Using Software Modules

There are many software packages installed on the RC supercomputer that are available through the software modules system.

New packages are added regularly.

1 Listing available modules
2 Loading a module
3 Listing Loaded Modules
4 Purging Loaded Modules
5 Using Modules in SBATCH scripts

Modules that install into/through python or anaconda are not managed through the software modules. To see if we have a conda environment for a python program load an anaconda module and list conda environments e.g.

module load anaconda3-2021.05-gcc-11.2.0
conda info --envs

You can also create and manage your own conda environments. For more information see https://asurc.atlassian.net/wiki/spaces/RC/pages/125829137

Listing available modules

The following commands will list the software modules that are available on Agave:

module -l avail

$ module -l avail
- Package/Alias -----------------------.- Versions --------.- Last mod. -------
/packages/modulefiles:
jupyter/2022-04-15                                          2022/04/15 21:36:08
jupyter/latest                                              2022/04/15 21:36:08
mamba/0.22.1                                                2022/04/15 21:40:41

/packages/spack/share/spack/modules/linux-rocky8-zen:
gcc-11.2.0-gcc-8.5.0                                        2022/04/20 09:40:44

/packages/spack/share/spack/modules/linux-rocky8-zen3:
anaconda3-2021.05-gcc-11.2.0                                2022/04/20 09:40:43
blaze-3.8-gcc-11.2.0                                        2022/04/20 09:40:44
bowtie-1.3.0-gcc-11.2.0                                     2022/04/20 09:40:44
bowtie2-2.4.2-gcc-11.2.0                                    2022/04/20 09:40:44
bzip2-1.0.8-gcc-11.2.0                                      2022/04/20 09:40:44
curl-7.79.0-gcc-11.2.0                                      2022/04/20 09:40:44
dmidecode-3-2-gcc-11.2.0                                    2022/04/20 09:40:44
dos2unix-7.4.2-gcc-11.2.0                                   2022/04/20 09:40:44
...

Loading a module

The following command will load the module for gcc 6.5.0

module load gcc-6.5.0-gcc-11.2.0

Previously, on Agave, modules are listed like “gcc/6.5.0”, while on Sol the name is extended and uses hyphens (-) This is because package installer suite called Spack is employed to help manage applications. The new module name now adds on the suffix of the compiler used to compile a given program. While the package name has become more lengthy, this greatly reduces runtime incompatibilities by ensuring that an app and all dependencies are using a uniform compiler.

Listing Loaded Modules

The following command will list the modules that are currently loaded:

Purging Loaded Modules

To clear out the modules that are currently loaded, perhaps because you want to load others, use the following command:

Using Modules in SBATCH scripts

Many sbatch scripts will include a module load command as part of the script.

An example of this can be found here: Creating SBATCH scripts.