[gmx-users] GPU Command
zaved at tezu.ernet.in
zaved at tezu.ernet.in
Wed Apr 18 09:47:23 CEST 2018
On Thu, Apr 12, 2018 at 4:47 PM <zaved at tezu.ernet.in> wrote:
>> Dear Gromacs Users
>> We have a GPU Server (Intel(R) Xeon(R) CPU E5-2609 v4 @ 1.70GHz, 16
>> with 2 NVIDIA Tesla P100 (12GB) cards.
>> What should be my final mdrun command so that it should utilize both the
>> cards for the run? (As of now it detects both the cards, but auto
>> only 1)
>> As of now I am using the following command:
>> gmx_mpi mdrun -v -deffnm run -gpu_id 0 1
> You mentioned auto selection of GPU usage, but you are selecting the GPU
> usage here, and you are requiring it to use only GPU 0. If you would look
> at the examples in the user guide you would see how to use -gpu_id. If you
> want permit mdrun to use its auto-selection, then don't use -gpu_id.
Thank you Mark for your kind response. However if I use the command
without the gpu id (gmx_mpi mdrun -v -deffnm md), it still selects only 1
card, and the log file throws a message as follows:
Using 1 MPI process
Using 16 OpenMP threads
2 compatible GPUs are present, with IDs 0,1
1 GPU auto-selected for this run.
Mapping of GPU ID to the 1 PP rank in this node: 0
NOTE: potentially sub-optimal launch configuration, gmx mdrun started with
less PP MPI process per node than GPUs available.
Each PP MPI process can use only one GPU, 1 GPU per node will be used.
Will do PME sum in reciprocal space for electrostatic interactions.
Dept.of Molecular Biology and Biotechnology
>> I am using Gromacs 2016.4 version.
>> For gromacs installation, used the following:
>> CC=/usr/bin/mpicc F77=/usr/bin/f77 CXX=/usr/bin/mpicxx
>> MPICC=/usr/bin/mpicc CMAKE_PREFIX_PATH=/soft/fftw337/lib cmake ..
>> -DCMAKE_INSTALL_PREFIX=/soft/gmx164 -DGMX_X11=OFF
>> -DCMAKE_CXX_COMPILER=/usr/bin/mpicxx -DCMAKE_C_COMPILER=/usr/bin/mpicc
>> -DGMX_MPI=ON -DGMX_DOUBLE=OFF -DGMX_DEFAULT_SUFFIX=ON
>> -DGMX_PREFER_STATIC_LIBS=ON -DGMX_SIMD=SSE2 -DGMX_SIMD=AVX2_256
>> -DGMX_USE_RDTSCP=OFF -DGMX_GPU=ON
> Use only one GMX_SIMD setting - the one that matches the capabilities of
> the CPU.
>> Do I need to provide any other option (openMPI) while installing
> You already chose to use your MPI library.
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