error in uploading the Kerdon SOM results?
Added by Anonymous over 12 years ago
Hi,
When I run a feature analysis with 12 x 12 clusters with 23000 negative stain particles, it works fine till the creation of montage with EMAN, then it crashes with below error. It worked well for 5 x 5 cluster and results are fine. How to solve this error?
Traceback (most recent call last):
File "/usr/local/bin/kerdenSOM.py", line 383, in ?
kerdenSOM.start()
File "/usr/local/bin/kerdenSOM.py", line 374, in start
self.insertKerDenSOM(binned=binned)
File "/usr/local/bin/kerdenSOM.py", line 68, in insertKerDenSOM
projectid = apProject.getProjectIdFromAlignStackId(self.params['alignstackid'])
File "/usr/lib/python2.4/site-packages/appionlib/apProject.py", line 74, in getProjectIdFromAlignStackId
alignstackdata = appiondata.ApAlignStackData.direct_query(alignstackid)
File "/usr/lib/python2.4/site-packages/sinedon/data.py", line 403, in direct_query
result = db.direct_query(cls, dbid, **kwargs)
File "/usr/lib/python2.4/site-packages/sinedon/dbdatakeeper.py", line 59, in direct_query
result = self.dbd.multipleQueries(queryinfo, readimages=readimages)
File "/usr/lib/python2.4/site-packages/sinedon/sqldict.py", line 245, in multipleQueries
return _multipleQueries(self.db, queryinfo, readimages)
File "/usr/lib/python2.4/site-packages/sinedon/sqldict.py", line 504, in init
self.execute()
File "/usr/lib/python2.4/site-packages/sinedon/sqldict.py", line 517, in execute
c = self._cursor()
File "/usr/lib/python2.4/site-packages/sinedon/sqldict.py", line 507, in _cursor
self.db.ping()
_mysql_exceptions.OperationalError: (2006, 'MySQL server has gone away')
regards,
venkata
Replies (3)
RE: error in uploading the Kerdon SOM results? - Added by Anchi Cheng over 12 years ago
Hi, Venkata,
'MySQL server has gone away' means exactly that. Did this run take a long time? You should be able to change mysql timeout according to
http://dev.mysql.com/doc/refman/5.0/en/gone-away.html
to solve this problem.
Anchi
RE: error in uploading the Kerdon SOM results? - Added by Anchi Cheng over 12 years ago
If the actual Kerdon SOM did not take long, I might not be solving your problem in the previous reply. The query it was performing was an easy one but it is true that it might not need database interaction for a long time during the actual run. If the last reply didn't help, please confirm that the alignstackId you inputted is valid. If not, it might be why it is stuck.
Anchi
RE: error in uploading the Kerdon SOM results? - Added by Anonymous over 12 years ago
Dear Anchi,
Yes, it is a long time run of more than 10 hrs. I will take a look for how to change it as per instructions in the link and try.
thanks,
regards
venkata