Bug #9703

[Crunch2] CWL workflow failed with Crunch2, but passed with Crunch1

Added by Radhika Chippada about 5 years ago. Updated over 3 years ago.

Status:
Resolved
Priority:
Normal
Assigned To:
-
Category:
-
Target version:
-
Start date:
Due date:
% Done:

0%

Estimated time:
Story points:
-
Release:
Release relationship:
Auto

History

#1 Updated by Radhika Chippada about 5 years ago

I ran Jiayong's varscan CWL workflow (main-goCallVars.cwl) in 9tee4.

When I used the command "arvados-cwl-runner --local --wait --debug main-goCallVars.cwl test-input-yml/main-goCallVars-job.yml" the pipeline instance https://workbench.9tee4.arvadosapi.com/pipeline_instances/9tee4-d1hrv-wgvlm9an4a6caw6 was created and succeeded. It had 7 successful jobs.

When I it ran using "--api containers", i.e. Crunch2, it created a container request https://workbench.9tee4.arvadosapi.com/container_requests/9tee4-xvhdp-hdeyli0ct23pwsf . This had two children (freebayes and varscan) and the freebayes CR is failing.

(venv)radhika@shell.9tee4:~/goCallVars/goCallVars$ arvados-cwl-runner --local --wait --debug --api containers main-goCallVars.cwl test-input-yml/main-goCallVars-job.yml
(venv)radhika@shell.9tee4:~/goCallVars/goCallVars$ arvados-cwl-runner --api containers --submit --no-wait main-goCallVars.cwl test-input-yml/main-goCallVars-job.yml

#2 Updated by Brett Smith about 5 years ago

9tee4 is currently trying and failing to dispatch a container for one of these workflows because it does not specify a number of CPUs in its runtime constraints. Once we upgrade the API server here, this container request wouldn't even be valid.

I think the bug here is that arvados-cwl-runner needs to fill in default constraints in cases where the workflow doesn't specify them. Otherwise, it might end up trying to submit invalid container requests to the API server.

#3 Updated by Nico C├ęsar almost 5 years ago

Isn't this resolved?

#4 Updated by Peter Amstutz over 3 years ago

  • Status changed from New to Resolved

a-c-r sets resource defaults

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