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

[Stephen N. Floor]

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