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Merge branch 'develop' into feature/pnorris/update-to-RRTMGP-v1.6
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@sdrabenh
sdrabenh authored May 17, 2023
2 parents ed18fe6 + 125544a commit 31c6bbb
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5 changes: 3 additions & 2 deletions AGCM.rc.tmpl
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Expand Up @@ -128,13 +128,14 @@ OGCM.JM_WORLD: @OGCM_JM
OGCM.LM: @OGCM_LM
@COUPLED OGCM.NX: @OGCM_NX
@COUPLED OGCM.NY: @OGCM_NY
@COUPLED OGCM.GRIDSPEC: MAPL_Tripolar.nc
@MOM5 OGCM.GRIDSPEC: MAPL_Tripolar.nc
@MOM6 OGCM.GRIDSPEC: MAPL_Tripolar.nc
@MIT OGCM.GRIDSPEC: mit.ascii
@DATAOCEAN @LATLON_OGCM OGCM.POLE: 'PE'
@DATAOCEAN @LATLON_OGCM OGCM.DATELINE: 'DE'
@DATAOCEAN @CUBE_OGCM OGCM.NF: @OGCM_NF
OGCM_RUN_DT: @OCEAN_DT
###########################################################

##############################################################################################
#### ####
#### SST REMAPPING ####
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194 changes: 183 additions & 11 deletions gcm_run.j
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Expand Up @@ -318,8 +318,13 @@ setenv EMISSIONS @EMISSIONS
@MOM5setenv OBCSDIR @COUPLEDIR/ocean_bcs/MOM5/${OGCM_IM}x${OGCM_JM}
@MOM6setenv ABCSDIR @COUPLEDIR/atmosphere_bcs/@LSMBCS/MOM6/@ATMOStag_@OCEANtag
@MOM6setenv OBCSDIR @COUPLEDIR/ocean_bcs/MOM6/${OGCM_IM}x${OGCM_JM}
@COUPLEDsetenv SSTDIR @COUPLEDIR/SST/MERRA2/${OGCM_IM}x${OGCM_JM}
@COUPLEDsetenv BCTAG `basename $ABCSDIR`
@MOM5setenv SSTDIR @COUPLEDIR/SST/MERRA2/${OGCM_IM}x${OGCM_JM}
@MOM6setenv SSTDIR @COUPLEDIR/SST/MERRA2/${OGCM_IM}x${OGCM_JM}
@MOM5setenv BCTAG `basename $ABCSDIR`
@MOM6setenv BCTAG `basename $ABCSDIR`
#this is hard-wired for NAS for now - should make it more general
@MITsetenv GRIDDIR /nobackupp18/afahad/GEOSMITgcmFiles/GRIDDIR/a${AGCM_IM}x${AGCM_JM}_o${OGCM_IM}x${OGCM_JM}
@MITsetenv BCTAG `basename $GRIDDIR`
@DATAOCEANsetenv BCTAG `basename $BCSDIR`

