From 40fb2fdcd6d4239c660f4005f289ff47849256fd Mon Sep 17 00:00:00 2001
From: Martin Schupfner <k204212@levante2.lvt.dkrz.de>
Date: Wed, 23 Oct 2024 06:01:59 +0200
Subject: [PATCH] mpiesm: added scripts for
transient-deglaciation-interactive_r1i1p1f1-CR
---
cmor/mpiesm/scripts/ncatted_CS.sh | 151 ++++
...laciation-interactive_r1i1p1f1-CR.cmor_ctl | 64 ++
...iation-interactive_r1i1p1f1-CR.cmor_ctl.mk | 44 ++
...deglaciation-interactive_r1i1p1f1-CR.runpp | 724 ++++++++++++++++++
...iation-interactive_r1i1p1f1-CR_cdocmorinfo | 113 +++
5 files changed, 1096 insertions(+)
create mode 100644 cmor/mpiesm/scripts/ncatted_CS.sh
create mode 100755 cmor/mpiesm/scripts/transient-deglaciation-interactive_r1i1p1f1-CR.cmor_ctl
create mode 100755 cmor/mpiesm/scripts/transient-deglaciation-interactive_r1i1p1f1-CR.cmor_ctl.mk
create mode 100755 cmor/mpiesm/scripts/transient-deglaciation-interactive_r1i1p1f1-CR.runpp
create mode 100644 cmor/mpiesm/scripts/transient-deglaciation-interactive_r1i1p1f1-CR_cdocmorinfo
diff --git a/cmor/mpiesm/scripts/ncatted_CS.sh b/cmor/mpiesm/scripts/ncatted_CS.sh
new file mode 100644
index 0000000..a4f327a
--- /dev/null
+++ b/cmor/mpiesm/scripts/ncatted_CS.sh
@@ -0,0 +1,151 @@
+#!/bin/bash
+set -ue
+
+module load nco
+
+
+# Attributes
+TITLE="MPI-ESM1-2-1 output prepared for PalMod2"
+REFERENCES="The paper ist currently in open discussion under the following citation:\nMikolajewicz, U., Kapsch, M.-L., Schannwell, C., Six, K. D., Ziemen, F. A., Bagge, M., Baudouin, J.-P., Erokhina, O., Gayler, V., Klemann, V., Meccia, V. L., Mouchet, A., and Riddick, T.: Deglaciation and abrupt events in a coupled comprehensive atmosphere–ocean–ice sheet–solid earth model, Clim. Past Discuss. [preprint], https://doi.org/10.5194/cp-2024-55, in review, 2024"
+#NOMINAL_RESOLUTION="500 km" # echam6, jsbach, mpiom, hamocc
+#NOMINAL_RESOLUTION="km" # vilma
+#NOMINAL_RESOLUTION="25 km" # mPISM
+SOURCE="MPI-ESM1.2.1-CR (2022): \naerosol: none, prescribed Kinne (2010)\natmos: ECHAM6.3 (spectral T31; 96 x 48 longitude/latitude; 31 levels; top level 10 hPa)\natmosChem: none\nland: JSBACH3.20\nlandIce: none/prescribed\nocean: MPIOM1.63 (bipolar GR3.0, approximately 300km; 122 x 101 longitude/latitude; 40 levels; top grid cell 0-15 m)\nocnBgchem: none\nseaIce: unnamed (thermodynamic (Semtner zero-layer) dynamic (Hibler 79) sea ice model)\nsolidLand: none/prescribed"
+CONVENTIONS="CF-1.7 PalMod-2.0"
+CREATION_DATE="2024-09-20T18:00:00Z"
+HISTORY="2024-09-20T18:00:00Z ; 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
+#dreqversion="00.00.02"
+#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"
+# 00.00.03
+dreqversion="00.00.03"
+TABLE_INFO[AERmon]="Creation Date:(1 February 2023) MD5:437d9b7f4524e7483e04d57b09f4aaaa"
+TABLE_INFO[Amon]="Creation Date:(1 February 2023) MD5:437d9b7f4524e7483e04d57b09f4aaaa"
+TABLE_INFO[centennial]="Creation Date:(1 February 2023) MD5:437d9b7f4524e7483e04d57b09f4aaaa"
+TABLE_INFO[dec]="Creation Date:(1 February 2023) MD5:437d9b7f4524e7483e04d57b09f4aaaa"
+TABLE_INFO[Emon]="Creation Date:(1 February 2023) MD5:437d9b7f4524e7483e04d57b09f4aaaa"
+TABLE_INFO[EmonZ]="Creation Date:(1 February 2023) MD5:437d9b7f4524e7483e04d57b09f4aaaa"
+TABLE_INFO[fx]="Creation Date:(1 February 2023) MD5:437d9b7f4524e7483e04d57b09f4aaaa"
+TABLE_INFO[IcenAnt]="Creation Date:(1 February 2023) MD5:437d9b7f4524e7483e04d57b09f4aaaa"
+TABLE_INFO[IcenGre]="Creation Date:(1 February 2023) MD5:437d9b7f4524e7483e04d57b09f4aaaa"
+TABLE_INFO[IdecAnt]="Creation Date:(1 February 2023) MD5:437d9b7f4524e7483e04d57b09f4aaaa"
+TABLE_INFO[IdecGre]="Creation Date:(1 February 2023) MD5:437d9b7f4524e7483e04d57b09f4aaaa"
+TABLE_INFO[IyrAnt]="Creation Date:(1 February 2023) MD5:437d9b7f4524e7483e04d57b09f4aaaa"
+TABLE_INFO[IyrGre]="Creation Date:(1 February 2023) MD5:437d9b7f4524e7483e04d57b09f4aaaa"
+TABLE_INFO[LImon]="Creation Date:(1 February 2023) MD5:437d9b7f4524e7483e04d57b09f4aaaa"
+TABLE_INFO[Lmon]="Creation Date:(1 February 2023) MD5:437d9b7f4524e7483e04d57b09f4aaaa"
+TABLE_INFO[Odec]="Creation Date:(1 February 2023) MD5:437d9b7f4524e7483e04d57b09f4aaaa"
+TABLE_INFO[Ofx]="Creation Date:(1 February 2023) MD5:437d9b7f4524e7483e04d57b09f4aaaa"
+TABLE_INFO[Omon]="Creation Date:(1 February 2023) MD5:437d9b7f4524e7483e04d57b09f4aaaa"
+TABLE_INFO[Oyr]="Creation Date:(1 February 2023) MD5:437d9b7f4524e7483e04d57b09f4aaaa"
+TABLE_INFO[SImon]="Creation Date:(1 February 2023) MD5:437d9b7f4524e7483e04d57b09f4aaaa"
+# 00.00.04
+dreqversion="00.00.04"
+TABLE_INFO[AERmon]="Creation Date:(18 September 2024) MD5:028d52f4a33ef4da346678b341512dda"
+TABLE_INFO[Amon]="Creation Date:(18 September 2024) MD5:028d52f4a33ef4da346678b341512dda"
+TABLE_INFO[centennial]="Creation Date:(18 September 2024) MD5:028d52f4a33ef4da346678b341512dda"
+TABLE_INFO[dec]="Creation Date:(18 September 2024) MD5:028d52f4a33ef4da346678b341512dda"
+TABLE_INFO[Emon]="Creation Date:(18 September 2024) MD5:028d52f4a33ef4da346678b341512dda"
+TABLE_INFO[EmonZ]="Creation Date:(18 September 2024) MD5:028d52f4a33ef4da346678b341512dda"
+TABLE_INFO[fx]="Creation Date:(18 September 2024) MD5:028d52f4a33ef4da346678b341512dda"
+TABLE_INFO[IcenAnt]="Creation Date:(18 September 2024) MD5:028d52f4a33ef4da346678b341512dda"
+TABLE_INFO[IcenGre]="Creation Date:(18 September 2024) MD5:028d52f4a33ef4da346678b341512dda"
+TABLE_INFO[IdecAnt]="Creation Date:(18 September 2024) MD5:028d52f4a33ef4da346678b341512dda"
+TABLE_INFO[IdecGre]="Creation Date:(18 September 2024) MD5:028d52f4a33ef4da346678b341512dda"
+TABLE_INFO[IyrAnt]="Creation Date:(18 September 2024) MD5:028d52f4a33ef4da346678b341512dda"
+TABLE_INFO[IyrGre]="Creation Date:(18 September 2024) MD5:028d52f4a33ef4da346678b341512dda"
+TABLE_INFO[LImon]="Creation Date:(18 September 2024) MD5:028d52f4a33ef4da346678b341512dda"
+TABLE_INFO[Lmon]="Creation Date:(18 September 2024) MD5:028d52f4a33ef4da346678b341512dda"
+TABLE_INFO[Odec]="Creation Date:(18 September 2024) MD5:028d52f4a33ef4da346678b341512dda"
+TABLE_INFO[Ofx]="Creation Date:(18 September 2024) MD5:028d52f4a33ef4da346678b341512dda"
+TABLE_INFO[Omon]="Creation Date:(18 September 2024) MD5:028d52f4a33ef4da346678b341512dda"
+TABLE_INFO[Oyr]="Creation Date:(18 September 2024) MD5:028d52f4a33ef4da346678b341512dda"
+TABLE_INFO[SImon]="Creation Date:(18 September 2024) MD5:028d52f4a33ef4da346678b341512dda"
+TABLE_INFO[SLdec]="Creation Date:(18 September 2024) MD5:028d52f4a33ef4da346678b341512dda"
+#TABLE_INFO[]=
+declare -A VARIANT_INFO
+VARIANT_INFO["4"]="The data are from a synchronously coupled model simulation of the last deglaciation with the MPI-ESM1.2.1-CR-mPISM-VILMA setup, hence, including interactive ice sheets and solid earth components. The simulation was forced with time-varying volcanic forcing (Schindlbeck-Belo et al., 2024). GHG forcing is after Koehler et al. (2017), Orbit after Berger (1978)."
