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ReproNim / containers

Containers "distribution" for reproducible neuroimaging
Apache License 2.0
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Need to avoid/tolerate race condition in calling git config #43

Closed yarikoptic closed 4 years ago

yarikoptic commented 4 years ago 
(git-annex)lena:…11ea-be9b-ff519d1f6bc9[master].reproman/jobs/local/20200522-000958-46c0
$> grep 'not lock' -3 stderr.1
> 00:10:34.142854375 [2357873] echo '[ReproMan] executing command containers/scripts/singularity_cmd run containers/images/bids/bids-mriqc--0.15.0.sing '\''data/bids'\'' '\''data/mriqc'\'' participant --participant_label '\''13'\'' -w work'
> 00:10:34.146979943 [2357873] echo '[ReproMan] ... within /home/yoh/.reproman/run-root/0a372e4e-9be2-11ea-be9b-ff519d1f6bc9'
> 00:10:34.149859825 [2357873] /bin/sh -c 'containers/scripts/singularity_cmd run containers/images/bids/bids-mriqc--0.15.0.sing '\''data/bids'\'' '\''data/mriqc'\'' participant --participant_label '\''13'\'' -w work'
error: could not lock config file /home/yoh/.reproman/run-root/0a372e4e-9be2-11ea-be9b-ff519d1f6bc9/containers/binds/HOME/.gitconfig: File exists
> 00:10:34.211776551 [2357873] echo 'failed: 255'
> 00:10:34.214277774 [2357873] mkdir -p /home/yoh/.reproman/run-root/0a372e4e-9be2-11ea-be9b-ff519d1f6bc9/.reproman/jobs/local/20200522-000958-46c0/failed
> 00:10:34.216103284 [2357873] touch /home/yoh/.reproman/run-root/0a372e4e-9be2-11ea-be9b-ff519d1f6bc9/.reproman/jobs/local/20200522-000958-46c0/failed/1

probably due to https://github.com/ReproNim/containers/blob/master/scripts/singularity_cmd#L49

see more info in https://github.com/ReproNim/reproman/issues/511

most likely should just try for X (5 should be enough ;)) times with some random sleep between

yarikoptic commented 4 years ago

fixed for it in ff700a4ade5a76883120644c700c5fcf6af20006, forgot to add Closes