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I am trying to build GraphChi on OS X Yosemite but get the following error:

fatal error: 'omp.h' file not found

From this question - How to include omp.h in OS X? - I learned that Yosemite uses Clang instead of gcc, which does not include omp.h.

$ which gcc
/usr/bin/gcc
$ gcc -v
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 6.0 (clang-600.0.56) (based on LLVM 3.5svn)
Target: x86_64-apple-darwin14.1.0
Thread model: posix

Next, I installed gcc via Homebrew

$ brew info gcc
gcc: stable 4.9.2 (bottled)
http://gcc.gnu.org
/usr/local/Cellar/gcc/4.9.2_1 (1092 files, 177M)
Built from source with: --without-multilib

and updated $PATH to include the path to the new gcc version

$ echo $PATH
/usr/local/Cellar/gcc/4.9.2_1:usr/local/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin

however, gcc -v and which gcc still point to the old version, and building GraphChi still doesn't work due to the missing omp.h file

Does anyone know what else I need to do?

Update

locate omp.h returned: 

/usr/local/Cellar/apple-gcc42/4.2.1-5666.3/lib/gcc/i686-apple-darwin11/4.2.1/include/omp.h
/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.1.0/4.9.2/include/omp.h
/usr/local/Cellar/gfortran/4.8.2/gfortran/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2/include/omp.h

my ~/.profile: 

export PATH=/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.1.0/4.9.2/include:/usr/local/Cellar/gcc/4.9.2_1/bin:usr/local/bin:/opt/local/bin:/opt/local/sbin:$PATH
Community
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Stephanie Embgen
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4 Answers4

3

I solved this with installing gcc with homebrew:

brew install gcc --without-multilib

and then building the source code with

CC=gcc-5 CXX=g++-5 cmake ..
CC=gcc-5 CXX=g++-5 make -j7
shrx
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Once you have installed gcc-4.9 with homebrew, it will automatically be in your path. To use OpenMP, you just need to make sure you are using the newly installed gcc-4.9, and it will be able to find omp.h.

In the case of GraphChi, you will have to go change line 3 of the Makefile to be gcc-4.9. From there, running make should just work. They describe this in their README, but at least the version they describe is out of date https://github.com/GraphChi/graphchi-cpp#problems-compiling-on-mac.

user2548418
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clang does not support OpenMP yet. Also gcc by default links to Apple's LLVM clang compiler (not the GCC installed from brew). Instead gcc-4.9 would link to GCC. I think if -fopenmp is specified omp.h is included automatically.

It is possible to manually build a version of clang with OpenMP support, see http://clang-omp.github.io

tmlen
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You shouldn't add the include path to PATH; instead, specify it as CFLAGS, including the -I option. You can export the CFLAGS variable, or set it on the fly.

Depending on how you compile things, you could do

CFLAGS=-I/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.1.0/4.9.2/include/omp.h gcc <whatever>

Of course, in this case you can specify it directly on the gcc command (as -I/usr/local/....), but the CFLAGS variable also works with configure (as configure often won't have an option to specify where it should look for specific include files); probably with make, or even for those installing a Python package: CFLAGS=-I... pip install <some-package>.

Other flags to consider are

  • CXXFLAGS: C++ specific pre-processor flags
  • LDFLAGS: linker specific flags (e.g. LDFLAGS=-L/some/path/... for linking with dynamic libraries).
  • CC: specify the C compiler to use. This is an easy way to avoid the built-in gcc alias for clang on OS X. Just use CC=/usr/local/bin/gcc-4 make or similar.
  • CXX: specify the C++ compiler to use.