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

[Friedrich F. <foe...@bi...>]

Dustin is probably essentially right.
the problem may be that the header of your file(s), where the file
dimensions are stored, does not follow the standard conventions. it may
well be that these numbers are somewhat insane and pytom tries to allocate
humongous amounts of memory. the mrc format (i guess that is what you are
using) has a lot of different flavors, which are not necessarily all
supported in pytom. for the em format, assignment of the 'magic number' at
the very beginning is sometimes a problem on macs.
best try to read in your files interactively in pytom and see if there any
complaints. when you found the culprit try to write it out or convert it
with a different program.

best wishes

friedrich



On Thu, Mar 17, 2016 at 4:40 AM, Dustin Morado <dus...@gm...>
wrote:

> 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!
> > >
> > >
> > >
> > >
> > >
> ------------------------------------------------------------------------------
> > > Transform Data into Opportunity.
> > > Accelerate data analysis in your applications with
> > > Intel Data Analytics Acceleration Library.
> > > Click to learn more.
> > >
> http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140_______________________________________________
> > > Pytom-mail mailing list
> > > Pyt...@li...
> > > https://lists.sourceforge.net/lists/listinfo/pytom-mail
> >
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Transform Data into Opportunity.
> > Accelerate data analysis in your applications with
> > Intel Data Analytics Acceleration Library.
> > Click to learn more.
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140_______________________________________________
> > Pytom-mail mailing list
> > Pyt...@li...
> > https://lists.sourceforge.net/lists/listinfo/pytom-mail
>
>
>
> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140
> _______________________________________________
> Pytom-mail mailing list
> Pyt...@li...
> https://lists.sourceforge.net/lists/listinfo/pytom-mail
>



-- 
Dr. Friedrich Foerster
Max-Planck Institut fuer Biochemie
Am Klopferspitz 18
D-82152 Martinsried

Tel: +49 89 8578 2632
Fax: +49 89 8578 2641

www.biochem.mpg.de/foerster

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

[Dustin M. <dus...@gm...>]

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!
> >
> >
> >
> >
> > ------------------------------------------------------------------------------
> > Transform Data into Opportunity.
> > Accelerate data analysis in your applications with
> > Intel Data Analytics Acceleration Library.
> > Click to learn more.
> > http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140_______________________________________________
> > Pytom-mail mailing list
> > Pyt...@li...
> > https://lists.sourceforge.net/lists/listinfo/pytom-mail
> 
> 
> 
> 
> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140_______________________________________________
> Pytom-mail mailing list
> Pyt...@li...
> https://lists.sourceforge.net/lists/listinfo/pytom-mail

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

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

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!
>>> >
>>> >
>>> >
>>> >
>>> >
>>> ------------------------------------------------------------------------------
>>> > Transform Data into Opportunity.
>>> > Accelerate data analysis in your applications with
>>> > Intel Data Analytics Acceleration Library.
>>> > Click to learn more.
>>> >
>>> http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140_______________________________________________
>>> > Pytom-mail mailing list
>>> > Pyt...@li...
>>> > https://lists.sourceforge.net/lists/listinfo/pytom-mail
>>>
>>>
>>
>

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

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

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!
>> >
>> >
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> > Transform Data into Opportunity.
>> > Accelerate data analysis in your applications with
>> > Intel Data Analytics Acceleration Library.
>> > Click to learn more.
>> >
>> http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140_______________________________________________
>> > Pytom-mail mailing list
>> > Pyt...@li...
>> > https://lists.sourceforge.net/lists/listinfo/pytom-mail
>>
>>
>

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!
> >
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Transform Data into Opportunity.
> > Accelerate data analysis in your applications with
> > Intel Data Analytics Acceleration Library.
> > Click to learn more.
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140_______________________________________________
> > Pytom-mail mailing list
> > Pyt...@li...
> > https://lists.sourceforge.net/lists/listinfo/pytom-mail
>
>

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!
> >
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Transform Data into Opportunity.
> > Accelerate data analysis in your applications with
> > Intel Data Analytics Acceleration Library.
> > Click to learn more.
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140_______________________________________________
> > Pytom-mail mailing list
> > Pyt...@li...
> > https://lists.sourceforge.net/lists/listinfo/pytom-mail
>
>

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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> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
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[Pytom-mail] MPI Errors and Particle File Viewing

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

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!

[Pytom-mail] Localize.pytom.org maintenance

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

Hi everyone,

We will be maintaining your favorite cryoET webserver - localize.pytom.org from tomorrow. 
The maintenance may take a few days. Please use your own PyTom installation for urgent localization tasks.

Best,
Thomas

Re: [Pytom-mail] pytom.basic.transformations.project numpy error

[Friedrich F. <foe...@bi...>]

dear dustin,

the project function is still experimental and not used anywhere else.
nevertheless, your fix should be fine - if you look at the volume in
chimera you probably will end up with many z-layers showing the same 2d
data.
this and other functions will have more support when we have hired a
full-time developer for pytom.

cheers

friedrich



On Fri, Feb 26, 2016 at 9:54 PM, Dustin Morado <dus...@gm...>
wrote:

> Hi all,
>
> When I try to project a subvolume I get the following error:
>
> ---------------------------------------------------------------------------
> ValueError                                Traceback (most recent call last)
> <ipython-input-9-c7d5e1885a02> in <module>()
> ----> 1 sv2d = project(sv, r)
>
> /opt/pytom/basic/transformations.py in project(v, rot, verbose)
>     611     npprojection = ndarray([v.sizeX(), v.sizeY(), 1],
> dtype=float32, buffer=None, offset=0, strides=npvol.strides,
>     612                            order='F')
> --> 613     proj(npvol, axis=2, dtype=float32, out=npprojection)
>     614     projection = npy2vol(npprojection,3)
>     615     return projection
>
> /usr/lib/python2.7/dist-packages/numpy/core/fromnumeric.pyc in sum(a,
> axis, dtype, out, keepdims)
>    1712     else:
>    1713         return _methods._sum(a, axis=axis, dtype=dtype,
> -> 1714                             out=out, keepdims=keepdims)
>    1715
>    1716 def product (a, axis=None, dtype=None, out=None, keepdims=False):
>
> /usr/lib/python2.7/dist-packages/numpy/core/_methods.pyc in _sum(a, axis,
> dtype, out, keepdims)
>      23 def _sum(a, axis=None, dtype=None, out=None, keepdims=False):
>      24     return um.add.reduce(a, axis=axis, dtype=dtype,
> ---> 25                             out=out, keepdims=keepdims)
>      26
>      27 def _prod(a, axis=None, dtype=None, out=None, keepdims=False):
>
> ValueError: output parameter for reduction operation add has too many
> dimensions
>
> If I add ‘keepdims=True’ to the sum call I get a projection, but is this
> OK to do?
>
> —
> Cheers,
> Dustin
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
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>



