Allow for a per-job memory limit for LSF executor

[mfoll]

LSF implements both a per-process or a per-job memory limit: https://www.ibm.com/support/knowledgecenter/#!/SSETD4_9.1.3/lsf_config_ref/lsf.conf.lsb_job_memlimit.5.dita

Currently nextflow assumes it's a per-process limit and therefore divides the amount of memory requested by the number of cpus requested (

nextflow/src/main/groovy/nextflow/executor/LsfExecutor.groovy

Line 66 in c49f561

// LSF specify per-process (per-core) memory limit (in MB)

).

It would be useful to have a flag in the nextflow config file to control for this and avoid dividing if the limit is per-job.

[pditommaso]

OK. I've uploaded a new snapshot including this patch.

You can switch to the per-job memory limit mode adding the following config setting in your nextflow.config file.

executor {
     perJobMemLimit=true
}

To use this snapshot prepend the variable NXF_VER=0.18.0-SNAPSHOT to your nextflow command line, for example:

NXF_VER=0.18.0-SNAPSHOT nextflow run .. 

Could you please give it a try to verify that this and #124 are working as expected?

[mfoll]

Thanks, I just tried and it's working great! Just one thing for #124, when perJobMemLimit=false you should still not divide the memory by the number of cpus for the reservation.

[pditommaso]

Oops, you are right. Thanks!