+VARIANT_INFO["1"]="The data are from a synchronously coupled model simulation of the last deglaciation with the MPI-ESM1.2.1-CR-mPISM-VILMA setup, hence, including interactive ice sheets and solid earth components. The simulation used climatological volcanic forcing representing PI. GHG forcing is after Koehler et al. (2017), Orbit after Berger (1978)."
+echo "------------------------"
+echo $TITLE
+echo $REFERENCES
+#echo $NOMINAL_RESOLUTION
+echo $SOURCE
+echo $CONVENTIONS
+echo $CREATION_DATE
+echo $HISTORY
+echo ${TABLE_INFO[@]}
+echo "-------------------------"
+
+exp_id=transient-deglaciation-interactive_r1i1p4f2-CR
+
+ifolder=/work/kd1292/ESGF_Buff/k204212/palmod_CS/${exp_id}/PalMod2/
+
+ifiles=($(find $ifolder -type f))
+echo ${#ifiles[@]} files found.
+i=0
+for ifile in ${ifiles[@]}; do
+i=$((i+1))
+echo $i $ifile
+ table=$(echo $ifile | rev | cut -d '/' -f 1 | rev | cut -d '_' -f 2)
+ memberid=$(echo $ifile | rev | cut -d '/' -f 1 | rev | cut -d '_' -f 5)
+ physics_index=${memberid:5:1}
+ forcing_index=${memberid:7:1}
+ realization_index=${memberid:1:1}
+ init_index=${memberid:3:1}
+ variantlabel=r${realization_index}i${init_index}p${physics_index}f${forcing_index}
+ uuid="hdl:21.14105/$(uuidgen)"
+
+ # Run ncatted
+ #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 $ifile"
+ #ncatted -O -h -a tracking_id,global,m,c,"$uuid" $ifile || echo "ERROR $ifile"
+ #ncatted -O -h -a parent_experiment_id,global,m,c,"${PARENTEXPID}" -a source,global,m,c,"$SOURCE" -a references,global,m,c,"$REFERENCES" -a variant_info,global,m,c,"${VARIANT_INFO[$physics_index]}" -a table_info,global,m,c,"${TABLE_INFO[$table]}" -a data_specs_version,global,m,c,${dreqversion} -a history,global,m,c,"$HISTORY" -a creation_date,global,m,c,"$CREATION_DATE" -a Conventions,global,m,c,"$CONVENTIONS" -a title,global,m,c,"$TITLE" -a tracking_id,global,m,c,"$uuid" $ifile || echo "ERROR $ifile"
+
+ # Adjust filename timestamp
+ if [[ "$table" != *"fx"* ]]; then
+ trunk=$(echo $ifile | rev | cut -d '_' -f 2- | rev)
+ timestamp=$(echo $ifile | rev | cut -d '.' -f 2 | cut -d '_' -f 1 | rev)
+ time1=$(echo $timestamp | cut -d '-' -f 1 | sed 's/^0*//' )
+ time2=$(echo $timestamp | cut -d '-' -f 2 | sed 's/^0*//' )
+ echo $time1 $time2
+ # Case 1 - Decadal data
+ if [[ "$table" == *"dec"* ]]; then
+ 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" ${time2} )
+ fi
+ # Case 2 - the rest - annual and monthly data
+ elif [[ "$table" == *"mon"* ]]; then
+ newtime1=$(printf "%07d" ${time1} )
+ newtime2=$(printf "%07d" ${time2} )
+ elif [[ "$table" == *"yr"* ]]; then
+ newtime1=$(printf "%05d" ${time1} )
+ newtime2=$(printf "%05d" ${time2} )
+ elif [[ "$table" == *"day"* ]]; then
+ newtime1=$(printf "%09d" ${time1} )
+ newtime2=$(printf "%09d" ${time2} )
+ elif [[ "$table" == *"hr"* ]]; then
+ newtime1=$(printf "%011d" ${time1} )
+ newtime2=$(printf "%011d" ${time2} )
+ else
+ echo "ERROR: ${table}: no timestamp renaming rule!"
+ continue
+ fi
+ # mv command
+ ifile_new=${trunk}_${newtime1}-${newtime2}.nc
+ [[ "$ifile" != "$ifile_new" ]] && {
+ mv -v $ifile $ifile_new || echo "ERROR renaming $ifile to $ifile_new"
+ }
+ fi
+done
diff --git a/cmor/mpiesm/scripts/transient-deglaciation-interactive_r1i1p1f1-CR.cmor_ctl b/cmor/mpiesm/scripts/transient-deglaciation-interactive_r1i1p1f1-CR.cmor_ctl
new file mode 100755
index 0000000..72de2fd
--- /dev/null
+++ b/cmor/mpiesm/scripts/transient-deglaciation-interactive_r1i1p1f1-CR.cmor_ctl
@@ -0,0 +1,64 @@
+#! /bin/sh -e
+#SBATCH --account=bm0021
+#SBATCH --qos=esgf
+#SBATCH --time=48:00:00
+#SBATCH --partition=shared
+#SBATCH --mail-type=FAIL
+#SBATCH --output=%x_%j.log
+
+# Number of sub-simulations
+n_subsim=4
+#initial and final year of the experiment
+spinup=1000
+iniyeararr=( $((4000+spinup)) 2000 2000 2000 )
+finyeararr=( 8999 8999 8999 8999 )
+iniyearoffset=1000
+iniyear=$(( 1 + $iniyearoffset + $spinup ))
+finyear=$(( 26000 + $iniyearoffset - $spinup ))
+#offset compared to startyear
+inioffsetarr=( $(( -3999 + $iniyearoffset )) $(( 3001 + $iniyearoffset )) $(( 10001 + $iniyearoffset )) $(( 17001 + $iniyearoffset )) )
+# Time axis (26000-1 BP)
+## exp time total yrs new exp time offset
+#a - 26000-21001 BP - 5000 yrs - 1- 5000 - - 3999
+#b - 21000-14001 BP - 7000 yrs - 5001-12000 - 3001
+#c - 14000- 7001 BP - 7000 yrs - 12001-19000 - 10001
+#d - 7000- 1 BP - 7000 yrs - 19001-26000 - 17001
+
+# Chunksize
+# Note that there are prerequisites concerning the chunksize:
+# - the defined decadal timeslizes may not overlap between two chunks!
+# - decadal bounds have to be defined accordingly - "???01231" in this case
+# - usually this is the case by default due to decadal model output!