-- 
Dr. Friedrich Foerster
Max-Planck Institut fuer Biochemie
Am Klopferspitz 18
D-82152 Martinsried

Tel: +49 89 8578 2632
Fax: +49 89 8578 2641

www.biochem.mpg.de/foerster

[Pytom-mail] pytom.basic.transformations.project numpy error

[Dustin M. <dus...@gm...>]

Hi all,

When I try to project a subvolume I get the following error:

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-9-c7d5e1885a02> in <module>()
----> 1 sv2d = project(sv, r)

/opt/pytom/basic/transformations.py in project(v, rot, verbose)
    611     npprojection = ndarray([v.sizeX(), v.sizeY(), 1], dtype=float32, buffer=None, offset=0, strides=npvol.strides,
    612                            order='F')
--> 613     proj(npvol, axis=2, dtype=float32, out=npprojection)
    614     projection = npy2vol(npprojection,3)
    615     return projection

/usr/lib/python2.7/dist-packages/numpy/core/fromnumeric.pyc in sum(a, axis, dtype, out, keepdims)
   1712     else:
   1713         return _methods._sum(a, axis=axis, dtype=dtype,
-> 1714                             out=out, keepdims=keepdims)
   1715 
   1716 def product (a, axis=None, dtype=None, out=None, keepdims=False):

/usr/lib/python2.7/dist-packages/numpy/core/_methods.pyc in _sum(a, axis, dtype, out, keepdims)
     23 def _sum(a, axis=None, dtype=None, out=None, keepdims=False):
     24     return um.add.reduce(a, axis=axis, dtype=dtype,
---> 25                             out=out, keepdims=keepdims)
     26 
     27 def _prod(a, axis=None, dtype=None, out=None, keepdims=False):

ValueError: output parameter for reduction operation add has too many dimensions

If I add ‘keepdims=True’ to the sum call I get a projection, but is this OK to do?
 
—
Cheers,
Dustin

Re: [Pytom-mail] error on the first attempt at tutorial

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

Hi Elizabeth (and everyone),

a new, stable(r) version 0.971 from yesterday is available with the most recent bug fixes.

Please test that by pulling the master branch or downloading the package from sourceforge. 
It will fix most of the more recent problems that were raised through the mailing list.

Cheers
Thomas

> On Feb 17, 2016, at 6:12 PM, Villa, Elizabeth <ev...@uc...> wrote:
> 
> hi all,  
> 
> We’re trying pytom for the first time and we seem to have issues. First we pulled the master branch, and now the devel branch, and we seem to have issues.  Can you please help?  We are following the website/tutorial instructions. 
> 
> Cheers, 
> Elizabeth 
> 
> 
> 
> 
> PyTom v0.97
> 
> This license affects the software package PyTom and all the herein distributed source / data files.
> Authors: 
> Thomas Hrabe
> Yuxiang Chen
> Friedrich Foerster
> 
> Copyright (c) 2008-2016
> Max-Planck-Institute for Biochemistry
> Dept. Molecular Structural Biology
> 82152 Martinsried, Germany
> http://www.pytom.org
> 
> This program is free software: you can redistribute it and/or modify
> it under the terms of the GNU General Public License as published by
> the Free Software Foundation, either version 3 of the License, or
> (at your option) any later version.
> 
> This program is distributed in the hope that it will be useful,
> but WITHOUT ANY WARRANTY; without even the implied warranty of
> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
> GNU General Public License for more details.
> 
> The complete license can be obtained from 
> http://www.gnu.org/licenses/gpl-3.0.html.
> 
> sys.version_info(major=2, minor=7, micro=5, releaselevel='final', serial=0)
> option --tiltSeriesPath not recognized
> RibosFromLysate/reconstructTomo> 
> 
> 
> 
> 
>> Begin forwarded message:
>> 
>> From: Elizabeth Villa <ev...@uc...>
>> Subject: Re: error on the first attempt at tutorial
>> Date: February 17, 2016 at 5:16:39 PM PST
>> To: Thomas Hrabe <th...@sb...>
>> Cc: Ittipat Meewan <im...@uc...>
>> 
>> Hmm.. I just pulled it from the git repository..  Will email the pytom list in the future.. 
>> 
>> thanks! 
>> E
>> 
>> 
>> 
>>> On Feb 17, 2016, at 5:06 PM, Thomas Hrabe <th...@sb...> wrote:
>>> 
>>> Hi E,
>>> 
>>> haven’t played with the reconstruction before for a while.
>>> Seems there’s a unset parameter. Obvious what it does, but do we have a different version running? In my release I find the line in row 178. The file is attached.
>>> 
>>> Please go through the mailing list next time, that’s the best way to get feedback from either of us, including Yuxiang and the whole pytom community (sometimes :) ).
>>> 
>>> My file is attached, or you can download the development branch from the GIT repository on sourceforge.
>>> 
>>> Thomas
>>> 
>>> 
>>> 
>>>> On Feb 17, 2016, at 4:23 PM, Villa, Elizabeth <ev...@uc...> wrote:
>>>> 
>>>> hi T, 
>>>> 
>>>> We just installed pytom and downloaded the tutorial. In the first attempt at reconstructing the tomo, I get:
>>>> 
>>>> The complete license can be obtained from 
>>>> http://www.gnu.org/licenses/gpl-3.0.html.
>>>> 
>>>> Tilt Series: ../projections/tomo01_sorted 1-41
>>>> Index of Reference Projection21
>>>> Marker Filename:../projections/markfile_temp.mark, Index of Reference Marker:1
>>>> Handflip:False
>>>> Projection Targets: ./alignedProjections/tomo01
>>>> FineAlignmentFile: None
>>>> Binning Factor of Projections: 4, lowpass filter (in Ny): 0.5
>>>> Name of Reconstruction Volume: tomogram.em of Filetype: em
>>>> Reconstruction size: ['512', '512', '128']
>>>> Reconstruction center: ['0', '0', '0']
>>>> Traceback (most recent call last):
>>>>  File "/usr/local/pytom/bin/reconstructTomogram.py", line 138, in <module>
>>>>    print "write only projections out: "+str(onlyWeightedProjections)
>>>> NameError: name 'onlyWeightedProjections' is not defined
>>>> [evilla@pordoi reconstructTomo]$ 
>>>> 
>>>> 
>>>> The weird thing is that onlyWeightedProjections  is not a flag in the script, so it must have been a default option that got dropped?  
>>>> 
>>>> Should we contact Frido’s group about this? 
>>>> 
>>>> Thanks! 
>>>> E
>>>> 
>>>> 
>>>> 
>>>> --
>>>> Elizabeth Villa
>>>> Department of Chemistry and Biochemistry
>>>> University of California San Diego 
>>>> 
>>>> w: villalab.ucsd.edu
>>>> v:  +1 (858) 246-1843
>>>> f: +1 (858) 534-4864
>>>> 
>>>> 
>>>> 
>>> 
>>> <reconstructTomogram.py>
>> 
>> --
>> Elizabeth Villa
>> Department of Chemistry and Biochemistry
>> University of California San Diego 
>> 
>> w:	villalab.ucsd.edu
>> v: 	+1 (858) 246-1843
>> f:	+1 (858) 534-4864
>> 
>> 
>> 
> 
> --
> Elizabeth Villa
> Department of Chemistry and Biochemistry
> University of California San Diego 
> 
> w:	villalab.ucsd.edu
> v: 	+1 (858) 246-1843
> f:	+1 (858) 534-4864
> 
> 
> 
> ------------------------------------------------------------------------------
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Re: [Pytom-mail] Pytom-mail post from khannakanika11@gmail.com requires approval

