[Dockdev] Can DOCK be run a compute cluster?

[Ricardo Nicoluci]

Hi,

I think that cluster solutions with technologies like OpenMosix would
help in the load balacing question. Here in our Institute the dock
program GOLD runs using PVM (Paralel Virtual Machine) just to allow us
to run more then one process and all the management is made by
OpenMosix.
All the dock process are split around the cluster nodes and the load
is equal on each one, so it runs as fast as it can. Also noting that
the developing programs to take advantage of this technolige, only
needs to know how to use the fork() C++ function instead of the all
parameters of MPI. We can also talk about the problem of that with
fork() functions you have no garantees of what data will finish first,
but depending of the problem it can be a simple solution.

Ricardo Nicoluci


On Wed, 2 Mar 2005 06:39:56 -0800, John Irwin <jji at cgl.ucsf.edu> wrote:
> Hi Faye
> 
> DOCK5 can be run in fine-grain parallel with MPI. Previous versions of DOCK
> can be run in coarse-grain parallel by splitting the database up, running
> each on a separate node, and combining the results at the end.
> 
> Hope this helps!
> 
> John Irwin http://johnirwin.compbio.ucsf.edu
> 
> > -----Original Message-----
> > From: dockdev-bounces at docking.org
> > [mailto:dockdev-bounces at docking.org] On Behalf Of Faye Schilkey
> > Sent: Tuesday, March 01, 2005 5:00 PM
> > To: dockdev at docking.org
> > Subject: [Dockdev] Can DOCK be run a compute cluster?
> >
> > Greetings,
> >
> > Can DOCK be run on Linux Redhat compute cluster with 128 nodes?
> >
> > Any information related to this would be great!
> >
> > Thanks,
> > -Faye
> >
> > _______________________________________________
> > Dockdev mailing list
> > Dockdev at docking.org
> > http://blur.compbio.ucsf.edu/mailman/listinfo/dockdev
> >
> 
> _______________________________________________
> Dockdev mailing list
> Dockdev at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dockdev
>