Run NEON sample end to end in Dev #355
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@mbthornton-lbl this failed, there is no output directory. cromwell run directory is 41ec9955-f8b4-4676-86c3-f2714a67b016 |
This was referenced Jan 22, 2025
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Root cause is mismatching input key names between the wdl and the workflows.yaml |
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@vlilanl @mbthornton-lbl please check on this, there are no records {'was_informed_by': 'nmdc:omprc-11-qww9t685'} in workflow_execution_set on mongo dev. |
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Run on Dev: test 1 (from before the Jan NERSC maintenance): nmdc:omprc-11-hcjd7y28 Scheduler Log: Watcher Log: Job Failed: |
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test 2: nmdc:omprc-11-rejajm76 Scheduler Log: Watcher Log: |
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Test 2 Also Failed: Cromwell exec path: |
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@mbthornton-lbl What does the cromwell API report about 7b84f6e2-7a5f-4741-8cdd-aca4a7117c3d? On the file system the exit code for the last task is 0 so I would expect the status of this job to be successful in our logging. |
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@aclum {"status":"Failed","id":"7b84f6e2-7a5f-4741-8cdd-aca4a7117c3d"} Here is the response from https://nmdc-cromwell.freeddns.org:8443/api/workflows/v1/7b84f6e2-7a5f-4741-8cdd-aca4a7117c3d/logs |
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@aclum Here is the submission details now being logged: |
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moved this from In Progress
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in 2025 - Sprint 56 - Feb 10-21,2025
mbthornton-lbl
moved this from Done
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in 2025 - Sprint 56 - Feb 10-21,2025
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The tasks have a zero exit code but the final workflow level checks reveal that there is an issue with the wdl in the finish_rqc step, the links to the data don't resolve. "submission": "2025-02-10T18:21:55.908Z", (nersc-python) nmdcda@perlmutter:login32:/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_rqcfilter/7b84f6e2-7a5f-4741-8cdd-aca4a7117c3d/call-finish_rqc/execution> ls -ltr |
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Action here is to update the cromwell config, restart cromwell, and submit an new test dataset (see query in the description of this ticket to get the next test id) |
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Cromwell / Condor services restarted - submitted next NEON sample: |
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Watcher Log: |
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Update scheduler logging and re-started on |
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Watcher Finds and Submits the 4 scheduled jobs: |
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there is no cromwell job folder so this is likely a mismatch between the wdl and inputs json made by workflow automation. @mbthornton-lbl please take over #298 and sort out passing the boolean flag to the inputs.json so it matches the wdl. |
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if you get a printout of the inputs.json you can use womtool or jaws validate to check that an inputs json file is valid against a given wdl |
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Start with the following Data Gen ID:
test 1 (from before the Jan NERSC maintenance): nmdc:omprc-11-hcjd7y28
test 2: nmdc:omprc-11-rejajm76
test 3: nmdc:omprc-11-qww9t685
If more test IDs are needed used the next record from this aggregation query:
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