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Allow increments to be added for ocean and ice cycling. #1308

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merged 10 commits into from
Feb 15, 2023
Merged

Allow increments to be added for ocean and ice cycling. #1308

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311657d
cyc with ocn-ice
guillaumevernieres Feb 11, 2023
364df4e
Update ush/forecast_postdet.sh
guillaumevernieres Feb 13, 2023
015e0bd
Update parm/config/config.base.emc.dyn
guillaumevernieres Feb 13, 2023
19c4748
addressed review comments
guillaumevernieres Feb 14, 2023
46b1e7e
Update parm/mom6/MOM_input_template_025
guillaumevernieres Feb 14, 2023
b04954b
Update parm/mom6/MOM_input_template_050
guillaumevernieres Feb 14, 2023
55df592
Update parm/mom6/MOM_input_template_100
guillaumevernieres Feb 14, 2023
acbeb76
Update parm/mom6/MOM_input_template_500
guillaumevernieres Feb 14, 2023
6be7442
Update ush/forecast_postdet.sh
guillaumevernieres Feb 14, 2023
b8963ee
typos + remove export
guillaumevernieres Feb 14, 2023
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2 changes: 1 addition & 1 deletion jobs/rocoto/ocnanalbmat.sh
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Expand Up @@ -13,7 +13,7 @@ export jobid="${job}.$$"

###############################################################
# Execute the JJOB
#"${HOMEgfs}"/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_BMAT
"${HOMEgfs}"/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_BMAT
echo "BMAT gets run here"
status=$?
exit "${status}"
32 changes: 28 additions & 4 deletions parm/mom6/MOM_input_template_025
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Expand Up @@ -406,7 +406,7 @@ GILL_EQUATORIAL_LD = True ! [Boolean] default = False
! radius, otherwise, if false, use Pedlosky's definition. These definitions
! differ by a factor of 2 in front of the beta term in the denominator. Gill's
! is the more appropriate definition.
INTERNAL_WAVE_SPEED_BETTER_EST = False ! [Boolean] default = True
INTERNAL_WAVE_SPEED_BETTER_EST = False ! [Boolean] default = True
! If true, use a more robust estimate of the first mode wave speed as the
! starting point for iterations.

Expand Down Expand Up @@ -731,7 +731,7 @@ NSTAR = 0.06 ! [nondim] default = 0.2
! The portion of the buoyant potential energy imparted by surface fluxes that is
! available to drive entrainment at the base of mixed layer when that energy is
! positive.
EPBL_MLD_BISECTION = True ! [Boolean] default = False
EPBL_MLD_BISECTION = True ! [Boolean] default = False
! If true, use bisection with the iterative determination of the self-consistent
! mixed layer depth. Otherwise use the false position after a maximum and
! minimum bound have been evaluated and the returned value or bisection before
Expand Down Expand Up @@ -833,6 +833,30 @@ ENERGYSAVEDAYS = 1.00 ! [days] default = 1.0

! === module ocean_model_init ===

! === module MOM_oda_incupd ===
ODA_INCUPD = @[ODA_INCUPD] ! [Boolean] default = False
! If true, oda incremental updates will be applied
! everywhere in the domain.
ODA_INCUPD_FILE = "inc.nc" ! The name of the file with the T,S,h increments.
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ODA_TEMPINC_VAR = "Temp" ! default = "ptemp_inc"
! The name of the potential temperature inc. variable in
! ODA_INCUPD_FILE.
ODA_SALTINC_VAR = "Salt" ! default = "sal_inc"
! The name of the salinity inc. variable in
! ODA_INCUPD_FILE.
ODA_THK_VAR = "h" ! default = "h"
! The name of the int. depth inc. variable in
! ODA_INCUPD_FILE.
ODA_INCUPD_UV = false !
!ODA_UINC_VAR = "u" ! default = "u_inc"
! The name of the zonal vel. inc. variable in
! ODA_INCUPD_UV_FILE.
!ODA_VINC_VAR = "v" ! default = "v_inc"
! The name of the meridional vel. inc. variable in
! ODA_INCUPD_UV_FILE.
ODA_INCUPD_NHOURS = @[ODA_INCUPD_NHOURS] ! default=3.0

