Cime compress namelist

CIME/Tools/noresm2netcdf4.sh

@@ -0,0 +1,85 @@
+#!/bin/bash -fvx
+# zip restart files?
+set -e 
+ZIPRES=1 
+
+# remove log files? 
+RMLOGS=0
+
+# Set script name
+sn=noresm2netcdf4
+
+# archive path of case
+ABASE=$1
+
+if [ ! -d $ABASE ]; then
+  echo "${sn}: ${ABASE} is not a directory." >&2
+  exit 1
+fi
+cd $ABASE
+
+# Set arguments
+nthreads=4
+
+# Set various variables
+ncdump=`which ncdump`
+nccopy=`which nccopy`
+complevel=5 # 1-9
+lid="`date +%y%m%d-%H%M%S`"
+
+# Functions 
+
+convert_cmd () {
+  echo convert $ncfile
+  rm -f ${ncfile}_tmp
+  set -e
+  ncks -a -h -O -4 -L $complevel $ncfile ${ncfile}_tmp
+  mv ${ncfile}_tmp ${ncfile}
+  chmod go+r ${ncfile}
+}
+
+compress_cmd () {
+  if [ $ZIPRES -eq 1 ] ; then 
+    echo zip $ncfile
+    gzip $ncfile
+    chmod go+r ${ncfile}.gz
+  fi
+}
+
+convert_loop () {
+  set -e
+  # loop over cases 
+  for ncfile in `find . -wholename '*/hist/*.nc' -print`; do
+    if [[ "`$ncdump -k $ncfile`" != 'netCDF-4' && "`$ncdump -k $ncfile`" != 'netCDF-4 classic model' ]] ; then
+      while :; do
+        if [ `jobs -p|wc -l` -lt $nthreads ]; then
+          convert_cmd &
+          break
+        fi
+        sleep 0.1s
+      done
+    fi
+  done
+  for ncfile in `find . -wholename '*/rest/*.nc' -print`; do
+      while :; do
+        if [ `jobs -p|wc -l` -lt $nthreads ]; then
+          compress_cmd & 
+          break
+        fi
+        sleep 0.1s
+      done
+  done
+  for logfile in `find . -wholename '*/logs/*' -print`; do
+      if [ $RMLOGS -eq 1 ] ; then 
+        rm -f $logfile
+      fi
+  done
+
+  wait
+  echo "${sn}: conversion completed."
+}
+
+# Execute the convert loop as a backgroud process
+echo `date` > $ABASE/archive.log.$lid
+convert_loop >> $ABASE/archive.log.$lid 
+echo `date` >> $ABASE/archive.log.$lid

CIME/case/case.py

@@ -1671,6 +1671,7 @@ def _create_caseroot_tools(self):
             os.path.join(toolsdir, "xmlchange"),
             os.path.join(toolsdir, "xmlquery"),
             os.path.join(toolsdir, "pelayout"),
+            os.path.join(toolsdir, "noresm2netcdf4.sh"),
         )
         try:
             for exefile in exefiles:

CIME/case/case_st_archive.py

@@ -1077,6 +1077,20 @@ def case_st_archive(
                 )
             else:
                 self.submit(resubmit=True)
+    if self.get_value('COMPRESS_ARCHIVE_FILES'):
+        archiveroot = self.get_value('DOUT_S_ROOT')
+        convert='/noresm2netcdf4.sh'
+        cmd_convert=caseroot+convert
+        cmd="%s %s" %(cmd_convert,archiveroot)
+        logger.info("cmd={}".format(cmd))
+        run_cmd_no_fail(cmd)
+
+    if self.get_value('COPY_CASE_FOLDER'):
+        archiveroot = self.get_value('DOUT_S_ROOT')
+        sync='rsync -avh'
+        cmd="%s %s %s %s" %(sync,caseroot, archiveroot+'/case','>'+archiveroot+'/case.log')
+        logger.info("cmd={}".format(cmd))
+        run_cmd_no_fail(cmd)
 
     return True