ctffind 4.1.14 segfault

Thanks for this information. I setup a Docker container with exactly that version of CentOS (8) and gcc. 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 had to do the following before being able to build ctffind:

yum -y install sudo epel-release
yum -y install fftw fftw-devel wxGTK3 wxGTK3-devel libtiff libtiff-devel cmake make gcc git which diffutils gcc-c++ libjpeg-turbo-devel

Then I did:

../configure --enable-debugmode --enable-openmp

make -j2

This completed without error (starting from the ctffind-4.1.14_200525.tar.gz archive I shared the other day).

I was then able to run the resulting binary executable on both yours and Grigory's test images, with no crashes or errors.

For reference, here are more details about the container I built and the toolchain, as well as the libraries the binary links against:

[developer@2a6e5732349b 200512_ctffind_dbg]$ ldd /mnt/ext_home/work/tmp/centos_ctffind/ctffind-4.1.14/build/ctffind
    linux-vdso.so.1 (0x00007fff9331d000)
    libwx_baseu-3.0.so.0 => /lib64/libwx_baseu-3.0.so.0 (0x00007f5b091a3000)
    libwx_baseu_net-3.0.so.0 => /lib64/libwx_baseu_net-3.0.so.0 (0x00007f5b08f57000)
    libtiff.so.5 => /lib64/libtiff.so.5 (0x00007f5b08cde000)
    libjpeg.so.62 => /lib64/libjpeg.so.62 (0x00007f5b08a75000)
    libz.so.1 => /lib64/libz.so.1 (0x00007f5b0885e000)
    libdl.so.2 => /lib64/libdl.so.2 (0x00007f5b0865a000)
    libfftw3f.so.3 => /lib64/libfftw3f.so.3 (0x00007f5b08243000)
    libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f5b07eae000)
    libm.so.6 => /lib64/libm.so.6 (0x00007f5b07b2c000)
    libgomp.so.1 => /lib64/libgomp.so.1 (0x00007f5b078f4000)
    libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f5b076dc000)
    libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f5b074bc000)
    libc.so.6 => /lib64/libc.so.6 (0x00007f5b070f9000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f5b0964c000)
    libjbig.so.2.1 => /lib64/libjbig.so.2.1 (0x00007f5b06eed000)
[developer@2a6e5732349b 200512_ctffind_dbg]$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/8/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-redhat-linux
Configured with: ../configure --enable-bootstrap --enable-languages=c,c++,fortran,lto --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-shared --enable-threads=posix --enable-checking=release --enable-multilib --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-gcc-major-version-only --with-linker-hash-style=gnu --enable-plugin --enable-initfini-array --with-isl --disable-libmpx --enable-offload-targets=nvptx-none --without-cuda-driver --enable-gnu-indirect-function --enable-cet --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux
Thread model: posix
gcc version 8.3.1 20190507 (Red Hat 8.3.1-4) (GCC)
[developer@2a6e5732349b 200512_ctffind_dbg]$ uname -a
Linux 2a6e5732349b 4.19.76-linuxkit #1 SMP Tue May 26 11:42:35 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
[developer@2a6e5732349b 200512_ctffind_dbg]$ rpm -q centos-release
centos-release-8.1-1.1911.0.8.el8.x86_64

[ TLDR: edit lines 270, 274, 2422 and 2765 of ctffind-4.1.14/src/programs/ctffind/ctffind.cpp and replace the bool at the beginning of those lines with void, then recompile. ]

I might have found the issue here - I at least had a similar experience and managed to fix it for our installation.

I recently built ctffind with a somewhat similar gcc version (8.3.0) and also experienced crashes.  I believe the reason for my crashes was undefined code in ctffind-4.1.14/src/programs/ctffind/ctffind.cpp:

The function ComputeRotationalAverageOfPowerSpectrum() (starting at line 2765) is declared as bool (matching the declaration in line 270), but it never returns anything, this is undefined behavior.  Going by its purpose, it doesn't have to return anything, it is only called once, in line 1757, and no return value is assigned there, and judging by the comment in the function in line 2824, it is planned to make it return something here (that should then also happen at the end of the function) and then evaluate that return value in the caller.

The same is true for RescaleSpectrumAndRotationalAverage().

All of this applies not only to ctffind 4.1.14 but also to 4.1.13.  In version 4.1.10 the two functions are correctly declared as void.

Here is a simple program visualizing the issue:

#include <iostream>

bool f() {
std::cout << "test" << std::endl;
}

int main()
{
f();
return 0;
}

Compiling this with <code>g++ -O1 -o test test.cpp</code> and running it fails in "random" ways - on x86-64 this causes an "infinite loop" (well, until the stack is exhausted) and on ppc64 it gives an "illegal instruction".  It appears to work if I compile with <code>-O0</code>. Unfortunately gcc only *warns* about this but compiles it nevertheless.

I hope this helps some people who are having problems (segfaults or other crashes) with 4.1.14.