Project

General

Profile

Actions

Bug #4248

closed

crash on large substack database insertion

Added by Neil Voss over 8 years ago. Updated over 8 years ago.

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?


Related issues 1 (1 open0 closed)

Related to Appion - Bug #3938: Aligned particle problemNew02/08/2016

Actions
Actions

Also available in: Atom PDF