+chunksize=100
+
+# Create list
+for i in $(seq 0 $(( n_subsim - 1 )) )
+do
+ for yyyy in $(seq ${iniyeararr[$i]} ${finyeararr[$i]} )
+ do
+ paramarr+=( "$i $yyyy" )
+ done
+done
+
+rm -f cmor_ctl_list_interactive_synch_r1i1p1f1
+in=0
+for i in $(seq $((iniyear-iniyear)) $chunksize $((finyear-iniyear)))
+do
+ [[ $i -eq $((iniyear-iniyear)) ]] && continue
+ li=$(echo ${paramarr[$in]} | cut -d " " -f1)
+ ly=$(echo ${paramarr[$in]} | cut -d " " -f2)
+ ui=$(echo ${paramarr[$((i-1))]} | cut -d " " -f1)
+ uy=$(echo ${paramarr[$((i-1))]} | cut -d " " -f2)
+ in=$i
+ echo "$li $ui $ly $uy" >> cmor_ctl_list_interactive_synch_r1i1p1f1
+done
+[[ $i -ne $((finyear-iniyear)) ]] && {
+ li=$(echo ${paramarr[$in]} | cut -d " " -f1)
+ ly=$(echo ${paramarr[$in]} | cut -d " " -f2)
+ ui=$(echo ${paramarr[$((finyear-iniyear))]} | cut -d " " -f1)
+ uy=$(echo ${paramarr[$((finyear-iniyear))]} | cut -d " " -f2)
+ echo "$li $ui $ly $uy" >> cmor_ctl_list_interactive_synch_r1i1p1f1
+}
+
+make -k -j 19 -f transient-deglaciation-interactive_r1i1p1f1-CR.cmor_ctl.mk "$@"
+
diff --git a/cmor/mpiesm/scripts/transient-deglaciation-interactive_r1i1p1f1-CR.cmor_ctl.mk b/cmor/mpiesm/scripts/transient-deglaciation-interactive_r1i1p1f1-CR.cmor_ctl.mk
new file mode 100755
index 0000000..4b25f01
--- /dev/null
+++ b/cmor/mpiesm/scripts/transient-deglaciation-interactive_r1i1p1f1-CR.cmor_ctl.mk
@@ -0,0 +1,44 @@
+EXP_ID = transient-deglaciation-interactive_r1i1p1f1-CR
+
+ACCOUNT = bm0021
+PARTITION = compute
+
+SUFFIX =
+ARCHIVE_SUFFIX =
+
+TARGET_STEP=cmor
+NUMCHUNKS=$(shell cat cmor_ctl_list_interactive_synch_r1i1p1f1 | wc -l )
+
+AGGR_TIME = 00:10:00
+DIAGS_TIME = 00:30:00
+CMOR_TIME = 02:30:00
+
+CMOR_FLAGS =
+
+SBATCHFLAGS=-W
+
+MESSAGE = $$(date +%Y-%m-%dT%H:%M:%S): CMIP6 diagnostics and CMOR rewriting ($(SUFFIX:_%=%))
+
+.PHONY: all
+.PRECIOUS: targets/$(EXP_ID).aggr$(SUFFIX).% targets/$(EXP_ID).diags$(SUFFIX).% targets/$(EXP_ID).cmor$(SUFFIX).%
+
+
+
+all:
+ @echo "$(MESSAGE) started"
+ mkdir -vp targets
+ $(MAKE) $(MFLAGS) -f $(MAKEFILE_LIST) $(addprefix targets/$(EXP_ID).$(TARGET_STEP)$(SUFFIX).,$(shell seq 1 $(NUMCHUNKS)))
+ @echo "$(MESSAGE) finished"
+
+targets/$(EXP_ID).aggr$(SUFFIX).%:
+ sbatch $(SBATCHFLAGS) --time=$(AGGR_TIME) --job-name=$(EXP_ID)_runpp_aggr$(SUFFIX) --output=%x_%j.log --comment=$* $(EXP_ID).runpp -s '$(SUFFIX)' -S '$(ARCHIVE_SUFFIX)' -A $(shell sed -n '$(*)'p < cmor_ctl_list_interactive_synch_r1i1p1f1)
+ @touch $@
+
+targets/$(EXP_ID).diags$(SUFFIX).%: targets/$(EXP_ID).aggr$(SUFFIX).%
+ sbatch $(SBATCHFLAGS) --time=$(DIAGS_TIME) --job-name=$(EXP_ID)_runpp_diag$(SUFFIX) --output=%x_%j.log --comment=$* $(EXP_ID).runpp -s '$(SUFFIX)' -S '$(ARCHIVE_SUFFIX)' -d $(shell sed -n '$(*)'p < cmor_ctl_list_interactive_synch_r1i1p1f1)
+ @touch $@
+
+targets/$(EXP_ID).cmor$(SUFFIX).%: targets/$(EXP_ID).diags$(SUFFIX).%
+ sbatch $(SBATCHFLAGS) --time=$(CMOR_TIME) --job-name=$(EXP_ID)_runpp_cmor$(SUFFIX) --output=%x_%j.log --comment=$* $(EXP_ID).runpp -s '$(SUFFIX)' -S '$(ARCHIVE_SUFFIX)' -c $(CMOR_FLAGS) $(shell sed -n '$(*)'p < cmor_ctl_list_interactive_synch_r1i1p1f1)
+ @touch $@
+
diff --git a/cmor/mpiesm/scripts/transient-deglaciation-interactive_r1i1p1f1-CR.runpp b/cmor/mpiesm/scripts/transient-deglaciation-interactive_r1i1p1f1-CR.runpp
new file mode 100755
index 0000000..293934f
--- /dev/null
+++ b/cmor/mpiesm/scripts/transient-deglaciation-interactive_r1i1p1f1-CR.runpp
@@ -0,0 +1,724 @@
+#!/bin/ksh
+#
+# PalMod .runpp
+#
+# Wrapper Script Agg+Diag+CMOR MPI-ESM1-2 by Martin Schupfner, DKRZ
+#
+### Batch Queuing System is SLURM
+#SBATCH --partition=compute
+#SBATCH --nodes=1
+#SBATCH --mem=100G
+#SBATCH --time=01:30:00
+#SBATCH --mail-type=none
+#SBATCH --account=bm0021
+#SBATCH --qos=esgf
+#SBATCH --exclusive
+#SBATCH --output=transient-deglaciation-interactive_r1i1p1f1-CR.runpp_%j.log
+
+DEBUG_LEVEL=${DEBUG_LEVEL:-0}
+
+# Support log style output
+export LANG=C
+print () { command print "$(date +'%F %T'):" "$@"; }
+print_re='^[0-9]+-[0-9]{2}-[0-9]{2} [0-9]{2}:[0-9]{2}:[0-9]{2}'
+
+warn () { print 'Hey:' "$@" >&2; }
+die () { print 'Oops:' "$@" >&2; return 1; }
+
+# Bail out on error
+trap 'print Error at line $LINENO >&2' ERR
+set -eu
+
+# Disable core file creation
+ulimit -c 0
+
+# Print command info
+[[ $DEBUG_LEVEL -ge 2 ]] && set -x
+
+#module load nco || { echo "Oops: Could not load NCO!" && exit 1 ; }
+alias ncatted=/sw/spack-levante/nco-5.0.6-3xkdth/bin/ncatted
+
+#########################################
+# Define specifics about the simulation
+#########################################
+
+#Root directory of all scripts, outdata, logs etc
+EXP_ID=transient-deglaciation-prescribed-glac1d_r1i1p1f1-CR
+#EXP_DIR_TRUNK=/work/bk1192/k204212/palmod_CS/transient-deglaciation-interactive_r1i1p1f1-CR
+EXP_DIR_TRUNK=/work/kd1292/ESGF_Buff/k204212/palmod_CS/transient-deglaciation-interactive_r1i1p1f1-CR
+
+#initial files for aggregation
+INPUT_DIR_TRUNK=/work/bk1192/WP1.1/MPIM_transient_deglaciation_synchronous
+
+# RAW Data - path and sub-simulations
+RAW_EXP_DIR_TRUNK=/work/bk1192/WP1.1/MPIM_transient_deglaciation_synchronous
+# As usually the Experiment is composed of several sub-simulations, define them as array
+RAW_EXP_IDS=( pmo0007a pmo0007b pmo0007c pmo0007d )
+# Parent experiment that the first RAW_EXP_ID branched from
+# (used for input data of the parent that is required for aggregation)
+# !! spinup - the aggregation will fail if the spinup period
+# !! is as long or longer than
+# !! the length of the first sub simulation!
