cmor mpiesm mpism - update to runpp regarding time axis

cmor/mpiesm/scripts/ncatted.sh

@@ -14,6 +14,7 @@ SOURCE="MPI-ESM1.2-CR (2017): \naerosol: none, prescribed Kinne (2010)\natmos: E
 CONVENTIONS="CF-1.7 PalMod-2.0"
 CREATION_DATE="2022-02-22T22:00:00Z"
 HISTORY="2022-02-22T22:00:00Z ; CMOR rewrote data to be consistent with PalMod2, CF-1.7 PalMod-2.0 and CF standards."
+PARENTEXPID="no parent"
 declare -A TABLE_INFO
 # 00.00.02
 TABLE_INFO[Amon]="Creation Date:(14 February 2022) MD5:26bac4b397da7babac4e36561826e6b0"
@@ -23,6 +24,18 @@ TABLE_INFO[dec]="Creation Date:(14 February 2022) MD5:26bac4b397da7babac4e365618
 TABLE_INFO[fx]="Creation Date:(14 February 2022) MD5:26bac4b397da7babac4e36561826e6b0"
 TABLE_INFO[Ofx]="Creation Date:(14 February 2022) MD5:26bac4b397da7babac4e36561826e6b0"
 # 00.00.03
+TABLE_INFO[Amon]="Creation Date:(14 February 2022) MD5:26bac4b397da7babac4e36561826e6b0"
+TABLE_INFO[Omon]="Creation Date:(14 February 2022) MD5:26bac4b397da7babac4e36561826e6b0"
+TABLE_INFO[Lmon]="Creation Date:(14 February 2022) MD5:26bac4b397da7babac4e36561826e6b0"
+TABLE_INFO[dec]="Creation Date:(14 February 2022) MD5:26bac4b397da7babac4e36561826e6b0"
+TABLE_INFO[fx]="Creation Date:(14 February 2022) MD5:26bac4b397da7babac4e36561826e6b0"
+TABLE_INFO[Ofx]="Creation Date:(14 February 2022) MD5:26bac4b397da7babac4e36561826e6b0"
+TABLE_INFO[Odec]="Creation Date:(14 February 2022) MD5:26bac4b397da7babac4e36561826e6b0"
+TABLE_INFO[dec]="Creation Date:(14 February 2022) MD5:26bac4b397da7babac4e36561826e6b0"
+TABLE_INFO[LImon]="Creation Date:(14 February 2022) MD5:26bac4b397da7babac4e36561826e6b0"
+TABLE_INFO[SImon]="Creation Date:(14 February 2022) MD5:26bac4b397da7babac4e36561826e6b0"
+TABLE_INFO[Emon]="Creation Date:(14 February 2022) MD5:26bac4b397da7babac4e36561826e6b0"
+TABLE_INFO[AERmon]="Creation Date:(14 February 2022) MD5:26bac4b397da7babac4e36561826e6b0"
 # 
 #TABLE_INFO[]=
 declare -A VARIANT_INFO
@@ -44,6 +57,8 @@ echo "-------------------------"
 exp_id=transient-deglaciation-prescribed-glac1d_r1i1p1f1-CR
 ifolder=/work/bk1192/k204212/palmod/${exp_id}/archive/PalMod2/
 ifolder=/work/bk1192/k204212/palmod_secondBatch/${exp_id}/archive/PalMod2/
+ifolder=/work/bk1192/k204212/palmod_thirdBatch/${exp_id}/archive/PalMod2/
+ifolder=/work/kd1292/k204212/palmod_errataBatch/${exp_id}/archive/PalMod2/
 #ifolder=/work/ik1017/ESGF_Buff/k204212/PalMod2_test
 
 ifiles=($(find $ifolder -type f))
@@ -57,7 +72,7 @@ echo $i $ifile
     physics_index=${memberid:5:1}
 
