Slurm testing on Travis, update SLURM templates

mllg / batchtools

Tools for computation on batch systems

https://mllg.github.io/batchtools/

GNU Lesser General Public License v3.0

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Slurm testing on Travis, update SLURM templates #252

Open tdhock opened 4 years ago

tdhock commented 4 years ago

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)

tdhock commented 4 years ago

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

coveralls commented 4 years ago

Coverage increased (+0.3%) to 87.839% when pulling 62ae838da98cb2efbcae5673e47d61b6f0929a12 on tdhock:slurm-registry-paths into 7f45a72290a061a85baf0bde2091b1d79af1d198 on mllg:master.

tdhock commented 4 years ago

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.