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Add debug #70

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binli2337 merged 15 commits into from
Apr 27, 2020
Merged

Add debug #70

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77b5efa
Update ufs-s2s-model
binli2337 Jan 28, 2020
5e1bd90
update FV3, MOM6 and NEMS
binli2337 Jan 28, 2020
a05d12a
Merge remote-tracking branch 'upstream/develop' into develop
binli2337 Feb 3, 2020
b5deed6
Merge branch 'develop' of https://github.com/ufs-community/ufs-s2s-mo…
binli2337 Feb 29, 2020
21c5620
Merge branch 'develop' of https://github.com/ufs-community/ufs-s2s-mo…
binli2337 Mar 21, 2020
288874f
Merge branch 'develop' of https://github.com/ufs-community/ufs-s2s-mo…
binli2337 Mar 26, 2020
8e0df44
Merge branch 'develop' of https://github.com/ufs-community/ufs-s2s-mo…
binli2337 Apr 9, 2020
fdcabca
Updated FV3.
binli2337 Apr 9, 2020
a3a964c
Merge branch 'develop' of https://github.com/ufs-community/ufs-s2s-mo…
binli2337 Apr 16, 2020
8f0b2eb
Revised compsets/fv3mom6cice5_ccpp.input, compsets/nemscommon.input.
binli2337 Apr 21, 2020
c07a6cc
Updated conf/before_components.mk.
binli2337 Apr 21, 2020
7efd277
Revised compsets/all.input and compsets/fv3mom6cice5_ccpp.input.
binli2337 Apr 24, 2020
5d37c48
Revised compsets/nemscommon.input and added log files.
binli2337 Apr 25, 2020
879140c
Update NEMS and .gitmodules.
binli2337 Apr 27, 2020
11bd1c7
Update .gitmodules and NEMS.
binli2337 Apr 27, 2020
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4 changes: 2 additions & 2 deletions .gitmodules
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@
branch = develop
[submodule "NEMS"]
path = NEMS
url = https://github.com/NOAA-EMC/NEMS.git
branch = develop
url = https://github.com/MinsukJi-NOAA/NEMS.git
branch = feature/s2s_debug
[submodule "CICE_SRC"]
path = CICE_SRC
url = https://github.com/NOAA-EMC/CICE5.git
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2 changes: 1 addition & 1 deletion NEMS
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Submodule NEMS updated 25 files
+3 −0 .gitignore
+1 −1 .gitmodules
+7 −0 GNUmakefile
+2,445 −0 doc/Doxyfile.IN
+64 −0 doc/Makefile
+48 −0 doc/architecture.md
+15 −0 doc/cap-doc.md
+95 −0 doc/configuring.md
+12 −0 doc/documentation.dox
+76 −0 doc/introduction.md
+3 −0 doc/make-images-fit.css
+239 −0 doc/mediator.md
+21 −0 doc/nemsmain.md
+234 −0 doc/prep_inputs.py
+34 −0 doc/scan_repo.pl
+1 −0 src/MAIN_NEMS.F90
+6 −0 src/conf/module-setup.csh.inc
+6 −0 src/conf/module-setup.sh.inc
+1 −0 src/incmake/buildenv.mk
+10 −0 src/incmake/env/ssec/detect.mk
+7 −0 src/incmake/env/ssec/s4.intel.mk
+9 −0 src/incmake/relist_components.mk
+2 −0 src/module_NEMS_GRID_COMP.F90
+1 −1 src/module_NEMS_Rusage.F90
+1 −1 tests/produtil/NCEPLIBS-pyprodutil
5 changes: 5 additions & 0 deletions compsets/all.input
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Original file line number Diff line number Diff line change
Expand Up @@ -98,6 +98,11 @@ run cpld_fv3_ccpp_384_mom6_cice_ww3_1d_bmark_rt @ fv3, coupledapp, warm384, phys
#run cpld_fv3_ccpp_mom6_cice_1d_gfdlmprad_gwd @ fv3, coupledapp, warm, physics
#run cpld_fv3_ccpp_mom6_cice_1d_gfdlmprad_noahmp @ fv3, coupledapp, warm, physics

