These are chat archives for nextflow-io/nextflow

8th
Sep 2015
Andrew Stewart
@andrewcstewart
Sep 08 2015 17:08
Anyone ever see "-bash: fork: retry: Resource temporarily unavailable" errors on CentOS while running nextflow?
seems related to having a lot of filehandles open
Paolo Di Tommaso
@pditommaso
Sep 08 2015 17:39
@andrewcstewart No. However did you check the max number of allowed open files?
You should be able to verify it with ulimit -n
or ulimit -a to see all limits
Andrew Stewart
@andrewcstewart
Sep 08 2015 18:01
@pditommaso yeah.. I think ill have to get my sysadmin in on this.
just wondering if its a common occurance
Paolo Di Tommaso
@pditommaso
Sep 08 2015 18:07
I've seen this kind of error, but not with nextflow
usually it's enough to increase the max number of open files
Are you running it within a container ?
Andrew Stewart
@andrewcstewart
Sep 08 2015 19:19
nah, just vanilla
runs fine on one of the host's siblings
but it's a new addition to the rack so it might need some configuration tuning somewhere
Andrew Stewart
@andrewcstewart
Sep 08 2015 20:07
would something like this work for dynamically setting the storeDir directive? storeDir { "${params.results}/$sample_id/bam" }
Paolo Di Tommaso
@pditommaso
Sep 08 2015 20:08
I think so
Andrew Stewart
@andrewcstewart
Sep 08 2015 20:09
I get confused with how string interpolation is supposed to work here
and I think the closure is also necessary
Paolo Di Tommaso
@pditommaso
Sep 08 2015 20:11
dynamic direri
oops
dynamic directives evaluation have been improved
Andrew Stewart
@andrewcstewart
Sep 08 2015 20:13
cool
Paolo Di Tommaso
@pditommaso
Sep 08 2015 20:14
interpolated string values are equivalent to closures
actually they are turned automatically to closures behind the scene