[Pytom-mail] MPI Errors and Particle File Viewing

[Kanika K. <kk...@uc...>]

Hello all,

1. When I try to execute my job using the following command
mpirun --host HostName -c 4 pytom localization.py PathToJobFile 2 2 2

I get the following error:
Traceback (most recent call last):
  File "/usr/local/pytom/bin/localization.py", line 82, in <module>
    startLocalizationJob(jobName, splitX, splitY, splitZ,
doSplitAngles=False)
  File "/usr/local/pytom/bin/localization.py", line 11, in
startLocalizationJob
    job.check()
  File "/usr/local/pytom/localization/peak_job.py", line 184, in check
Traceback (most recent call last):
  File "/usr/local/pytom/bin/localization.py", line 82, in <module>
    raise IOError('File: ' + str(self.volume) + ' not found!')
IOError: File: <Volume Binning="[0, 0, 0]" Filename="PY79.mrc"
Sampling="[0, 0, 0]" Subregion="[0, 0, 0, 0, 0, 0]"/>
 not found!
    startLocalizationJob(jobName, splitX, splitY, splitZ,
doSplitAngles=False)
  File "/usr/local/pytom/bin/localization.py", line 11, in
startLocalizationJob
    job.check()
  File "/usr/local/pytom/localization/peak_job.py", line 184, in check
    raise IOError('File: ' + str(self.volume) + ' not found!')
IOError: File: <Volume Binning="[0, 0, 0]" Filename="PY79.mrc"
Sampling="[0, 0, 0]" Subregion="[0, 0, 0, 0, 0, 0]"/>
 not found!
Traceback (most recent call last):
  File "/usr/local/pytom/bin/localization.py", line 82, in <module>
    startLocalizationJob(jobName, splitX, splitY, splitZ,
doSplitAngles=False)
  File "/usr/local/pytom/bin/localization.py", line 11, in
startLocalizationJob
    job.check()
  File "/usr/local/pytom/localization/peak_job.py", line 184, in check
    raise IOError('File: ' + str(self.volume) + ' not found!')
IOError: File: <Volume Binning="[0, 0, 0]" Filename="PY79.mrc"
Sampling="[0, 0, 0]" Subregion="[0, 0, 0, 0, 0, 0]"/>
 not found!
-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/pytom/bin/localization.py", line 82, in <module>
    startLocalizationJob(jobName, splitX, splitY, splitZ,
doSplitAngles=False)
  File "/usr/local/pytom/bin/localization.py", line 11, in
startLocalizationJob
    job.check()
  File "/usr/local/pytom/localization/peak_job.py", line 184, in check
    raise IOError('File: ' + str(self.volume) + ' not found!')
IOError: File: <Volume Binning="[0, 0, 0]" Filename="PY79.mrc"
Sampling="[0, 0, 0]" Subregion="[0, 0, 0, 0, 0, 0]"/>
 not found!
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status,
thus causing
the job to be terminated. The first process to do so was:

  Process name: [[27852,1],3]
  Exit code:    1


Any idea how I can circumvent this? Or what exactly might be going wrong?

2. Once you have the pl.xml file generated after extraction of particles,
we have the script VolumeDialog.py for viewing it in Chimera. I already
installed it in the Volume Viewer folder. How exactly are we suppose to use
it? Also, there were a couple of existing files of the same name in the
folder existing previously (is that the case with everyone here?). Anything
to do with them?

Thanks!