ADL: CUDA compiling

Jan-Philip Gehrcke jgehrcke at googlemail.com
Fri Feb 21 10:00:49 PST 2014


It's not only about interest. The most important question is if the 
search and scoring algorithms used in docking tools (e.g. Vina) can take 
significant(!) advantage when being re-implemented for GPU architecture 
at all. My initial guess is that scoring can profit a lot (pairwise sums 
and such things) whereas the search might not be suitable for GPU 
re-implementation. If one then only implements scoring for GPU and 
leaves search for CPU, large amounts of data need to be transferred from 
and to the GPU all the times. Due to this communication overhead, there 
might be none of a overall performance gain compared to the classical 
method.

Just my two cents, one has to think about this before.

On 21.02.2014 18:23, Brian Moldover wrote:
> Is there a lot of interest in such a project? We've talked about doing it,
> but it's been a pretty low ( i.e. unfunded) priority.
>
> -Brian
>
> -----Original Message-----
> From: autodock-bounces at scripps.edu [mailto:autodock-bounces at scripps.edu] On
> Behalf Of Oleg Trott
> Sent: Thursday, February 20, 2014 8:26 PM
> To: autodock at scripps.edu
> Subject: Re: ADL: CUDA compiling
>
> Not to my knowledge
>
> On Thu, Feb 20, 2014 at 6:45 AM, Jean DESSOLIN
> <j.dessolin at iecb.u-bordeaux.fr> wrote:
>> Dear Autodockers and Vina fans,
>>
>> I cannot find in the archives any mention about compiling Vina for GPU use
> ?
>> I found an old one about autodock, but nothing about vina and cuda.
>>
>> Thus, did anybody recompiled/rewrote vina for CUDA calculations ?
>>
>> Best regards.
>>
>> Jean
>> ________________________________________________
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>> ---
>
>
>
> --
> Oleg Trott, Ph.D. (Columbia University)
>
> Staff Scientist in the Olson Lab
> The Scripps Research Institute
>
> http://olegtrott.com
> ________________________________________________
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>
> ________________________________________________
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