Failed to find loop device: could not attach image file to loop device: no loop devices available

[yasu-sh]

@felixleopoldo Thanks for your works, benchpress. It works fine on the machines. I was using benchpress and issues on WSL2 at win11 with docker. So now I moved to native Ubuntu machine with docker-image as the instruction manual at benchpress.

One symptom is worth telling you on some cases.

• countermeasure-1 reduce cores - worked.
  • snakemake --cores 4 --use-singularity --configfile config/config.json
• countermeasure-2 install as Linux(Ubuntu) on WSL - worked!
  • Straightforwardly used miniforge(mambaforge) instead of miniconda since both conda make corruption of base environment at conda.
  • Apptainer version 1.2.3 installed with non-setuid installation

I guess the root cause has not been solved yet. But it in some cases updates makes a solutions. I hope my report be a help for benchpress users. https://github.com/sylabs/singularity/issues/67 <- the same symptoms.

When I run the code as below:

(snakemake) root@:/mnt# snakemake --cores all --use-singularity --configfile config/config.json

Then I faced the error as below. Both have the same. loop device was not enough.

• Win11 on Docke Desktop with WSL2, volume mounted at Windows file system PS > docker run -it -w /mnt --privileged -v F:/benchpress:/mnt bpimages/snakemake:v7.32.3

• Win11 on Docke Desktop with WSL2, volume mounted at WSL2 file system docker run -it -w /mnt --privileged --name bntab -v /home/path/benchpress:/mnt bpimages/snakemake:v7.32.3

• Symptom:

  
  (omit)
  [Fri Sep 29 05:17:07 2023]
  Finished job 112.
  1 of 346 steps (0.3%) done
  FATAL:   container creation failed: mount /proc/self/fd/3->/opt/conda/envs/snakemake/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

(snakemake) root@d6f240d00620:/mnt# lscpu Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian Address sizes: 48 bits physical, 48 bits virtual CPU(s): 12 On-line CPU(s) list: 0-11 Thread(s) per core: 2 Core(s) per socket: 6 Model name: AMD Ryzen 5 5500 CPU MHz: 3593.164

Memory 64GB / GPU nvidia 8GB

The loop device increased from 8 to 255.
```bash
(snakemake) root@:/mnt# ls /dev/loop*
/dev/loop-control  /dev/loop119  /dev/loop140  /dev/loop162  /dev/loop184  /dev/loop205  /dev/loop227  /dev/loop249  /dev/loop40  /dev/loop62  /dev/loop84
/dev/loop0         /dev/loop12   /dev/loop141  /dev/loop163  /dev/loop185  /dev/loop206  /dev/loop228  /dev/loop25   /dev/loop41  /dev/loop63  /dev/loop85
(omit)
/dev/loop118       /dev/loop14   /dev/loop161  /dev/loop183  /dev/loop204  /dev/loop226  /dev/loop248  /dev/loop4    /dev/loop61  /dev/loop83

[felixleopoldo]

Thanks for this report. I also experienced a loop device error before, both when running through Docker on Linux and natively on Linux. I didn't find out exactly what the solution is but it seemed to work when I created a new conda environment or when updating Apptainer. I was not able to reproduce the error once it worked.

[felixleopoldo]

If anyone experience a similar problem, please make a comment here and we can try to figure out how to solve it.