[gmx-users] Install Gromacs Cuda MacBook pro with eGPU OS X 10.13.4

[Szilárd Páll]

Hi,

The issue is a limitation imposed by the CUDA toolkit; you could try using
the native clang support by passing GMX_CLANG_CUDA=ON to cmake.

Also note that:
- I might not remember correctly the reviews, but isn't NVIDIA officially
unsupported in eGPUs (might still work, but beware)?
- you only get at best 4 lane PCIe on TB3 so simulation performance will be
affected by that

Cheers,

--
Szilárd

On Wed, May 30, 2018 at 10:18 PM, Владимир Богданов <
bogdanov-vladimir at yandex.ru> wrote:

>
>
> Hey! Maybe somewhere could help me. I have some problems when I try to
> compile gromacs on OS X with eGPU:
>
>
> Copyright (c) 2005-2017 NVIDIA Corporation
>
> Built on Tue_Dec_19_21:36:29_CST_2017
>
> Cuda compilation tools, release 9.1, V9.1.128
>
>
>
> when I use clang/clang++ compilers:
>
>
>
> clang -v
>
> clang version 6.0.0 (tags/RELEASE_600/final)
>
> Target: x86_64-apple-darwin17.5.0
>
> Thread model: posix
>
> InstalledDir: /usr/local/Cellar/llvm/6.0.0/bin
>
> Found CUDA installation: /usr/local/cuda, version unknown
> I can found OpenMP:
>
> -- Found OpenMP_C: -fopenmp=libomp (found version "3.1")
>
> -- Found OpenMP_CXX: -fopenmp=libomp (found version "3.1")
>
> -- Found OpenMP: TRUE (found version "3.1")
> but:
>
> -- Check for working NVCC/C compiler combination
>
> -- Check for working NVCC/C compiler combination - broken
>
> CMake Error at cmake/gmxManageGPU.cmake:291 (message):
>
>   CUDA compiler does not seem to be functional.
>
>
>
>
>
> -- Configuring incomplete, errors occurred!
>
>
> when I use   llvm-gcc/llvm-g++ or CC/C++ compilers:
>
>
> c++ -v
>
> Apple LLVM version 9.0.0 (clang-900.0.39.2)
>
> Target: x86_64-apple-darwin17.5.0
>
> Thread model: posix
>
> InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin
>
> Found CUDA installation: /usr/local/cuda, version unknown
>
>
>
> llvm-gcc -v
>
> Apple LLVM version 9.0.0 (clang-900.0.39.2)
>
> Target: x86_64-apple-darwin17.5.0
>
> Thread model: posix
>
> InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin
>
> Found CUDA installation: /usr/local/cuda, version unknown
>
> I can not find OpenMP:
>
>
> -- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES)
> (found version "1.0")
>
> -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS
> OpenMP_CXX_LIB_NAMES) (found version "1.0")
>
>
>
> and when I do make:
>
>
>
> [  3%] Building C object src/gromacs/CMakeFiles/tng_io_
> obj.dir/__/external/tng_io/src/lib/md5.c.o
>
> [  3%] Built target tng_io_obj
>
> [  3%] Generating baseversion-gen.c
>
> [  3%] Building NVCC (Device) object src/gromacs/CMakeFiles/
> libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o
>
> /Users/<user>/Downloads/gromacs-2018.1/src/gromacs/mdlib/nbnxn_cuda/
> nbnxn_cuda_kernel_pruneonly.cu(41): error: explicit instantiation
> definition directive for __global__ functions with clang host compiler is
> not yet supported
>
>
>
> /Users/<user>/Downloads/gromacs-2018.1/src/gromacs/mdlib/nbnxn_cuda/
> nbnxn_cuda_kernel_pruneonly.cu(42): error: explicit instantiation
> definition directive for __global__ functions with clang host compiler is
> not yet supported
>
>
>
> 2 errors detected in the compilation of "/var/folders/ls/_
> pffbhc9613d67c9jh2jhbyr0000gn/T//tmpxft_0001457e_00000000-13
> _nbnxn_cuda.compute_70.cpp1.ii".
>
> CMake Error at libgromacs_generated_nbnxn_cuda.cu.o.Release.cmake:282
> (message):
>
>   Error generating file
>
>   /Users/<user>/Downloads/gromacs-2018.1/build/src/
> gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/./
> libgromacs_generated_nbnxn_cuda.cu.o
>
>
>
>
>
> make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_
> cuda/libgromacs_generated_nbnxn_cuda.cu.o] Error 1
>
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
>
> make: *** [all] Error 2
>
>
> --
> Thanks,
> Vlad
>
> --
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