These are instruction on how to use modules that are installed at SISSA, both on workstations and on hpc cluster, and are meant to be used within the group. The scripts directory contains the scripts that were used to install the modules.
On workstations:
module use /u/b/bussi/shared_modules/modules
On cluster:
module use /home/bussi/shared_modules
module load python/3.9
Once loaded, other modules will become available and compatible with this python version.
Notice that executable is named python3, and not python!
module load py-base
This is versioned according to the date on which the tools were packages were installed. It contains a number of general purpose tools (numpy, pandas, jupyter, barnaba, etc). Notice that, due to the way the PYTHONPATH environment variable work, it is easy to override these modules with more recent versions if you need them.
When this module is installed first, a new file is written in the scripts directory documenting the exact version of each tool. For instance, this is the file corresponding to the module installed on Nov 29, 2022.
module load py-bussilab
The tools documented here.
I left them as a separate module so that I can update them more frequently than the py-base
module.
module load cudamat
Versioned according to the date and on the cuda drivers used.
module load jax
Versioned according to the version of both jax and jaxlib. Notice that, in order to use the cuda version currently available on our machines, older jax/jaxlib versions are installed
module load gromacs
Versioned according to the GROMACS version and possible modifications. Notice that one can load a different version of PLUMED by loading a suitable module. However, it is important to record which version of PLUMED was used for patching since patches themselves evolve with time:
gromacs/2020/2020.7-cr-p-2.8.1version 2020.7, patched with plumed 2.8.1 (compatible with any plumed version) and with crescale barostat (will be available by default in version 2021).
module load plumed
Versioned according to PLUMED version. We might have more ad hoc versions in the future. It should be possible to combine any PLUMED version with any GROMACS version:
plumed/2.8/2.8.1version 2.8.1, all external modules enabledplumed/2.8/2.8.2version 2.8.2, all external modules enabled
It is also recommended to setup plumed command autocompletion and, if you are using VIM, vim syntax. This has to be done once in your .bashrc and .vimrc files.
module load ViennaRNA
Versioned according to ViennaRNA and to the version of python for which the python wrappers were compiled.
module load htop
htop is a better replacement of top.
module load ncdu
ncdu shows disk usage graphically in the terminal.