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ZIH
hpcsupport
hpc-compendium
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e52373a3
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e52373a3
authored
2 years ago
by
Lars Jitschin
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Put the Data Lifecycle example for Gaussian on Gaussian's page
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Check ws allocation
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doc.zih.tu-dresden.de/docs/software/nanoscale_simulations.md
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@@ -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
intermediates and transition structures.
Gaussian is currently not installed as a module. Please, contact
[
hpcsupport@zih.tu-dresden.de
](
mailto:hpcsupport@zih.tu-dresden.de
)
if you need assistance.
Access to the Gaussian installation on our system is limited to members
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
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