[gridengine users] Debugging crash when running program through GridEngine

Simon Andrews simon.andrews at babraham.ac.uk
Fri May 4 13:45:24 UTC 2018


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.

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