I want to install xgboost in Python 3.5. This requires gcc to support -fopenmp option. Default gcc does not support it. So I am using
brew install gcc --without-multilib
But I get Warning: gcc: this formula has no '--without-multilib' option so it will be ignored! Any ideas?
The option no longer exists, since 8/2017. Many older 3rd-party xgboost instructions are outdated. Just do brew install gcc without options and be amazed that everything still works.
Related
I installed the gcc compiler via xcode-select --install but the version installed is 4.2.1 then it isn't possible to use the OpenMp flag -fopenmp for compile the source code.
I tried to install the compile via Homebrew and link this to the gcc exported but it doesn't work. I tried to install gcc building the latest GNU release but after building the operative system asked me if I would install gcc using xcode-select --install.
Moreover, I follow the answer to this question but I have this error:
Error: No available formula with the name "clang-omp"
Is there any solution or suggestion I can follow to execute the OpenMP code on my Mac and on any unix-like device without having to install particular dependencies because in this answer there is a solution but the user can install dependencies?
OpenMP code can be compiled with AppleClang on mojave. Xcode includes an openmp-aware preprocessor which must be invoked.
You must have an omp installed; libomp is the most common. I have also used libiomp5.
Adjust the flags in cmake to point to your openmp solution.:
cmake .. -DCMAKE_C_COMPILER="clang" -DCMAKE_CXX_COMPILER="clang++" -DOpenMP_C_FLAGS=-fopenmp=lomp -DOpenMP_CXX_FLAGS=-fopenmp=lomp -DOpenMP_C_LIB_NAMES="libomp" -DOpenMP_CXX_LIB_NAMES="libomp" -DOpenMP_libiomp5_LIBRARY="/opt/local/lib/libomp.dylib" -DOpenMP_CXX_FLAGS="-Xpreprocessor -fopenmp /opt/local/lib/libomp.dylib -I/opt/local/include" -DOpenMP_CXX_LIB_NAMES="libomp" -DOpenMP_omp_LIBRARY=/opt/local/lib/libomp.dylib -DOpenMP_C_FLAGS="-Xpreprocessor -fopenmp /opt/local/lib/libomp.dylib -I/opt/local/include"
Similar flags for libiomp5: See this line.
Thanks to Richard answer, I was able to compile a project that uses OpenMP on Mojave. I'm adding this answer because some of his flags are currently wrong or useless.
-DOpenMP_C_LIB_NAMES "libomp"
-DOpenMP_CXX_LIB_NAMES "libomp"
-DOpenMP_C_FLAGS "-Xpreprocessor -fopenmp -I/usr/local/include"
-DOpenMP_CXX_FLAGS "-Xpreprocessor -fopenmp -I/usr/local/include"
-DOpenMP_omp_LIBRARY "/usr/local/lib/libomp.dylib"
-DOpenMP_libomp_LIBRARY "/usr/local/lib/libomp.dylib"
libomp was installed with brew install libomp.
My ultimate goal is to get python package graph_tool working on my system and also on ipynb if possible. I have already brew install graph-tool, as indicated here, but that's still insufficient.
So I follow conda instructions here, and I make decent progress, until I encounter a compiler issue with the configuration.
$ conda create -n py36env python=3.6.3 anaconda
(py36env) $ conda install -c conda-forge cgal
... and so forth with the other required libraries
(py36env) Tams-MacBook-Pro:graph-tool-2.25 tamtam$ ./configure --prefix=/Users/tamtam/anaconda3/envs/py36env/ --with-python-module-path=/Users/tamtam/anaconda3/envs/py36env/lib/python3.6/site-packages
.
.
.
checking whether g++ supports C++14 features by default... no
checking whether g++ supports C++14 features with -std=gnu++14... no
checking whether g++ supports C++14 features with -std=gnu++1y... no
configure: error: *** A compiler with support for C++14 language features is required.
I'm not very familiar with compiler things, but I check my system as follows:
(py36env) Tams-MacBook-Pro:graph-tool-2.25 tamtam$ conda list | grep gcc
gcc 4.8.5 8
And outside of the conda env:
$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/Users/tamtam/anaconda3/envs/py36env/bin/../libexec/gcc/x86_64-apple-darwin11.4.2/4.8.5/lto-wrapper
Target: x86_64-apple-darwin11.4.2
Configured with: ./configure --prefix=/Users/ray/mc-x64-3.5/conda-bld/gcc-4.8_1477649012852/
Thread model: posix
gcc version 4.8.5 (GCC)
And with Homebrew
$ brew list --versions | grep gcc
gcc 7.1.0 7.2.0
$ /usr/local/bin/gcc-7 --version
gcc-7 (Homebrew GCC 7.2.0) 7.2.0
$ echo $PATH
/Users/tamtam/anaconda3/bin:/Users/tamtam/anaconda/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin
So my questions are: EDITS INCLUDED
1) What's the difference between the conda gcc 4.8.5 and Homebrew gcc 7.2 on my system? I'm confused because they're each up-to-date packages.
