Illegal instruction (core dumped) on linux

[belatulipo]

I'm trying to compile ANTs on ubuntu 18.04 using the instructions. I have searched and searched and I've done everything I can think of. Please help me understand what the problem is.
I have a laptop and a desktop computer with the same OS. With my laptop the system just crashed after the "make" command. With the desktop I get this error:

Illegal instruction (core dumped)
Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeFiles/hdf5-static.dir/build.make:61: recipe for target 'Modules/ThirdParty/HDF5/src/itkhdf5/H5Tinit.c' failed
make[5]: *** [Modules/ThirdParty/HDF5/src/itkhdf5/H5Tinit.c] Error 132
make[5]: *** Deleting file 'Modules/ThirdParty/HDF5/src/itkhdf5/H5Tinit.c'
CMakeFiles/Makefile2:7779: recipe for target 'Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeFiles/hdf5-static.dir/all' failed
make[4]: *** [Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeFiles/hdf5-static.dir/all] Error 2
make[4]: *** Waiting for unfinished jobs....
.
.
.
[ 58%] Built target gdcmDSED
Makefile:151: recipe for target 'all' failed
make[3]: *** [all] Error 2
CMakeFiles/ITKv5.dir/build.make:112: recipe for target 'ITKv5-prefix/src/ITKv5-stamp/ITKv5-build' failed
make[2]: *** [ITKv5-prefix/src/ITKv5-stamp/ITKv5-build] Error 2
CMakeFiles/Makefile2:109: recipe for target 'CMakeFiles/ITKv5.dir/all' failed
make[1]: *** [CMakeFiles/ITKv5.dir/all] Error 2
Makefile:116: recipe for target 'all' failed
make: *** [all] Error 2

[gdevenyi]

likely overheating. Not an ANTs bug.

[belatulipo]

I tried again after shutting down the whole system for hours and I got the exact same error. I don't think it's overheating. Any suggestions?

[gdevenyi]

Building ANTs on 18.04 does not result in such issues on any systems I admin, or during our automated builds. Given that, I suspect it is an issue with your system.

Check "dmesg" for signs of thermal throttling.

Another possibility is bad ram, check memtest86+

[cookpa]

@belatulipo is this native Linux or a VM / WSL?

[belatulipo]

Building ANTs on 18.04 does not result in such issues on any systems I admin, or during our automated builds. Given that, I suspect it is an issue with your system.

Check "dmesg" for signs of thermal throttling.

Another possibility is bad ram, check memtest86+

Thank you I will try that.
I was able to successfully compile it on 16.04 at the research center. But I prefer to have it on my own computer as well.

[belatulipo]

@belatulipo is this native Linux or a VM / WSL?
Native linux.

[cookpa]

Thanks. I'm working on a VM, where I can successfully compile using 18.04 / GCC 7:

$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/7/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 7.4.0-1ubuntu1~18.04.1' --with-bugurl=file:///usr/share/doc/gcc-7/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++ --prefix=/usr --with-gcc-major-version-only --program-suffix=-7 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 7.4.0 (Ubuntu 7.4.0-1ubuntu1~18.04.1) 

It might be related to this issue

#764

I can't test this because I can't reproduce the problem.

[cookpa]

This commit might fix the problem, at least for some machines

691c865#diff-821bb4259dcdb7f026034ba1b16e553c

CC: @ronangarrison

[gdevenyi]

This problem was actually introduced earlier:
2d54c16

[gdevenyi]

To be clear, the devs believe the issue is that your CPU is older than corei7, which is what our default "arch" setting is:
https://github.com/ANTsX/ANTs/blob/master/CMake/ITKSetStandardCompilerFlags.cmake#L245

You can adjust this by adding "-march=native" to your compile options.

[cookpa]

Found a test case and fix for this issue:

https://github.com/ANTsX/ANTs/wiki/Compiling-ANTs-on-Linux-and-Mac-OS#compilation-fails-or-run-time-errors-occur-with-illegal-instruction-errors