diff --git a/doc.zih.tu-dresden.de/docs/data_lifecycle/workspaces.md b/doc.zih.tu-dresden.de/docs/data_lifecycle/workspaces.md
index 537c298287fb742d49bd62fd1f7c8bfbdc18600d..d4342395370661c0aa7247f503f69b84a4ce12d6 100644
--- a/doc.zih.tu-dresden.de/docs/data_lifecycle/workspaces.md
+++ b/doc.zih.tu-dresden.de/docs/data_lifecycle/workspaces.md
@@ -213,33 +213,69 @@ There are three typical options for the use of workspaces:
### Per-Job Storage
A batch job needs a directory for temporary data. This can be deleted afterwards.
+To help you to write your own [(Slurm) job file](../jobs_and_resources/slurm.md#job-files),
+suited to your own needs, we came up with
+the following example (which works [for the program g16](../software/nanoscale_simulations.md)).
+You will probably want to adjust it in a few places (e.g. what software you want to
+[load](../software/modules.md), inserting the path to your input file and actually
+calling the actual software to do your computation).
-!!! example "Use with Gaussian"
+!!! example "Using temporary workspaces for I/O intensive tasks"
- ```
+ ```bash
#!/bin/bash
+
#SBATCH --partition=haswell
- #SBATCH --time=96:00:00
+ #SBATCH --time=48:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
+ ## The optional constraint for the filesystem feature depends
+ ## on the filesystem on which you want to use a workspace.
+ ## Documentation here https://doc.zih.tu-dresden.de/jobs_and_resources/slurm/#available-features
+ #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
-
- COMPUTE_DIR=gaussian_$SLURM_JOB_ID
- export GAUSS_SCRDIR=$(ws_allocate -F ssd $COMPUTE_DIR 7)
- echo $GAUSS_SCRDIR
-
- srun g16 inputfile.gjf logfile.log
-
- test -d $GAUSS_SCRDIR && rm -rf $GAUSS_SCRDIR/*
- ws_release -F ssd $COMPUTE_DIR
+ module load <modules>
+
+ # Adjust the path to where your input file is located
+ INPUTFILE="/path/to/my/inputfile.data"
+
+ test ! -f "${INPUTFILE}" && echo "Error: Could not find the input file ${INPUTFILE}" && exit 1
+
+ # Allocate workspace. Adjust time span to time limit of the job (-d <N>).
+ WSNAME=computation_$SLURM_JOB_ID
+ export WSDDIR=$(ws_allocate -F ssd -n ${WSNAME} -d 2)
+ echo ${WSDIR}
+
+ # Check allocation
+ test -z "${WSDIR}" && echo "Error: Cannot allocate workspace ${WSDIR}" && exit 1
+
+ # Change to workspace directory
+ cd ${WSDIR}
+
+ # Adjust the following line to invoke the program you want to run
+ srun <application> < "${INPUTFILE}" > logfile.log
+
+ # Save result files, e.g. into your user home
+ # Compress results with bzip2 (which includes CRC32 Checksums)
+ bzip2 --compress --stdout -4 "${WSDIR}" > $HOME/gaussian_job-$SLURM_JOB_ID.bz2
+ RETURN_CODE=$?
+ COMPRESSION_SUCCESS="$(if test ${RETURN_CODE} -eq 0; then echo 'TRUE'; else echo 'FALSE'; fi)"
+
+ # Clean up workspace
+ if [ "TRUE" = ${COMPRESSION_SUCCESS} ]; then
+ test -d ${WSDIR} && rm -rf ${WSDIR}/*
+ # Reduces grace period to 1 day!
+ ws_release -F ssd ${WSNAME}
+ else
+ echo "Error with compression and writing of results"
+ echo "Please check the folder \"${WSDIR}\" for any partial(?) results."
+ exit 1
+ fi
```
-Likewise, other jobs can use temporary workspaces.
-
### Data for a Campaign
For a series of jobs or calculations that work on the same data, you should allocate a workspace
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 9727d2d35f03fa334a79385ffd960625fc958348..d7a90eb4bf0af3fe417fe9e6c89d7c44a400be28 100644
--- a/doc.zih.tu-dresden.de/docs/software/nanoscale_simulations.md
+++ b/doc.zih.tu-dresden.de/docs/software/nanoscale_simulations.md
@@ -106,8 +106,68 @@ 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
+
+ # Load the software you need here
+ module purge
+ module load modenv/hiera
+ module load Gaussian
+
+ # 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 ${INPUTFILE}" && exit 1
+
+ # Allocate workspace. Adjust time span to time limit of the job (-d <N>).
+ COMPUTE_DIR=gaussian_${SLURM_JOB_ID}
+ export GAUSS_SCRDIR=$(ws_allocate -F ssd -n ${COMPUTE_DIR} -d 7)
+ echo ${GAUSS_SCRDIR}
+
+ # Check allocation.
+ test -z "${GAUSS_SCRDIR}" && echo "Error: Cannot allocate workspace ${COMPUTE_DIR}" && exit 1
+
+ # Change to workspace directory and execute application
+ cd ${GAUSS_SCRDIR}
+ srun g16 < "${INPUTFILE}" > logfile.log
+
+ # Save result files into user home
+ # 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)"
+
+ # Clean up workspace
+ 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
@@ -116,9 +176,9 @@ of motion for systems with hundreds to millions of particles. It is primarily de
biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded
interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that
usually dominate simulations), many groups are also using it for research on non-biological systems,
-e.g., polymers. For documentations see [Gromacs homepage](https://www.gromacs.org/).
+e.g., polymers. For documentations see [GROMACS homepage](https://www.gromacs.org/).
-GROMACSS is available as [modules](modules.md). Available packages can be listed and loaded with the
+GROMACS is available as [modules](modules.md). Available packages can be listed and loaded with the
following commands:
```console
@@ -195,16 +255,16 @@ standard quantum chemical methods ranging from semiempirical methods to DFT to s
multireference correlated ab initio methods. It can also treat environmental and relativistic
effects.
-To run Orca jobs in parallel, you have to specify the number of processes in your input file (here
+To run ORCA jobs in parallel, you have to specify the number of processes in your input file (here
for example 16 processes):
```Bash
%pal nprocs 16 end
```
-Note, that Orca spawns MPI processes itself, so you must not use `srun` to launch it in your batch
+Note, that ORCA spawns MPI processes itself, so you must not use `srun` to launch it in your batch
file. Just set `--ntasks` to the same number as in your input file and call the `orca` executable
-directly. For parallel runs, it must be called with the full path:
+directly. For parallel runs, it must be called with the full path:
```Bash
#!/bin/bash
diff --git a/doc.zih.tu-dresden.de/wordlist.aspell b/doc.zih.tu-dresden.de/wordlist.aspell
index 08d177bd12347df1539edcbb077d76f8add8766b..5dc9d446f03b1fd9a57e50e6fff19bdac1b31406 100644
--- a/doc.zih.tu-dresden.de/wordlist.aspell
+++ b/doc.zih.tu-dresden.de/wordlist.aspell
@@ -285,6 +285,7 @@ openmpi
OpenMPI
OpenSSH
Opteron
+ORCA
OST
OSTs
OTF