It maybe caused by the environment variables. One simple way may be adding something like:
>source myscriptforenv.sh (bash) in your job script. On Fri, May 4, 2018 at 9:45 AM, Simon Andrews <simon.andr...@babraham.ac.uk> 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 > > -- Best, Feng
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