Linking Homebrew-compiled openmpi (or mpich2) to Homebrew's gcc

Question

I'm new to Homebrew (I usually use Macports, but I'm trying out Homebrew on a 2nd computer), and I wish to install the openmpi (or mpich2) package. Steps are as follows (carried out on Mac OS X Yosemite with Xcode 6 installed):

brew install gcc
brew install openmpi

However, I suspect the linking may have been done incorrectly, due to the following reasons:

1. The symbolic link for /usr/local/bin/gcc is missing:

   $ which gcc
   /usr/bin/gcc
   $ gcc --version
   Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/c++/4.2.1
   Apple LLVM version 6.0 (clang-600.0.54) (based on LLVM 3.5svn)
   Target: x86_64-apple-darwin14.0.0
   Thread model: posix
   
   $ which gcc-4.9
   /usr/local/bin/gcc-4.9
   $ gcc-4.9 --version
   gcc-4.9 (Homebrew gcc 4.9.2) 4.9.2
   Copyright (C) 2014 Free Software Foundation, Inc.
   This is free software; see the source for copying conditions.  There is NO
   warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
   

2. mpicc may have been linked to the Apple gcc:

   $ which mpicc
   /usr/local/bin/mpicc
   $ mpicc --version
   Apple LLVM version 6.0 (clang-600.0.54) (based on LLVM 3.5svn)
   Target: x86_64-apple-darwin14.0.0
   Thread model: posix
   

My questions are as follows:

1. How do I get the /usr/local/bin/gcc symbolic link? Or is Homebrew deliberately avoiding this for certain reasons? e.g. if Homebrew is compiling all its packages using Apple gcc, which is assumed to be in the path, would changing the path to gcc-4.9 mean that Homebrew now compiles its packages with gcc-4.9 instead?

2. Is the Homebrew-installed Open MPI linked to the Apple gcc (and not the Homebrew gcc)? If yes, is it possible (or advisable) to change the linking?

3. Alternatively, how necessary is it to fix the linkages? Could I run into certain problems if I choose not to fix it? For example, I'm considering using ln -s to forcibly create the /usr/local/bin/gcc symbolic link. But is this a good idea (*)?

(*) I understand there are likely to be issues when linking object files created by different compilers. So with (1), (2) and (3), I'm hoping to find a solution that avoids combinations whereby I'm creating object files with different compilers (some with gcc-4.9 and some with the Apple gcc).

Underclay

Answer 1

You need to do the following:

1) Add environment variables for homebrew (you can also add these lines to your ~\.bashrc):

$ export HOMEBREW_CC=gcc-4.9
$ export HOMEBREW_CXX=g++-4.9

2) Rebuild and reinstall openmpi and its dependencies from source

$ brew reinstall openmpi --build-from-source

3) In the end you will get a message like:

==> Reinstalling open-mpi
==> Using Homebrew-provided fortran compiler.
This may be changed by setting the FC environment variable.
==> Downloading http://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.
Already downloaded: /Library/Caches/Homebrew/open-mpi-1.8.4.tar.bz2
==> ./configure --prefix=/usr/local/Cellar/open-mpi/1.8.4 --disable-silent-rules 
==> make all
==> make check
==> make install
Warning: open-mpi dependency gcc was built with a different C++ standard
library (libstdc++ from clang). This may cause problems at runtime.
🍺  /usr/local/Cellar/open-mpi/1.8.4: 785 files, 23M, built in 41.2 minutes

$ mpicc --showme 
gcc-4.9 -I/usr/local/Cellar/open-mpi/1.8.4/include -L/usr/local/opt/libevent/lib -L/usr/local/Cellar/open-mpi/1.8.4/lib -lmpi

On my MacBook I had some conflicts with XCode 6.2, which were solved following this instructions

If you want to install mpich

$ unlink openmpi
$ brew unlink gcc
$ brew install homebrew/versions/gcc5
$ brew install mpich --build-from-source   
$ mpicc -v
mpicc for MPICH version 3.2
Using built-in specs.
COLLECT_GCC=gcc-5
COLLECT_LTO_WRAPPER=/usr/local/Cellar/gcc5/5.4.0/libexec/gcc/x86_64-apple-darwin14.5.0/5.4.0/lto-wrapper
Target: x86_64-apple-darwin14.5.0
Configured with: ../configure --build=x86_64-apple-darwin14.5.0 --prefix=/usr/local/Cellar/gcc5/5.4.0 --libdir=/usr/local/Cellar/gcc5/5.4.0/lib/gcc/5 --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-5 --with-gmp=/usr/local/opt/gmp --with-mpfr=/usr/local/opt/mpfr --with-mpc=/usr/local/opt/libmpc --with-isl=/usr/local/opt/isl014 --with-system-zlib --enable-libstdcxx-time=yes --enable-stage1-checking --enable-checking=release --enable-lto --disable-werror --with-pkgversion='Homebrew gcc5 5.4.0' --with-bugurl=https://github.com/Homebrew/homebrew-versions/issues --enable-plugin --disable-nls --enable-multilib
Thread model: posix
gcc version 5.4.0 (Homebrew gcc5 5.4.0) 

Kirtley

is it the same for mpich? for some strange reason, my mac only works with MPICH but not openmpi – Musicology

I use open-mpi , perhaps you want to brew unlink mpich before using open-mpi – Kirtley

@Musicology updating answer to install mpich – Kirtley

Answer 2

It would probably be cleaner if you simply modify the configuration file for the Open MPI compiler wrapper and make it invoke gcc-4.9 instead of simply gcc. As I have no idea where exactly Homebrew puts Open MPI and therefore cannot give you the correct path directly, you should search for it:

$ find /usr/local -name mpicc-wrapper-data.txt

Once you have found mpicc-wrapper-data.txt, find the line that starts with compiler= and modify it to read:

compiler=gcc-4.9

You should also modify all other files that match the shell glob mpi*-wrapper-data.txt and modify the compiler=... line accordingly. Use g++-4.9 in mpic++, mpicxx, and mpiCC. Use gfortran-4.9 (if installed) in mpif77 and mpif90 (for Open MPI versions < 1.8) or for mpifort (for versions >= 1.8).

Mixing object code produced by different compilers on the same platform should be fine as long as all of them adhere to the same ABI, which is more or less the case with Clang and GCC. In the end, all programs are linked against the system libraries that come with OS X and those are compiled with Clang only.

Epileptoid

What would you do if you want to build open-mpi using gcc-4.9 only? – Kirtley

I would just build it from source. Some of the core Open MPI developers are actually Mac users and they do it on a regular basis. – Epileptoid