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levinboimtomer / JUST

A tool for constructing and executing experiment pipelines on a cluster
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workdir cannot contain / when using qsub #9

Open KentonMurray opened 7 years ago

KentonMurray commented 7 years ago

Here's the stacktrace. Removing the trailing slash from the workdir fixes the problem.

[kmurray4@crcfe01 il3]$ python ../../../../../../software/just/just.py basic_moses.just --workdir test_just/ --q '@@nlp' JUST: running: qsub -q @@nlp -N s1.train.wd=test_just/ -v workdir=test_just/ test_just//s1.train.sh qsub: ERROR! argument to -N option must not contain /

levinboimtomer commented 7 years ago

As the error message informs, the problem is with qsub's -N switch which assigns a name to the submitted job, and prohibits using "/". How about replacing "/" with "_" at line 206: cmdargs.workdir.replace("/", "\").

KentonMurray commented 7 years ago

Yeah, I think that's fine. This is only a minor bug ... you just get the / when you tab complete.