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

$> 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]

apptainer/singularity#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 #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