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

Thank you! Will explore the FAQ section too.

On Wednesday, February 24, 2016, Thomas Hrabe <th...@gm...> wrote:

> Please go to
>
> pytom.org -> Documentation -> Guide & Tutorials -> FAQ and search for the
>
> LD_PRELOAD
>
> part.
>
> I think this MPI bug was previously fixed with setting LD_PRELOAD to your
> libmpi.so .
>
> Use locate libmpi.so to find it. If locate does not give you the location
> of the library, the paths.csh file in pytom/bin should list one of the
> directories in LD_LIBRARY_PATH where libmpi.so is.
>
> Thomas
>
>
> On Feb 24, 2016, at 2:37 PM, Kanika Khanna <kk...@uc...
> <javascript:_e(%7B%7D,'cvml','kk...@uc...');>> wrote:
>
> Hello,
>
> So I am trying localization with the tutorial data set itself. I did not
> use the hostfile as I am running on only one host. Hence, I specified the
> host and no. of CPUs as per the following command
>
> mpirun --host 'HostName' -c 4 pytom /usr/local/pytom/bin/localization.py
> 'PathToJobFile'/job.xml 2 2 2
>
> I get the following error:
>
> It looks like orte_init failed for some reason; your parallel process is
> likely to abort.  There are many reasons that a parallel process can
> fail during orte_init; some of which are due to configuration or
> environment problems.  This failure appears to be an internal failure;
> here's some additional information (which may only be relevant to an
> Open MPI developer):
>
>   opal_init failed
>   --> Returned value Error (-1) instead of ORTE_SUCCESS
> --------------------------------------------------------------------------
> *** An error occurred in MPI_Init
> *** on a NULL communicator
> *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
> ***    and potentially your MPI job)
> [pordoi:29128] Local abort before MPI_INIT completed successfully; not
> able to aggregate error messages, and not able to guarantee that all other
> processes were killed!
>
>
> On Tue, Feb 23, 2016 at 3:44 PM, Dustin Morado <dus...@gm...
> <javascript:_e(%7B%7D,'cvml','dus...@gm...');>> wrote:
>
>> Hi Kanika,
>>
>> What was the command you ran exactly? It looks like there’s an error with
>> your host file. Are you running this on a cluster, or just a workstation
>> with openmpi?
>>
>> If it’s the latter you can simply run it like this:
>> mpirun --hostfile localhost -c 8 pytomlocalization.py job.xml 2 2 2
>>
>> which will send one of each of the 8 chunks of the tomogram to a
>> processor.
>>
>> If you are on a cluster, you might want to ask the cluster admin if
>> there’s a specific submit script you need to run to have access to the
>> correct default hostfile.
>>
>> —
>> Cheers,
>> Dustin
>>
>>
>> > Thanks you for that. When I run the process with openmpi, i get the
>> following
>> > error message:
>> > Open RTE detected a parse error in the hostfile:
>> /home/kkhanna/Documents/Pytom/Bacillus_ribosome/job.xml It occured on line
>> number 37 on token 1.
>> > —————————————————————————————————————
>> > [pordoi:25878] [[4037,0],0] ORTE_ERROR_LOG: Error in file
>> base/rmaps_base_support_fns.c at line 176
>> > [pordoi:25878] [[4037,0],0] ORTE_ERROR_LOG: Error in file rmaps_rr.c at
>> line 121
>> > [pordoi:25878] [[4037,0],0] ORTE_ERROR_LOG: Error in file
>> base/rmaps_base_map_job.c at line 379
>> > [pordoi:25878] 2 more processes have sent help message
>> help-hostfile.txt / parse_error
>> > [pordoi:25878] Set MCA parameter "orte_base_help_aggregate" to 0 to see
>> all help / error messages
>>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
>
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________
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> Pyt...@li...
> <javascript:_e(%7B%7D,'cvml','Pyt...@li...');>
> https://lists.sourceforge.net/lists/listinfo/pytom-mail
>
>
>

Re: [Pytom-mail] Pytom-mail post from khannakanika11@gmail.com requires approval

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

Please go to 

pytom.org -> Documentation -> Guide & Tutorials -> FAQ and search for the 

LD_PRELOAD 

part.

I think this MPI bug was previously fixed with setting LD_PRELOAD to your libmpi.so .

Use locate libmpi.so to find it. If locate does not give you the location of the library, the paths.csh file in pytom/bin should list one of the directories in LD_LIBRARY_PATH where libmpi.so is.

