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Bug #4500

closed

gautomatch fails

Added by Saikat Chowdhury over 7 years ago. Updated over 6 years ago.

Status:
Closed
Priority:
High
Assignee:
Saikat Chowdhury
Category:
Image Processing
Target version:
Appion/Leginon 3.3
Start date:
10/04/2016
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.3
Show in known bugs:
No
Workaround:

Description

We were trying to run gautomatch through appion on a gpu node and it didn't work.

Following is the command we were trying to run to test on a micrograph:

$ gautomatch.py --overlapmult=1 --lp=30 --hp=1000 --pre_lp=8 --pre_hp=1000 --speed=1 --lsigma_D=200 --lsigma_cutoff=1.3 --lave_D=400 --runname=gauto1 --rundir=/gpfs/group/em/appion/saikat/16sep29g/extract/gauto1 --projectid=328 --session=16sep29g --no-rejects --no-commit --no-continue --mrclist=16sep29g_10a_00019gr_00007sq_00026hl_00003esup-b.mrc

This is the error we were getting.

  • ... Time stamp: 16oct03t51
    ... Function name: gautomatch
    ... Appion directory: /gpfs/home/glander/myami/appion
    ... Processing hostname: nodeb1203
    !!! WARNING: There is more than one appion directory in your PYTHONPATH
    ['/gpfs/home/glander/myami/appion/appionlib', '/gpfs/home/glander/myami/appion']
    Traceback (most recent call last):
    File "/gpfs/home/glander/myami/appion/bin/gautomatch.py", line 9, in <module>
    imgLoop = apGautomatch.GautomatchLoop()
    File "/gpfs/home/glander/myami/appion/appionlib/particleLoop2.py", line 92, in init
    appionLoop2.AppionLoop.__init__(self)
    File "/gpfs/home/glander/myami/appion/appionlib/appionLoop2.py", line 27, in init
    appionScript.AppionScript.__init__(self)
    File "/gpfs/home/glander/myami/appion/appionlib/appionScript.py", line 67, in init
    self.setParams(optargs,useglobalparams)
    File "/gpfs/home/glander/myami/appion/appionlib/appionScript.py", line 340, in setParams
    self.setupParserOptions()
    File "/gpfs/home/glander/myami/appion/appionlib/apGautomatch.py", line 98, in setupParserOptions
    self.parser.add_option("--minthresh",dest="minthresh",help="Cross-correlation cutoff, 0.2~0.4 normally; Try to select several typical micrographs to optimize this value.")
    File "/usr/lib64/python2.6/optparse.py", line 1020, in add_option
    self._check_conflict(option)
    File "/usr/lib64/python2.6/optparse.py", line 995, in _check_conflict
    option)
    optparse.OptionConflictError: option --minthresh: conflicting option string(s): --minthresh *
    We were also using python/2.6.6.

Seems like an issue with the appion wrapper

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