+spinup=1000
+RAW_EXP_ID_PARENT=( None pmo0007a pmo0007b pmo0007c ) # cmorizing 26000-1 BP as 1-26000 AD
+if [[ $spinup -ne 0 ]]; then
+ RAW_EXP_ID_PARENT[0]=${RAW_EXP_IDS[0]} # cmorizing (26000-spinup)-1 BP as 1-(26000-spinup) AD
+fi
+
+echo ${RAW_EXP_IDS[@]}
+echo ${RAW_EXP_ID_PARENT[@]}
+
+#Work dir
+WORK_DIR_TRUNK=$EXP_DIR_TRUNK/work
+
+#Where to find the scripts (runpp etc.)
+SCRIPT_DIR=${EXP_DIR_TRUNK}/scripts
+SCRIPT_DIR=/work/bm0021/PalMod2/cmor/mpiesm/scripts
+
+
+
+############################
+#Define necessary variables
+############################
+
+#Where to find cdo (incl. CMOR operator), eg.:
+cdo="/work/bm0021/cdo_incl_cmor/cdo-2022-09-20_cmor3.6.0_gcc/bin/cdo -v" # surely working version
+#cdo="/work/bm0021/cdo_incl_cmor/cdo-2024-09-11_cmor3.9.0_gcc/bin/cdo -v" # latest version
+cdozg="/sw/spack-levante/cdo-1.9.10-j5frmz/bin/cdo -v"
+
+# Base directory for DataRequest related headers/scripts
+SCRIPT_ROOT=${SCRIPT_DIR}
+
+#Where to find the functions
+fpath=/work/bm0021/PalMod2/cmor/functions
+
+#Where to find the configuration
+cpath=${SCRIPT_ROOT}/conf
+
+#Models
+atmmod=echam6
+ocemod=mpiom
+srfmod=jsbach
+esmod=MPI-ESM1-2
+icemod=mpism
+slmod=vilma
+
+#Chunks
+chunks+=([echam6]=" 0 1 2 3 4 5 6 7 8 9 ")
+chunks+=([jsbach]=" 0 1 2 3 4 5 6 7 8 9 ")
+chunks+=([mpiom]=" 0 ")
+chunks+=([jsbachdec]=" 0 ")
+atmmod_dec_chunk="???0123124"
+srfmod_dec_chunk="???0123124"
+srfmod_input_dec_chunk="???0123124"
+ocemod_dec_chunk="???1123124"
+icemod_dec_chunk="???1123124"
+slmod_dec_chunk="???1123124"
+slmod_input_dec_chunk="???0123124"
+ocemod_fxyear=3000
+chunks+=([mpism]=" 0 ")
+chunks+=([vilma]=" 0 1 ")
+chunks+=([vilmadec]=" 0 ")
+
+#InfoTable(s)
+# Define here the "cdocmorinfo"-File or "eum"-Files
+# Multiple files possible with "," as delimiter, eg:
+# it=expinfo.txt,userinfo.txt,modelinfo.txt
+it_temp="${SCRIPT_ROOT}/transient-deglaciation-interactive_r1i1p1f1-CR_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_mpism_CR")
+ca+=([vilma]="${SCRIPT_ROOT}/cdocmorinfo_vilma_CR")
+
+#Experiment etc
+experiment=transient-deglaciation-interactive
+member=r1i1p1f1
+mip=PalMod2
+vd=v20240920
+#vd=v$(date '+%Y%m%d') #CMOR version directory name, should be a date in format YYYYMMDD
+
+#Where to store errors
+errdir=${EXP_DIR_TRUNK}/logs/errors
+errdir_cmor=${errdir}_cmor
+errdir_diag=${errdir}_diag
+errdir_agg=${errdir}_agg
+
+#initial and final year of the experiment
+iniyeararr=($((4000+spinup)) 2000 2000 2000) # 26000-1 BP
+finyeararr=(8999 8999 8999 8999)
+iniyearoffset=0 # additional optional offset
+iniyear=$(( $iniyearoffset + 1 ))
+finyear=$(( 26000 + $iniyearoffset - $spinup ))
+#offset compared to startyear
+inioffsetarr=( $(( -3999 + $iniyearoffset )) $(( 3001 + $iniyearoffset )) $(( 10001 + $iniyearoffset )) $(( 17001 + $iniyearoffset )) ) # 26000-1 BP
+# Time axis (26000-1 BP)
+## exp time total yrs new exp time offset
+#a - 26000-21001 BP - 5000 yrs - 1- 5000 - - 3999
+#b - 21000-14001 BP - 7000 yrs - 5001-12000 - 3001
+#c - 14000- 7001 BP - 7000 yrs - 12001-19000 - 10001
+#d - 7000- 1 BP - 7000 yrs - 19001-26000 - 17001
+
+#pmo0007a-d: Transient simulation of the last deglaciation with interactive ice
+#sheets and synchronous coupling between MPI-ESM and the ice sheet-solid earth model.
+#GHG forcing is after Koehler et al. (2017), Orbit after Berger (1978).
+#They are structured as follows.
+#
+# pmo0007a: Simulation year 4000-8999 spans the time period 26000
+# years BP to 21000 years BP.
+# pmo0007b: Simulation years 2000-8999; years 21000 to 14000 BP
+# pmo0007c: Simulation years 2000-8999; years 14000 to 7000 BP
+# pmo0007d: Simulation years 2000-8999; years 7000 BP to 0 BP
+#
+
+# Command line options
+RUN_AGG=true
+RUN_DIAGS=true
+RUN_CMOR=true
+SUFFIX=
+CLIMSUFFIX=
+ARCHIVE_SUFFIX=
+USE_CHUNKS=false
+REMOVE_CHUNKS=false
+PROCESS_CLIM=false
+while [[ "$1" == -* ]]
+do
+ OPT=
+ ARG=
+ case "$1" in
+ -d|--diags|--diags-only) RUN_CMOR=false; RUN_AGG=false;;
+ -c|--cmor|--cmor-only) RUN_DIAGS=false; RUN_AGG=false;;
+ -A|--agg|--agg-only) RUN_DIAGS=false; RUN_CMOR=false;;
+ -C|--clim) PROCESS_CLIM=true;;
+ -s|--suffix) OPT=-s; ARG=SUFFIX;;
+ -S|--archive-suffix) OPT=-S; ARG=ARCHIVE_SUFFIX;;
+ -f|--force) REMOVE_CHUNKS=true;;
+ -a|--append) USE_CHUNKS=true;;
+ --) shift; break;;
+ -*) die "invalid option '$1'";;
+ esac
+ if [[ -n "$OPT" ]]
+ then
+ shift
+ [[ $# -lt 1 ]] && die "missing argument for option '$OPT'"
+ eval "$ARG='$1'"
+ fi
+ shift
+done
+
+echo "-----------------"
+echo $0 $1 $2 $3 $4
+echo "-----------------"
+
+#Write Output to:
+dr_trunk=${EXP_DIR_TRUNK}/archive$ARCHIVE_SUFFIX
+
+
+
+###############################################################################
+# No user input beyond this line necessary (usually)
+###############################################################################
+
+# Store parameters
+par1=$1
+par2=$2
+par3=$3
+par4=$4
+n_arr=${#inioffsetarr[@]}
+
+#time interval of the experiment to standardize
+if [[ ${#iniyeararr[@]} != ${#inioffsetarr[@]} ]] || [[ ${#iniyeararr[@]} != ${#finyeararr[@]} ]] || [[ ${#iniyeararr[@]} != ${#RAW_EXP_IDS[@]} ]]; then
+ die 'Each sub-simulation needs a specified iniyear, finyear and inioffset!'
