Comments (10)
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
from bohrium.
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.
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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.
from bohrium.
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.
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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
from bohrium.
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:
from bohrium.
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
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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.
from bohrium.
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
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Thank you, works now!
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Related Issues (20)
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