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Bug #2547

open

jobs crash for specific session (13sep27e)

Added by Gira Bhabha about 11 years ago. Updated about 11 years ago.

Status:
In Test
Priority:
High
Assignee:
Category:
-
Target version:
-
Start date:
10/04/2013
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.0.0
Show in known bugs:
No
Workaround:

Description

ctffind and dogpicker jobs crash for session 13sep27e, with the following error.

----------------------------
AttributeError: 'module' object has no attribute 'MoverParamsData'
----------------------------

jobs end within a few seconds (on goby & guppy)

details:
----------------------------
[gbhabha@goby ~]$ /opt/myamisnap/bin/appion dogPicker.py --projectid=382 --preset=en --session=13sep27e --runname=dogrun1 --rundir=/ami/exdata/appion/13sep27e/extract/dogrun1 --no-rejects --no-wait --commit --continue --peaktype=centerofmass --maxthresh=1.5 --thresh=0.5 --median=2 --lowpass=15 --highpass=0 --planereg --bin=4 --diam=140 --pixlimit=4.0 --kfactor=1.5 --expid=12404 --jobtype=dogpicker

... Time stamp: 13oct04l33
... Function name: dogPicker
... Appion directory: /opt/myamisnap/lib
... Using split database
Connected to database: 'ap382'
... Committing data to database
!!! WARNING: lowpass filter value greater than zero; will ignore
... Found project id=382 for session 13sep27e in 5.64 msec
... Run directory: /ami/exdata/appion/13sep27e/extract/dogrun1
!!! WARNING: directory '/ami/exdata/appion/13sep27e/extract/dogrun1' already exists.
... Writing function log to: dogPicker.log
... Running on host: goby.amigroup.scripps.edu
... Uploading ScriptData....
... Running on host: goby.amigroup.scripps.edu
... Found 16 processors on this machine
!!! WARNING: More than one cluster job has this path
... Running Appion version 'trunk'
... Reading old done dictionary: dogPicker.donedict
... Found 1 done dictionary entries
... Querying database for preset 'en' images from session '13sep27e' ...

Traceback (most recent call last):
File "/opt/myamisnap/bin/dogPicker.py", line 78, in <module>
imgLoop.run()
File "/opt/myamisnap/lib/appionlib/appionLoop2.py", line 65, in run
self._getAllImages()
File "/opt/myamisnap/lib/appionlib/appionLoop2.py", line 486, in _getAllImages
self.imgtree = apDatabase.getImagesFromDB(self.params['sessionname'], self.params['preset'])
File "/opt/myamisnap/lib/appionlib/apDatabase.py", line 83, in getImagesFromDB
imgtree = imgquery.query(readimages=False)
File "/opt/myamisnap/lib/sinedon/data.py", line 395, in query
results = db.query(self, **kwargs)
File "/opt/myamisnap/lib/sinedon/dbdatakeeper.py", line 95, in query
result = self._query(*args, **kwargs)
File "/opt/myamisnap/lib/sinedon/dbdatakeeper.py", line 118, in _query
myresult = result.fetchall()
File "/opt/myamisnap/lib/sinedon/sqldict.py", line 577, in fetchall
cursorresult = self._format(subfetch, qikey)
File "/opt/myamisnap/lib/sinedon/sqldict.py", line 650, in _format
result = map(sql2data, sqlresult, qikeylist, qinfolist)
File "/opt/myamisnap/lib/sinedon/sqldict.py", line 1282, in sql2data
content = datatype(in_dict, join=join, parentclass=parentclass)
File "/opt/myamisnap/lib/sinedon/sqldict.py", line 1372, in datatype
dclass = findDataClass(modulename, dclassname)
File "/opt/myamisnap/lib/sinedon/sqldict.py", line 1308, in findDataClass
cls = getattr(mod, classname)
AttributeError: 'module' object has no attribute 'MoverParamsData'
----------------------------

Actions #1

Updated by Sargis Dallakyan about 11 years ago

  • Assignee set to Anchi Cheng

MoverParamsData seems to be a new table in dbemdata. I don't know what it is used for; couldn't find any reference to it. Maybe this needs an entry in leginon/leginondata.py for it to work.

Actions #2

Updated by Anchi Cheng about 11 years ago

  • Assignee changed from Anchi Cheng to Sargis Dallakyan
  • Affected Version changed from Appion/Leginon 2.2.0 to Appion/Leginon 3.0.0

Just checked,

On guppy head node, /opt/myamisnap/lib/leginon/leginondata.py does have MoverParamsData
Also good on guppy-29. I was able to run dogpicker of my session o.k.

I don't have goby account, but asked Jeff to check for me on goby
Neighther the headnode nor one of the node we got on with qsub -I has MoverParamsData.

MoverParamsData was added in r17925, dated on Monday. Maybe goby is not up to date?

Actions #3

Updated by Sargis Dallakyan about 11 years ago

  • Status changed from New to In Test
  • Assignee changed from Sargis Dallakyan to Gira Bhabha

Thanks Anchi. I have copied /opt/myamisnap from guppy to goby and I see MoverParamsData in /opt/myamisnap/lib/leginon/leginondata.py now.

Gira, please try again and change the status of this bug report to closed if it works for you. Thanks.

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