar='file', default=None, - help="output file path; default is 'run_summary_.csv'\ - or 'run_summary_.csv' if sync dir path is invalid;\ - WARNING: will be overwritten") + help="output file path; default is\ + 'run_summary_.csv';\ + overrides --outfile_syncdir if set.\ + WARNING: output file will be overwritten") + parser.add_argument('--outfile_syncdir', + action='store_true', default=False, + help="set output file path to\ + 'run_summary_.csv'\ + or 'run_summary_.csv' if sync dir\ + path is invalid;\ + ignored if '-o', '--outfile' is set.\ + WARNING: output file will be overwritten") parser.add_argument('path', metavar='path', type=str, nargs='*', help='zero or more ACCESS-OM2 control directory paths; default is current working directory') args = parser.parse_args() @@ -931,29 +940,15 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, lst = vars(args)['list'] dump_all = vars(args)['dump_all'] outfile = vars(args)['outfile'] + outfile_syncdir = vars(args)['outfile_syncdir'] basepaths = vars(args)['path'] # a list of length >=0 since nargs='*' - if outfile is None: - if basepaths is None: - run_summary(show_fails=show_fails, list_available=lst, - dump_all=dump_all) - else: - for bp in basepaths: - try: - run_summary(show_fails=show_fails, basepath=bp, - list_available=lst, dump_all=dump_all) - except: - print('\nFailed. Error:', sys.exc_info()) - else: - if basepaths is None: - run_summary(show_fails=show_fails, outfile=outfile, - list_available=lst, dump_all=dump_all) - else: - for bp in basepaths: - try: - run_summary(show_fails=show_fails, basepath=bp, - outfile=outfile, list_available=lst, - dump_all=dump_all) - except: - print('\nFailed. Error:', sys.exc_info()) - -# TODO: run_diff : git diff between 2 runs \ No newline at end of file + if not basepaths: + basepaths = [os.getcwd()] + for bp in basepaths: + try: + run_summary(show_fails=show_fails, basepath=bp, + outfile=outfile, list_available=lst, + dump_all=dump_all, + outfile_syncdir=outfile_syncdir) + except: + print('\nFailed. Error:', sys.exc_info()) From 91b28ecf59bdf4317964599346096459083e800d Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Wed, 17 Jun 2020 08:38:55 +1000 Subject: [PATCH 075/111] increase memory from 500GB to 1000GB --- config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config.yaml b/config.yaml index 851b4b2e..a9153840 100644 --- a/config.yaml +++ b/config.yaml @@ -5,7 +5,7 @@ queue: normal walltime: 3:00:00 jobname: 1deg_jra55_iaf -mem: 500GB +mem: 1000GB # Force payu to always find, and save, files in this scratch project directory # shortpath: /scratch/w35 From d8bf17262771ce06c5ece5b3155fd60dac31df06 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Thu, 18 Jun 2020 17:59:05 +1000 Subject: [PATCH 076/111] improve .gitignore --- .gitignore | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/.gitignore b/.gitignore index d12dc6e2..a8658446 100644 --- a/.gitignore +++ b/.gitignore @@ -1,9 +1,8 @@ archive work +__pycache__ access-om2.err access-om2.out -*deg_jra55_*.[eo][0-9]+ -output_to_gdata.[eo][0-9]+ -restarts_to_gdata.[eo][0-9]+ +*.[eo][0-9]* .DS_Store -._.DS_Store +._* From 3ce3e15e0096454311e96ac30bbc53250787cbf1 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Thu, 18 Jun 2020 20:01:22 +1000 Subject: [PATCH 077/111] update and sync run_summary with sync_data.sh --- sync_data.sh | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/sync_data.sh b/sync_data.sh index dcbcb296..02d6ac69 100755 --- a/sync_data.sh +++ b/sync_data.sh @@ -3,7 +3,7 @@ #PBS -l ncpus=1 #PBS -l wd #PBS -l walltime=4:00:00,mem=4GB -#PBS -l storage=gdata/hh5+gdata/ik11+scratch/v45 +#PBS -l storage=gdata/hh5+gdata/ik11+scratch/v45+scratch/x77+scratch/g40 #PBS -N sync # Set SYNCDIR to the path you want your data copied to. @@ -100,6 +100,17 @@ rsync -vrltoD --safe-links pbs_logs ${SYNCDIR} cd ${SYNCDIR} || exit 1 ls git-runlog || git clone $sourcepath git-runlog cd git-runlog -git pull +git pull --no-rebase -echo $0" completed successfully" \ No newline at end of file +# update and sync run summary - do this last in case it doesn't work +cd $sourcepath +module use /g/data/hh5/public/modules +module load conda/analysis3 +module load python3-as-python +./run_summary.py +rsync -vrltoD --safe-links run_summary*.csv ${SYNCDIR} +git add run_summary*.csv +git commit -m "update run summary" +cd ${SYNCDIR}/git-runlog && git pull --no-rebase + +echo $0" completed successfully" From 1397888d557de82d3570adc8488fd2ca861bff44 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Thu, 18 Jun 2020 20:43:27 +1000 Subject: [PATCH 078/111] improve help in tidy_restarts.py and set default k=1 --- tidy_restarts.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/tidy_restarts.py b/tidy_restarts.py index 290da3f6..ebca097d 100755 --- a/tidy_restarts.py +++ b/tidy_restarts.py @@ -1,7 +1,7 @@ #!/usr/bin/env python """ -Tidy up restart directories - see argparse desciption below. +Tidy up restart directories - see argparse description below. This is best used with restart_freq: 1 in config.yaml. @@ -14,7 +14,7 @@ import sys from glob import glob -def tidy(yearskip=1, keeplast=6): +def tidy(yearskip=1, keeplast=1): yearskip = abs(yearskip) keeplast = max(1, abs(keeplast)) # always keep the last restart restarts = glob('archive/restart???') @@ -61,10 +61,10 @@ def tidy(yearskip=1, keeplast=6): This is best used with restart_freq: 1 in config.yaml.') parser.add_argument('-y', '--year-skip', type=int, metavar='n', default=1, - help="keep one restart every n years") + help="keep one restart every n years (default=1)") parser.add_argument('-k', '--keep-last', type=int, - metavar='n', default=6, - help="keep last n restarts") + metavar='m', default=1, + help="keep last m >= 1 restarts (default=1)") args = parser.parse_args() yearskip = vars(args)['year_skip'] keeplast = vars(args)['keep_last'] From bb215d34d68cd897b70b7efb03bc9c5ebac20fd8 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Thu, 18 Jun 2020 20:50:11 +1000 Subject: [PATCH 079/111] auto-resubmit on atmosphere/input.nml error https://github.com/payu-org/payu/issues/274 --- resub.sh | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/resub.sh b/resub.sh index e106fa43..38681542 100755 --- a/resub.sh +++ b/resub.sh @@ -8,9 +8,10 @@ MAX_RESUBMISSIONS=2 date >> ${logfile} # Define errors from which a resubmit is appropriate -declare -a errors=( +declare -a errors=( "Segmentation fault: address not mapped to object" "Transport retry count exceeded" + "atmosphere/input.nml" ) resub=false @@ -48,10 +49,9 @@ then ${PAYU_PATH}/payu sweep >> ${logfile} ${PAYU_PATH}/payu run -n ${PAYU_N_RUNS} >> ${logfile} # Decrement resub counter and save to counter file - ((PAYU_N_RESUB=PAYU_N_RESUB-1)) + ((PAYU_N_RESUB=PAYU_N_RESUB-1)) echo "${PAYU_N_RESUB}" > ${counterfile} else echo "Resubmit limit reached ... " >> ${logfile} rm ${counterfile} fi - From d9255d80739b37f30ebe65e4744efcccf59f40e1 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Thu, 18 Jun 2020 21:04:33 +1000 Subject: [PATCH 080/111] improved comments in config.yaml --- config.yaml | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/config.yaml b/config.yaml index a9153840..d30abaef 100644 --- a/config.yaml +++ b/config.yaml @@ -1,15 +1,18 @@ # PBS configuration -# If submitting to a different project to your default uncomment line below -# and change project code as appropriate -# project: w35 + +# If submitting to a different project to your default, uncomment line below +# and change project code as appropriate; also set shortpath below +# project: v45 + +# Force payu to always find, and save, files in this scratch project directory +# (you may need to add the corresponding PBS -l storage flag in sync_data.sh) +# shortpath: /scratch/v45 + queue: normal walltime: 3:00:00 jobname: 1deg_jra55_iaf mem: 1000GB -# Force payu to always find, and save, files in this scratch project directory -# shortpath: /scratch/w35 - # Model configuration name: common model: access-om2 @@ -66,6 +69,5 @@ userscripts: error: resub.sh run: rm -f resubmit.count -# DANGER! Do not uncomment this without checking the script is synching -# to the correct location! +# DANGER! Do not uncomment this without checking the script is syncing to the correct location! # postscript: sync_data.sh From 2c3295f8d2530e4c638859c620ead33747899a21 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Wed, 24 Jun 2020 10:48:22 +1000 Subject: [PATCH 081/111] update run_summary.py --- run_summary.py | 107 +++++++++++++++++++++++++++++++++++++++---------- 1 file changed, 85 insertions(+), 22 deletions(-) diff --git a/run_summary.py b/run_summary.py index fa8c76f8..4602766e 100755 --- a/run_summary.py +++ b/run_summary.py @@ -286,9 +286,9 @@ def parse_mom_time_stamp(paths): try: d1 = dateutil.parser.parse(parsed_items[keys[0]]) d2 = dateutil.parser.parse(parsed_items[keys[1]]) - len = d2-d1 # BUG: presumably assumes Gregorian calendar with leap years and time in UTC - parsed_items['Model run length (s)'] = len.total_seconds() - parsed_items['Model run length (days)'] = len.total_seconds()/3600/24 + duration = d2-d1 # BUG: presumably assumes Gregorian calendar with leap years and time in UTC + parsed_items['Model run length (s)'] = duration.total_seconds() + parsed_items['Model run length (days)'] = duration.total_seconds()/3600/24 except KeyError: pass return parsed_items @@ -541,11 +541,13 @@ def keylistssuperset(d): def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, - dump_all=False, show_fails=False, outfile_syncdir=False): + dump_all=False, show_fails=False, outfile_syncdir=False, + no_header=False): """ Generate run summary """ basepath = os.path.abspath(basepath) + archive_path = os.path.realpath(os.path.join(basepath, 'archive')) print('Generating run summary of ' + basepath, end='') # get jobname from config.yaml -- NB: we assume this is the same for all jobs @@ -581,7 +583,7 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, # NB: match jobname[:15] because in some cases the pbs log files use a shortened version of the jobname in config.yaml # e.g. see /home/157/amh157/payu/025deg_jra55_ryf8485 # NB: logs in archive may be duplicated in sync_path, in which case the latter is used - logfiles = glob.glob(os.path.join(basepath, 'archive/pbs_logs', jobname[:15] + '*.o*'))\ + logfiles = glob.glob(os.path.join(archive_path, 'pbs_logs', jobname[:15] + '*.o*'))\ + glob.glob(os.path.join(basepath, jobname[:15] + '*.o*')) if sync_path: logfiles += glob.glob(os.path.join(sync_path, 'pbs_logs', jobname[:15] + '*.o*')) @@ -592,6 +594,11 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, run_data[jobid] = dict() run_data[jobid]['PBS log'] = parse_pbs_log(f) run_data[jobid]['PBS log']['PBS log file'] = f + # fudge: these paths might actually apply only to the latest job + run_data[jobid]['paths'] = dict() + run_data[jobid]['paths']['Control path'] = basepath + run_data[jobid]['paths']['Sync path'] = sync_path + run_data[jobid]['paths']['Archive path'] = archive_path # get run data for all jobs for jobid in run_data: @@ -604,10 +611,39 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, # BUG: assumes the time zones match - no timezone specified in date - what does git assume? UTC? if pbs['Exit Status'] == 0: # output dir belongs to this job only if Exit Status = 0 outdir = 'output' + str(pbs['Run number']).zfill(3) + restartdir = 'restart' + str(pbs['Run number']).zfill(3) paths = [] + if sync_path: - paths += [os.path.join(sync_path, outdir)] - paths += [os.path.join(basepath, 'archive', outdir)] + sync_output_path = os.path.join(sync_path, outdir) + if os.path.isdir(sync_output_path): + paths += [sync_output_path] + run_data[jobid]['paths']['Sync output path'] =\ + sync_output_path + sync_restart_path = os.path.join(sync_path, restartdir) + if os.path.isdir(sync_restart_path): + run_data[jobid]['paths']['Sync restart path'] =\ + sync_restart_path + + archive_output_path = os.path.join(archive_path, outdir) + if os.path.isdir(archive_output_path): + paths += [archive_output_path] + run_data[jobid]['paths']['Archive output path'] =\ + archive_output_path + archive_restart_path = os.path.join(archive_path, restartdir) + if os.path.isdir(archive_restart_path): + run_data[jobid]['paths']['Archive restart path'] =\ + archive_restart_path + + # 'Sync output path' if it exists, otherwise 'Archive output path' + run_data[jobid]['paths']['Output path'] =\ + run_data[jobid]['paths'].get('Sync output path') or\ + run_data[jobid]['paths'].get('Archive output path') + # 'Sync restart path' if it exists, otherwise 'Archive restart path' + run_data[jobid]['paths']['Restart path'] =\ + run_data[jobid]['paths'].get('Sync restart path') or\ + run_data[jobid]['paths'].get('Archive restart path') + run_data[jobid]['MOM_time_stamp.out'] = parse_mom_time_stamp(paths) run_data[jobid]['config.yaml'] = parse_config_yaml(paths) run_data[jobid]['namelists'] = parse_nml(paths) @@ -687,7 +723,8 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, # make a 'timing' entry to contain model timestep and run length for both MATM and YATM runs # run length is [years, months, days, seconds] to accommodate both MATM and YATM - for jobid in run_data: + prevjobid = -1 + for jobid in sortedjobids: r = run_data[jobid] timing = dict() if r['namelists']['accessom2.nml'] is None: # non-YATM run @@ -701,7 +738,18 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, yrs = r['MOM_time_stamp.out']['Model run length (days)']/365.25 # FUDGE: assumes 365.25-day year timing['SU per model year'] = r['PBS log']['Service Units']/yrs timing['Walltime (hr) per model year'] = r['PBS log']['Walltime Used (hr)']/yrs + + if prevjobid >= 0: # also record time including wait between runs + d1 = dateutil.parser.parse(run_data[prevjobid]['PBS log']['Run completion date']) + d2 = dateutil.parser.parse(r['PBS log']['Run completion date']) + tot_walltime = (d2-d1).total_seconds()/3600 + timing['Walltime (hr) between this completion and previous completion'] = tot_walltime + timing['Wait (hr) between this run and previous'] = tot_walltime - r['PBS log']['Walltime Used (hr)'] + timing['SU per calendar day'] = r['PBS log']['Service Units']/tot_walltime*24 + timing['Model years per calendar day'] = yrs/tot_walltime*24 + r['timing'] = timing + prevjobid = jobid # include changes in all git commits since previous run for i, jobid in enumerate(sortedjobids): @@ -715,7 +763,7 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, # BUG: always have zero count between two successful runs straddling a jobid rollover # BUG: first run also counts all fails after a rollover prevjobid = -1 - for i, jobid in enumerate(sortedjobids): + for jobid in sortedjobids: c = [e for e in all_run_data.keys() if e > prevjobid and e < jobid and e not in run_data] c.sort() @@ -768,20 +816,29 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, # L___ job ID dict # L___ ... etc output_format = OrderedDict([ - ('Run number', ['PBS log', 'Run number']), + ('Run', ['PBS log', 'Run number']), ('Run start', ['MOM_time_stamp.out', 'Model start time']), ('Run end', ['MOM_time_stamp.out', 'Model end time']), - ('Run length (years, months, days, seconds)', ['timing', 'Run length']), + ('Run length (y, m, d, s)', ['timing', 'Run length']), ('Run length (days)', ['MOM_time_stamp.out', 'Model run length (days)']), - ('Job Id', ['PBS log', 'Job Id']), - ('Failed previous jobs', ['PBS log', 'Failed previous jobs']), - ('Failed previous jobids', ['PBS log', 'Failed previous jobids']), + ('Control directory', ['paths', 'Control path']), + # ('Archive directory', ['paths', 'Archive path']), + # ('Sync directory', ['paths', 'Sync path']), + ('Output directory', ['paths', 'Output path']), + ('Restart directory', ['paths', 'Restart path']), + ('Run by', ['git log', 'Author']), ('Run completion date', ['PBS log', 'Run completion date']), + ('Job Id', ['PBS log', 'Job Id']), + # ('Failed jobs', ['PBS log', 'Failed previous jobs']), + ('Failed jobids', ['PBS log', 'Failed previous jobids']), ('Queue', ['config.yaml', 'queue']), ('Service Units', ['PBS log', 'Service Units']), ('Walltime Used (hr)', ['PBS log', 'Walltime Used (hr)']), ('SU per model year', ['timing', 'SU per model year']), ('Walltime (hr) per model year', ['timing', 'Walltime (hr) per model year']), + ('Wait (hr) between runs', ['timing', 'Wait (hr) between this run and previous']), + ('SU per calendar day', ['timing', 'SU per calendar day']), + ('Model years per calendar day', ['timing', 'Model years per calendar day']), ('Memory Used (Gb)', ['PBS log', 'Memory Used (Gb)']), ('NCPUs Used', ['PBS log', 'NCPUs Used']), ('MOM NCPUs', ['config.yaml', 'submodels-by-name', 'ocean', 'ncpus']), @@ -808,8 +865,8 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, ('Payu version', ['PBS log', 'payu version']), ('Git hash of run', ['git log', 'Commit']), ('Commit date', ['git log', 'Date']), - ('Git-tracked file changes since previous run', ['git diff', 'Changed files']), - ('Git log messages since previous run', ['git diff', 'Messages']), + ('Git-tracked file changes', ['git diff', 'Changed files']), + ('Git log messages', ['git diff', 'Messages']), ]) ########################################################################### @@ -891,11 +948,12 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, # output csv file according to output_format above print('\nWriting', outfile) with open(outfile, 'w', newline='') as csvfile: - csvw = csv.writer(csvfile, dialect='excel') - csvw.writerow(['Summary report generated by run_summary.py, https://github.com/aekiss/run_summary']) - csvw.writerow(['report generated:', datetime.datetime.now().replace(microsecond=0).astimezone().isoformat()]) - csvw.writerow(['control directory path:', basepath, 'git branch:', git_branch]) - csvw.writerow(['output path:', sync_path]) + csvw = csv.writer(csvfile, dialect='excel', lineterminator='\n') + if not no_header: + csvw.writerow(['Summary report generated by run_summary.py, https://github.com/aekiss/run_summary']) + csvw.writerow(['report generated:', datetime.datetime.now().replace(microsecond=0).astimezone().isoformat()]) + csvw.writerow(['control directory path:', basepath, 'git branch:', git_branch]) + csvw.writerow(['output path:', sync_path]) csvw.writerow(output_format.keys()) # header for jobid in sortedjobids: csvw.writerow([dictget(run_data, [jobid] + keylist) for keylist in output_format.values()]) @@ -933,6 +991,9 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, path is invalid;\ ignored if '-o', '--outfile' is set.\ WARNING: output file will be overwritten") + parser.add_argument('--no_header', + action='store_true', default=False, + help="don't output header in output .csv") parser.add_argument('path', metavar='path', type=str, nargs='*', help='zero or more ACCESS-OM2 control directory paths; default is current working directory') args = parser.parse_args() @@ -941,6 +1002,7 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, dump_all = vars(args)['dump_all'] outfile = vars(args)['outfile'] outfile_syncdir = vars(args)['outfile_syncdir'] + no_header = vars(args)['no_header'] basepaths = vars(args)['path'] # a list of length >=0 since nargs='*' if not basepaths: basepaths = [os.getcwd()] @@ -949,6 +1011,7 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, run_summary(show_fails=show_fails, basepath=bp, outfile=outfile, list_available=lst, dump_all=dump_all, - outfile_syncdir=outfile_syncdir) + outfile_syncdir=outfile_syncdir, + no_header=no_header) except: print('\nFailed. Error:', sys.exc_info()) From 7bcb8159d3ac61d5d68ba24a98cf28321ecf1ecb Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Wed, 24 Jun 2020 10:55:50 +1000 Subject: [PATCH 082/111] update sync_data.sh to sync only collated .nc files --- sync_data.sh | 47 ++++++++++++++++++++++------------------------- 1 file changed, 22 insertions(+), 25 deletions(-) diff --git a/sync_data.sh b/sync_data.sh index 02d6ac69..7b5bb58a 100755 --- a/sync_data.sh +++ b/sync_data.sh @@ -15,7 +15,8 @@ SYNCDIR=/ERROR/SET/SYNCDIR/IN/sync_data.sh exitcode=0 help=false -restarts=false +dirtype=output +exclude="--exclude *.nc.*" rmlocal=false # parse argument list @@ -26,7 +27,11 @@ while [ $# -ge 1 ]; do ;; -r) echo "syncing restarts instead of output directories" - restarts=true + dirtype=restart + ;; + -u) + echo "syncing collated and uncollated .nc files" + exclude="" ;; -D) # --remove-source-files tells rsync to remove from the sending side the files (meaning non-directories) @@ -43,12 +48,10 @@ while [ $# -ge 1 ]; do ;; -*) echo $1": invalid option" - help=true exitcode=1 ;; *) echo $1": invalid argument" - help=true exitcode=1 ;; esac @@ -56,40 +59,34 @@ while [ $# -ge 1 ]; do done if [ $exitcode != "0" -o $help == true ]; then - echo $0": rsync model run outputs (and optionally restarts) to another location." + echo "$0: rsync model run outputs (and optionally restarts) to another location." echo " Must be invoked from a control directory." - echo " "$0" should be edited to set SYNCDIR." + echo " $0 should be edited to set SYNCDIR." echo " Default will rsync all output directories, leaving local copies intact." + echo " Uncollated .nc files are not rsynced unless the -u option is used." echo " Also rsyncs error_logs and pbs_logs." echo " Also updates git-runlog, a git clone of the control directory (whose git history documents all changes in the run)." - echo "usage: "$0" [-h] [-r] [-D]" + echo " Also updates, rsyncs and commits run summary" + echo "usage: $0 [-h] [-r] [-u] [-D]" echo " -h: show this help message and exit" - echo " -r: sync all restart directories (default syncs output directories)" + echo " -r: sync all restart directories instead of output directories" + echo " -u: sync collated and uncollated .nc files (default is collated only)" echo " -D: delete local copies of synced files in all but the most recent synced directories (outputs or restarts, depending on -r). Must be done interactively. (Default leaves local copies intact.)" exit $exitcode fi sourcepath="$PWD" -mkdir -p ${SYNCDIR} || exit 1 +mkdir -p ${SYNCDIR} || { echo "Error: cannot create ${SYNCDIR} - edit $0 to set SYNCDIR"; exit 1; } cd archive || exit 1 # first delete any cice log files that only have a 105-character header and nothing else find output* -size 105c -iname "ice.log.task_*" -delete -if [ $restarts == true ]; then - # only sync/remove restarts - rsync -vrltoD --safe-links restart* ${SYNCDIR} - if [ $rmlocal == true ]; then - # Now do removals. Don't remove final local copy, so we can continue run. - rsync --remove-source-files --exclude `\ls -1d restart[0-9][0-9][0-9] | tail -1` -vrltoD --safe-links restart* ${SYNCDIR} - fi -else - # default - only sync/remove outputs - rsync --exclude "*.nc.*" -vrltoD --safe-links output* ${SYNCDIR} - if [ $rmlocal == true ]; then - # Now do removals. Don't remove final local copy, so we can continue run. - rsync --remove-source-files --exclude `\ls -1d output[0-9][0-9][0-9] | tail -1` --exclude "*.nc.*" -vrltoD --safe-links output* ${SYNCDIR} - fi +# copy all collated outputs/restarts +rsync $exclude -vrltoD --safe-links $dirtype[0-9][0-9][0-9] ${SYNCDIR} +if [ $rmlocal == true ]; then + # Now do removals. Don't remove final local copy, so we can continue run. + rsync --remove-source-files --exclude `\ls -1d $dirtype[0-9][0-9][0-9] | tail -1` $exclude -vrltoD --safe-links $dirtype[0-9][0-9][0-9] ${SYNCDIR} fi # Also sync error and PBS logs @@ -107,10 +104,10 @@ cd $sourcepath module use /g/data/hh5/public/modules module load conda/analysis3 module load python3-as-python -./run_summary.py +./run_summary.py --no_header rsync -vrltoD --safe-links run_summary*.csv ${SYNCDIR} git add run_summary*.csv git commit -m "update run summary" cd ${SYNCDIR}/git-runlog && git pull --no-rebase -echo $0" completed successfully" +echo "$0 completed successfully" From 448a8cce40593ef9b9510c669e7b8143ba82358c Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Mon, 29 Jun 2020 20:55:07 +1000 Subject: [PATCH 083/111] collate on normal queue as wait time is negligible on gadi --- config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config.yaml b/config.yaml index d30abaef..a57dd696 100644 --- a/config.yaml +++ b/config.yaml @@ -54,7 +54,7 @@ collate: walltime: 1:00:00 mem: 30GB ncpus: 4 - queue: express + queue: normal exe: /g/data/ik11/inputs/access-om2/bin/mppnccombine # Misc From 0d544be18c84e52b846d5cea98aaf3f7376b457a Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Mon, 6 Jul 2020 18:16:28 +1000 Subject: [PATCH 084/111] extend forcing end date to 2019-01-01T00:00:00 --- accessom2.nml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/accessom2.nml b/accessom2.nml index 5707cca8..5bad2798 100644 --- a/accessom2.nml +++ b/accessom2.nml @@ -5,7 +5,7 @@ &date_manager_nml forcing_start_date = '1958-01-01T00:00:00' - forcing_end_date = '2018-01-01T00:00:00' + forcing_end_date = '2019-01-01T00:00:00' ! Runtime for a single segment/job/submit, format is years, months, seconds, ! two of which must be zero. From 5ae8e79b6f467561ad363e8aac795a2d9e2c243e Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Mon, 6 Jul 2020 20:13:11 +1000 Subject: [PATCH 085/111] move timestep details from README.md to accessom2.nml --- README.md | 2 +- accessom2.nml | 7 +++++++ 