Re: [Pytom-mail] MPI Errors and Particle File Viewing

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

Hi Thomas,

I have been able to resolve issue 1. I just killed all the processes and
started again. It worked that time.

On Sat, Mar 12, 2016 at 1:05 AM, Thomas Hrabe <th...@gm...> wrote:

> Hi Kanika,
>
>
> 1.
> to me, it looks like that you are trying to open a file called
>
> > <Volume Binning="[0, 0, 0]" Filename="PY79.mrc" Sampling="[0, 0, 0]"
> Subregion="[0, 0, 0, 0, 0, 0]"/>
>
>
> Can you please attach the xml file?
>
> 2.
> I have to look into the script as well. I must re-install it before I can
> advice about how to use it.
>
> Cheers,
> Thomas
>
> > On Mar 11, 2016, at 11:15 AM, Kanika Khanna <kk...@uc...> wrote:
> >
> > 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!
> >
> >
> >
> >
> >
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