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Bug #3938

open

Aligned particle problem

Added by Scott Stagg almost 9 years ago. Updated almost 9 years ago.

Status:
New
Priority:
Normal
Assignee:
-
Category:
-
Target version:
-
Start date:
02/08/2016
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.2
Show in known bugs:
No
Workaround:

Description

Does anybody else get this when making a new stack from selected particles from an alignment?
... Assembling database insertion command
... Inserting particle information into database
Traceback (most recent call last):
File "/panfs/storage.local/imb/stagg/software/myami-3.2/appion/bin/alignSubStack.py", line 314, in <module>
subStack.start()
File "/panfs/storage.local/imb/stagg/software/myami-3.2/appion/bin/alignSubStack.py", line 306, in start
apStack.commitSubStack(self.params,included=includeParticle)
File "/panfs/storage.local/imb/stagg/software/myami-3.2/appion/appionlib/apStack.py", line 569, in commitSubStack
sinedon.directq.complexMysqlQuery('appiondata',sqlcmd)
File "/panfs/storage.local/imb/stagg/software/myami-3.2/sinedon/directq.py", line 24, in complexMysqlQuery
results = cur.selectall(query)
File "/panfs/storage.local/imb/stagg/software/myami-3.2/sinedon/sqldb.py", line 42, in selectall
self.c.execute(strSQL, param)
File "/usr/lib64/python2.7/site-packages/MySQLdb/cursors.py", line 174, in execute
self.errorhandler(self, exc, value)
File "/usr/lib64/python2.7/site-packages/MySQLdb/connections.py", line 36, in defaulterrorhandler
raise errorclass, errorvalue
_mysql_exceptions.OperationalError: (2006, 'MySQL server has gone away')>

If I revert to myami-3.1, there is no problem because it does the inserts one at a time instead of making one big MySQL insert statement. This only seems to happen for bigger stacks.


Related issues 1 (0 open1 closed)

Related to Appion - Bug #4248: crash on large substack database insertionClosed06/08/2016

Actions
Actions #1

Updated by Anchi Cheng almost 9 years ago

How big is big ? So that I can ask people around here.

Actions #2

Updated by Scott Stagg almost 9 years ago

90,000 particles

Actions #3

Updated by Scott Stagg almost 9 years ago

Update, Donny changed the MySQL configuration, and I think that fixed it. From Donny:

line 14 in the server configuration file: /etc/my.cnf.d/server.cnf

It was set to 8M and I changed it to
max_allowed_packet = 32M

Actions #4

Updated by Neil Voss over 8 years ago

  • Related to Bug #4248: crash on large substack database insertion added
Actions

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