     # Run ncatted
-    #ncatted -O -h -a variant_info,global,m,c,"${VARIANT_INFO[$physics_index]}" -a history,global,m,c,"$HISTORY" -a creation_date,global,m,c,"$CREATION_DATE" -a physics_index,global,m,c,"$physics_index" -a variant_label,global,m,c,"$memberid" -a table_info,global,m,c,"${TABLE_INFO[$table]}" -a Conventions,global,m,c,"$CONVENTIONS" -a title,global,m,c,"$TITLE" -a references,global,m,c,"$REFERENCES" -a source,global,m,c,"$SOURCE" -a nominal_resolution,global,m,c,"$NOMINAL_RESOLUTION" $ifile || echo "ERROR $ifile"
+    #ncatted -O -h -a parent_experiment_id,global,m,c,"${PARENTEXPID}" -a variant_info,global,m,c,"${VARIANT_INFO[$physics_index]}" -a history,global,m,c,"$HISTORY" -a creation_date,global,m,c,"$CREATION_DATE" -a physics_index,global,m,c,"$physics_index" -a variant_label,global,m,c,"$memberid" -a table_info,global,m,c,"${TABLE_INFO[$table]}" -a Conventions,global,m,c,"$CONVENTIONS" -a title,global,m,c,"$TITLE" -a references,global,m,c,"$REFERENCES" -a source,global,m,c,"$SOURCE" -a nominal_resolution,global,m,c,"$NOMINAL_RESOLUTION" $ifile || echo "ERROR $ifile"
     #ncatted -O -h -a variant_info,global,m,c,"${VARIANT_INFO[$physics_index]}" $ifile || echo "ERROR $ifile"
 
     # Adjust filename timestamp
@@ -69,9 +84,9 @@ echo $i $ifile
         echo $time1 $time2
         # Case 1 - Decadal data
         if [[ "$table" == *"dec"* ]]; then
-            if [[ "${time1: -1}" == "5" ]]; then
-                newtime1=$(printf "%05d" $(expr $time1 - 4))
-                newtime2=$(printf "%05d" $(expr $time2 + 5))
+            if [[ "${time1: -1}" == "6" ]]; then
+                newtime1=$(printf "%05d" $(expr $time1 - 5))
+                newtime2=$(printf "%05d" $(expr $time2 + 4))
             else
                 newtime1=$(printf "%05d" ${time1} )
                 newtime2=$(printf "%05d" ${time2} )

cmor/mpiesm/scripts/palmod2_diagnostic_MPI-ESM1-2_mpism_auto.h

@@ -2,6 +2,9 @@
 # Editor Note: This variable needs to be converted to the correct units. So it should bmelt*ice_density (917)*secondsperyear. Requires aggregation to account for leap years. Added recipe just for testing.
 { (if_requested $member $icemod IdecAnt libmassbffl $chunk '???1123124' && {
   find_file -e            "$sdir" "pism_ant_${period}*.nc" ifile
+  echo "$cdo -f nc -O \
+    -expr,'libmassbffl=bmelt*917*86400*365;' \
+       $ifile ${sdir}/out_diag/IdecAnt_libmassbffl_${period}.nc"
   $cdo -f nc -O \
     -expr,'libmassbffl=bmelt*917*86400*365;' \
        $ifile ${sdir}/out_diag/IdecAnt_libmassbffl_${period}.nc || echo ERROR
@@ -11,6 +14,9 @@
 # Editor Note: This variable needs to be converted to the correct units. So it should bmelt*ice_density (917)*secondsperyear. Requires aggregation to account for leap years. Added recipe just for testing.
 { (if_requested $member $icemod IdecGre libmassbffl $chunk '???1123124' && {
   find_file -e            "$sdir" "pism_nh_${period}*.nc" ifile
+  echo "$cdo -f nc -O \
+    -expr,'libmassbffl=bmelt*917*86400*365;' \
+       $ifile ${sdir}/out_diag/IdecGre_libmassbffl_${period}.nc"
   $cdo -f nc -O \
     -expr,'libmassbffl=bmelt*917*86400*365;' \
        $ifile ${sdir}/out_diag/IdecGre_libmassbffl_${period}.nc || echo ERROR
@@ -19,6 +25,9 @@
 #-- Diagnostic for mpism (ESM: MPI-ESM1-2) variable sftgifIt / table IdecAnt
 { (if_requested $member $icemod IdecAnt sftgifIt $chunk '???1123124' && {
   find_file -e            "$sdir" "pism_ant_${period}*.nc" ifile
+  echo "$cdo -f nc -O \
+    ${cdochain-} -expr,'ifl=mask==0;gi=mask==2;fi=mask==3;o=mask==4;' \
+    $ifile ${sdir}/out_diag/IdecAnt_sftgifIt_$period.nc"
   $cdo -f nc -O \
     ${cdochain-} -expr,'ifl=mask==0;gi=mask==2;fi=mask==3;o=mask==4;' \
     $ifile ${sdir}/out_diag/IdecAnt_sftgifIt_$period.nc || echo ERROR
@@ -27,6 +36,9 @@
 #-- Diagnostic for mpism (ESM: MPI-ESM1-2) variable sftgifIt / table IdecGre
 { (if_requested $member $icemod IdecGre sftgifIt $chunk '???1123124' && {
   find_file -e            "$sdir" "pism_nh_${period}*.nc" ifile
+  echo "$cdo -f nc -O \
+    ${cdochain-} -expr,'ifl=mask==0;gi=mask==2;fi=mask==3;o=mask==4;' \
+    $ifile ${sdir}/out_diag/IdecGre_sftgifIt_$period.nc"
   $cdo -f nc -O \
     ${cdochain-} -expr,'ifl=mask==0;gi=mask==2;fi=mask==3;o=mask==4;' \
     $ifile ${sdir}/out_diag/IdecGre_sftgifIt_$period.nc || echo ERROR

