Software

Software is a critical component of any HPC environment and programming project. We manage and provide a set of software packages that are available to all cluster users — see the Modules section for details. If you need additional software, please contact us at hpc-support@amsterdamumc.nl. You also have the option to install your own software using Conda, RStudio, or containers.

Modules

Modules can be loaded into your environment so that they become available to use. To check all available modules on the cluster, use the following command:

module avail 

Look for your software of interest, for example Python:

module avail | grep -i python

Now load the module

module load python/3.9.16

Info

Type python into the terminal. What version is being displayed? Is it the same as the module you loaded?

You can always unload the module

module unload python/3.9.16

Check which modules I have loaded:

module list

Report all the versions + detailed information for the modules that match the name

module spider python/3.9.16

Clear all loaded modules

module purge

Conda environment

To install your personal miniconda, please follow the installation protocol on the conda user documentation.

If you are curious how to use conda environments with batch jobs (e.g. via sbatch scripts), please refer to our [dedicated page] for instructions.

Rstudio libraries

When using the RStudio interactive application on Open OnDemand, a Bioconductor container is launched in the background with a specific Bioconductor and R version. You can install any R package compatible with these versions. Installed packages will be placed in your home directory:

/home/[P-number]/R/x86_64-pc-linux-gnu-library/[R-version]

If you want to use the same environment in batch jobs (e.g. via sbatch scripts), please refer to our [dedicated page] for instructions.

Containers

In construction