[gmx-users] gromacs on GPU

[Szilárd Páll]

Dear James,

On Wed, Jan 9, 2013 at 6:17 PM, James Starlight <jmsstarlight at gmail.com>wrote:

> Roland,
>
> indeed the error was that I'have compilate mdrun-openmm which is not
> the native gpu.
>
> now I've made mdrun via
>
> cmake CMakeLists.txt -DGMX_GPU=ON
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.0
>
> and obtain workable gromacs.
>
> My test system consist of calmodulin (charmm27) solvated in tip3p
> water. total size of the system: 67752 atoms.
> I have set below values on the mdp file as grompp told me
>
> nstlist = 20
> cutoff-scheme = Verlet   ; !not quite sure whai is this!
>

Again RTM:
http://www.gromacs.org/Documentation/Cut-off_schemes<http://www.gromacs.org/Documentation/Cut-off_schemes?highlight=verlet+scheme>


> vdwtype         = cut-off
>
>
>  Now on the mdrun output I have
>
> Using 1 MPI thread
> Using 4 OpenMP threads
>
> 1 GPU detected:
>   #0: NVIDIA GeForce GTX 670, compute cap.: 3.0, ECC:  no, stat: compatible
>
> 1 GPU auto-selected to be used for this run: #0
>
> does it mean that all 4 cores of my CPU + gpu are used at same time ?
>

Yes.


> is there any other ways to increase performance ? ( e.g I'm not quite
> sure if open_mpi is used with that build because during compilation
> cmake asked me only about fftw3 libs).
>

There could be, but I/we can't well without more information on what and
how you compiled and ran. The minimum we need is a log file.


>
> Is there any ways to monitor total performance ( e.g separate cpu and
> gpu usage ) ?
>

See the performance table and summary at the end of the log file. For
further CPU monitoring you can use top, for GPUs the nvidia-smi tool that
comes together with the driver has some monitoring capabilities.


Finally, I would strongly suggest that you check the links I posted in the
first mail. There is plenty of documentation and general description on
the heterogeneous (CPU+GPU) acceleration on the wiki and mailing list; the
google results of the searches I hinted will get you exactly that and more.

Let me reiterate: while questions and general interest are appreciated, the
*minimum* expectation is that you at least read the relevant part of the
documentation and related mailing list posts, especially if this has been
already suggested to you. Please do us and yourself a favor and browse
through the available resources.

Cheers,
--
Szilárd


>
>
> Thanks for suggestions,
>
> James
>
> 2013/1/9 Roland Schulz <roland at utk.edu>:
> > On Wed, Jan 9, 2013 at 3:17 AM, James Starlight <jmsstarlight at gmail.com
> >wrote:
> >
> >> As I understood that gromacs version already has included openMM so
> >> the installation of the external openMM sources is not needed, isnt it
> >> ?
> >>
> >
> > No the new build in GPU implementation and openMM are two different
> things.
> > The Gromacs-OpenMM interface isn't actively maintained and thus not
> > recommended.
> >
> >
> >> also I wounder to know what exactly CUDA version is needed ? For
> >> example I've tried lattest cuda-5.0 but with that version i've obtain
> >> error from mdrun-openmm that platform cuda was not detected (gromacs
> >> was compilated without any errors).
> >>
> > with the natived gpu implementation (GMX_GPU) cuda 5.0 works fine.
> >
> >
> >> by the way is it possible to compilate gromacs-4.6 agains other
> >> platgorm ( e.g openCL) ? I have no problems with the compatibility of
> >> the openCL and openMM.
> >>
> > GMX_GPU doesn't support openCL.
> >
> > Roland
> >
> >
> >>
> >> James
> >>
> >> 2013/1/9 Szilárd Páll <szilard.pall at cbr.su.se>:
> >> > On Tue, Jan 8, 2013 at 3:22 PM, James Starlight <
> jmsstarlight at gmail.com
> >> >wrote:
> >> >
> >> >> So could someone provide me more about gpu-accelerated MD implemented
> >> >> in the 4.6 gromacs ? Does it require openMM (what version is
> supported
> >> >>
> >> >
> >> > FYI, if nobody can, trust G:
> >> > http://lmgtfy.com/?q=gromacs+4.6+gpu+acceleration
> >> > http://lmgtfy.com/?q=gromacs+4.6+installation+instructions
> >> >
> >> > The wiki and mailing list contains quite extensive information
> (indexed
> >> by
> >> > G).
> >> >
> >> > Otherwise, release notes (not final):
> >> > http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x
> >> >
> >> > Install guide is at the expected location:
> >> > http://www.gromacs.org/Documentation/Installation_Instructions
> >> >
> >> > Cheers,
> >> > --
> >> > Szilárd
> >> >
> >> >
> >> >> for that gromacs release ?) installed? By the way at present time I
> >> >> force with the problem of compilation 4.1.1 openMM (i need to compile
> >> >> openMM because of cuda-5.0 ). If someone have done it (openMM 4.11
> >> >> +cuda 5.0 + gromacs-4.5 for lattest geforces) please let me know.
> >> >>
> >> >>
> >> >> James
> >> >>
> >> >> 2013/1/7 James Starlight <jmsstarlight at gmail.com>:
> >> >> > Hi Szilárd!
> >> >> >
> >> >> > As I understood you correctly gromacs-4.6 have specific algorithm
> >> >> > (independent on openMM?) for gpu-based calculations havent ? If it
> >> >> > true how I should compilate such new gpu-based gromacs? In the
> >> >> > gromacs-4.6-beta-3 folder I've found instructuon for the standart
> >> >> > installation via cmake
> >> >> >
> >> >> > cmake PATH_TO_SOURCE_DIRECTORY -DGMX_OPENMM=ON -DGMX_THREADS=OFF
> >> >> >
> >> >> >
> >> >> > James
> >> >> >
> >> >> > 2013/1/7 Szilárd Páll <szilard.pall at cbr.su.se>:
> >> >> >> Szilárd
> >> >> --
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> >>
> >>
> >
> >
> > --
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