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Merge pull request #48 from GEOS-ESM/feature/mmanyin/setup_and_run
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Updates to the setup script and the run script
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@mmanyin
mmanyin authored Jan 12, 2023
2 parents b8fab44 + 92aea98 commit 113abb9
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Showing 2 changed files with 68 additions and 72 deletions.
12 changes: 6 additions & 6 deletions src/Applications/GEOSctm_App/ctm_run.j
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Original file line number Diff line number Diff line change
Expand Up @@ -581,23 +581,23 @@ if( ${DRIVING_DATASETS} == MERRA2) then
set oldstring = `cat CAP.rc | grep EXTDATA_CF:`
set COMPNAME = `grep COMPNAME CAP.rc | awk '{print $2}'`

if( $startYear > 1979 && $startYear < 1992 ) then
if( $startYear >= 1980 && $startYear < 1992 ) then
set sYear = 1980
set sMonth = jan79
set MERRA2type = MERRA2_100
set data_Transition_Date = 19920101
else if( $startYear > 1991 && $startYear < 2000 ) then
else if( $startYear >= 1992 && $startYear < 2000 ) then
set sYear = 1992
set sMonth = jan91
set MERRA2type = MERRA2_200
set data_Transition_Date = 20000101
else if( $startYear > 1999 && $startYear < 2010 ) then
else if( $startYear >= 2000 && $startYear < 2011 ) then
set sYear = 2000
set sMonth = jan00
set MERRA2type = MERRA2_300
set data_Transition_Date = 20100101
else if( $startYear > 2009 ) then
set sYear = 2010
set data_Transition_Date = 20110101
else if( $startYear >= 2011 ) then
set sYear = 2011
set sMonth = jan10
set MERRA2type = MERRA2_400
set data_Transition_Date = 20500101
Expand Down
128 changes: 62 additions & 66 deletions src/Applications/GEOSctm_App/ctm_setup
View file
Original file line number Diff line number Diff line change
Expand Up @@ -236,13 +236,13 @@ echo "Enter the ${C1}Atmospheric Horizontal Resolution${CN} code:"
echo "--------------------------------------"
echo " Cubed-Sphere"
echo "--------------------------------------"
echo " ${C2}c12 -- 8 deg ${CN}"
echo " ${C2}c24 -- 4 deg ${CN}"
echo " ${C2}c48 -- 2 deg ${CN}"
echo " ${C2}c90 -- 1 deg ${CN}"
echo " ${C2}c180 -- 1/2 deg (${C1}56-km${C2}) ${CN}"
echo " ${C2}c360 -- 1/4 deg (${C1}28-km${C2}) ${CN} "
echo " ${C2}c720 -- 1/8 deg (${C1}14-km${C2}) ${CN}"
echo " ${C2}c12 -- 8 deg ${CN}"
echo " ${C2}c24 -- 4 deg ${CN}"
echo " ${C2}c48 -- 2 deg ${CN}"
echo " ${C2}c90 -- 1 deg ${CN}"
echo " ${C2}c180 -- 1/2 deg (${C1}56-km${C2}) ${CN}"
echo " ${C2}c360 -- 1/4 deg (${C1}28-km${C2}) ${CN} "
echo " ${C2}c720 -- 1/8 deg (${C1}14-km${C2}) ${CN}"
echo " ${C2}c1440 - 1/16 deg (${C1} 7-km${C2}) ${CN}"
echo " ${C2} DYAMOND Grids "
echo " ${C2}c768 -- 1/8 deg (${C1}12-km${C2}) ${CN}"
Expand Down Expand Up @@ -294,10 +294,10 @@ echo "Use ${C1}Hydrostatic Atmosphere${CN}? (Default: ${C2}${DEFAULT_HYDROSTATIC
set USE_HYDROSTATIC = $<

if( .$USE_HYDROSTATIC == . ) then
set USE_HYDROSTATIC = $DEFAULT_HYDROSTATIC
set USE_HYDROSTATIC = $DEFAULT_HYDROSTATIC
else
set USE_HYDROSTATIC = `echo $USE_HYDROSTATIC | tr "[:lower:]" "[:upper:]"`
if( $USE_HYDROSTATIC == "Y" | \
set USE_HYDROSTATIC = `echo $USE_HYDROSTATIC | tr "[:lower:]" "[:upper:]"`
if( $USE_HYDROSTATIC == "Y" | \
$USE_HYDROSTATIC == "YES" | \
$USE_HYDROSTATIC == "T" | \
$USE_HYDROSTATIC == "TRUE" ) set USE_HYDROSTATIC = TRUE
Expand Down Expand Up @@ -416,13 +416,13 @@ else if ( $SITE == 'NAS' ) then

