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clusterOptions does not work with CLI flags (LSF executor) #4935

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timini opened this issue Apr 19, 2024 · 3 comments · Fixed by #4993
Closed

clusterOptions does not work with CLI flags (LSF executor) #4935

timini opened this issue Apr 19, 2024 · 3 comments · Fixed by #4993
Labels
executor/lsf
Milestone
24.04.0

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@timini
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timini commented Apr 19, 2024

Bug report

when specigying a clusterOptions which includes a flag the Grid executor header is constructed wrongly by nextflow

e.g profile.config :

clusterOptions = { "-g /${_queue_group} -app ${params.fast_track ? params.lsf_fast_track_profile : task.process.tokenize(':')[-1].toLowerCase()} -sp ${params.hpc_priority} -P ${params.lsf_project_name} -rn" }

results in the following BSUB command (LSF executor)

#!/bin/bash
#BSUB -o /home/tim/nextflow/13/e0aeb3d2121ed180dc3272e28de8a0/.command.log
#BSUB -q high
#BSUB -W 24:00
#BSUB -J nf-DELIVERY_INTEGRITY_MOVE_DELIVERY_(HX23697398_LP5221738-DNA_H07)
#BSUB -rn -g
#BSUB /high -app
# NEXTFLOW TASK: DELIVERY_INTEGRITY:MOVE_DELIVERY (HX23697398/LP5221738-DNA_H07)
set -e
set -u
NXF_DEBUG=${NXF_DEBUG:=0}; [[ $NXF_DEBUG > 1 ]] && set -x
NXF_ENTRY=${1:-nxf_main}

Expected behavior and actual behavior

I would expect flags (keys with no values) to be correctly rendered in the BSUB option lists

#!/bin/bash
#BSUB -o /home/tim/nextflow/13/e0aeb3d2121ed180dc3272e28de8a0/.command.log
#BSUB -q high
#BSUB -W 24:00
#BSUB -J nf-DELIVERY_INTEGRITY_MOVE_DELIVERY_(HX23697398_LP5221738-DNA_H07)
#BSUB -rn 
#BSUB -g /high
#BSUB  -app something
# NEXTFLOW TASK: DELIVERY_INTEGRITY:MOVE_DELIVERY (HX23697398/LP5221738-DNA_H07)
set -e
set -u
NXF_DEBUG=${NXF_DEBUG:=0}; [[ $NXF_DEBUG > 1 ]] && set -x
NXF_ENTRY=${1:-nxf_main}

Steps to reproduce the problem

(Provide a test case that reproduce the problem either with a self-contained script or GitHub repository)

Program output

(Copy and paste here output produced by the failing execution. Please highlight it as a code block. Whenever possible upload the .nextflow.log file.)

Environment

  • Nextflow version: [?]
  • Java version: [?]
  • Operating system: [macOS, Linux, etc]
  • Bash version: (use the command $SHELL --version)

Additional context

(Add any other context about the problem here)
@timini timini mentioned this issue Apr 19, 2024
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@bentsherman
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It is because the abstract grid executor assumes the cluster options are provided as key-value pairs:

nextflow/modules/nextflow/src/main/groovy/nextflow/executor/AbstractGridExecutor.groovy

Lines 95 to 116 in 7c9d965

String getHeaders( TaskRun task ) {
final token = getHeaderToken()
def result = new StringBuilder()
def header = new ArrayList(2)
def dir = getDirectives(task)
def len = dir.size()-1
for( int i=0; i<len; i+=2) {
def opt = dir[i]
def val = dir[i+1]
if( opt ) header.add(opt)
if( val ) header.add(wrapHeader(val))
if( header ) {
result << token << ' ' << header.join(' ') << '\n'
}
header.clear()
}
return result.toString()
}

So you can probably make clusterOptions work by inserting a blank value after -rn:

clusterOptions = { "-g /${_queue_group} -app ${params.fast_track ? params.lsf_fast_track_profile : task.process.tokenize(':')[-1].toLowerCase()} -sp ${params.hpc_priority} -P ${params.lsf_project_name} -rn ''" }

@bentsherman
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@pditommaso what if we allow clusterOptions to be a list of strings, then it becomes clear how to map the options to the directive lines:

clusterOptions = { [
  "-g /${_queue_group}",
  "-app ${params.fast_track ? params.lsf_fast_track_profile : task.process.tokenize(':')[-1].toLowerCase()}",
  "-sp ${params.hpc_priority}",
  "-P ${params.lsf_project_name}",
  "-rn" ] }

@pditommaso
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It makes sense

@bentsherman bentsherman mentioned this issue May 1, 2024
Closed
@pditommaso pditommaso mentioned this issue May 11, 2024
Merged
@bentsherman bentsherman linked a pull request May 11, 2024 that will close this issue
Implements clusterOptions as a list #4993
Merged
@pditommaso pditommaso added this to the 24.04.0 milestone May 12, 2024
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24.04.0
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@timini @pditommaso @bentsherman