HPC & reproducible research in Guix 0.16.0

Ludovic Courtès — December 7, 2018

Version 0.16.0 of Guix was released yesterday. It’s slated to be the last release before 1.0, and as usual, it brings noteworthy packages and features for HPC and reproducible research.

Packages

Of the 985 packages were added and 1,945 upgraded, here are the noteworthy HPC and bioinformatics changes:

  • FEniCS and related packages were contributed by Paul Garlick of Tourbillion Technology.
  • petsc-openmpi is now configured with support for the HYPRE preconditioner, for the MUMPS solver, and for the HDF5 data format.
  • SLEPc and PETSc were upgraded to 3.10.1 and 3.10.2.
  • MPI4Py was added.
  • ngless, a domain-specific language (DSL) for working with next generation sequencing data is now available.
  • A handful of packages for Nanopore processing have been added, including Filtlong, Nanopolish, Poretools, and Porechop.
  • Hundreds of bioinformatics and R packages and upgrades were contributed in particular by Mădălin Ionel Patrașcu and Ricardo Wurmus of the Max Delbrück Center for Molecular Medicine (MDC).

Reproducible scientific workflows

A lot of core Guix work has gone into improving tools in support of reproducible development and deployment workflows—a prerequisite, in our view, for reproducible research.

The new channels facility solves several problems:

As an example, if I want to use packages from the Guix-HPC repository at Inria, all I need to do is create a ~/.config/guix/channels.scm file containing this:

;; Add Guix-HPC to the official Guix channel.
(cons (channel
        (name 'guix-hpc)
        (url "https://gitlab.inria.fr/guix-hpc/guix-hpc.git"))
      %default-channels)

From then on, guix pull will take care of pulling from both Guix and Guix-HPC.

Previously you could already replicate Guix using guix pull --commit=XYZ but integration with channels streamlines this. Specifically, the new guix describe command provides a complete description of the channels in use:

$ guix describe
Generation 23   Dec 07 2018 11:07:27    (current)
  guix 5118e26
    repository URL: https://git.savannah.gnu.org/git/guix.git
    branch: master
    commit: 5118e26f83cc2b4ec835df56bee2a4003c1325b9
  guix-hpc 779f4df
    repository URL: https://gitlab.inria.fr/guix-hpc/guix-hpc.git
    branch: master
    commit: 779f4df63892a95de6efba259abf82e64951d4be

Now let’s imagine Bob has a setup that works for him on his laptop and wants to share it with Alice for use on a supercomputer. Bob captures his setup as a “pinned” channel specification in a file:

bob@laptop$ guix describe --format=channels > bob-channels.scm

He then sends bob-channels.scm over to Alice who, on the supercomputer, feeds it to guix pull:

alice@supercomputer$ guix pull --channels=bob-channels.scm
Updating channel 'guix' from Git repository at 'https://git.savannah.gnu.org/git/guix.git'...
Updating channel 'guix-hpc' from Git repository at 'https://gitlab.inria.fr/guix-hpc/guix-hpc.git'...
Building from these channels:
  guix      https://git.savannah.gnu.org/git/guix.git   5118e26
  guix-hpc  https://gitlab.inria.fr/guix-hpc/guix-hpc.git       779f4df
…

Alice now has the exact same Guix as Bob, which in turn means she can deploy the exact same pieces of software as Bob and yet have complete provenance tracking of the binaries she runs—something “container images” fail to provide.

The good thing with having access to all the package definitions is that one can easily experiment with them, which is often a key aspect of research work. The package transformation options should serve that need, and the new --with-branch and --with-commit options that allow a package to be built straight from its Git repository are another step in that direction.

Last but not least, Guix now supports Software Heritage as a back-end to fetch Git repositories from. That makes Guix resilient to vanishing upstream repositories, which is unfortunately not uncommon. Along with reproducible builds, this secures reproducible software deployment from source to binaries.

Do not miss the release notes to learn about the other goodies that the release brings.

Enjoy the new release!

  • MDC
  • Inria
  • UBC