Help setting apptainer cache dir

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1

question on config variable setting~

I need to use nextflow v22.10.4 for a non-nf-core pipeline. I set my conda/singularity cache dirs in my config file, but am getting the following error indicating that apptainer is looking at the wrong directory (/$HOME/$USER/ instead of specified dir which is on a different node called /ceph/)

FATAL:   While making image from oci registry: error fetching image to cache: while building SIF from layers: while creating SIF: while unloading container: close /dicos_ui_home/ewissel/.apptainer/cache/oci-tmp/tmp_3980167945: disk quota exceeded

I tried to update the apptainer cache in my config file but must have done so unsuccessfully as I got the same error on a rerun. Can someone help me fix the apptainer cache directory? I used the singularity/conda cache dir commands as a template, so I don’t quite understand where I’m going wrong here.

## relevant partt of nextflow.config
profiles {
  standard {
    conda {
      useMamba = false
      conda.enabled = true
      // Allow longer conda creation timeout
      createTimeout = '2 h'
      cacheDir = "/ceph/work/IBMS-PHLab/emily/nf_conda/"
      }
      params.enable_conda = true
      singularity.enabled = false
      singularity.automounts = false
      docker.enabled = false
      podman.enabled = false
      shifter.enabled = false
      charliecloud.enabled = false
  }
  conda {
    conda {
    useMamba = false
    conda.enabled = true
    // Allow longer conda creation timeout
    createTimeout = '2 h'
    cacheDir = "/ceph/work/IBMS-PHLab/emily/nf_conda/"
    }
    params.enable_conda = true
    singularity.enabled = false
    singularity.automounts = false
    docker.enabled = false
    podman.enabled = false
    shifter.enabled = false
    charliecloud.enabled = false
  }
  singularity {
    singularity.enabled = true
    singularity.autoMounts = true
    singularity.runOptions = "--bind /ceph/sharedfs/work/IBMS-PHLab/emily/tmp:/tmp"
    singularity.cacheDir = "/ceph/work/IBMS-PHLab/emily/singularity-images/"
    params.enable_container=true
    docker.enabled = false
    podman.enabled = false
    shifter.enabled = false
    charliecloud.enabled = false
  }
  docker {
    singularity.enabled = false
    singularity.autoMounts = false
    docker.enabled = true
    params.enable_container=true
    podman.enabled = false
    shifter.enabled = false
    charliecloud.enabled = false
  }
  apptainer  {
    apptainer.cacheDir =  "/ceph/work/IBMS-PHLab/emily/singularity-images/"    ## what I added
 }
}

When I run nextflow, i specify -profile singularity, so I’m not sure if the apptainer cache needs to be connected to the singularity profile in this instead of how it is now? Thanks for the help!

2

Hey @ewissel.

What you’re actually doing is apptainer.apptainer.cacheDir = ".... You should do instead:

apptainer {
  cacheDir = "/ceph/work/IBMS-PHLab/emily/singularity-images/"
}

Or you can also set your cache directory for apptainer with an environment variable: NXF_APPTAINER_CACHEDIR.

Could you please try again and let me know if it worked?

3

this worked, and is a big “duh” in hindsight. Thank you!!

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4

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