[gmx-users] Pme on gpu performance
Jones de Andrade
johannesrs at gmail.com
Mon Nov 28 20:55:12 CET 2011
Hi.
I'm another one waiting for the OpenCL version here.
4.6 will support only CUDA.
>
> OpenCL GPU implementations have yet match CUDA; on CPU it would hardly
> match the performance of the hand-tuned SSE kernels, moreover, CPU &
> GPU algorithms are not the same.
>
If you allow me, the (second and third!) argument is not strong enough,
since also cuda for cpu would not match the performance of all tricks from
gromacs. Also, I think that the cpu and cuda algorithms are not the same.
>From my point of view, the only really strong argument would be the first
one: "OpenCL GPU implementations have yet match CUDA!", despite the fact
that I would like to see it better explained if possible (even a link would
be suffice).
More important: does this mean that openMM and gromacs gpu development are
"breaking apart"? What can we really expect from that, other than easier
installation and usage?
Thanks a lot!
Sincerely yours,
Jones
>
> --
> Szilárd
>
>
>
> On Sun, Nov 27, 2011 at 11:25 PM, Alexey Shvetsov
> <alexxy at omrb.pnpi.spb.ru> wrote:
> > Hi!
> >
> > Will it use CUDA or OpenCL? Second one will be more common since it will
> > work with wider range of platfroms (cpu, gpu, fcpga)
> >
> > Szilárd Páll писал 27.11.2011 23:50:
> >>
> >> Native acceleration = not relying on external libraries. ;)
> >>
> >> --
> >> Szilárd
> >>
> >>
> >>
> >> On Sun, Nov 27, 2011 at 9:33 PM, Peter C. Lai <pcl at uab.edu> wrote:
> >>>
> >>> Random hijack:
> >>>
> >>> Will the CUDA acceleration support CMAP or will it still be limited to
> >>> the limitations of OpenMM that it currently has?
> >>>
> >>> On 2011-11-27 12:10:47PM -0600, Szilárd Páll wrote:
> >>>>
> >>>> Hi Andrzej,
> >>>>
> >>>> GROMACS 4.6 is work in progress, it will have native CUDA acceleration
> >>>> with multi-GPU support along a few other improvements. You can expect
> >>>> a speedup in the ballpark of 3x. We will soon have the code available
> >>>> for testing.
> >>>>
> >>>> I'm a little skeptical about the 5x of ACEMD. What setting did you
> >>>> use? AFAIR they were using large time-steps without contraints in
> >>>> their benchmarks.
> >>>>
> >>>> Cheers,
> >>>> --
> >>>> Szilárd
> >>>>
> >>>>
> >>>>
> >>>> On Thu, Nov 24, 2011 at 9:53 AM, Andrzej Rzepiela
> >>>> <Andrzej.Rzepiela at physik.uni-freiburg.de> wrote:
> >>>> > Dears,
> >>>> >
> >>>> > I would like to ask what performance improvement is expected for
> >>>> > future
> >>>> > releases (e.g. 4.6) for PME calculations on gpu cards. Last week I
> >>>> > sent
> >>>> > benchmark results for dhfr to the list, which show no performance
> gain
> >>>> > when
> >>>> > the newest versions of tesla cards vs intel xeon R are used (more or
> >>>> > less in
> >>>> > agreement of what is presented on the gromacs website). However, for
> >>>> > the
> >>>> > same system simulations with different gpu code, acemd, on a very
> >>>> > similar
> >>>> > machine can be about 5 times faster, as benchmarked recently by my
> >>>> > colleagues, suggesting that performance of gromacs may soon improve.
> >>>> > is that
> >>>> > correct ?
> >>>> >
> >>>> >
> >>>> > Andrzej
> >>>> > --
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> >>>> >
> >>>> --
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> >>>
> >>> --
> >>> ==================================================================
> >>> Peter C. Lai | University of Alabama-Birmingham
> >>> Programmer/Analyst | KAUL 752A
> >>> Genetics, Div. of Research | 705 South 20th Street
> >>> pcl at uab.edu | Birmingham AL 35294-4461
> >>> (205) 690-0808 |
> >>> ==================================================================
> >>>
> >>> --
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> >>>
> >
> > --
> > Best Regards,
> > Alexey 'Alexxy' Shvetsov
> > Petersburg Nuclear Physics Institute, Russia
> > Department of Molecular and Radiation Biophysics
> > Gentoo Team Ru
> > Gentoo Linux Dev
> > mailto:alexxyum at gmail.com
> > mailto:alexxy at gentoo.org
> > mailto:alexxy at omrb.pnpi.spb.ru
> > --
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