Skip to main content

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 (old)

R is provided via the DCSR software stack Interactive mode To load R: module load r R # Then...

R on the clusters

R is provided via the DCSR software stack Interactive mode To load R: $> module load r-light ...

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...

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 Text Analysis with LLMs

You can do the practicals on various computing platforms. However, since the participants may use...

Course software for Image Analysis with CNNs

You can do the practicals on various computing platforms. However, since the participants may use...

Performance of LLM backends and models in Curnagl

TODO Introduction (Cristian) Backends and models tested (Margot) Hardware description (Margot)...