Here we don't provide a complete list of available software. To check, what is currently available, please also check the output of
module avail
Compiler
We currently provide the following compilers:
| Name | Version | module | Notes |
|---|---|---|---|
| gcc | 8.5.0 | - | system default |
| 12.1.0 | gcc/12.1.0 | activated support for offloading on Nvidia GPUs (nvptx) | |
| intel-oneapi | 2022.1.0 | intel-oneapi-compilers/2022.1.0 | |
| nvhpc | 22.3 | nvhpc/22.3 | |
| aocc | 3.2.0 | aocc/3.2.0 |
MPI
Spack
Python, R, conda, Jupyter
Conda is a package manager for Python, R, and Julia software. You can use it on our HPC system by:
$ module load conda
Thereafter, you should be able to use conda to manage your Python/R/Julia environments. Typically you will want to install software via:
$ conda install -c conda-forge <PACKAGE_NAME>
Note that this allows you to install both Python as well as R packages.
Jupyter is an interactive computing environment which lets you execute notebooks which can mix code, text, graphics, and LaTeX all in a single document. To start a local Jupyter server, ensure that you have Jupyter installed in your currently activated conda environment, and then run:
$ jupyter lab --no-browser --ip 0.0.0.0 /path/to/start/from
The printed output will direct you to a website where you can then open up the Jupyter interface. We are currently working on an experimental JupyterHub which will allow you to log on to the login nodes and run notebooks directly from the browser. If you want to test this out, you can try here: http://paleosrv3.dmawi.de/jupyterhub-hpc Note that VPN is required!
Singularity
Singularity (now renamed Apptainer) is a containerization software similar to Docker but with several additional security features which make it feasible to use on HPC systems. You can find more information about the software here: https://apptainer.org/docs/user/main/
We offer Apptainer/Singularity as a module which can be loaded with:
$ module load apptainer
Thereafter, you should have both the singularity and apptainer executables available to you so you can download and run containers. These programs are interchangeable.
Important note about building containers from scratch: Building requires root privileges! However, the generated container files are portable and can be copied from (e.g.) your personal laptop to the HPC system. Alternatively, you can consider to use the "remote builder" hosted at Sylabs.io: https://cloud.sylabs.io/builder