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