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 4cf4c995..38ec2a14 100644 --- a/README.md +++ b/README.md @@ -3,6 +3,6 @@ Standard configuration for 1 degree [ACCESS-OM2](https://github.com/COSIMA/acces For usage instructions, see the [ACCESS-OM2 wiki](https://github.com/COSIMA/access-om2/wiki). -Run length and timestep are set in `accessom2.nml`. The timestep is normally set to a factor of the JRA55-do forcing period of 3hr = 10800s, for example one of 100, 108, 120, 135, 144, 150, 180, 200, 216, 225, 240, 270, 300, 360, 400, 432, 450, 540, 600, 675, 720, 900, 1080, 1200, 1350, 1800, 2160, 2700, 3600 or 5400s. The default timestep for this configuration is 5400 seconds, and the model is stable with this timestep right from the start. However if you alter the configuration you may need a shorter timestep during the first year or two of model equilibration. +Run length and timestep are set in `accessom2.nml`. The default timestep for this configuration is 5400 seconds, and the model is stable with this timestep right from the start. However if you alter the configuration you may need a shorter timestep during the first year or two of model equilibration. **NOTE:** All ACCESS-OM2 model components and configurations are undergoing continual improvement. We strongly recommend that you "watch" this repo (see button at top of screen; ask to be notified of all conversations) and also watch [ACCESS-OM2](https://github.com/COSIMA/access-om2), all the [component models](https://github.com/COSIMA/access-om2/tree/master/src), and [payu](https://github.com/payu-org/payu) to be kept informed of updates, problems and bug fixes as they arise. diff --git a/accessom2.nml b/accessom2.nml index 5bad2798..ff41df1e 100644 --- a/accessom2.nml +++ b/accessom2.nml @@ -1,5 +1,12 @@ &accessom2_nml log_level = 'DEBUG' + + ! ice_ocean_timestep defines the MOM baroclinic timestep, CICE thermodynamic timestep + ! and MOM-CICE coupling interval, in seconds. + ! ice_ocean_timestep is normally a factor of the JRA55-do forcing period of 3hr = 10800s, + ! e.g. one of 100, 108, 120, 135, 144, 150, 180, 200, 216, 225, 240, 270, 300, 360, 400, 432, + ! 450, 540, 600, 675, 720, 900, 1080, 1200, 1350, 1800, 2160, 2700, 3600 or 5400 seconds. + ! The model is usually stable with a 5400s timestep, including in the initial spinup from rest. ice_ocean_timestep = 5400 &end From 8f43503f9a1df4c2e0c44eb45c10135d5a8a26c8 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Tue, 7 Jul 2020 17:36:03 +1000 Subject: [PATCH 086/111] fix namcouple comment - closes https://github.com/COSIMA/access-om2/issues/211 --- namcouple | 1 - 1 file changed, 1 deletion(-) diff --git a/namcouple b/namcouple index a096ecc0..2a44983a 100644 --- a/namcouple +++ b/namcouple @@ -16,7 +16,6 @@ ### 11 fields atm -> ice ### 17 fields ice -> ocn ### 7 fields ocn -> ice -### 1 fields ice -> atm 35 $END ######################################################################### From a5a2555c11dec62446c51f1412677218446ba42f Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Wed, 8 Jul 2020 14:42:01 +1000 Subject: [PATCH 087/111] add metadata.yaml and sync it --- metadata.yaml | 20 ++++++++++++++++++++ sync_data.sh | 28 ++++++++++++++++------------ 2 files changed, 36 insertions(+), 12 deletions(-) create mode 100644 metadata.yaml diff --git a/metadata.yaml b/metadata.yaml new file mode 100644 index 00000000..874e1a4c --- /dev/null +++ b/metadata.yaml @@ -0,0 +1,20 @@ +contact: Add your name here +email: Add your email address here +created: Add the date you started the experiment here (YYYY-MM-DD) +description: >- + 1 degree ACCESS-OM2 global model configuration under interannual forcing. + The configuration is based on that described in Kiss et al. (2020), + https://doi.org/10.5194/gmd-13-401-2020, but with many improvements. + Initial conditions are WOA13v2 potential temperature and practical salinity. + Run with JRA55-do v1.4.0 interannually-varying forcing with all solid runoff + converted to liquid runoff with no heat transfer. + Spin up starts 1 Jan 1958 and runs to 1 Jan 2019. +note: >- + Provide details here of any important problems or changes during the experiment, + e.g. when additional dignostics are output +keywords: + - one + - cosima + - access-om2-1 + - jra55-do-v1.4.0 + - iaf diff --git a/sync_data.sh b/sync_data.sh index 7b5bb58a..7d0ba345 100755 --- a/sync_data.sh +++ b/sync_data.sh @@ -10,6 +10,7 @@ # This must be a unique absolute path for your set of runs. # To share your data, sync to a subdirectory in /g/data/ik11/outputs/ # but first add an experiment description - see /g/data/ik11/outputs/README +# and make sure metadata.yaml is correct. # DOUBLE-CHECK SYNCDIR PATH IS UNIQUE SO YOU DON'T OVERWRITE EXISTING OUTPUT! SYNCDIR=/ERROR/SET/SYNCDIR/IN/sync_data.sh @@ -17,6 +18,7 @@ exitcode=0 help=false dirtype=output exclude="--exclude *.nc.*" +rsyncflags="-vrltoD --safe-links" rmlocal=false # parse argument list @@ -30,7 +32,7 @@ while [ $# -ge 1 ]; do dirtype=restart ;; -u) - echo "syncing collated and uncollated .nc files" + echo "ignoring exclusions - syncing collated and uncollated .nc files" exclude="" ;; -D) @@ -70,31 +72,33 @@ if [ $exitcode != "0" -o $help == true ]; then echo "usage: $0 [-h] [-r] [-u] [-D]" echo " -h: show this help message and exit" echo " -r: sync all restart directories instead of output directories" - echo " -u: sync collated and uncollated .nc files (default is collated only)" + echo " -u: ignore exclusions - sync collated and uncollated .nc files (default is collated only)" echo " -D: delete local copies of synced files in all but the most recent synced directories (outputs or restarts, depending on -r). Must be done interactively. (Default leaves local copies intact.)" exit $exitcode fi sourcepath="$PWD" -mkdir -p ${SYNCDIR} || { echo "Error: cannot create ${SYNCDIR} - edit $0 to set SYNCDIR"; exit 1; } +mkdir -p $SYNCDIR || { echo "Error: cannot create $SYNCDIR - edit $0 to set SYNCDIR"; exit 1; } cd archive || exit 1 # first delete any cice log files that only have a 105-character header and nothing else find output* -size 105c -iname "ice.log.task_*" -delete # copy all collated outputs/restarts -rsync $exclude -vrltoD --safe-links $dirtype[0-9][0-9][0-9] ${SYNCDIR} +rsync $exclude $rsyncflags $dirtype[0-9][0-9][0-9] $SYNCDIR if [ $rmlocal == true ]; then # Now do removals. Don't remove final local copy, so we can continue run. - rsync --remove-source-files --exclude `\ls -1d $dirtype[0-9][0-9][0-9] | tail -1` $exclude -vrltoD --safe-links $dirtype[0-9][0-9][0-9] ${SYNCDIR} + rsync --remove-source-files --exclude `\ls -1d $dirtype[0-9][0-9][0-9] | tail -1` $exclude $rsyncflags $dirtype[0-9][0-9][0-9] $SYNCDIR fi -# Also sync error and PBS logs -rsync -vrltoD --safe-links error_logs ${SYNCDIR} -rsync -vrltoD --safe-links pbs_logs ${SYNCDIR} +# Also sync error and PBS logs and metadata.yaml +rsync $rsyncflags error_logs $SYNCDIR +rsync $rsyncflags pbs_logs $SYNCDIR +cd $sourcepath +rsync $rsyncflags metadata.yaml $SYNCDIR -# create/update a clone of the run history in ${SYNCDIR}/git-runlog -cd ${SYNCDIR} || exit 1 +# create/update a clone of the run history in $SYNCDIR/git-runlog +cd $SYNCDIR || exit 1 ls git-runlog || git clone $sourcepath git-runlog cd git-runlog git pull --no-rebase @@ -105,9 +109,9 @@ module use /g/data/hh5/public/modules module load conda/analysis3 module load python3-as-python ./run_summary.py --no_header -rsync -vrltoD --safe-links run_summary*.csv ${SYNCDIR} +rsync $rsyncflags run_summary*.csv $SYNCDIR git add run_summary*.csv git commit -m "update run summary" -cd ${SYNCDIR}/git-runlog && git pull --no-rebase +cd $SYNCDIR/git-runlog && git pull --no-rebase echo "$0 completed successfully" From a7ba596d3c9e9c8f4a3e25edce156c1ebdbbfcaa Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Mon, 13 Jul 2020 14:39:32 +1000 Subject: [PATCH 088/111] keep all restarts --- config.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/config.yaml b/config.yaml index a57dd696..205e309d 100644 --- a/config.yaml +++ b/config.yaml @@ -60,6 +60,7 @@ collate: # Misc runlog: true stacksize: unlimited +restart_freq: 1 # use tidy_restarts.py instead qsub_flags: -W umask=027 # set number of cores per node (28 for normalbw, 48 for normal on gadi) platform: From 66841b7280d3fe4c81d1d3157a68b3c57e3e0623 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Mon, 13 Jul 2020 14:46:56 +1000 Subject: [PATCH 089/111] auto-resubmit on Segmentation fault: invalid permissions for mapped object error --- resub.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/resub.sh b/resub.sh index 38681542..55b2ed9a 100755 --- a/resub.sh +++ b/resub.sh @@ -10,6 +10,7 @@ date >> ${logfile} # Define errors from which a resubmit is appropriate declare -a errors=( "Segmentation fault: address not mapped to object" + "Segmentation fault: invalid permissions for mapped object" "Transport retry count exceeded" "atmosphere/input.nml" ) From 8d2b1b3d6c65a54c05269d359d2cd6618b927b40 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Tue, 14 Jul 2020 14:36:14 +1000 Subject: [PATCH 090/111] update run_summary.py --- run_summary.py | 148 ++++++++++++++++++++++++++++++++----------------- 1 file changed, 98 insertions(+), 50 deletions(-) diff --git a/run_summary.py b/run_summary.py index 4602766e..29197fc7 100755 --- a/run_summary.py +++ b/run_summary.py @@ -8,10 +8,7 @@ Apache 2.0 License http://www.apache.org/licenses/LICENSE-2.0.txt """ -# TODO: collect data on storage use on hh5 (and short?) with du -bs -# TODO: use starting date/time for determining git commit # TODO: use PAYU_N_RUNS - does this tell you whether the run is part of a sequence? if so we can determine queue wait for runs in a sequence - but sometimes it is None -# TODO: summary stats: specify list of excel commands e.g. ['sum', 'average', 'min', 'max'] as optional third tuple element in output_format and insert formulas for these. Or just calculate them in python? might as well, as Execel will save formulas as values if formulas aren't displayed... from __future__ import print_function import sys @@ -33,6 +30,7 @@ import copy try: + import numpy as np import yaml import f90nml # from https://f90nml.readthedocs.io/en/latest/ except ImportError: # BUG: don't get this exception if payu module loaded, even if on python 2.6.6 @@ -294,20 +292,22 @@ def parse_mom_time_stamp(paths): return parsed_items -def parse_config_yaml(paths): +def parse_yaml(paths, filename): """ - Return dict of items from parsed config.yaml. + Return dict of items from parsed yaml file. paths: list of base paths + filename: yaml filename to attempt to read from base paths - output: dict parsed from first matching config.yaml in paths + output: dict parsed from first matching filename in paths """ parsed_items = dict() for path in paths: - fname = os.path.join(path, 'config.yaml') - if os.path.isfile(fname): - with open(fname, 'r') as infile: - parsed_items = yaml.load(infile, Loader=yaml.FullLoader) + fpath = os.path.join(path, filename) + if os.path.isfile(fpath): + with open(fpath, 'r') as infile: + # Need to use load_all to handle manifests. Only return final part. + parsed_items = list(yaml.load_all(infile, Loader=yaml.FullLoader))[-1] break return parsed_items @@ -540,9 +540,19 @@ def keylistssuperset(d): return [s.split('\b') for s in all] +def tryfunc(func, arg): + """ + Return func(arg) or None if there's an exception. + """ + try: + return func(arg) + except: + return None + + def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, dump_all=False, show_fails=False, outfile_syncdir=False, - no_header=False): + no_header=False, no_stats=False): """ Generate run summary """ @@ -599,6 +609,7 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, run_data[jobid]['paths']['Control path'] = basepath run_data[jobid]['paths']['Sync path'] = sync_path run_data[jobid]['paths']['Archive path'] = archive_path + run_data[jobid]['storage'] = dict() # get run data for all jobs for jobid in run_data: @@ -644,11 +655,25 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, run_data[jobid]['paths'].get('Sync restart path') or\ run_data[jobid]['paths'].get('Archive restart path') + # find GiB for output and restart + for k in ['Output path', 'Restart path']: + path = run_data[jobid]['paths'][k] + if path: + p = subprocess.Popen('du -bs ' + path, + stdout=subprocess.PIPE, shell=True) + ret = p.communicate()[0].decode('ascii') + bytes = int(ret.split()[0]) + run_data[jobid]['storage'][k + ' GiB'] = \ + round(bytes/1073741824, 