Fantastic - thanks for the update! I hope it is okay - I am cc'ing the
-dev list so if people search on this problem in the future and search
the can see what the problem turned out to be and how to fix it. Enjoy
your job killing.
On Fri, Aug 15, 2014 at 12:47 PM, Michael Mason
Just an update on the hypothesis. Our server guy figured out that the nfs
memory setting was such that Galaxy used all the memory. He believes this
resulted in no memory for jobs to be killed. He changed the setting so
that there is some leftover memory when I am using Galaxy at an all out
pace and I was able to kill jobs this morning.
On 8/15/14 9:32 AM, "John Chilton" <jmchilton(a)gmail.com> wrote:
>Very interesting - whenever you get a chance I would try to kill
>simple jobs when Galaxy is not under load to verify the problem is
>related to Galaxy's job load. If you still have problems I would then
>try again to get that stack trace.
>On Wed, Aug 13, 2014 at 6:46 PM, Michael Mason
>> Hi John,
>> We actually went ahead and recovered an archived instance from Friday.
>> This should should be the same build though. Because of the archived
>> instance I believe we lost the stack trace but I'll check with the IT
>> Thanks for your help. Below is the tip call. BTW we are using Galaxy
>> fastq's from a Fluidigm's C1 machine. This means we often run 100-200
>> libraries on a single flow cell. The resulting 100-200 libraries tend to
>> tax Galaxy. But it tends to handle it though this may be the root cause
>> our difficulty killing jobs.
>> On 8/13/14 1:39 PM, "John Chilton" <jmchilton(a)gmail.com> wrote:
>>>When was the last time you updated Galaxy - we fixed a bug that would
>>>be causing this behavior several releases ago.
>>>Otherwise - additional information would help - like are you using the
>>>DRMAA job runner or the newer specialized Slurm job runner and are
>>>there any details in the Galaxy log that might be helpful? I would
>>>expect to see a stack trace of some kind if there are problems like
>>>this. If there are no stack traces and you have an update-to-date
>>>Galaxy - perhaps checking the SLURM logs for errors might also provide
>>>On Tue, Aug 12, 2014 at 12:10 PM, Michael Mason
>>>> Hello all,
>>>> I am running a Galaxy instance on slurm. I am unable to stop jobs via
>>>> admin "Manage Jobs" window. Via postgres, there are no jobs in
>>>> table. Any thoughts?
>>>> I realize this may not be dev but I am at a loss of what to do.
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