From: dongsheng lei (laidongshengs_at_gmail.com)
Date: Fri Dec 14 2012 - 03:42:08 CST
Dear Aron and Axel,
Thank you very much for your detailed explanations. I will try LAMMPS
and OpenMM before obtaining a nvidia video card and do not just hope that
companys will do all the things we wished.
Good luck to you and all NAMD users,
Dongsheng Lei
2012/12/14 Aron Broom <broomsday_at_gmail.com>
> Yes, I'd agree that OpenMM's speed advantage is most fully demonstrated
> with implicit solvent (or even no solvent at all, provided there is also no
> non-bonded cutoff). I didn't find it horrible for explicit solvent.
>
> It's unfortunate that while GPU acceleration has actually been quite
> successful in my mind, it was perhaps hyped up to an insane degree and so
> was never going to be able to really meet expectations. It seems though,
> that the 600 series (or at leas the 670 and 680) nVidia cards perform quite
> well when most of the calculations are single precision, and so still offer
> a good return on investment compared to a small cluster if you're certain
> you're ok with running at that precision level (I think default AMBER for
> instance is SPDP or SPFP or something that benefits quite well from those
> cards).
>
> So with any hope it will just be the GP-GPU specific market that dies off
> and we'll all keep happily using consumer cards (albeit ones with larger
> than average memory sizes).
>
> ~Aron
>
>
> On Fri, Dec 14, 2012 at 4:04 AM, Axel Kohlmeyer <akohlmey_at_gmail.com>wrote:
>
>> On Fri, Dec 14, 2012 at 9:49 AM, Aron Broom <broomsday_at_gmail.com> wrote:
>> > I believe that at the moment this is true.
>> >
>> > For the time being, you can consider some alternatives. I believe
>> OpenMM
>> > will function with ATI cards, and hence, I suspect the GPU enhanced
>>
>> OpenMM only used to work well (and fast) for folding_at_home calculations,
>> which are all implicit solvent jobs (well, at least that is what i am
>> seeing on
>> the machine that i am co-managing).
>>
>> > functions in GROMACS will also do the same. I thought also that LAMMPS
>> > allows ATI cards?
>>
>> LAMMPS has two different GPU support modules (with different
>> functionality).
>> one of them can be retargeted to generate either CUDA or OpenCL code,
>> which
>> in turn makes it work on ATI/AMD. indeed, i have one node with 4x firepro
>> cards
>> and you can run LAMMPS on them. there is support for the usual "bio" force
>> fields, but CHARMM support is (currently) lacking CMAP support.
>>
>> > OpenCL used to be fairly inferior to CUDA by all accounts (I'm speaking
>> from
>> > 2nd hand knowledge, so could easily be very wrong) but my impression is
>> that
>> > things are much more equivalent now, so perhaps both will be supported
>> > eventually. From a GPU computing perspective this can only be a good
>> thing,
>> > as nVidia's pseudo-monopoly is not ideal.
>>
>> don't get your hopes up. considering the financial woes that AMD is in,
>> they simply don't have the funds to support proper development of the
>> drivers and utilities. they've been letting people go left and right.
>>
>> even nvidia's attempts to entice people to jump onto the GPU bandwagon
>> these days have a ring of desperation to it.
>>
>> axel.
>>
>> >
>> > ~Aron
>> >
>> >
>> > On Fri, Dec 14, 2012 at 3:28 AM, dongsheng lei <laidongshengs_at_gmail.com
>> >
>> > wrote:
>> >>
>> >> Hello,
>> >>
>> >> I want to run GPU accelerated NAMD on my computer which has a ATI video
>> >> card. However, according to the NAMD user guide and online
>> information, GPU
>> >> accelerated NAMD can only function with nvidia video cards, which are
>> >> CUDA-capable. I want to know does it mean that we can not run GPU
>> >> accelerated NAMD by using ATI video card in any case, currently?
>> >>
>> >> I heard that NVIDIA Contributes CUDA Compiler to Open Source Community
>> and
>> >> wish we can use ATI video cards to run NAMD with GPU acceleration in
>> the
>> >> future.
>> >>
>> >> Best wishes to you,
>> >>
>> >> Dongsheng Lei
>> >
>> >
>> >
>> >
>> > --
>> > Aron Broom M.Sc
>> > PhD Student
>> > Department of Chemistry
>> > University of Waterloo
>> >
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> International Centre for Theoretical Physics, Trieste. Italy.
>>
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
>
>
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