FATAL: container creation failed with singularity profile

[Fiwx]

Discussed in #3914

^{Originally posted by nhhaidee May 3, 2023}

Bug report

Can not run pipeline with singularity profile

Expected behavior and actual behavior

Run pipeline (https://github.com/CFIA-NCFAD/nf-flu) with singularity profile but it failed with error

Steps to reproduce the problem

Run pipeline with -profile singularity

Program output

Command error: FATAL: container creation failed: mount /proc/self/fd/3->/usr/local/var/singularity/mnt/session/rootfs error: while mounting image /proc/self/fd/3: failed to find loop device: could not attach image file to loop device: no loop devices available

Environment

• Nextflow version: 23.04.1.5866
• Java version: openjdk 11.0.9.1-internal 2020-11-04
• Operating system: Ubuntu 22.04
• Bash version: 5.1.16(1)-release (x86_64-pc-linux-gnu)

Additional context

There is no problem with Docker profile

Other users say:

We have the same issue, singularity profile does not work on our cluster system. We looked at the solution proposed here:
sylabs/singularity#1499

But it does not yield a consistent solution for Nextflow. Test singularity containers will run after this intervention but no full Nextflow runs.

I have the same issue. Only test runs will work, but not full Nextflow runs. Here is the error:

FATAL: container creation failed: mount /proc/self/fd/4->/usr/local/var/singularity/mnt/session/rootfs error: while mounting image /proc/se