########################################################################
# Two debug tests
run cpld_fv3_ccpp_mom6_cice_cold_debug @ fv3, coupledapp, cold, physics
run cpld_fv3_ccpp_mom6_cice_6h_debug @ fv3, coupledapp, warm, physics

########################################################################
#Run the Benchmark-like inputs for a single date
#These can be run separately from the baseline test cases
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195 changes: 195 additions & 0 deletions compsets/fv3mom6cice5_ccpp.input
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Expand Up @@ -109,6 +109,20 @@ build fv3_ccpp_mom6_cice_ww3_repro.exe {
OPTS="app=coupledFV3_CCPP_MOM6_CICE_WW3_repro",md5sum="@[md5sum]")
}

build fv3_ccpp_mom6_cice_debug.exe {
# Use NEMSAppBuilder to build a coupled app.
use plat
# Note:
# plat%EXECrt = temporary directory for executables and md5 sums
# plat%INCrt = temporary directory for modulefiles
target="@[plat%EXECrt]/fv3_ccpp_mom6_cice_debug.exe"
modules.nems="@[plat%INCrt]/modules_fv3_ccpp_mom6_cice_debug"
md5sum="@[target].md5"

# The NEMSAppBuilder is another embedded bash script in nemscommon.input
build=NEMSAppBuilder_debug(NEMS.x="@[target]",modules.nems="@[modules.nems]",
OPTS="app=coupledFV3_CCPP_MOM6_CICE_debug",md5sum="@[md5sum]")
}
########################################################################
#NOTE: DO NOT UPDATE the fv3_default variables for coupled fiels,
#update them within the tests themselves. The fv3_default variables
Expand Down Expand Up @@ -387,6 +401,187 @@ test cpld_fv3_ccpp_mom6_cice_1d_satmedmf: fv3_ccpp_mom6_cice.exe {
}
}
########################################################################
# cold c96 debug

test cpld_fv3_ccpp_mom6_cice_cold_debug: fv3_ccpp_mom6_cice_debug.exe {
use cpld_fv3_ccpp_mom6_cice_cold_atm_flux
TEST_DESCR="Fully coupled FV3-CCPP-MOM6-CICE system - debug"
CNTL_NAME="RT-Baselines_cold_debug_ccpp"
CNTL="@[plat%BASELINE]/@[CNTL_NAME]"
CNTLMED="@[plat%BASELINE]/MEDIATOR_debug_ccpp"

build=fv3_ccpp_mom6_cice_debug.exe

prep=fv3cpld_prep(
RUNDIR="@[RUNDIR]",modules="@[fv3_ccpp_mom6_cice_debug.exe%modules.nems]",
CNTL="@[CNTL]")

