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glennhickey / progressiveCactus

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
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runProgressiveCactus.sh never returns when run with thread/cpu options #92

Open malcook opened 6 years ago

malcook commented 6 years ago

running:

runProgressiveCactus.sh --overwrite examples/blanchette00.txt ./test/blanchette00 ./test/blanchette00/msa.hal  --defaultCpu=20  --maxThreads=20  --logInfo --logFile ./test/blanchette00_LOG.txt

never returns, leaving 21 idle python processes, and a runProgressiveCactus.sh idle process, etc

The job otherwise seems to have completed, with last line in cactus.log being:

2017-10-07 16:43:03.890871: Finished HAL Export

which file passes halValidate

If I run without any cpu/thread/logging options the process returns and the cactus log similarly ends after "Finished HAL Export".

So, I suspect this is something to do with management of process pool take-down upon completion.

joelarmstrong commented 6 years ago

Interesting! This is probably yet another jobTree bug.