NorESMhub · TomasTorsvik · May 16, 2025
diff --git a/README.md b/README.md
@@ -5,6 +5,7 @@ Miscellaneous pre- and post-processing scripts for NorESM
     - mg_budget_plot.py: Script for plotting the the tendency terms that contribute to the total tendencies of the cloud microphysics scheme by Morrison and Gettelman in NorESM2/CAM6
 - PostProc: Scripts for post processing model output
     - rcat_noresm.sh: Concatenate and compress NorESM model output
+- RunScript: sample run scripts
 - Utilities: Miscellaneous scripts and programs
     - buildCPRNC_NIRD.sh: File to build the cprnc tool needed by rcat_noresm.sh
     - test_rcat_noresm.sh: Unit tests for rcat_noresm.sh
diff --git a/RunScript/run_noresm/run_noresm3.sh b/RunScript/run_noresm/run_noresm3.sh
@@ -0,0 +1,253 @@
+#!/usr/bin/env bash
+set -eu -o pipefail; shopt -s failglob
+
+## Account settings
+PROJECT="nn9560k"    # Where source code is located
+ACCOUNT="nn9560k"    # Who pays for CPU hours
+## See .../query_testlists --list machine
+MACHINE=${MACHINE:-"betzy"}
+## See .../query_testlists --list compiler
+COMPILER=${COMPILER:-"intel"}
+
+## What base tag version of NorESM are we testing
+TAG=${TAG:-"noresm3_0_alpha03b"}
+SRC_LABEL=${TAG}
+
+## LABEL is the case name that will be used for the test
+LABEL=${LABEL:-"3.0a03b"}
+
+## Case label (overwrite)
+LABEL="rest-NOIIAJRARYF6162OC_20250506.${LABEL}"
+#LABEL="hybrid_fates-nocomp.${LABEL}"
+# LABEL="hybrid_fatesnocomp.${LABEL}"
+timestamp=$(date +"%Y%m%d")
+
+## Compset long name
+CSHORT=${CSHORT:-"n1850"}
+CTIME=${CTIME:-"1850"}
+CATM=${CATM:-"CAM70%LT%NORESM%CAMoslo"}
+#CLND=${CLND:-"CLM60%FATES-NOCOMP"}
+CLND=${CLND:-"CLM60%FATES"}
+CICE=${CICE:-"CICE"}
+COCE=${COCE:-"BLOM%HYB%ECO"}
+CROF=${CROF:-"MOSART"}
+CGLC=${CFLC:-"DGLC%NOEVOLVE"}
+CWAV=${CWAV:-"SWAV"}
+COMPSET=${COMPSET:-"${CTIME}_${CATM}_${CLND}_${CICE}_${COCE}_${CROF}_${CGLC}_${CWAV}_SESP"}
+
+## Resolution
+RES=${RES:-"ne30pg3_tn14"}
+RES_LABEL=${RES_LABEL:-"ne30_tn14"}
+
+## Component settings
+## BLOM_TAG: This can be either a tag or a branch
+##    tag: "<tag_name>"
+##    branch: "develop/<branch_name>"
+## BLOM_REPO: source for development version, either url to remote
+##            repository or local path
+BLOM_DEVELOP="no"
+if [ "${BLOM_DEVELOP}" == "yes" ]; then
+    #BLOM_LABEL=${BLOM_LABEL:-"output_switches"}
+    #BLOM_LABEL=${BLOM_LABEL:-"master"}
+    #BLOM_TAG=${BLOM_TAG:-"${BLOM_LABEL}"}           # Use this for tags
+    #BLOM_TAG=${BLOM_TAG:-"develop/${BLOM_LABEL}"}   # Use this for branches
+    BLOM_REPO=${BLOM_REPO:-"https://github.com/NorESMhub/BLOM"}
+    #BLOM_REPO=${BLOM_REPO:-"https://github.com/TomasTorsvik/BLOM-TTfork"}
+    #BLOM_REPO=${BLOM_REPO:-"https://github.com/jmaerz/BLOM"}
+    SRC_LABEL="${SRC_LABEL}.BLOM-${BLOM_LABEL}"
+fi
+
+## Decide if you run model in debug mode
+## - Debug flags enabled
+RUN_DEBUG_MODE="no"
+
+## Decied if we run with the --run-unsupported flag
+## This should be used for compsets for which there are no
+## science supported experiments available
+RUN_UNSUPPORTED="yes"
+
+## Decide whether or not to run manage_externals/checkout_externals
+## While this is not perfect, it works if used consistently
+## NB: If you check out the target tag from outside the script,
+## be sure to run checkout_externals yourself, this script might
+## miss it.