# Specify output files:
criteria output {
# WORKFILE .comparison. TARGET
'phyf001.tile1.nc' .bitcmp. "@[CNTL]"
'phyf001.tile2.nc' .bitcmp. "@[CNTL]"
'phyf001.tile3.nc' .bitcmp. "@[CNTL]"
'phyf001.tile4.nc' .bitcmp. "@[CNTL]"
'phyf001.tile5.nc' .bitcmp. "@[CNTL]"
'phyf001.tile6.nc' .bitcmp. "@[CNTL]"
'dynf001.tile1.nc' .bitcmp. "@[CNTL]"
'dynf001.tile2.nc' .bitcmp. "@[CNTL]"
'dynf001.tile3.nc' .bitcmp. "@[CNTL]"
'dynf001.tile4.nc' .bitcmp. "@[CNTL]"
'dynf001.tile5.nc' .bitcmp. "@[CNTL]"
'dynf001.tile6.nc' .bitcmp. "@[CNTL]"
'RESTART/coupler.res' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/fv_core.res.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/fv_core.res.tile1.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/fv_core.res.tile2.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/fv_core.res.tile3.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/fv_core.res.tile4.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/fv_core.res.tile5.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/fv_core.res.tile6.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/fv_srf_wnd.res.tile1.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/fv_srf_wnd.res.tile2.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/fv_srf_wnd.res.tile3.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/fv_srf_wnd.res.tile4.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/fv_srf_wnd.res.tile5.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/fv_srf_wnd.res.tile6.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/fv_tracer.res.tile1.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/fv_tracer.res.tile2.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/fv_tracer.res.tile3.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/fv_tracer.res.tile4.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/fv_tracer.res.tile5.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/fv_tracer.res.tile6.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/phy_data.tile1.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/phy_data.tile2.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/phy_data.tile3.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/phy_data.tile4.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/phy_data.tile5.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/phy_data.tile6.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/sfc_data.tile1.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/sfc_data.tile2.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/sfc_data.tile3.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/sfc_data.tile4.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/sfc_data.tile5.nc' .bitcmp. "@[CNTL]/RESTART/"
'RESTART/sfc_data.tile6.nc' .bitcmp. "@[CNTL]/RESTART/"
'mediator_FBAtm_a_restart.tile1.nc' .bitcmp. "@[CNTLMED]/"
'mediator_FBAtm_a_restart.tile2.nc' .bitcmp. "@[CNTLMED]/"
'mediator_FBAtm_a_restart.tile3.nc' .bitcmp. "@[CNTLMED]/"
'mediator_FBAtm_a_restart.tile4.nc' .bitcmp. "@[CNTLMED]/"
'mediator_FBAtm_a_restart.tile5.nc' .bitcmp. "@[CNTLMED]/"
'mediator_FBAtm_a_restart.tile6.nc' .bitcmp. "@[CNTLMED]/"
'mediator_FBAtmOcn_o_restart.nc' .bitcmp. "@[CNTLMED]/"
'mediator_FBIce_i_restart.nc' .bitcmp. "@[CNTLMED]/"
'mediator_FBOcn_o_restart.nc' .bitcmp. "@[CNTLMED]/"
'mediator_scalars_restart.txt' .bitcmp. "@[CNTLMED]/"
# Executable validation. This makes an MD5 sum of the fv3.exe
# for comparison against the MD5 sum made in the build job.
# This is to ensure the executable did not change during the
# test suite.
"@[build%target]" .md5cmp. "@[fv3_ccpp_mom6_cice_debug.exe%md5sum]"
}
}
########################################################################
# warm 6h c96 debug

test cpld_fv3_ccpp_mom6_cice_6h_debug: fv3_ccpp_mom6_cice_debug.exe {
use cpld_fv3_ccpp_mom6_cice_2d_atm_flux
DAYS='0.25' # run for 0.25 day
FHMAX='6'
NFHOUT_HF='1'
walltime=2400 # seconds
TEST_DESCR="Fully coupled FV3-CCPP-MOM6-CICE system - debug"
CNTL_NAME="RT-Baselines_6h_warm_debug_ccpp"
CNTL="@[plat%BASELINE]/@[CNTL_NAME]"

MED_restart_data="@[plat%BASELINE]/MEDIATOR_debug_ccpp"

build=fv3_ccpp_mom6_cice_debug.exe

prep=fv3cpld_prep(
RUNDIR="@[RUNDIR]",modules="@[fv3_ccpp_mom6_cice_debug.exe%modules.nems]",
CNTL="@[CNTL]")

# Specify output files:

@DeniseWorthen DeniseWorthen Apr 27, 2020 •
edited
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You are not comparing the CICE restart file. I believe that is because you have not created one because the default compset you are using has:
DUMPFREQ_N="@[DAYS]"
DUMPFREQ='d'

In order to generate a CICE restart for a 6 hour run, you need to set
DUMPFREQ_N ="@[FHMAX]"
DUMPFREQ='h'

@binli2337 binli2337 Apr 27, 2020

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You are correct. The cice_in will be updated in the next commit this week.

