cpu_set_t not found when building on OSX

[bh107]

cpu_set_t not found when building on OSX

[kenkendk]

I don't think the Cluster VEM compiles on OSX. At least I know that I have not tested it, and I do most of the OSX fixes.

Normally the build will just skip the Cluster VEM because MPI is not found.

Below is my output from cmake, does yours differ?

-- The following RECOMMENDED packages have been found:

 * OpenCL , Open Computing Language , <www.khronos.org/opencl/>
   Enables the GPU-VE.
 * NumPy , Numerical Python , <www.numpy.org>
   Enables the Python/NumPy bridge (together with Python and SWIG).
 * SWIG , Simplified Wrapper and Interface Generator , <www.swig.org>
   Enables the Python/NumPy bridge (together with Python and NumPy).
 * Cython , C-Extensions for Python , <cython.org>
   Enables the Python/NumPy bridge (together with Python and SWIG).
 * Mono , An open source implementation the CLR , <www.mono-project.com>
   Enables the NumCIL package

-- The following REQUIRED packages have been found:

 * Boost , Boost C++ source libraries , <www.boost.org>
   Boost is required to build Bohrium
 * Cheetah , Cheetah is a template module for Python , <www.cheetahtemplate.org>
   Cheetah is required to build Bohrium
 * GLUT
 * OpenGL , Open Graphics Library , <www.opengl.org>
   Required by OpenCL/GPU-VE.
 * PythonInterp , Python Programming Language , <www.python.org>
   Python is required to build Bohrium

-- The following OPTIONAL packages have not been found:

 * OpenMP

-- The following RECOMMENDED packages have not been found:

 * MPI , Message Passing Interface , <www.mpi-forum.org>
   Enables the Cluster-VEM.
 * FFTW , Fastest Fourier Transform in the West , <www.fftw.org>
   Enables the FFTW extended method

[fjarri]

That's what I have:

  -- The following RECOMMENDED packages have been found:

   * MPI , Message Passing Interface , <www.mpi-forum.org>
     Enables the Cluster-VEM.
   * OpenCL , Open Computing Language , <www.khronos.org/opencl/>
     Enables the GPU-VE.
   * OpenGL , Open Graphics Library , <www.opengl.org>
     Required by OpenCL/GPU-VE.
   * NumPy , Numerical Python , <www.numpy.org>
     Enables the Python/NumPy bridge (together with Python and SWIG).
   * SWIG , Simplified Wrapper and Interface Generator , <www.swig.org>
     Enables the Python/NumPy bridge (together with Python and NumPy).
   * Cython , C-Extensions for Python , <cython.org>
     Enables the Python/NumPy bridge (together with Python and SWIG).

  -- The following REQUIRED packages have been found:

   * Boost , Boost C++ source libraries , <www.boost.org>
     Boost is required to build Bohrium
   * Cheetah , Cheetah is a template module for Python , <www.cheetahtemplate.org>
     Cheetah is required to build Bohrium
   * PythonInterp , Python Programming Language , <www.python.org>
     Python is required to build Bohrium

  -- The following OPTIONAL packages have not been found:

   * OpenMP

  -- The following RECOMMENDED packages have not been found:

   * FFTW , Fastest Fourier Transform in the West , <www.fftw.org>
     Enables the FFTW extended method
     FFTW was found, but not enabled. 
     Manually enable FFTW with FFTW_INCLUDES and FFTW_LIBRARIES
     if you have a clang multi-arch FFTW binary.
   * Mono , An open source implementation the CLR , <www.mono-project.com>
     Enables the NumCIL package

So I do have MPI, but no OpenMP. I installed OpenMPI specifically for Bohrium via Homebrew, but I can remove it if it prevents the compilation — I don't use it otherwise.

[fjarri]

I installed OpenMPI specifically for Bohrium via Homebrew, but I can remove it if it prevents the compilation

Actually, scratch that. I uninstalled openmpi from homebrew, and cmake is still able to find it.

[kenkendk]

In the folder where you checked out Bohrium, you should be able to do:

mkdir build
cd build
cmake -DVEM_CLUSTER=false ..
make install

Alternatively, you can use ccmake . to configure the build, and disable VEM_CLUSTER.

[fjarri]

Thanks, now the build passes. There's a (seemingly) related problem though: import bohrium passes, but when I try to use it, Python crashes with:

Error in [node:impl]: dlopen(/Users/bogdan/.local/lib/libbh_vem_node.dylib, 2): Library not loaded: libbh.dylib
  Referenced from: /Users/bogdan/.local/lib/libbh_vem_node.dylib
  Reason: image not found

[kenkendk]

Try to clean out your install, i.e.:

rm -rf ~/.local/lib/libbh* ~/.local/var/bohrium ~/.bohrium

Then make install again.

If the file /Users/bogdan/.local/lib/libbh_vem_node.dylib exists, then it is most likely some issue with 64-vs-32 bit. You can see what version of Python you are running, with this snippet:

https://stackoverflow.com/questions/1405913/how-do-i-determine-if-my-python-shell-is-executing-in-32bit-or-64bit-mode-on-os

[fjarri]

I'm using Py2.7.9, using the tests from your link it's 64 bit. After removing everything and doing the clean install, the problem persists. The libraries in question seem to be multi-arch:

> file /Users/bogdan/.local/lib/libbh_vem_node.dylib
/Users/bogdan/.local/lib/libbh_vem_node.dylib: Mach-O universal binary with 2 architectures
/Users/bogdan/.local/lib/libbh_vem_node.dylib (for architecture i386):  Mach-O dynamically linked shared library i386
/Users/bogdan/.local/lib/libbh_vem_node.dylib (for architecture x86_64):    Mach-O 64-bit dynamically linked shared library x86_64
> file /Users/bogdan/.local/lib/libbh.dylib
/Users/bogdan/.local/lib/libbh.dylib: Mach-O universal binary with 2 architectures
/Users/bogdan/.local/lib/libbh.dylib (for architecture i386):   Mach-O dynamically linked shared library i386
/Users/bogdan/.local/lib/libbh.dylib (for architecture x86_64): Mach-O 64-bit dynamically linked shared library x86_64

[kenkendk]

VEM stands for "Vector Engine Manager".
Currently there are two implementations of a VEM: Node and Cluster.
The Cluster VEM distributes (using MPI) work to multiple Node VEM's, which hands the work to the Vector Engine (VE).

So you get Python -> Bridge -> VEM -> VE.
Using the config.ini file you can change which VEM and VE you use, but you cannot skip the Node VEM (which, does not do anything but pass on the work).

I am trying a clean build to see if I can reproduce the issue.

[kenkendk]

I can reproduce. The problem is that when you are building from source, the install goes into ~/.local.
On Linux the ~/.local/lib folder is used automatically, but it is not on OSX.

To fix it, you need to set the environment variable DYLD_LIBRARY_PATH.

To set it, run:
export DYLD_LIBRARY_PATH=~/.local/lib

Or add it each time you run a command:
DYLD_LIBRARY_PATH=~/.local/lib python ~/.local/share/bohrium/test/python/numpytest.py

[fjarri]

Thank you, works now!