[gmx-users] compilation issues with GCC/clang/CUDA on OSX

[Anders Gabrielsson]

Hi!
Note that the warnings are only suggesting that your build may give suboptimal performance. (as in having no compatible GPU or non-openmp enabled compiler).
In my experience, you can actually ignore the first one about not finding GPUs. That never worked for me either (on mac os x).

Did you try proceed to 'make' anything?
The openmp-related warning suggest to me that either cmake is confused about what compiler to use (clear out the build dir and try again?) or your gcc installation is somehow broken.

Happy compiling!
Anders


On 24 Apr 2014, at 21:41, Stephen N. Floor <floor at berkeley.edu> wrote:

> Hello -
> 
> I am trying to compile gromacs 4.6.5 with CUDA support for a new
> graphics card on OSX 10.8.5 with CUDA 6.0.37 using gcc 4.8.2 from fink
> (gcc-4 and g++-4) for OpenMP support and clang for CUDA as recommended
> previously.
> 
> I am starting cmake like this:
> 
> export CC=/sw/bin/gcc-4
> export CXX=/sw/bin/g++-4
> 
> cmake -DGMX_GPU=ON -DCMAKE_C_COMPILER=${CC}
> -DCMAKE_CXX_COMPILER=${CXX} -DCUDA_HOST_COMPILER=/usr/bin/clang
> -DCUDA_PROPAGATE_HOST_FLAGS=OFF ..
> 
> I am having two issues:
> 
> 1) cmake does not detect any video cards:
> 
> -- Looking for NVIDIA GPUs present in the system
> -- Could not detect NVIDIA GPUs
> -- Found CUDA: /usr/local/cuda (found suitable version "6.0", minimum
> required is "3.2")
> 
> While I can likely continue with compilation, this seems to suggest an
> underlying issue that may rear its head later.
> 
> 2) OpenMP is not detected
> 
> { snipped many openmp flag test results that are all failures }
> 
> CMake Warning at CMakeLists.txt:273 (message):
>  The compiler you are using does not support OpenMP parallelism.  This might
>  hurt your performance a lot, in particular with GPUs.  Try using a more
>  recent version, or a different compiler.  For now, we are proceeding by
>  turning off OpenMP.
> 
> compiler info:
> 
> [snf at waipio gromacs/gromacs-4.6.5/build-cmake-gpu]$ gcc-4 --version -v
> Using built-in specs.
> COLLECT_GCC=gcc-4
> COLLECT_LTO_WRAPPER=/sw/lib/gcc4.8/libexec/gcc/x86_64-apple-darwin12.5.0/4.8.2/lto-wrapper
> gcc-4 (GCC) 4.8.2
> Copyright (C) 2013 Free Software Foundation, Inc.
> This is free software; see the source for copying conditions.  There is NO
> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
> 
> 
> Target: x86_64-apple-darwin12.5.0
> Configured with: ../gcc-4.8.2/configure --prefix=/sw
> --prefix=/sw/lib/gcc4.8 --mandir=/sw/share/man
> --infodir=/sw/lib/gcc4.8/info
> --enable-languages=c,c++,fortran,lto,objc,obj-c++,java --with-gmp=/sw
> --with-libiconv-prefix=/sw --with-isl=/sw --with-cloog=/sw
> --with-mpc=/sw --with-system-zlib --x-includes=/usr/X11R6/include
> --x-libraries=/usr/X11R6/lib --program-suffix=-fsf-4.8
> Thread model: posix
> gcc version 4.8.2 (GCC)
> COLLECT_GCC_OPTIONS='-mmacosx-version-min=10.8.5' '--version' '-v'
> '-mtune=core2'
> /sw/lib/gcc4.8/libexec/gcc/x86_64-apple-darwin12.5.0/4.8.2/cc1 -quiet
> -v -D__DYNAMIC__ help-dummy -fPIC -quiet -dumpbase help-dummy
> -mmacosx-version-min=10.8.5 -mtune=core2 -auxbase help-dummy -version
> --version -o /var/folders/bj/fl_w4q152yx6cg787vx5c12h0000gq/T//ccQjwwGf.s
> GNU C (GCC) version 4.8.2 (x86_64-apple-darwin12.5.0)
>        compiled by GNU C version 4.8.2, GMP version 5.1.3, MPFR
> version 3.1.2, MPC version 1.0.2
> GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
> COLLECT_GCC_OPTIONS='-mmacosx-version-min=10.8.5' '--version' '-v'
> '-mtune=core2'
> as -arch x86_64 -force_cpusubtype_ALL --version -o
> 
> Thanks for any insight!
> -Stephen
> 
> --
> Stephen N. Floor
> HHWF Postdoctoral Fellow, Doudna Group
> http://doudna.berkeley.edu
> -- 
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