! === module MOM_surface_forcing ===
OCEAN_SURFACE_STAGGER = "A" ! default = "C"
! A case-insensitive character string to indicate the
Expand Down Expand Up @@ -868,8 +892,8 @@ LIQUID_RUNOFF_FROM_DATA = @[MOM6_RIVER_RUNOFF] ! [Boolean] default = False
! the data_table using the component name 'OCN'.
! === module ocean_stochastics ===
DO_SPPT = @[DO_OCN_SPPT] ! [Boolean] default = False
! If true perturb the diabatic tendencies in MOM_diabadic_driver
PERT_EPBL = @[PERT_EPBL] ! [Boolean] default = False
! If true perturb the diabatic tendencies in MOM_diabadic_driver
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MOM_diabatic_driver or is it diabadic?

PERT_EPBL = @[PERT_EPBL] ! [Boolean] default = False
! If true perturb the KE dissipation and destruction in MOM_energetic_PBL
! === module MOM_restart ===
RESTART_CHECKSUMS_REQUIRED = False
Expand Down
34 changes: 29 additions & 5 deletions parm/mom6/MOM_input_template_050
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Expand Up @@ -419,7 +419,7 @@ GILL_EQUATORIAL_LD = True ! [Boolean] default = False
! radius, otherwise, if false, use Pedlosky's definition. These definitions
! differ by a factor of 2 in front of the beta term in the denominator. Gill's
! is the more appropriate definition.
INTERNAL_WAVE_SPEED_BETTER_EST = False ! [Boolean] default = True
INTERNAL_WAVE_SPEED_BETTER_EST = False ! [Boolean] default = True
! If true, use a more robust estimate of the first mode wave speed as the
! starting point for iterations.

Expand Down Expand Up @@ -757,7 +757,7 @@ MSTAR2_COEF1 = 0.29 ! [nondim] default = 0.3
MSTAR2_COEF2 = 0.152 ! [nondim] default = 0.085
! Coefficient in computing mstar when only rotation limits the total mixing
! (used if EPBL_MSTAR_SCHEME = OM4)
EPBL_MLD_BISECTION = True ! [Boolean] default = False
EPBL_MLD_BISECTION = True ! [Boolean] default = False
! If true, use bisection with the iterative determination of the self-consistent
! mixed layer depth. Otherwise use the false position after a maximum and
! minimum bound have been evaluated and the returned value or bisection before
Expand Down Expand Up @@ -858,8 +858,32 @@ USE_NEUTRAL_DIFFUSION = True ! [Boolean] default = False
! If true, enables the neutral diffusion module.

! === module ocean_model_init ===

RESTART_CHECKSUMS_REQUIRED = False

! === module MOM_oda_incupd ===
ODA_INCUPD = @[ODA_INCUPD] ! [Boolean] default = False
! If true, oda incremental updates will be applied
! everywhere in the domain.
ODA_INCUPD_FILE = "inc.nc" ! The name of the file with the T,S,h increments.
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ODA_TEMPINC_VAR = "Temp" ! default = "ptemp_inc"
! The name of the potential temperature inc. variable in
! ODA_INCUPD_FILE.
ODA_SALTINC_VAR = "Salt" ! default = "sal_inc"
! The name of the salinity inc. variable in
! ODA_INCUPD_FILE.
ODA_THK_VAR = "h" ! default = "h"
! The name of the int. depth inc. variable in
! ODA_INCUPD_FILE.
ODA_INCUPD_UV = false !
!ODA_UINC_VAR = "u" ! default = "u_inc"
! The name of the zonal vel. inc. variable in
! ODA_INCUPD_UV_FILE.
!ODA_VINC_VAR = "v" ! default = "v_inc"
! The name of the meridional vel. inc. variable in
! ODA_INCUPD_UV_FILE.
ODA_INCUPD_NHOURS = @[ODA_INCUPD_NHOURS] ! default=3.0

! === module MOM_lateral_boundary_diffusion ===
! This module implements lateral diffusion of tracers near boundaries

Expand Down Expand Up @@ -913,8 +937,8 @@ LIQUID_RUNOFF_FROM_DATA = @[MOM6_RIVER_RUNOFF] ! [Boolean] default = False
! the data_table using the component name 'OCN'.
! === module ocean_stochastics ===
DO_SPPT = @[DO_OCN_SPPT] ! [Boolean] default = False
! If true perturb the diabatic tendencies in MOM_diabadic_driver
PERT_EPBL = @[PERT_EPBL] ! [Boolean] default = False
! If true perturb the diabatic tendencies in MOM_diabadic_driver
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again

