Code

merge ak-dev branch#6

Code

Merged

aekiss merged 121 commits intomasterCOSIMA/1deg_jra55_iaf:masterfrom ak-devCOSIMA/1deg_jra55_iaf:ak-devCopy head branch name to clipboardNov 12, 2020

+3,909-4,399

Commits

Commits on Aug 2, 2019

• Set CICE output compression with history_deflate_level = 1; see COSIMA/cice5#33

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  committed
  ae98ee0

Commits on Aug 6, 2019

• use frazil_3d_int_z in diag_table - see COSIMA/access-om2#139

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• disable net_sfc_heating and total_net_sfc_heating in diag_table - see COSIMA/access-om2#139

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  8681ca9

Commits on Aug 7, 2019

• use use relative winds in CICE (highfreq=true) - see COSIMA/access-om2#138

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  fa2b5b9

Commits on Aug 8, 2019

• set zmax_pen = 1.0e6 (the default) in ocean/input.nml

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  b7b7921

Commits on Aug 12, 2019

• more harmonisation across default configurations

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  4b696b6

• set neutralrho_min=1028.0 and neutralrho_max=1038.0; see COSIMA/access-om2#135

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  3bd5382

Commits on Aug 13, 2019

• Fix Rayleigh damping - see COSIMA/access-om2#156

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  5cb4ac5

Commits on Aug 21, 2019

• small tweaks

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  3a725f9

• Merge branch 'master' into ak-dev

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• README.md: add recommendation to watch repos

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• README tweak

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  474c510

• Use safer min_thickness = 1.0e-3; see COSIMA/access-om2#161

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  04fac56

Commits on Sep 10, 2019

• Merge branch 'master' into ak-dev

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  03d8303

Commits on Oct 3, 2019

• Don't compress MOM outputs/restarts until collation - COSIMA/access-om2#168

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  55837b7

Commits on Oct 31, 2019

• added tidy_restarts.py

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  ebf3623

Commits on Dec 9, 2019

• remove trailing comma in atmosphere/forcing.json

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  bbff9d6

Commits on Dec 13, 2019

• merge gadi-transition

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  090b4d2

Commits on Dec 16, 2019

• merge gadi-transition again

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  2e4157b

• use input_rc for inputs (temporary - for testing)

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Commits on Dec 17, 2019

• increase memory request for sync_output_to_gdata.sh from 2Gb to 4Gb

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  547eddf

Commits on Dec 20, 2019

• revert cice commit COSIMA/cice5@ab473434 - see COSIMA/cice5#38

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  c093ff7

Commits on Jan 12, 2020

• sync_output_to_gdata.sh: set PBS flag for storage on gadi; exit if paths inaccessible

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  307e3a2

Commits on Jan 14, 2020

• 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 COSIMA/access-om2#171

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  2ea5aa9

Commits on Feb 12, 2020

• Merge branch 'gadi-transition' into ak-dev

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  6794913

Commits on Feb 24, 2020

• fix /g/data paths for gadi - COSIMA/access-om2#188

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  e92b910

Commits on Feb 27, 2020

• Merge branch 'gadi-transition' into ak-dev

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  488d0f1

Commits on Mar 16, 2020

• remove references to /g/data3

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Commits on Mar 17, 2020

• stop using qsub_flags: -lother=hyperthread - see COSIMA/access-om2#191

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Commits on Mar 19, 2020

• rename sync_to_gdata.sh to sync_data.sh and recommend syncing to /g/data/ik11 rather than hh5

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Commits on Mar 20, 2020

• remove payu workaround for gadi storage issue - see payu-org/payu#215

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Commits on Mar 26, 2020

• clarify comment in sync_data.sh

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• use normal queue

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Commits on Apr 20, 2020

• more helpful README

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  cc26e6b

Commits on Apr 28, 2020

• Automatically sweep and resubmit on specific errors - payu-org/payu#241

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• Merge branch 'feat-155-JRA55-v1p4' into ak-dev

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  41218bf

Commits on Apr 29, 2020

• compress restarts - see COSIMA/access-om2#168

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  cf26870

• update manifests

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• fix resub.sh - payu-org/payu#241 (comment)

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• Simpified/generalised namcouple

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• Further clean-ups to namcouple

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Commits on Apr 30, 2020

• Fix merge

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  76aa595

Commits on May 5, 2020

• improve CICE diagnostic consistency across configs

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  59e7684

Commits on May 6, 2020

• Remove redundant neutral physics namelist entries - see COSIMA/access-om2#197

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Commits on May 14, 2020

• put namelists in a consistent format with nmltab.py --tidy_overwrite - should work identically to before

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  f9bd1e0

• remove repeated history_deflate_level in cice_in.nml

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• Add pot_temp to diag_table since we're using conservative temperature as the prognostic variable COSIMA/access-om2#97

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Commits on May 15, 2020

• Merge branch 'tidy-namelists' into ak-dev

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• remove unused cdbot and default cdbot_roughness_length and use_geothermal_heating in input.nml - see COSIMA/access-om2#200

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• remove empty namelist groups from ocean/input.nml

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• delete any cice log files that only have a 105-character header and nothing else

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  f32846d

Commits on May 17, 2020

• improve alignment of namelists, using ./nmltab.py --tidy_overwrite with aekiss/nmltab@cb35a12

