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Bug #1964

open

Import Eman on Centos6 gives segmentation fault

Added by Amber Herold about 12 years ago. Updated about 12 years ago.

Status:
Assigned
Priority:
Low
Assignee:
Sargis Dallakyan
Category:
-
Target version:
-
Start date:
08/03/2012
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 2.1.0
Show in known bugs:
No
Workaround:

Description

  1. Log into defcon4
  2. Start python
  3. import EMAN

Does EMAN need to be compiled, perhaps there is a newer?

Discovered this while centering a stack:

Center stack (redux version) has segmentation fault

[amber@defcon4 ~]$ centerParticleStack.py --stack-id=87 --mask=59 --maxshift=5 --description="center stack for redux test" --commit --rundir=/ami/data00/appion/zz07jul25b/stacks/centered87 --runname=centered87 --projectid=303 --expid=8556 --jobtype=makestack
/home/amber/workspace/myami/pyami/tifffile.py:903: UserWarning: Failed to import _tifffile.decodepackbits
  warnings.warn("Failed to import %s" % module_function)
/home/amber/workspace/myami/pyami/tifffile.py:903: UserWarning: Failed to import _tifffile.decodelzw
  warnings.warn("Failed to import %s" % module_function)

 ... Time stamp: 12aug03j59
 ... Function name: centerParticleStack
 ... Appion directory: /home/amber/workspace/myami/appion
 ... Using split database
Connected to database: 'ap303'
 ... Committing data to database
 ... Run directory: /ami/data00/appion/zz07jul25b/stacks/centered87
 ... Writing function log to: centerParticleStack.log
 ... Running on host: defcon4
 ... Uploading ScriptData....
 ... Running on host: defcon4
 ... Found 4 processors on this machine
 ... Running on host: defcon4
 ... Running Appion version 'trunk-r16801:17002M'
 ... Getting stack data for stackid=87
Old stack info: 'test redux'
Segmentation fault (core dumped)

This runs on non-redux code with CentOS 5 fine.

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 #1

Updated by Sargis Dallakyan about 12 years ago

  • Priority changed from Immediate to Low

Unable to reproduce this. 

[sargis@defcon4 ~]$ python
Python 2.6.6 (r266:84292, Dec  7 2011, 20:48:22) 
[GCC 4.4.6 20110731 (Red Hat 4.4.6-3)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import EMAN
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named EMAN

I also did su amber:
[amber@defcon4 ~]$ centerParticleStack.py --stack-id=87 --mask=59 --maxshift=5 --description="center stack for redux test" --commit --rundir=/ami/data00/appion/zz07jul25b/stacks/centered87 --runname=centered87 --projectid=303 --expid=8556 --jobtype=makestack
centerParticleStack.py: Command not found.

Need more info to reproduce this. Please run which centerParticleStack.py to find out which centerParticleStack.py is giving this error message.

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