+else
+ for y in $(seq 0 $(( n_arr - 1 )) ); do
+ SDIR+=( ${EXP_DIR_TRUNK}/${RAW_EXP_IDS[$y]} )
+ RAWSDIR+=( ${RAW_EXP_DIR_TRUNK}/${RAW_EXP_IDS[$y]} )
+ WORK_DIR+=( ${WORK_DIR_TRUNK}/${RAW_EXP_IDS[$y]} )
+ done
+ [[ -z "$2" ]] && [[ "$PROCESS_CLIM" == "false" ]] && die 'invalid number of parameters; need index of start and end simulations, start year (of first index) and end year (of second index) as YYYY'
+ [[ -z "$3" ]] && [[ "$PROCESS_CLIM" == "false" ]] && die 'invalid number of parameters; need index of start and end simulations, start year (of first index) and end year (of second index) as YYYY'
+ [[ -z "$4" ]] && [[ "$PROCESS_CLIM" == "false" ]] && die 'invalid number of parameters; need index of start and end simulations, start year (of first index) and end year (of second index) as YYYY'
+ for y in $(seq 0 $(( n_arr - 1 )) ); do
+ if [[ $y -lt $par1 ]] || [[ $y -gt $par2 ]]; then
+ lrel=-1
+ urel=-1
+ labs=-1
+ uabs=-1
+ elif [[ $y -eq $1 ]] && [[ $1 -eq $2 ]]; then
+ lrel=$3
+ urel=$4
+ labs=$(( $3 + ${inioffsetarr[$y]} - $spinup ))
+ uabs=$(( $4 + ${inioffsetarr[$y]} - $spinup ))
+ elif [[ $y -eq $1 ]]; then
+ lrel=$3
+ urel=${finyeararr[$y]}
+ labs=$(( $3 + ${inioffsetarr[$y]} - $spinup ))
+ uabs=$(( ${finyeararr[$y]} + ${inioffsetarr[$y]} - $spinup ))
+ elif [[ $y -eq $2 ]]; then
+ lrel=${iniyeararr[$y]}
+ urel=$4
+ labs=$(( ${iniyeararr[$y]} + ${inioffsetarr[$y]} - $spinup ))
+ uabs=$(( $4 + ${inioffsetarr[$y]} - $spinup ))
+ else
+ lrel=${iniyeararr[$y]}
+ urel=${finyeararr[$y]}
+ labs=$(( ${iniyeararr[$y]} + ${inioffsetarr[$y]} - $spinup ))
+ uabs=$(( ${finyeararr[$y]} + ${inioffsetarr[$y]} - $spinup ))
+ fi
+ [[ $urel -lt $lrel ]] && die 'iniyear, finyear arrays not properly set up!'
+ [[ $uabs -lt $labs ]] && die 'iniyear, finyear arrays not properly set up!'
+ SUB_SIM_REL_L+=( $lrel )
+ SUB_SIM_REL_U+=( $urel )
+ SUB_SIM_ABS_L+=( $labs )
+ SUB_SIM_ABS_U+=( $uabs )
+ [[ $lrel -eq -1 ]] && continue
+ [[ "$PROCESS_CLIM" == "false" ]] && { [[ ${SUB_SIM_REL_L[$y]} -lt ${iniyeararr[$y]} ]] || [[ ${SUB_SIM_REL_L[$y]} -gt ${finyeararr[$y]} ]] ; } && die 'erroneous input - input does not make sense along with the configured iniyear, finyear arrays'
+ [[ "$PROCESS_CLIM" == "false" ]] && { [[ ${SUB_SIM_REL_U[$y]} -lt ${iniyeararr[$y]} ]] || [[ ${SUB_SIM_REL_U[$y]} -gt ${finyeararr[$y]} ]] ; } && die 'erroneous input - input does not make sense along with the configured iniyear, finyear arrays'
+ done
+ echo ${SUB_SIM_REL_L[@]}
+ echo ${SUB_SIM_REL_U[@]}
+ echo ${SUB_SIM_ABS_L[@]}
+ echo ${SUB_SIM_ABS_U[@]}
+ [[ $1 -ge ${#iniyeararr[@]} ]] && die 'erroneous input - input does not make sense along with the configured iniyear, finyear arrays'
+ [[ $2 -ge ${#iniyeararr[@]} ]] && die 'erroneous input - input does not make sense along with the configured iniyear, finyear arrays'
+ [[ $1 -gt $2 ]] && die 'erroneous input - input does not make sense along with the configured iniyear, finyear arrays'
+ cmorstart=$(( $3 + ${inioffsetarr[$1]} - $spinup ))
+ cmorend=$(( $4 + ${inioffsetarr[$2]} -spinup ))
+fi
+MESSAGE='PalMod2'
+$RUN_AGG && MESSAGE+=' - Aggregation - '
+$RUN_DIAGS && MESSAGE+=' - Diagnostics - '
+$RUN_CMOR && MESSAGE+=" - CMOR rewriting - "
+$PROCESS_CLIM && MESSAGE+=' for only climatological variables'
+print "$(date +%Y-%m-%dT%H:%M:%S): $MESSAGE started for ${cmorstart}-${cmorend} $SUFFIX"
+print " ... translating to ${RAW_EXP_IDS[$1]}@$3 to ${RAW_EXP_IDS[$2]}@$4"
+
+#exit 0
+
+
+
+##############################
+# Load the required functions
+# function_Read_request_config: read data request / user configuration and initialize the if_requested check
+# function_if_requested: checks if the currently processed variable is requested for the current timestep
+# function_find_file: searches for inputfiles
+##############################
+. $fpath/function_Read_request_config_palmod
+. $fpath/function_if_requested
+. $fpath/function_find_file
+
+#Load predefined timeslices (depends on $iniyear/$finyear)
+. $cpath/TimeSlices.h
+
+##Additionally define custom TimeSlices
+## Example on how to define TimeSlices
+## format: YYYYMMDDHH-YYYYMMDDHH
+##
+#TimeSlices+=([custom1]=(1850010100-1850010100))
+#TimeSlices+=([custom2]=(1850010100-1850123124))
+##TimeSlice dependend on variable
+#TimeSlices+=([custom3]=(${iniyear}010100-${iniyear}123124))
+##TimeSlice dependend on arithmetics using variable
+#TimeSlices+=([custom4]=($((iniyear+121))010100-$((iniyear+150))123124))
+
+##Define SettingsContainer
+## The following Option 3hrtest will activate the listed 3hr variables and deactivate any other variable for the given member (= realisation)
+## The UserSettings for the given experiment have to contain the line:
+## Option: 3hrtest = True
+## or the setting will not be active!
+#SettingsContainer+=([3hrtest]=([3hr]=(clt hfls hfss pr prc ps rlds rlus rsds rsus tas tos uas vas)))
+#SettingsContainer[3hrtest]+=([${member}]=(${member}:False))
+
+#Define Settings for Requested_vars.conf
+ism=True # Produce PISM vars
+slm=True # Produce vilma vars
+
+#Initialize DataRequest/User Configuration for the if_requested function
+# This will read all SettingsContainers, TimeSlices and the configuration file
+rrc_option=-s
+[[ $DEBUG_LEVEL -ge 1 ]] && rrc_option=
+[[ $DEBUG_LEVEL -ge 2 ]] && rrc_option=-v
+rrc_option=-v
+
+
+#################################
+# Run agg, diag and cmor-rewrite
+#################################
+
+function run_agg
+{
+ # Loop over file output periods and load diagnostic script fragment
+ if $RUN_AGG; then
+
+ for y in $(seq ${par1} ${par2}); do
+
+ 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", $0 }')123124
+ l_chunk=$(echo $chunk | cut -d "-" -f1)
+ r_chunk=$(echo $chunk | cut -d "-" -f2)
+
+ l_chunk_year=${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 (legacy) $period (latest)"
+
+ # Clean up stdout/stderr from previous run of this script
+ errtemp_agg="${errdir_agg}${SUFFIX}${CLIMSUFFIX}/${RAW_EXP_IDS[$y]}/${RAW_EXP_IDS[$y]}_${period}"
+ mkdir -p ${errtemp_agg}
+ err="${errtemp_agg}/err${period}"
+ rm -f ${err}*
+
+ # Read input file
+ if [[ "${iniyeararr[$y]}" == "$period" ]]
+ then
+ echo "Reading from parent ${RAW_EXP_ID_PARENT[$y]} jsbach_T31GR30_11tiles_5layers_natural-veg_$period.nc"
+ input_file_jsbach=$INPUT_DIR_TRUNK/${RAW_EXP_ID_PARENT[$y]}/restart/topo/jsbach_T31GR30_11tiles_5layers_natural-veg_$period.nc
+ input_file_glac_fx=$INPUT_DIR_TRUNK/${RAW_EXP_ID_PARENT[$y]}/restart/topo/GLAC_$((period+9)).nc
+ input_file_glac=$INPUT_DIR_TRUNK/${RAW_EXP_ID_PARENT[$y]}/restart/topo/GLAC_$period.nc
+ input_file_topo=$INPUT_DIR_TRUNK/${RAW_EXP_ID_PARENT[$y]}/restart/topo/TOPO_$period.nc
+ else
+ echo "Reading from ${RAW_EXP_IDS[$y]} jsbach_T31GR30_11tiles_5layers_natural-veg_$period.nc"
+ input_file_jsbach=$INPUT_DIR_TRUNK/${RAW_EXP_IDS[$y]}/restart/topo/jsbach_T31GR30_11tiles_5layers_natural-veg_$period.nc
+ input_file_glac_fx=$INPUT_DIR_TRUNK/${RAW_EXP_IDS[$y]}/restart/topo/GLAC_$((period+9)).nc
+ input_file_glac=$INPUT_DIR_TRUNK/${RAW_EXP_IDS[$y]}/restart/topo/GLAC_$period.nc
+ input_file_topo=$INPUT_DIR_TRUNK/${RAW_EXP_IDS[$y]}/restart/topo/TOPO_$period.nc
+ fi
+
+ # Perform aggregation for each submodel
+ for submodel in $icemod $slmod $atmmod $ocemod $srfmod; do
+
+ if [[ "$submodel" == "$icemod" ]]; then
+ period=$(( inv_chunk_year - 10 ))
+ # perform time shift for selected variables
+ cdochain="-shifttime,-5year -shifttime,${finyear}year" # for decadal time intervals only!
