Squashfs files no longer work with singularity 3.x

Squashfs files no longer work with singularity 3.x

[Shane Sturrock]

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

Re: Squashfs files no longer work with singularity 3.x

[Ricardo Wurmus]

Hi Shane,

> 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 can reproduce this with singularity version 3.1.0-1.el7.centos.

> $ 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

This works for me:

    image=$(guixr pack -f squashfs --entry-point=bin/sh -S /bin=bin samtools bash)
    singularity exec $image /bin/samtools

Hope this helps!

--
Ricardo

Re: Squashfs files no longer work with singularity 3.x

[Shane Sturrock]

Thanks Richardo, the --entry-point=bin/sh was the key. I can just call samtools without the leading /bin just fine:

$ singularity --silent exec $image samtools --version
samtools 1.9
Using htslib 1.9
Copyright (C) 2018 Genome Research Ltd.

Regards,

Shane

> On 15/07/2019, at 2:26 PM, Ricardo Wurmus <rekado@elephly.net> wrote:
> 
> 
> Hi Shane,
> 
>> 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 can reproduce this with singularity version 3.1.0-1.el7.centos.
> 
>> $ 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
> 
> This works for me:
> 
>    image=$(guixr pack -f squashfs --entry-point=bin/sh -S /bin=bin samtools bash)
>    singularity exec $image /bin/samtools
> 
> Hope this helps!
> 
> --
> Ricardo
> 

Shane Sturrock, Ph.D
Director of Bio-it
m +64 21 648 466
e shane.sturrock@realtimegenomics.com