cmor/mpiesm/scripts/pismtest

@@ -11,12 +11,12 @@
 n_subsim=1
 #initial and final year of the experiment
 spinup=0
-iniyeararr=( $(( 4000 + spinup )) )
-finyeararr=( 4999 )
+iniyeararr=( $(( 1 + spinup )) )
+finyeararr=( 1000 )
 iniyear=$(( 1 + spinup ))
 finyear=26000
 #offset compared to startyear
-inioffsetarr=( -3999 )
+inioffsetarr=( 0 )
 
 # Time axis (26000-1 BP)
 ##     exp time       total yrs   new exp time   offset
@@ -37,7 +37,7 @@ chunksize=100
 for i in 0
 do
   #for yyyy in $(seq ${iniyeararr[$i]} ${finyeararr[$i]} )
-  for yyyy in $(seq 4100 4299)
+  for yyyy in $(seq 4000 4199)
   do
     paramarr+=( "$i $yyyy" )
   done

cmor/mpiesm/scripts/pismtest.runpp

@@ -13,7 +13,7 @@
 #SBATCH --account=bm0021
 #SBATCH --qos=esgf
 #SBATCH --exclusive
-#SBATCH --output=transient-deglaciation-prescribed-glac1d_r1i1p1f1-CR.runpp_%j.log
+#SBATCH --output=pismtest.runpp_%j.log
 
 DEBUG_LEVEL=${DEBUG_LEVEL:-0}
 
@@ -113,7 +113,7 @@ it_temp="${SCRIPT_ROOT}/pismtest_cdocmorinfo"
 ca+=([mpiom]="${SCRIPT_ROOT}/cdocmorinfo_mpiom_CR")
 ca+=([echam6]="${SCRIPT_ROOT}/cdocmorinfo_echam6_CR")
 ca+=([jsbach]="${SCRIPT_ROOT}/cdocmorinfo_jsbach_CR")
-ca+=([mpism]="${SCRIPT_ROOT}/cdocmorinfo_jsbach_CR")
+ca+=([mpism]="${SCRIPT_ROOT}/cdocmorinfo_mpism_CR")
 
 #Experiment etc
 experiment=transient-deglaciation-prescribed-glac1d
@@ -329,9 +329,6 @@ function run_agg
 
     for y in $(seq ${par1} ${par2}); do
 
-    # perform time shift for selected variables
-    cdochain="-shifttime,$((inioffsetarr[$y] - spinup))year -shifttime,-3day"
-
     for period in $(seq ${SUB_SIM_REL_L[$y]} ${SUB_SIM_REL_U[$y]}); do
         # Define the chunk that is tested by if_requested (YYYYMMDDHH-YYYYMMDDHH)
         chunk=$( echo $(( ${period} + ${inioffsetarr[$y]} - $spinup )) | awk '{ printf "%06d", $0 }')010100-$( echo $(( ${period} + ${inioffsetarr[$y]} - $spinup )) | awk '{ printf "%06d", $0 }')123124
@@ -340,6 +337,8 @@ function run_agg
 
         l_chunk_year=${l_chunk%??????}
         r_chunk_year=${r_chunk%??????}
+        period_bk=$period
+
 
         inv_chunk_year=$(( 1 + ${finyear} - ${l_chunk_year##+(0)} ))
         print "Aggregation $chunk ($period): Reading forcing/input of year $inv_chunk_year"
@@ -353,6 +352,16 @@ function run_agg
         # Perform aggregation for each submodel
         for submodel in $icemod; do #$atmmod $ocemod $srfmod $bgcmod; do
 
