ADL: MPI.Autodock4

Mark Swingle mswingle at jaguar1.usouthal.edu
Fri Apr 17 13:36:35 PDT 2009


Barbara,

For virtual screening, an MPI version of autodock is not needed. VS is what 
one might call embarassingly parallel. You simply need to divide your ligand 
database into small segments and run autodock processes with a segment on 
each available processor core. This can be done with simple scripting 
(numerous examples are floating around) or with something like DOVIS that is 
specifically geared to VS. My guess is that multiple instances of "plain 
vanilla" autodock running in parallel on many processors would be a bit 
faster than a single instance of an MPI version of autodock utilizing the 
same number of processors, simply because of the increased overhead due to 
MPI.

Regards,

Mark

On Friday 17 April 2009 09:34:51 am Collignon, Barbara C. wrote:
> For VS
>
> Barbara
>
>
> -----Original Message-----
> From: autodock-bounces at scripps.edu on behalf of M. Shahid
> Sent: Fri 4/17/2009 2:59 AM
> To: autodock at scripps.edu
> Subject: Re: ADL: MPI.Autodock4
>
> Do you need it for single run on how many processors? or you need one for
> VS?
>
>
> On Thu, Apr 16, 2009 at 10:52 PM, Collignon, Barbara C. <
>
> collignonbc at ornl.gov> wrote:
> > Sorry , I am confused.
> >
> > May someone give me the link to download MPI.Autodock4 ?
> >
> > Barbara
> >
> >
> >
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
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>
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