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Maybe somebody had a cold when writing that namelist @CoryMartin-NOAA

PERT_EPBL = @[PERT_EPBL] ! [Boolean] default = False
! If true perturb the KE dissipation and destruction in MOM_energetic_PBL
! === module MOM_restart ===

Expand Down
28 changes: 25 additions & 3 deletions parm/mom6/MOM_input_template_100
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Expand Up @@ -76,7 +76,7 @@ SAVE_INITIAL_CONDS = False ! [Boolean] default = False
! If true, write the initial conditions to a file given by IC_OUTPUT_FILE.

! === module MOM_oda_incupd ===
ODA_INCUPD = @[MOM_IAU] ! [Boolean] default = False
ODA_INCUPD = @[ODA_INCUPD] ! [Boolean] default = False
! If true, oda incremental updates will be applied
! everywhere in the domain.
ODA_INCUPD_FILE = "mom6_increment.nc" ! The name of the file with the T,S,h increments.
Expand All @@ -97,7 +97,7 @@ ODA_UINC_VAR = "u_inc" ! default = "u_inc"
ODA_VINC_VAR = "v_inc" ! default = "v_inc"
! The name of the meridional vel. inc. variable in
! ODA_INCUPD_UV_FILE.
ODA_INCUPD_NHOURS = @[MOM_IAU_HRS] ! default=3.0
ODA_INCUPD_NHOURS = @[ODA_INCUPD_NHOURS] ! default=3.0
! Number of hours for full update (0=direct insertion).

! === module MOM_domains ===
Expand Down Expand Up @@ -430,7 +430,7 @@ VISC_RES_FN_POWER = 2 ! [nondim] default = 100
! used, although even integers are more efficient to calculate. Setting this
! greater than 100 results in a step-function being used. This function affects
! lateral viscosity, Kh, and not KhTh.
INTERNAL_WAVE_SPEED_BETTER_EST = False ! [Boolean] default = True
INTERNAL_WAVE_SPEED_BETTER_EST = False ! [Boolean] default = True
! If true, use a more robust estimate of the first mode wave speed as the
! starting point for iterations.

Expand Down Expand Up @@ -829,6 +829,28 @@ ENERGYSAVEDAYS = 0.25 ! [days] default = 1.0
! other globally summed diagnostics.

! === module ocean_model_init ===
ODA_INCUPD = @[ODA_INCUPD] ! [Boolean] default = False
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So usually the MOM_input_template_* is a copy of what is in ufs-weather-model. Do these updates need a corresponding test in ufs-weather-model?

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Thanks for jumping in @JessicaMeixner-NOAA , I should have thought about adding you when I started modifying the mom namelist! Sorry.
Is there a MOM6 IAU test in the ufs-weather model?

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I think there is one here: https://github.com/ufs-community/ufs-weather-model/blob/develop/tests/tests/datm_cdeps_iau_gefs but it looks like the settings are different

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It seems close enough to me @JessicaMeixner-NOAA but up to you if you think it needs an update to the RT.
@aerorahul was trying to bring the naming nomenclature closer to what the atmosphere DA is doing, which does make sense.

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That sounds like a great idea to me too. I think it's important that we are testing in ufs-weather-model what we're actually going to be running and having consistency makes updating the model in the future easier. I believe there was talk at one point to actually point to the MOM_template files in ufs-eather-model instead of having a second copy of these, but I'm not sure if that's still going to be a future development for g-w or not. Either way, I just wanted to flag this as something to be aware of, but I don't think it should hold up this PR.

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Thanks @JessicaMeixner-NOAA
We can let this PR pass and I can open a follow up PR removing these files from global-workflow and using the ones from ufs-weather-model.
Would you be able to provide a branch of the ufs-weather-model that allows for this flexibility?
The ufs-weather-model RT parm/ files may need an update.

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We'd need the following:

  1. A PR to ufs-weather-model updating the template files to use these new settings
  2. A PR to global-workflow then updating the model version
  3. A PR having the global-workflow update to then use the ufs-weather-model parm files (I actually thought this was on the workflow teams radar to do?)

