On 9/12/13 10:35 AM, "Peter Cock" <p.j.a.c...@googlemail.com> wrote:

>On Thu, Sep 12, 2013 at 2:01 PM, Mathieu Bahin <mathieu.ba...@irisa.fr>
>> Hi all,
>> We have been developing our own Galaxy instance for a while now. We
>>have a
>> cluster on which the job are sent to be executed, it is managed through
>> Usually, communication between SGE and DRMAA is ok and we don't have any
>> problem with that.
>> When a job is deleted by the user, most of the times, the job
>>disappears but
>> sometimes, we don't know why, the job stays and has the status 'dr'
>> SGE. If we don't kill it 'manually', it stays forever. It is not always
>> same tools which produces this error.
>> Have you any idea why how manage it ?
>I have noticed problem with our DRMMA/SGE setup where a
>user can cancel a large job (using the job splitter in at least some
>cases), but Galaxy does not seem to cancel the jobs on the cluster.
>I've not tried to diagnose this yet - it could be a similar issue though.

Also, in our DRMAA/LSF setup (using a fork of the latest galaxy-dist) jobs
generated by the current workflow step continue running on the cluster
after history is deleted.


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