[gmx-users] gromacs on GPU

[Szilárd Páll]

On Wed, Jan 9, 2013 at 9:17 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
> ?
>

The manual and wiki guides are meant to be read. Although they are a bit
dated, the main body of information is still valid. Please read the
documentation; aka RT(F)M:
http://www.gromacs.org/gpu#Compiling_and_installation_of_GROMACS-GPU_from_source


> 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). I've seen that erorr in other
> posts in the mailing list but could not found any possible sollutions.
>

It surely works with the (admittedly dated) versions the docs suggest,
you mileage may vary with other versions, but in principle everything
should work with the latest compilers, CUDA, and OpenMM (myself and others
have built and ran successfully).


>
> 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.
>

No, RTM. OpenMM does have an OpenCL plugin, but that's not supported in
GROMACS, if you want to use it you'll have to write your own code around
the OpenMM library. We
have no resources to implement it ATM, but as GROMACS is OSS anyone is
welcome to contribute it.

And let me reiterate, if you're running explicit solvent you should be
using the native GPU acceleration as you've been told before.

Cheers,
Szilard


> 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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