+            if [[ "$submodel" == "$icemod" ]]; then
+                period=$(( inv_chunk_year - 10 ))
+                # perform time shift for selected variables
+                cdochain="-shifttime,-5year -shifttime,${finyear}year" # for decadal time intervals only!
+            else
+                period=$period_bk
+                # perform time shift for selected variables
+                cdochain="-shifttime,$((inioffsetarr[$y] - spinup))year -shifttime,-3day"
+            fi
+
             # Chunking
             [[ "${chunks[$submodel]}" == *" ${period: -1} "* ]] && {
 
@@ -374,11 +383,11 @@ function run_agg
 
             # Create softlinks to raw model output - PISM requires special treatment
             if [[ $submodel == "mpism" ]]; then
-              #ln -sf $rawsdir_pism_ant/pism_-$(printf "%06d" ${inv_chunk_year})/pism_-$(printf "%06d" ${inv_chunk_year}).nc $sdir/pism_ant_${period}.nc
-              #ln -sf $rawsdir_pism_nh/pism_-$(printf "%06d" ${inv_chunk_year})/pism_-$(printf "%06d" ${inv_chunk_year}).nc $sdir/pism_nh_${period}.nc
-              cp -v $rawsdir_pism_ant/pism_-$(printf "%06d" ${inv_chunk_year})/pism_-$(printf "%06d" ${inv_chunk_year}).nc $sdir/pism_ant_${period}.nc
+              #ln -sf $rawsdir_pism_ant/pism_-$(printf "%06d" $((inv_chunk_year - 10)))/pism_-$(printf "%06d" $((inv_chunk_year - 10))).nc $sdir/pism_ant_${period}.nc
+              #ln -sf $rawsdir_pism_nh/pism_-$(printf "%06d" $((inv_chunk_year - 10)))/pism_-$(printf "%06d" $((inv_chunk_year - 10))).nc $sdir/pism_nh_${period}.nc
+              cp -v $rawsdir_pism_ant/pism_-$(printf "%06d" $((inv_chunk_year - 10)))/pism_-$(printf "%06d" $((inv_chunk_year - 10))).nc $sdir/pism_ant_${period}.nc
               ncatted -O -h -a scale_factor_at_projection_origin,mapping,o,d,1.0 $sdir/pism_ant_${period}.nc || { echo "ERROR ncatted $sdir/pism_ant_${period}.nc" ; exit 1 ; }
-              cp -v $rawsdir_pism_nh/pism_-$(printf "%06d" ${inv_chunk_year})/pism_-$(printf "%06d" ${inv_chunk_year}).nc $sdir/pism_nh_${period}.nc
+              cp -v $rawsdir_pism_nh/pism_-$(printf "%06d" $((inv_chunk_year - 10)))/pism_-$(printf "%06d" $((inv_chunk_year - 10))).nc $sdir/pism_nh_${period}.nc
               ncatted -O -h -a ellipsoid,mapping,o,c,WGS84 -a grid_mapping_name,mapping,o,c,polar_stereographic -a false_easting,mapping,o,d,0. -a false_northing,mapping,o,d,0. -a latitude_of_projection_origin,mapping,o,d,90. -a standard_parallel,mapping,o,d,70. -a straight_vertical_longitude_from_pole,mapping,o,d,-45. -a scale_factor_at_projection_origin,mapping,o,d,1.0 $sdir/pism_nh_${period}.nc || { echo "ERROR ncatted $sdir/pism_nh_${period}.nc" ; exit 1 ; }
             else
               ln -sf $rawsdir/*_${period}* $sdir/ 2>/dev/null 1>&2 || { echo "ERROR creating links for $period ${RAW_EXP_IDS[$y]} $submodel" && exit 1 ; }
@@ -408,6 +417,7 @@ function run_diag
 
         l_chunk=$(echo $chunk | cut -d "-" -f1)
         r_chunk=$(echo $chunk | cut -d "-" -f2)
+        period_bk=$period
 
         l_chunk_year=${l_chunk%??????}
         r_chunk_year=${r_chunk%??????}
@@ -423,6 +433,16 @@ function run_diag
         # Perform diagnostic for each submodel
         for submodel in $icemod; do #$atmmod $ocemod $srfmod $bgcmod; do
 
+            if [[ "$submodel" == "$icemod" ]]; then
+                period=$(( inv_chunk_year - 10 ))
+                # perform time shift for selected variables
+                cdochain="-shifttime,-5year -shifttime,${finyear}year" # for decadal time intervals only!
+            else
+                period=$period_bk
+                # perform time shift for selected variables
+                cdochain="-shifttime,$((inioffsetarr[$y] - spinup))year -shifttime,-3day"
+            fi
+
             # Chunking
             [[ "${chunks[$submodel]}" == *" ${period: -1} "* ]] && {
 
