Support for OpenLava versions 2.2/3.x?

[Andrew MacBride]

Hello,

I was looking at running one of my existing NextFlow pipelines on an LSF cluster (OpenLava 2.2/3.x), but the current LsfExecutor.groovy seems to generate bsub commands in .command.run that OpenLava 2.2/3.1 doesn't understand.

In particular, it's trying to the set the CWD:

result << '-cwd' << task.workDir.toString()

...but the current versions of OpenLava's bsub don't support it. (It interprets it as a CPULIMIT specifier, the -c flag).

bsub -I "ls /tmp"

Job <3> is submitted to default queue <normal>.

vs.

bsub -I -cwd "/tmp" "ls /tmp"

wd: Bad CPULIMIT specification. Job not submitted.

The generated script:

#!/bin/bash

#BSUB -cwd /nfs/nextflow/work/4a/544a1111e5ba226fd60be0f9627282

#BSUB -o /nfs/nextflow/work/4a/544a1111e5ba226fd60be0f9627282/.command.log

#BSUB -J nf-startup_(1)

[etc.]

Is there any workaround? (Or am I missing something?)

Thanks,

Andrew

[Paolo Di Tommaso]

Hi Andrew, 

It looks that Open Lava is not 100% with LSF. There's no immediate workaround but this could be a good opportunity to implement an explicit support for it in Nextflow.  

What is directive that OpenLava expects to set the job working directory? 

Cheers,

Paolo

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[Andrew MacBride]

Hi Paolo,

I haven't found anything obvious that allows one to set the working directory, but I've asked on the OpenLava list, and will let you know if I hear anything. (The $LS_SUBCWD env var shows the submission directory, but it's read-only.)

Many thanks,

Andrew

[Andrew MacBride]

I've fiddled around myself, and this seems to work (adding an explicit cd to the command), but is somewhat awkward.

bsub  -I 'cd /tmp; pwd'

Would that suffice for a future OpenLavaExecutor.groovy?

Best,

Andrew

[Paolo Di Tommaso]

Actually the setting of the working directory is redundant because the job is launched in that folder. 

I'm wondering if could be enough to remove the `-cwd` option from the LSF executor to make it compatible with OpenLava. 

Please let's continue this discussion here 

https://github.com/nextflow-io/nextflow/issues/152

Cheers, p