*** buffer overflow detected ***: in relion_run_motioncorr_mpi upon generation of the logfile.pdf

[Alex Shkumatov]

Hi

I get the following error when running motioncorr wrapper from RELION3.0_beta (see below). Now, if I checkout, build and run the older version (RELION 2.1.0), it works without any error.

As i was writing this i also were doing more tests and figured out why this bug is appearing, namely when the file corrected_micrographs_hist_rlnAccumMotionEarly.eps is empty, e.g. when i am skipping first 3 frames.

Let me know if you need more details. Thanks, Alex

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... skipped. .. Correcting beam-induced motions using Shawn Zheng's MOTIONCOR2 ... 20/ 20 sec ............................................................(,_,"> Generating logfile.pdf ... 000/??? sec (,_,"> [oo][jekyll:36791] Process received signal [jekyll:36791] Signal: Aborted (6) [jekyll:36791] Signal code: (-6) [jekyll:36791] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x12890)[0x7f1acb2e6890] [jekyll:36791] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7f1ac9fa7e97] [jekyll:36791] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x141)[0x7f1ac9fa9801] [jekyll:36791] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x89897)[0x7f1ac9ff2897] [jekyll:36791] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x134cff)[0x7f1aca09dcff] [jekyll:36791] [ 5] /lib/x86_64-linux-gnu/libc.so.6(+0x134d21)[0x7f1aca09dd21] [jekyll:36791] [ 6] /lib/x86_64-linux-gnu/libc.so.6(+0x132a10)[0x7f1aca09ba10] [jekyll:36791] [ 7] /lib/x86_64-linux-gnu/libc.so.6(+0x131f29)[0x7f1aca09af29] [jekyll:36791] [ 8] /lib/x86_64-linux-gnu/libc.so.6(_IO_default_xsputn+0x74)[0x7f1ac9ff7494] [jekyll:36791] [ 9] /lib/x86_64-linux-gnu/libc.so.6(+0x609dc)[0x7f1ac9fc99dc] [jekyll:36791] [10] /lib/x86_64-linux-gnu/libc.so.6(_IO_vfprintf+0x1677)[0x7f1ac9fc5a07] [jekyll:36791] [11] /lib/x86_64-linux-gnu/libc.so.6(__vsprintf_chk+0x9b)[0x7f1aca09afcb] [jekyll:36791] [12] /lib/x86_64-linux-gnu/libc.so.6(__sprintf_chk+0x8a)[0x7f1aca09aefa] [jekyll:36791] [13] /home/software/relion/git-relion-3.0_beta/build-relion3.0_beta-20181024_cu92/bin/relion_run_motioncorr_mpi(_ZN7CPlot2D23ComputeLabelTickSpacingEddPdS0_S0_iNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x278)[0x556390424bb8] [jekyll:36791] [14] /home/software/relion/git-relion-3.0_beta/build-relion3.0_beta-20181024_cu92/bin/relion_run_motioncorr_mpi(_ZN7CPlot2D20PrecomputeDimensionsEv+0x277)[0x556390425057] [jekyll:36791] [15] /home/software/relion/git-relion-3.0_beta/build-relion3.0_beta-20181024_cu92/bin/relion_run_motioncorr_mpi(_ZN7CPlot2D20OutputPostScriptPlotENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x51)[0x556390425381] [jekyll:36791] [16] /home/software/relion/git-relion-3.0_beta/build-relion3.0_beta-20181024_cu92/bin/relion_run_motioncorr_mpi(_ZN16MotioncorrRunner35generateLogFilePDFAndWriteStarFilesEv+0xb08)[0x5563903e4698] [jekyll:36791] [17] /home/software/relion/git-relion-3.0_beta/build-relion3.0_beta-20181024_cu92/bin/relion_run_motioncorr_mpi(_ZN19MotioncorrRunnerMpi3runEv+0x382)[0x5563904096a2] [jekyll:36791] [18] /home/software/relion/git-relion-3.0_beta/build-relion3.0_beta-20181024_cu92/bin/relion_run_motioncorr_mpi(main+0x4f)[0x5563903bac2f] [jekyll:36791] [19] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7f1ac9f8ab97] [jekyll:36791] [20] /home/software/relion/git-relion-3.0_beta/build-relion3.0_beta-20181024_cu92/bin/relion_run_motioncorr_mpi(_start+0x2a)[0x5563903bb30a] [jekyll:36791] End of error message

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mpirun noticed that process rank 0 with PID 0 on node jekyll exited on signal 6 (Aborted).

[Takanori Nakane]

Thank you very much for the report. Meanwhile, please specify --dose_motionstats_cutoff such that you have at least two frames in the 'early' phase of the motion.