+ elif [[ "$submodel" == "$slmod" ]]; then
+ period=$(( inv_chunk_year - 10 ))
+ # perform no time shift
+ cdochain=""
+ echo "--------- $period $period_bk $chunk"
+ else
+ period=$period_bk
+ # perform time shift for selected variables
+ cdochain="-shifttime,$((inioffsetarr[$y] - spinup))year -shifttime,-3day"
+ fi
+
+ # Chunking
+ [[ "${chunks[$submodel]}" == *" ${period: -1} "* ]] && {
+
+ # Show progress
+ print "$(date +%Y-%m-%dT%H:%M:%S): Aggregation started for ${RAW_EXP_IDS[$y]} $submodel $chunk ($period) ..."
+ sh -c 'scontrol update JobId=$SLURM_JOB_ID Comment="$*"' scomment aggr/${RAW_EXP_IDS[$y]}/$submodel/$period
+
+ # Location of input/output
+ sdir=${SDIR[$y]}/outdata/$submodel
+ rawsdir=${RAWSDIR[$y]}/outdata/$submodel
+ rawsdir_pism_ant=$(echo $rawsdir | rev | cut -d "/" -f 3- | rev)/PISM_ANT
+ rawsdir_pism_nh=$(echo $rawsdir | rev | cut -d "/" -f 3- | rev)/PISM_NH
+ echo "... writing output to $sdir/out_aggr"
+ echo "... writing log to $errtemp_agg"
+
+ # Create output dirs
+ mkdir -p ${sdir}/tmp_aggr
+ mkdir -p ${sdir}/out_aggr
+
+ # Create softlinks to raw model output - PISM requires special treatment
+ if [[ $submodel == "$icemod" ]]; then
+ #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" $((inv_chunk_year - 10)))/pism_-$(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 ; }
+ elif [[ $submodel == "vilma" ]]; then
+ if [[ "${chunks[${submodel}dec]}" == *" ${period: -1} "* ]]; then
+ ln -vsf $rawsdir/vilma_-$(printf "%06d" $((inv_chunk_year - 10)))/delta_rsl.nc $sdir/delta_rsl_${period_bk}.nc || echo "ERROR ln -vsf $rawsdir/vilma_-$(printf \"%06d\" $((inv_chunk_year - 10)))/delta_rsl.nc $sdir/delta_rsl_${period_bk}.nc"
+ fi
+ else
+ ln -sf $rawsdir/*_${period}* $sdir/ 2>/dev/null 1>&2 || { echo "ERROR creating links for $period ${RAW_EXP_IDS[$y]} $submodel" && exit 1 ; }
+ fi
+
+ # Load and run the aggr ScriptFragment
+ . ${SCRIPT_DIR}/palmod2_aggregation_${esmod}_${submodel}.h
+ wait
+ print "$(date +%Y-%m-%dT%H:%M:%S): Aggregation ended for ${RAW_EXP_IDS[$y]} $submodel $chunk ($period) ..."
+ }
+
+ done # submodel
+ done # period
+ done # EXP ID Index y
+ fi # if RUN_AGG
+}
+
+function run_diag
+{
+ # Loop over file output periods and load diagnostic script fragment
+ if $RUN_DIAGS; then
+ for y in $(seq ${par1} ${par2}); do
+
+ 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", $0 }')123124
+
+ l_chunk=$(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%??????}
+
+ inv_chunk_year=$(( 1 + ${finyear} - ${l_chunk_year##+(0)} ))
+
+ # Clean up stdout/stderr from previous run of this script
+ errtemp_diag="${errdir_diag}${SUFFIX}${CLIMSUFFIX}/${RAW_EXP_IDS[$y]}/${RAW_EXP_IDS[$y]}_${period}"
+ mkdir -p ${errtemp_diag}
+ err="${errtemp_diag}/err${period}"
+ rm -f ${err}*
+
+ # Perform diagnostic for each submodel
+ for submodel in $icemod $slmod $atmmod $ocemod $srfmod; do
+
+ if [[ "$submodel" == "$icemod" ]]; then
+ period=$(( inv_chunk_year - 10 ))
+ # perform time shift for selected variables
+ cdochain="-shifttime,-5year -shifttime,${finyear}year" # for decadal time intervals only!
+ elif [[ "$submodel" == "$slmod" ]]; then
+ period=$period_bk
+ # create time-axis
+ cdochain=""
+ else
+ period=$period_bk
+ # perform time shift for selected variables
+ cdochain="-shifttime,$((inioffsetarr[$y] - spinup))year -shifttime,-3day"
+ fi
+
+ # Chunking
+ [[ "${chunks[$submodel]}" == *" ${period: -1} "* ]] && {
+
+ # Show progress
+ print "$(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
+
+ #Location of input/output
+ sdir=${SDIR[$y]}/outdata/$submodel
+ rawsdir=${RAWSDIR[$y]}/outdata/$submodel
+ echo "... writing output to $sdir/out_diag"
+ echo "... writing log to $errtemp_diag"
+
+ # Diagnostic Output
+ mkdir -p ${sdir}/tmp_diag
+ mkdir -p ${sdir}/out_diag
+
+ # Load and run the diag ScriptFragment
+ . ${SCRIPT_DIR}/palmod2_diagnostic_${esmod}_${submodel}_auto.h
+ wait
+ print "$(date +%Y-%m-%dT%H:%M:%S): Diagnostic ended for ${RAW_EXP_IDS[$y]} $submodel $chunk ($period) ..."
