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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -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 | ||
|
|
@@ -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 | ||
|
|
@@ -382,16 +398,7 @@ cat << _EOF_ > $FILE | |
| @COUPLED/bin/ln -sf $ABCSDIR/ndvi_clim_@RES_DATELINE.data ndvi.data | ||
| >>>GCMRUN_CATCHCN<<<if ( -f $BCSDIR/$BCRSLV/lnfm_clim_@RES_DATELINE.data ) /bin/ln -sf $BCSDIR/$BCRSLV/lnfm_clim_@RES_DATELINE.data lnfm.data | ||
| >>>GCMRUN_CATCHCN<<<if (-f $BCSDIR/$BCRSLV/MODISVISmean_${AGCM_IM}x${AGCM_JM}.dat ) /bin/ln -s MODISVISmean.dat | ||
| >>>GCMRUN_CATCHCN<<<if (-f $BCSDIR/$BCRSLV/MODISVISstd_${AGCM_IM}x${AGCM_JM}.dat ) /bin/ln -s MODISVISstd.dat | ||
| >>>GCMRUN_CATCHCN<<<if (-f $BCSDIR/$BCRSLV/MODISNIRmean_${AGCM_IM}x${AGCM_JM}.dat ) /bin/ln -s MODISNIRmean.dat | ||
| >>>GCMRUN_CATCHCN<<<if (-f $BCSDIR/$BCRSLV/MODISNIRstd_${AGCM_IM}x${AGCM_JM}.dat ) /bin/ln -s MODISNIRstd.dat | ||
| >>>GCMRUN_CATCHCN<<<if (-f $BCSDIR/$BCRSLV/MODELFPARmean_${AGCM_IM}x${AGCM_JM}.dat) /bin/ln -s MODELFPARmean.dat | ||
| >>>GCMRUN_CATCHCN<<<if (-f $BCSDIR/$BCRSLV/MODELFPARstd_${AGCM_IM}x${AGCM_JM}.dat ) /bin/ln -s MODELFPARstd.dat | ||
| >>>GCMRUN_CATCHCN<<<if (-f $BCSDIR/$BCRSLV/MODISFPARmean_${AGCM_IM}x${AGCM_JM}.dat) /bin/ln -s MODISFPARmean.dat | ||
| >>>GCMRUN_CATCHCN<<<if (-f $BCSDIR/$BCRSLV/MODISFPARstd_${AGCM_IM}x${AGCM_JM}.dat ) /bin/ln -s MODISFPARstd.dat | ||
| >>>GCMRUN_CATCHCN<<</bin/ln -s /discover/nobackup/projects/gmao/ssd/land/l_data/LandBCs_files_for_mkCatchParam/V001/CO2_MonthlyMean_DiurnalCycle.nc4 | ||
| >>>GCMRUN_CATCHCN<<</bin/ln -s /discover/nobackup/projects/gmao/ssd/land/l_data/LandBCs_files_for_mkCatchParam/V001/FPAR_CDF_Params-M09.nc4 | ||
| >>>GCMRUN_CATCHCN<<</bin/ln -s /discover/nobackup/projects/gmao/bcs_shared/make_bcs_inputs/land/CO2/v1/CO2_MonthlyMean_DiurnalCycle.nc4 | ||
| @DATAOCEAN/bin/ln -sf $BCSDIR/$BCRSLV/topo_DYN_ave_@RES_DATELINE.data topo_dynave.data | ||
| @DATAOCEAN/bin/ln -sf $BCSDIR/$BCRSLV/topo_GWD_var_@RES_DATELINE.data topo_gwdvar.data | ||
|
|
@@ -797,7 +804,9 @@ 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 | ||
|
|
@@ -819,7 +828,7 @@ else | |
|
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||
| # 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 | ||
| # ------------------------------------------------- | ||
|
|
@@ -939,6 +948,78 @@ 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 # --------------------------------------------------- | ||
|
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||
| # Set OMP_NUM_THREADS | ||
| # ------------------- | ||
| setenv OMP_NUM_THREADS 1 | ||
|
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||
| # Run GEOSgcm.x | ||
|
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@@ -965,6 +1046,88 @@ else | |
| endif | ||
| echo GEOSgcm Run Status: $rc | ||
|
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||
| @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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