Bug #4470
closed
[Crunch] tmpdir not writable running jobs in Docker
Description
https://workbench.qr1hi.arvadosapi.com/pipeline_instances/qr1hi-d1hrv-e3jx9on6hkp9c8o#Components
$ arv run --local /bin/bash ./vartovcf.sh -- <collection hash1> <collection hash2>
qr1hi-8i9sb-lzelnxp2m7y01xp 19126 0 stderr Traceback (most recent call last):
qr1hi-8i9sb-lzelnxp2m7y01xp 19126 0 stderr File "/tmp/crunch-job-4009/src/crunch_scripts/run-command", line 43, in <module>
qr1hi-8i9sb-lzelnxp2m7y01xp 19126 0 stderr os.mkdir("tmpdir")
qr1hi-8i9sb-lzelnxp2m7y01xp 19126 0 stderr OSError: [Errno 13] Permission denied: 'tmpdir'
2014-11-07 21:44:41 +0000 -- pipeline_instance qr1hi-d1hrv-e3jx9on6hkp9c8o
command qr1hi-8i9sb-lzelnxp2m7y01xp failed 2014-11-07T21:44:37Z
Pipeline is Failed
No output
I can provide full log on request (contains hashes).
Some indication on Workbench that this was run locally might be nice too.
Related issues
Updated by Peter Amstutz over 9 years ago
- Target version set to 2014-11-19 sprint
Updated by Peter Amstutz over 9 years ago
- Subject changed from arv run --local results in run-command OSError, permission denied to [Crunch] tmpdir not writable running crunch-job in local mode
- Category changed from SDKs to Crunch
- Target version deleted (
2014-11-19 sprint)
Updated by Peter Amstutz over 9 years ago
- Target version set to 2014-11-19 sprint
Updated by Tom Clegg over 9 years ago
- Assigned To changed from Nancy Ouyang to Tom Clegg
- Priority changed from Normal to High
Updated by Peter Amstutz over 9 years ago
On further research, this is a general problem, the data volume shows up as being owned by root inside the container, so the crunch user can't write to the data volume.
Updated by Peter Amstutz over 9 years ago
- Subject changed from [Crunch] tmpdir not writable running crunch-job in local mode to [Crunch] tmpdir not writable running jobs in Docker
Updated by Tom Clegg over 9 years ago
Should be fixed by 3824-task-work branch on #3824
Updated by Peter Amstutz over 9 years ago
- Status changed from New to Resolved
I agree, I'm pretty certain this is resolved. (Tested running local jobs, and using arv run).