Thomas


> On Feb 24, 2016, at 2:37 PM, Kanika Khanna <kk...@uc...> wrote:
> 
> Hello,
> 
> So I am trying localization with the tutorial data set itself. I did not use the hostfile as I am running on only one host. Hence, I specified the host and no. of CPUs as per the following command
> 
> mpirun --host 'HostName' -c 4 pytom /usr/local/pytom/bin/localization.py 'PathToJobFile'/job.xml 2 2 2
> 
> I get the following error:
> 
> It looks like orte_init failed for some reason; your parallel process is
> likely to abort.  There are many reasons that a parallel process can
> fail during orte_init; some of which are due to configuration or
> environment problems.  This failure appears to be an internal failure;
> here's some additional information (which may only be relevant to an
> Open MPI developer):
> 
>   opal_init failed
>   --> Returned value Error (-1) instead of ORTE_SUCCESS
> --------------------------------------------------------------------------
> *** An error occurred in MPI_Init
> *** on a NULL communicator
> *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
> ***    and potentially your MPI job)
> [pordoi:29128] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed!
> 
> 
> On Tue, Feb 23, 2016 at 3:44 PM, Dustin Morado <dus...@gm... <mailto:dus...@gm...>> wrote:
> Hi Kanika,
> 
> What was the command you ran exactly? It looks like there’s an error with your host file. Are you running this on a cluster, or just a workstation with openmpi?
> 
> If it’s the latter you can simply run it like this:
> mpirun --hostfile localhost -c 8 pytomlocalization.py job.xml 2 2 2
> 
> which will send one of each of the 8 chunks of the tomogram to a processor.
> 
> If you are on a cluster, you might want to ask the cluster admin if there’s a specific submit script you need to run to have access to the correct default hostfile.
> 
> —
> Cheers,
> Dustin
> 
> 
> > Thanks you for that. When I run the process with openmpi, i get the following
> > error message:
> > Open RTE detected a parse error in the hostfile: /home/kkhanna/Documents/Pytom/Bacillus_ribosome/job.xml It occured on line number 37 on token 1.
> > —————————————————————————————————————
> > [pordoi:25878] [[4037,0],0] ORTE_ERROR_LOG: Error in file base/rmaps_base_support_fns.c at line 176
> > [pordoi:25878] [[4037,0],0] ORTE_ERROR_LOG: Error in file rmaps_rr.c at line 121
> > [pordoi:25878] [[4037,0],0] ORTE_ERROR_LOG: Error in file base/rmaps_base_map_job.c at line 379
> > [pordoi:25878] 2 more processes have sent help message help-hostfile.txt / parse_error
> > [pordoi:25878] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
> 
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________
> Pytom-mail mailing list
> Pyt...@li...
> https://lists.sourceforge.net/lists/listinfo/pytom-mail

Re: [Pytom-mail] Pytom-mail post from khannakanika11@gmail.com requires approval

[Dustin M. <dus...@gm...>]

You need to do this command in your terminal due to something in mpi4py. 

bourne-shell (bash, zsh, etc.)
export LD_PRELOAD='<path to libmpi.so>'

csh (csh, tcsh, etc.)
setenv LD_PRELOAD '<path to libmpi.so>'

where the path to the library is something like ‘/usr/lib/openmpi/lib/libmpi.so’ on my ubuntu 14.04 system.

If you forget again (I always do), it’s also mentioned in the pytom FAQ

—
Cheers,
Dustin

> On Feb 24, 2016, at 4:37 PM, Kanika Khanna <kk...@uc...> wrote:
> 
> Hello,
> 
> So I am trying localization with the tutorial data set itself. I did not use the hostfile as I am running on only one host. Hence, I specified the host and no. of CPUs as per the following command
> 
> mpirun --host 'HostName' -c 4 pytom /usr/local/pytom/bin/localization.py 'PathToJobFile'/job.xml 2 2 2
> 
> I get the following error:
> 
> It looks like orte_init failed for some reason; your parallel process is
> likely to abort.  There are many reasons that a parallel process can
> fail during orte_init; some of which are due to configuration or
> environment problems.  This failure appears to be an internal failure;
> here's some additional information (which may only be relevant to an
> Open MPI developer):
> 
>   opal_init failed
>   --> Returned value Error (-1) instead of ORTE_SUCCESS
> --------------------------------------------------------------------------
> *** An error occurred in MPI_Init
> *** on a NULL communicator
> *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
> ***    and potentially your MPI job)
> [pordoi:29128] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed!
> 
> 
> On Tue, Feb 23, 2016 at 3:44 PM, Dustin Morado <dus...@gm...> wrote:
> Hi Kanika,
> 
> What was the command you ran exactly? It looks like there’s an error with your host file. Are you running this on a cluster, or just a workstation with openmpi?
> 
> If it’s the latter you can simply run it like this:
> mpirun --hostfile localhost -c 8 pytomlocalization.py job.xml 2 2 2
> 
> which will send one of each of the 8 chunks of the tomogram to a processor.
> 
> If you are on a cluster, you might want to ask the cluster admin if there’s a specific submit script you need to run to have access to the correct default hostfile.
> 
> —
> Cheers,
> Dustin
> 
> 
> > Thanks you for that. When I run the process with openmpi, i get the following
> > error message:
> > Open RTE detected a parse error in the hostfile: /home/kkhanna/Documents/Pytom/Bacillus_ribosome/job.xml It occured on line number 37 on token 1.
> > —————————————————————————————————————
> > [pordoi:25878] [[4037,0],0] ORTE_ERROR_LOG: Error in file base/rmaps_base_support_fns.c at line 176
> > [pordoi:25878] [[4037,0],0] ORTE_ERROR_LOG: Error in file rmaps_rr.c at line 121
> > [pordoi:25878] [[4037,0],0] ORTE_ERROR_LOG: Error in file base/rmaps_base_map_job.c at line 379
> > [pordoi:25878] 2 more processes have sent help message help-hostfile.txt / parse_error
> > [pordoi:25878] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
> 

Re: [Pytom-mail] Pytom-mail post from khannakanika11@gmail.com requires approval

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

Hello,

So I am trying localization with the tutorial data set itself. I did not
use the hostfile as I am running on only one host. Hence, I specified the
host and no. of CPUs as per the following command

mpirun --host 'HostName' -c 4 pytom /usr/local/pytom/bin/localization.py
'PathToJobFile'/job.xml 2 2 2

I get the following error:

It looks like orte_init failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems.  This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

  opal_init failed
  --> Returned value Error (-1) instead of ORTE_SUCCESS
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
***    and potentially your MPI job)
[pordoi:29128] Local abort before MPI_INIT completed successfully; not able
to aggregate error messages, and not able to guarantee that all other
processes were killed!


