Guix-HPC is an effort to optimize GNU Guix for reproducible scientific workflows in high-performance computing (HPC). Our introductory article explains how we got started and gives an overview of what we want to achieve. We regularly publish articles on this Web site highlighting specific features or achievements. Stay tuned!
Guix-HPC is a joint software development project currently involving three research institutes: Inria, the Max Delbrück Center for Molecular Medicine (MDC), University of Tennessee Health Science Center (UTHSC) and the Utrecht Bioinformatics Center (UBC).
Talks & Papers
The material below covers our work and motivation for Guix-HPC:
- [Re] Storage Tradeoffs in a Collaborative Backup Service for Mobile Devices, ReScience C, June 2020
- Towards reproducible Jupyter notebooks, FOSDEM, Feb. 2020
- PiGx: Reproducible Genomics Analysis Pipelines with GNU Guix, GigaScience ICG-13 (video), Dec. 2018
- Beyond Bundles—Reproducible Software Environments with GNU Guix, CERN Computing Seminars, May 2018
- Reproducible genomics analysis pipelines with GNU Guix, Apr. 2018
- Tying software deployment to scientific workflows, FOSDEM, Feb. 2018
- Reproducible and user-controlled software management in HPC with GNU Guix (PDF), BOSC, July 2017
- Optimized and Reproducible HPC Deployment, FOSDEM, Feb. 2017
- Workflow Management with GNU Guix, FOSDEM, Feb. 2017
- Reproducible and User-Controlled Software Environments in HPC with Guix (slides), paper presented at the 2nd International Workshop on Reproducibility in Parallel Computing (RepPar), Aug. 2015
Most of the code developed for Guix-HPC aims to consolidate the code base and package collection of Guix proper, and thus be pushed upstream. This has already given rise to a large collection of bioinformatics, algebra, and R packages, as well as features to simplify Guix deployment on clusters.
Some auxiliary tools and package sets are maintained elsewhere, or kept in a staging area until they are mature enough to be submitted for inclusion in Guix:
- The Guix Workflow Language, a lightweight framework implementing reproducible computational pipelines.
- hpcguix-web is a web interface that allows users to search for packages and guides them the installation and the job submission process.
- The Guix-Science channel is a joint effort to provide free scientific packages that are not or not yet available in Guix proper. Read more.
- The Guix-HPC repository currently contains packages for HPC tools and run-time support and linear algebra libraries developed by research teams at Inria.
- The Guix-BIMSB repository currently contains packages for bioinformatics tools and package variants used at the Berlin Institute for Medical Systems Biology of the Max Delbrück Center for Molecular Medicine.
- This UMCU Genetics repository has more bioinformatics packages in use at the Center for Molecular Medicine at UMC Utrecht.
- The ACE repository provides packages used by the Australian Centre for Ecogenomics.
- Genenetwork repository contains bioinformatics and HPC packages used by Genenetwork at the University of Tennessee.
- Genomics repository for pangenome bioinformatics
- The Guix-ZPID contains packages in use at the Leibniz Institute for Psychology Information.
- The Guix Past channel contains definitions for old core packages.
All this is free software that you are welcome to use and contribute to!
Here are known deployments of Guix on clusters and contact information:
- 250-node cluster + workstations
- contact: Ricardo Wurmus
Utrecht Bioinformatics Center (The Netherlands)
- 68-node cluster (1,000+ cores)
- contact: Roel Janssen
Australian Centre for Ecogenomics (Australia)
- 21-node cluster (1,000 cores)
- contact: Ben Woodcroft
- 120-node heterogeneous cluster (3,000+ cores)
- contact: Ludovic Courtès
- 72-node “Dahu” cluster (1,000+ cores)
- contact: Violaine Louvet, Pierre-Antoine Bouttier
- 230-node cluster (4,000+ cores)
- contact: Yann Dupont
31 clusters, 828 nodes (12,000+ cores)
contact: Dimitri Delabroye, Lucas Nussbaum
If you would like to be listed here, please email us at
If you are using Guix in an HPC context at your workplace, or if you would like to discuss ways to address your own HPC use cases, or if you are an HPC vendor interested in improving the software deployment experience for your users, please consider joining us!
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