+ }
+
+ done # submodel
+ done # period
+ done # EXP ID Index y
+ fi # if RUN_DIAG
+}
+
+function run_cmor
+{
+ # Loop over file output periods and load CMOR-Rewrite script fragment
+ if $RUN_CMOR; then
+
+ for y in $(seq ${par1} ${par2}); do
+
+ # Use working directory to hold .CHUNK and other tmp files
+ current_dir=${WORK_DIR[$y]}/cmor${SUFFIX}_${cmorstart}-${cmorend}${CLIMSUFFIX}
+ if [[ -e $current_dir ]] && [[ "$PROCESS_CLIM" == "false" ]]
+ then
+ if $USE_CHUNKS
+ then
+ warn "appending to existing chunk"
+ elif $REMOVE_CHUNKS
+ then
+ warn "moving chunk info to backup"
+ mkdir -p ${WORK_DIR[$y]}/backup
+ mv -v --backup=numbered $current_dir ${WORK_DIR[$y]}/backup
+ else
+ die "please check if cmor is running or has already been run for this chunk. Use --force to re-run"
+ fi
+ else
+ if $USE_CHUNKS
+ then
+ die "cannot find chunk info for appending"
+ fi
+ fi
+ mkdir -p $current_dir
+ previous_dir=$PWD
+ # Link gridinfo files
+ ln -sf $SCRIPT_DIR/gridinfo*nc $current_dir/
+ cd $current_dir
+
+ # Define DRS root dir
+ dr=$dr_trunk/cmor${SUFFIX}_${cmorstart}-${cmorend}${CLIMSUFFIX}
+ mkdir -p $dr
+
+ 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", $0 }')123124
+
+ l_chunk=$(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%??????}
+
+ inv_chunk_year=$(( 1 + ${finyear} - ${l_chunk_year##+(0)} ))
+
+ # Define decadal interval
+ dioce="$(( ${period} + ${inioffsetarr[$y]} - $spinup )),$(( ${period} + ${inioffsetarr[$y]} - $spinup + 9 ))"
+ disl=${l_chunk_year##+(0)},$(( ${l_chunk_year##+(0)} + 9 ))
+
+ # Clean up stdout/stderr from previous run of this script
+ errtemp_cmor="${errdir_cmor}${SUFFIX}${CLIMSUFFIX}/${RAW_EXP_IDS[$y]}/${RAW_EXP_IDS[$y]}_${period}"
+ mkdir -p ${errtemp_cmor}
+ err="${errtemp_cmor}/err${period}"
+ rm -f ${err}*
+
+ # Perform CMOR rewrite for each submodel
+ for submodel in $icemod $slmod $atmmod $ocemod $srfmod; do
+
+ if [[ "$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)},$(( ${l_chunk_year##+(0)} + 9 ))
+ elif [[ "$submodel" == "$slmod" ]]; then
+ period=$(( inv_chunk_year - 10 ))
+ # create time-axis
+ cdochain="-shifttime,$((inioffsetarr[$y] - spinup -5 ))year -shifttime,-3day"
+ di="$(( ${period_bk} + ${inioffsetarr[$y]} - 9 - $spinup )),$(( ${period_bk} + ${inioffsetarr[$y]} - $spinup ))"
+ else
+ period=$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]}" == *" ${period: -1} "* ]] && {
+
+ # Show progress
+ print "$(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
+
+ #Location of input/output
+ sdir=${SDIR[$y]}/outdata/$submodel
+ rawsdir=${RAWSDIR[$y]}/outdata/$submodel
+ echo "... writing output to $dr/$submodel"
+ echo "... writing log to $errtemp_cmor"
+
+ # Output
+ mkdir -p $dr/$submodel
+
+ #Location of Mapping table:
+ mt="${SCRIPT_DIR}/tables/${esmod}_${submodel}_${mip}_mapping.txt"
+
+ #Define cdocmorinfo
+ it="${it_temp},${ca[${submodel}]}"
+
+ # Load and run the CMOR-Rewrite ScriptFragment
+ . ${SCRIPT_DIR}/palmod2_cmor-rewrite_${esmod}_${submodel}_auto.h
+ wait
+ print "$(date +%Y-%m-%dT%H:%M:%S): CMORisation ended for ${RAW_EXP_IDS[$y]} $submodel $chunk ($period) ..."
+ }
+
+ done # submodel
+ done # period
+ cd $previous_dir
+ done # EXP ID Index y
+
+ # Run NCO ncatted cleanup of unappropriate/unnecessary attributes
+ # this is necessary since CMOR sets attributes necessary only for CMIP6
+ # that are unnecessary/wrong for PalMod
+ post_nco
+
+ fi # if RUN_CMOR
+}
+
+function post_nco {
+
+print "$(date +%Y-%m-%dT%H:%M:%S): NCO cleanup started for $dr"
+# Load nco
+#module load nco || { echo "Oops: Could not load NCO!" && exit 1 ; }
+
+# Post Processing with ncatted
+#Find netCDF files in DRS directory
+flist=( $( find $dr -name "*.nc" -type f | sort ) )
+
+#Loop and run ncatted
+echo "-> Looping over ${#flist[@]} netCDF files!"
+for f in ${flist[@]}
+do
+ echo "... editing $f"
+ ncatted -O -h -a further_info_url,global,d,, $f && echo "... deleted 'further_info_url'." || echo "... failed (ERROR)"
+ [[ "$(basename $f)" == *"cen"* ]] && {
+ ncatted -O -h -a frequency,global,m,c,"cen" $f && echo "... changed frequency to 'cen'." || echo "... failed (ERROR)"
+ }
+done
+
+print "$(date +%Y-%m-%dT%H:%M:%S): NCO cleanup ended for $dr"
+
+}
+
+
+
+#Initialize DataRequest/User Configuration for the if_requested function
+# This will read all SettingsContainers, TimeSlices and the configuration file
+# Thereafter run aggregation, diagnostic, cmorization
+if $PROCESS_CLIM
+then
+ # Overwrite cmorstart/cmorend:
+ cmorstart=$iniyear
+ cmorend=$finyear
+
+ # Read settings for clim1
+ CLIMSUFFIX=_clim
+ Read_request_config $rrc_option AllExp ${cpath}/${mip}_requested_vars_AllExp_ISM_SLM${SUFFIX}${CLIMSUFFIX}.conf || die "error while reading request config"
+ # Run diag&cmor
+ run_diag
+ run_cmor
+
+ if [[ "$experiment" != "ssp"* ]]
+ then
+ # Reset Read_requested_config
+ l_linu=0
+ unset DreqSettings
+ unset SliceSettings
+ unset UserSettings
+ unset TimeSlicesBounds
+ unset PriorityOrder
+
+ # Read settings for clim2
+ CLIMSUFFIX=_clim2
+ Read_request_config $rrc_option AllExp ${cpath}/${mip}_requested_vars_AllExp_ISM_SLM${SUFFIX}${CLIMSUFFIX}.conf || die "error while reading request config"
+ # Run diag&cmor
+ run_diag
+ run_cmor
+ fi
+else
+ Read_request_config $rrc_option AllExp ${cpath}/${mip}_requested_vars_AllExp_ISM_SLM$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"
+ $RUN_CMOR && run_cmor || echo "Could not run cmor"
+ wait
+fi
+
+
+
+print "$(date +%Y-%m-%dT%H:%M:%S): $MESSAGE finished for $cmorstart-$cmorend$SUFFIX"
+
+# Update run dates and submit job scripts
+
+# $Id$
+
+
diff --git a/cmor/mpiesm/scripts/transient-deglaciation-interactive_r1i1p1f1-CR_cdocmorinfo b/cmor/mpiesm/scripts/transient-deglaciation-interactive_r1i1p1f1-CR_cdocmorinfo
new file mode 100644
index 0000000..84d2c8f
--- /dev/null
+++ b/cmor/mpiesm/scripts/transient-deglaciation-interactive_r1i1p1f1-CR_cdocmorinfo
@@ -0,0 +1,113 @@
+#
+# experiment info:
+#
+_CONTROLLED_VOCABULARY_FILE=PalMod2_CV.json
+_FORMULA_VAR_FILE=PalMod2_formula_terms.json
+_AXIS_ENTRY_FILE=PalMod2_coordinate.json
+CONVENTIONS="CF-1.7 PalMod-2.0"
+TITLE="MPI-ESM1-2-1 output prepared for PalMod2"
+_history_template="%s ; CMOR rewrote data to be consistent with <activity_id>, <Conventions> and CF standards."
+
+EXPERIMENT_ID=transient-deglaciation-interactive
+EXPERIMENT="synchronously coupled transient deglaciation with interactive ice sheets and solid earth"
+#Specify VARIANT_LABEL explicitly or realization_index, physics_index, initialization_index and forcing_index:
+VARIANT_LABEL=r1i1p1f1
+REALIZATION_INDEX=1
+INITIALIZATION_INDEX=1
+PHYSICS_INDEX=1
+FORCING_INDEX=1
+VARIANT_INFO="The data are from a synchronously coupled model simulation of the last deglaciation with the MPI-ESM1.2.1-CR-mPISM-VILMA setup, hence, including interactive ice sheets and solid earth components. The simulation used climatological volcanic forcing representing PI. GHG forcing is after Koehler et al. (2017), Orbit after Berger (1978)."
+COMMENT="Earth viscosity configuration for the solid earth model VILMA. The vertical viscosity structure is piecewise constant for the following specified layers of the earth: (1) 0 to 3.480000e+06 m from earth core: 1.000000e+19 Pa s. (2) 3.480000e+06 to 5.701000e+06 m from earth core: 1.000000e+22 Pa s. (3) 5.701000e+06 to 6.291000e+06 m from earth core: 4.000000e+20 Pa s. (4) 6.291000e+06 to 6.371000e+06 m from earth core: 1.000000e+30 Pa s."