On Tue, Feb 23, 2016 at 3:44 PM, Dustin Morado <dus...@gm...>
wrote:

> Hi Kanika,
>
> What was the command you ran exactly? It looks like there’s an error with
> your host file. Are you running this on a cluster, or just a workstation
> with openmpi?
>
> If it’s the latter you can simply run it like this:
> mpirun --hostfile localhost -c 8 pytomlocalization.py job.xml 2 2 2
>
> which will send one of each of the 8 chunks of the tomogram to a processor.
>
> If you are on a cluster, you might want to ask the cluster admin if
> there’s a specific submit script you need to run to have access to the
> correct default hostfile.
>
> —
> Cheers,
> Dustin
>
>
> > Thanks you for that. When I run the process with openmpi, i get the
> following
> > error message:
> > Open RTE detected a parse error in the hostfile:
> /home/kkhanna/Documents/Pytom/Bacillus_ribosome/job.xml It occured on line
> number 37 on token 1.
> > —————————————————————————————————————
> > [pordoi:25878] [[4037,0],0] ORTE_ERROR_LOG: Error in file
> base/rmaps_base_support_fns.c at line 176
> > [pordoi:25878] [[4037,0],0] ORTE_ERROR_LOG: Error in file rmaps_rr.c at
> line 121
> > [pordoi:25878] [[4037,0],0] ORTE_ERROR_LOG: Error in file
> base/rmaps_base_map_job.c at line 379
> > [pordoi:25878] 2 more processes have sent help message help-hostfile.txt
> / parse_error
> > [pordoi:25878] Set MCA parameter "orte_base_help_aggregate" to 0 to see
> all help / error messages
>

Re: [Pytom-mail] Tutorial files

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

Deleting it from the call worked...

On Wed, Feb 24, 2016 at 12:36 PM, Thomas Hrabe <th...@gm...> wrote:

> The parameter is case sensitive -> fileType ?
>
>
>
> On Feb 24, 2016, at 12:01 PM, Kanika Khanna <kk...@uc...> wrote:
>
> Sorry! Thanks for pointing that out. But now it is showing a different
> error!
>
> option --filetype Not recognized
>
> On Wed, Feb 24, 2016 at 11:39 AM, Thomas Hrabe <th...@gm...> wrote:
>
>> Hm, I see theres a gap between - and projectionTargets in your call?
>>
>>
>>
>> On Feb 24, 2016, at 11:09 AM, Thomas Hrabe <th...@gm...> wrote:
>>
>> Kanika,
>>
>> attached is the fixed call for your reconstruction.
>>
>> The two first parameters had to be replaced
>>
>> reconstructTomogram.py
>> --tiltSeriesName
>> /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/tomo01_sorted
>> --tiltSeriesFormat em
>> --firstIndex 1 --lastIndex 41 --referenceIndex 21 --markerFile
>> /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/markfile_temp.mark
>> --referenceMarkerIndex 1 -- projectionTargets ./alignedProjections/tomo01
>> --projectionBinning 4 --lowpassFilter 0.5 --tomogramFile tomogram.em
>> --filetype em --tomogramSizeX 512 --tomogramSizeY 512 --tomogramSizeZ 128
>> --reconstructionCenterX 0 --reconstructionCenterY 0 reconstructCenterZ 0
>>
>> Works? (Worked for me)
>>
>> The tutorial will be fixed in a bit.
>>
>> Thomas
>>
>> On Feb 24, 2016, at 10:32 AM, Kanika Khanna <kk...@uc...> wrote:
>>
>> Hi,
>>
>> I used the following command as per the tutorial.
>>
>> reconstructTomogram.py --tiltSeriesPath
>> /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/
>> --tiltSeriesPrefix tomo01_sorted --firstIndex 1 --lastIndex 41
>> --referenceIndiex 21 --markerFile
>> /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/markfile_temp.mark
>> --referenceMarkerIndex 1 -- projectionTargets ./alignedProjections/tomo01
>> --projectionBinning 4 --lowpassFilter 0.5 --tomogramFile tomogram.em
>> --filetype em --tomogramSizeX 512 --tomogramSizeY 512 --tomogramSizeZ 128
>> --reconstructionCenterX 0 --reconstructionCenterY 0 reconstructCenterZ 0
>>
>>
>> On Wed, Feb 24, 2016 at 10:17 AM, Thomas Hrabe <th...@gm...> wrote:
>>
>>> Hi Kanika,
>>>
>>> can you please send the full terminal command and output you processed?
>>>
>>> Thomas
>>>
>>> On Feb 24, 2016, at 10:13 AM, Kanika Khanna <kk...@uc...> wrote:
>>>
>>> Hi,
>>>
>>> I downloaded the tutorial file.
>>>
>>> I have been trying to use it to reconstruct the tutorial data and I get
>>> the following error when I run the script reconstructTomo.
>>>
>>>
>>>
>>> *sys.version_info(major=2, minor=7, micro=5, releaselevel='final',
>>> serial=0)option --tiltSeriesPath not recognized*
>>>
>>> ------------------------------------------------------------------------------
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>> Monitor end-to-end web transactions and take corrective actions now
>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>
>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________
>>> Pytom-mail mailing list
>>> Pyt...@li...
>>> https://lists.sourceforge.net/lists/listinfo/pytom-mail
>>>
>>>
>>>
>>
>>
>>
>
>

Re: [Pytom-mail] Tutorial files

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

The parameter is case sensitive -> fileType ?



