Feature #9308
closed
[CWL] Crunchrunner supports using writable keep mount for output
Added by Peter Amstutz almost 9 years ago.
Updated over 8 years ago.
Estimated time:
(Total: 0.00 h)
Description
Crunchrunner used by crunch v1 for CWL jobs does not support using the writable keep mount as the output directory.
- Define a job runtime constraint that requests use of writable keep mount.
- Update crunchrunner to use writable keep mount as the output directory if the runtime constraint is set
- Update arvados-cwl-runner to set the job runtime constraint for writable keep when there is an appropriate hint in the CWL document (depends on #9307)
- Description updated (diff)
- Assigned To set to Peter Amstutz
- Target version set to 2016-10-12 sprint
Some observations:
- File
sdk/go/crunchrunner/crunchrunner.go
func setupCommand: Is it possible that the file copy return some error? Maybe it’s convenient to check for that and return it if exist.func getKeepTmp: Can be the case of a corrupted json data being read from ‘buf’ making json.Unmarshall return an error?
- File
sdk/cwl/arvados_cwl/arv-cwl-schema.yml
- There’s a repeated “this” word on the
OutputDirType documentation (line 25)
- Status changed from New to Resolved
Applied in changeset arvados|commit:74ec5b86db46257f75ea1eb94c136ce18e65c906.
- Status changed from Resolved to In Progress
Running bcl2fastq on e51c5 after this was deployed causes the job to deadlock/hang with 4 cores spinning solidly burning sys time with no user time or I/O
- Status changed from In Progress to Resolved
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Updated by Tom Morris