I’d like to use
datalad containers-run to execute a singularity container for fmriprep-1.5.0 on my BIDS-formatted dataset, but have a couple issues. Apologies if these would be better presented as separate posts…
I can execute a SLURM array of fmriprep jobs on my BIDS-formatted dataset (a la https://fmriprep.readthedocs.io/en/latest/singularity.html), but would like to use
datalad containers-run to wrap the command. I created a virtual environment for datalad via conda-forge, updated datalad to version 0.12.0rc6, and installed the datalad-containers extension on our hpc (CentOS 7), but am a little uncertain how/where to specify appropriate bind mounts.
Do I need to include the
--bind arguments with the
--cmd-fmt flag when I add the fmriprep singularity image via
datalad containers-add, or can I specify bind mounts in the
datalad containers-run call?
I’m also having trouble using
datalad containers-add to pull the fmriprep singularity image, although I can successfully
datalad containers-add an fmriprep image that I built ahead of time by specifying its path rather than using the
I can add a
heudiconv container with no problem via
datalad containers-add -d . heudiconv --url docker://nipy/heudiconv:0.5.4, but when I try to add an fmriprep container via
datalad containers-add -d . fmriprep --url docker://poldracklab/fmriprep:latest, I receive the following error:
ERROR: build: failed to make environment files: open /tmp/sbuild-432867294/fs/etc/resolv.conf: permission denied FATAL: While performing build: packer failed to pack: while inserting base environment: build: failed to make environment files: open /tmp/sbuild-432867294/fs/etc/resolv.conf: permission denied
The only hit I could find for a similar error is for a closed singularity issue (https://github.com/sylabs/singularity/issues/4532), but I’m not sure if it applies, since I have a more recent version of singularity installed.
I’ve attached a
datalad_containers-add_fmriprep_errors.txt file with the error message in it’s entirety in case this isn’t the heart of the issue (but it’s pretty lengthy), and also a
singularity version: 3.4.1-1.el7
datalad version: 0.12.0rc6