echo "Enter the ${C1}Processor Type${CN} you wish to run on:"
if( "$BUILT_ON_ROME" != "TRUE" ) then
echo " ${C2}has (Haswell)${CN}"
echo " ${C2}bro (Broadwell)${CN}"
echo " ${C2}sky (Skylake)${CN} (default)"
echo " ${C2}cas (Cascade Lake)${CN}"
echo " "
echo " NOTE: Due to how FV3 is compiled by default, Sandy Bridge"
echo " and Ivy Bridge are not supported by current GEOS"
echo " ${C2}has (Haswell)${CN}"
echo " ${C2}bro (Broadwell)${CN}"
echo " ${C2}sky (Skylake)${CN} (default)"
echo " ${C2}cas (Cascade Lake)${CN}"
echo " "
echo " NOTE: Due to how FV3 is compiled by default, Sandy Bridge"
echo " and Ivy Bridge are not supported by current GEOS"
else
echo " ${C2}rom (AMD Rome)${CN} (default)"
endif
Expand All @@ -431,16 +431,16 @@ else if ( $SITE == 'NAS' ) then
set MODEL = `echo $MODEL | tr "[:upper:]" "[:lower:]"`
if ( .$MODEL == .) then
if( "$BUILT_ON_ROME" != "TRUE" ) then
set MODEL = 'sky'
set MODEL = 'sky'
else
set MODEL = 'rom'
endif
endif

if( "$BUILT_ON_ROME" != "TRUE" ) then
if( $MODEL != 'has' & \
$MODEL != 'bro' & \
$MODEL != 'sky' & \
if( $MODEL != 'has' & \
$MODEL != 'bro' & \
$MODEL != 'sky' & \
$MODEL != 'cas' ) goto ASKPROC
else
if( $MODEL != 'rom' ) goto ASKPROC
Expand Down Expand Up @@ -487,6 +487,10 @@ endif

# The CTM for now seems to only use Reynolds
set OCEAN_TAG = Reynolds
# To simplify comparison w/ ctm_setup:
set OGCM = FALSE
set OGCM_NX = 0
set OGCM_NY = 0

# Set DEFAULT SHMEM Parameter
# ---------------------------
Expand Down Expand Up @@ -578,12 +582,18 @@ if( $GEOSCTM_IM == "c90" ) then
set DT = 450
set SOLAR_DT = 3600
set IRRAD_DT = 3600
set OCEAN_DT = $IRRAD_DT
set CHEM_DT = $DT
set GEOSCTM_IM = 90
set GEOSCTM_JM = `expr $GEOSCTM_IM \* 6`
set NX = 4
set NY = `expr $NX \* 6`
if( $OGCM == TRUE ) then
set NX = $OGCM_NY
set NY = $OGCM_NX
set OCEAN_DT = $DT
else
set NX = 4
set NY = `expr $NX \* 6`
set OCEAN_DT = $IRRAD_DT
endif
set CHEM_DT = $DT
set HYDROSTATIC = $USE_HYDROSTATIC
set HIST_IM = `expr $GEOSCTM_IM \* 4`
set HIST_JM = `expr $GEOSCTM_IM \* 2 + 1`
Expand All @@ -597,12 +607,18 @@ if( $GEOSCTM_IM == "c180" ) then
set DT = 450
set SOLAR_DT = 3600
set IRRAD_DT = 3600
set OCEAN_DT = $IRRAD_DT
set CHEM_DT = $DT
set GEOSCTM_IM = 180
set GEOSCTM_JM = `expr $GEOSCTM_IM \* 6`
set NX = 6
set NY = `expr $NX \* 6`
if( $OGCM == TRUE ) then
set NX = $OGCM_NY
set NY = $OGCM_NX
set OCEAN_DT = $DT
else
set NX = 6
set NY = `expr $NX \* 6`
set OCEAN_DT = $IRRAD_DT
endif
set HYDROSTATIC = $USE_HYDROSTATIC
set HIST_IM = `expr $GEOSCTM_IM \* 4`
set HIST_JM = `expr $GEOSCTM_IM \* 2 + 1`
Expand Down Expand Up @@ -795,9 +811,9 @@ set JOB_SGMT = "$JOB_SGMT 000000"
set FV_NWAT = ""
set FV_ZTRACER = "z_tracer = .T."
if ( "$USE_HYDROSTATIC" == "TRUE" ) then
set FV_MAKENH = "Make_NH = .F."
set FV_HYDRO = "hydrostatic = .T."
set FV_SATADJ = "do_sat_adj = .F."
set FV_MAKENH = "Make_NH = .F."
set FV_HYDRO = "hydrostatic = .T."
set FV_SATADJ = "do_sat_adj = .F."
else
# Logic for NH runs based on build type
if ( "$DEFAULT_HYDROSTATIC" == "TRUE") then
Expand Down Expand Up @@ -1122,7 +1138,7 @@ endif

