Script to do HDF5 to netCDF4 conversion of MOHID results in MIDOSS project Monte-Carlo results tree. Created for post-processing of the `north_strait_5th362` batch of runs for which the in-job conversion failed because the `SLURM_TMPDIR` local scratch storage on the node filled.

backfill_hdf5-to-netcdf4.sh

#!/bin/bash

RESULTS_DIR="/scratch/dlatorne/MIDOSS/runs/monte-carlo/north_strait_5th362_2021-06-14T150753/results/north_strait_5th362"
HDF5_TO_NETCDF4="${HOME}/.local/bin/hdf5-to-netcdf4"

module load python/3.8.2
module load nco/4.9.5

TMPDIR="${SLURM_TMPDIR}"

for n in {0..361}
do
    if test -f ${RESULTS_DIR}-${n}/Lagrangian*.hdf5
    then
	LAGRANGIAN=$(find ${RESULTS_DIR}-${n} -type f -name Lagrangian*.hdf5 | xargs basename -s .hdf5)
	echo ${LAGRANGIAN}
	echo "Results hdf5 to netCDF4 conversion started at $(date)"
	cp -v ${RESULTS_DIR}-${n}/${LAGRANGIAN}.hdf5 ${SLURM_TMPDIR}/ && \
	${HDF5_TO_NETCDF4} -v info \
	    ${SLURM_TMPDIR}/${LAGRANGIAN}.hdf5 \
	    ${SLURM_TMPDIR}/${LAGRANGIAN}.nc && \
	mv -v ${SLURM_TMPDIR}/${LAGRANGIAN}.nc ${RESULTS_DIR}-${n}/
	rm -v ${RESULTS_DIR}-${n}/${LAGRANGIAN}.hdf5
      echo "Results hdf5 to netCDF4 conversion ended at $(date)"
    fi
done