[ADAM-1442] Fix thread pool deadlock in GenomicRDD.pipe #1443
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Resolves bigdatagenomics#1442. Eliminates use of thread pool in GenomicRDD and instead launches the InFormatterRunner (which extends `Callable`) as a thread and runs the OutFormatterRunner in the original thread that launched the piped subprocess. Additionally, rewrote the `AnySAMOutFormatter` to improve performance.
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Test FAILed. Build result: FAILURE[...truncated 16 lines...] > /home/jenkins/git2/bin/git rev-parse origin/pr/1443/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 27a25d8d1f707bfe451f787b310ef7f5689a5c5e # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1443/merge^{commit} # timeout=10Checking out Revision 27a25d8d1f707bfe451f787b310ef7f5689a5c5e (origin/pr/1443/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 27a25d8d1f707bfe451f787b310ef7f5689a5c5eFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.3.0,2.11,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.3.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.11,2.0.0,centosTriggering ADAM-prb ? 2.6.0,2.10,2.0.0,centosTriggering ADAM-prb ? 2.3.0,2.10,1.6.1,centosTriggering ADAM-prb ? 2.6.0,2.11,1.6.1,centosADAM-prb ? 2.3.0,2.11,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.10,2.0.0,centos completed with result SUCCESSADAM-prb ? 2.3.0,2.10,1.6.1,centos completed with result SUCCESSADAM-prb ? 2.6.0,2.11,1.6.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Test FAILed. |
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Jenkins, retest this please. |
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Test PASSed. |
heuermh
approved these changes
Mar 21, 2017
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Thank you, @fnothaft! |
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Resolves #1442. Eliminates use of thread pool in GenomicRDD and instead launches the InFormatterRunner (which extends
Callable) as a thread and runs the OutFormatterRunner in the original thread that launched the piped subprocess.Additionally, rewrote the
AnySAMOutFormatterto improve performance.With this, BWA-on-Cannoli works (https://github.com/heuermh/cannoli/pull/2).