Hi,
can PMEMD.cuda and sander.MPI be configured together on a GPU?
On Tue, Sep 25, 2012 at 3:47 AM, Robert Crovella <RCrovella.nvidia.com>wrote:
> You can still run sander.MPI on your GPU based systems. You won't see any
> particular GPU acceleration in that case, but the system should behave the
> same as if the GPUs were not installed.
>
> If you want to configure and build sander.MPI, just follow the regular
> instructions provided with AMBER.
>
> -----Original Message-----
> From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
> Sent: Monday, September 24, 2012 1:57 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] cuda
>
> Hi,
>
> CUDA is the programming langauge that essentially allows a program to run
> on GPUs. PMEMD has CUDA code; SANDER does not, so SANDER will not function
> on GPUs. GPU architecture is substantially different than CPU, so it can
> require a lot of rewriting to get CPU code ported over to GPU. There are
> currently no plans to add CUDA code to SANDER since as Ross mentioned it
> would be far too much work to do efficiently.
>
> -Dan
>
> On Mon, Sep 24, 2012 at 11:52 AM, Mary Varughese <maryvj1985.gmail.com>
> wrote:
> > Sir,
> >
> > I need one more clarification.
> > >From what you said I understand
> > Cuda applies for PMEMD only. Its better to switch to PMEMD, because of
> > its efficiency.
> >
> > But If NVIDA CUDA is applied on a GPU with multicores(~4000) and
> > amber(11) is installed ; although cuda is for pmemd only surely
> > sander.MPI will work efficiently (installed under cuda doesnt mean we
> > cant configure sander.MPI) isn't it?
> >
> > Is there any problem in this?
> >
> > thanking you.
> > your suggestions are much valuable.
> >
> >
> >
> > On Mon, Sep 24, 2012 at 9:38 PM, Ross Walker <ross.rosswalker.co.uk>
> wrote:
> >
> >> Hi Mary,
> >>
> >> Unfortunately the nature of GPUs is such that one has to rewrite the
> >> entire code to run on the GPU in order to obtain efficiency. Why we
> >> would love to rewrite sander to run it would be a monumental task and
> >> we simply don't have the resources or manpower to do it. One can do
> >> 'tricks' in which just part of the calculation runs on the GPU (say
> >> the direct space) but this needs stupidly big atom counts to see any
> >> real performance improvement and also tends to be inefficient in
> >> terms of the number of GPUs used. We have decided not to go down this
> >> route since we believe it better to focus on accelerating the types
> >> of calculations that most people run rather than going after simple
> headline numbers.
> >>
> >> For this reason we used PMEMD as our base point since the code is
> >> much cleaner and it was easy to implement the majority of the
> >> features without many clashes. For example, sander has so many
> >> options we'd be forever chasing which ones work with GPUs which don't
> >> etc and we would never gotten to having a fully working code. Our
> >> intention is to slowly migrate over features that are widely used
> >> (like TI for example) into PMEMD. This is a much efficient use of
> >> resources than trying to hack the support into Sander. Thus please stay
> tuned for more additions to PMEMD to come.
> >>
> >> With regards to other parts of AMBER on GPUs. At present the code is
> >> just in PMEMD. We are working on a library that we plan to release
> >> open source under AmberTools for people to add GPU support to their
> >> own codes. Of course this will suffer from the fact that copying back
> >> and forth from GPU will destroy performance and so if one wanted to
> >> add their own specific features this would likely need them to edit
> >> the cuda code to achieve this. Unfortunately there are no magic
> >> bullets. So ultimately once the library is completed the cuda code
> >> will be released under an open source license. It will likely take us a
> while to get this done however.
> >>
> >> All the best
> >> Ross
> >>
> >>
> >>
> >> On 9/24/12 7:41 AM, "Mary Varughese" <maryvj1985.gmail.com> wrote:
> >>
> >> >Sir,
> >> >
> >> >Then sander would have no improvement in efficiency?
> >> >Also the amber11 licenced is using or is there any other version for
> >> >using with cuda.
> >> >
> >> >Thanking you
> >> >On Mon, Sep 24, 2012 at 11:08 AM, filip fratev
> >> ><filipfratev.yahoo.com>wrote:
> >> >
> >> >> Hi,
> >> >> Only pmemd.cuda.
> >> >>
> >> >> All the best,
> >> >>
> >> >>
> >> >>
> >> >> ________________________________
> >> >> From: Mary Varughese <maryvj1985.gmail.com>
> >> >> To: AMBER Mailing List <amber.ambermd.org>
> >> >> Sent: Monday, September 24, 2012 7:03 AM
> >> >> Subject: [AMBER] cuda
> >> >>
> >> >> Sir,
> >> >>
> >> >> Does installing AMBER11 with NVIDA CUDA on GPU machine works fine
> >> >>for sander too for parallel. On going through details i notice
> >> >>only pmemd.cuda and not any sander.cuda.
> >> >> Would you please clear this. It will help me to understand the
> >> >>situation.
> >> >>
> >> >> Thanking you
> >> >> --
> >> >> Mary Varughese
> >> >> Research Scholar
> >> >> School of Pure and Applied Physics Mahatma Gandhi University India
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
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> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> >
> >> >
> >> >
> >> >--
> >> >Mary Varughese
> >> >Research Scholar
> >> >School of Pure and Applied Physics
> >> >Mahatma Gandhi University
> >> >India
> >> >_______________________________________________
> >> >AMBER mailing list
> >> >AMBER.ambermd.org
> >> >http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> _______________________________________________
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> >
> >
> >
> > --
> > Mary Varughese
> > Research Scholar
> > School of Pure and Applied Physics
> > Mahatma Gandhi University
> > India
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
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--
Mary Varughese
Research Scholar
School of Pure and Applied Physics
Mahatma Gandhi University
India
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Received on Mon Sep 24 2012 - 22:00:02 PDT
