ROOT_Numpy Installation Atomic File missing! Fatal Error


I’m trying to install root_numpy.

sudo ROOTSYS=$ROOTSYS python install

and got

In file included from root_numpy/src/_librootnumpy.cpp:460:
In file included from /Users/DC/Downloads/build/include/TClass.h:25:
In file included from /Users/DC/Downloads/build/include/TDictionary.h:45:
In file included from /Users/DC/Downloads/build/include/TNamed.h:26:
In file included from /Users/DC/Downloads/build/include/TObject.h:18:
/Users/DC/Downloads/build/include/Rtypes.h:37:10: fatal error: 'atomic' file not found
#include <atomic>
1 warning and 1 error generated.
error: command 'gcc' failed with exit status 1

I already updated my gcc. Is there any way for me to get that mysterious atomic file and put it in it’s place?



The gcc that’s used to build numpy is too old. Which version of gcc do you use?

Cheers, Axel

Hi the gcc version I recently installed is:

Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin14.5.0
Thread model: posix

But I am not sure if that is what has been used to build numpy? I have installed anaconda/jupyter with python2 along with different packages before I got this latest version. Any suggestions?

Now my version is.

which gcc
DC@DCUsers-iMac:~$ gcc -v 
Using built-in specs.
Target: x86_64-apple-darwin14.5.0
Configured with: ../configure --build=x86_64-apple-darwin14.5.0 --prefix=/usr/local/Cellar/gcc/6.3.0_1 --libdir=/usr/local/Cellar/gcc/6.3.0_1/lib/gcc/6 --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-6 --with-gmp=/usr/local/opt/gmp --with-mpfr=/usr/local/opt/mpfr --with-mpc=/usr/local/opt/libmpc --with-isl=/usr/local/opt/isl --with-system-zlib --enable-libstdcxx-time=yes --enable-stage1-checking --enable-checking=release --enable-lto --with-build-config=bootstrap-debug --disable-werror --with-pkgversion='Homebrew GCC 6.3.0_1' --with-bugurl= --enable-plugin --disable-nls --enable-multilib
Thread model: posix
gcc version 6.3.0 (Homebrew GCC 6.3.0_1) 

But I figured I had to uninstall and reinstall anaconda to rebuild numpy I guess and I sort of screwed things up more as the notebook can’t find the gcc file. So I can’t work with root_numpy in the root --notebook.


Ah macos, that’s a relevant piece of information I missed… You should not use gcc if you built or downloaded the default configuration of ROOT on macos. Instead you should teach numpy to build with clang.

If you install gcc from whatever package manager you also need to build your own ROOT with it, tell python to use that etc. It’s a mess…

Cheers, Axel

Perhaps I have a very basic question now, how do you build numpy with clang exactly? My idea is to build from source again but I am not sure how to teach it to build with clang.

So I guess I’ll just skip building with gcc.


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