SGE syntax

[DustinSokolowski]

Hey!

I am trying to run TOGA on the SGE cluster, which relies on nextflow. My cluster has some relatively specific cluster options (see clusterOptions, but the amount of memory needs to be passed into nextflow memory = "${_MEMORY_}G". I am unable to pass the memory command into clusterOptions (e.g., clusterOptions = { "-V -l h_vmem "${_MEMORY_}G" -V -P simpsonlab -l h_stack=32M -l h_rt=48:00:00" }. Do you know the syntax for this?

Thank you
Dustin

process {
    executor = "sge"
    penv = "smp"
    memory = "${_MEMORY_}G"
    cpus = '1'
    time = '24h'
    clusterOptions = { "-V -l h_vmem=64G -V -P simpsonlab -l h_stack=32M -l h_rt=48:00:00" }
}

executor {
    name = "sge"
    queueSize = 1000
    queueStatInterval = "10s"
}

[bentsherman]

Not sure if you're asking a Nextflow question or an SGE question. But here is how Nextflow defines the memory options:

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

Lines 78 to 82 in 5a01f27

	// task max memory
	if( task.config.getMemory() ) {
	final mem = "${task.config.getMemory().mega}M".toString()
	result << "-l" << "h_rss=$mem,mem_free=$mem".toString()
	}