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Bug #3025

open

MySQL server has gone away

Added by Melody Campbell over 9 years ago. Updated over 9 years ago.

Status:
In Test
Priority:
High
Assignee:
Melody Campbell
Category:
-
Target version:
-
Start date:
03/22/2015
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.1.0
Show in known bugs:
No
Workaround:

Description

Hi,
I think we might have had an issue with this earlier but I can't seem to find it. My cl2d jobs (both xmipp2 and xmipp3) won't upload to appion when I run them (from garibaldi). I get the following error:

Traceback (most recent call last):
File "/opt/applications/myami/trunk/bin/runXmipp3CL2D.py", line 634, in <module>
cl2d.start()
File "/opt/applications/myami/trunk/bin/runXmipp3CL2D.py", line 605, in start
self.apix = apStack.getStackPixelSizeFromStackId(self.runparams['stackid'])*self.runparams['bin']
File "/opt/applications/myami/trunk/lib/python2.6/site-packages/appionlib/apStack.py", line 560, in getStackPixelSizeFromStackId
stackdata = getOnlyStackData(stackId, msg=msg)
File "/opt/applications/myami/trunk/lib/python2.6/site-packages/appionlib/apStack.py", line 144, in getOnlyStackData
stackdata = appiondata.ApStackData.direct_query(stackid)
File "/opt/applications/myami/trunk/lib/python2.6/site-packages/sinedon/data.py", line 428, in direct_query
result = db.direct_query(cls, dbid, **kwargs)
File "/opt/applications/myami/trunk/lib/python2.6/site-packages/sinedon/dbdatakeeper.py", line 59, in direct_query
result = self.dbd.multipleQueries(queryinfo, readimages=readimages)
File "/opt/applications/myami/trunk/lib/python2.6/site-packages/sinedon/sqldict.py", line 246, in multipleQueries
return multipleQueries(self.db, queryinfo, readimages)
File "/opt/applications/myami/trunk/lib/python2.6/site-packages/sinedon/sqldict.py", line 520, in init
self.execute()
File "/opt/applications/myami/trunk/lib/python2.6/site-packages/sinedon/sqldict.py", line 533, in execute
c = self._cursor()
File "/opt/applications/myami/trunk/lib/python2.6/site-packages/sinedon/sqldict.py", line 523, in _cursor
self.db.ping()
_mysql_exceptions.OperationalError: (2006, 'MySQL server has gone away')
Exception _mysql_exceptions.OperationalError: (2006, 'MySQL server has gone away') in <bound method CL2D._del__ of <__main__.CL2D object at 0x1b0c210>> ignored

The directory is here: /gpfs/group/em/appion/15mar13a/align/cl2d3-why

Dmitry had written a script to upload the results to appion even if it crashed in this way, but it doesn't seem to work for me. Perhaps it is related to this issue and has to do with the server being reset? #2414

Thanks!
Melody

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