set FILE = linkbcs
Expand All @@ -331,13 +336,24 @@ cat << _EOF_ > $FILE
/bin/mkdir -p ExtData
/bin/ln -sf $CHMDIR/* ExtData
@COUPLED/bin/ln -sf $OBCSDIR/SEAWIFS_KPAR_mon_clim.${OGCM_IM}x${OGCM_JM} SEAWIFS_KPAR_mon_clim.data
@COUPLED/bin/ln -sf $ABCSDIR/@[email protected] tile.data
@COUPLED/bin/ln -sf $ABCSDIR/@[email protected] runoff.bin
@COUPLED/bin/ln -sf $OBCSDIR/MAPL_Tripolar.nc .
@COUPLED/bin/ln -sf $OBCSDIR/vgrid${OGCM_LM}.ascii ./vgrid.ascii
@MOM5#/bin/ln -s @COUPLEDIR/a@HIST_IMx@HIST_JM_o${OGCM_IM}x${OGCM_JM}/DC0@HIST_IMxPC0@[email protected] tile_hist.data
@MOM6#/bin/ln -s @COUPLEDIR/MOM6/DC0@HIST_IMxPC0@HIST_JM_@OCEANtag/DC0@HIST_IMxPC0@[email protected] tile_hist.data
@MOM5/bin/ln -sf $OBCSDIR/SEAWIFS_KPAR_mon_clim.${OGCM_IM}x${OGCM_JM} SEAWIFS_KPAR_mon_clim.data
@MOM6/bin/ln -sf $OBCSDIR/SEAWIFS_KPAR_mon_clim.${OGCM_IM}x${OGCM_JM} SEAWIFS_KPAR_mon_clim.data
@MIT/bin/ln -sf /nobackupp18/afahad/GEOSMITgcmFiles/SEAWIFS_KPAR_mon_clim.data SEAWIFS_KPAR_mon_clim.data
@MOM5/bin/ln -sf $ABCSDIR/@[email protected] tile.data
@MOM6/bin/ln -sf $ABCSDIR/@[email protected] tile.data
## Should include this >>>MOM5<<</bin/ln -s @COUPLEDIR/a@HIST_IMx@HIST_JM_o${OGCM_IM}x${OGCM_JM}/DC0@HIST_IMxPC0@[email protected] tile_hist.data
## Should include this >>>MOM6<<</bin/ln -s @COUPLEDIR/MOM6/DC0@HIST_IMxPC0@HIST_JM_@OCEANtag/DC0@HIST_IMxPC0@[email protected] tile_hist.data
@MIT/bin/ln -sf /nobackupp18/afahad/GEOSMITgcmFiles/CF0090x6C_LL5400xLL0015-Pfafstetter.til tile.data
@MOM5/bin/ln -sf $ABCSDIR/@[email protected] runoff.bin
@MOM6/bin/ln -sf $ABCSDIR/@[email protected] runoff.bin
@MIT/bin/ln -sf /nobackupp18/afahad/GEOSMITgcmFiles/CF0090x6C_LL5400xLL0015-Pfafstetter.TRN runoff.bin
@MOM5/bin/ln -sf $OBCSDIR/MAPL_Tripolar.nc .
@MOM6/bin/ln -sf $OBCSDIR/MAPL_Tripolar.nc .
@MIT/bin/ln -sf $GRIDDIR/mit.ascii
@MOM5/bin/ln -sf $OBCSDIR/vgrid${OGCM_LM}.ascii ./vgrid.ascii
@MOM6/bin/ln -sf $OBCSDIR/vgrid${OGCM_LM}.ascii ./vgrid.ascii
@MIT/bin/ln -sf $GRIDDIR/vgrid${OGCM_LM}.ascii ./vgrid.ascii
@MIT/bin/ln -sf /nobackupp18/afahad/GEOSMITgcmFiles/DC0360xPC0181_LL5400x15-LL.bin DC0360xPC0181_LL5400x15-LL.bin
# Precip correction
#/bin/ln -s /discover/nobackup/projects/gmao/share/gmao_ops/fvInput/merra_land/precip_CPCUexcludeAfrica-CMAP_corrected_MERRA/GEOSdas-2_1_4 ExtData/PCP
Expand Down Expand Up @@ -797,7 +813,9 @@ setenv YEAR $yearc

if (! -e tile.bin) then
$GEOSBIN/binarytile.x tile.data tile.bin
@MOM5 $GEOSBIN/binarytile.x tile_hist.data tile_hist.bin
### @MIT $GEOSBIN/binarytile.x tile_hist.data tile_hist.bin
### @MOM5 $GEOSBIN/binarytile.x tile_hist.data tile_hist.bin
### @MOM6 $GEOSBIN/binarytile.x tile_hist.data tile_hist.bin
endif

# If running in dual ocean mode, link sst and fraci data here
Expand All @@ -819,7 +837,7 @@ else

# If saltwater_internal_rst is in EXPDIR move to SCRDIR
# -----------------------------------------------------
if ( -e $EXPDIR/saltwater_internal_rst ) /bin/mv $EXPDIR/saltwater_internal_rst $SCRDIR
if ( -e $EXPDIR/saltwater_internal_rst ) /bin/cp $EXPDIR/saltwater_internal_rst $SCRDIR

# The splitter script requires an OutData directory
# -------------------------------------------------
Expand Down Expand Up @@ -939,6 +957,78 @@ endif

