Hello and Happy New Year to everyone!
I have a seg fault at the last refinement iteration when using the option --dont_combine_weights_via_disc, see below.
My volume is not that huge: 318 pixels. I get this with a 20,000 particles dataset, and a 5000 particles dataset.
I tried rebooting the nodes and it had no effect.
Removing the option --dont_combine_weights_via_disc solved the problem, but the maximization took ~3-5 hours just by itself.
Best,
Amedee
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Auto-refine: Iteration= 18
Auto-refine: Resolution= 23.9257 (no gain for 7 iter)
Auto-refine: Changes in angles= 1.08112 degrees; and in offsets= 0.734029 pixels (no gain for 3 iter)
Auto-refine: Refinement has converged, entering last iteration where two halves will be combined...
Auto-refine: The last iteration will use data to Nyquist frequency, which may take more CPU and RAM.
Estimating accuracies in the orientational assignment ...
2.98/2.98 min ............................................................~~(,_,">
Auto-refine: Estimated accuracy angles= 2.822 degrees; offsets= 2.114 pixels
Auto-refine: Angular step= 1.875 degrees; local searches= true
Auto-refine: Offset search range= 4.5 pixels; offset step= 1.5 pixels
Estimated required memory for expectation step= 4.96788 Gb, maximum allowed memory = 16 Gb.
CurrentResolution= 23.9257 Angstroms, which requires orientationSampling of at least 6.2069 degrees for a particle of diameter 440 Angstroms
Oversampling= 0 NrHiddenVariableSamplingPoints= 663552
OrientationalSampling= 3.75 NrOrientations= 145
TranslationalSampling= 3 NrTranslations= 9
=============================
Oversampling= 1 NrHiddenVariableSamplingPoints= 21233664
OrientationalSampling= 1.875 NrOrientations= 1160
TranslationalSampling= 1.5 NrTranslations= 36
=============================
Expectation iteration 18
11.63/11.63 min ............................................................~~(,_,">
[node61:03488] *** Process received signal ***
[node61:03488] Signal: Segmentation fault (11)
[node61:03488] Signal code: (128)
[node61:03488] Failing at address: (nil)
[node60:03446] *** Process received signal ***
[node60:03446] Signal: Segmentation fault (11)
[node60:03446] Signal code: (128)
[node60:03446] Failing at address: (nil)
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mpirun noticed that process rank 4 with PID 3488 on node node61 exited on signal 11 (Segmentation fault).
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2 total processes killed (some possibly by mpirun during cleanup)
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