That actually helps. I don't have any choice in running LSF but knowing that
it didn't work because LSF is rejecting it helps when I talk to my boss about
why I couldn't do it.
On 5/03/2014, at 10:28 pm, Charles Girardot <charles.girar...@embl.de> wrote:
> Hi Shane,
> 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
>> Please keep all replies on the list by using "reply all"
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> Charles Girardot
> Head of Genome Biology Computational Support (GBCS)
> European Molecular Biology Laboratory
> Tel: +49 6221 387 -8585
> Fax: +49-(0)6221-387-8166
> Email: charles.girar...@embl.de
> Room V205
> Meyerhofstraße 1,
> 69117 Heidelberg, Germany
Dr Shane Sturrock
Tel: +64 (0) 9 379 5064
76 Anzac Ave
Please keep all replies on the list by using "reply all"
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