Python scripts that submit Slurm job scripts to the Slurm Workload
Manager reside in the same directory as the job scripts and start with
submit_*.py. All (documented) Python submit scripts are listed
in the Python Submit Scripts section.
How to find a suitable Slurm job script? How is this project structured?
The two main directories that contain Slurm job scripts are
analysis. As the names suggests,
simulation contains job scripts that run the actual simulations
analysis contains job scripts that run analysis tasks. The
corresponding Python submit scripts reside in the same directory as the
Slurm job scripts that they submit.
Slurm job scripts to analyze MD simulations and their corresponding Python submit scripts.
Bash scripts that are used by the Slurm job scripts.
Directory containing this documentation.
Bash scripts that can be sourced to load Lmod modules into the current shell.
Python modules that are used by the Python submit scripts.
Slurm job scripts to run MD simulations and their corresponding Python submit scripts.
Each top-level directory should contain a
README file that
explains the contents and the structure of this directory.
You should not change the directory structure or move scripts around, because the scripts call and import other scripts based on relative paths.
If you are submitting jobs on Palma2, another important directory
directory contains Bash scripts that can be sourced to load the required
Lmod modules for your job. By selecting the corresponding Lmod source
script, you can specify which version of a software package to use for
your simulation or analysis. For example
lmod/palma/2019a/gmx2018-8_foss.sh loads Gromacs 2018.8 compiled
and linked with free and open source software (foss), whereas
lmod/palma/2020a/gmx2020-1_foss.sh loads Gromacs 2020.1.
You can run the Python scripts simply by:
If you have made the scripts executable with
chmod u+x path/to/script.py
you can also run the scripts in the following way:
Give one or more examples how to use the scripts.