if( $SITE == 'NAS' ) then
setenv BATCH_CMD "qsub" # PBS Batch command
setenv BATCH_GROUP "PBS -W group_list=" # PBS Syntax for GROUP
setenv BATCH_GROUP "PBS -W group_list=" # PBS Syntax for GROUP
setenv BATCH_TIME "PBS -l walltime=" # PBS Syntax for walltime
setenv BATCH_JOBNAME "PBS -N " # PBS Syntax for job name
setenv BATCH_OUTPUTNAME "PBS -o " # PBS Syntax for job output name
Expand All @@ -1134,10 +1150,10 @@ if( $SITE == 'NAS' ) then
setenv ARCHIVE_T "8:00:00" # Wallclock Time for ctm_archive.j
if( $GPU == "TRUE" ) then
set NCPUS_PER_NODE = 16 # CPUS per node
set MODEL = "san_gpu" # Model of CPU
set QTYPE = "gpu_k40" # Queue to use
set MODEL = "san_gpu" # Model of CPU
set QTYPE = "gpu_k40" # Queue to use
else
set QTYPE = "normal" # Queue to use
set QTYPE = "normal" # Queue to use
endif

#@ NODES = `echo "($MODEL_NPES + $NCPUS_PER_NODE - 1)/$NCPUS_PER_NODE" | bc`
Expand All @@ -1158,9 +1174,6 @@ if( $SITE == 'NAS' ) then
setenv MOVE_P "PBS -l select=1:ncpus=1" # PE Configuration for ctm_moveplot.j

setenv BCSDIR /nobackup/gmao_SIteam/ModelData/bcs/${LSM_BCS}/${LSM_BCS}_${OCEAN_TAG} # location of Boundary Conditions
setenv REPLAY_ANA_EXPID ONLY_MERRA2_SUPPORTED # Default Analysis Experiment for REPLAY
setenv REPLAY_ANA_LOCATION ONLY_MERRA2_SUPPORTED # Default Analysis Location for REPLAY
setenv M2_REPLAY_ANA_LOCATION /nobackup/gmao_SIteam/ModelData/verification/MERRA-2 # Default Analysis Location for M2 REPLAY

setenv CHMDIR /nobackup/gmao_SIteam/ModelData/fvInput_nc3 # locations of Aerosol Chemistry BCs
setenv WRKDIR /nobackup/$LOGNAME # user work directory
Expand Down Expand Up @@ -1202,9 +1215,6 @@ else if( $SITE == 'NCCS' ) then
setenv MOVE_P "SBATCH --ntasks=1" # PE Configuration for ctm_moveplot.j

setenv BCSDIR /discover/nobackup/ltakacs/bcs/${LSM_BCS}/${LSM_BCS}_${OCEAN_TAG} # location of Boundary Conditions
setenv REPLAY_ANA_EXPID x0039 # Default Analysis Experiment for REPLAY
setenv REPLAY_ANA_LOCATION /discover/nobackup/projects/gmao/g6dev/ltakacs/x0039 # Default Analysis Location for REPLAY
setenv M2_REPLAY_ANA_LOCATION /discover/nobackup/projects/gmao/share/gmao_ops/verification/MERRA-2 # Default Analysis Location for M2 REPLAY

setenv CHMDIR $SHARE/dao_ops/fvInput_nc3 # locations of Aerosol Chemistry BCs
setenv WRKDIR /discover/nobackup/$LOGNAME # user work directory
Expand Down Expand Up @@ -1237,9 +1247,6 @@ else if( $SITE == 'AWS' ) then
setenv MOVE_P "SBATCH --ntasks=1" # PE Configuration for ctm_moveplot.j

setenv BCSDIR /ford1/share/gmao_SIteam/ModelData/bcs/${LSM_BCS}/${LSM_BCS}_${OCEAN_TAG} # location of Boundary Conditions
setenv REPLAY_ANA_EXPID REPLAY_UNSUPPORTED # Default Analysis Experiment for REPLAY
setenv REPLAY_ANA_LOCATION REPLAY_UNSUPPORTED # Default Analysis Location for REPLAY
setenv M2_REPLAY_ANA_LOCATION REPLAY_UNSUPPORTED # Default Analysis Location for M2 REPLAY

