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.
-John
On Fri, Aug 15, 2014 at 12:47 PM, Michael Mason MMason@benaroyaresearch.org wrote:
Hi John,
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. Thanks again. Mike
On 8/15/14 9:32 AM, "John Chilton" jmchilton@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.
Good luck,
-John
On Wed, Aug 13, 2014 at 6:46 PM, Michael Mason MMason@benaroyaresearch.org wrote:
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 folks. Thanks for your help. Below is the tip call. BTW we are using Galaxy with 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 of our difficulty killing jobs.
tip 13753:d3b1f484c4b6bbb3daa50fa167eef97a384890b3 latest_2014.06.02 13742:8a863a311a6c9f14b302799bffcf94df9186fef7 release_2014.06.02 13712:7e257c7b10badb65772b1528cb61d58175a42e47 latest_2014.04.14 13085:68a8b0397947c732b28207d465d3f3c4e2a7a8a0 release_2014.04.14 13064:9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.02.10 12440:5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2013.11.04 11218:26f58e05aa1068761660681583821e21e6cbf7ab release_2013.08.12 10392:1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 release_2013.06.03 9943:524f246ca85395082719ae7a6ff72260d7ad5612 security_2013.04.08 9292:2cc8d10988e03257dc7b97f8bb332c7df745d1dd release_2013.04.01 9231:75f09617abaadbc8cc732bb8ee519decaeb56ea7 release_2013.02.08 8794:1c717491139269651bb59687563da9410b84c65d release_2013.01.13 8530:a4113cc1cb5eaa68091c9a73375f00555b66dd11
On 8/13/14 1:39 PM, "John Chilton" jmchilton@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 additional insight.
-John
On Tue, Aug 12, 2014 at 12:10 PM, Michael Mason MMason@benaroyaresearch.org wrote:
Hello all,
I am running a Galaxy instance on slurm. I am unable to stop jobs via the admin "Manage Jobs" window. Via postgres, there are no jobs in the job table. Any thoughts? I realize this may not be dev but I am at a loss of what to do. Thanks Mike ________________________________ --CONFIDENTIALITY NOTICE--: The information contained in this email is intended for the exclusive use of the addressee and may contain confidential information. If you are not the intended recipient, you are hereby notified that any form of dissemination of this communication is strictly prohibited. www.benaroyaresearch.org
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--CONFIDENTIALITY NOTICE--: The information contained in this email is intended for the exclusive use of the addressee and may contain confidential information. If you are not the intended recipient, you are hereby notified that any form of dissemination of this communication is strictly prohibited. www.benaroyaresearch.org
--CONFIDENTIALITY NOTICE--: The information contained in this email is intended for the exclusive use of the addressee and may contain confidential information. If you are not the intended recipient, you are hereby notified that any form of dissemination of this communication is strictly prohibited. www.benaroyaresearch.org