[gmx-users] gromacs on GPU

[Szilárd Páll]

Hi James,

Don't use the OpenMM accelerated mdrun for explicit solvent simulations.
For such runs any modern CPU with 4-8 cores will probably be as fast or
faster than most GPUs.

However, do consider the 4.6 *native* heterogeneous GPU-accelerated code.
This new efficient code can provide 2-4x speedup and uses both CPU and GPU.

To get the latest 4.6 version use the 4.6-beta3 release (http://goo.gl/XFPoe)
or even better, get the code from git (git clone git://
git.gromacs.org/gromacs -b release-4-6).

Let us know how things worked out!

Cheers,

--
Szilárd


On Mon, Jan 7, 2013 at 8:05 AM, James Starlight <jmsstarlight at gmail.com>wrote:

> Today I've tried to test gpu performance on the benchmark system (
> explicit solvent with pme )
>
> grompp-gpu -f md_sd.mdp -c conf -p topol.top -o md_test
> mdrun-gpu -device
> "OpenMM:platform=Cuda,DeviceID=1,Memtest=15,force-device=no" -v
> -deffnm md_test
>
> that produce the error
>
> Program mdrun-gpu, VERSION 4.5.5
> Source code file: /home/own/gromacs_gpu/src/kernel/openmm_wrapper.cpp,
> line: 1365
>
> Fatal error:
> OpenMM exception caught while initializating: cudaMemcpyToSymbol:
> SetSim copy to cSim failed invalid device symbol
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> In the mailing list archive I've found the same error with the same
> card posted some time ago
>
> http://article.gmane.org/gmane.science.biology.gromacs.user/55577/match=openmm+exception+caught+while+initializating+cudaMemcpyToSymbol+setsim+copy+cSim+failed+invalid+device+symbol
>
> >From that topic I've understood that 670 graphic card is not supported
> yet in Gromacs (4.55). I've checked the manual for the 4.6 beta
> version and does not found anything about supporting of that card in
> the lattest gromacs realeses as well. IS there any ways to solve that
> problem ? Could that error be linked with some others ?  E.g I've
> installed nvidia drivers + cuda first and openMM 4.01 than. During
> gromacs compilation I've not forced with any errors.
>
> Thanks for help
> James
>
>  2013/1/6 Justin Lemkul <jalemkul at vt.edu>:
> >
> >
> > On 1/6/13 1:53 PM, James Starlight wrote:
> >>
> >> OK!
> >>
> >> I've compilated gromacs-gpu from the source using that tutorial for
> >> the Debian OS
> >>
> >>
> http://verahill.blogspot.ru/2012/01/debian-testing-64-wheezy-compiling_20.html
> >>
> >> The only thing that it lack is the installation mdrun_d-gpu  but i'm
> >> not sure that double precission can be used with gpu.
> >>
> >> Could someone provide me with some tutorial which would show me basic
> >> mdrun options with the calculation on my gpu as well as some testing
> >> system?
> >>
> >
> > Everything you need to know (including benchmark systems) is posted at
> > http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GPUs.
> >
> > The invocation of mdrun-gpu is like any other mdrun, with GPU-specific
> > information available by reading mdrun-gpu -h.
> >
> >
> > -Justin
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > --
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