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Seg fault in 2.0.3 and 2.1 #304

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max1c opened this issue Nov 3, 2017 · 1 comment
Closed

Seg fault in 2.0.3 and 2.1 #304

max1c opened this issue Nov 3, 2017 · 1 comment

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@max1c
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max1c commented Nov 3, 2017

Command:
mpirun relion_refine_mpi --o Class3D/job129/run --i Select/job119/particles.star --ref PM_1.26_200.mrc --firstiter_cc --dont_combine_weights_via_disc --ini_high 40 --pool 100 --ctf --iter 25 --tau2_fudge 4 --particle_diameter 180 --K 4 --flatten_solvent --zero_mask --strict_highres_exp 4 --oversampling 1 --healpix_order 3 --offset_range 5 --offset_step 2 --sym D2 --norm --scale --j 4

Error:
"mpirun noticed that process rank 0 with PID 32434 on node c21a-s5 exited on signal 11 (Segmentation fault)."

Backtrace from the 2.1.0 segfault shows that the issue manifests itself during plot generation:
#0 0x00002aaaaabee74f in CDataSet::GetDataPoint(int) () at /relion/2.1.0/relion/src/CPlot2D.h:160
#1 0x00002aaaaabe7c2c in CPlot2D::DrawDataPostScript() () at /relion/2.1.0/relion/src/CPlot2D.cpp:286
#2 0x00002aaaaabe6dfa in CPlot2D::OutputPostScriptPlot(std::__cxx11::basic_string<char, std::char_traits, std::allocator >) () at /relion/2.1.0/relion/src/CPlot2D.cpp:168
#3 0x00002aaaaaecb5c4 in Postprocessing::writeOutput() () at /distapps/relion/2.1.0/relion/src/postprocessing.cpp:806
#4 0x00002aaaaaecee60 in Postprocessing::run() () at /relion/2.1.0/relion/src/postprocessing.cpp:1179
#5 0x000000000040ade3 in main () at /relion/2.1.0/relion/src/apps/postprocess.cpp:34

@biochem-fan
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Refine3D should not generate any PDF files.

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