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

[Szilárd Páll]

Uliano,

Thanks for the update! Such info is always useful to share.

Weird indeed and as I have not much OS X experience I can't comment on
most of this stuff -- except one bash-ism that may help rendering your
shell useless after setting the dynamic library path.

[env] MY_ENV_VAR=value gmx mdrun ...

will set the MY_ENV_VAR variable only for the process you prefix it with!

Cheers,
--
Szilárd


On Sat, Jun 11, 2016 at 8:09 AM, Uliano Guerrini
<uliano.guerrini at unimi.it> wrote:
> 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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>
>
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