SGE - problem specifying parallel environment

[lonsbio]

From [email protected] on 2014-04-15T18:25:20Z

Hi,

switched our cluster to SGE the other day and wanted to run a simple bpipe pipeline. However, specifying resources as described in the documentation yields an error. For example, we have a PE called 'nodejob', so I specify:

procs="nodejob 8"

When running this, I get

An error occurred executing your pipeline:

                               For input string: "nodejob 8"                                    

Please see the details below for more information.

========================================== Error Details ===========================================

java.lang.NumberFormatException: For input string: "nodejob 8" at bpipe.PipelineContext.async(PipelineContext.groovy:1468) at bpipe.PipelineContext.async(PipelineContext.groovy) at bpipe.PipelineContext.exec(PipelineContext.groovy:1272) at bpipe.PipelineContext.exec(PipelineContext.groovy:1221) at bpipe.PipelineContext.invokeMethod(PipelineContext.groovy) at bpipe.PipelineDelegate.methodMissing(PipelineDelegate.groovy:133) at bpipe.PipelineDelegate.invokeMethod(PipelineDelegate.groovy) at Script1$_run_closure2_closure8.doCall(Script1.groovy:35) at Script1$_run_closure2_closure8.doCall(Script1.groovy) [SNIP]

Bpipe version: 0.9.8.6_beta_3 Grid engine version: OGS/GE 2011.11

Original issue: http://code.google.com/p/bpipe/issues/detail?id=96

[lonsbio]

From [email protected] on 2014-04-15T23:05:48Z

Further investigation has tracked this down to a formatting issue in the 'exec' command - i.e. when changing the order of some variables set in the command, it could execute fine on SGE. The same file ran fine on Slurm and locally prior to this change. However the problem could not be reproduced. Please close.

[gdevenyi]

Solved be new template system, can be closed.