Changeset 9048

Timestamp:

2017-12-14T14:40:24+01:00 (5 years ago)

Author:

timgraham

Message:

New version of rebuild_nemo

Location:

branches/2017/dev_merge_2017/NEMOGCM/TOOLS/REBUILD_NEMO

Files:

• BATCH_TEMPLATES (copied) (copied from branches/UKMO/dev_r7681_rebuild_nemo/NEMOGCM/TOOLS/REBUILD_NEMO/BATCH_TEMPLATES)
• rebuild_nemo (modified) (5 diffs)
• src/rebuild_nemo.F90 (copied) (copied from branches/UKMO/dev_r7681_rebuild_nemo/NEMOGCM/TOOLS/REBUILD_NEMO/src/rebuild_nemo.F90)
• src/rebuild_nemo.f90 (deleted)

branches/2017/dev_merge_2017/NEMOGCM/TOOLS/REBUILD_NEMO/rebuild_nemo

@@ -1 +1 @@
 #!/bin/ksh
-#
-#  Script to run the NEMO rebuild tool to rebuild NEMO
-#  diagnostic or restart files.
-#
-#  The scripts creates the nam_rebuild namelist based upon
-#  the command line options you give it (see usage below)
-#
-#  Ed Blockley, September 2011
-#
-#
+
+# CALLS: rebuild_nemo.exe
 
 #set -ax
@@ -18 +10 @@
    echo "  ************"
    echo
-   echo "  usage: ${0##*/} [-t -c] filebase ndomain [rebuild dimensions]"
+   echo "  usage: ${0##*/} [-l -t -c -m -n] filebase ndomain [rebuild dimensions]"
    echo
-   echo "  flags:  -t num      use num threads"
-   echo "          -c num      split 4D vars into time chuncks of size num"
+   echo "  flags:    -l                 submit to compute node"
+   echo "            -t num             use num threads"
+   echo "            -c num             split 4D vars into time chuncks of size num"
+   echo "            -m                 force masking of global arrays (zero if no mdi)"
+   echo "            -d deflate_level   deflate level for output files (key_netcdf4 only)"
+   echo "            -n namelist        full path to namelist file to be created (otherwise default nam_rebuild+_process_id is used)"
+   echo "            -r memory          Memory to request on compute node including units (Default = 10Gb)"
    echo
    exit 1
 }
 
-while getopts c:t: opt
+while getopts c:n:t:d:r:lm opt
 do
   case ${opt} in
+      l) 
+         BATCH="yes"
+         BATCH_CMD="qsub" 
+         ARCH="XC40_METO"
+         echo "Submitting job to compute node"
+      ;;
       t)
          OMP_NUM_THREADS=${OPTARG}
@@ -35 +38 @@
          NCHUNKSIZE=${OPTARG}
       ;;
+      m) 
+         NMASK="TRUE"
+         echo "mask"
+      ;;
+      d)
+         DEFLATE=${OPTARG}
+      ;;
+      n)
+         nam_rebuild=${OPTARG}
+      ;;
+      r)
+         MEMORY=${OPTARG}
+      ;;
   esac
 done
 shift $(expr ${OPTIND} - 1)
 
-if [[ $# < 2 ]] ; then
+if [[ $# -lt 2 ]] ; then
    usage
 fi
@@ -49 +65 @@
 DIM1=$3
 DIM2=$4
-export OMP_NUM_THREADS=${OMP_NUM_THREADS:-16}
+export OMP_NUM_THREADS=${OMP_NUM_THREADS:-1}
+nam_rebuild=${nam_rebuild:-nam_rebuild_$$}
+MEMORY=${MEMORY:-10Gb}
+
+#Find out the maximum number of files that can be opened and increase if necessary)
+nopen=$(ulimit -n)
+if [[ $ndomain -gt $nopen ]] ; then
+  nopen=$((ndomain+2))
+fi
 
 if [[ -n ${DIM1} && -n ${DIM2} ]] ; then
    dim_str=" dims '${DIM1}','${DIM2}'"
    dims="dims='${DIM1}','${DIM2}'"
-   echo ${dim_str} >> nam_rebuild
 fi
 
 echo "file ${file},  num_domains ${ndomain}, num_threads ${OMP_NUM_THREADS}${dim_str}"
 
-cat > nam_rebuild << EOC
+cat > $nam_rebuild << EOC
 &nam_rebuild
 filebase='${file}'
@@ -65 +88 @@
 EOC
 if [[ -n ${dims} ]] ; then
-   echo ${dims} >> nam_rebuild
+   echo ${dims} >> $nam_rebuild
 fi
 if [[ -n ${NCHUNKSIZE} ]] ; then
-   echo " nchunksize=${NCHUNKSIZE}" >> nam_rebuild
+   echo " nchunksize=${NCHUNKSIZE}" >> $nam_rebuild
 fi
-echo "/" >> nam_rebuild
+if [[ -n ${NMASK} ]] ; then
+   echo " l_maskout=.true." >> $nam_rebuild
+fi
+if [[ -n ${DEFLATE} ]] ; then
+   echo " deflate_level=${DEFLATE}" >> $nam_rebuild
+fi
 
-# run the rebuild code
-${script_dir}/rebuild_nemo.exe 
+echo "/" >> $nam_rebuild
+
+if [[ ${BATCH} == "yes" ]] ; then
+   batch_file=rebuild_nemo_batch_${ARCH}
+
+   #Create a modified local copy of the batch submission file
+   #The process ID is appended to the end of the file name so it is unique
+   cat ${script_dir}/BATCH_TEMPLATES/${batch_file} | sed -e"s/NTHREADS/${OMP_NUM_THREADS}/" \
+      -e"s/MEMORY/${MEMORY}/" \
+      -e"s:INDIR:${script_dir}:" \
+      -e"s/NOPEN/${nopen}/" \
+      -e"s/NAMELIST/${nam_rebuild}/" > ${batch_file}_$$.sh
+   
+   #Submit the job
+   $BATCH_CMD ${batch_file}_$$.sh
+
+else
+   ulimit -n $nopen
+   ${script_dir}/rebuild_nemo.exe $nam_rebuild
+fi
+