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

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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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>>>
>>
>

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

http://www.sciencedirect.com/science/article/pii/S1047847711003492

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