Bug #2555
closedDatabase issues (user-specific)
0%
Description
Helen Kim (helenkim@scripps.edu) reported this; I'm relaying it to AMI. I just ran a test to confirm there isn't something globally broken with, say, DoG Picking, when ran from my account.
She collected data to a Garibaldi path (/gpfs/group/em/leginon/helenkim/13oct10b/rawdata/) and then ran dogPicker.py on an interactive node. She can view the data on longboard/gammamyami
nodea1402 home/helenkim> dogPicker.py --projectid=396 --preset=en --session=13oct10b --runname=dogrun1 --rundir=/gpfs/group/em/appion/helenkim/13oct10b/extract/dogrun1 --no-rejects --no-wait --commit --continue --peaktype=centerofmass --maxthresh=1.7 --thresh=0.9 --median=2 --lowpass=15 --highpass=0 --planereg --bin=4 --diam=120 --pixlimit=4.0 --expid=12465 --jobtype=dogpicker
... Time stamp: 13oct10m03
... Function name: dogPicker
... Appion directory: /opt/applications/myami/2.2/lib/python2.6/site-packages
... Load average is high 5.15
!!! WARNING: Using split database
Connected to database: 'ap396'
... Committing data to database
!!! WARNING: lowpass filter value greater than zero; will ignore
... Found project id=396 for session 13oct10b in 7.0 msec
... Run directory: /gpfs/group/em/appion/helenkim/13oct10b/extract/dogrun1
!!! WARNING: directory '/gpfs/group/em/appion/helenkim/13oct10b/extract/dogrun1' already exists.
... Writing function log to: dogPicker.log
... Uploading ScriptData....
... Found 16 processors on this machine
... Running Appion version '2.2.0'
... Reading old done dictionary: dogPicker.donedict
... Found 1 done dictionary entries
... Querying database for preset 'en' images from session '13oct10b' ...
Traceback (most recent call last):
File "/opt/applications/myami/2.2/bin/dogPicker.py", line 78, in <module>
imgLoop.run()
File "/opt/applications/myami/2.2/lib/python2.6/site-packages/appionlib/appionLoop2.py", line 45, in run
self._getAllImages()
File "/opt/applications/myami/2.2/lib/python2.6/site-packages/appionlib/appionLoop2.py", line 461, in _getAllImages
self.imgtree = apDatabase.getImagesFromDB(self.params['sessionname'], self.params['preset'])
File "/opt/applications/myami/2.2/lib/python2.6/site-packages/appionlib/apDatabase.py", line 83, in getImagesFromDB
imgtree = imgquery.query(readimages=False)
File "/opt/applications/myami/2.2/lib/python2.6/site-packages/sinedon/data.py", line 395, in query
results = db.query(self, **kwargs)
File "/opt/applications/myami/2.2/lib/python2.6/site-packages/sinedon/dbdatakeeper.py", line 95, in query
result = self._query(*args, **kwargs)
File "/opt/applications/myami/2.2/lib/python2.6/site-packages/sinedon/dbdatakeeper.py", line 118, in _query
myresult = result.fetchall()
File "/opt/applications/myami/2.2/lib/python2.6/site-packages/sinedon/sqldict.py", line 576, in fetchall
cursorresult = self._format(subfetch, qikey)
File "/opt/applications/myami/2.2/lib/python2.6/site-packages/sinedon/sqldict.py", line 649, in _format
result = map(sql2data, sqlresult, qikeylist, qinfolist)
File "/opt/applications/myami/2.2/lib/python2.6/site-packages/sinedon/sqldict.py", line 1278, in sql2data
content = datatype(in_dict, join=join, parentclass=parentclass)
File "/opt/applications/myami/2.2/lib/python2.6/site-packages/sinedon/sqldict.py", line 1368, in datatype
dclass = findDataClass(modulename, dclassname)
File "/opt/applications/myami/2.2/lib/python2.6/site-packages/sinedon/sqldict.py", line 1304, in findDataClass
cls = getattr(mod, classname)
AttributeError: 'module' object has no attribute 'MoverParamsData'Updated by Gabriel Lander about 11 years ago
Can you try replacing "module load myami" with "module load myami/trunk" in your .cshrc?
Updated by Gabriel Lander about 11 years ago
- Assignee set to Anchi Cheng
using trunk doesn't fix this problem - Anchi, do you have any clue what might be going on?
Updated by Anchi Cheng about 11 years ago
This turns out to be an old sinedon bug surfaced because my new change. See #2557. I've asked JC to update both myami/trunk and myami/2.2 on garibaldi with the fix. Hopefully it would be fixed by tomorrow.
Garibaldi modules are not updated daily to keep it more stable.
I will let you know when JC says he has done the update.
Updated by Ryan Hoffman about 11 years ago
Not sure if this is related...seems that data collection is now broken:
bash-4.1$ /ami/sw/bin/betaleginon
/ami/sw/packages/myamitrunk:/ami/sw/lib64/python2.6/site-packages
Traceback (most recent call last):
File "/ami/sw/packages/myamitrunk/leginon/start.py", line 13, in <module>
import leginon.gui.wx.Manager
File "/ami/sw/packages/myamitrunk/leginon/gui/wx/Manager.py", line 20, in <module>
from leginon import manager
File "/ami/sw/packages/myamitrunk/leginon/manager.py", line 19, in <module>
import launcher
File "/ami/sw/packages/myamitrunk/leginon/launcher.py", line 13, in <module>
import node
File "/ami/sw/packages/myamitrunk/leginon/node.py", line 27, in <module>
import correctorclient
File "/ami/sw/packages/myamitrunk/leginon/correctorclient.py", line 18, in <module>
import leginon.session
File "/ami/sw/packages/myamitrunk/leginon/session.py", line 14, in <module>
projectdata = leginon.project.ProjectData()
File "/ami/sw/packages/myamitrunk/leginon/project.py", line 36, in __init__
raise NotConnectedError(e)
leginon.project.NotConnectedError: (2003, "Can't connect to MySQL server on '137.131.205.164' (113)")
Updated by Gabriel Lander about 11 years ago
This latest error is unrelated, it appears that cronus4, which hosts the database, went down at some point last night.
Updated by Anchi Cheng about 11 years ago
- Status changed from New to In Test
- Assignee changed from Anchi Cheng to Ryan Hoffman
Ryan,
JC has updated myami/trunk and myami/2.2 on garibaldi. It should be good to go. Helen is not on redmine, so I am assigning you to test.
Updated by Ryan Hoffman about 11 years ago
- Status changed from In Test to Closed
Helen can run a job at the Garibaldi CLI with no problems. The results immediately display on Appion. So I think this bug (pertaining to database issues) is closed.
It seems she can't run the DoG picking from the web interface, however, but I think that should be treated as a different bug. Someone should confirm that there's an reproducible problem with submitting jobs to Garibaldi from the Appion interface. I can't do it over the next few hours, however (I'm currently heading out.) Her attempts to do so are for the same session as was examined here (/gpfs/group/em/appion/helenkim/13oct10b/extract); dogrun1 and dogrun3 are failed runs from Appion, and dogrun2 is the successful one on the CLI.