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  e609d07

• remove redundant clutter in input.nml; no change in results expected

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  b95f0e9

Commits on May 18, 2020

• remove redundant ocean_albedo_nml in input.nml

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• remove redundant monin_obukhov_nml in input.nml

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Commits on May 19, 2020

• reinstate unused namelist groups in input.nml

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  ea3eeeb

• remove redundant zero_pressure_force = .false. in input.nml

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  e59d76e

Commits on May 20, 2020

• undo sorting of namelist groups in cice_in.nml

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  cf5ff4d

• let payu determine the total ncpus - see payu-org/payu#97

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Commits on May 22, 2020

• Raise limits on number of MOM output files

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Commits on May 26, 2020

• new diag_table generated from diag_table_source.yaml with make_diag_table.py

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Commits on May 27, 2020

• diag_table tweaks - see COSIMA/access-om2#203

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  c93239c

• increase max_axes to 400 in input.nml

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Commits on May 29, 2020

• more diag_table tweaks

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• yet more diag_table tweaks

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• even more diag_table tweaks

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• another diag_table update - see COSIMA/access-om2#203

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Commits on May 30, 2020

• add tx_trans to diag_table

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• use inputs from input_20200530

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• update input manifests

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Commits on Jun 3, 2020

• improve sync_data.sh

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Commits on Jun 4, 2020

• more diag_table tweaks

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• remove old test data

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Commits on Jun 6, 2020

• output MOM scalar diags as daily snapshots

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Commits on Jun 7, 2020

• use Large and Yeager (2009) latitude-dependent ocean albedo (cst_ocn_albedo=false) - COSIMA/access-om2#172

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• update ice diagnostics - see COSIMA/access-om2#207

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• use latest model executables

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Commits on Jun 9, 2020

• use latest executables

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  bfbc4f0

• update manifests/exe.yaml

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  448f759

• update libaccessom2 again

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  2fe0b86

Commits on Jun 11, 2020

• add run_summary.py

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Commits on Jun 12, 2020

• remove calving diagnostics

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  5b95929

Commits on Jun 16, 2020

• add nmltab.py and update run_summary.py

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  10f74f0

• increase memory from 500GB to 1000GB

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  91b28ec

Commits on Jun 18, 2020

• improve .gitignore

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  d8bf172

• update and sync run_summary with sync_data.sh

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• improve help in tidy_restarts.py and set default k=1

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• auto-resubmit on atmosphere/input.nml error payu-org/payu#274

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• improved comments in config.yaml

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Commits on Jun 24, 2020

• update run_summary.py

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• update sync_data.sh to sync only collated .nc files

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Commits on Jun 29, 2020

• collate on normal queue as wait time is negligible on gadi

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Commits on Jul 6, 2020

• extend forcing end date to 2019-01-01T00:00:00

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• move timestep details from README.md to accessom2.nml

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Commits on Jul 7, 2020

• fix namcouple comment - closes COSIMA/access-om2#211

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Commits on Jul 8, 2020

• add metadata.yaml and sync it

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Commits on Jul 13, 2020

• keep all restarts

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  a7ba596

• auto-resubmit on Segmentation fault: invalid permissions for mapped object error

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Commits on Jul 14, 2020

• update run_summary.py

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Commits on Aug 4, 2020

• output monthly mean temp_xflux_gm_int_z, temp_yflux_gm_int_z, temp_xflux_submeso_int_z, temp_yflux_submeso_int_z

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Commits on Aug 10, 2020

• fix typo

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  c1945e6

• backward sync support in sync_data.sh

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Commits on Sep 4, 2020

• add eta_nonbouss monthly diagnostic

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• improve legibility of resubmit.log

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  f4c6fe8

• tweak run_summary.py outputs

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Commits on Sep 6, 2020

• fix daily max bottom_temp, sea_level, surface_temp diagnostics and add daily min surface_temp diagnostic

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Commits on Sep 7, 2020

• fix diag_table: change u_surf, v_surf to usurf, vsurf

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Commits on Sep 9, 2020

• Merge branch 'master' into ak-dev

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Commits on Sep 15, 2020

• fix notes field in metadata.yaml

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Commits on Sep 16, 2020

• update metadata.yaml

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Commits on Oct 6, 2020

• add conditions of use to metadata

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Commits on Oct 20, 2020

• output surface_pot_temp instead of (conservative) surface_temp - see COSIMA/access-om2#203 (comment)

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Commits on Oct 22, 2020

• switch to input_20201022

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Commits on Oct 28, 2020

• concatenate ice daily files in sync_data.sh; sync_data.sh -r now removes individual daily ice files if they have been concatenated

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Commits on Oct 30, 2020

• add conditions of use to README.md

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Commits on Nov 5, 2020

• update model executables (MOM exe now includes WOMBAT BGC: mom-ocean/MOM5#317; CICE uses PIO: COSIMA/cice5#34); configuration changes to support PIO in CICE

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• use input_20201102

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• don't output vorticity_z_surf (it doesn't exist)

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• update manifests

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Commits on Nov 11, 2020

• sort diagnostics

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Commits on Nov 12, 2020

• use history_chunksize_x = 180, history_chunksize_y = 150 - see COSIMA/cice5#34 (comment)

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