[gmx-users] gromacs on multiple gpus

[Kutzner, Carsten]

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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