[gridengine users] Debugging crash when running program through GridEngine

Feng Zhang prod.feng at gmail.com
Fri May 4 13:54:56 UTC 2018


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.andrews at 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.
>
>
>
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-- 
Best,

Feng
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