I was then able to run the resulting binary executable on both yours and Grigory's test images, with no crashes or errors.įor reference, here are more details about the container I built and the toolchain, as well as the libraries the binary links 200512_ctffind_dbg]$ ldd /mnt/ext_home/work/tmp/centos_ctffind/ctffind-4.1.14/build/ctffind
Bugzilla mrc archive#
This completed without error (starting from the ctffind-4.1.14_ archive I shared the other day).
Bugzilla mrc install#
Yum -y install fftw fftw-devel wxGTK3 wxGTK3-devel libtiff libtiff-devel cmake make gcc git which diffutils gcc-c++ libjpeg-turbo-devel I had to do the following before being able to build ctffind: I believe I'm now using the same environment as you, and yet I am unable to reproduce the crashes using the latest version I shared with you a few days ago. I setup a Docker container with exactly that version of CentOS (8) and gcc. OpenMP is not available - will not use parallel threads.
Use a restraint on astigmatism? : noĭo you want to set expert options? : no Size of amplitude spectrum to compute : 512ĭo you know what astigmatism is present? : no Input image file name : /root/MotionCorr/job019/relionrelated/tutorialdata/relion30_tutorial/Movies/20170629_00049_frameImage.mrc I know Alexis can make ctffind 4.1.14 workable with my tiff in Alexis's computer, but I hope Alexis can make it workable in every computer (or every liux). I have tried the ctffind ( ) using my posted tiff in this forum initiated by me, as it still gave segmentation fault, as following. Could you try to reproduce with 4.1.14, and, assuming it reproduces, could you please send the input image and runtime parameters so that I can investigate further? I believe if you start a new forum topic you'll have the option to attach files to the initial post in the topic. Thanks for taking time to investigate this - it does look like a bug. I have number_of_bins = 363, but the counter on the line 2852 still goes outside of range:Ģ854 MyDebugAssertFalse(std::isnan(average_rank),"AverageRank is NaN for bin %i\n",counter) Ģ853 MyDebugAssertFalse(std::isnan(average),"Average is NaN for bin %i\n",counter) The produced defocus though seems correct (compared to cistem results) The output mrc is empty file and the output txt has no numbers in it, just the header. Size of amplitude spectrum to compute :ĭo you know what astigmatism is present? :ĭo you want to set expert options? :įailed Assert at src/programs/ctffind/ctffind.cpp:2854īool ComputeRotationalAverageOfPowerSpectrum(Image*, CTF*, Image*, Image*, int, double*, double*, double*, double*, float*, float*) configure -with-wx-config=/usr/bin/wx-config -enable-openmp -enable-debugmode then make. So far I was unable to run standalone ctffind on any mic, the only working binary for me is from inside cistem (4.1.8 I believe)ġ) the linu圆4 binary from the website segfaults straight away when I execute it.Ģ) I've downloaded the src, run.
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