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Bug #4248
closedcrash on large substack database insertion
Status:
Closed
Priority:
Normal
Assignee:
-
Category:
-
Target version:
-
Start date:
06/08/2016
Due date:
% Done:
0%
Estimated time:
Affected Version:
Appion/Leginon 3.3
Show in known bugs:
No
Workaround:
Description
I was running the mean stdev substack program on a 128 box stack with 20,876 particles. Command:
stackFilter.py --old-stack-id=1 --description="remove extreme mean stdev" --minx=2200 --maxx=5300 --miny=340 --maxy=700 --commit --rundir=/emg/data/appion/artemia2/stacks/meanfilt1 --runname=meanfilt1 --projectid=1 --expid=3 --jobtype=makestack
Most of the particles with kept:
... received 20876 stack particles in 5.69 sec 20263 included
Error message:
got old stackdata in 2.47 msec ... created new stackdata in 8.05 msec ... Getting list of particles to include ... Completed in 49.61 msec ... Retrieving original stack information ... Completed in 53.38 msec ... Assembling database insertion command ... Inserting particle information into database connecting Traceback (most recent call last): File "/emg/sw/myami/appion/bin/stackFilter.py", line 102, in <module> subStack.start() File "/emg/sw/myami/appion/bin/stackFilter.py", line 91, in start apStack.commitSubStack(self.params, newname, oldstackparts=stackparts) File "/usr/lib64/python2.6/site-packages/appionlib/apStack.py", line 590, in commitSubStack sinedon.directq.complexMysqlQuery('appiondata',sqlcmd) File "/usr/lib/python2.6/site-packages/sinedon/directq.py", line 24, in complexMysqlQuery results = cur.selectall(query) File "/usr/lib/python2.6/site-packages/sinedon/sqldb.py", line 42, in selectall self.c.execute(strSQL, param) File "/usr/lib64/python2.6/site-packages/MySQLdb/cursors.py", line 173, in execute self.errorhandler(self, exc, value) File "/usr/lib64/python2.6/site-packages/MySQLdb/connections.py", line 36, in defaulterrorhandler raise errorclass, errorvalue _mysql_exceptions.OperationalError: (1153, "Got a packet bigger than 'max_allowed_packet' bytes")
Not sure who I should assign this to, but any suggestions to fix?
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