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maxTime flag propagates to Bacalhau Job.Spec.Timeout#636

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acashmoney merged 3 commits intomainfrom
635-lab-596-configure-bacalhau-job-timeout-value-equal-to-maxtime-flag
Sep 7, 2023
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maxTime flag propagates to Bacalhau Job.Spec.Timeout#636
acashmoney merged 3 commits intomainfrom
635-lab-596-configure-bacalhau-job-timeout-value-equal-to-maxtime-flag

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@acashmoney acashmoney commented Sep 7, 2023

Summary

This is a sister PR to #633.

In the previous PR, the maxTime flag updates the time plex (client-side) waits for a Bacalhau job to complete. However, the Bacalhau job spec defaults to a timeout of 1800 sec (30 min).

This change connects the maxTime flag to Bacalhau's Job.Spec.Timeout value. Now Job.Spec.Timeout aligns with plex max wait time for job completion.

Example

Initialize a diffdock job, which generally takes 10+ min.

./plex init -t tools/diffdock.json -i '{"protein": ["testdata/binding/pdbbind_processed_size1/6d08/6d08_protein_processed.pdb"], "small_molecule": ["testdata/binding/pdbbind_processed_size1/6d08/6d08_ligand.sdf"]}' --scatteringMethod=crossProduct                            
Plex version (v0.10.2) up to date.
Pinned IO JSON CID: QmaAZVjACY5bS2eNnvCqYRGxAXDgL4W7WYAuDENKYs3Nbp

Set maxTime flag to 1 min.

./plex run -i QmaAZVjACY5bS2eNnvCqYRGxAXDgL4W7WYAuDENKYs3Nbp -m 1 -a test
Plex version (v0.10.2) up to date.
Created working directory:  /Users/aakaash/Desktop/code/OPENLAB/plex/jobs/c602e946-fb2c-4dea-b60a-aaf272540c9d
Initialized IO file at:  /Users/aakaash/Desktop/code/OPENLAB/plex/jobs/c602e946-fb2c-4dea-b60a-aaf272540c9d/io.json
Processing IO Entries
Starting to process IO entry 0 
Job running...
Bacalhau job id: 0b29d97f-021a-4cbd-b5ad-3bab9b807a09 
Error processing IO entry 0 
error getting Bacalhau job results: bacalhau job did not finish within the expected time (~1 min); please check the job status manually with `bacalhau describe 0b29d97f-021a-4cbd-b5ad-3bab9b807a09`
Finished processing, results written to /Users/aakaash/Desktop/code/OPENLAB/plex/jobs/c602e946-fb2c-4dea-b60a-aaf272540c9d/io.json
Completed IO JSON CID: QmXpgknt7B1XDkiU9V66PDdx5jkNXYcRdcme4NSRxFy5st

Expected behavior of a job timeout occurs.

@acashmoney acashmoney linked an issue Sep 7, 2023 that may be closed by this pull request
[LAB-596] configure bacalhau job timeout value equal to maxTime flag #635
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linear bot commented Sep 7, 2023

LAB-596 configure bacalhau job timeout value equal to `maxTime` flag

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vercel bot commented Sep 7, 2023 •
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@acashmoney acashmoney temporarily deployed to ci September 7, 2023 08:15 — with GitHub Actions Inactive
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@acashmoney acashmoney merged commit 273161c into main Sep 7, 2023
@acashmoney acashmoney deleted the 635-lab-596-configure-bacalhau-job-timeout-value-equal-to-maxtime-flag branch September 7, 2023 08:23
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[LAB-596] configure bacalhau job timeout value equal to maxTime flag

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