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Bug #3436
closedmemory error for ctfpower.py
Start date:
08/26/2015
Due date:
% Done:
0%
Estimated time:
Affected Version:
Appion/Leginon 3.2
Show in known bugs:
No
Workaround:
Description
image attached
ctfestimate.py --runname=ctffindrun2 --rundir=/emg/data00/appion/rice/15aug25g/ctf/ctffindrun2 --commit --preset=en --projectid=5 --session=15aug25g --no-rejects --no-wait --continue --ampcarbon=0.15 --ampice=0.07 --fieldsize=512 --medium=ice --bin=8 --resmin=100 --resmax=10 --defstep=1000 --numstep=25 --dast=500 --expid=605 --jobtype=ctfestimate
[CTF param] def1: 9.54e-07 | def2: 1.01e-06 | angle: -76.5 | ampcontr 0.07 | defratio 1.054
Final params: def1: 9.54e-07 | def2: 1.01e-06 | angle: -76.5 | defratio 1.05
... Defocus Astig Percent Diff 2.61 -- 9.540e-07, 1.005e-06
Computing power spectra in 1024x1024 blocks...................................
... Computing median of power spectra series
Traceback (most recent call last):
File "/emg/sw/packages/myamitrunk/appion/bin/ctfestimate.py", line 449, in <module>
imgLoop.run()
File "/emg/sw/packages/myamitrunk/appion/appionlib/appionLoop2.py", line 93, in run
self.loopCommitToDatabase(imgdata)
File "/emg/sw/packages/myamitrunk/appion/appionlib/appionLoop2.py", line 143, in loopCommitToDatabase
return self.commitToDatabase(imgdata)
File "/emg/sw/packages/myamitrunk/appion/bin/ctfestimate.py", line 349, in commitToDatabase
ctfinsert.validateAndInsertCTFData(imgdata, self.ctfvalues, self.ctfrun, self.params['rundir'])
File "/emg/sw/packages/myamitrunk/appion/appionlib/apCtf/ctfinsert.py", line 45, in validateAndInsertCTFData
ctfvalues = runCTFdisplayTools(imgdata, ctfvalues, opimagedir, fftpath, fftfreq)
File "/emg/sw/packages/myamitrunk/appion/appionlib/apCtf/ctfinsert.py", line 83, in runCTFdisplayTools
ctfdisplaydict = ctfdisplay.makeCtfImages(imgdata, ctfvalues, fftpath, fftfreq)
File "/emg/sw/packages/myamitrunk/appion/appionlib/apCtf/ctfdisplay.py", line 1267, in makeCtfImages
ctfdisplaydict = a.CTFpowerspec(imgdata, ctfdata, fftpath, fftfreq, twod=twod)
File "/emg/sw/packages/myamitrunk/appion/appionlib/apCtf/ctfdisplay.py", line 1131, in CTFpowerspec
self.outerAngstrom1D, self.apix)
File "/emg/sw/packages/myamitrunk/appion/appionlib/apCtf/ctftools.py", line 204, in powerSpectraToOuterResolution
data, freq = ctfpower.power(image, apix, fieldsize)
File "/emg/sw/packages/myamitrunk/appion/appionlib/apCtf/ctfpower.py", line 137, in power
poweravg = numpy.median(psdlist, axis=0)
File "/usr/lib64/python2.6/site-packages/numpy/lib/function_base.py", line 2803, in median
sorted = sort(a, axis=axis)
File "/usr/lib64/python2.6/site-packages/numpy/core/fromnumeric.py", line 574, in sort
a = asanyarray(a).copy()
File "/usr/lib64/python2.6/site-packages/numpy/core/numeric.py", line 312, in asanyarray
return array(a, dtype, copy=False, order=order, subok=True)
MemoryError
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Updated by Neil Voss over 9 years ago
- Assignee changed from Neil Voss to Anchi Cheng
Is this reproducible? I wonder if it was caused by another program using too much memory? Because looks like it should have had plenty of memory.
Updated by Anchi Cheng over 9 years ago
- Assignee changed from Anchi Cheng to Neil Voss
- Priority changed from Immediate to Urgent
Hi, Neil,
emgbox02 where this occur did have 1GB of memory used by other program. Strangely by pbs_scheduler. I didn't know this computer only has total of 2GB memory. The rest is from swap.
I tried the same on j3200leginon with had all 4GB memory for itself and it ran past that point. How much memory does this part of program need ?
There is another problem though. I will start a new issue for it.
Updated by Neil Voss almost 9 years ago
- Status changed from Assigned to Won't Fix or Won't Do
- Priority changed from Urgent to Normal
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