[gmx-users] [gmx-developers] GTX 680 non detected on OS X

[Uliano Guerrini]

HI all, I’m resuming this thread with some updates

I “believed" to have set them, however for (silly?) security reason since OSX 10.11 with the introduction of System Integrity Protection (SIP) Apple disallows the user to see the content od environment variables starting with DYLD* and to propagate their modification from one process to the child, so setting them in .bash_profile is useless

however I was able to run with GPU by

cmake ../gromacs-5.1.2 -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DGMX_GPU=on -DCMAKE_PREFIX_PATH="/opt/local;/Developer/NVIDIA/CUDA-7.5/lib"  -DCUDA_TOOLKIT_ROOT_DIR=/Developer/NVIDIA/CUDA-7.5 -DCMAKE_INSTALL_PREFIX=/opt/gromacs  -DCUDA_HOST_COMPILER=/usr/bin/clang++ -DCUDA_USE_STATIC_CUDA_RUNTIME=OFF

and then 

export DYLD_LIBRARY_PATH=/Developer/NVIDIA/CUDA-7.5/lib:$DYLD_LIBRARY_PATH 

in the shell just before issuing

gmx mdrun

however that shell become completely useless for most part of other commands as it has lost any previous $DYLD_LIBRARY_PATH (being not accessible it is copied an empty string)

What I find puzzling is that while the dynamic linking works (helped by the $DYLD_LIBRARY_PATH) there appears to be no trace of libcudart.dylib in the executable
uliano at MacPro:/opt/gromacs/bin$ otool -L gmx
gmx:
	@rpath/libgromacs.1.dylib (compatibility version 1.0.0, current version 1.2.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1226.10.1)
	/opt/local/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.8)
	/opt/local/lib/libfftw3f.3.dylib (compatibility version 8.0.0, current version 8.4.0)
	/System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate (compatibility version 1.0.0, current version 4.0.0)
	/opt/local/lib/libomp/libomp.dylib (compatibility version 5.0.0, current version 5.0.0)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.1.0)
uliano at MacPro:/opt/gromacs/bin$ 

I have tried different options in the cmake command line hoping to have it included in the executable (as all other shared library actually are!) but without success

Uliano

> Il giorno 01 giu 2016, alle ore 17:35, Uliano Guerrini <uliano.guerrini at unimi.it> ha scritto:
> 
> 
>> Il giorno 01 giu 2016, alle ore 11:18, Mark Abraham <mark.j.abraham at gmail.com> ha scritto:
>> 
>> Hi,
>> 
>> Googling around, I see that some places recommend things such as
>> 
>> export PATH=/Developer/NVIDIA/CUDA-6.0/bin:$PATH
>> export DYLD_LIBRARY_PATH=/Developer/NVIDIA/CUDA-6.0/lib:$DYLD_LIBRARY_PATH
>> 
>> 
>> Does that seem adaptable to your setup as a possible fix for getting
>> dynamic linking to work?
>> 
>> Mark
> 
> I had already set them
> 
> Uliano
> 
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