date:20140808

Re: [galaxy-dev] sql server timeout

2014-08-08 Thread Dannon Baker

Hi Don,

Haven't seen this before myself, but I did a little digging here:
http://docs.sqlalchemy.org/en/rel_0_8/faq.html#mysql-server-has-gone-away

So, to differentiate between those two issues, does this happen very
frequently or only after a long idle?

-Dannon


On Wed, Aug 6, 2014 at 3:15 PM, Shrum, Donald C dcsh...@admin.fsu.edu
wrote:

 On occasion I'm getting and 'Internal Server error' on login with my
 production galaxy server.
 If I refresh the page I'm able to login just fine.

 This instance of galaxy has an apache frontend and a mysql server on the
 back end.   If I look at my log files I see:

 OperationalError: (OperationalError) (2006, 'MySQL server has gone away')
 'SELECT galaxy_session.id AS galaxy_session_id.

 It looks like perhaps galaxy is trying to use a stale session or something
 like that.  Has anyone else seen this problem and is there an easy solution
 aside from having users refresh the page?

 Thanks,
 Don
 FSU Research Computing Center


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Re: [galaxy-dev] bug?

2014-08-08 Thread Dannon Baker

Hey Brad,

So I've dug around and replicated all the requests in the web log you sent
(central#default tip -- what revision are you running?), but I'm not seeing
any unencoded id queries my sql logs (expected this more or less, w/ all of
the requests in your web log being 200 OK's).  The next guess is that it
has to do with job metrics or metadata.  The job itself failed, do you know
why that is?  What job metrics do you have enabled?  And has this been a
consistent issue, or you just happened to notice the error this one time?

-Dannon


On Tue, Aug 5, 2014 at 5:53 PM, Langhorst, Brad langho...@neb.com wrote:

  I tried to do some time correlation between galaxy logs and postgres
 logs…

  postgres
 2014-08-01 17:15:15.643 EDT


  handler1.log
  galaxy.jobs.output_checker INFO 2014-08-01 17:15:08,875 Job 123681:
 Fatal error: Exit code 1 (Interval subtraction error)
 galaxy.jobs DEBUG 2014-08-01 17:15:08,948 setting dataset state to ERROR
 galaxy.jobs INFO 2014-08-01 17:15:09,196 Collecting job metrics for
 galaxy.model.Job object at 0x7fcbacccbb50
 galaxy.jobs DEBUG 2014-08-01 17:15:09,208 job 123681 ended
 galaxy.datatypes.metadata DEBUG 2014-08-01 17:15:09,208 Cleaning up
 external metadata files
 galaxy.jobs.runners.drmaa DEBUG 2014-08-01 17:17:32,338 (123678/1521440)
 state change: job finished normally

  handler0.log
  laxy.datatypes.metadata DEBUG 2014-08-01 17:14:40,572 loading metadata
 from file for: HistoryDatasetAssociation 192134
 galaxy.jobs INFO 2014-08-01 17:14:40,804 Collecting job metrics for
 galaxy.model.Job object at 0x7f15fc281850
 galaxy.jobs DEBUG 2014-08-01 17:14:40,815 job 123680 ended
 galaxy.datatypes.metadata DEBUG 2014-08-01 17:14:40,815 Cleaning up
 external metadata files
 python path is:
 /mnt/galaxy/data/galaxy/galaxy-dist/eggs/kombu-3.0.12-py2.7.egg,
 /mnt/galaxy/data/galaxy/galaxy-dist/eggs/anyjson-0.3.3-py2.7.egg,
 /mnt/galaxy/data/galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs2.egg,
 /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs2.egg,
 /mnt/galaxy/data/galaxy/galaxy-dist/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs2.egg,
 /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs2.egg,
 /mnt/galaxy/data/galaxy/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs2.egg,
 /mnt/galaxy/data/galaxy/galaxy-dist/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs2.egg,
 /mnt/galaxy/data/galaxy/galaxy-dist/eggs/amqp-1.4.3-py2.7.egg,
 /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pexpect-2.4-py2.7.egg,
 /mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg,
 /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Babel-1.3-py2.7.egg,
 /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pytz-2013.9-py2.7.egg,
 /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg,
 /mnt/galaxy/data/galaxy/galaxy-dist/eggs/WebHelpers-1.3-py2.7.egg,
 /mnt/galaxy/data/galaxy/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs2.egg,
 /mnt/galaxy/data/galaxy/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg,
 /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Routes-1.12.3-py2.7.egg,
 /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg,
 /mnt/galaxy/data/galaxy/galaxy-dist/eggs/wchartype-0.1-py2.7.egg,
 /mnt/galaxy/data/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg,
 /mnt/galaxy/data/galaxy/galaxy-dist/eggs/docutils-0.7-py2.7.egg,
 /mnt/galaxy/data/galaxy/galaxy-dist/eggs/PasteDeploy-1.5.0-py2.7.egg,
 /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg,
 /mnt/galaxy/data/galaxy/galaxy-dist/lib,
 /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages/cutadapt-1.3-py2.7-linux-x86_64.egg,
 /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages/distribute-0.6.10-py2.7.egg,
 /mnt/galaxy/data/galaxy/sw/lib/python27.zip,
 /mnt/galaxy/data/galaxy/sw/lib/python2.7,
 /mnt/galaxy/data/galaxy/sw/lib/python2.7/plat-linux2,
 /mnt/galaxy/data/galaxy/sw/lib/python2.7/lib-tk, /mnt/galaxy/da

  ta/galaxy/sw/lib/python2.7/lib-old,
 /mnt/galaxy/data/galaxy/sw/lib/python2.7/lib-dynload,
 /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages

  web0.log
  172.17.130.113 - - [01/Aug/2014:17:14:58 -0400] GET
 /api/histories/39a249c523d1b262/contents HTTP/1.0 200 - 
 http://galaxy.neb.com/root/index; Mozilla/5.0 (Macintosh; Intel Mac OS X
 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chr
 ome/36.0.1985.125 Safari/537.36
 172.17.130.113 - - [01/Aug/2014:17:15:03 -0400] GET
 /datasets/49b19822485c7897/display/?preview=True HTTP/1.0 200 - 
 http://galaxy.neb.com/root/index; Mozilla/5.0 (Macintosh; Intel Mac OS X
 10_9_4) AppleWebKit/537.36 (KHTML, like Ge
 cko) Chrome/36.0.1985.125 Safari/537.36
 172.17.131.223 - - [01/Aug/2014:17:15:03 -0400] GET
 /api/histories/11ff4619ea0fcba9/contents HTTP/1.0 200 - 
 http://galaxy.neb.com/; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_3)
 AppleWebKit/537.76.4 (KHTML, like Gecko) Version/7.0
 .4 Safari/537.76.4
 172.17.130.113 - - [01/Aug/2014:17:15:04

Re: [galaxy-dev] sql server timeout

Re: [galaxy-dev] bug?

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