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

[Thomas H. <th...@gm...>]

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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