[gmx-users] cmake + Intel + CUDA + gcc 4.1.2 = bad time

[Malcolm Tobias]

Mark,

Upgrading to the latest/greatest cmake (2.8.11.1) fixed the problem in my case.

Thanks,
Malcolm

On Tuesday 02 July 2013 14:20:44 Mark Abraham wrote:
> Following http://www.gromacs.org/Documentation/Installation_Instructions#.c2.a7_4.6._Native_GPU_acceleration
> could help. The FindCUDA.cmake in CMake 2.8.1 might not work properly
> - we don't test that combination. Trying a newer CMake could help, but
> I would avoid 2.8.7, 2.8.9 and 2.8.10 because they have known issues
> (http://www.cmake.org/Wiki/CMake_Version_Compatibility_Matrix/StandardCMakeModulesA).
> There are some hard-coded gcc-isms in CUDA, too, but I would not think
> that is the issue here.
> 
> Mark
> 
> On Tue, Jul 2, 2013 at 8:59 PM, Malcolm Tobias <mtobias at wustl.edu> wrote:
> >
> > All,
> >
> > I'm attempting to build gromacs 4.6.2 with a bit of everything: CUDA support, MPI, Intel compilers, etc. using the new cmake system.  I've set CC and CXX to specify the Intel compilers:
> >
> > [root at login002 build]# echo $CC
> > icc
> >
> > [root at login002 build]# echo $CXX
> > icc
> >
> > and sourced the setup script for good measure:
> >
> > /export/intel/composer_xe_2013.1.117/bin/compilervars.sh intel64
> >
> > During cmake, everything appears to be happy:
> >
> > [root at login002 build]# /export/cmake-2.8.1/bin/cmake -DGMX_GPU=ON DCUDA_TOOLKIT_ROOT_DIR=/export/cuda-5.0 -DGMX_BUILD_OWN_FFTW=ON -DGMX_FFT_LIBRARY=mkl -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/export/gromacs-4.6.2 .. | tee cmake.out
> > ...
> > -- The C compiler identification is Intel
> > -- Check for working C compiler: /export/intel/composer_xe_2013.1.117/bin/intel64/icc
> > -- Check for working C compiler: /export/intel/composer_xe_2013.1.117/bin/intel64/icc -- works
> > ...
> > -- Looking for NVIDIA GPUs present in the system
> > -- Could not detect NVIDIA GPUs
> > -- Found CUDA: /usr/local/cuda
> > ...
> > -- MPI is not compatible with thread-MPI. Disabling thread-MPI.
> > -- Found MPI: /export/openmpi-1.4.3/lib/libmpi_cxx.so
> > ...
> > -- Setting the nvcc host compiler to: /export/intel/composer_xe_2013.1.117/bin/intel64/icc
> > -- Setting Intel Compiler compatibity mode to gcc 4.5 for nvcc host compilation
> > ...
> > -- Using external FFT library - Intel MKL
> >
> > But I quickly get a compile-time error:
> >
> > [root at login002 build]# make
> > -- Configuring done
> > -- Generating done
> > -- Build files have been written to: /export/src/gromacs-4.6.2/build
> > [  0%] Building NVCC (Device) object src/gmxlib/cuda_tools/./cuda_tools_generated_copyrite_gpu.cu.o
> > /usr/include/c++/4.1.2/bits/cpp_type_traits.h(358): error: expected an identifier
> >
> > /usr/include/c++/4.1.2/bits/cpp_type_traits.h(371): error: expected an identifier
> >
> > So something about the cmake process is reverting to the default GNU compilers (4.1.2) when it's trying to build some of the CUDA stuff.  I tried tricking it to use something more recent:
> >
> > alias /usr/bin/gcc44 gcc
> > alias g++=/usr/bin/g++44
> >
> > But I still see the path pointing to 4.1.2.  Any suggestions on things to try?
> >
> > Thanks,
> > Malcolm
> >
> > --
> > Malcolm Tobias
> > 314.362.1594
> >
> > --
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-- 
Malcolm Tobias
314.362.1594