Modification to ICL hpc helper scripts.

Author: madDipanjan

tools/hpc_execute.sh

@@ -22,7 +22,7 @@ set -e
 if (( $# < 1 ))
 then
  echo "The experiment directory must be set."
- echo "usage: FROM THE TOP LEVEL DIRECTORY run: bash ./u-dales/tools/hpc_execute.sh <PATH_TO_CASE>"
+ echo "usage: FROM THE TOP LEVEL DIRECTORY run: u-dales/tools/hpc_execute.sh <PATH_TO_CASE>"
  exit 1
 fi
 
@@ -53,7 +53,7 @@ if [ -z $DA_BUILD ]; then
     exit 1
 fi;
 if [ -z $DA_TOOLSDIR ]; then
-    echo "Script directory DA_TOOLSDIR must be set inside $outdir/config.sh"
+    echo "Script directory DA_TOOLSDIR must be set inside $inputdir/config.sh"
     exit 1
 fi;
 if [ -z $NNODE ]; then
@@ -76,26 +76,23 @@ fi;
 ## set the output directory
 outdir=$DA_WORKDIR/$exp
 
-## copy files to execution and output directory
-mkdir -p $outdir
-cp -r $inputdir/* $outdir
-pushd $outdir
-
 echo "writing job.$exp."
 
 ## write new job.exp file for HPC
 cat <<EOF > job.$exp
 #!/bin/bash
 #PBS -l walltime=${WALLTIME}
 #PBS -l select=${NNODE}:ncpus=${NCPU}:mem=${MEM}
-module load intel/2025a netCDF/4.9.2-iimpi-2023a netCDF-Fortran/4.6.1-iimpi-2023a FFTW/3.3.9-intel-2021a CMake/3.29.3-GCCcore-13.3.0 git/2.45.1-GCCcore-13.3.0 NCO/5.2.9-foss-2024a GSL/2.8-GCC-13.3.0
+module load intel/2025a netCDF/4.9.2-iimpi-2023a netCDF-Fortran/4.6.1-iimpi-2023a FFTW/3.3.9-intel-2021a CMake/3.29.3-GCCcore-13.3.0 git/2.45.1-GCCcore-13.3.0
+mkdir -p $outdir
+cp -r $inputdir/* $outdir
+pushd $outdir
 mpiexec -n $(( $NCPU * $NNODE )) $DA_BUILD $outdir/namoptions.$exp > $outdir/output.$exp 2>&1
+module load NCO/5.2.9-foss-2024a GSL/2.8-GCC-13.3.0
 $DA_TOOLSDIR/gather_outputs.sh $outdir
 EOF
 
 ## submit job.exp file to queue
 qsub job.$exp
 
 echo "job.$exp submitted."
-
-popd

tools/hpc_gather.sh

@@ -21,62 +21,69 @@ set -e
 
 if (( $# < 1 ))
 then
- echo "The output case directory must be set."
- echo "usage: FROM THE TOP LEVEL DIRECTORY run: bash ./u-dales/tools/hpc_gather.sh <PATH_TO_OUTPUT_CASE>"
+ echo "The experiment directory must be set."
+ echo "usage: FROM THE TOP LEVEL DIRECTORY run: u-dales/tools/hpc_gather.sh <PATH_TO_CASE>"
  exit 1
 fi
 
-## go to output case directory
+## go to experiment directory
 pushd $1
-outdir=$(pwd)
+inputdir=$(pwd)
 
 ## set experiment number via path
-exp="${outdir: -3}"
+exp="${inputdir: -3}"
 
 echo "experiment number: $exp"
 
 ## read in additional variables
 if [ -f config.sh ]; then
     source config.sh
 else
-    echo "config.sh must be there inside $outdir"
+    echo "config.sh must be there inside $inputdir"
     exit 1
 fi
 
 ## check if required variables are set
+if [ -z $DA_WORKDIR ]; then
+    echo "Script directory DA_WORKDIR must be set inside $inputdir/config.sh"
+    exit 1
+fi;
 if [ -z $DA_TOOLSDIR ]; then
-    echo "Script directory DA_TOOLSDIR must be set inside $outdir/config.sh"
+    echo "Script directory DA_TOOLSDIR must be set inside $inputdir/config.sh"
     exit 1
 fi;
 if [ -z $NNODE ]; then
-    echo "Script directory NNODE must be set inside $outdir/config.sh"
+    echo "Script directory NNODE must be set inside $inputdir/config.sh"
     exit 1
 fi;
 if [ -z $NCPU ]; then
-    echo "Script directory NCPU must be set inside $outdir/config.sh"
+    echo "Script directory NCPU must be set inside $inputdir/config.sh"
     exit 1
 fi;
 if [ -z $WALLTIME ]; then
-    echo "Script directory WALLTIME must be set inside $outdir/config.sh"
+    echo "Script directory WALLTIME must be set inside $inputdir/config.sh"
     exit 1
 fi;
 if [ -z $MEM ]; then
-    echo "Script directory MEM must be set inside $outdir/config.sh"
+    echo "Script directory MEM must be set inside $inputdir/config.sh"
     exit 1
 fi;
 
+## set the output directory
+outdir=$DA_WORKDIR/$exp
+
+echo "writing post-job.$exp."
+
 ## write post-job.exp file for HPC
 cat <<EOF > post-job.$exp
 #!/bin/bash
 #PBS -l walltime=${WALLTIME}
 #PBS -l select=${NNODE}:ncpus=${NCPU}:mem=${MEM}
-module load intel/2024a netCDF/4.9.2-iimpi-2023a netCDF-Fortran/4.6.1-iimpi-2023a NCO/5.2.9-foss-2024a GSL/2.8-GCC-13.3.0
+module load NCO/5.2.9-foss-2024a GSL/2.8-GCC-13.3.0
 $DA_TOOLSDIR/gather_outputs.sh $outdir
 EOF
 
 ## submit post-job.exp file to queue
 qsub post-job.$exp
 
 echo "post-job.$exp submitted."
-
-popd