> On Feb 24, 2016, at 12:01 PM, Kanika Khanna <kk...@uc...> wrote:
> 
> Sorry! Thanks for pointing that out. But now it is showing a different error! 
> 
> option --filetype Not recognized
> 
> On Wed, Feb 24, 2016 at 11:39 AM, Thomas Hrabe <th...@gm... <mailto:th...@gm...>> wrote:
> Hm, I see theres a gap between - and projectionTargets in your call?
> 
> 
> 
>> On Feb 24, 2016, at 11:09 AM, Thomas Hrabe <th...@gm... <mailto:th...@gm...>> wrote:
>> 
>> Kanika,
>> 
>> attached is the fixed call for your reconstruction.
>> 
>> The two first parameters had to be replaced
>> 
>> reconstructTomogram.py 
>> --tiltSeriesName /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/tomo01_sorted 
>> --tiltSeriesFormat em 
>> --firstIndex 1 --lastIndex 41 --referenceIndex 21 --markerFile /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/markfile_temp.mark --referenceMarkerIndex 1 -- projectionTargets ./alignedProjections/tomo01 --projectionBinning 4 --lowpassFilter 0.5 --tomogramFile tomogram.em --filetype em --tomogramSizeX 512 --tomogramSizeY 512 --tomogramSizeZ 128 --reconstructionCenterX 0 --reconstructionCenterY 0 reconstructCenterZ 0
>> 
>> Works? (Worked for me) 
>> 
>> The tutorial will be fixed in a bit.
>> 
>> Thomas
>> 
>>> On Feb 24, 2016, at 10:32 AM, Kanika Khanna <kk...@uc... <mailto:kk...@uc...>> wrote:
>>> 
>>> Hi,
>>> 
>>> I used the following command as per the tutorial. 
>>> 
>>> reconstructTomogram.py --tiltSeriesPath /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/ --tiltSeriesPrefix tomo01_sorted --firstIndex 1 --lastIndex 41 --referenceIndiex 21 --markerFile /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/markfile_temp.mark --referenceMarkerIndex 1 -- projectionTargets ./alignedProjections/tomo01 --projectionBinning 4 --lowpassFilter 0.5 --tomogramFile tomogram.em --filetype em --tomogramSizeX 512 --tomogramSizeY 512 --tomogramSizeZ 128 --reconstructionCenterX 0 --reconstructionCenterY 0 reconstructCenterZ 0
>>> 
>>> 
>>> On Wed, Feb 24, 2016 at 10:17 AM, Thomas Hrabe <th...@gm... <mailto:th...@gm...>> wrote:
>>> Hi Kanika,
>>> 
>>> can you please send the full terminal command and output you processed?
>>> 
>>> Thomas
>>> 
>>>> On Feb 24, 2016, at 10:13 AM, Kanika Khanna <kk...@uc... <mailto:kk...@uc...>> wrote:
>>>> 
>>>> Hi,
>>>> 
>>>> I downloaded the tutorial file.
>>>> 
>>>> I have been trying to use it to reconstruct the tutorial data and I get the following error when I run the script reconstructTomo.
>>>> 
>>>> sys.version_info(major=2, minor=7, micro=5, releaselevel='final', serial=0)
>>>> option --tiltSeriesPath not recognized
>>>> 
>>>> ------------------------------------------------------------------------------
>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>> Monitor end-to-end web transactions and take corrective actions now
>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________ <http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________>
>>>> Pytom-mail mailing list
>>>> Pyt...@li... <mailto:Pyt...@li...>
>>>> https://lists.sourceforge.net/lists/listinfo/pytom-mail <https://lists.sourceforge.net/lists/listinfo/pytom-mail>
>>> 
>>> 
>> 
> 
> 

Re: [Pytom-mail] Tutorial files

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

Sorry! Thanks for pointing that out. But now it is showing a different
error!

option --filetype Not recognized

On Wed, Feb 24, 2016 at 11:39 AM, Thomas Hrabe <th...@gm...> wrote:

> Hm, I see theres a gap between - and projectionTargets in your call?
>
>
>
> On Feb 24, 2016, at 11:09 AM, Thomas Hrabe <th...@gm...> wrote:
>
> Kanika,
>
> attached is the fixed call for your reconstruction.
>
> The two first parameters had to be replaced
>
> reconstructTomogram.py
> --tiltSeriesName
> /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/tomo01_sorted
> --tiltSeriesFormat em
> --firstIndex 1 --lastIndex 41 --referenceIndex 21 --markerFile
> /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/markfile_temp.mark
> --referenceMarkerIndex 1 -- projectionTargets ./alignedProjections/tomo01
> --projectionBinning 4 --lowpassFilter 0.5 --tomogramFile tomogram.em
> --filetype em --tomogramSizeX 512 --tomogramSizeY 512 --tomogramSizeZ 128
> --reconstructionCenterX 0 --reconstructionCenterY 0 reconstructCenterZ 0
>
> Works? (Worked for me)
>
> The tutorial will be fixed in a bit.
>
> Thomas
>
> On Feb 24, 2016, at 10:32 AM, Kanika Khanna <kk...@uc...> wrote:
>
> Hi,
>
> I used the following command as per the tutorial.
>
> reconstructTomogram.py --tiltSeriesPath
> /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/
> --tiltSeriesPrefix tomo01_sorted --firstIndex 1 --lastIndex 41
> --referenceIndiex 21 --markerFile
> /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/markfile_temp.mark
> --referenceMarkerIndex 1 -- projectionTargets ./alignedProjections/tomo01
> --projectionBinning 4 --lowpassFilter 0.5 --tomogramFile tomogram.em
> --filetype em --tomogramSizeX 512 --tomogramSizeY 512 --tomogramSizeZ 128
> --reconstructionCenterX 0 --reconstructionCenterY 0 reconstructCenterZ 0
>
>
> On Wed, Feb 24, 2016 at 10:17 AM, Thomas Hrabe <th...@gm...> wrote:
>
>> Hi Kanika,
>>
>> can you please send the full terminal command and output you processed?
>>
>> Thomas
>>
>> On Feb 24, 2016, at 10:13 AM, Kanika Khanna <kk...@uc...> wrote:
>>
>> Hi,
>>
>> I downloaded the tutorial file.
>>
>> I have been trying to use it to reconstruct the tutorial data and I get
>> the following error when I run the script reconstructTomo.
>>
>>
>>
>> *sys.version_info(major=2, minor=7, micro=5, releaselevel='final',
>> serial=0)option --tiltSeriesPath not recognized*
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________
>> Pytom-mail mailing list
>> Pyt...@li...
>> https://lists.sourceforge.net/lists/listinfo/pytom-mail
>>
>>
>>
>
>
>

Re: [Pytom-mail] Tutorial files

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

Hm, I see theres a gap between - and projectionTargets in your call?