# Establish safe default number of OpenMP threads
# -----------------------------------------------
@MIT # ---------------------------------------------------
@MIT # For MITgcm restarts - before running GEOSgcm.x
@MIT # ---------------------------------------------------
@MIT
@MIT # set time interval for segment in seconds
@MIT
@MIT set yearc = `echo $nymdc | cut -c1-4`
@MIT set monthc = `echo $nymdc | cut -c5-6`
@MIT set dayc = `echo $nymdc | cut -c7-8`
@MIT set hourc = `echo $nhmsc | cut -c1-2`
@MIT set minutec = `echo $nhmsc | cut -c3-4`
@MIT set secondc = `echo $nhmsc | cut -c5-6`
@MIT
@MIT set yearf = `echo $nymdf | cut -c1-4`
@MIT set monthf = `echo $nymdf | cut -c5-6`
@MIT set dayf = `echo $nymdf | cut -c7-8`
@MIT set hourf = `echo $nhmsf | cut -c1-2`
@MIT set minutef = `echo $nhmsf | cut -c3-4`
@MIT set secondf = `echo $nhmsf | cut -c5-6`
@MIT
@MIT set yearf = `echo $nymdf | cut -c1-4`
@MIT
@MIT set time1 = `date -u -d "${yearc}-${monthc}-${dayc}T${hourc}:${minutec}:${secondc}" "+%s"`
@MIT set time2 = `date -u -d "${yearf}-${monthf}-${dayf}T${hourf}:${minutef}:${secondf}" "+%s"`
@MIT
@MIT @ mitdt = $time2 - $time1
@MIT echo "Segment time: $mitdt"
@MIT
@MIT
@MIT # Set-up MITgcm run directory
@MIT if (! -e mitocean_run) mkdir -p mitocean_run
@MIT cd mitocean_run
@MIT
@MIT # link mit configuration and initialization files
@MIT ln -sf $EXPDIR/mit_input/* .
@MIT # link mitgcm restarts if exist
@MIT /bin/ln -sf $EXPDIR/restarts/pic* .
@MIT # make an archive folder for mitgcm run
@MIT mkdir $EXPDIR/mit_output
@MIT
@MIT # Calculate segment time steps
@MIT set mit_nTimeSteps = `cat ${SCRDIR}/AGCM.rc | grep OGCM_RUN_DT: | cut -d: -f2 | tr -s " " | cut -d" " -f2`
@MIT @ mit_nTimeSteps = ${mitdt} / $mit_nTimeSteps
@MIT
@MIT #change namelist variables in data - nTimeSteps, chkptFreq and monitorFreq
@MIT sed -i "s/nTimeSteps.*/nTimeSteps = ${mit_nTimeSteps},/" data
@MIT sed -i "s/chkptFreq.*/chkptFreq = ${mitdt}.0,/" data
@MIT sed -i "s/pChkptFreq.*/pChkptFreq = ${mitdt}.0,/" data
@MIT # get nIter0
@MIT
@MIT if (! -e ${EXPDIR}/restarts/MITgcm_restart_dates.txt ) then
@MIT set nIter0 = `grep nIter0 data | tr -s " " | cut -d"=" -f2 | cut -d"," -f1 | awk '{$1=$1;print}'`
@MIT else
@MIT set nIter0 = `grep "$nymdc $nhmsc" ${EXPDIR}/restarts/MITgcm_restart_dates.txt | cut -d" " -f5`
@MIT if ( $nIter0 == "" ) then
@MIT echo "No ocean restart file for $nymdc $nhmsc, exiting"
@MIT echo "If this is a new initialized experiment, delete:"
@MIT echo "${EXPDIR}/restarts/MITgcm_restart_dates.txt"
@MIT echo "and restart"
@MIT exit
@MIT else
@MIT sed -i "s/nIter0.*/ nIter0 = ${nIter0},/" data
@MIT endif
@MIT endif
@MIT
@MIT cd ..
@MIT # ---------------------------------------------------
@MIT # End MITgcm restarts - before running GEOSgcm.x
@MIT # ---------------------------------------------------

