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Re: [Pytom-mail] MPI Errors and Particle File Viewing
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From: Kanika K. <kk...@uc...> - 2016-03-11 20:01:59
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Hi
I am sorry but the job did start running and it gave this weird error then
and aborted again! :(
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
node_0: send number of 50 rotations to node 2
node_0: send number of 25 rotations to node 1
node_2: send number of 25 rotations to node 3
node_0: starting to calculate 25 rotations
node_3: starting to calculate 25 rotations
node_1: starting to calculate 25 rotations
node_2: starting to calculate 25 rotations
Traceback (most recent call last):
File "/usr/local/pytom/bin/localization.py", line 82, in <module>
startLocalizationJob(jobName, splitX, splitY, splitZ,
doSplitAngles=False)
File "/usr/local/pytom/bin/localization.py", line 21, in
startLocalizationJob
leader.parallelRun(job, splitX, splitY, splitZ, verbose)
File "/usr/local/pytom/localization/parallel_extract_peaks.py", line
1046, in parallelRun
result = self.run(verbose)
File "/usr/local/pytom/localization/parallel_extract_peaks.py", line 104,
in run
[resV, orientV, sumV, sqrV] = extractPeaks(v, ref, rot, scoreFnc, m,
mIsSphere, wedg, nodeName=self.name, verboseMode=verbose, moreInfo=moreInfo)
File "/usr/local/pytom/localization/extractPeaks.py", line 130, in
extractPeaks
meanV = meanUnderMask(volume, maskV, p);
File "/usr/local/pytom/basic/correlation.py", line 244, in meanUnderMask
result = iftshift(ifft(fMask*fft(volume)))/(size*p)
File "/usr/local/pytom/pytomc/swigModules/pytom_volume.py", line 342, in
__mul__
return _pytom_volume.vol_comp___mul__(self, *args)
RuntimeError: std::bad_alloc
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
On Fri, Mar 11, 2016 at 11:56 AM, Kanika Khanna <kk...@uc...> wrote:
> Hi Thomas,
>
> I have been able to resolve issue 1. I just killed all the processes and
> started again. It worked that time.
>
> On Sat, Mar 12, 2016 at 1:05 AM, Thomas Hrabe <th...@gm...> wrote:
>
>> Hi Kanika,
>>
>>
>> 1.
>> to me, it looks like that you are trying to open a file called
>>
>> > <Volume Binning="[0, 0, 0]" Filename="PY79.mrc" Sampling="[0, 0, 0]"
>> Subregion="[0, 0, 0, 0, 0, 0]"/>
>>
>>
>> Can you please attach the xml file?
>>
>> 2.
>> I have to look into the script as well. I must re-install it before I can
>> advice about how to use it.
>>
>> Cheers,
>> Thomas
>>
>> > On Mar 11, 2016, at 11:15 AM, Kanika Khanna <kk...@uc...> wrote:
>> >
>> > Hello all,
>> >
>> > 1. When I try to execute my job using the following command
>> > mpirun --host HostName -c 4 pytom localization.py PathToJobFile 2 2 2
>> >
>> > I get the following error:
>> > Traceback (most recent call last):
>> > File "/usr/local/pytom/bin/localization.py", line 82, in <module>
>> > startLocalizationJob(jobName, splitX, splitY, splitZ,
>> doSplitAngles=False)
>> > File "/usr/local/pytom/bin/localization.py", line 11, in
>> startLocalizationJob
>> > job.check()
>> > File "/usr/local/pytom/localization/peak_job.py", line 184, in check
>> > Traceback (most recent call last):
>> > File "/usr/local/pytom/bin/localization.py", line 82, in <module>
>> > raise IOError('File: ' + str(self.volume) + ' not found!')
>> > IOError: File: <Volume Binning="[0, 0, 0]" Filename="PY79.mrc"
>> Sampling="[0, 0, 0]" Subregion="[0, 0, 0, 0, 0, 0]"/>
>> > not found!
>> > startLocalizationJob(jobName, splitX, splitY, splitZ,
>> doSplitAngles=False)
>> > File "/usr/local/pytom/bin/localization.py", line 11, in
>> startLocalizationJob
>> > job.check()
>> > File "/usr/local/pytom/localization/peak_job.py", line 184, in check
>> > raise IOError('File: ' + str(self.volume) + ' not found!')
>> > IOError: File: <Volume Binning="[0, 0, 0]" Filename="PY79.mrc"
>> Sampling="[0, 0, 0]" Subregion="[0, 0, 0, 0, 0, 0]"/>
>> > not found!
>> > Traceback (most recent call last):
>> > File "/usr/local/pytom/bin/localization.py", line 82, in <module>
>> > startLocalizationJob(jobName, splitX, splitY, splitZ,
>> doSplitAngles=False)
>> > File "/usr/local/pytom/bin/localization.py", line 11, in
>> startLocalizationJob
>> > job.check()
>> > File "/usr/local/pytom/localization/peak_job.py", line 184, in check
>> > raise IOError('File: ' + str(self.volume) + ' not found!')
>> > IOError: File: <Volume Binning="[0, 0, 0]" Filename="PY79.mrc"
>> Sampling="[0, 0, 0]" Subregion="[0, 0, 0, 0, 0, 0]"/>
>> > not found!
>> > -------------------------------------------------------
>> > Primary job terminated normally, but 1 process returned
>> > a non-zero exit code.. Per user-direction, the job has been aborted.
>> > -------------------------------------------------------
>> > Traceback (most recent call last):
>> > File "/usr/local/pytom/bin/localization.py", line 82, in <module>
>> > startLocalizationJob(jobName, splitX, splitY, splitZ,
>> doSplitAngles=False)
>> > File "/usr/local/pytom/bin/localization.py", line 11, in
>> startLocalizationJob
>> > job.check()
>> > File "/usr/local/pytom/localization/peak_job.py", line 184, in check
>> > raise IOError('File: ' + str(self.volume) + ' not found!')
>> > IOError: File: <Volume Binning="[0, 0, 0]" Filename="PY79.mrc"
>> Sampling="[0, 0, 0]" Subregion="[0, 0, 0, 0, 0, 0]"/>
>> > not found!
>> >
>> --------------------------------------------------------------------------
>> > mpirun detected that one or more processes exited with non-zero status,
>> thus causing
>> > the job to be terminated. The first process to do so was:
>> >
>> > Process name: [[27852,1],3]
>> > Exit code: 1
>> >
>> >
>> > Any idea how I can circumvent this? Or what exactly might be going
>> wrong?
>> >
>> > 2. Once you have the pl.xml file generated after extraction of
>> particles, we have the script VolumeDialog.py for viewing it in Chimera. I
>> already installed it in the Volume Viewer folder. How exactly are we
>> suppose to use it? Also, there were a couple of existing files of the same
>> name in the folder existing previously (is that the case with everyone
>> here?). Anything to do with them?
>> >
>> > Thanks!
>> >
>> >
>> >
>> >
>> >
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