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Use "$NCPUS" if defined to set GALAXY_SLOTS #2145

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merged 1 commit into from Apr 14, 2016

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commented Apr 13, 2016

On our PBS cluster we do not have $PBS_NCPUS, and $PBS_NODEFILE contains the
hostname of the nodes the task runs on. But we do have "$NCPUS" with the
correct number of CPUS.

Use "$NCPUS" if defined to set GALAXY_SLOTS
On our PBS cluster we do not have $PBS_NCPUS, and $PBS_NODEFILE contains the
hostname of the nodes the task runs on. But we do have "$NCPUS" with the
correct number of CPUS.

@galaxybot galaxybot added this to the 16.07 milestone Apr 13, 2016

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commented Apr 13, 2016

@natefoo

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commented Apr 14, 2016

Makes me wonder how slots ever worked with PBSPro.

@nsoranzo nsoranzo merged commit 148d4ee into galaxyproject:dev Apr 14, 2016

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commented Apr 14, 2016

Hmm, maybe if you request mpiprocs in the same time?

The number of lines in PBS_NODEFILE is the sum of the val-ues of mpiprocs for all chunks requested by the job. For each chunk with mpiprocs=P, the host name for that chunk is written to the PBS_NODEFILEP times.

martenson added a commit that referenced this pull request Apr 15, 2016

@mvdbeek mvdbeek deleted the mvdbeek:pbs_ncpu branch Nov 23, 2016

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