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Slurm testing on Travis, update SLURM templates #252

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@tdhock tdhock commented Dec 9, 2019

Hi @mllg this PR was motivated by an application in which I am using batchtools with SLURM on some data stored in a path that has some unusual characters (spaces, parentheses).

It provides a fix for the slurm templates, by using shQuote on the log file path.

It also provides test cases in test_slurm.R which use a local 1-node slurm cluster running on travis CI. (I updated the travis config file so that slurm is installed and configured)

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tdhock commented Dec 9, 2019

my fork/branch passes travis with 1 new NOTE about MPI that I was unsure of how to fix, https://travis-ci.org/tdhock/batchtools/jobs/622901681#L1033

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Coverage Status

Coverage increased (+0.3%) to 87.839% when pulling 62ae838 on tdhock:slurm-registry-paths into 7f45a72 on mllg:master.

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tdhock commented Dec 9, 2019

you may consider adding a test/shQuote for the --name parameter in the slurm templates, which also causes problems if there are spaces.

More generally it would be easier for the user to understand how to fix the problem if batchtools could detect these situations and give an informative error message.

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