Software
DCSR Software Stack
What is it? The DCSR provides a software environment including commonly used scientific tools an...
Old software stack
The old (Vital-IT) software stack can be accessed on Curnagl via the following commands $ source...
Compiling and running MPI codes
To illustrate the procedure we will compile and run a MPI hello world example from mpitutorial.co...
MATLAB on the clusters
The full version of MATLAB is only installed on the login and interactive nodes so in order to ru...
Using Conda and Anaconda
Conda is a package manager system for Python and other tools and is widely used in some areas suc...
Using Mamba to install Conda packages
Mamba is an alternative to Conda package manager. The main advantage is its speed regarding depen...
Deep Learning with GPUs
The training phase of your deep learning model may be very time consuming. To accelerate this pro...
AlphaFold
The project home page where you can find the latest information is at https://github.com/deepmind...
R on the clusters
R is provided via the DCSR software stack Interactive mode To load R: module load gcc r R # ...
Software local installation
This page gives an example of a local installation of a software, i.e. a software that will be on...
DCSR GitLab service
What is it? The DCSR hosted version control service (https://gitlab.dcsr.unil.ch) is primarily i...
Running Busco
A Singularity container is available for version 4.0.6 of Busco. To run it, you need to proceed a...
Offline installation on Jura
Installing new software on Jura is complicated because the cluster does not have Internet access....
SWITCHfilesender from the cluster
Switch Filesender Filesender is a service provided by SWITCH to transfer files over http. Normal...
Filetransfer from the cluster
filetransfer.dcsr.unil.ch https://filetransfer.dcsr.unil.ch is a service provided by the DCSR to...
CryoSPARC
First of all, if you plan to use CryoSPARC on the cluster, please contact us to get a port number...
Sandbox containers
Container basics For how to use Singularity/Apptainer containers please see our course at: htt...
Course software for decision trees / random forests
In the practicals, we will use only a small dataset and we will need only little computation powe...
Course software for introductory deep learning
In the practicals, we will use only a small dataset and we will need only little computation powe...
Rstudio on the Curnagl cluster
Rstudio can be run on the curnagl cluster from within a singularity container, with an interactiv...
Rstudio on the Urblauna cluster
Rstudio can be run on the Urblauna cluster from within a singularity container, with an interacti...
JupyterLab on the curnagl cluster
JupyterLab can be run on the curnagl cluster for testing purposes, only as an intermediate step i...
JupyterLab with C++ on the curnagl cluster
JupyterLab can be run on the curnagl cluster for testing purposes, only as an intermediate step i...
Dask on curnagl
In order to use Dask in Curnagl you have to use the following packages: dask dask-jobqueue Not...
Running the Isca framework on the cluster
Isca is a framework for the idealized modelling of the global circulation of planetary atmosphere...
Running the MPAS framework on the cluster
The Model for Prediction Across Scales (MPAS) is a collaborative project for developing atmospher...
Run OpenFOAM codes on Curnagl
Script to run OpenFOAM code You are using OpenFOAM on your computer and you need more ressources...
Compiling software using cluster libraries
If you see the following error when compiling a code on the cluster: fatal error: XXXX.h: No suc...
Course software for Image Analysis with CNNs
You can do the practicals on various computing platforms. However, since the participants may use...