Hi,
indeed, you are right. In the database, the "job_runner_external_id"
column is empty for all jobs causing the crash of Galaxy when they are
stopped. I tried to launch the instance without the --daemon option and
I have got this segmentation fault as you suspected:
run.sh: line 77: 19622 Segmentation fault (core dumped)
/local/python/2.7-bis/bin/python ./scripts/paster.py serve
universe_wsgi.ini
If I understand, we can't delete a job with the state "new" (associated
with an empty "job_runner_external_id" column)?
Thanks,
Cyril
On 01/09/2013 07:51 PM, Nate Coraor wrote:
Hi Cyril,
If you start the server in the foreground (no --daemon option), is there a
segfault when the process dies? If so, this is most likely a problem where a
job is attempting to be stopped that does not have an external job ID set.
Could you check this in the database for one of the jobs that's causing this
(e.g. 3065)?
Thanks,
--nate
On Jan 9, 2013, at 4:39 AM, MONJEAUD wrote:
Hello All,
after more researchs, I found that the crash of the galaxy server was caused by
stopping jobs. We are working with our own SGE cluster.
It's weird because we can kill jobs via history or administration panel without
problem.
In the paster.log, we just got this message before the crash of the server :
galaxy.jobs.handler DEBUG 2013-01-08 16:52:39,877 Stopping job 3065:
galaxy.jobs.handler DEBUG 2013-01-08 16:52:39,877 stopping job 3065 in drmaa
runner
I think this problem comes when there is many jobs in "running", "new" and
"queued" states.
Cheers,
Cyril
On 01/08/2013 04:11 PM, MONJEAUD wrote:
Hello All,
I'm trying to deploy my instance of Galaxy in production. Some tests we've done
show that when the number of person connected is high (>20 together), the
server stops itself.
Sometimes, I have this error in the paster.log:
Exception happened during processing of request from ('127.0.0.1', 60575)
Traceback (most recent call last):
File "/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line
1053, in process_request_in_thread
self.finish_request(request, client_address)
File "/local/python/2.7-bis/lib/python2.7/SocketServer.py", line 323, in
finish_request
self.RequestHandlerClass(request, client_address, self)
File "/local/python/2.7-bis/lib/python2.7/SocketServer.py", line 641, in
__init__
self.finish()
File "/local/python/2.7-bis/lib/python2.7/SocketServer.py", line 694, in
finish
self.wfile.flush()
File "/local/python/2.7-bis/lib/python2.7/socket.py", line 301, in flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
Do you have any ideas about this and how resolve it?
Cheers!!
Cyril
--
Cyril Monjeaud
Equipe Symbiose / Plate-forme GenOuest
Bureau D156
IRISA-INRIA, Campus de Beaulieu
35042 Rennes cedex, France
Tél: +33 (0) 2 99 84 74 17
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--
Cyril Monjeaud
Equipe Symbiose / Plate-forme GenOuest
Bureau D156
IRISA-INRIA, Campus de Beaulieu
35042 Rennes cedex, France
Tél: +33 (0) 2 99 84 74 17
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
