pbs.sh

#!/bin/bash
#PBS -S /bin/bash
#PBS -q alpha
#PBS -l select=1:ncpus=128
#PBS -l walltime=00:50:00
#PBS -N dipha_bench
#PBS -j oe

# load appropriate modules
module purge
# mpt must be loaded before openMPI to avoid mixing MPI implementations
module load mpt openMPI gcc

# move to PBS_O_WORKDIR
cd $PBS_O_WORKDIR

# Define scratch space
PROJECT=dipha
SCRATCH=/scratchalpha/$USER/$PROJECT
mkdir -p $SCRATCH

# working directory
WD=$HOME/pdiags_bench

# copy some input files to  $SCRATCH directory
cp -r $WD/raws $SCRATCH

# env variables
INSTDIR=/home/guilloup/install
TTK_BUILD=/home/guilloup/ttk-guillou/build
PY38=python3.8/site-packages
export LD_LIBRARY_PATH=$INSTDIR/lib64:$INSTDIR/lib:$TTK_BUILD/lib64:$LD_LIBARY_PATH
export PATH=$INSTDIR/bin:$WD/build_dipha:$TTK_BUILD/bin:$PATH
export PYTHONPATH=$INSTDIR/lib64/$PY38:$INSTDIR/lib/$PY38:$TTK_BUILD/lib64/$PY38
export PV_PLUGIN_PATH=$TTK_BUILD/lib64/TopologyToolKit

# execute your program
cd $SCRATCH || exit 1

# prepare datasets
mkdir datasets

for raw in raws/*.raw; do
    echo "Converting $raw..."
    time python $WD/convert_datasets.py $raw datasets
    raw_stem=${raw#raws/}
    out=$WD/log/${raw_stem}_${PBS_JOBID}_${NCPUS}.out
    err=$WD/log/${raw_stem}_${PBS_JOBID}_${NCPUS}.err
    vtu=datasets/${raw_stem%.raw}_order_expl.vtu
    for nt in 1 16 32 48 64 80 96 112 128; do
        echo "Processing $vtu with TTK with $nt threads..." >> $out
        omplace -nt $nt \
                ttkPersistenceDiagramCmd -i $vtu -t $nt \
                1>> $out 2>> $err
        rm $vtu
    done
done

# copy some output files to submission directory
# cp -p $PBS_JOBNAME.out $PBS_JOBNAME.err $PBS_O_WORKDIR || exit 1

# clean the temporary directory
rm -rf "$SCRATCH"/*