EDIT: Nowhere online that I perused explicitly states this, but I am understanding (aka educated guess bc it's 3am and I need sleep) conda gcc 4.8.5 to just be equivalent to brew gcc 4.8.5, and that Anaconda is just way behind on developing an 'official' gcc supporting C++14. In the meantime I conda install -c salford_systems gcc-5 and ./configure seems to find itself a C++14 compiler. YAY (but this also led me to a new problem T.B.A.)
NOTE: I had also tried running the ./configure file with both conda gcc 4.8.5 and brew gcc 7.2.0 (switching of default gcc compiler guided here), but still same error of ./configure not finding C++14 compile (so ignore this)
2) I also have Xcode 8.3.3 that also comes with clang, which is what gcc is symlinked to... ?? No idea about the setup/relation
3) How can I adjust my system (for example, paths) so that the configuration process will detect a C++14 compiler? EDIT: resolved per 1)
(This solution is also included within the edits at the bottom of my question.)
Nowhere online that I perused explicitly states this, but I am understanding (aka educated guess bc it's 3am and I need sleep) conda gcc 4.8.5 to just be equivalent to brew gcc 4.8.5, and that Anaconda is just way behind on developing an 'official' gcc supporting C++14. In the meantime I conda install -c salford_systems gcc-5 and ./configure seems to find itself a C++14 compiler. YAY (but this also led me to a new problem)
NOTE: I had also tried running the ./configure file with both conda gcc 4.8.5 and brew gcc 7.2.0 (switching of default gcc compiler guided here), but still same error of ./configure not finding C++14 compile arises (so ignore this)
As a rule of thumb, if a product provides its own build tools (compiler, C headers, static libraries, include/library paths etc) instead of using the system's ones, you should use those when building things to use within its environment.
That's because, depending on include files, compiler, compiler version, compiler flags, predefined macros etc the same sources and libraries built with different toolchains can be binary incompatible. This goes double for C++ where there are no ABI standards at all. (In C, there are de facto ones for most platforms where there are competing compilers due to the need to do system calls.)
Now, what you have on your system:
The system's stock gcc (if any) is at /usr/bin (so includes are at /usr/include, static libraries at /usr/lib etc)
Homebrew's gcc 7.2 at /usr/local/bin (includes are probably at /usr/local/include)
Anaconda also has a gcc package that, if installed, would reside somewhere like /Users/<login>/anaconda3/envs/<env name>/bin
If an environment provides an own toolchain, it provides some way to make build scripts select that toolchain when building things. A common way is to set relevant environment variables (PATH, INCLUDE, LIB) - either directly or through some tool that the environment provides. Homebrew executables reside in /usr/local/bin which is always present in UNIX PATH as per the FHS; Anaconda adds itself to PATH whenever its environment is activated.
So, as you yourself guessed, since Anaconda provides its own gcc packages (thus enforces the compatibility of their output with its binary packages via package metadata - if there are known incompatibilities, the installation will fail due to requirement conflicts), you need to install one that meets graph-tool requirements -- which is gcc 5, available via gcc-5 package from salford_systems channel. Then specify --prefix as you already have.
You may need to install other dependencies, too, if you didn't already or you need optional features that they're required for.
I was trying to use the omh.h header file and I realized it was missing. I tried reinstalling gcc on my mac using brew. This is the message I got at the end of the installation.
..
GCC has been built with multilib support. Notably, OpenMP may not work:
https://gcc.gnu.org/bugzilla/show_bug.cgi?id=60670
If you need OpenMP support you may want to
brew reinstall gcc --without-multilib
==> Summary
🍺 /usr/local/Cellar/gcc/4.9.2_1: 1156 files, 203M
It suggests that if I need OpenMP support I need to install brew reinstall gcc --without-multilib. I am not able to understand the meaning of --without-multilib. How is it different from simply installing gcc?