+ACTIVITY_ID=PalMod2
+#MIP_ERA=PalMod2 #ONLY CMIP6
+PROJECT_ID=PalMod2
+REQUIRED_TIME_UNITS="days since 1-1-1 00:00:00"
+#FURTHER_INFO_URL="https://furtherinfo.es-doc.org/<mip_era>.<institution_id>.<source_id>.<experiment_id>.<sub_experiment_id>.<variant_label>
+#Branch Info: If needed use the following 2 attributes to define the branch time
+# in Parent_Time_Units and Required_Time_Units (=child)
+# else use BRANCH_DATES to give the dates in YYYYMMDD,YYYYMMDD format
+#BRANCH_TIME_IN_PARENT=
+#BRANCH_TIME_IN_CHILD=
+#BRANCH_DATES=19000101,18500101
+#BRANCH_METHOD="standard"
+#PARENT_MIP_ERA=none #ONLY CMIP6
+#PARENT_ACTIVITY_ID=none
+#PARENT_EXPERIMENT=none
+#cmip6-spinup-HR
+#PARENT_EXPERIMENT_ID=none
+#PARENT_SOURCE_ID=none
+#PARENT_TIME_UNITS="days since 1850-1-1 00:00:00"
+#PARENT_VARIANT_LABEL=none
+SUB_EXPERIMENT_ID=none
+SUB_EXPERIMENT=none
+#
+#model info:
+#
+SOURCE_ID=MPI-ESM1-2-1-CR
+#MODEL_ID=MPI-ESM1-2-1-CR
+REFERENCES="The paper ist currently in open discussion under the following citation:\nMikolajewicz, U., Kapsch, M.-L., Schannwell, C., Six, K. D., Ziemen, F. A., Bagge, M., Baudouin, J.-P., Erokhina, O., Gayler, V., Klemann, V., Meccia, V. L., Mouchet, A., and Riddick, T.: Deglaciation and abrupt events in a coupled comprehensive atmosphere–ocean–ice sheet–solid earth model, Clim. Past Discuss. [preprint], https://doi.org/10.5194/cp-2024-55, in review, 2024"
+SOURCE="MPI-ESM1.2.1-CR (2022): \naerosol: none, prescribed Kinne (2010)\natmos: ECHAM6.3 (spectral T31; 96 x 48 longitude/latitude; 31 levels; top level 10 hPa)\natmosChem: none\nland: JSBACH3.20\nlandIce: none/prescribed\nocean: MPIOM1.63 (bipolar GR3.0, approximately 300km; 122 x 101 longitude/latitude; 40 levels; top grid cell 0-15 m)\nocnBgchem: none\nseaIce: unnamed (thermodynamic (Semtner zero-layer) dynamic (Hibler 79) sea ice model)\nsolidLand: none/prescribed"
+SOURCE_TYPE="AOGCM ISM SLM"
+#CALENDAR=proleptic_gregorian
+#MAPPING_TABLE_DIR=cmip6_mapping_tables
+#MAPPING_TABLE=MPIESM1_CMIP6.txt
+#GRID_FILE_DIR=__GRID_FILE_DIR
+#GRID_FILE=__GRID_FILE
+GRID=gn
+GRID_LABEL=gn
+#NOMINAL_RESOLUTION read from external file
+#For MPIOM/HAMOCC CR / GR30
+#NOMINAL_RESOLUTION="500 km"
+#For ECHAM6/JSBACH CR / T31
+#NOMINAL_RESOLUTION="500 km"
+CHAR_AXIS_TYPELICE="ice_free_land","ice_sheet","floating_ice","ice_free_sea"
+CHAR_AXIS_VEGTYPE=bare_land,glacier,tropical_evergreen_trees,tropical_deciduous_trees,extra-tropical_evergreen_trees,extra-tropical_deciduous_trees,raingreen_shrubs,deciduous_shrubs,C3_grass,C4_grass,C3_pasture,C4_pasture,C3_crops,C4_crops
+CHAR_AXIS_SOILPOOLS=acid-soluble_below_ground_leaf_litter,acid-soluble_below_ground_woody_litter,water-soluble_below_ground_leaf_litter,water-soluble_below_ground_woody_litter,ethanol-soluble_below_ground_leaf_litter,ethanol-soluble_below_ground_woody_litter,non-soluble_below_ground_leaf_litter,non-soluble_below_ground_woody_litter,humus_from_leaf_litter,humus_from_woody_litter
+CHAR_AXIS_LANDUSE=primary_and_secondary_land,crops,pastures,urban
+CHAR_AXIS_BASIN=global_ocean,atlantic_arctic_ocean,indian_pacific_ocean
+CHAR_AXIS_OLINE=barents_opening,bering_strait,canadian_archipelago,denmark_strait,drake_passage,english_channel,pacific_equatorial_undercurrent,faroe_scotland_channel,florida_bahamas_strait,fram_strait,iceland_faroe_channel,indonesian_throughflow,mozambique_channel,taiwan_luzon_straits,windward_passage
+CHAR_AXIS_SILINE=barents_opening,bering_strait,canadian_archipelago,fram_strait
+#spectband for the 3 aeropt variables
+CHAR_AXIS_SPECTBAND_aeroptbnd=1818182
+CHAR_AXIS_SPECTBAND_aeroptbnd_BOUNDS=2262443,1600000
+CHAR_AXIS_SPECTBAND_aeroptbnd_UNITS="m-1"
+CHAR_AXIS_SPECTBAND_aerssabnd=1818182
+CHAR_AXIS_SPECTBAND_aerssabnd_BOUNDS=2262443,1600000
+CHAR_AXIS_SPECTBAND_aerssabnd_UNITS="m-1"
+CHAR_AXIS_SPECTBAND_aerasymbnd=1818182
+CHAR_AXIS_SPECTBAND_aerasymbnd_BOUNDS=2262443,1600000
+CHAR_AXIS_SPECTBAND_aerasymbnd_UNITS="m-1"
+# 2d-spectband for the albedos
+CHAR_AXIS_SPECTBAND_albdirbnd=3225689,766690
+CHAR_AXIS_SPECTBAND_albdirbnd_BOUNDS=5000000,1451379,1451379,82001
+CHAR_AXIS_SPECTBAND_albdirbnd_UNITS="m-1"
+CHAR_AXIS_SPECTBAND_albdiffbnd=3225689,766690
+CHAR_AXIS_SPECTBAND_albdiffbnd_BOUNDS=5000000,1451379,1451379,82001
+CHAR_AXIS_SPECTBAND_albdiffbnd_UNITS="m-1"
+CHAR_AXIS_SPECTBAND_solbnd=1818182
+CHAR_AXIS_SPECTBAND_solbnd_BOUNDS=2262443,1600000
+CHAR_AXIS_SPECTBAND_solbnd_UNITS="m-1"
+#T_AXIS="cmip" causes the time axis to be rewritten according to the requested time stamps
+T_AXIS="cmip"
+#OUTPUT_MODE="r"
+OUTPUT_MODE="a"
+MAX_SIZE=0
+SAVE_CHUNK="n"
+#For files without time axis, if one is requested:
+#firsttimeval=1 (1850-01-02 00:00:00 wenn days since 1850-01-01 00:00:00)
+FIRSTTIMEVAL=1
+#
+# institution and contact info:
+#
+# none of these can be set in the command line
+#
+DEFLATE_LEVEL=1
+CONTACT=palmod2-mpi-esm@dkrz.de
+#
+# MPI-M
+#
+INSTITUTION_ID=MPI-M
+INSTITUTION="Max Planck Institute for Meteorology, Hamburg 20146, Germany"
+LICENSE="PalMod2 model data produced by MPI-M is licensed under a Creative Commons Attribution ShareAlike 4.0 International License (https://creativecommons.org/licenses). The data producers and data providers make no warranty, either express or implied, including, but not limited to, warranties of merchantability and fitness for a particular purpose. All liabilities arising from the supply of the information (including any liability arising in negligence) are excluded to the fullest extent permitted by law."
+#MIP_TABLE_DIR="/pool/data/CMIP6/cmip6-cmor-tables/Tables/"
+MIP_TABLE_DIR="/work/bm0021/PalMod2/cmor_tables/"
--
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