3) + run_data[jobid]['MOM_time_stamp.out'] = parse_mom_time_stamp(paths) - run_data[jobid]['config.yaml'] = parse_config_yaml(paths) run_data[jobid]['namelists'] = parse_nml(paths) run_data[jobid]['access-om2.out'] = parse_accessom2_out(paths) run_data[jobid]['ice_diag.d'] = parse_ice_diag_d(paths) + run_data[jobid]['metadata.yaml'] = parse_yaml([basepath, sync_path], 'metadata.yaml') + for fn in ['config.yaml', 'env.yaml', 'job.yaml', + 'manifests/exe.yaml', 'manifests/input.yaml', 'manifests/restart.yaml']: + run_data[jobid][fn] = parse_yaml(paths, fn) all_run_data = copy.deepcopy(run_data) # all_run_data includes failed jobs @@ -738,6 +763,9 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, yrs = r['MOM_time_stamp.out']['Model run length (days)']/365.25 # FUDGE: assumes 365.25-day year timing['SU per model year'] = r['PBS log']['Service Units']/yrs timing['Walltime (hr) per model year'] = r['PBS log']['Walltime Used (hr)']/yrs + storagekeys = list(r['storage'].keys()) + for k in storagekeys: + timing[k + ' per model year'] = round(r['storage'][k]/yrs, 3) if prevjobid >= 0: # also record time including wait between runs d1 = dateutil.parser.parse(run_data[prevjobid]['PBS log']['Run completion date']) @@ -747,6 +775,8 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, timing['Wait (hr) between this run and previous'] = tot_walltime - r['PBS log']['Walltime Used (hr)'] timing['SU per calendar day'] = r['PBS log']['Service Units']/tot_walltime*24 timing['Model years per calendar day'] = yrs/tot_walltime*24 + for k in storagekeys: + timing[k + ' per calendar day'] = round(r['storage'][k]/tot_walltime*24, 3) r['timing'] = timing prevjobid = jobid @@ -772,13 +802,15 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, prevjobid = jobid if list_available: - print('\nInformation which can be tabulated if added to output_format:') - keyliststr = [] + print('\nAvailable data which can be tabulated if added to output_format') + print('(but you may need to edit some keys to ensure uniqueness):') + keylist = [] for k in keylistssuperset(run_data): - keyliststr.append("['" + "', '".join(k) + "']") - keyliststr.sort() - for k in keyliststr: - print(k) + keylist.append((k[-1], "['" + "', '".join(k) + "']")) + keylist.sort(key = lambda x: x[1]) + maxkeywidth = max([len(k[0]) for k in keylist]) + for k in keylist: + print(" ('" + k[0] + "', " + " "*(maxkeywidth-len(k[0])) + k[1] + "),") if dump_all: dumpoutfile = os.path.splitext(outfile)[0]+'.yaml' @@ -789,32 +821,11 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, ########################################################################### # Specify the output format here. ########################################################################### - # output_format is a list of (key, value) tuples, one for each column. - # keys are headers (must be unique) + # output_format is a OrderedDict of (key, value) tuples, one for each column. + # keys are column headers (arbitrary but must be unique) # values are lists of keys into run_data (omitting job id) - # - # run_data dict structure (use list_available for full details): - # - # run_data dict - # L___ job ID dict - # L___ 'PBS log' dict - # L___ 'git log' dict - # L___ 'git diff' dict - # L___ 'MOM_time_stamp.out' dict - # L___ 'config.yaml' dict - # L___ 'access-om2.out' dict - # L___ 'timing' dict - # L___ 'namelists' dict - # L___ 'accessom2.nml' namelist (or None if non-YATM run) - # L___ 'atmosphere/atm.nml' namelist (only if YATM run) - # L___ 'atmosphere/input_atm.nml' namelist (only if MATM run) - # L___ '/ice/cice_in.nml' namelist - # L___ 'ice/input_ice.nml' namelist - # L___ 'ice/input_ice_gfdl.nml' namelist - # L___ 'ice/input_ice_monin.nml' namelist - # L___ 'ocean/input.nml' namelist - # L___ job ID dict - # L___ ... etc + # "run_summary.py --list" will list all available data you can add here + # (but you may need to edit some keys to ensure uniqueness) output_format = OrderedDict([ ('Run', ['PBS log', 'Run number']), ('Run start', ['MOM_time_stamp.out', 'Model start time']), @@ -825,7 +836,9 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, # ('Archive directory', ['paths', 'Archive path']), # ('Sync directory', ['paths', 'Sync path']), ('Output directory', ['paths', 'Output path']), + ('Output GiB', ['storage', 'Output path GiB']), ('Restart directory', ['paths', 'Restart path']), + ('Restart GiB', ['storage', 'Restart path GiB']), ('Run by', ['git log', 'Author']), ('Run completion date', ['PBS log', 'Run completion date']), ('Job Id', ['PBS log', 'Job Id']), @@ -868,8 +881,17 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, ('Git-tracked file changes', ['git diff', 'Changed files']), ('Git log messages', ['git diff', 'Messages']), ]) + stats = OrderedDict([ # tuples: (label, function) + ('Total', sum), + ('Mean', np.mean), + ('Median', np.median), + ('Min', min), + ('Max', max), + ('Std dev', np.std) + ]) ########################################################################### - + if no_stats: + stats = OrderedDict([]) if show_fails: # output crash-related info (redefines order of any keys already in output_format) output_format_prefix = OrderedDict([ @@ -947,18 +969,39 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, # output csv file according to output_format above print('\nWriting', outfile) + + if len(stats) > 0: + lhcol = [None] + else: + lhcol = [] # don't allow space for stats headings if we don't have any + with open(outfile, 'w', newline='') as csvfile: csvw = csv.writer(csvfile, dialect='excel', lineterminator='\n') + if not no_header: csvw.writerow(['Summary report generated by run_summary.py, https://github.com/aekiss/run_summary']) csvw.writerow(['report generated:', datetime.datetime.now().replace(microsecond=0).astimezone().isoformat()]) csvw.writerow(['control directory path:', basepath, 'git branch:', git_branch]) csvw.writerow(['output path:', sync_path]) - csvw.writerow(output_format.keys()) # header - for jobid in sortedjobids: - csvw.writerow([dictget(run_data, [jobid] + keylist) for keylist in output_format.values()]) - print('Done.') + csvw.writerow(lhcol + list(output_format.keys())) # header + for jobid in sortedjobids: # output a row for each jobid + csvw.writerow(lhcol + [dictget(run_data, [jobid] + keylist) for keylist in output_format.values()]) + + if len(stats) > 0: + # calculate and save summary stats + statsdata = copy.deepcopy(output_format) + for k, keylist in output_format.items(): # calculate summary stats + coldata = [dictget(run_data, [jobid] + keylist) for jobid in sortedjobids] + coldata = [c for c in coldata if c is not None] + statsdata[k] = {label:tryfunc(func, coldata) for (label, func) in stats.items()} + # write summary stats + csvw.writerow(lhcol + [None]*len(list(output_format.keys()))) # blank row + csvw.writerow(lhcol + list(output_format.keys())) # header + for s in stats: + csvw.writerow([s] + [statsdata[k][s] for k in statsdata.keys()]) + + print('Done.') return @@ -993,7 +1036,10 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, WARNING: output file will be overwritten") parser.add_argument('--no_header', action='store_true', default=False, - help="don't output header in output .csv") + help="don't write header rows in output .csv") + parser.add_argument('--no_stats', + action='store_true', default=False, + help="don't output summary statistics") parser.add_argument('path', metavar='path', type=str, nargs='*', help='zero or more ACCESS-OM2 control directory paths; default is current working directory') args = parser.parse_args() @@ -1003,6 +1049,7 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, outfile = vars(args)['outfile'] outfile_syncdir = vars(args)['outfile_syncdir'] no_header = vars(args)['no_header'] + no_stats = vars(args)['no_stats'] basepaths = vars(args)['path'] # a list of length >=0 since nargs='*' if not basepaths: basepaths = [os.getcwd()] @@ -1012,6 +1059,7 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, outfile=outfile, list_available=lst, dump_all=dump_all, outfile_syncdir=outfile_syncdir, - no_header=no_header) + no_header=no_header, + no_stats=no_stats) except: print('\nFailed. Error:', sys.exc_info()) From 4bf95f3bf50776a661a0877cbcac3a7beced5d36 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Tue, 4 Aug 2020 21:11:17 +1000 Subject: [PATCH 091/111] output monthly mean temp_xflux_gm_int_z, temp_yflux_gm_int_z, temp_xflux_submeso_int_z, temp_yflux_submeso_int_z --- ocean/diag_table | 12 ++++++++++++ ocean/diag_table_source.yaml | 8 ++++---- 2 files changed, 16 insertions(+), 4 deletions(-) diff --git a/ocean/diag_table b/ocean/diag_table index 09cd16d4..f0f496e2 100644 --- a/ocean/diag_table +++ b/ocean/diag_table @@ -247,15 +247,27 @@ ACCESS-OM2 "ocean-2d-temp_xflux_adv_int_z-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "temp_xflux_adv_int_z", "temp_xflux_adv_int_z", "ocean-2d-temp_xflux_adv_int_z-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-2d-temp_xflux_gm_int_z-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "temp_xflux_gm_int_z", "temp_xflux_gm_int_z", "ocean-2d-temp_xflux_gm_int_z-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + "ocean-2d-temp_xflux_ndiffuse_int_z-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "temp_xflux_ndiffuse_int_z", "temp_xflux_ndiffuse_int_z", "ocean-2d-temp_xflux_ndiffuse_int_z-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-2d-temp_xflux_submeso_int_z-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "temp_xflux_submeso_int_z", "temp_xflux_submeso_int_z", "ocean-2d-temp_xflux_submeso_int_z-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + "ocean-2d-temp_yflux_adv_int_z-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "temp_yflux_adv_int_z", "temp_yflux_adv_int_z", "ocean-2d-temp_yflux_adv_int_z-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-2d-temp_yflux_gm_int_z-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "temp_yflux_gm_int_z", "temp_yflux_gm_int_z", "ocean-2d-temp_yflux_gm_int_z-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + "ocean-2d-temp_yflux_ndiffuse_int_z-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "temp_yflux_ndiffuse_int_z", "temp_yflux_ndiffuse_int_z", "ocean-2d-temp_yflux_ndiffuse_int_z-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-2d-temp_yflux_submeso_int_z-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "temp_yflux_submeso_int_z", "temp_yflux_submeso_int_z", "ocean-2d-temp_yflux_submeso_int_z-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + "ocean-2d-tx_trans_int_z-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "tx_trans_int_z", "tx_trans_int_z", "ocean-2d-tx_trans_int_z-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 diff --git a/ocean/diag_table_source.yaml b/ocean/diag_table_source.yaml index afbf06c8..6352df9c 100755 --- a/ocean/diag_table_source.yaml +++ b/ocean/diag_table_source.yaml @@ -220,13 +220,13 @@ diag_table: tau_y: temp_int_rhodz: temp_xflux_adv_int_z: - # temp_xflux_gm_int_z: + temp_xflux_gm_int_z: temp_xflux_ndiffuse_int_z: - # temp_xflux_submeso_int_z: + temp_xflux_submeso_int_z: temp_yflux_adv_int_z: - # temp_yflux_gm_int_z: + temp_yflux_gm_int_z: temp_yflux_ndiffuse_int_z: - # temp_yflux_submeso_int_z: + temp_yflux_submeso_int_z: tx_trans_int_z: ty_trans_int_z: wfiform: From c1945e6b508ffbd363ebe1b505cb36b4546068fc Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Mon, 10 Aug 2020 10:42:59 +1000 Subject: [PATCH 092/111] fix typo --- metadata.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metadata.yaml b/metadata.yaml index 874e1a4c..3ce126c5 100644 --- a/metadata.yaml +++ b/metadata.yaml @@ -11,7 +11,7 @@ description: >- Spin up starts 1 Jan 1958 and runs to 1 Jan 2019. note: >- Provide details here of any important problems or changes during the experiment, - e.g. when additional dignostics are output + e.g. when additional diagnostics are output keywords: - one - cosima From 1fb7f543dff78744944db5d8ce12c9c1035e6297 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Mon, 10 Aug 2020 15:56:28 +1000 Subject: [PATCH 093/111] backward sync support in sync_data.sh --- sync_data.sh | 82 ++++++++++++++++++++++++++++++++-------------------- 1 file changed, 51 insertions(+), 31 deletions(-) diff --git a/sync_data.sh b/sync_data.sh index 7d0ba345..58964caf 100755 --- a/sync_data.sh +++ b/sync_data.sh @@ -20,6 +20,7 @@ dirtype=output exclude="--exclude *.nc.