Squashfs files no longer work with singularity 3.x

[Shane Sturrock <shane.sturrock@realtimegenomics.com>]

I’ve previously used guix pack -f squashfs to create files that Singularity 3.x would run although it complains about the lack of exec with "WARNING: container does not have /.singularity.d/actions/exec, calling samtools directly” where samtools is the program installed in the file by Guix. That warning can be silenced with the --silent flag when running the singularity exec command.

However, the most recent updates/installs of Guix produce a file that fails with "FATAL:   exec /.singularity.d/actions/exec failed: no such file or directory”. I’ve still got previously created squashfs files which still work but any new ones I make won’t. The ones that work were made back on May 15th 2019 so the change has happened since then. I’ve confirmed this on multiple systems we have Guix installed on and even did a completely fresh install in a VM just to be sure and that also had the issue.

Here’s the command I used and what happens when I try and run it with Singularity 3.1 (also happens with 3.2) - CentOS 7.6.1810 release:

$ guix pack -f squashfs -S /bin=bin samtools
/gnu/store/7wpn9a4nlpyr0hgzcl65qi8fqmqz6swg-squashfs-pack.gz.squashfs
$ singularity exec /gnu/store/7wpn9a4nlpyr0hgzcl65qi8fqmqz6swg-squashfs-pack.gz.squashfs samtools
WARNING: passwd file doesn't exist in container, not updating
WARNING: group file doesn't exist in container, not updating
FATAL:   exec /.singularity.d/actions/exec failed: no such file or directory
$ singularity --version
singularity version 3.1.1-1.1.el7

Hopefully there’s a solution because one of the big selling points for us was the ability to create these files for running on a cluster with Singularity installed.

Regards,

Shane Sturrock