High performance computing - HPC
Ce service permet d’accéder aux infrastructures de calcul haute performance (clusters) de l’UNIL pour le traitement de données de recherche non sensibles.
Getting Started
DCSR? Kesako?
The full name is the Division de Calcul et Soutien à la Recherche / Computing and Research Suppor...
How to access the clusters
The DCSR maintains a general purpose cluster (Curnagl) which is described here. Researchers need...
I'm a PI and would like to use the clusters - what do I do?
It's easy! Please fill in the request form at https://requests.dcsr.unil.ch and we'll get back in...
Help!
Infrastructure and Resources
Curnagl
Kesako? Curnagl (Romanche), or Chocard à bec jaune in French, is a sociable bird known for its...
Curnagl - 2022
Following the migration to the CCT datacenter there are a number of things that have changed that...
Storage on Curnagl
Where is data stored The recommended place to store all important data is on the DCSR NAS which ...
Jura
Jura is a cluster for the analysis of sensitive data and is primarily used by the CHUV. The Jura...
Urblauna
Kesako? Urblauna (Romanche), or Lagopède Alpin in French, is a bird known for its changing plumag...
Using the Clusters
How to run a job on Curnagl
Overview Suppose that you have finished writing your code, say a python code called <my_code.py>...
What projects am I part of and what is my default account?
In order to find out what projects you are part of on the clusters then you can use the Sproject ...
Providing access to external collaborators
In order to allow non UNIL collaborators to use the HPC clusters there are three steps which are ...
Requesting and using GPUs
GPU Nodes Both Curnagl and Urblauna have nodes with GPUs - on Curnagl these are in a separate ...
How do I run a job for more that 3 days?
The simple answer is that you can't without special authorisation. Please do not submit such jobs...
Access NAS DCSR from the cluster
The NAS is available from the login node only under /nas. The folder hierarchy is: /nas/FAC/<you...
SSH connection to DCSR cluster
This page presents how to connect to DCSR cluster depending on your operating system. Linux SSH...
Checkpoint SLURM jobs
Introduction As you probably noticed, execution time for jobs in DCSR clusters is limited to 3 d...
Urblauna access and data transfer
Connecting to Urblauna The Urblauna cluster is intended for the processing of sensitive data and ...
Jura to Urblauna Migration
Migration schedule and deadlines Once the Urblauna cluster is officially in service the decomm...
Job Templates
Here you can find example job script templates for a variety of job types Single-threaded tasks ...
Urblauna Guacamole / RDP issues
Resolving connnection problems There can sometimes be communication issues between the web based ...
Urblauna migration
Urblauna Urblauna is the new UNIL cluster for sensitive data and will replace the Jura cluster. s...
Transfer files to/from Curnagl
How do I transfer my code to Curnagl? How do I get my results back on my computer? There are ...
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 Image Analysis with CNNs
You can do the practicals on various computing platforms. However, since the participants may use...
Course software for Text Analysis with LLMs
You can do the practicals on various computing platforms. However, since the participants may use...
Performance of LLM backends and models in Curnagl
Introduction This page shows performance of Llama and mistral models on Curnagl hardware. We have...