Software and Containers

Environment Modules

The HPC does not rely on the OS distribution's package repositories for software, as they typically provide only a single version of each package. Instead, the HPC uses Environment Modules to manage software with support for multiple versions. To set up modules, export the following variable in your .bashrc file (and remember to source the file again):

MODULEPATH=/share/apps/Modules/noarch/:/share/apps/Modules/linux-debian12-zen3

To explore the available packages, run module avail to list all installed software. To search for a specific package, try:

$ module avail llvm
-------------------------------------------------------------------------------------------- /share/apps/Modules/linux-debian12-zen3 --------------------------------------------------------------------------------------------
llvm/16.0.6-gcc-12.2.0-re62fk5  llvm/18.1.8-gcc-12.2.0-mx7panm

Key:
modulepath

$ module avail cuda
-------------------------------------------------------------------------------------------- /share/apps/Modules/linux-debian12-zen3 --------------------------------------------------------------------------------------------
cuda/12.5.1-gcc-12.2.0-tk2uq2c

Key:
modulepath

To load a module (make sure to the desired version is provided):

$ module load llvm/18.1.8-gcc-12.2.0-mx7panm
Loading llvm/18.1.8-gcc-12.2.0-mx7panm
  Loading requirement: glibc/2.36-gcc-12.2.0-4jbapu4 gcc-runtime/12.2.0-gcc-12.2.0-ujkkx2r zlib/1.3.1-gcc-12.2.0-62cb2vq zstd/1.5.6-gcc-12.2.0-ihynyhi binutils/2.42-gcc-12.2.0-h5uryxy libpciaccess/0.17-gcc-12.2.0-x4no44r
    xz/5.4.6-gcc-12.2.0-bi4mbkf libxml2/2.10.3-gcc-12.2.0-j4po5v7 ncurses/6.5-gcc-12.2.0-yh57hvp hwloc/2.9.3-gcc-12.2.0-dmfv7ll libedit/3.1-20230828-gcc-12.2.0-vtr2gfz libffi/3.4.6-gcc-12.2.0-li2rwog
    nghttp2/1.62.0-gcc-12.2.0-wxj7b5x openssl/3.3.1-gcc-12.2.0-mbbi2oa curl/8.7.1-gcc-12.2.0-smtz4u6 readline/8.2-gcc-12.2.0-vyqw5tr unzip/6.0-gcc-12.2.0-eothgfx lua/5.3.6-gcc-12.2.0-loj6p3p pcre2/10.43-gcc-12.2.0-zqzpqjh
    swig/4.1.1-gcc-12.2.0-4zpscua

Multiple versions of packages, cross-compile are supported. Please contact us for more information.

Apptainer

Apptainer (also known as Singularity) is the container engine for the HPC environment. We maintain a collection of commonly used container images, which can be found here:

Please check out the Official User Guide.

Bind Paths and Mounts

For making the directories available inside the container, visit: https://apptainer.org/docs/user/main/bind_paths_and_mounts.html#bind-examples