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Make it easier to use job re-submission conditions. #3319

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commented Dec 15, 2016

Two commits, two ways to make it easier.

  • The first commit adds more documentation for job re-submission. This covers all the expressions and variables added in #3291. Yes I know job_conf.xml.sample_advanced is already very complicated - it absolutely should be replaced by a series of examples documented in the Sphinx docs - but I think that is outside the scope of this PR.
  • The second commit adds a default re-submission condition that applies for all job destinations by default. It makes it easier to say simple things like "just retry all jobs that fail quickly a few times" - as documented in galaxy.ini.sample.

@jmchilton jmchilton added this to the 17.01 milestone Dec 15, 2016

@jmchilton jmchilton force-pushed the jmchilton:job_resubmission_refinement_0 branch 3 times, most recently from 73abe91 to d4ea021 Dec 16, 2016

is available). These expressions include math and logical operators, numbers,
strings, etc.... The following variables are available in these expressions:
- "walltime_reached" (True if and only the job runner indicates a walltime maximum was reached)

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@bgruening

bgruening Jan 4, 2017

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Should this be iff, True, if and only if the job ...?

strings, etc.... The following variables are available in these expressions:
- "walltime_reached" (True if and only the job runner indicates a walltime maximum was reached)
- "memory_limit_reached" (True if and only the job runner indicates a memory limit was hit)

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bgruening Jan 4, 2017

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Some here, is a if missing?

<destination id="retry_on_unknown_problems" runner="slurm">
<!-- Just retry the job 5 times if un-categories errors occur backing
off by 30 more seconds between attempts. -->
<resubmit condition="unknown_error and attempt &lt;= 5 and " delay="attempt * 30" />

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@bgruening

bgruening Jan 4, 2017

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what does the leading and is doing?

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@jmchilton

jmchilton Jan 4, 2017

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Yup - that is just broken. I'll fix that.

@jmchilton jmchilton force-pushed the jmchilton:job_resubmission_refinement_0 branch from d4ea021 to 34f0b0f Jan 4, 2017

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commented Jan 4, 2017

@bgruening Thanks for the review - I believe I have made the requested changes and rebased.

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commented Jan 4, 2017

@galaxybot test this

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commented Jan 6, 2017

@galaxybot test this

@bgruening bgruening merged commit bb5d450 into galaxyproject:dev Jan 8, 2017

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