# Set OMP_NUM_THREADS
# -------------------
setenv OMP_NUM_THREADS 1

# Run GEOSgcm.x
Expand All @@ -965,6 +1055,88 @@ else
endif
echo GEOSgcm Run Status: $rc

@MIT # ---------------------------------------------------
@MIT # For MITgcm restarts - after running GEOSgcm.x
@MIT # ---------------------------------------------------
@MIT
@MIT set STEADY_STATE_OCEAN=`grep STEADY_STATE_OCEAN AGCM.rc | cut -d':' -f2 | tr -d " "`
@MIT
@MIT # update ocean only if activated. Otherwize use the same pickups (passive ocean).
@MIT if ( ${STEADY_STATE_OCEAN} != 0 ) then
@MIT
@MIT if ( ${rc} == 0 ) then
@MIT
@MIT # Update nIter0 for next segment
@MIT set znIter00 = `echo $nIter0 | awk '{printf("%010d",$1)}'`
@MIT @ nIter0 = $nIter0 + $mit_nTimeSteps
@MIT set znIter0 = `echo $nIter0 | awk '{printf("%010d",$1)}'`
@MIT
@MIT # to update MITgcm restart list file
@MIT sed -i "/${nIter0}/d" ${EXPDIR}/restarts/MITgcm_restart_dates.txt
@MIT echo "Date_GEOS5 $nymdf $nhmsf NITER0_MITgcm ${nIter0}" >> ${EXPDIR}/restarts/MITgcm_restart_dates.txt
@MIT
@MIT /bin/mv $SCRDIR/mitocean_run/STDOUT.0000 $EXPDIR/mit_output/STDOUT.${znIter00}
@MIT
@MIT endif
@MIT
@MIT cd $SCRDIR/mitocean_run
@MIT
@MIT # Check existance of roling pickups
@MIT set nonomatch rp = ( pickup*ckptA* )
@MIT echo $rp
@MIT # Rename and move them if exist
@MIT if ( -e $rp[1] ) then
@MIT set timeStepNumber=`cat pickup.ckptA.meta | grep timeStepNumber | tr -s " " | cut -d" " -f5 | awk '{printf("%010d",$1)}'`
@MIT foreach fname ( pickup*ckptA* )
@MIT set bname = `echo ${fname} | cut -d "." -f1 | cut -d "/" -f2`
@MIT set aname = `echo ${fname} | cut -d "." -f3`
@MIT echo $EXPDIR/restarts/${bname}.${timeStepNumber}.${aname}
@MIT /bin/mv ${fname} $EXPDIR/restarts/${bname}.${timeStepNumber}.${aname}
@MIT end
@MIT endif
@MIT
@MIT # Check existance of permanent pickups
@MIT set nonomatch pp = ( pickup* )
@MIT echo $pp
@MIT # Move them if exist
@MIT if ( -e $pp[1] ) then
@MIT foreach fname ( pickup* )
@MIT if ( ! -e $EXPDIR/restarts/${fname} ) /bin/mv ${fname} $EXPDIR/restarts/${fname}
@MIT end
@MIT endif
@MIT
@MIT /bin/mv T.* $EXPDIR/mit_output/
@MIT /bin/mv S.* $EXPDIR/mit_output/
@MIT /bin/mv U.* $EXPDIR/mit_output/
@MIT /bin/mv V.* $EXPDIR/mit_output/
@MIT /bin/mv W.* $EXPDIR/mit_output/
@MIT /bin/mv PH* $EXPDIR/mit_output/
@MIT /bin/mv Eta.* $EXPDIR/mit_output/
@MIT
@MIT /bin/mv AREA.* $EXPDIR/mit_output/
@MIT /bin/mv HEFF.* $EXPDIR/mit_output/
@MIT /bin/mv HSNOW.* $EXPDIR/mit_output/
@MIT /bin/mv UICE.* $EXPDIR/mit_output/
@MIT /bin/mv VICE.* $EXPDIR/mit_output/
@MIT
@MIT #copy mit output to mit_output
@MIT foreach i (`grep -i filename data.diagnostics | grep "^ " | cut -d"=" -f2 | cut -d"'" -f2 | awk '{$1=$1;print}'`)
@MIT /bin/mv ${i}* $EXPDIR/mit_output/
@MIT end
@MIT
@MIT foreach i (`grep -i stat_fName data.diagnostics | grep "^ " | cut -d"=" -f2 | cut -d"'" -f2 | awk '{$1=$1;print}'`)
@MIT /bin/mv ${i}* $EXPDIR/mit_output/
@MIT end
@MIT
@MIT cd $SCRDIR
@MIT
@MIT endif
@MIT
@MIT # ---------------------------------------------------
@MIT # End MITgcm restarts - after running GEOSgcm.x
@MIT # ---------------------------------------------------


#######################################################################
# Rename Final Checkpoints => Restarts for Next Segment and Archive
# Note: cap_restart contains the current NYMD and NHMS
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