@DeniseWorthen DeniseWorthen Apr 27, 2020

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So we will update the test to produce the ice restart file and also compare it, correct?

criteria output {
# WORKFILE .comparison. TARGET
'phyf006.tile1.nc' .bitcmp. "@[CNTL]"
'phyf006.tile2.nc' .bitcmp. "@[CNTL]"
'phyf006.tile3.nc' .bitcmp. "@[CNTL]"
'phyf006.tile4.nc' .bitcmp. "@[CNTL]"
'phyf006.tile5.nc' .bitcmp. "@[CNTL]"
'phyf006.tile6.nc' .bitcmp. "@[CNTL]"
'dynf006.tile1.nc' .bitcmp. "@[CNTL]"
'dynf006.tile2.nc' .bitcmp. "@[CNTL]"
'dynf006.tile3.nc' .bitcmp. "@[CNTL]"
'dynf006.tile4.nc' .bitcmp. "@[CNTL]"
'dynf006.tile5.nc' .bitcmp. "@[CNTL]"
'dynf006.tile6.nc' .bitcmp. "@[CNTL]"
'RESTART/coupler.res' .bitcmp. "@[CNTL]/RESTART"
'RESTART/fv_core.res.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/fv_core.res.tile1.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/fv_core.res.tile2.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/fv_core.res.tile3.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/fv_core.res.tile4.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/fv_core.res.tile5.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/fv_core.res.tile6.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/fv_srf_wnd.res.tile1.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/fv_srf_wnd.res.tile2.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/fv_srf_wnd.res.tile3.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/fv_srf_wnd.res.tile4.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/fv_srf_wnd.res.tile5.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/fv_srf_wnd.res.tile6.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/fv_tracer.res.tile1.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/fv_tracer.res.tile2.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/fv_tracer.res.tile3.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/fv_tracer.res.tile4.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/fv_tracer.res.tile5.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/fv_tracer.res.tile6.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/phy_data.tile1.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/phy_data.tile2.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/phy_data.tile3.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/phy_data.tile4.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/phy_data.tile5.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/phy_data.tile6.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/sfc_data.tile1.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/sfc_data.tile2.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/sfc_data.tile3.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/sfc_data.tile4.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/sfc_data.tile5.nc' .bitcmp. "@[CNTL]/RESTART"
'RESTART/sfc_data.tile6.nc' .bitcmp. "@[CNTL]/RESTART"
'MOM6_RESTART/MOM.res.nc' .bitcmp. "@[CNTL]/RESTART"
'MOM6_RESTART/MOM.res_1.nc' .bitcmp. "@[CNTL]/RESTART"
'MOM6_RESTART/MOM.res_2.nc' .bitcmp. "@[CNTL]/RESTART"
'MOM6_RESTART/MOM.res_3.nc' .bitcmp. "@[CNTL]/RESTART"
'mediator_FBaccumAtm_restart.tile1.nc' .bitcmp. "@[CNTL]/RESTART"
'mediator_FBaccumAtm_restart.tile2.nc' .bitcmp. "@[CNTL]/RESTART"
'mediator_FBaccumAtm_restart.tile3.nc' .bitcmp. "@[CNTL]/RESTART"
'mediator_FBaccumAtm_restart.tile4.nc' .bitcmp. "@[CNTL]/RESTART"
'mediator_FBaccumAtm_restart.tile5.nc' .bitcmp. "@[CNTL]/RESTART"
'mediator_FBaccumAtm_restart.tile6.nc' .bitcmp. "@[CNTL]/RESTART"
'mediator_FBaccumOcn_restart.nc' .bitcmp. "@[CNTL]/RESTART"
'mediator_FBaccumIce_restart.nc' .bitcmp. "@[CNTL]/RESTART"
'mediator_FBaccumLnd_restart.nc' .bitcmp. "@[CNTL]/RESTART"
'mediator_FBaccumHyd_restart.nc' .bitcmp. "@[CNTL]/RESTART"
'mediator_FBaccumAtmOcn_restart.nc' .bitcmp. "@[CNTL]/RESTART"
'mediator_FBAtm_a_restart.tile1.nc' .bitcmp. "@[CNTL]/RESTART"
'mediator_FBAtm_a_restart.tile2.nc' .bitcmp. "@[CNTL]/RESTART"
'mediator_FBAtm_a_restart.tile3.nc' .bitcmp. "@[CNTL]/RESTART"
'mediator_FBAtm_a_restart.tile4.nc' .bitcmp. "@[CNTL]/RESTART"
'mediator_FBAtm_a_restart.tile5.nc' .bitcmp. "@[CNTL]/RESTART"
'mediator_FBAtm_a_restart.tile6.nc' .bitcmp. "@[CNTL]/RESTART"
'mediator_FBIce_i_restart.nc' .bitcmp. "@[CNTL]/RESTART"
'mediator_FBOcn_o_restart.nc' .bitcmp. "@[CNTL]/RESTART"
'mediator_FBLnd_l_restart.nc' .bitcmp. "@[CNTL]/RESTART"
'mediator_FBHyd_h_restart.nc' .bitcmp. "@[CNTL]/RESTART"
'mediator_FBAtmOcn_o_restart.nc' .bitcmp. "@[CNTL]/RESTART"
# Executable validation. This makes an MD5 sum of the fv3.exe
# for comparison against the MD5 sum made in the build job.
# This is to ensure the executable did not change during the
# test suite.
"@[build%target]" .md5cmp. "@[fv3_ccpp_mom6_cice_debug.exe%md5sum]"
}
}
########################################################################
# cold c384

