These are chat archives for nextflow-io/nextflow

28th
Dec 2015
wuyilei
@wuyilei
Dec 28 2015 05:43
Hi guys, I’v encountered a problem when using nextflow on SGE cluster. Not sure whether appropriate to ask here.
My script used the parameter cpus as mentioned in official document on the page of Processes->Directives. But after submit, nextflow always report “use parallel environments instead of requesting slots explicitly”. Our cluster consists of 6 nodes, with grid engine 6.2u5p3 deployed. It seems this version of SGE doesn’t support “#$ -l slots=12”, is that true? Would somebody help on this question? thanks a lot.
Paolo Di Tommaso
@pditommaso
Dec 28 2015 08:30
@wuyilei That is an error message reported by SGE. You need to specify the parallel environment in your script using the penv directive.