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

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

Hi

I am attaching the job file here.

FYI, I tried to run my previous job files as well which ran well then
(including tutorial data set). But everything, gives the same kind of error
now.

On Fri, Mar 11, 2016 at 11:35 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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