Bug #4470
closed
[Crunch] tmpdir not writable running jobs in Docker
100%
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.
Updated by Peter Amstutz about 10 years ago
- Target version set to 2014-11-19 sprint
Updated by Peter Amstutz about 10 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 about 10 years ago
- Target version set to 2014-11-19 sprint
Updated by Tom Clegg about 10 years ago
- Assigned To changed from Nancy Ouyang to Tom Clegg
- Priority changed from Normal to High
Updated by Peter Amstutz about 10 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 about 10 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 about 10 years ago
Should be fixed by 3824-task-work branch on #3824
Updated by Peter Amstutz about 10 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).