Container path not expanded properly with Singularity on Uppmax
Closed this issue · 3 comments
Hammarn commented
As the title says. Log output:
Container : docker://
Pulling Singularity image docker:// [cache /crex2/proj/sllstore2017079/nobackup/private/rickard/test_phil_PR/NGI-RNAseq/tests/work/singularity/.img]
ERROR ~ Error executing process > 'trim_galore (SRR4238351_subsamp)'
Caused by:
Failed to pull singularity image
command: singularity pull --name .img docker:// > /dev/null
message:
WARNING: pull for Docker Hub is not guaranteed to produce the
WARNING: same image on repeated pull. Use Singularity Registry
WARNING: (shub://) to pull exactly equivalent images.
ERROR Could not parse image ""! Exiting.
ERROR: pulling container failed!
Hammarn commented
This was apparently several separate issues. The path not being expanded is fixed in Nextflow v 0.28.
The second problem is that since the Singularity cache was not set then each time a process is started it tries to pull the image again for each compute node.
If the user sets singularity.cacheDir in their own then it works fine - I tested that myself on Rackham.
I do think that it would be nice to set the cache dir in the working directory instead, but it work as it is now.
ewels commented
Problems reproducing this. Note that the docker build has been failing for some time (separate issue): https://hub.docker.com/r/scilifelab/ngi-rnaseq/builds/