[gmx-users] Problem compiling Gromacs 4.6.3 with CUDA

[Mark Abraham]

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.
> > > > >
> > > > > --
> > > > > gmx-users mailing list    gmx-users at gromacs.org
> > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > > > * Please search the archive at
> > > > > http://www.gromacs.org/Support/Mailing_Lists/Search before
> posting!
> > > > > * Please don't post (un)subscribe requests to the list. Use the
> > > > > www interface or send it to gmx-users-request at gromacs.org.
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > --
> > > > gmx-users mailing list    gmx-users at gromacs.org
> > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > > > * Please don't post (un)subscribe requests to the list. Use the
> > > > www interface or send it to gmx-users-request at gromacs.org.
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > --
> > > gmx-users mailing list    gmx-users at gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > > * Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>