fails to run (mriqc) singularity container through docker

[yarikoptic]

initially reported by @dnkennedy and then troubleshooted locally on Linux REPRONIM_USE_DOCKER=1 of our example in README.md

full dump from terminal

```shell $> REPRONIM_USE_DOCKER=1 ./containers-test.sh > mktemp -d /home/yoh/.tmp/repro-XXXXXXX > cd /home/yoh/.tmp/repro-6XkWWkE > datalad create -d ds000003-qc -c text2git [INFO ] Creating a new annex repo at /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc [INFO ] Scanning for unlocked files (this may take some time) [INFO ] Running procedure cfg_text2git [INFO ] == Command start (output follows) ===== [INFO ] == Command exit (modification check follows) ===== create(ok):../ /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc (dataset) > cd ds000003-qc > datalad install -d . ///repronim/containers [INFO ] Scanning for unlocked files (this may take some time) install(ok): /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc/containers (dataset) add(ok): /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc/containers (file) add(ok): /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc/.gitmodules (file) save(ok): /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc (dataset) action summary: add (ok: 2) install (ok: 1) save (ok: 1) > datalad run -m Downgrade/Freeze mriqc container version containers/scripts/freeze_versions bids-mriqc=0.15.1 [INFO ] == Command start (output follows) ===== I: bids-mriqc -> 0.15.1 [INFO ] == Command exit (modification check follows) ===== add(ok):../ /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc/containers/.datalad/config (file) save(ok): /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc/containers (dataset) add(ok): /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc/containers (file) save(ok): /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc (dataset) action summary: add (ok: 2) save (ok: 2) > datalad install -d . -s https://github.com/ReproNim/ds000003-demo sourcedata [INFO ] Scanning for unlocked files (this may take some time) [INFO ] Remote origin not usable by git-annex; setting annex-ignore [INFO ] access to 1 dataset sibling s3-PRIVATE not auto-enabled, enable with: | datalad siblings -d "/home/yoh/.tmp/repro-6XkWWkE/ds000003-qc/sourcedata" enable -s s3-PRIVATE install(ok): /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc/sourcedata (dataset) add(ok): /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc/sourcedata (file) add(ok): /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc/.gitmodules (file) save(ok): /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc (dataset) action summary: add (ok: 2) install (ok: 1) save (ok: 1) > datalad containers-run -n containers/bids-mriqc --input sourcedata --output . {inputs} {outputs} participant group [INFO ] Making sure inputs are available (this may take some time) get(ok): /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc/sourcedata/sub-02/anat/sub-02_T1w.nii.gz (file) [from s3-PUBLIC...] get(ok): /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc/sourcedata/sub-02/anat/sub-02_inplaneT2.nii.gz (file) [from s3-PUBLIC...] get(ok): /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc/sourcedata/sub-02/func/sub-02_task-rhymejudgment_bold.nii.gz (file) [from s3-PUBLIC...] get(ok): /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc/sourcedata/sub-13/anat/sub-13_T1w.nii.gz (file) [from s3-PUBLIC...] get(ok): /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc/sourcedata/sub-13/anat/sub-13_inplaneT2.nii.gz (file) [from s3-PUBLIC...] get(ok): /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc/sourcedata/sub-13/func/sub-13_task-rhymejudgment_bold.nii.gz (file) [from s3-PUBLIC...] get(ok): /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc/containers/images/bids/bids-mriqc--0.15.1.sing (file) [from origin...] [INFO ] == Command start (output follows) ===== FATAL: container creation failed: mount /proc/self/fd/5->/usr/local/singularity/var/singularity/mnt/session/rootfs error: can't mount image /proc/self/fd/5: failed to mount squashfs filesystem: invalid argument [INFO ] == Command exit (modification check follows) ===== [INFO ] The command had a non-zero exit code. If this is expected, you can save the changes with 'datalad save -d . -r -F .git/COMMIT_EDITMSG' CommandError: 'containers/scripts/singularity_cmd run containers/images/bids/bids-mriqc--0.15.1.sing 'sourcedata' '' participant group' failed with exitcode 255 under /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc REPRONIM_USE_DOCKER=1 ./containers-test.sh 36.18s user 43.33s system 14% cpu 9:27.22 total ```

[yarikoptic]

https://github.com/hpcng/singularity/issues/5408 suggests that we need freshier singularity since we have

$> docker run --privileged --rm -e UID=47521 -e GID=47522 -v /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc:/home/yoh/.tmp/repro-6XkWWkE/ds000003-qc -v /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc/containers:/home/yoh/.tmp/repro-6XkWWkE/ds000003-qc/containers -v /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc/containers/binds/HOME:/home/yoh/.tmp/repro-6XkWWkE/ds000003-qc/containers/binds/HOME -w /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc -v /etc/localtime --entrypoint singularity mjtravers/singularity-shim:latest --version
singularity version 3.3.0-1

[yarikoptic]

damn -- I guess https://github.com/ReproNim/containers/pull/42 was intended to fix it all but was "forgotten". will get back to it now.

[yarikoptic]

42 and followup commits + updated docker build of the repronim/containers should have addressed this issue