setenv CHMDIR /ford1/share/gmao_SIteam/ModelData/fvInput_nc3 # locations of Aerosol Chemistry BCs
setenv WRKDIR /home/$LOGNAME # user work directory
Expand Down Expand Up @@ -1278,15 +1285,12 @@ else
setenv MOVE_P NULL # PE Configuration for ctm_moveplot.j

setenv BCSDIR /ford1/share/gmao_SIteam/ModelData/bcs/${LSM_BCS}/${LSM_BCS}_${OCEAN_TAG} # location of Boundary Conditions
setenv REPLAY_ANA_EXPID REPLAY_UNSUPPORTED # Default Analysis Experiment for REPLAY
setenv REPLAY_ANA_LOCATION REPLAY_UNSUPPORTED # Default Analysis Location for REPLAY
setenv M2_REPLAY_ANA_LOCATION REPLAY_UNSUPPORTED # Default Analysis Location for M2 REPLAY

setenv CHMDIR /ford1/share/gmao_SIteam/ModelData/fvInput_nc3 # locations of Aerosol Chemistry BCs
setenv WRKDIR /home/$LOGNAME # user work directory
setenv COUPLEDIR /ford1/share/gmao_SIteam/ModelData/Forcings # Coupled Ocean/Atmos Forcing
set NX = 1
set NY = 6
set NX = 1
set NY = 6
set CNV_NX = ${NX}
set CNV_NY = ${NY}
setenv CPEXEC /bin/cp # Copy utility for large copies
Expand Down Expand Up @@ -1356,10 +1360,10 @@ while( $check == FALSE )
echo $HISTORYrc > $HOME/.HISTORYrc
/bin/cp -f $HISTORYrc/HISTORY.GEOSCTM.rc.tmpl $TMPHIST
else
echo "This condition is based on updating HISTORY.GEOSCTM.rc.tmpl with CVS"
echo "This has no equivalent in git at present. Please contact Matt"
echo "Thompson or Larry Takacs to help resolve this."
exit 2
echo "This condition is based on updating HISTORY.GEOSCTM.rc.tmpl with CVS"
echo "This has no equivalent in git at present. Please contact Matt"
echo "Thompson or Larry Takacs to help resolve this."
exit 2
endif
endif
end
Expand Down Expand Up @@ -1497,7 +1501,7 @@ setenv CNVDIR $EXPDIR/convert
set GEOSDIR = $NUGEOSDIR
endif

set check = FALSE
set check = FALSE

GEOSDIR:
while( $check == FALSE )
Expand Down Expand Up @@ -1568,12 +1572,12 @@ echo $GROUP > $HOME/.GROUProot
# Copy Model Executable and RC Files to Experiment Directory
#######################################################################

mkdir -p $EXPDIR/RC
rsync -ax $GEOSDIR/etc/*.rc $EXPDIR/RC
mkdir -p $EXPDIR/RC
rsync -ax $GEOSDIR/etc/*.rc $EXPDIR/RC
if( .$EMISSIONS != . ) then
/bin/cp $GEOSDIR/etc/$EMISSIONS/*.rc $EXPDIR/RC
/bin/cp $GEOSDIR/etc/$EMISSIONS/*.rc $EXPDIR/RC
else
set EMISSIONS = g5chem
set EMISSIONS = g5chem
endif

if ( $LINKX == "TRUE" ) then
Expand Down Expand Up @@ -1871,13 +1875,6 @@ s?>>>EMIP_OLDLAND<<<?$EMIP_OLDLAND?g
s?>>>EMIP_NEWLAND<<<?$EMIP_NEWLAND?g
s?@LSM_PARMS?$LSM_PARMS?g
s?>>>4DIAUDAS<<<?#DELETE?g
s?>>>REGULAR_REPLAY<<<?#?g
s?>>>REGULAR_REPLAY_GMAO<<<?#?g
s?>>>REGULAR_REPLAY_NCEP<<<?#DELETE?g
s?>>>REGULAR_REPLAY_ECMWF<<<?#DELETE?g
s?ana4replay.eta.%y4%m2%d2_%h2z.nc4?/discover/nobackup/projects/gmao/share/gmao_ops/verification/MERRA2_MEANS/ana/Y%y4/M%m2/MERRA-2.ana.eta.%y4%m2%d2_%h2z.nc4?g
s?@OX_RELAXTIME?259200.?g
s?@PCHEM_CLIM_YEARS?228?g
Expand Down Expand Up @@ -1995,7 +1992,6 @@ foreach FILE ($FILES)
exit 2
endif


sed -f $HOMDIR/sedfile $HOMDIR/tmpfile > $HOMDIR/$FILE

echo "Creating ${C1}${FILE}${CN} for Experiment: $EXPID "
Expand Down

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