[gmx-users] Problem compiling Gromacs 4.6.3 with CUDA

[Jones de Andrade]

Did it a few days ago. Not so much of a problem here.

But I compiled everything, including fftw, with it. The only error I got
was that I should turn off the separable compilation, and that the user
must be in the group video.

My settings are (yes, I know it should go better with openmp, but openmp
goes horrobly in our cluster, I don't know why):

setenv CC  "/opt/intel/bin/icc"
setenv CXX "/opt/intel/bin/icpc"
setenv F77 "/opt/intel/bin/ifort"
setenv CMAKE_PREFIX_PATH /storage/home/johannes/lib/fftw/vanilla/
mkdir build
cd build
cmake .. -DGMX_GPU=ON -DCUDA_SEPARABLE_COMPILATION=OFF
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_OPENMP=OFF -DGMX_MPI=ON
-DGMX_THREAD_MPI=OFF -DMPIEXEC_MAX_NUMPROCS=1024 -DBUILD_SHARED_LIBS=OFF
-DGMX_PREFER_STATIC_LIBS=ON
-DCMAKE_INSTALL_PREFIX=/storage/home/johannes/bin/gromacs/vanilla/
make
make install
cd ..
rm -rf build


On Thu, Nov 7, 2013 at 3:02 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> icc and CUDA is pretty painful. I'd suggest getting latest gcc.
>
> Mark
>
>
> On Thu, Nov 7, 2013 at 2:42 PM, <ahmed.sajid at stfc.ac.uk> wrote:
>
> > Hi,
> >
> > I'm having trouble compiling v 4.6.3 with GPU support using CUDA 5.5.22.
> >
> > The configuration runs okay and I have made sure that I have set paths
> > correctly.
> >
> > I'm getting errors:
> >
> > $ make
> > [  0%] Building NVCC (Device) object
> >
> src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o
> > icc: command line warning #10006: ignoring unknown option '-dumpspecs'
> > /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In
> > function `_start':
> > (.text+0x20): undefined reference to `main'
> > CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206
> (message):
> >   Error generating
> >
> >
> /apps/src/gromacs/gromacs-4.6.3/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o
> >
> >
> > make[2]: ***
> >
> [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o]
> > Error 1
> > make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error
> 2
> > make: *** [all] Error 2
> >
> > Any help would be appreciated.
> >
> > Regards,
> > Ahmed.
> >
> > --
> > Scanned by iCritical.
> >
> > --
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