+RUN_CHECKOUT="no"
+
+## Source and case directories
+REPO=${REPO:-"https://github.com/NorESMhub/NorESM"}
+SRCROOT="/cluster/projects/${PROJECT}/${USER}/NorESM/src/${SRC_LABEL}"
+CASEROOT="/cluster/projects/${PROJECT}/${USER}/NorESM/cases"
+CASENAME="${CSHORT}.${RES_LABEL}.${LABEL}.${timestamp}"
+CASEDIR="${CASEROOT}/${CASENAME}"
+RUNDIR="/cluster/work/users/${USER}/noresm/${CASENAME}/run/"
+
+## Include usermods?
+USE_USERMODS="yes"
+if [ "${USE_USERMODS}" == "yes" ]; then
+    USERMODS="${SRCROOT}/cime_config/usermods_dirs/reduced_out_devsim/"
+fi
+
+# Copy this run script to CASEDIR
+COPY_THIS_FILE="yes"
+this_file="${PWD}/"; this_file+=$(basename "$0")
+echo "Running ${this_file}"
+
+
+##--- Function: Check for execution errors ---
+perror() {
+    ## Print an error message and exit if a non-zero error code is passed
+    if [ $1 -ne 0 ]; then
+        echo "ERROR (${1}): ${2}"
+        exit $1
+    fi
+}
+
+##--- Checkout model source code ---
+## (make sure that clone exists, otherwise, clone REPO)
+if [ ! -d "${SRCROOT}" ]; then
+    git clone -o NorESM ${REPO} ${SRCROOT}
+    perror $? "running 'git clone -o NorESM ${REPO} ${SRCROOT}'"
+    RUN_CHECKOUT="yes"
+fi
+
+## Ensure correct source is checked out
+cd ${SRCROOT}
+if [ "${RUN_CHECKOUT}" != "no" ]; then
+    if [ "$( git describe )" != "${TAG}" ]; then
+        git checkout ${TAG}
+        perror $? "running 'git checkout ${TAG}'"
+    fi
+
+    #--- Checkout TAG version ---
+    ./bin/git-fleximod update
+    perror $? "running './bin/git-fleximod update'"
+
+    #--- Checkout BLOM development version ---
+    if [ "${BLOM_DEVELOP}" == "yes" ]; then
+        cd components/blom
+        ## Remove old "develop" repo if present
+        if git config remote.develop.url > /dev/null; then
+            git remote rm develop
+        fi
+        git remote add develop ${BLOM_REPO}
+        git fetch --all
+        git fetch --tags --all
+        git checkout --detach ${BLOM_TAG}
+        git submodule update
+        cd ${SRCROOT}
+    fi
+fi
+
+
+##--- Create your case
+cd ${SRCROOT}
+if [ ! -d "${CASEDIR}" ]; then
+    ## Only run create_newcase if the case does not exist
+    echo "=== Creating new case ==="
+    cn_args=" --case ${CASEDIR} --compset ${COMPSET} --res ${RES} --project ${ACCOUNT} --machine ${MACHINE} --compiler ${COMPILER}"
+    if [ "${RUN_UNSUPPORTED}" == "yes" ]; then
+        cn_args="${cn_args} --run-unsupported"
+    fi
+    if [ "${USE_USERMODS}" == "yes" ]; then
+        cn_args="${cn_args} --user-mods-dir ${USERMODS}"
+    fi
+    ./cime/scripts/create_newcase ${cn_args}
+    perror $? "running './cime/scripts/create_newcase ${cn_args}'"
+fi
+
+
+## Move to your case directory
+cd ${CASEDIR}
+perror $? "trying 'cd ${CASEDIR}'"
+if [ "${COPY_THIS_FILE}" == "yes" ]; then
+    cp ${this_file} ${CASEDIR}
+    perror $? "running 'cp ${this_file} ${CASEDIR}'"
+fi
+
+
+## Copy noresm setup files
+#NORESM_SETUP_DIR="/cluster/projects/nn9560k/tomast/NorESM/src/"
+#cp -r ${NORESM_SETUP_DIR}/SourceMods/hybrid_wavparam_fatessp/* ./SourceMods/
+
+
+## Any PE changes must go here
+./xmlchange NTASKS=1920
+./xmlchange NTASKS_OCN=256
+./xmlchange ROOTPE=0
+./xmlchange ROOTPE_OCN=1920
+
+## Set up the case as configured so far
+echo "=== Setup for new case ==="
+./case.setup
+perror $? "trying './case.setup'"
+
+## Changes that affect the build go here
+./xmlchange STOP_OPTION=nyears
+./xmlchange STOP_N=4
+./xmlchange REST_N=1
+./xmlchange REST_OPTION=nyears
+./xmlchange RESUBMIT=0
+./xmlchange --subgroup case.run JOB_WALLCLOCK_TIME=48:00:00
+./xmlchange --subgroup case.st_archive JOB_WALLCLOCK_TIME=03:00:00
+
+## Changes to user_nl_* files goes here
+cat <<EOF >> user_nl_cam
+use_aerocom = .false.
