Do you have any memory limits (in particular, h_vmem) imposed on your batch jobs?
On Fri, May 04, 2018 at 01:45:24PM +0000, Simon Andrews wrote: > I've got a strange problem on our cluster where some python programs are > segfaulting when run through qsub, but work fine on the command line, or even > if run remotely through SSH. > > Really simple (hello world) programs work OK, but anything which does a > significant amount of imports seems to fail. So for example; > > htseq-count > > works locally, but > > qsub -o test.log -cwd -V -j y -b y htseq-count > > Produces a segfault in the executed program. > > ssh compute-0-0 htseq-count > > ..works fine (we're using ssh to launch jobs on our cluster) > > Any suggestions for how to go about trying to track this down? > > Thanks > > Simon. > > The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT > Registered Charity No. 1053902. > The information transmitted in this email is directed only to the addressee. > If you received this in error, please contact the sender and delete this > email from your system. The contents of this e-mail are the views of the > sender and do not necessarily represent the views of the Babraham Institute. > Full conditions at: www.babraham.ac.uk<http://www.babraham.ac.uk/terms> > _______________________________________________ > users mailing list > users@gridengine.org > https://gridengine.org/mailman/listinfo/users -- -- Skylar Thompson (skyl...@u.washington.edu) -- Genome Sciences Department, System Administrator -- Foege Building S046, (206)-685-7354 -- University of Washington School of Medicine _______________________________________________ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users
