about.md 6.11 KB
Newer Older
Ludovic Courtès's avatar
Ludovic Courtès committed
1 2 3
title: About
---

Ludovic Courtès's avatar
Ludovic Courtès committed
4
Guix-HPC is an effort to optimize [GNU Guix](https://gnu.org/s/guix) for
Ludovic Courtès's avatar
Ludovic Courtès committed
5
_reproducible scientific workflows in high-performance computing_ (HPC).
6
Our [introductory article](/blog/2017/09/guix-hpc-debut) explains how we got
Ludovic Courtès's avatar
Ludovic Courtès committed
7 8
started and gives an overview of what we want to achieve.  We
regularly publish [articles](/blog) on this Web site highlighting specific
Ludovic Courtès's avatar
Ludovic Courtès committed
9 10 11
features or achievements.  Stay tuned!

Guix-HPC is a joint software development project currently involving
12
three research institutes: [Inria](https://www.inria.fr/en/centre/bordeaux/news/towards-reproducible-software-environments-in-hpc-with-guix),
Ludovic Courtès's avatar
Ludovic Courtès committed
13
the
14 15
[Max Delbrück Center for Molecular Medicine (MDC)](https://www.mdc-berlin.de/47864296/en/news/2017/20170905-wissenschaftliches-rechnen-erfolgreich-reproduzieren),
and the [Utrecht Bioinformatics Center (UBC)](https://ubc.uu.nl/reproducible-software-environments-in-hpc-with-guix/).
16

17 18
# Talks & Papers

19
The material below covers our work and motivation for Guix-HPC:
20

21 22 23 24 25
  - [_PiGx: Reproducible Genomics Analysis Pipelines with
    GNU Guix_](https://doi.org/10.1093/gigascience/giy123), GigaScience
    [ICG-13](http://www.icg-13.org/)
    ([video](https://hpc.guix.info/blog/2019/01/pigx-paper-awarded-at-the-international-conference-on-genomics-icg-13/)),
    Dec. 2018
Ludovic Courtès's avatar
Ludovic Courtès committed
26 27 28
  - [_Beyond Bundles—Reproducible Software Environments with
    GNU Guix_](https://cds.cern.ch/record/2316926), [CERN Computing
    Seminars](http://cseminar.web.cern.ch/cseminar/), May 2018
29 30 31 32 33 34
  - [_Reproducible genomics analysis pipelines with
    GNU Guix_](https://www.biorxiv.org/content/early/2018/04/11/298653),
    Apr. 2018
  - [_Tying software deployment to scientific
    workflows_](https://fosdem.org/2018/schedule/event/guix_workflows/),
    [FOSDEM](https://fosdem.org/2018/), Feb. 2018
35 36 37 38 39
  - [_Reproducible and user-controlled software management in HPC with GNU Guix_](https://www.youtube.com/watch?v=cH6wCL6GeOQ&list=PLir-OOQiOhXZX_2zmUJz0fx8RLALi3tkK&index=26) ([PDF](https://www.gnu.org/software/guix/guix-bosc-20170724.pdf)),
    [BOSC](https://www.open-bio.org/wiki/BOSC_2017_Schedule), July 2017
  - [_Optimized and Reproducible HPC Deployment_](https://archive.fosdem.org/2017/schedule/event/hpc_deployment_guix/),
	[FOSDEM](https://fosdem.org/2017),
	Feb. 2017
40 41 42
  - [_Workflow Management with GNU Guix_](https://archive.fosdem.org/2017/schedule/event/guixworkflowmanagement/),
	[FOSDEM](https://fosdem.org/2017),
	Feb. 2017
43 44 45 46 47 48
  - [_Reproducible and User-Controlled Software Environments in HPC with Guix_](https://hal.inria.fr/hal-01161771/en)
    ([slides](https://www.gnu.org/software/guix/guix-reppar-20150825.pdf)),
	paper presented at the 2nd International Workshop on Reproducibility
	in Parallel Computing ([RepPar](http://www.reppar.org/2015/)),
	Aug. 2015

49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69
# Code

Most of the code developed for Guix-HPC aims to consolidate [the code
base](https://git.savannah.gnu.org/cgit/guix.git/)
and [package collection](https://gnu.org/software/guix/packages) 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](https://www.guixwl.org/), a lightweight
    framework implementing reproducible computational pipelines.
  - [hpcguix-web](https://github.com/UMCUGenetics/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-HPC repository](https://gitlab.inria.fr/guix-hpc/guix-hpc)
    currently contains packages for HPC tools and run-time support
    and linear algebra libraries developed by research teams
70
    at [Inria](https://www.inria.fr/en/).
71 72 73 74 75
  - The [Guix-BIMSB repository](https://github.com/BIMSBbioinfo/guix-bimsb)
    currently contains packages for bioinformatics tools and package
    variants used at the
    [Berlin Institute for Medical Systems Biology](https://www.mdc-berlin.de/bimsb)
    of the
76 77 78 79 80 81 82 83 84 85 86 87 88 89
    [Max Delbrück Center for Molecular
    Medicine](https://www.mdc-berlin.de).
  - This [UMCU Genetics
    repository](https://github.com/UMCUGenetics/guix-additions) has more
    bioinformatics packages in use at the [Center for Molecular Medicine
    at UMC
    Utrecht](http://www.umcutrecht.nl/en/Research/Research-centers/Center-for-Molecular-Medicine).
  - The [ACE repository](https://github.com/Ecogenomics/ace-guix)
    provides packages used by the [Australian Centre for
    Ecogenomics](http://ecogenomic.org/).
  - This [Genenetwork
    repository](https://gitlab.com/genenetwork/guix-bioinformatics)
    contains bioinformatics and HPC packages used by
    [Genenetwork](http://genenetwork.org/).
90 91 92 93

All this is [free software](https://www.gnu.org/philosophy/free-sw.html)
that you are welcome to use and contribute to!

94 95 96 97 98 99 100 101 102 103
# Cluster Deployments

Here are deployments of Guix on clusters and contact information:

  - [Max Delbrück Center for Molecular Medicine](https://www.mdc-berlin.de) (Germany)
      - 250-node cluster + workstations
      - contact: Ricardo Wurmus
  - [Utrecht Bioinformatics Center](https://ubc.uu.nl) (The Netherlands)
      - 68-node cluster (1,000+ cores)
      - contact: Roel Janssen
104
  - [Australian Centre for Ecogenomics](http://ecogenomic.org/) (Australia)
105
      - 21-node cluster (1,000 cores)
106
      - contact: Ben Woodcroft
107 108 109
  - [PlaFRIM cluster](https://www.plafrim.fr/en/home/) (France)
	  - 120-node heterogeneous cluster (3,000+ cores)
	  - contact: Ludovic Courtès
110 111 112
  - [GriCAD](https://gricad.univ-grenoble-alpes.fr/) (France)
	  - 72-node “Dahu” cluster (1,000+ cores)
	  - contact: Violaine Louvet, Pierre-Antoine Bouttier
113 114 115

If you would like to be listed here, please email us at `guix-hpc@gnu.org`.

116 117
# Join us!

118
If you are using Guix in an HPC context at your workplace, or if you
119
would like to discuss ways to address your own HPC use cases, or if you are
Ludovic Courtès's avatar
Ludovic Courtès committed
120 121 122
an HPC vendor interested in improving the software deployment experience
for your users, please consider joining us!  Email us at
`guix-hpc@gnu.org`.