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Re: [Pytom-mail] MPI Errors and Particle File Viewing
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From: Dustin M. <dus...@gm...> - 2016-03-17 03:40:50
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Anything with alloc in the error is usually a memory error. Do you have enough RAM to fit everything? If you use binning does it work?
--
Cheers,
Dustin
> On Mar 16, 2016, at 7:47 PM, Kanika Khanna <kk...@uc...> wrote:
>
> Hello
>
> I have been trying endlessly to run the localization job with parallel processing, but it is always giving an 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 21, in startLocalizationJob
> leader.parallelRun(job, splitX, splitY, splitZ, verbose)
> File "/usr/local/pytom/localization/parallel_extract_peaks.py", line 1046, in parallelRun
> result = self.run(verbose)
> File "/usr/local/pytom/localization/parallel_extract_peaks.py", line 104, in run
> [resV, orientV, sumV, sqrV] = extractPeaks(v, ref, rot, scoreFnc, m, mIsSphere, wedg, nodeName=self.name, verboseMode=verbose, moreInfo=moreInfo)
> File "/usr/local/pytom/localization/extractPeaks.py", line 130, in extractPeaks
> meanV = meanUnderMask(volume, maskV, p);
> File "/usr/local/pytom/basic/correlation.py", line 244, in meanUnderMask
> result = iftshift(ifft(fMask*fft(volume)))/(size*p)
> File "/usr/local/pytom/basic/fourier.py", line 122, in fft
> returnValue = pytom_volume.vol_comp(theTuple.complexVolume.sizeX(),theTuple.complexVolume.sizeY(),theTuple.complexVolume.sizeZ())
> File "/usr/local/pytom/pytomc/swigModules/pytom_volume.py", line 234, in __init__
> this = _pytom_volume.new_vol_comp(*args)
> RuntimeError: std::bad_alloc
> --------------------------------------------------------------------------
> 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: [[6894,1],0]
> Exit code: 1
>
>
> On Fri, Mar 11, 2016 at 12:00 PM, Kanika Khanna <kk...@uc...> wrote:
> Hi
>
> I am sorry but the job did start running and it gave this weird error then and aborted again! :(
> Primary job terminated normally, but 1 process returned
> a non-zero exit code.. Per user-direction, the job has been aborted.
>
> node_0: send number of 50 rotations to node 2
> node_0: send number of 25 rotations to node 1
> node_2: send number of 25 rotations to node 3
> node_0: starting to calculate 25 rotations
> node_3: starting to calculate 25 rotations
> node_1: starting to calculate 25 rotations
> node_2: starting to calculate 25 rotations
> 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 21, in startLocalizationJob
> leader.parallelRun(job, splitX, splitY, splitZ, verbose)
> File "/usr/local/pytom/localization/parallel_extract_peaks.py", line 1046, in parallelRun
> result = self.run(verbose)
> File "/usr/local/pytom/localization/parallel_extract_peaks.py", line 104, in run
> [resV, orientV, sumV, sqrV] = extractPeaks(v, ref, rot, scoreFnc, m, mIsSphere, wedg, nodeName=self.name, verboseMode=verbose, moreInfo=moreInfo)
> File "/usr/local/pytom/localization/extractPeaks.py", line 130, in extractPeaks
> meanV = meanUnderMask(volume, maskV, p);
> File "/usr/local/pytom/basic/correlation.py", line 244, in meanUnderMask
> result = iftshift(ifft(fMask*fft(volume)))/(size*p)
> File "/usr/local/pytom/pytomc/swigModules/pytom_volume.py", line 342, in __mul__
> return _pytom_volume.vol_comp___mul__(self, *args)
> RuntimeError: std::bad_alloc
> -------------------------------------------------------
> Primary job terminated normally, but 1 process returned
> a non-zero exit code.. Per user-direction, the job has been aborted.
>
>
> On Fri, Mar 11, 2016 at 11:56 AM, Kanika Khanna <kk...@uc...> wrote:
> 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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> > Accelerate data analysis in your applications with
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>
>
>
> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
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