I can do all of the above, but it will be a while before I personally have time to do this. Again, there's no reason this PR should not proceed.

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Yes. 3. is on our radar.
We need atleast 1. for 3.
There is a lot more work in the ufs-weather-model than in the global-workflow to achieve this.
I can create issues in the global-workflow and ufs-weather-model and assign us respectively if that is ok?

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That sounds great. Just know this isn't anywhere near the top of my priority list at the moment.

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@JessicaMeixner-NOAA
#1312
ufs-community/ufs-weather-model#1613
have been created

! If true, oda incremental updates will be applied
! everywhere in the domain.
ODA_INCUPD_FILE = "inc.nc" ! The name of the file with the T,S,h increments.
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ODA_TEMPINC_VAR = "Temp" ! default = "ptemp_inc"
! The name of the potential temperature inc. variable in
! ODA_INCUPD_FILE.
ODA_SALTINC_VAR = "Salt" ! default = "sal_inc"
! The name of the salinity inc. variable in
! ODA_INCUPD_FILE.
ODA_THK_VAR = "h" ! default = "h"
! The name of the int. depth inc. variable in
! ODA_INCUPD_FILE.
ODA_INCUPD_UV = false !
!ODA_UINC_VAR = "u" ! default = "u_inc"
! The name of the zonal vel. inc. variable in
! ODA_INCUPD_UV_FILE.
!ODA_VINC_VAR = "v" ! default = "v_inc"
! The name of the meridional vel. inc. variable in
! ODA_INCUPD_UV_FILE.
ODA_INCUPD_NHOURS = @[ODA_INCUPD_NHOURS] ! default=3.0

! === module MOM_surface_forcing ===
OCEAN_SURFACE_STAGGER = "A" ! default = "C"
Expand Down
6 changes: 4 additions & 2 deletions parm/mom6/MOM_input_template_500
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Expand Up @@ -492,7 +492,9 @@ MAXTRUNC = 1000 ! [truncations save_interval-1] default = 0
! to stop if there is any truncation of velocities.

! === module ocean_model_init ===
ODA_INCUPD = @[MOM_IAU] ! [Boolean] default = False

! === module MOM_oda_incupd ===
ODA_INCUPD = @[ODA_INCUPD] ! [Boolean] default = False
! If true, oda incremental updates will be applied
! everywhere in the domain.
ODA_INCUPD_FILE = "inc.nc" ! The name of the file with the T,S,h increments.
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Expand All @@ -513,7 +515,7 @@ ODA_INCUPD_UV = false !
!ODA_VINC_VAR = "v" ! default = "v_inc"
! The name of the meridional vel. inc. variable in
! ODA_INCUPD_UV_FILE.
ODA_INCUPD_NHOURS = @[MOM_IAU_HRS] ! default=3.0
ODA_INCUPD_NHOURS = @[ODA_INCUPD_NHOURS] ! default=3.0

! === module MOM_surface_forcing ===
OCEAN_SURFACE_STAGGER = "A" ! default = "C"
Expand Down
10 changes: 10 additions & 0 deletions ush/forecast_postdet.sh
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Expand Up @@ -769,6 +769,16 @@ MOM6_postdet() {
;;
esac

# Link increment
if [[ "${DO_JEDIOCNVAR:-NO}" = "YES" ]]; then
if [[ ! -f "${ROTDIR}/${CDUMP}.${PDY}/${cyc}/ocean/${CDUMP}.t${cyc}z.ocninc.nc" ]]; then
echo "FATAL ERROR: Ocean increment not found, ABORT!"
exit 111
fi
$NLN "${ROTDIR}/${CDUMP}.${PDY}/${cyc}/ocean/${CDUMP}.t${cyc}z.ocninc.nc" "${DATA}/INPUT/inc.nc"
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export ODA_INCUPD="true"
fi

# Copy MOM6 fixed files
$NCP -pf $FIXmom/$OCNRES/* $DATA/INPUT/

Expand Down
3 changes: 2 additions & 1 deletion ush/load_ufsda_modules.sh
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@@ -1,7 +1,8 @@
#! /usr/bin/env bash

###############################################################
if [[ "${DEBUG_WORKFLOW:-NO}" == "NO" ]]; then
export DEBUG_WORKFLOW="${DEBUG_WORKFLOW:-NO}"
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is this a lint thing?