@@ -430,11 +450,6 @@ function run_diag
             print "$(date +%Y-%m-%dT%H:%M:%S): Diagnostic started for ${RAW_EXP_IDS[$y]} $submodel $chunk ($period) ..."
             sh -c 'scontrol update JobId=$SLURM_JOB_ID Comment="$*"' scomment diag/${RAW_EXP_IDS[$y]}/$submodel/$period
 
-            # cdochain - perform a timeshift
-            cdochain="-shifttime,$((inioffsetarr[$y] - spinup))year -shifttime,-3day"
-            # for PISM
-            [[ "$submodel" == "$icemod" ]] && cdochain="-shifttime,${l_chunk_year}year -shifttime,-5year -shifttime,${inv_chunk_year}year"
-
             #Location of input/output
             sdir=${SDIR[$y]}/outdata/$submodel
             rawsdir=${RAWSDIR[$y]}/outdata/$submodel
@@ -501,6 +516,7 @@ function run_cmor
 
         l_chunk=$(echo $chunk | cut -d "-" -f1)
         r_chunk=$(echo $chunk | cut -d "-" -f2)
+        period_bk=$period
 
         l_chunk_year=${l_chunk%??????}
         r_chunk_year=${r_chunk%??????}
@@ -508,7 +524,6 @@ function run_cmor
         inv_chunk_year=$(( 1 + ${finyear} - ${l_chunk_year##+(0)} ))
 
         # Define decadal interval
-        di="$(( ${period} + ${inioffsetarr[$y]} - 9 - $spinup )),$(( ${period} + ${inioffsetarr[$y]} - $spinup ))"
         dioce="$(( ${period} + ${inioffsetarr[$y]} - $spinup )),$(( ${period} + ${inioffsetarr[$y]} - $spinup + 9 ))"
 
         # Clean up stdout/stderr from previous run of this script
@@ -520,6 +535,18 @@ function run_cmor
         # Perform CMOR rewrite for each submodel
         for submodel in $icemod; do #$atmmod $ocemod $srfmod $bgcmod; do
 
+            if [[ "$submodel" == "$icemod" ]]; then
+                period=$(( inv_chunk_year - 10 ))
+                # perform time shift for selected variables
+                cdochain="-shifttime,-5year -shifttime,${finyear}year" # for decadal time intervals only!
+                di=${l_chunk_year##+(0)},$(( ${l_chunk_year##+(0)} + 9 ))
+            else
+                period=$period_bk
+                # perform time shift for selected variables
+                cdochain="-shifttime,$((inioffsetarr[$y] - spinup))year -shifttime,-3day"
+                di="$(( ${period} + ${inioffsetarr[$y]} - 9 - $spinup )),$(( ${period} + ${inioffsetarr[$y]} - $spinup ))"
+            fi
+
             # Chunking
             [[ "${chunks[$submodel]}" == *" ${period: -1} "* ]] && {
 
@@ -527,11 +554,6 @@ function run_cmor
             print "$(date +%Y-%m-%dT%H:%M:%S): CMORisation started for ${RAW_EXP_IDS[$y]} $submodel $chunk ($period) ..."
             sh -c 'scontrol update JobId=$SLURM_JOB_ID Comment="$*"' scomment cmor/${RAW_EXP_IDS[$y]}/$submodel/$period
 
-            # cdochain - perform a timeshift
-            cdochain="-shifttime,$((inioffsetarr[$y] - spinup))year -shifttime,-3day"
-            # for PISM
-            [[ "$submodel" == "$icemod" ]] && cdochain="-shifttime,${l_chunk_year}year -shifttime,-5year -shifttime,${inv_chunk_year}year"
-
             #Location of input/output
             sdir=${SDIR[$y]}/outdata/$submodel
             rawsdir=${RAWSDIR[$y]}/outdata/$submodel
@@ -624,7 +646,7 @@ then
         run_cmor
     fi
 else
-    Read_request_config $rrc_option AllExpPISM ${cpath}/${mip}_requested_vars_AllExp$SUFFIX.conf || die "error while reading request config"
+    Read_request_config $rrc_option AllExp ${cpath}/${mip}_requested_vars_AllExpPISM$SUFFIX.conf || die "error while reading request config"
     $RUN_AGG && run_agg || echo "Could not run agg"
     $RUN_DIAGS && run_diag || echo "Could not run diag"
     $RUN_CMOR && run_cmor || echo "Could not run cmor"