Merge branch 'master' of https://github.com/uDALES/u-dales into heatpump

Author: madDipanjan

.gitmodules

@@ -2,6 +2,7 @@
 	path = 2decomp-fft
 	url = https://github.com/uDALES/2decomp-fft.git
 
-[submodule "View3D"]
+[submodule "tools/View3D"]
 	path = tools/View3D
-	url = https://github.com/jasondegraw/View3D
+	url = https://github.com/uDALES/View3D.git
+	branch = master

tools/View3D

@@ -41,10 +41,10 @@ build_type=$2
 
 if [ $system == "icl" ]
 then
-    module load cmake/3.18.2 git/2.14.3 intel-suite/2020.2 mpi/intel-2019.8.254
+    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
     FC=mpiifort
-    NETCDF_DIR=/apps/netcdf/4.4.1-c
-    NETCDF_FORTRAN_DIR=/apps/netcdf/4.4.4-fortran
+    NETCDF_DIR=/sw-eb/software/netCDF/4.9.2-iimpi-2023a
+    NETCDF_FORTRAN_DIR=/sw-eb/software/netCDF-Fortran/4.6.1-iimpi-2023a
 
 elif [ $system == "archer" ]
 then

tools/build_executable.sh

@@ -40,29 +40,21 @@ if [ -f config.sh ]; then
 fi
 
 ## set the output directory
-outdir=$EPHEMERAL/$exp
+outdir=$DA_WORKDIR/$exp
 
 echo "writing job.$exp."
 
 ## write new job.exp file for HPC
-echo "#PBS -l walltime=${WALLTIME}" > job.$exp
-echo "#PBS -l select=${NNODE}:ncpus=${NCPU}:mem=${MEM}" >> job.$exp
-
-## load modules required for the execution
-echo "module load intel-suite/2017.6 mpi/intel-2018 cmake/3.14.0 git/2.14.3" >> job.$exp
-
-## copy files to execution and output directory
-echo "mkdir -p $outdir" >> job.$exp
-echo "cp -r $inputdir/* $outdir" >> job.$exp
-
-## go to execution and output directory
-echo "pushd $outdir" >> job.$exp
-
-## execute program with mpi
-echo "mpiexec -n $(( $NCPU * $NNODE )) $DA_BUILD $outdir/namoptions.$exp > $outdir/output.$exp 2>&1" >> job.$exp
-
-## gather output files from cores in a single file
-echo "$DA_TOOLSDIR/gather_outputs.sh $outdir " >> job.$exp
+cat <<EOF > job.$exp
+#PBS -l walltime=${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
+mkdir -p $outdir
+cp -r $inputdir/* $outdir
+pushd $outdir
+mpiexec -n $(( $NCPU * $NNODE )) $DA_BUILD $outdir/namoptions.$exp > $outdir/output.$exp 2>&1
+$DA_TOOLSDIR/gather_outputs.sh $outdir
+EOF
 
 ## submit job.exp file to queue
 qsub job.$exp

tools/hpc_execute.sh

@@ -70,15 +70,17 @@ popd
 
 if [ $start == "c" ]; then
 
+	cd $inputdir
+
 ###### RUN MATLAB SCRIPT through HPC job script
 cat <<EOF > pre-job.$iexpnr
 
 #PBS -l walltime=24:00:00
-#PBS -l select=1:ncpus=8:mem=50gb
+#PBS -l select=1:ncpus=8:mem=64gb
 
 module load tools/prod
-module load MATLAB/2023a_Update_3
-module load gcc/11.2.0
+module load MATLAB/2024b
+module load GCC/14.2.0
 
 cd $DA_TOOLSDIR
 
@@ -88,11 +90,6 @@ export MATLAB_USE_USERWORK=0
 
 matlab -nodesktop -nojvm -nosplash -r "expnr=$iexpnr; write_inputs; quit"
 
-cd $DA_EXPDIR
-cd ..
-
-mv pre-job.$iexpnr* $DA_EXPDIR/$iexpnr
-
 EOF
 
 ## submit job.exp file to queue
@@ -101,8 +98,8 @@ EOF
 
 elif [ $start == "l" ]; then
 	module load tools/prod
-	module load MATLAB/2023a_Update_3
-	module load gcc/11.2.0
+	module load MATLAB/2024b
+	module load GCC/14.2.0
 	export MATLAB_USE_USERWORK=0
 	cd $DA_TOOLSDIR
 	matlab -nodesktop -nojvm -nosplash -r "expnr=$iexpnr; write_inputs; quit"