> On Feb 24, 2016, at 11:09 AM, Thomas Hrabe <th...@gm...> wrote:
> 
> Kanika,
> 
> attached is the fixed call for your reconstruction.
> 
> The two first parameters had to be replaced
> 
> reconstructTomogram.py 
> --tiltSeriesName /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/tomo01_sorted 
> --tiltSeriesFormat em 
> --firstIndex 1 --lastIndex 41 --referenceIndex 21 --markerFile /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/markfile_temp.mark --referenceMarkerIndex 1 -- projectionTargets ./alignedProjections/tomo01 --projectionBinning 4 --lowpassFilter 0.5 --tomogramFile tomogram.em --filetype em --tomogramSizeX 512 --tomogramSizeY 512 --tomogramSizeZ 128 --reconstructionCenterX 0 --reconstructionCenterY 0 reconstructCenterZ 0
> 
> Works? (Worked for me) 
> 
> The tutorial will be fixed in a bit.
> 
> Thomas
> 
>> On Feb 24, 2016, at 10:32 AM, Kanika Khanna <kk...@uc... <mailto:kk...@uc...>> wrote:
>> 
>> Hi,
>> 
>> I used the following command as per the tutorial. 
>> 
>> reconstructTomogram.py --tiltSeriesPath /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/ --tiltSeriesPrefix tomo01_sorted --firstIndex 1 --lastIndex 41 --referenceIndiex 21 --markerFile /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/markfile_temp.mark --referenceMarkerIndex 1 -- projectionTargets ./alignedProjections/tomo01 --projectionBinning 4 --lowpassFilter 0.5 --tomogramFile tomogram.em --filetype em --tomogramSizeX 512 --tomogramSizeY 512 --tomogramSizeZ 128 --reconstructionCenterX 0 --reconstructionCenterY 0 reconstructCenterZ 0
>> 
>> 
>> On Wed, Feb 24, 2016 at 10:17 AM, Thomas Hrabe <th...@gm... <mailto:th...@gm...>> wrote:
>> Hi Kanika,
>> 
>> can you please send the full terminal command and output you processed?
>> 
>> Thomas
>> 
>>> On Feb 24, 2016, at 10:13 AM, Kanika Khanna <kk...@uc... <mailto:kk...@uc...>> wrote:
>>> 
>>> Hi,
>>> 
>>> I downloaded the tutorial file.
>>> 
>>> I have been trying to use it to reconstruct the tutorial data and I get the following error when I run the script reconstructTomo.
>>> 
>>> sys.version_info(major=2, minor=7, micro=5, releaselevel='final', serial=0)
>>> option --tiltSeriesPath not recognized
>>> 
>>> ------------------------------------------------------------------------------
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>> Monitor end-to-end web transactions and take corrective actions now
>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________ <http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________>
>>> Pytom-mail mailing list
>>> Pyt...@li... <mailto:Pyt...@li...>
>>> https://lists.sourceforge.net/lists/listinfo/pytom-mail <https://lists.sourceforge.net/lists/listinfo/pytom-mail>
>> 
>> 
> 

Re: [Pytom-mail] Tutorial files

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

Hello

Thank you! But there is still this error for me :(

Traceback (most recent call last):
  File "/usr/local/pytom/bin/reconstructTomogram.py", line 186, in <module>
    outMarkerFileName=outMarkerFileName, verbose=True)
  File "/usr/local/pytom/reconstruction/reconstructionFunctions.py", line
192, in alignWeightReconstruct
    vol_bp = tiltSeries.reconstructVolume(dims=voldims,
reconstructionPosition=recCent, binning=1)
  File "/usr/local/pytom/reconstruction/TiltAlignmentStructures.py", line
440, in reconstructVolume
    binning=binning)
  File "/usr/local/pytom/reconstruction/reconstructionStructures.py", line
423, in reconstructVolume
    vol_bp = vol(dims[0], dims[1], dims[2])
  File "/usr/local/pytom/pytomc/swigModules/pytom_volume.py", line 85, in
__init__
    this = _pytom_volume.new_vol(*args)
RuntimeError: Initialize of volume failed. Specified size is 0,0,0!

On Wed, Feb 24, 2016 at 11:09 AM, Thomas Hrabe <th...@gm...> wrote:

> Kanika,
>
> attached is the fixed call for your reconstruction.
>
> The two first parameters had to be replaced
>
> reconstructTomogram.py
> --tiltSeriesName
> /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/tomo01_sorted
> --tiltSeriesFormat em
> --firstIndex 1 --lastIndex 41 --referenceIndex 21 --markerFile
> /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/markfile_temp.mark
> --referenceMarkerIndex 1 -- projectionTargets ./alignedProjections/tomo01
> --projectionBinning 4 --lowpassFilter 0.5 --tomogramFile tomogram.em
> --filetype em --tomogramSizeX 512 --tomogramSizeY 512 --tomogramSizeZ 128
> --reconstructionCenterX 0 --reconstructionCenterY 0 reconstructCenterZ 0
>
> Works? (Worked for me)
>
> The tutorial will be fixed in a bit.
>
> Thomas
>
> On Feb 24, 2016, at 10:32 AM, Kanika Khanna <kk...@uc...> wrote:
>
> Hi,
>
> I used the following command as per the tutorial.
>
> reconstructTomogram.py --tiltSeriesPath
> /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/
> --tiltSeriesPrefix tomo01_sorted --firstIndex 1 --lastIndex 41
> --referenceIndiex 21 --markerFile
> /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/markfile_temp.mark
> --referenceMarkerIndex 1 -- projectionTargets ./alignedProjections/tomo01
> --projectionBinning 4 --lowpassFilter 0.5 --tomogramFile tomogram.em
> --filetype em --tomogramSizeX 512 --tomogramSizeY 512 --tomogramSizeZ 128
> --reconstructionCenterX 0 --reconstructionCenterY 0 reconstructCenterZ 0
>
>
> On Wed, Feb 24, 2016 at 10:17 AM, Thomas Hrabe <th...@gm...> wrote:
>
>> Hi Kanika,
>>
>> can you please send the full terminal command and output you processed?
>>
>> Thomas
>>
>> On Feb 24, 2016, at 10:13 AM, Kanika Khanna <kk...@uc...> wrote:
>>
>> Hi,
>>
>> I downloaded the tutorial file.
>>
>> I have been trying to use it to reconstruct the tutorial data and I get
>> the following error when I run the script reconstructTomo.
>>
>>
>>
>> *sys.version_info(major=2, minor=7, micro=5, releaselevel='final',
>> serial=0)option --tiltSeriesPath not recognized*
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________
>> Pytom-mail mailing list
>> Pyt...@li...
>> https://lists.sourceforge.net/lists/listinfo/pytom-mail
>>
>>
>>
>
>

Re: [Pytom-mail] Tutorial files

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

Kanika,

attached is the fixed call for your reconstruction.

The two first parameters had to be replaced

reconstructTomogram.py 
--tiltSeriesName /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/tomo01_sorted 
--tiltSeriesFormat em 
--firstIndex 1 --lastIndex 41 --referenceIndex 21 --markerFile /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/markfile_temp.mark --referenceMarkerIndex 1 -- projectionTargets ./alignedProjections/tomo01 --projectionBinning 4 --lowpassFilter 0.5 --tomogramFile tomogram.em --filetype em --tomogramSizeX 512 --tomogramSizeY 512 --tomogramSizeZ 128 --reconstructionCenterX 0 --reconstructionCenterY 0 reconstructCenterZ 0

Works? (Worked for me) 

The tutorial will be fixed in a bit.