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@CoryMartin-NOAA , nope, that was an issue before you added a default to the other places where DEBUG_WORKFLOW is used. I'll remove that line.

if [[ "${DEBUG_WORKFLOW}" == "NO" ]]; then
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I think this was a mistake to merge this change in... did anyone test? @jiaruidong2017 seems to be having an issue here

echo "Loading modules quietly..."
set +x
fi
Expand Down
8 changes: 4 additions & 4 deletions ush/parsing_namelists_MOM6.sh
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Expand Up @@ -15,8 +15,8 @@ MOM6_ALLOW_LANDMASK_CHANGES=${MOM6_ALLOW_LANDMASK_CHANGES:-'False'}
DO_OCN_SPPT=${DO_OCN_SPPT:-'False'}
PERT_EPBL=${PERT_EPBL:-'False'}

MOM_IAU=${MOM_IAU:-"false"}
MOM_IAU_HRS=${MOM_IAU_HRS:-'3.0'}
ODA_INCUPD=${ODA_INCUPD:-"false"}
ODA_INCUPD_NHOURS=${ODA_INCUPD_NHOURS:-'3.0'}

if [ $cplwav = ".true." ] ; then
MOM6_USE_WAVES='True'
Expand Down Expand Up @@ -134,8 +134,8 @@ sed -e "s/@\[DT_THERM_MOM6\]/$DT_THERM_MOM6/g" \
-e "s/@\[CHLCLIM\]/$CHLCLIM/g" \
-e "s/@\[DO_OCN_SPPT\]/$OCN_SPPT/g" \
-e "s/@\[PERT_EPBL\]/$PERT_EPBL/g" \
-e "s/@\[MOM_IAU_HRS\]/$MOM_IAU_HRS/g" \
-e "s/@\[MOM_IAU\]/$MOM_IAU/g" $DATA/INPUT/MOM_input_template_$OCNRES > $DATA/INPUT/MOM_input
-e "s/@\[ODA_INCUPD_NHOURS\]/$ODA_INCUPD_NHOURS/g" \
-e "s/@\[ODA_INCUPD\]/$ODA_INCUPD/g" $DATA/INPUT/MOM_input_template_$OCNRES > $DATA/INPUT/MOM_input
rm $DATA/INPUT/MOM_input_template_$OCNRES

#data table for runoff:
Expand Down
5 changes: 2 additions & 3 deletions workflow/rocoto/workflow_tasks.py
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Expand Up @@ -649,9 +649,8 @@ def _fcst_cycled(self):
dependencies = rocoto.create_dependency(dep=dep)

if self.app_config.do_jediocnvar:
dep_dict = {'type': 'task', 'name': f'{self.cdump}ocnanalrun'}
dep = rocoto.add_dependency(dep_dict)
dependencies = rocoto.create_dependency(dep=dep)
dep_dict = {'type': 'task', 'name': f'{self.cdump}ocnanalpost'}
dependencies.append(rocoto.add_dependency(dep_dict))

if self.app_config.do_gldas and self.cdump in ['gdas']:
dep_dict = {'type': 'task', 'name': f'{self.cdump}gldas'}
Expand Down
8 changes: 8 additions & 0 deletions workflow/setup_expt.py
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Expand Up @@ -120,6 +120,14 @@ def link_files_from_src_to_dst(src_dir, dst_dir):
makedirs_if_missing(dst_dir)
link_files_from_src_to_dst(src_dir, dst_dir)

# First 1/2 cycle needs a MOM6 increment
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why? is it not a cold start?

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No, it's a warm start.

incdir = f'{inputs.cdump}.{idatestr[:8]}/{idatestr[8:]}'
incfile = f'{inputs.cdump}.t{idatestr[8:]}z.ocninc.nc'
src_file = os.path.join(inputs.icsdir, incdir, 'ocean', incfile)
dst_file = os.path.join(comrot, incdir, 'ocean', incfile)
makedirs_if_missing(os.path.join(comrot, incdir, 'ocean'))
os.symlink(src_file, dst_file)

# Link ice files
if do_ice:
detdir = f'{inputs.cdump}.{rdatestr[:8]}/{rdatestr[8:]}'
Expand Down