test cpld_fv3_ccpp_384_mom6_cice_cold_atm_flux: fv3_ccpp_mom6_cice.exe {
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19 changes: 19 additions & 0 deletions compsets/nemscommon.input
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Original file line number Diff line number Diff line change
Expand Up @@ -38,3 +38,22 @@ embed bash NEMSAppBuilder(NEMS.x,modules.nems,OPTS,md5sum)
cp -fp conf/modules.nems "@[modules.nems]"
md5sum "@[NEMS.x]" > "@[md5sum]"
]]]
embed bash NEMSAppBuilder_debug(NEMS.x,modules.nems,OPTS,md5sum)
[[[
mkdir -p "@[plat%EXECrt]" "@[plat%INCrt]"
rm -f "@[NEMS.x]" "@[modules.nems]"
cd @[plat%HOMEnems]
export S2S_DEBUG_MODULE=true

# NOTE: Replace "rebuild" with "norebuild" to disable "gmake clean"
@[plat%execution_time_modules]
if ( which aprun ) && [[ @[plat%PLATFORM_NAME] == wcoss.cray ]] ; then
aprun -n 1 -j 1 -N 1 -d 24 bash -c "./NEMS/NEMSAppBuilder rebuild $OPTS"
else
./NEMS/NEMSAppBuilder rebuild $OPTS
fi
cd @[plat%SRCnems]
cp -fp ../exe/NEMS.x "@[NEMS.x]"
cp -fp conf/modules.nems "@[modules.nems]"
md5sum "@[NEMS.x]" > "@[md5sum]"
]]]
9 changes: 7 additions & 2 deletions conf/before_components.mk
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,13 @@

# ----------------------------------------------------------------------
# Decide the conf and modulefile names.

CHOSEN_MODULE=$(BUILD_TARGET)/fv3_coupled
# S2S_DEBUG_MODULE is defined in GNUmakefile
ifeq ($(S2S_DEBUG_MODULE),false)
CHOSEN_MODULE=$(BUILD_TARGET)/fv3_coupled
else
CHOSEN_MODULE=$(BUILD_TARGET)/fv3_coupled_debug
endif
$(info CHOSEN_MODULE is $(CHOSEN_MODULE))

CONFIGURE_NEMS_FILE=configure.fv3_coupled.$(BUILD_TARGET)

Expand Down
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