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[15.05] Split initialization of galaxy queue worker. #198

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merged 3 commits into from May 5, 2015

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@dannon
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commented May 1, 2015

Should finally put down my white whale. Also includes logging improvements.

@dannon dannon changed the title Split initialization of galaxy queue worker. [15.05] Split initialization of galaxy queue worker. May 1, 2015

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commented May 1, 2015

I would love for someone that has managed to reliably(ish) reproduce this issue to give it a test. I have seen it once on my own hardware in total, and make a terrible test case for it.

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commented May 5, 2015

So I would say this happens to me once every ~30 times I started Galaxy (your previous re-arrangement or other dev setup config changes seemed to decrease this frequency from once every ~15 times). I just switched to this branch and started and killed Galaxy lets say 50 times without hitting the deadlock.

So 👍 - happy to merge this now - or we can wait for a more reliable tester if you think that is going to come.

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commented May 5, 2015

Thanks for testing! I'm comfortable with the reorganization even if it doesn't resolve the issue, though I really hope it does, so yeah, let's go ahead and get it in there and hopefully get more hands testing it whether they want it or not ;)

dannon added a commit that referenced this pull request May 5, 2015

Merge pull request #198 from dannon/kombuaaaaarrgh
[15.05] Split initialization of galaxy queue worker.

@dannon dannon merged commit 69c5952 into galaxyproject:release_15.05 May 5, 2015

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commented May 6, 2015

@dannon - sorry for the delay. Started galaxy 40 times with these changes with no issue. That on the machine that was, and still is giving errors at least every 10 restarts before any of your changes.

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commented May 6, 2015

That's fantastic! Hopefully this is the end of these issues. Thanks for testing!

jmchilton added a commit to jmchilton/galaxy that referenced this pull request May 7, 2015

Fix problem with twill's custom subprocess module.
There has been for some time a scary warning when testing (http://dev.list.galaxyproject.org/run-test-sh-ImportError-cannot-import-name-args-from-interpreter-flags-td4666277.html) that I now understand is the result of Twill being packaged with its own custom subprocess module that conflicts with modules using multiprocessing (e.g. kombu).

After the galaxyproject#198 this scary warning has become an exception that prevents exception of tests (see https://travis-ci.org/galaxyproject/planemo/jobs/61547827 for instance). Importing subprocess seems to force Python to use the system module instead of twills - which seems to prevent these problems.

There have been other reports of this problem with Twill in other projects and removing the subprocess module didn't seem to break anything for them either.

@jmchilton jmchilton added the kind/bug label Aug 12, 2015

@dannon dannon deleted the dannon:kombuaaaaarrgh branch Mar 1, 2016

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