*" rsyncflags="-vrltoD --safe-links" rmlocal=false +backward=false # parse argument list while [ $# -ge 1 ]; do @@ -35,12 +36,16 @@ while [ $# -ge 1 ]; do echo "ignoring exclusions - syncing collated and uncollated .nc files" exclude="" ;; + -b) + echo "backward sync (from SYNCDIR to local)" + backward=true + ;; -D) # --remove-source-files tells rsync to remove from the sending side the files (meaning non-directories) # that are a part of the transfer and have been successfully duplicated on the receiving side. # This option should only be used on source files that are quiescent. # Require interaction here to avoid syncing and removing partially-written files. - echo "DELETING LOCAL COPIES OF SYNCED FILES!" + echo "DELETING SOURCE COPIES OF SYNCED FILES!" echo "WARNING: to avoid losing data, do not proceed if there are any running jobs or collations underway." read -p "Proceed? (y/n) " yesno case $yesno in @@ -73,7 +78,8 @@ if [ $exitcode != "0" -o $help == true ]; then echo " -h: show this help message and exit" echo " -r: sync all restart directories instead of output directories" echo " -u: ignore exclusions - sync collated and uncollated .nc files (default is collated only)" - echo " -D: delete local copies of synced files in all but the most recent synced directories (outputs or restarts, depending on -r). Must be done interactively. (Default leaves local copies intact.)" + echo " -b: backward sync, i.e. from SYNCDIR to local dir (default is from local to SYNCDIR)." + echo " -D: delete all source copies (i.e. local copies, or copies on SYNCDIR if -b is used) of synced output or restart files (depending on -r), retaining only the empty directories. Must be done interactively. If -b is not used, the most recent synced local files are not deleted, so model run can continue. Does not delete non-output/restart files. (Default leaves all source copies intact.)" exit $exitcode fi @@ -81,37 +87,51 @@ sourcepath="$PWD" mkdir -p $SYNCDIR || { echo "Error: cannot create $SYNCDIR - edit $0 to set SYNCDIR"; exit 1; } cd archive || exit 1 -# first delete any cice log files that only have a 105-character header and nothing else -find output* -size 105c -iname "ice.log.task_*" -delete - -# copy all collated outputs/restarts -rsync $exclude $rsyncflags $dirtype[0-9][0-9][0-9] $SYNCDIR -if [ $rmlocal == true ]; then - # Now do removals. Don't remove final local copy, so we can continue run. - rsync --remove-source-files --exclude `\ls -1d $dirtype[0-9][0-9][0-9] | tail -1` $exclude $rsyncflags $dirtype[0-9][0-9][0-9] $SYNCDIR -fi +# copy all outputs/restarts +if [ $backward == true ]; then + rsync $exclude $rsyncflags $SYNCDIR/${dirtype}[0-9][0-9][0-9] . + if [ $rmlocal == true ]; then + rsync --remove-source-files $exclude $rsyncflags $SYNCDIR/${dirtype}[0-9][0-9][0-9] . + fi + # Also sync error and PBS logs and metadata.yaml and run summary + rsync $rsyncflags $SYNCDIR/error_logs . + rsync $rsyncflags $SYNCDIR/pbs_logs . + cd $sourcepath + rsync $rsyncflags $SYNCDIR/metadata.yaml . + rsync $rsyncflags $SYNCDIR/run_summary*.csv . +else + # normal case: forward sync from current dir to SYNCDIR + # first delete any cice log files that only have a 105-character header and nothing else + find output* -size 105c -iname "ice.log.task_*" -delete -# Also sync error and PBS logs and metadata.yaml -rsync $rsyncflags error_logs $SYNCDIR -rsync $rsyncflags pbs_logs $SYNCDIR -cd $sourcepath -rsync $rsyncflags metadata.yaml $SYNCDIR + rsync $exclude $rsyncflags ${dirtype}[0-9][0-9][0-9] $SYNCDIR + if [ $rmlocal == true ]; then + # Now do removals. Don't remove final local copy, so we can continue run. + rsync --remove-source-files --exclude `\ls -1d ${dirtype}[0-9][0-9][0-9] | tail -1` $exclude $rsyncflags ${dirtype}[0-9][0-9][0-9] $SYNCDIR + fi + # Also sync error and PBS logs and metadata.yaml and run summary + rsync $rsyncflags error_logs $SYNCDIR + rsync $rsyncflags pbs_logs $SYNCDIR + cd $sourcepath + rsync $rsyncflags metadata.yaml $SYNCDIR + rsync $rsyncflags run_summary*.csv $SYNCDIR -# create/update a clone of the run history in $SYNCDIR/git-runlog -cd $SYNCDIR || exit 1 -ls git-runlog || git clone $sourcepath git-runlog -cd git-runlog -git pull --no-rebase + # create/update a clone of the run history in $SYNCDIR/git-runlog + cd $SYNCDIR || exit 1 + ls git-runlog || git clone $sourcepath git-runlog + cd git-runlog + git pull --no-rebase -# update and sync run summary - do this last in case it doesn't work -cd $sourcepath -module use /g/data/hh5/public/modules -module load conda/analysis3 -module load python3-as-python -./run_summary.py --no_header -rsync $rsyncflags run_summary*.csv $SYNCDIR -git add run_summary*.csv -git commit -m "update run summary" -cd $SYNCDIR/git-runlog && git pull --no-rebase + # update and sync run summary - do this last in case it doesn't work + cd $sourcepath + module use /g/data/hh5/public/modules + module load conda/analysis3 + module load python3-as-python + ./run_summary.py --no_header + rsync $rsyncflags run_summary*.csv $SYNCDIR + git add run_summary*.csv + git commit -m "update run summary" + cd $SYNCDIR/git-runlog && git pull --no-rebase +fi echo "$0 completed successfully" From 486f7a2e397fb341eb10423e923ac97c36de0f6c Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Fri, 4 Sep 2020 13:57:58 +1000 Subject: [PATCH 094/111] add eta_nonbouss monthly diagnostic --- ocean/diag_table | 3 +++ ocean/diag_table_source.yaml | 1 + 2 files changed, 4 insertions(+) diff --git a/ocean/diag_table b/ocean/diag_table index f0f496e2..b315844f 100644 --- a/ocean/diag_table +++ b/ocean/diag_table @@ -151,6 +151,9 @@ ACCESS-OM2 "ocean-2d-ekman_we-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "ekman_we", "ekman_we", "ocean-2d-ekman_we-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-2d-eta_nonbouss-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "eta_nonbouss", "eta_nonbouss", "ocean-2d-eta_nonbouss-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + "ocean-2d-evap_heat-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "evap_heat", "evap_heat", "ocean-2d-evap_heat-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 diff --git a/ocean/diag_table_source.yaml b/ocean/diag_table_source.yaml index 6352df9c..4c03d9d6 100755 --- a/ocean/diag_table_source.yaml +++ b/ocean/diag_table_source.yaml @@ -188,6 +188,7 @@ diag_table: bmf_u: bmf_v: ekman_we: + eta_nonbouss: evap_heat: evap: fprec_melt_heat: From f4c6fe85d49c1ef546f611be59ce7a42a11fd7e5 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Fri, 4 Sep 2020 14:02:49 +1000 Subject: [PATCH 095/111] improve legibility of resubmit.log --- resub.sh | 2 ++ 1 file changed, 2 insertions(+) diff --git a/resub.sh b/resub.sh index 55b2ed9a..e70f56a8 100755 --- a/resub.sh +++ b/resub.sh @@ -56,3 +56,5 @@ else echo "Resubmit limit reached ... " >> ${logfile} rm ${counterfile} fi + +echo "" >> ${logfile} From 294df5000a2921f43ef106e2738d03dcbe5a2840 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Fri, 4 Sep 2020 14:09:42 +1000 Subject: [PATCH 096/111] tweak run_summary.py outputs --- run_summary.py | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/run_summary.py b/run_summary.py index 29197fc7..53d8fb30 100755 --- a/run_summary.py +++ b/run_summary.py @@ -842,7 +842,7 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, ('Run by', ['git log', 'Author']), ('Run completion date', ['PBS log', 'Run completion date']), ('Job Id', ['PBS log', 'Job Id']), - # ('Failed jobs', ['PBS log', 'Failed previous jobs']), + ('Failed jobs', ['PBS log', 'Failed previous jobs']), ('Failed jobids', ['PBS log', 'Failed previous jobids']), ('Queue', ['config.yaml', 'queue']), ('Service Units', ['PBS log', 'Service Units']), @@ -867,15 +867,15 @@ def run_summary(basepath=os.getcwd(), outfile=None, list_available=False, ('Timestep (s)', ['timing', 'Timestep']), ('MOM barotropic split', ['namelists', 'ocean/input.nml', 'ocean_model_nml', 'barotropic_split']), ('CICE dynamic split (ndtd)', ['namelists', 'ice/cice_in.nml', 'setup_nml', 'ndtd']), - ('ktherm', ['namelists', 'ice/cice_in.nml', 'thermo_nml', 'ktherm']), - ('Common inputs', ['config.yaml', 'input']), - ('Atmosphere executable', ['config.yaml', 'submodels-by-name', 'atmosphere', 'exe']), - ('Atmosphere inputs', ['config.yaml', 'submodels-by-name', 'atmosphere', 'input']), - ('MOM executable', ['config.yaml', 'submodels-by-name', 'ocean', 'exe']), - ('MOM inputs', ['config.yaml', 'submodels-by-name', 'ocean', 'input']), - ('CICE executable', ['config.yaml', 'submodels-by-name', 'ice', 'exe']), - ('CICE inputs', ['config.yaml', 'submodels-by-name', 'ice', 'input']), - ('Payu version', ['PBS log', 'payu version']), + # ('ktherm', ['namelists', 'ice/cice_in.nml', 'thermo_nml', 'ktherm']), + # ('Common inputs', ['config.yaml', 'input']), + # ('Atmosphere executable', ['config.yaml', 'submodels-by-name', 'atmosphere', 'exe']), + # ('Atmosphere inputs', ['config.yaml', 'submodels-by-name', 'atmosphere', 'input']), + # ('MOM executable', ['config.yaml', 'submodels-by-name', 'ocean', 'exe']), + # ('MOM inputs', ['config.yaml', 'submodels-by-name', 'ocean', 'input']), + # ('CICE executable', ['config.yaml', 'submodels-by-name', 'ice', 'exe']), + # ('CICE inputs', ['config.yaml', 'submodels-by-name', 'ice', 'input']), + # ('Payu version', ['PBS log', 'payu version']), ('Git hash of run', ['git log', 'Commit']), ('Commit date', ['git log', 'Date']), ('Git-tracked file changes', ['git diff', 'Changed files']), From c775d25701629470f3b45695d365b063b551a944 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Sun, 6 Sep 2020 21:16:13 +1000 Subject: [PATCH 097/111] fix daily max bottom_temp, sea_level, surface_temp diagnostics and add daily min surface_temp diagnostic --- ocean/diag_table | 27 ++++++++++++++++++--------- ocean/diag_table_source.yaml | 21 ++++++++++++++++++--- 2 files changed, 36 insertions(+), 12 deletions(-) diff --git a/ocean/diag_table b/ocean/diag_table index b315844f..99706cb7 100644 --- a/ocean/diag_table +++ b/ocean/diag_table @@ -295,9 +295,6 @@ ACCESS-OM2 # daily 2d fields -"ocean-2d-bottom_temp_max-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" -"ocean_model", "bottom_temp_max", "bottom_temp_max", "ocean-2d-bottom_temp_max-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 - "ocean-2d-bottom_temp-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" "ocean_model", "bottom_temp", "bottom_temp", "ocean-2d-bottom_temp-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 @@ -310,9 +307,6 @@ ACCESS-OM2 "ocean-2d-pme_river-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" "ocean_model", "pme_river", "pme_river", "ocean-2d-pme_river-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-2d-sea_level_max-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" -"ocean_model", "sea_level_max", "sea_level_max", "ocean-2d-sea_level_max-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 - "ocean-2d-sea_level-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" "ocean_model", "sea_level", "sea_level", "ocean-2d-sea_level-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 @@ -328,9 +322,6 @@ ACCESS-OM2 "ocean-2d-surface_salt-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" "ocean_model", "surface_salt", "surface_salt", "ocean-2d-surface_salt-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-2d-surface_temp_max-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" -"ocean_model", "surface_temp_max", "surface_temp_max", "ocean-2d-surface_temp_max-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 - "ocean-2d-surface_temp-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" "ocean_model", "surface_temp", "surface_temp", "ocean-2d-surface_temp-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 @@ -344,6 +335,24 @@ ACCESS-OM2 "ocean_model", "vorticity_z_surf", "vorticity_z_surf", "ocean-2d-vorticity_z_surf-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 +# daily 2d maximum fields + +"ocean-2d-bottom_temp-1-daily-max-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "bottom_temp", "bottom_temp", "ocean-2d-bottom_temp-1-daily-max-ym%4yr%2mo", "all", "max", "none", 2 + +"ocean-2d-sea_level-1-daily-max-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "sea_level", "sea_level", "ocean-2d-sea_level-1-daily-max-ym%4yr%2mo", "all", "max", "none", 2 + +"ocean-2d-surface_temp-1-daily-max-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "surface_temp", "surface_temp", "ocean-2d-surface_temp-1-daily-max-ym%4yr%2mo", "all", "max", "none", 2 + + +# daily 2d minimum fields + +"ocean-2d-surface_temp-1-daily-min-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "surface_temp", "surface_temp", "ocean-2d-surface_temp-1-daily-min-ym%4yr%2mo", "all", "min", "none", 2 + + # daily scalar snapshots "ocean-scalar-1-daily-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" diff --git a/ocean/diag_table_source.yaml b/ocean/diag_table_source.yaml index 4c03d9d6..cc7effd8 100755 --- a/ocean/diag_table_source.yaml +++ b/ocean/diag_table_source.yaml @@ -246,22 +246,37 @@ diag_table: output_freq: 1 # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run) output_freq_units: days # time units for output: years, months, days, hours, minutes, or seconds fields: - bottom_temp_max: bottom_temp: frazil_3d_int_z: mld: pme_river: - sea_level_max: sea_level: sfc_hflux_coupler: sfc_hflux_from_runoff: sfc_hflux_pme: surface_salt: - surface_temp_max: surface_temp: u_surf: v_surf: vorticity_z_surf: + 'daily 2d maximum fields': + defaults: # these can be overridden for individual fields below + file_name_dimension: 2d # descriptor for filename, e.g. 3d, 2d, scalar + output_freq: 1 # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run) + output_freq_units: days # time units for output: years, months, days, hours, minutes, or seconds + reduction_method: max # mean, snap, rms, pow##, min, max, or diurnal## + fields: + bottom_temp: + sea_level: + surface_temp: + 'daily 2d minimum fields': + defaults: # these can be overridden for individual fields below + file_name_dimension: 2d # descriptor for filename, e.g. 3d, 2d, scalar + output_freq: 1 # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run) + output_freq_units: days # time units for output: years, months, days, hours, minutes, or seconds + reduction_method: min # mean, snap, rms, pow##, min, max, or diurnal## + fields: + surface_temp: # min for comparison with foundation temperature 'daily scalar snapshots': # snapshots of global integrals give better parallel performance defaults: # these can be overridden for individual fields below file_name_dimension: scalar # descriptor for filename, e.g. 3d, 2d, scalar From 76571ce05587de79bf8e572ee9a292af47cda165 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Mon, 7 Sep 2020 10:14:28 +1000 Subject: [PATCH 098/111] fix diag_table: change u_surf, v_surf to usurf, vsurf --- ocean/diag_table | 8 ++++---- ocean/diag_table_source.yaml | 4 ++-- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/ocean/diag_table b/ocean/diag_table index 99706cb7..7b322b33 100644 --- a/ocean/diag_table +++ b/ocean/diag_table @@ -325,11 +325,11 @@ ACCESS-OM2 "ocean-2d-surface_temp-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" "ocean_model", "surface_temp", "surface_temp", "ocean-2d-surface_temp-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-2d-u_surf-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" -"ocean_model", "u_surf", "u_surf", "ocean-2d-u_surf-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-2d-usurf-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "usurf", "usurf", "ocean-2d-usurf-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-2d-v_surf-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" -"ocean_model", "v_surf", "v_surf", "ocean-2d-v_surf-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-2d-vsurf-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "vsurf", "vsurf", "ocean-2d-vsurf-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 "ocean-2d-vorticity_z_surf-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" "ocean_model", "vorticity_z_surf", "vorticity_z_surf", "ocean-2d-vorticity_z_surf-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 diff --git a/ocean/diag_table_source.yaml b/ocean/diag_table_source.yaml index cc7effd8..1bfed851 100755 --- a/ocean/diag_table_source.yaml +++ b/ocean/diag_table_source.yaml @@ -256,8 +256,8 @@ diag_table: sfc_hflux_pme: surface_salt: surface_temp: - u_surf: - v_surf: + usurf: + vsurf: vorticity_z_surf: 'daily 2d maximum fields': defaults: # these can be overridden for individual fields below From 3a05b1fd415409ad49157df59396d9ac78f58029 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Tue, 15 Sep 2020 12:16:03 +1000 Subject: [PATCH 099/111] fix notes field in metadata.yaml --- metadata.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metadata.yaml b/metadata.yaml index 3ce126c5..98e79f16 100644 --- a/metadata.yaml +++ b/metadata.yaml @@ -9,7 +9,7 @@ description: >- Run with JRA55-do v1.4.0 interannually-varying forcing with all solid runoff converted to liquid runoff with no heat transfer. Spin up starts 1 Jan 1958 and runs to 1 Jan 2019. -note: >- +notes: >- Provide details here of any important problems or changes during the experiment, e.g. when additional diagnostics are output keywords: From 06eb4cebf26e1c295667ebe3ac261ee8a640078f Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Wed, 16 Sep 2020 11:38:17 +1000 Subject: [PATCH 100/111] update metadata.yaml --- metadata.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/metadata.yaml b/metadata.yaml index 98e79f16..82f96547 100644 --- a/metadata.yaml +++ b/metadata.yaml @@ -10,6 +10,8 @@ description: >- converted to liquid runoff with no heat transfer. Spin up starts 1 Jan 1958 and runs to 1 Jan 2019. notes: >- + Source code: https://github.com/COSIMA/access-om2 + License: Attribution-NonCommercial-NoDerivatives 4.0 International (http://creativecommons.org/licenses/by-nc-nd/4.0/legalcode) Provide details here of any important problems or changes during the experiment, e.g. when additional diagnostics are output keywords: From 6ef2abfe7a5bb617011abb79589025e353c7e374 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Tue, 6 Oct 2020 17:00:52 +1100 Subject: [PATCH 101/111] add conditions of use to metadata --- metadata.yaml | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/metadata.yaml b/metadata.yaml index 82f96547..5645e985 100644 --- a/metadata.yaml +++ b/metadata.yaml @@ -12,8 +12,16 @@ description: >- notes: >- Source code: https://github.com/COSIMA/access-om2 License: Attribution-NonCommercial-NoDerivatives 4.0 International (http://creativecommons.org/licenses/by-nc-nd/4.0/legalcode) - Provide details here of any important problems or changes during the experiment, - e.g. when additional diagnostics are output + Conditions of use: + We request that users of this or other ACCESS-OM2 model code or output data: + (a) consider citing Kiss et al. (2020) [http://doi.org/10.5194/gmd-13-401-2020] + (b) include an acknowledgement such as the following: + "The authors thank the Consortium for Ocean-Sea Ice Modelling in Australia (COSIMA; http://www.cosima.org.au) + for making the ACCESS-OM2 suite of models available at https://github.com/COSIMA/access-om2. + Model runs were undertaken with the assistance of resources from the National Computational Infrastructure (NCI), + which is supported by the Australian Government." + (c) let us know of any publications which use these models or data so we can add them to our list: + https://scholar.google.com/citations?hl=en&user=inVqu_4AAAAJ keywords: - one - cosima From c7be3342d7d3c3e6ea75e6f08a4337f0269ac44c Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Tue, 20 Oct 2020 15:48:58 +1100 Subject: [PATCH 102/111] output surface_pot_temp instead of (conservative) surface_temp - see https://github.com/COSIMA/access-om2/issues/203#issuecomment-707507691 --- ocean/diag_table | 20 ++++++++++---------- ocean/diag_table_source.yaml | 10 +++++----- 2 files changed, 15 insertions(+), 15 deletions(-) diff --git a/ocean/diag_table b/ocean/diag_table index 7b322b33..68208a81 100644 --- a/ocean/diag_table +++ b/ocean/diag_table @@ -232,8 +232,8 @@ ACCESS-OM2 "ocean-2d-surface_salt-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "surface_salt", "surface_salt", "ocean-2d-surface_salt-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-2d-surface_temp-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" -"ocean_model", "surface_temp", "surface_temp", "ocean-2d-surface_temp-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-2d-surface_pot_temp-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "surface_pot_temp", "surface_pot_temp", "ocean-2d-surface_pot_temp-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 "ocean-2d-swflx-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "swflx", "swflx", "ocean-2d-swflx-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 @@ -289,8 +289,8 @@ ACCESS-OM2 "ocean-2d-mld-1-monthly-max-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "mld", "mld", "ocean-2d-mld-1-monthly-max-ym%4yr%2mo", "all", "max", "none", 2 -"ocean-2d-surface_temp-1-monthly-min-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" -"ocean_model", "surface_temp", "surface_temp", "ocean-2d-surface_temp-1-monthly-min-ym%4yr%2mo", "all", "min", "none", 2 +"ocean-2d-surface_pot_temp-1-monthly-min-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "surface_pot_temp", "surface_pot_temp", "ocean-2d-surface_pot_temp-1-monthly-min-ym%4yr%2mo", "all", "min", "none", 2 # daily 2d fields @@ -322,8 +322,8 @@ ACCESS-OM2 "ocean-2d-surface_salt-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" "ocean_model", "surface_salt", "surface_salt", "ocean-2d-surface_salt-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-2d-surface_temp-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" -"ocean_model", "surface_temp", "surface_temp", "ocean-2d-surface_temp-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-2d-surface_pot_temp-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "surface_pot_temp", "surface_pot_temp", "ocean-2d-surface_pot_temp-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 "ocean-2d-usurf-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" "ocean_model", "usurf", "usurf", "ocean-2d-usurf-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 @@ -343,14 +343,14 @@ ACCESS-OM2 "ocean-2d-sea_level-1-daily-max-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" "ocean_model", "sea_level", "sea_level", "ocean-2d-sea_level-1-daily-max-ym%4yr%2mo", "all", "max", "none", 2 -"ocean-2d-surface_temp-1-daily-max-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" -"ocean_model", "surface_temp", "surface_temp", "ocean-2d-surface_temp-1-daily-max-ym%4yr%2mo", "all", "max", "none", 2 +"ocean-2d-surface_pot_temp-1-daily-max-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "surface_pot_temp", "surface_pot_temp", "ocean-2d-surface_pot_temp-1-daily-max-ym%4yr%2mo", "all", "max", "none", 2 # daily 2d minimum fields -"ocean-2d-surface_temp-1-daily-min-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" -"ocean_model", "surface_temp", "surface_temp", "ocean-2d-surface_temp-1-daily-min-ym%4yr%2mo", "all", "min", "none", 2 +"ocean-2d-surface_pot_temp-1-daily-min-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "surface_pot_temp", "surface_pot_temp", "ocean-2d-surface_pot_temp-1-daily-min-ym%4yr%2mo", "all", "min", "none", 2 # daily scalar snapshots diff --git a/ocean/diag_table_source.yaml b/ocean/diag_table_source.yaml index 1bfed851..3ba404cf 100755 --- a/ocean/diag_table_source.yaml +++ b/ocean/diag_table_source.yaml @@ -215,7 +215,7 @@ diag_table: sfc_salt_flux_ice: sfc_salt_flux_restore: surface_salt: - surface_temp: + surface_pot_temp: swflx: tau_x: tau_y: @@ -239,7 +239,7 @@ diag_table: output_freq_units: months # time units for output: years, months, days, hours, minutes, or seconds fields: mld: {reduction_method: max} # max avoids spurious small values due to rainfall - surface_temp: {reduction_method: min} # min for comparison with foundation temperature + surface_pot_temp: {reduction_method: min} # min for comparison with foundation temperature 'daily 2d fields': defaults: # these can be overridden for individual fields below file_name_dimension: 2d # descriptor for filename, e.g. 3d, 2d, scalar @@ -255,7 +255,7 @@ diag_table: sfc_hflux_from_runoff: sfc_hflux_pme: surface_salt: - surface_temp: + surface_pot_temp: usurf: vsurf: vorticity_z_surf: @@ -268,7 +268,7 @@ diag_table: fields: bottom_temp: sea_level: - surface_temp: + surface_pot_temp: 'daily 2d minimum fields': defaults: # these can be overridden for individual fields below file_name_dimension: 2d # descriptor for filename, e.g. 3d, 2d, scalar @@ -276,7 +276,7 @@ diag_table: output_freq_units: days # time units for output: years, months, days, hours, minutes, or seconds reduction_method: min # mean, snap, rms, pow##, min, max, or diurnal## fields: - surface_temp: # min for comparison with foundation temperature + surface_pot_temp: # min for comparison with foundation temperature 'daily scalar snapshots': # snapshots of global integrals give better parallel performance defaults: # these can be overridden for individual fields below file_name_dimension: scalar # descriptor for filename, e.g. 3d, 2d, scalar From 333fc18d64b3049e84bfecd5b6b5b8ea59b99d04 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Thu, 22 Oct 2020 15:58:24 +1100 Subject: [PATCH 103/111] switch to input_20201022 --- config.