Thomas

> On Feb 24, 2016, at 10:32 AM, Kanika Khanna <kk...@uc...> wrote:
> 
> Hi,
> 
> I used the following command as per the tutorial. 
> 
> reconstructTomogram.py --tiltSeriesPath /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/ --tiltSeriesPrefix tomo01_sorted --firstIndex 1 --lastIndex 41 --referenceIndiex 21 --markerFile /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/markfile_temp.mark --referenceMarkerIndex 1 -- projectionTargets ./alignedProjections/tomo01 --projectionBinning 4 --lowpassFilter 0.5 --tomogramFile tomogram.em --filetype em --tomogramSizeX 512 --tomogramSizeY 512 --tomogramSizeZ 128 --reconstructionCenterX 0 --reconstructionCenterY 0 reconstructCenterZ 0
> 
> 
> On Wed, Feb 24, 2016 at 10:17 AM, Thomas Hrabe <th...@gm... <mailto:th...@gm...>> wrote:
> Hi Kanika,
> 
> can you please send the full terminal command and output you processed?
> 
> Thomas
> 
>> On Feb 24, 2016, at 10:13 AM, Kanika Khanna <kk...@uc... <mailto:kk...@uc...>> wrote:
>> 
>> Hi,
>> 
>> I downloaded the tutorial file.
>> 
>> I have been trying to use it to reconstruct the tutorial data and I get the following error when I run the script reconstructTomo.
>> 
>> sys.version_info(major=2, minor=7, micro=5, releaselevel='final', serial=0)
>> option --tiltSeriesPath not recognized
>> 
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
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>> Monitor end-to-end web transactions and take corrective actions now
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>> Pytom-mail mailing list
>> Pyt...@li... <mailto:Pyt...@li...>
>> https://lists.sourceforge.net/lists/listinfo/pytom-mail <https://lists.sourceforge.net/lists/listinfo/pytom-mail>
> 
> 

[Pytom-mail] stable version?

[Villa, E. <ev...@uc...>]

hi,

We have recently downloaded both the stable and the development version of pytom and can’t get the tutorial to work.  As examples, in one case the functions called by the shell script (or described in the tutorial) don’t recognize certain flags that are specified there. I also looked briefly into some other scripts and found hard paths to the MPI NFS.

Is there any stable version somewhere? We’d really like to use pytom :-)

Cheers,
Elizabeth



--
Elizabeth Villa
Department of Chemistry and Biochemistry
University of California San Diego

w: villalab.ucsd.edu<http://villalab.ucsd.edu>
v:  +1 (858) 246-1843
f: +1 (858) 534-4864

Re: [Pytom-mail] Tutorial files

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

Yes, I see it on my computer, too.

The parameters were changed recently to accommodate IMOD reconstructions. I will look up a translation of the parameters from old to new and update the tutorial.

Thomas

> On Feb 24, 2016, at 10:32 AM, Kanika Khanna <kk...@uc...> wrote:
> 
> Hi,
> 
> I used the following command as per the tutorial. 
> 
> reconstructTomogram.py --tiltSeriesPath /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/ --tiltSeriesPrefix tomo01_sorted --firstIndex 1 --lastIndex 41 --referenceIndiex 21 --markerFile /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/markfile_temp.mark --referenceMarkerIndex 1 -- projectionTargets ./alignedProjections/tomo01 --projectionBinning 4 --lowpassFilter 0.5 --tomogramFile tomogram.em --filetype em --tomogramSizeX 512 --tomogramSizeY 512 --tomogramSizeZ 128 --reconstructionCenterX 0 --reconstructionCenterY 0 reconstructCenterZ 0
> 
> 
> On Wed, Feb 24, 2016 at 10:17 AM, Thomas Hrabe <th...@gm... <mailto:th...@gm...>> wrote:
> Hi Kanika,
> 
> can you please send the full terminal command and output you processed?
> 
> Thomas
> 
>> On Feb 24, 2016, at 10:13 AM, Kanika Khanna <kk...@uc... <mailto:kk...@uc...>> wrote:
>> 
>> Hi,
>> 
>> I downloaded the tutorial file.
>> 
>> I have been trying to use it to reconstruct the tutorial data and I get the following error when I run the script reconstructTomo.
>> 
>> sys.version_info(major=2, minor=7, micro=5, releaselevel='final', serial=0)
>> option --tiltSeriesPath not recognized
>> 
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________ <http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________>
>> Pytom-mail mailing list
>> Pyt...@li... <mailto:Pyt...@li...>
>> https://lists.sourceforge.net/lists/listinfo/pytom-mail <https://lists.sourceforge.net/lists/listinfo/pytom-mail>
> 
> 

Re: [Pytom-mail] Tutorial files

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

Hi,

I used the following command as per the tutorial.

reconstructTomogram.py --tiltSeriesPath
/home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/
--tiltSeriesPrefix tomo01_sorted --firstIndex 1 --lastIndex 41
--referenceIndiex 21 --markerFile
/home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/markfile_temp.mark
--referenceMarkerIndex 1 -- projectionTargets ./alignedProjections/tomo01
--projectionBinning 4 --lowpassFilter 0.5 --tomogramFile tomogram.em
--filetype em --tomogramSizeX 512 --tomogramSizeY 512 --tomogramSizeZ 128
--reconstructionCenterX 0 --reconstructionCenterY 0 reconstructCenterZ 0


On Wed, Feb 24, 2016 at 10:17 AM, Thomas Hrabe <th...@gm...> wrote:

> Hi Kanika,
>
> can you please send the full terminal command and output you processed?
>
> Thomas
>
> On Feb 24, 2016, at 10:13 AM, Kanika Khanna <kk...@uc...> wrote:
>
> Hi,
>
> I downloaded the tutorial file.
>
> I have been trying to use it to reconstruct the tutorial data and I get
> the following error when I run the script reconstructTomo.
>
>
>
> *sys.version_info(major=2, minor=7, micro=5, releaselevel='final',
> serial=0)option --tiltSeriesPath not recognized*
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
>
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________
> Pytom-mail mailing list
> Pyt...@li...
> https://lists.sourceforge.net/lists/listinfo/pytom-mail
>
>
>