+interpolate_nlat   = 192
+interpolate_nlon   = 288
+interpolate_output = .true.
+history_aerosol = .false.
+zmconv_c0_lnd  =  0.0075D0
+zmconv_c0_ocn  =  0.0300D0
+zmconv_ke =  5.0E-6
+zmconv_ke_lnd =  1.0E-5
+clim_modal_aero_top_press =  1.D-4
+micro_mg_dcs = 600.D-6
+bndtvg = '/cluster/shared/noresm/inputdata/atm/cam/ggas/noaamisc.r8.nc'
+EOF
+perror $? "adding variables to user_nl_cam"
+
+
+# cat <<EOF >> user_nl_blom
+# ICFILE = "/cluster/shared/noresm/inputdata/restart/NOIIAJRAOC20TR_TL319_tn14_ppm_20240816/rest/1775-01-01-00000/NOIIAJRAOC20TR_TL319_tn14_ppm_20240816.blom.r.1775-01-01-00000.nc"
+# EOF
+# cat <<EOF >> user_nl_blom
+# ICFILE = "/cluster/shared/noresm/inputdata/restart/NOIIAJRAOC_TL319_tn14_3.0a3_newmix_20250430/rest/0062-01-01-00000/NOIIAJRAOC_TL319_tn14_3.0a3_newmix_20250430.blom.r.0062-01-01-00000.nc"
+# EOF
+cat <<EOF >> user_nl_blom
+ICFILE = "/cluster/shared/noresm/inputdata/restart/NOIIAJRARYF6162OC.TL319_tn14.3.0a03a.20250506/rest/1774-01-01-00000/NOIIAJRARYF6162OC.TL319_tn14.3.0a03a.20250506.blom.r.1774-01-01-00000.nc"
+EOF
+perror $? "adding variables to user_nl_blom"
+
+# cat <<EOF >> user_nl_cice
+# ice_ic = "/cluster/shared/noresm/inputdata/restart/NOIIAJRAOC20TR_TL319_tn14_ppm_20240816/rest/1775-01-01-00000/NOIIAJRAOC20TR_TL319_tn14_ppm_20240816.cice.r.1775-01-01-00000.nc"
+# EOF
+# cat <<EOF >> user_nl_cice
+# ice_ic = "/cluster/shared/noresm/inputdata/restart/NOIIAJRAOC_TL319_tn14_3.0a3_newmix_20250430/rest/0062-01-01-00000/NOIIAJRAOC_TL319_tn14_3.0a3_newmix_20250430.cice.r.0062-01-01-00000.nc"
+# EOF
+cat <<EOF >> user_nl_cice
+ice_ic = "/cluster/shared/noresm/inputdata/restart/NOIIAJRARYF6162OC.TL319_tn14.3.0a03a.20250506/rest/1774-01-01-00000/NOIIAJRARYF6162OC.TL319_tn14.3.0a03a.20250506.cice.r.1774-01-01-00000.nc"
+EOF
+perror $? "adding variables to user_nl_cice"
+
+cat <<EOF >> user_nl_clm
+use_fates_nocomp = .true.
+use_fates_fixed_biogeog = .true.
+use_fates_luh = .false.
+fates_radiation_model = 'twostream'
+finidat = '/cluster/work/users/kjetisaa/archive/i1850.FATES-NOCOMP-noLU_cal15_twosteam.ne30pg3_tn14.noresm3_0_alpha01.20250326/rest/0101-01-01-00000/i1850.FATES-NOCOMP-noLU_cal15_twosteam.ne30pg3_tn14.noresm3_0_alpha01.20250326.clm2.r.0101-01-01-00000.nc'
+fates_history_dimlevel = 1,1
+EOF
+perror $? "adding variables to user_nl_clm"
+
+
+## Build and submit case
+echo "=== Build the case ==="
+./preview_namelists
+./case.build
+perror $? "trying './case.build'"
+
+
+echo "=== Submit the case ==="
+./case.submit
+perror $? "trying './case.submit'"