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Conda is a package manager system for Python and other tools and is widely used in some areas such as bioinformatics and data science. On personal computers it is a useful way to install a stack of tools. The full documentation can be found at https://docs.c...

The DCSR has deployed a new facility to provide researchers with a virtual machine (VM) service. Two kind of virtual machines are available: virtual workstations: the idea is to offer a workstation reachable from anywhere (even outside UNIL) from a simple Web...

Objectives of this course Learn the basic necessities of Linux to use UNIL HPC clusters in a command-line interface mode. Target audience Any PhD students, post-docs, researchers of UNIL and CHUV who need to use UNIL HPC clusters but who are not familiar wi...

Objectives of this course We explain the basics of version control using git and show how it can help both individual and collaborative research. Target audience Any PhD students, post-docs, researchers of UNIL and CHUV who have to deal with code developm...

This page presents how to connect to DCSR cluster depending on your operating system. Linux SSH is always installed by most commons Linux distributions, so no extra package should be installed. Connection with a password To connect using a password, just r...

R is provided via the DCSR software stack Interactive mode To load R: module load gcc r R # Then you can use R interactively > ... Batch mode While using R in batch mode, you have to use Rscript to launch your script. Here is an example of sbatch scrip...

This page gives an example of a local installation of a software, i.e. a software that will be only available to yourself. For simplicity we assume here that the software you want to install is available as a single binary file. To be executed from anywhere t...

A Singularity container is available for version 4.0.6 of Busco. To run it, you need to proceed as follows: $ module load singularity $ export SINGULARITY_BINDPATH="/scratch,/users,/work" Some configuration files included in the container must be copied in ...

This page presents the way to move data between your laptop (or a virtual machine/lab server) and the NAS. Accessing DCSR NAS from home or UNIL network Note: If you work from home, you first need to connect to UNIL's VPN using Pulse Secure (see VPN instruc...

The NAS is available from the login node only under /nas. The folder hierarchy is: /nas/FAC/<your_faculty>/<your_department>/<your_PI>/<your_project> Cluster -> NAS To copy a file to the new NAS: cp /path/to/file /nas/FAC/<your_faculty>/<your_department>/<...

Since november 2023, new research projects should store their data using Tresorit. Please see the detailed documentation : https://wiki.unil.ch/ci/books/research-data-storage/chapter/donnees-sensibles-tresorit  Current user of the NAS DCSR RECHERCHE-S/Boxcryp...

There are two administrative steps: The external collaborator must ask a UNIL account using this online form (go to "Obtenir un compte informatique personnel"). Warning: in the online form, the external collaborator have to write the name/email of the PI who ...

Jura is a cluster for the analysis of sensitive data and is primarily used by the CHUV. The Jura cluster is replaced by Urblauna  Computing ressources 10 compute nodes cpt01: CPUs=40 Boards=1 SocketsPerBoard=4 CoresPerSocket=10 ThreadsPerCore=1 RealMemory=...

Installing new software on Jura is complicated because the cluster does not have Internet access. This page covers the installation of R, BioConductor, and Python packages. R packages For packages in CRAN Since Jura cluster is not connected to the Internet,...

The DCSR team is able to help you regarding high performance computing topics including: using DCSR clusters when you're not able to perform your research and run computations on your local computer. harnessing the DCSR clusters (CPU and GPU) scaling your c...

Machine learning methods are nowadays used in a wide variety of scientific domains. For example, - Unsupervised machine learning methods may be used as tools for data exploration and visualisation (dimension reduction and clustering), - Supervised machine le...

First of all, if you plan to use CryoSPARC on the cluster, please contact us to get a port number (you will understand later why it's important). CryoSPARC can be used on Curnagl and take benefit from Nvidia A100 GPUs. This page presents the installation in t...

In progress

The DCSR provides support to researchers in the humanities for projects based on structured corpora (databases, digital libraries or collections, etc.). The DCSR carries out a technological watch to provide researchers and research groups in the humanities wi...

At some point, you might have to move data from one project to another one for various reasons. On NAS DCSR, such move is not possible by default because of a technical limitation. So depending on the volume of data to move, there are 2 options. But before go...