> Am 04.05.2018 um 16:10 schrieb Skylar Thompson <skyl...@uw.edu>: > > Do you have any memory limits (in particular, h_vmem) imposed on your batch > jobs?
Also worth to be checked is the setting of the stack size. Certain applications need a set stack size of 8 MB to 128 MB instead of being left as unlimited. You can compare the limits for the interactive access and a job submission by using: echo hard limits ulimit -aH echo soft limits ulimit -aS -- Reuti > > 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 _______________________________________________ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users
