diff --git a/doc.zih.tu-dresden.de/docs/software/nanoscale_simulations.md b/doc.zih.tu-dresden.de/docs/software/nanoscale_simulations.md index 6bf65b4151272d0ffff4ee7e4420a2fdb072d85d..c60714158eb1a02a19e208bb40660e1cf7f8dc80 100644 --- a/doc.zih.tu-dresden.de/docs/software/nanoscale_simulations.md +++ b/doc.zih.tu-dresden.de/docs/software/nanoscale_simulations.md @@ -107,20 +107,21 @@ compounds which are difficult or impossible to observe experimentally such as sh intermediates and transition structures. Access to the Gaussian installation on our system is limited to members -of the UNIX group s_gaussian. Please, contact +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). +[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 @@ -128,18 +129,19 @@ However hereafter we have an example on how that might look like for Gaussian: #SBATCH --constraint=fs_lustre_ssd #SBATCH --cpus-per-task=24 + # Load the software you need here module purge module load modenv/hiera module load Gaussian - # TODO: Adjust the path to where your input file is located + # 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 $GAUSS_SCRDIR + COMPUTE_DIR=gaussian_${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 ${COMPUTE_DIR}" && exit 1 @@ -148,19 +150,19 @@ However hereafter we have an example on how that might look like for Gaussian: srun g16 < "${INPUTFILE}" > logfile.log # Compress results with bzip2 (which includes CRC32 Checksums) - bzip2 --compress --stdout -4 "${GAUSS_SRCDIR}" > $HOME/gaussian_job-$SLURM_JOB_ID.bz2 + bzip2 --compress --stdout -4 "${GAUSS_SRCDIR}" > ${HOME}/gaussian_job-${SLURM_JOB_ID}.bz2 RETURN_CODE=$? - COMPRESSION_SUCCESS="$(if test $RETURN_CODE -eq 0; then echo 'TRUE'; else echo 'FALSE'; fi)" + COMPRESSION_SUCCESS="$(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/* + 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 + 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; + echo "Error with compression and writing of results" + echo "Please check the folder \"${GAUSS_SRCDIR}\" for any partial(?) results." + exit 1 + fi ``` ## GROMACS