[gmx-users] GPU Command

Mark Abraham mark.j.abraham at gmail.com
Thu Apr 12 17:54:45 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 cores)
> 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 selects
> 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.

> 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 ..
> -DFFTWF_INCLUDE_DIR=/soft/fftw337/include
> -DFFTWF_LIBRARIES=/soft/fftw337/lib/libfftw3.so
> -DCMAKE_CXX_COMPILER=/usr/bin/mpicxx -DCMAKE_C_COMPILER=/usr/bin/mpicc

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 groamcs?

You already chose to use your MPI library.


> Thank You
> Regards
> Zaved Hazarika
> PhD Scholar
> Dept.of Molecular Biology and Biotechnology
> Tezpur University
> Indi
> * * * D I S C L A I M E R * * *
> This e-mail may contain privileged information and is intended solely for
> the individual named. If you are not the named addressee you should not
> disseminate, distribute or copy this e-mail. Please notify the sender
> immediately by e-mail if you have received this e-mail in error and destroy
> it from your system. Though considerable effort has been made to deliver
> error free e-mail messages but it can not be guaranteed to be secure or
> error-free as information could be intercepted, corrupted, lost, destroyed,
> delayed, or may contain viruses. The recipient must verify the integrity of
> this e-mail message.
> --
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list