We had enabled this feature on our cluster working with PBS but since we
switched to LSF, we never managed to have it working again. Same error as yours
if I correctly remember. After hours spent looking into LSF, I think we
understood that LSF somehow catches the user change and rejects the job. We
finally gave up.
I am not sure this helps ...
On 5 Mar 2014, at 02:55, Shane Sturrock wrote:
> Has anyone had any success in getting cluster jobs running as the real user?
> I've got our server happily working with LSF via drmaa but all jobs run as
> the galaxy user and I would like to be able to separate out the jobs on a per
> user basis. I've followed the instructions at
> but I'm having no luck with it so was wondering if someone would know how I
> might debug it, like where could I find the script it is trying to execute?
> All I'm getting is code 18: invalid LSF job id although it does seem to be
> creating files in my databases/tmp directory owned by the user.
> Dr Shane Sturrock
> Senior Scientist
> Tel: +64 (0) 9 379 5064
> 76 Anzac Ave
> New Zealand
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Head of Genome Biology Computational Support (GBCS)
European Molecular Biology Laboratory
Tel: +49 6221 387 -8585
69117 Heidelberg, Germany
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