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/config.yaml b/config.yaml index fbd8c9cf..0ffea1ec 100644 --- a/config.yaml +++ b/config.yaml @@ -16,13 +16,13 @@ mem: 1000GB # Model configuration name: common model: access-om2 -input: /g/data/ik11/inputs/access-om2/input_20200530/common_1deg_jra55 +input: /g/data/ik11/inputs/access-om2/input_20201022/common_1deg_jra55 submodels: - name: atmosphere model: yatm exe: /g/data/ik11/inputs/access-om2/bin/yatm_a9d4b67.exe input: - - /g/data/ik11/inputs/access-om2/input_20200530/yatm_1deg + - /g/data/ik11/inputs/access-om2/input_20201022/yatm_1deg - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/rsds/gr/v20190429 - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/rlds/gr/v20190429 - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/prra/gr/v20190429 @@ -39,13 +39,13 @@ submodels: - name: ocean model: mom exe: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM_08cf2b5_libaccessom2_a9d4b67.x - input: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg + input: /g/data/ik11/inputs/access-om2/input_20201022/mom_1deg ncpus: 216 - name: ice model: cice5 exe: /g/data/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_26e6159_libaccessom2_a9d4b67.exe - input: /g/data/ik11/inputs/access-om2/input_20200530/cice_1deg + input: /g/data/ik11/inputs/access-om2/input_20201022/cice_1deg ncpus: 24 # Collation From d7d25ac106bc675f8ad684ebdbf64149e4be2e96 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Wed, 28 Oct 2020 13:08:00 +1100 Subject: [PATCH 104/111] concatenate ice daily files in sync_data.sh; sync_data.sh -r now removes individual daily ice files if they have been concatenated --- sync_data.sh | 35 +++++++++++++++++++++++++++++++---- 1 file changed, 31 insertions(+), 4 deletions(-) diff --git a/sync_data.sh b/sync_data.sh index 58964caf..12c822ea 100755 --- a/sync_data.sh +++ b/sync_data.sh @@ -2,8 +2,8 @@ #PBS -q copyq #PBS -l ncpus=1 #PBS -l wd -#PBS -l walltime=4:00:00,mem=4GB -#PBS -l storage=gdata/hh5+gdata/ik11+scratch/v45+scratch/x77+scratch/g40 +#PBS -l walltime=10:00:00,mem=12GB +#PBS -l storage=gdata/hh5+gdata/ik11+gdata/cj50+scratch/v45+scratch/x77+scratch/g40 #PBS -N sync # Set SYNCDIR to the path you want your data copied to. @@ -17,7 +17,7 @@ SYNCDIR=/ERROR/SET/SYNCDIR/IN/sync_data.sh exitcode=0 help=false dirtype=output -exclude="--exclude *.nc.*" +exclude="--exclude *.nc.* --exclude iceh.????-??-??.nc --exclude *-DEPRECATED --exclude *-DELETE --exclude *-IN-PROGRESS" rsyncflags="-vrltoD --safe-links" rmlocal=false backward=false @@ -41,7 +41,7 @@ while [ $# -ge 1 ]; do backward=true ;; -D) - # --remove-source-files tells rsync to remove from the sending side the files (meaning non-directories) + # --remove-source-files tells rsync to remove from the sending side the files (meaning non-directories) # that are a part of the transfer and have been successfully duplicated on the receiving side. # This option should only be used on source files that are quiescent. # Require interaction here to avoid syncing and removing partially-written files. @@ -85,6 +85,30 @@ fi sourcepath="$PWD" mkdir -p $SYNCDIR || { echo "Error: cannot create $SYNCDIR - edit $0 to set SYNCDIR"; exit 1; } + +# concatenate ice daily files +module load nco +for d in archive/output*/ice/OUTPUT; do + for f in $d/iceh.????-??.nc; do + if [[ -f ${f/.nc/-01.nc} ]] && [[ ! -f ${f/.nc/-IN-PROGRESS} ]] && [[ ! -f ${f/.nc/-daily.nc} ]]; + then + touch ${f/.nc/-IN-PROGRESS} + echo "doing ncrcat -O -L 5 -7 ${f/.nc/-??.nc} ${f/.nc/-daily.nc}" + ncrcat -O -L 5 -7 ${f/.nc/-??.nc} ${f/.nc/-daily.nc} && chmod g+r ${f/.nc/-daily.nc} && rm ${f/.nc/-IN-PROGRESS} + if [[ ! -f ${f/.nc/-IN-PROGRESS} ]] && [[ -f ${f/.nc/-daily.nc} ]]; + then + for daily in ${f/.nc/-??.nc} + do + # rename individual daily files - user to delete + mv $daily $daily-DELETE + done + else + rm ${f/.nc/-IN-PROGRESS} + fi + fi + done +done + cd archive || exit 1 # copy all outputs/restarts @@ -108,6 +132,9 @@ else if [ $rmlocal == true ]; then # Now do removals. Don't remove final local copy, so we can continue run. rsync --remove-source-files --exclude `\ls -1d ${dirtype}[0-9][0-9][0-9] | tail -1` $exclude $rsyncflags ${dirtype}[0-9][0-9][0-9] $SYNCDIR + for d in ${dirtype}[0-9][0-9][0-9]/ice/OUTPUT; do + rm $d/iceh.????-??-??.nc-DELETE + done fi # Also sync error and PBS logs and metadata.yaml and run summary rsync $rsyncflags error_logs $SYNCDIR From a9f59b507e7874bc59eec45ebe86de72cb9513ab Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Fri, 30 Oct 2020 11:59:42 +1100 Subject: [PATCH 105/111] add conditions of use to README.md --- README.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/README.md b/README.md index 38ec2a14..7ba2ff7e 100644 --- a/README.md +++ b/README.md @@ -6,3 +6,11 @@ For usage instructions, see the [ACCESS-OM2 wiki](https://github.com/COSIMA/acce Run length and timestep are set in `accessom2.nml`. The default timestep for this configuration is 5400 seconds, and the model is stable with this timestep right from the start. However if you alter the configuration you may need a shorter timestep during the first year or two of model equilibration. **NOTE:** All ACCESS-OM2 model components and configurations are undergoing continual improvement. We strongly recommend that you "watch" this repo (see button at top of screen; ask to be notified of all conversations) and also watch [ACCESS-OM2](https://github.com/COSIMA/access-om2), all the [component models](https://github.com/COSIMA/access-om2/tree/master/src), and [payu](https://github.com/payu-org/payu) to be kept informed of updates, problems and bug fixes as they arise. + +## Conditions of use + +We request that users of this or other ACCESS-OM2 model code: +1. consider citing Kiss et al. (2020) ([http://doi.org/10.5194/gmd-13-401-2020](http://doi.org/10.5194/gmd-13-401-2020)) +2. include an acknowledgement such as the following: +*The authors thank the Consortium for Ocean-Sea Ice Modelling in Australia (COSIMA; [http://www.cosima.org.au](http://www.cosima.org.au)) for making the ACCESS-OM2 suite of models available at [https://github.com/COSIMA/access-om2](https://github.com/COSIMA/access-om2).* +3. let us know of any publications which use these models or data so we can add them to [our list](https://scholar.google.com/citations?hl=en&user=inVqu_4AAAAJ). From 1e70e10619a8a2f321a8c696ee30baa9c3310aa5 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Thu, 5 Nov 2020 16:49:48 +1100 Subject: [PATCH 106/111] update model executables (MOM exe now includes WOMBAT BGC: https://github.com/mom-ocean/MOM5/pull/317; CICE uses PIO: https://github.com/COSIMA/cice5/issues/34); configuration changes to support PIO in CICE --- config.yaml | 7 ++++--- ice/cice_in.nml | 3 ++- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/config.yaml b/config.yaml index 0ffea1ec..af4e7735 100644 --- a/config.yaml +++ b/config.yaml @@ -20,7 +20,7 @@ input: /g/data/ik11/inputs/access-om2/input_20201022/common_1deg_jra55 submodels: - name: atmosphere model: yatm - exe: /g/data/ik11/inputs/access-om2/bin/yatm_a9d4b67.exe + exe: /g/data/ik11/inputs/access-om2/bin/yatm_2617f7c.exe input: - /g/data/ik11/inputs/access-om2/input_20201022/yatm_1deg - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/rsds/gr/v20190429 @@ -38,13 +38,13 @@ submodels: - name: ocean model: mom - exe: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM_08cf2b5_libaccessom2_a9d4b67.x + exe: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM-BGC_af3a94d_libaccessom2_2617f7c.x input: /g/data/ik11/inputs/access-om2/input_20201022/mom_1deg ncpus: 216 - name: ice model: cice5 - exe: /g/data/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_26e6159_libaccessom2_a9d4b67.exe + exe: /g/data/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_015877c_libaccessom2_2617f7c.exe input: /g/data/ik11/inputs/access-om2/input_20201022/cice_1deg ncpus: 24 @@ -61,6 +61,7 @@ collate: runlog: true stacksize: unlimited restart_freq: 1 # use tidy_restarts.py instead +mpirun: --mca io ompio --mca io_ompio_num_aggregators 1 qsub_flags: -W umask=027 # set number of cores per node (28 for normalbw, 48 for normal on gadi) platform: diff --git a/ice/cice_in.nml b/ice/cice_in.nml index 2bcc3864..65cd1472 100644 --- a/ice/cice_in.nml +++ b/ice/cice_in.nml @@ -11,6 +11,8 @@ hist_avg = .true. histfreq = 'd', 'm', 'x', 'x', 'x' histfreq_n = 1, 1, 1, 1, 1 + history_chunksize_x = 90 + history_chunksize_y = 300 history_deflate_level = 1 history_dir = './OUTPUT/' history_file = 'iceh' @@ -29,7 +31,6 @@ restart_dir = './RESTART/' restart_ext = .false. restart_file = 'iced' - restart_format = 'nc' runtype = 'initial' use_leap_years = .false. use_restart_time = .true. From ba94568b3ca69992a5361c53e3e069a6ed732b86 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Thu, 5 Nov 2020 16:53:26 +1100 Subject: [PATCH 107/111] use input_20201102 --- config.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/config.yaml b/config.yaml index af4e7735..74a5fa69 100644 --- a/config.yaml +++ b/config.yaml @@ -16,13 +16,13 @@ mem: 1000GB # Model configuration name: common model: access-om2 -input: /g/data/ik11/inputs/access-om2/input_20201022/common_1deg_jra55 +input: /g/data/ik11/inputs/access-om2/input_20201102/common_1deg_jra55 submodels: - name: atmosphere model: yatm exe: /g/data/ik11/inputs/access-om2/bin/yatm_2617f7c.exe input: - - /g/data/ik11/inputs/access-om2/input_20201022/yatm_1deg + - /g/data/ik11/inputs/access-om2/input_20201102/yatm_1deg - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/rsds/gr/v20190429 - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/rlds/gr/v20190429 - /g/data/qv56/replicas/input4MIPs/CMIP6/OMIP/MRI/MRI-JRA55-do-1-4-0/atmos/3hr/prra/gr/v20190429 @@ -39,13 +39,13 @@ submodels: - name: ocean model: mom exe: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM-BGC_af3a94d_libaccessom2_2617f7c.x - input: /g/data/ik11/inputs/access-om2/input_20201022/mom_1deg + input: /g/data/ik11/inputs/access-om2/input_20201102/mom_1deg ncpus: 216 - name: ice model: cice5 exe: /g/data/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_015877c_libaccessom2_2617f7c.exe - input: /g/data/ik11/inputs/access-om2/input_20201022/cice_1deg + input: /g/data/ik11/inputs/access-om2/input_20201102/cice_1deg ncpus: 24 # Collation From 7de128a3145a871f856a1fd0a184018939677bbf Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Thu, 5 Nov 2020 17:42:05 +1100 Subject: [PATCH 108/111] don't output vorticity_z_surf (it doesn't exist) --- ocean/diag_table | 3 --- ocean/diag_table_source.yaml | 1 - 2 files changed, 4 deletions(-) diff --git a/ocean/diag_table b/ocean/diag_table index 68208a81..1caa4863 100644 --- a/ocean/diag_table +++ b/ocean/diag_table @@ -331,9 +331,6 @@ ACCESS-OM2 "ocean-2d-vsurf-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" "ocean_model", "vsurf", "vsurf", "ocean-2d-vsurf-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-2d-vorticity_z_surf-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" -"ocean_model", "vorticity_z_surf", "vorticity_z_surf", "ocean-2d-vorticity_z_surf-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 - # daily 2d maximum fields diff --git a/ocean/diag_table_source.yaml b/ocean/diag_table_source.yaml index 3ba404cf..f0b0ee5b 100755 --- a/ocean/diag_table_source.yaml +++ b/ocean/diag_table_source.yaml @@ -258,7 +258,6 @@ diag_table: surface_pot_temp: usurf: vsurf: - vorticity_z_surf: 'daily 2d maximum fields': defaults: # these can be overridden for individual fields below file_name_dimension: 2d # descriptor for filename, e.g. 3d, 2d, scalar From 3b71194377be33047b7af3936faecd4ab4cdbaeb Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Thu, 5 Nov 2020 18:08:36 +1100 Subject: [PATCH 109/111] update manifests --- manifests/exe.yaml | 24 ++++++------ manifests/input.yaml | 92 ++++++++++++++++++++++++++++++-------------- 2 files changed, 76 insertions(+), 40 deletions(-) diff --git a/manifests/exe.yaml b/manifests/exe.yaml index a03d8ac5..307a0086 100644 --- a/manifests/exe.yaml +++ b/manifests/exe.yaml @@ -1,18 +1,18 @@ format: yamanifest version: 1.0 --- -work/atmosphere/yatm_a9d4b67.exe: - fullpath: /g/data/ik11/inputs/access-om2/bin/yatm_a9d4b67.exe +work/atmosphere/yatm_2617f7c.exe: + fullpath: /g/data/ik11/inputs/access-om2/bin/yatm_2617f7c.exe hashes: - binhash: 75722a5be452b46f55ce2fc0d3cbad44 - md5: 8137dfef69adc41912648e3642f79cc6 -work/ice/cice_auscom_360x300_24p_26e6159_libaccessom2_a9d4b67.exe: - fullpath: /g/data/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_26e6159_libaccessom2_a9d4b67.exe + binhash: 6ed3eddff1bc4b25b08ec4f0357d8016 + md5: 8596534a07539745b1a60dfaf1c9e3f1 +work/ice/cice_auscom_360x300_24p_015877c_libaccessom2_2617f7c.exe: + fullpath: /g/data/ik11/inputs/access-om2/bin/cice_auscom_360x300_24p_015877c_libaccessom2_2617f7c.exe hashes: - binhash: 9293e76448d4b655deef829122169429 - md5: f15ee94d35fc3569e06a323ba6a6ef2b -work/ocean/fms_ACCESS-OM_08cf2b5_libaccessom2_a9d4b67.x: - fullpath: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM_08cf2b5_libaccessom2_a9d4b67.x + binhash: 52ab2f69d54bf103c1c304ae0e44b6f0 + md5: e6a7b6ff6cb8792373a839e87841af96 +work/ocean/fms_ACCESS-OM-BGC_af3a94d_libaccessom2_2617f7c.x: + fullpath: /g/data/ik11/inputs/access-om2/bin/fms_ACCESS-OM-BGC_af3a94d_libaccessom2_2617f7c.x hashes: - binhash: 228d9788823a8d6f4ab3f8676006c76e - md5: 69c3a7020be150a02965e935cbab4052 + binhash: 0e1a697406cf0e5376252daab47cd8a9 + md5: ba2a8275e78cb22e1366d525b182d34a diff --git a/manifests/input.yaml b/manifests/input.yaml index ca9c39b0..cd059b1c 100644 --- a/manifests/input.yaml +++ b/manifests/input.yaml @@ -2,27 +2,27 @@ format: yamanifest version: 1.0 --- work/INPUT/JRA55_MOM1_conserve2nd.