Appion

I've tracked it down. Sometimes it crashes sometimes it does not. The problem occurs during the alignment of the class averages. I do this so that it two class averages are similar, they are in the same orientation; necessary for things like coran/PCA.

/emg/sw/relion/bin/relion_refine   --i part16aug18v24_it008_classes.mrcs  \
--o /emg/data/appion/06jul12a/align/maxlike2/ref16aug18v24  --angpix 4.8900  \
--iter 8  --K 1  --psi_step 5  --tau2_fudge 1.0  --particle_diameter 190.0  --j 1  --dont_check_norm 
 Running in double precision. 
 Estimating initial noise spectra 
   0/   0 sec ............................................................~~(,_,">
WARNING: There are only 9 particles in group 1
WARNING: You may want to consider joining some micrographs into larger groups to obtain more robust noise estimates. 
         You can do so by using the same rlnMicrographName label for particles from multiple different micrographs in the input STAR file. 
 Estimating accuracies in the orientational assignment ... 
   0/   0 sec ............................................................~~(,_,">
 Auto-refine: Estimated accuracy angles= 0.05 degrees; offsets= 0.05 pixels
 CurrentResolution= 65.2 Angstroms, which requires orientationSampling of at least 36 degrees for a particle of diameter 190 Angstroms
 Oversampling= 0 NrHiddenVariableSamplingPoints= 2088
 OrientationalSampling= 5 NrOrientations= 72
 TranslationalSampling= 2 NrTranslations= 29
=============================
 Oversampling= 1 NrHiddenVariableSamplingPoints= 66816
 OrientationalSampling= 2.5 NrOrientations= 576
 TranslationalSampling= 1 NrTranslations= 116
=============================
 Estimated memory for expectation step  > 0.10236 Gb, available memory = 2 Gb.
 Estimated memory for maximization step > 0.000152752 Gb, available memory = 2 Gb.
 Expectation iteration 1 of 8
000/??? sec ~~(,_,">                                                          [oo] exp_thisparticle_sumweight= nan
 part_id= 6
 group_id= 0 mymodel.scale_correction[group_id]= 1
 exp_ipass= 0
 sampling.NrDirections(0, true)= 1 sampling.NrDirections(0, false)= 1
 sampling.NrPsiSamplings(0, true)= 72 sampling.NrPsiSamplings(0, false)= 72
 mymodel.sigma2_noise[ipart]= 
      -nan
       nan
       nan
       nan
      -nan
       nan
       nan
       nan
      -nan
       nan
       nan
      -nan

 wsum_model.sigma2_noise[ipart]= 
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0
         0

 wsum_model.pdf_direction[ipart]= 
         0

written out Mweight.spi
 exp_thisparticle_sumweight= nan
 exp_min_diff2[ipart]= 9.9e+100
ERROR!!! zero sum of weights....
File: src/ml_optimiser.cpp line: 4103

In thread 0
^CTraceback (most recent call last):
  File "/emg/sw/myami/appion/bin/relionMaxlikeAlignment.py", line 386, in <module>
!!! WARNING: could not run eman command: /emg/sw/relion/bin/relion_refine   \
--i part16aug18v24_it008_classes.mrcs  --o /emg/data/appion/06jul12a/align/maxlike2/ref16aug18v24  \
--angpix 4.8900  --iter 8  --K 1  --psi_step 5  --tau2_fudge 1.0  --particle_diameter 190.0  \
--j 1  --dont_check_norm 
Traceback (most recent call last):
  File "/emg/sw/myami/appion/bin/uploadRelion2DMaxlikeAlign.py", line 537, in <module>
    maxLike.start()
  File "/emg/sw/myami/appion/bin/relionMaxlikeAlignment.py", line 381, in start
    maxLike.start()
  File "/emg/sw/myami/appion/bin/uploadRelion2DMaxlikeAlign.py", line 508, in start
    self.runUploadScript()
  File "/emg/sw/myami/appion/bin/relionMaxlikeAlignment.py", line 217, in runUploadScript
    self.alignReferences(runparams)
  File "/emg/sw/myami/appion/bin/uploadRelion2DMaxlikeAlign.py", line 437, in alignReferences
    proc.communicate()
  File "/usr/lib64/python2.6/subprocess.py", line 728, in communicate
    self.wait()
  File "/usr/lib64/python2.6/subprocess.py", line 1307, in wait
    pid, sts = _eintr_retry_call(os.waitpid, self.pid, 0)
  File "/usr/lib64/python2.6/subprocess.py", line 462, in _eintr_retry_call
    return func(*args)
KeyboardInterrupt
    apEMAN.executeEmanCmd(relioncmd, verbose=True, showcmd=True)
  File "/usr/lib64/python2.6/site-packages/appionlib/apEMAN.py", line 233, in executeEmanCmd
    out, err = emanproc.communicate()
  File "/usr/lib64/python2.6/subprocess.py", line 728, in communicate
    self.wait()
  File "/usr/lib64/python2.6/subprocess.py", line 1307, in wait
    pid, sts = _eintr_retry_call(os.waitpid, self.pid, 0)
  File "/usr/lib64/python2.6/subprocess.py", line 462, in _eintr_retry_call
    return func(*args)
KeyboardInterrupt