[gmx-users] problems for GPU simulations

[Berk Hess]

Hi,

You don't need SLI for multi-GPU simulations in Gromacs.
But you do need a real MPI library and configure Gromacs with -DGMX_MPI=on
Then you need to start Gromacs with (depending on you MPI library):
mpirun -np #GPUs mdrun

If anything, the performance of Gromacs should have gotten better from 4.6-beta to 4.6, not worse.

Cheers,

Berk

----------------------------------------
> Date: Thu, 7 Feb 2013 13:28:55 +0300
> Subject: Re: [gmx-users] problems for GPU simulations
> From: jmsstarlight at gmail.com
> To: gmx-users at gromacs.org
>
> Albert,
>
> thanks for information!
>
> So now it's only intresting to my how I should install multi-GPU's on
> my system to obtain best compatibility with gromacs.
>
> Also could you tell me what your system has performance (in gflops)
> and what system you have simulated on it (average atom number,
> presence of explicit membrane etc)?
>
>
> Thank you for help again,
>
> James
>
> 2013/2/7 Albert <mailmd2011 at gmail.com>:
> > On 02/07/2013 11:03 AM, James Starlight wrote:
> >>
> >> Hi Albert!
> >>
> >>
> >> As I understood your correctly you have run simulations with your 2
> >> GPU cards on Gromacs-beta but could not do it with final version
> >> havent it?
> >
> > not really. both versions could run with GPU. The 4.6 beta recognize my
> > number of GPU as 4, but final version as 2. And the efficiency for beta is
> > double comparing with final version.
> >
> >
> >
> >>
> >> Could you tell me how you installed both GPU in your work-station?
> >> Have you used SLI ? ( I've heard that gromacs is not suported the
> >> simulation in multi-GPU regime so I'll be very happy if it's not true
> >> :))
> >
> > both GPU version were compiled with the same command:
> >
> > cmake .. -DGMX_MPI=ON -DCMAKE_CXX_COMPILER=/soft/openmpi-1.4.3/bin/mpiCC
> > -DCMAKE_C_COMPILER=/soft/openmpi-1.4.3/bin/mpicc
> > -DCMAKE_INSTALL_PREFIX=/soft/gromacs4.6beta3 -DGMX_GPU=OFF
> > -DBUILD_SHARED_LIBS=OFF -DCMAKE_PREFIX_PATH=/soft/fftw-3.3.3
> >
> > I don't think I used SLI
> >
> >
> >>
> >> Also could you tell me about configuration of your workstation in more
> >> detailes ? ( what cpu and mb you use ? )
> >
> > there are 16 GB for the memory, I've got intel I7-960 for the workstation.
> > I don't specify how many core should be used, but both cases occupy full CPU
> > resources automatically.
> >
> >
> >
> >>
> >> James
> >
> >
> > --
> > 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