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Check ws allocation

Merged Martin Schroschk requested to merge check-ws-allocation into preview
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@@ -106,8 +106,63 @@ molecules and reactions under a wide range of conditions, including both stable
@@ -106,8 +106,63 @@ molecules and reactions under a wide range of conditions, including both stable
compounds which are difficult or impossible to observe experimentally such as short-lived
compounds which are difficult or impossible to observe experimentally such as short-lived
intermediates and transition structures.
intermediates and transition structures.
Gaussian is currently not installed as a module. Please, contact
Access to the Gaussian installation on our system is limited to members
[hpcsupport@zih.tu-dresden.de](mailto:hpcsupport@zih.tu-dresden.de) if you need assistance.
of the UNIX group s_gaussian. Please, contact
 
[hpcsupport@zih.tu-dresden.de](mailto:hpcsupport@zih.tu-dresden.de) if you can't
 
access it, yet wish to use it.
 
 
### Guidance on Data Management with Gaussian
 
 
We have a general description about
 
[how to utilize Workspaces for your I/O intensive Jobs](../data_lifecycle/workspaces.md).
 
However hereafter we have an example on how that might look like for Gaussian:
 
 
!!! example "Using Workspaces with Gaussian"
 
 
```
 
#!/bin/bash
 
#SBATCH --partition=haswell
 
#SBATCH --time=96:00:00
 
#SBATCH --nodes=1
 
#SBATCH --ntasks=1
 
#SBATCH --constraint=fs_lustre_ssd
 
#SBATCH --cpus-per-task=24
 
 
module purge
 
module load modenv/hiera
 
module load Gaussian
 
 
# TODO: Adjust the path to where your input file is located
 
INPUTFILE="/path/to/my/inputfile.gjf"
 
 
test ! -f "${INPUTFILE}" && echo "Error: Could not find the input file ${INPUTFILE}" && exit 1
 
 
COMPUTE_DIR=gaussian_$SLURM_JOB_ID
 
export GAUSS_SCRDIR=$(ws_allocate -F ssd $COMPUTE_DIR 7)
 
echo $GAUSS_SCRDIR
 
 
# Check allocation.
 
test -z "${GAUSS_SCRDIR}" && echo "Error: Cannot allocate workspace ${COMPUTE_DIR}" && exit 1
 
 
cd ${GAUSS_SCRDIR}
 
srun g16 < "${INPUTFILE}" > logfile.log
 
 
# Compress results with bzip2 (which includes CRC32 Checksums)
 
bzip2 --compress --stdout -4 "${GAUSS_SRCDIR}" > $HOME/gaussian_job-$SLURM_JOB_ID.bz2
 
RETURN_CODE=$?
 
COMPRESSION_SUCCESS="$(if test $RETURN_CODE -eq 0; then echo 'TRUE'; else echo 'FALSE'; fi)"
 
 
if [ "TRUE" = $COMPRESSION_SUCCESS ]; then
 
test -d $GAUSS_SCRDIR && rm -rf $GAUSS_SCRDIR/*
 
# Reduces grace period to 1 day!
 
ws_release -F ssd $COMPUTE_DIR
 
else
 
echo "Error with compression and writing of results";
 
echo "Please check the folder \"${GAUSS_SRCDIR}\" for any partial(?) results.";
 
exit 1;
 
fi;
 
```
 
## GROMACS
## GROMACS
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