some organization of drive-dates code in land spinup

.gitignore

@@ -43,6 +43,7 @@ perturb.*.nl
 nl.landspinup*
 !nl.landspinup.pm-cpu
 !nl.landspinup.derecho
+nl_dd.*
 
 ## Model namelists
 user_nl_cam

land-spinup/drive-dates.sh → land-spinup/drive-dates/drive-dates.sh

@@ -1,23 +1,31 @@
 #!/bin/bash
 
 set -e
-source ../utils.sh
-
-### Set vars here for now
-datesfile="dates.CHEY.VR28.NATL.REF.CAM5.4CLM5.0.dtime900.txt"
-CASEDIR="/global/homes/c/czarzyck/I-runs/ne128pg2-spinup_19840101_0000"
-path_to_rundir="/pscratch/sd/c/czarzyck/e3sm_scratch/pm-cpu/ne128pg2-spinup_19840101_0000/run"
-CIMEsubstring=""
-CIMEbatchargs=""
-betacast="/global/homes/c/czarzyck/betacast"
-WALLCLOCK="02:00:00"
-RUNQUEUE="regular"
-# Copy this last restart to a stash folder
-DIRSTASH=/global/cfs/cdirs/m2637/E3SM_SCREAM_files/finidat/ne128pg2/CHEY.VR28.NATL.REF.CAM5.4CLM5.0.dtime900/
-
-#--------
-
-cd $betacast/land-spinup/
+
+NAMELISTFILE=$1
+
+source ../../utils.sh
+
+# Read the namelist
+read_bash_nl "${NAMELISTFILE}"
+
+# Build relevant directories
+CASEDIR=$CASESRC/$CASENAME
+PATH_TO_RUNDIR=$BASERUN/$CASENAME/run/
+SCRIPTDIR=$BETACAST/land-spinup/drive-dates/
+
+echo $CASEDIR
+echo $PATH_TO_RUNDIR
+echo $SCRIPTDIR
+
+## Set defaults
+## Set these in your namelistfile if need to
+if [ -z "${CIMEsubstring+x}" ]; then CIMEsubstring=""; fi
+if [ -z "${CIMEbatchargs+x}" ]; then CIMEbatchargs=""; fi
+
+## Get to this directory
+cd $SCRIPTDIR
+
 # Parse dates file
 echo "Using dates in: "${datesfile}
 longdate=$(get_top_line_from_dates "${datesfile}")
@@ -31,15 +39,15 @@ cd $CASEDIR
 ./xmlchange --force JOB_QUEUE=${RUNQUEUE}
 ./xmlchange REST_OPTION="end"
 ./xmlchange STOP_DATE="$yearstr$monthstr$daystr"
-run_CIME2 "$path_to_rundir" "$CIMEsubstring" "$CIMEbatchargs" true
+run_CIME2 "$PATH_TO_RUNDIR" "$CIMEsubstring" "$CIMEbatchargs" true
 
 # Assuming run_CIME2 was successful, let's set CONTINUE_RUN to TRUE
 # this is because for a cold start we want FALSE, but every other run is TRUE
 # So there is no harm in doing this as long as the first run succeeds.
 ./xmlchange CONTINUE_RUN=TRUE
 
 # Copy restart files to some directory for stashing purposes
-cd $path_to_rundir
+cd $PATH_TO_RUNDIR
 
 # Assuming run was succesful, delete all other restarts except the last one
 delete_except_last "*.clm2.r.*,*.elm.r.*,*.elm.rh0.*,*.elm.rh1.*"
@@ -48,32 +56,11 @@ delete_except_last "*.cpl.r.*"
 
 echo "Done with delete_except_last"
 
+## Make stash directories if they don't exist
 if [ ! -d "$DIRSTASH" ]; then mkdir -v "$DIRSTASH"; fi
 if [ ! -d "$DIRSTASH/logs/" ]; then mkdir -v "$DIRSTASH/logs/"; fi
 
-function safe_cp2() {
-
-  local dest="$2"
-  # split on multiple input patterns if necessary
-  IFS=',' read -r -a patterns <<< "$1"
-
-  # Loop over all matching patterns
-  for pattern in "${patterns[@]}"; do
-
-    # Trim leading and trailing spaces from the pattern
-    pattern=$(echo "$pattern" | xargs)
-
-    # Collect all files matching the pattern, sorted
-    files=($(ls $pattern 2>/dev/null | sort))
-
-    if [ ${#files[@]} -eq 0 ]; then
-      echo "Error: ZERO files found matching pattern $pattern."
-    else
-      cp -v -- "${files[@]}" "$dest"
-    fi
-  done
-}
-
+## Copy relevant files over to dirstash, compress any uncompressed, and cleanup
 safe_cp2 "*.clm2.r.*,*.elm.r.*" $DIRSTASH
 safe_cp2 "*.mosart.r.*" $DIRSTASH
 for file in $DIRSTASH/*.nc; do
@@ -84,8 +71,8 @@ mv -fv *tar.gz $DIRSTASH/logs/
 rm -fv *.bin
 
 # Return to the script dir to do things and resubmit
-cd $betacast/land-spinup/
+cd $SCRIPTDIR
 remove_top_line_from_dates ${datesfile}
 
 echo "*-*-*-* Automatically resubbing next date!"
-exec ./drive-dates.sh
+exec ./drive-dates.sh "$NAMELISTFILE"

land-spinup/drive-dates/nl_dd.REF001.ne128pg2

@@ -0,0 +1,8 @@
+datesfile="dates.REF001.ne128pg2.txt"
+DIRSTASH="/global/cfs/cdirs/m2637/E3SM_SCREAM_files/finidat/ne128pg2/CHEY.VR28.NATL.REF.CAM5.4CLM5.0.dtime900/"
+CASENAME="ne128pg2-spinup_19840101_0000"
+CASESRC="/global/homes/c/czarzyck/I-runs/"
+BASERUN="/pscratch/sd/c/czarzyck/e3sm_scratch/pm-cpu/"
+BETACAST="/global/homes/c/czarzyck/betacast/"
+WALLCLOCK="02:00:00"
+RUNQUEUE="regular"

utils.sh

@@ -749,6 +749,32 @@ function delete_except_last() {
 }
 
 
+# Copy files given a set of patterns
+# Usage: safe_cp2 "*.clm2.r.*,*.elm.r.*" $DIRSTASH
+function safe_cp2() {
+
+  local dest="$2"
+  # split on multiple input patterns if necessary
+  IFS=',' read -r -a patterns <<< "$1"
+
+  # Loop over all matching patterns
+  for pattern in "${patterns[@]}"; do
+
+    # Trim leading and trailing spaces from the pattern
+    pattern=$(echo "$pattern" | xargs)
+
+    # Collect all files matching the pattern, sorted
+    files=($(ls $pattern 2>/dev/null | sort))
+
+    if [ ${#files[@]} -eq 0 ]; then
+      echo "Error: ZERO files found matching pattern $pattern."
+    else
+      cp -v -- "${files[@]}" "$dest"
+    fi
+  done
+}
+
+
 # Usage:
 # script_start=$(date +%s)
 # script_end=$(date +%s)