[gmx-users] Problem compiling Gromacs 4.6.3 with CUDA

[Jones de Andrade]

Ok, you convinced me. I'll really give it a try. I'm following this throw
the suposition that openMP implementation on intel compilers is not as good
as GNU compilers. I already tested intel openMP in our cluster, and it just
sucked in comparison to the pure MPI compilation.

Let's hope I can make it work together with the IMPI. I don't want to
install openmpi as just a user also (did it a long time ago as root, not in
limited space).

Thanks again!


On Fri, Nov 8, 2013 at 9:21 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> On Fri, Nov 8, 2013 at 12:02 AM, Jones de Andrade <johannesrs at gmail.com
> >wrote:
>
> > Really?
>
>
> Of course. With openmp gets to use all your cores for PME+bondeds+stuff
> while the GPU does PP. Any version without openmp gets to use one core per
> domain, which is bad.
>
>
> > An what about gcc+mpi? should I expect any improvement?
> >
>
> Run how and compared with what? Using an external MPI library within a
> single node is a complete waste of time compared with the alternatives
> (thread-MPI, OpenMP, or both).
>
> Mark
>
>
> >
> >
> > On Thu, Nov 7, 2013 at 6:51 PM, Mark Abraham <mark.j.abraham at gmail.com
> > >wrote:
> >
> > > You will do much better with gcc+openmp than icc-openmp!
> > >
> > > Mark
> > >
> > >
> > > On Thu, Nov 7, 2013 at 9:17 PM, Jones de Andrade <johannesrs at gmail.com
> > > >wrote:
> > >
> > > > 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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