[gmx-users] gromacs on multiple gpus

[Mark Abraham]

Hi,

And also see
http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-performance.html#examples-for-mdrun-on-more-than-one-node

Mark

On Tue, May 10, 2016 at 10:14 AM Kutzner, Carsten <ckutzne at gwdg.de> wrote:

> Hi,
>
> you can use the -gpu_id command line parameter to mdrun to map available
> GPUs to MPI ranks. In the simplest case with two MPI ranks:
>
> mdrun -gpu_id 01
>
> You will probably get much more performance by using more MPI ranks
> (check out 10.1002/jcc.24030). E.g. for 6 MPI ranks use -gpu_id 000111
>
> Carsten
>
>
> > On 10 May 2016, at 05:51, Neha Gandhi <n.gandhiau at gmail.com> wrote:
> >
> > Dear List,
> >
> > I have compiled GROMACS 5.0.7 using following options
> >
> > CMAKE_PREFIX_PATH=/home/gandhin/fftw cmake .. -DGMX_BUILD_OWN_FFTW=OFF
> > -DGMX_MPI=on -DGMX_GPU=on -DGMX_SIMD=AVX2_256
> > -DCMAKE_C_COMPILER=${MPICCDIR}mpicc
> -DCMAKE_CXX_COMPILER=${MPICCDIR}mpicxx
> > -DGMX_BUILD_MDRUN_ONLY=on
> -DCMAKE_INSTALL_PREFIX=/home/gandhin/gromacs-5.0.7
> >
> > The machine has two K40 gpus and 12 cpus per node. When I submit jobs
> using
> > mpirun gmx_mpi mdrun -v.. the program mdrun detects two gpus with ids #0
> > and #1 but it still runs the job with only one gpu i.e. gpu id #0. What
> is
> > the correct way of submitting job (using PBS) so that both gpus and 12
> > cores on the same node are utilised by mdrun for the simulation?
> >
> > My apologies to post this question to GROMACS mailing list, this post is
> > more related to the system admin who aren't able to help.
> >
> > Thank you for kind attention
> >
> > Regards,
> > Neha
> >
> >
> >
> >
> >
> > --
> > Regards,
> > Dr. Neha S. Gandhi,
> > Vice Chancellor's Research Fellow,
> > Queensland University of Technology,
> > 2 George Street, Brisbane, QLD 4000
> > Australia
> > LinkedIn
> > Research Gate
> > --
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