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_20200530/common_1deg_jra55/JRA55_MOM1_conserve2nd.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20201102/common_1deg_jra55/JRA55_MOM1_conserve2nd.nc hashes: binhash: abe66e4b33cbb75d25c010ea5f96f053 md5: 00be8ec0f1126055b65dc68178ce4eb5 work/INPUT/JRA55_MOM1_patch.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_20200530/common_1deg_jra55/JRA55_MOM1_patch.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20201102/common_1deg_jra55/JRA55_MOM1_patch.nc hashes: binhash: af316080d1711daa25abadbf0548718c md5: 6c345282e51521828f62b842e58dd734 work/INPUT/rmp_jra55_cice_1st_conserve.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_20200530/common_1deg_jra55/rmp_jra55_cice_1st_conserve.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20201102/common_1deg_jra55/rmp_jra55_cice_1st_conserve.nc hashes: binhash: bee0b815a97dc6eaf8c2417b4579a31f md5: 6404d936d4898e5ed31e62b585d630cf work/INPUT/rmp_jra55_cice_2nd_conserve.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_20200530/common_1deg_jra55/rmp_jra55_cice_2nd_conserve.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20201102/common_1deg_jra55/rmp_jra55_cice_2nd_conserve.nc hashes: binhash: 57da74118e8eb06d0c26255fd0b8e6db md5: 79885c8149d65a55d093244935f62360 work/INPUT/rmp_jra55_cice_patch.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_20200530/common_1deg_jra55/rmp_jra55_cice_patch.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20201102/common_1deg_jra55/rmp_jra55_cice_patch.nc hashes: binhash: f317a81f25961ba37f27b873b364a8d6 md5: aa91ea2e3cdef04f58ed5db8f8d7de6d @@ -2197,7 +2197,7 @@ work/atmosphere/INPUT/rlds_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_g binhash: f1a3c4313a4f6ff631f0fe887a849153 md5: 3d08213bdacd00ba2cfde806cf6d6b6f work/atmosphere/INPUT/rmp_jrar_to_cict_CONSERV.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_20200530/yatm_1deg/rmp_jrar_to_cict_CONSERV.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20201102/yatm_1deg/rmp_jrar_to_cict_CONSERV.nc hashes: binhash: d7b11ae77fba63aecab0892891135a1f md5: 10f0b5ea6b8102a03ad1140e5163a0f7 @@ -3441,73 +3441,109 @@ work/atmosphere/INPUT/vas_input4MIPs_atmosphericState_OMIP_MRI-JRA55-do-1-4-0_gr hashes: binhash: 987ff85784eff1316d6929f631fe1426 md5: b0e514bfac0d9dfbf538d36b8ecd17f9 +work/ice/RESTART/grid.nc: + copy: true + fullpath: /g/data/ik11/inputs/access-om2/input_20201102/cice_1deg/grid.nc + hashes: + binhash: e7108317ae28b1f9ae77711728925cb6 + md5: 1213e346055ee073fe33dc12578d99c6 +work/ice/RESTART/i2o.nc: + copy: true + fullpath: /g/data/ik11/inputs/access-om2/input_20201102/cice_1deg/i2o.nc + hashes: + binhash: 527d494c80b2a3418645b962fd8706d0 + md5: c96e06c3c80c0f680545db59ed3349e5 +work/ice/RESTART/kmt.nc: + copy: true + fullpath: /g/data/ik11/inputs/access-om2/input_20201102/cice_1deg/kmt.nc + hashes: + binhash: 13a23d6d9331abc9d677c6fd466a4433 + md5: 1f9806c646a620378e5257e480bc9df7 +work/ice/RESTART/monthly_sstsss.nc: + copy: true + fullpath: /g/data/ik11/inputs/access-om2/input_20201102/cice_1deg/monthly_sstsss.nc + hashes: + binhash: 66f44d84fada351d4ebf05f196762d8c + md5: 323d4c605f83f4d7d3126da70153c2ed +work/ice/RESTART/o2i.nc: + copy: true + fullpath: /g/data/ik11/inputs/access-om2/input_20201102/cice_1deg/o2i.nc + hashes: + binhash: 56f258e931a8eda2fc42b3a315d485eb + md5: 3498246dcd7da40d3b8c6b4a908b260f +work/ice/RESTART/u_star.nc: + copy: true + fullpath: /g/data/ik11/inputs/access-om2/input_20201102/cice_1deg/u_star.nc + hashes: + binhash: f93a19930c5c59e03751e70a123ab01f + md5: 68cf0ef92576f96ef085cd7f243d0c39 work/ocean/INPUT/chl.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/chl.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20201102/mom_1deg/chl.nc hashes: binhash: 05b3313121bbb9825a20f0fb58901b21 md5: a7aa5bcf4a3b9fa8102edd3b6b67c3a2 work/ocean/INPUT/grid_spec.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/grid_spec.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20201102/mom_1deg/grid_spec.nc hashes: binhash: 587ca8eb0cbc978232fe55a7bff054c9 md5: 027d2f8fb1eda3ef1cf0a3f520a217f7 work/ocean/INPUT/mask_table.24.16x15: - fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/mask_table.24.16x15 + fullpath: /g/data/ik11/inputs/access-om2/input_20201102/mom_1deg/mask_table.24.16x15 hashes: binhash: 77b929b930cd4fca59f185b3222dde49 md5: 2203b38758fb2b56a145ef16b7872af9 work/ocean/INPUT/ocean_hgrid.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/ocean_hgrid.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20201102/mom_1deg/ocean_hgrid.nc hashes: binhash: 87d66edc0ef57c97b758a3049bfe8a14 md5: 51f58be0f4ea6da2cb438a893f95c689 work/ocean/INPUT/ocean_mask.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/ocean_mask.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20201102/mom_1deg/ocean_mask.nc hashes: - binhash: 85321c4533642d2602df6b0086eca477 - md5: 1d9dfb140919f355037f72bc89f15db0 + binhash: ab10098b71d76ba5fcf0ea9e007a90e5 + md5: 411567441c64bcfa814259736c5ed1a3 work/ocean/INPUT/ocean_mask_table: - fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/ocean_mask_table + fullpath: /g/data/ik11/inputs/access-om2/input_20201102/mom_1deg/ocean_mask_table hashes: binhash: dc68931f1bb40bcd75a98d209b47d4c4 md5: 2203b38758fb2b56a145ef16b7872af9 work/ocean/INPUT/ocean_mosaic.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/ocean_mosaic.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20201102/mom_1deg/ocean_mosaic.nc hashes: binhash: 6aadd388078defe3f80df6f3de77b4bd md5: cb42e630ee31d3686156fcbdc2f9d07c work/ocean/INPUT/ocean_temp_salt.res.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/ocean_temp_salt.res.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20201102/mom_1deg/ocean_temp_salt.res.nc hashes: - binhash: c56262c68ab55b0998e32bec98dec07d - md5: c9814c04b393cf73fe3d16daf5d421af + binhash: 1530c856cbbc9b5073bdf3e7beb72cd7 + md5: c5f7e60b5427a4442f111adc65a2d067 work/ocean/INPUT/ocean_vgrid.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/ocean_vgrid.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20201102/mom_1deg/ocean_vgrid.nc hashes: - binhash: 115586f18cc20a6ca309194b4d59665b - md5: 6eebf039362b6572eaad5477740236bf + binhash: cd9ef67b8cf6d4ea0c78554ac38e1bc3 + md5: 339ff716e3019a86fc861498e674250a work/ocean/INPUT/roughness_amp.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/roughness_amp.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20201102/mom_1deg/roughness_amp.nc hashes: binhash: 73a425be9e5cf7a3d349d75a8ebeadd1 md5: 185dadeb53da2de75b47c53fd7085f89 work/ocean/INPUT/roughness_cdbot.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/roughness_cdbot.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20201102/mom_1deg/roughness_cdbot.nc hashes: binhash: 4ec236c3874fbd4dc5c2fcdec271f557 md5: b50f0595f3ebc872cbcf5f3223115643 work/ocean/INPUT/salt_sfc_restore.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/salt_sfc_restore.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20201102/mom_1deg/salt_sfc_restore.nc hashes: binhash: 13101e8424f559b6c172ef86d85b9a8f md5: b2bd35c44017597ba99b85fb61ed4d72 work/ocean/INPUT/tideamp.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/tideamp.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20201102/mom_1deg/tideamp.nc hashes: binhash: 0226a494f8a03f8fb9845060cb694389 md5: b2840af757d9b7b40207f33f1fc84c5c work/ocean/INPUT/topog.nc: - fullpath: /g/data/ik11/inputs/access-om2/input_20200530/mom_1deg/topog.nc + fullpath: /g/data/ik11/inputs/access-om2/input_20201102/mom_1deg/topog.nc hashes: - binhash: b03638decf5d3a74da46fb225625f445 - md5: f01ddc02cfe21d8db99c2976e9fcc828 + binhash: 8ab65e521a588943b533b188a619d361 + md5: 4e13d88001b646f3cf4f1c3b8db59f91 From 38ba88eeafa0c8242cbc596fac411846867cee6e Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Wed, 11 Nov 2020 16:25:49 +1100 Subject: [PATCH 110/111] sort diagnostics --- ocean/diag_table | 12 ++++++------ ocean/diag_table_source.yaml | 4 ++-- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/ocean/diag_table b/ocean/diag_table index 1caa4863..0083b40a 100644 --- a/ocean/diag_table +++ b/ocean/diag_table @@ -229,12 +229,12 @@ ACCESS-OM2 "ocean-2d-sfc_salt_flux_restore-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "sfc_salt_flux_restore", "sfc_salt_flux_restore", "ocean-2d-sfc_salt_flux_restore-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-2d-surface_salt-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" -"ocean_model", "surface_salt", "surface_salt", "ocean-2d-surface_salt-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 - "ocean-2d-surface_pot_temp-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "surface_pot_temp", "surface_pot_temp", "ocean-2d-surface_pot_temp-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-2d-surface_salt-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" +"ocean_model", "surface_salt", "surface_salt", "ocean-2d-surface_salt-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 + "ocean-2d-swflx-1-monthly-mean-ym%4yr%2mo", 1, "months", 1, "days", "time", 1, "years" "ocean_model", "swflx", "swflx", "ocean-2d-swflx-1-monthly-mean-ym%4yr%2mo", "all", "average", "none", 2 @@ -319,12 +319,12 @@ ACCESS-OM2 "ocean-2d-sfc_hflux_pme-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" "ocean_model", "sfc_hflux_pme", "sfc_hflux_pme", "ocean-2d-sfc_hflux_pme-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 -"ocean-2d-surface_salt-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" -"ocean_model", "surface_salt", "surface_salt", "ocean-2d-surface_salt-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 - "ocean-2d-surface_pot_temp-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" "ocean_model", "surface_pot_temp", "surface_pot_temp", "ocean-2d-surface_pot_temp-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 +"ocean-2d-surface_salt-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" +"ocean_model", "surface_salt", "surface_salt", "ocean-2d-surface_salt-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 + "ocean-2d-usurf-1-daily-mean-ym%4yr%2mo", 1, "days", 1, "days", "time", 1, "years" "ocean_model", "usurf", "usurf", "ocean-2d-usurf-1-daily-mean-ym%4yr%2mo", "all", "average", "none", 2 diff --git a/ocean/diag_table_source.yaml b/ocean/diag_table_source.yaml index f0b0ee5b..abce5f31 100755 --- a/ocean/diag_table_source.yaml +++ b/ocean/diag_table_source.yaml @@ -214,8 +214,8 @@ diag_table: sfc_salt_flux_coupler: sfc_salt_flux_ice: sfc_salt_flux_restore: - surface_salt: surface_pot_temp: + surface_salt: swflx: tau_x: tau_y: @@ -254,8 +254,8 @@ diag_table: sfc_hflux_coupler: sfc_hflux_from_runoff: sfc_hflux_pme: - surface_salt: surface_pot_temp: + surface_salt: usurf: vsurf: 'daily 2d maximum fields': From 0783553cc4abd279232e34d776a13c646cb6fab4 Mon Sep 17 00:00:00 2001 From: Andrew Kiss <31054815+aekiss@users.noreply.github.com> Date: Thu, 12 Nov 2020 14:21:01 +1100 Subject: [PATCH 111/111] use history_chunksize_x = 180, history_chunksize_y = 150 - see https://github.com/COSIMA/cice5/issues/34#issuecomment-725742030 --- ice/cice_in.nml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ice/cice_in.nml b/ice/cice_in.nml index 65cd1472..b5cc7456 100644 --- a/ice/cice_in.nml +++ b/ice/cice_in.nml @@ -11,8 +11,8 @@ hist_avg = .true. histfreq = 'd', 'm', 'x', 'x', 'x' histfreq_n = 1, 1, 1, 1, 1 - history_chunksize_x = 90 - history_chunksize_y = 300 + history_chunksize_x = 180 + history_chunksize_y = 150 history_deflate_level = 1 history_dir = './OUTPUT/' history_file = 'iceh'