[gmx-users] Pme on gpu performance

[Matt Larson]

Szilárd,

 Version 4.6, GPU without OpenMM sounds fantastic.  I am very excited!
I was having trouble getting simulations to work equivalently well on
the GPU as CPU because of having to make different choices with
cutoffs and mainly not being able to use the V-rescale thermostat.

 -Matt

On Sun, Nov 27, 2011 at 6:01 PM, Szilárd Páll <szilard.pall at cbr.su.se> wrote:
> Hi,
>
> 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.
>
> --
> 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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>>>>
>>>> --
>>>> ==================================================================
>>>> 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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