And apparently brew reinstall gcc --without-multilib takes forever to run and brew uninstall gcc && brew install gcc was lightning fast.
Multilib means support for multiple architectures, so you can compile binaries for them.
Given the bug you show, you should be safe as long you build binaries for AMD64 architecture (64-bit) and IA32, as that is what your machine is.
Otherwise, better to choose without multilib.
At the first,I used the default gcc on my mac.but it does't support openmp.
using "gcc -v",I get gcc 4.2.1
So, I used brew to install gcc. When it is done, using the "gcc -v",it has no changes.
the brew give tips to me "openmp may not be supported,using "brew reinstall gcc --without-muli"??
I don't remember the "muli???" accurately.I try that,but It doesn't help.
So, this is my question: What can I do to make my gcc to support openmp in my macbook?
Brew will install gcc under a slightly different name to not clobber the existing gcc. The easiest way to check for other gcc's is to type gcc- and then hit the TAB key to see what completions there are. I believe brew's current gcc is 4.9.1, so after installing gcc with brew you should be able to access it with gcc-4.9.
According to this post (https://github.com/mxcl/homebrew/pull/2953), the flag "--with-mpi" should enable boost_mpi build support for the related homebrew formula, so I am trying to install boost via homebrew like this:
brew install boost --with-mpi
However, the actual boost mpi library is not being build and can not be found.
There is currently some work being done around this, according to: https://github.com/mxcl/homebrew/pull/15689
In summary, I can currently build boost, but it seems the "--with-mpi" flag is being ignored. Could someone please check, if I should be able to build boost (with mpi support) on Mac OS X Mountain Lion (10.8)?
The (verbose) output generates these lines:
MPI auto-detection failed: unknown wrapper compiler mpic++
Please report this error to the Boost mailing list: http://www.boost.org
You will need to manually configure MPI support.
warning: skipping optional Message Passing Interface (MPI) library.
note: to enable MPI support, add "using mpi ;" to user-config.jam.
note: to suppress this message, pass "--without-mpi" to bjam.
note: otherwise, you can safely ignore this message.
Not sure how exactly I can fix this and get the mpi stuff to be build - any ideas?
Just in case this helps anyone else along the line, here's how I fixed this. The main error is MPI auto-detection failed: unknown wrapper compiler mpic++, any typing mpic++ at the command line verified that it was not working properly for me. I used brew to install open-mpi, but the same error was showing in the verbose output for installing boost. A run of brew doctor showed that openmpi was not linked properly, so I fixed those errors and reran brew -v install boost --with-mpi --without-single and it finally built and installed all of the libraries without a problem
To anyone that comes across this, the package migrated to boost-python and boost-mpi separate from boost. Use brew install boost-mpi
Just get it worked on OSX 10.11.5. I've tried brew, but with no luck.
Suppose you already have gcc installed. Here are what I've done:
1. Find and disable (but do not remove) clang
clang alway cause headaches. There would be a lot of warnings when building Boost.
which clang, which should give you /usr/bin/clang
Rename it: sudo mv clang clang_mac_remove, also for clang++: sudo mv clang++ clang++_mac_remove. You can change the names back if you need them in future.
2. Install OpenMPI
If you already installed using brew, uninstall first. Becasue it would have used clang as the compiler wrapper by default. You need to change the wrapper to gcc.
Download the package.
Specify the wrapper compiler to gcc and g++:
./configure CC=gcc CXX=g++ F77=ifort FC=ifort --prefix=/usr/local
Below may take a long time.
make all
sudo make install
Reference: https://wiki.helsinki.fi/display/HUGG/Open+MPI+install+on+Mac+OS+X
3. Install Boost MPI
Download the package.
Run ./bootstrap.sh (can open it first and specify the toolset to gcc, otherwise, the default option is darwin for mac).
Add using mpi ; in project-config.jam file. Then ./b2 —with-mpi will only build the mpi library.
Then, all built libraries can be found in the folder ~/Downloads/boost_1_61_0/stage/lib.
Copy or move them to /usr/local/lib or any other commonly used library path.
Reference: http://www.boost.org/doc/libs/1_61_0/doc/html/mpi/getting_started.html
4. Compile with Boost MPI
LIBRARY DIR = -L/usr/local/lib
INCLUDE = -I/usr/local/include/
LINKER = -lboost_mpi -lboost_serialization
e.g.
mpic++ -std=c++11 -I/usr/local/include/ -c boost_test.cpp -L/usr/local/lib -lboost_mpi -lboost_serialization
Good luck!