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Bug #5413

closed

lm-bfgs Particle Polisher bugs

Added by Zhening Zhang over 6 years ago. Updated over 5 years ago.

Status:
Closed
Priority:
High
Assignee:
Zhening Zhang
Category:
-
Target version:
Appion/Leginon 3.3
Start date:
01/05/2018
Due date:
% Done:

0%

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

Description

I got these error messages when I submit a job:
/opt/myamisnap/bin/appion polishStack.py --commit --micrographs_per_job=30 --particleradius=150 --expweight --localavg --localavgsigma=500 --framefirstali=0 --framefirstave=0 --smooth=1.0 --exaggerate=10 --rmax1=500 --rmax2=20 --bfactor=2000 --runname=rpp2 --stackid=15 --rundir=/gpfs/appion/afeklistov/17dec20a/rpp/rpp2 --projectid=333 --expid=5605 --jobtype=particlepolishing

... Time stamp: 18jan05j17
 ... Function name: polishStack
 ... Appion directory: /opt/myamisnap/lib
 ... Processing hostname: SEMC-head
 ... Using split database
Connected to database: 'nyap_333'
 ... Committing data to database
 ... Using split database
Connected to database: 'nyap_333'
Traceback (most recent call last):
  File "/opt/myamisnap/bin/polishStack.py", line 428, in <module>
    polisher = stackPolisherScript()
  File "/opt/myamisnap/lib/appionlib/appionScript.py", line 85, in init
    self.checkConflicts()
  File "/opt/myamisnap/bin/polishStack.py", line 105, in checkConflicts
    self.dd = apDDprocess.DDStackProcessing()
  File "/opt/myamisnap/lib/appionlib/apDDprocess.py", line 1357, in init
    super(DDStackProcessing,self).__init__()
  File "/opt/myamisnap/lib/appionlib/apDDprocess.py", line 65, in init
    self.setForcedFrameSessionPath(None)
AttributeError: 'DDStackProcessing' object has no attribute 'setForcedFrameSessionPath'
 ... Looking up session, 5605
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 #1

Updated by Anchi Cheng over 6 years ago

  • Status changed from New to In Test
  • Assignee set to Zhening Zhang
  • Target version set to Appion/Leginon 3.3

This should work now. But use with caution that it will start as many 1 processor job as needed and may clug the cluster if allowed to run wild. It is also not a nohup job, and will terminate if you close the terminal.

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 #2

Updated by Anchi Cheng over 5 years ago

  • Status changed from In Test to Closed

never got feedback, assume fixed

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