From owner-chemistry-!at!-ccl.net Mon Nov 5 06:24:00 2007 From: "=?ISO-8859-1?Q?Sina_T=FCreli?= sinatureli(-)gmail.com" To: CCL Subject: CCL: Massive parallelization. Message-Id: <-35558-071105050417-27073-ZimWDxG6+muC48MoJ2hOcA-,-server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?Sina_T=FCreli?=" Content-Type: multipart/alternative; boundary="----=_Part_11362_20306597.1194257018569" Date: Mon, 5 Nov 2007 12:03:38 +0200 MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?Sina_T=FCreli?=" [sinatureli(-)gmail.com] ------=_Part_11362_20306597.1194257018569 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline NAMD can be run on parallel machines and is free source http://www.ks.uiuc.edu/Research/namd/ On 11/5/07, Andreas Bick andreas.bick/ascienomics.com < owner-chemistry**ccl.net> wrote: > > > Sent to CCL by: Andreas Bick [andreas.bick . scienomics.com] > Hi Don, > > I think LAMMPS, a classical MD code (http://lammps.sandia.gov/) fulfills > your criteria. > > Regards > > Andreas > > >Sent to CCL by: "Don Steiger" [don.steiger~~gmail.com] > >I am looking for a program that would make a good test case for > >parallelization. I want to try out some parallelization ideas that uses > mpi-2 > >for intra-machine message passing, and Globus for inter-machine message > passing > >(i.e. over the internet). In addition, instead of using a passive > >synchronization, which mpi programs normally use, I want to try an > approach > >that uses a dedicated processor to coordinate the processing performed by > the > >individual processors. I'm hoping that this kind of parallelization > scales well > >when the number of processors are large and spread across multiple > machines. > > > >There are three key requirements for an appropriate test case: > > > > 1) the algorithm has an underlying parallel structure, > > > > 2) the scalar version of the code is reasonably bug free, and > > > > 3) the code must be either very well documented, or > > reasonably simple to figure out, or somebody familiar with > > the source be willing to take some time to provide > guidance. > > > >If you have, or know of, a scalar program that you would like to port to > a > >parallel environment, and want somebody else to do the work then let me > know. > > > > > >Don > >don.steiger- -gmail.com> > > > > > > > > > > > > > -- > Dr. Andreas Bick > Scienomics SARL > Sales and Marketing > mobile: +491621309945> > > > ------=_Part_11362_20306597.1194257018569 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
NAMD can be run on parallel machines and is free source
 
http://www.ks.uiuc.edu/Research/namd/

 
On 11/5/07, Andreas Bick andreas.bick/ascienomics.com <owner-chemistry**ccl.net> wrote:

Sent to CCL by: Andreas Bick [andreas.bick . scienomics.com]
Hi Don,

I think LAMMPS, a classical MD code (http://lammps.sandia.gov/) fulfills
your criteria.

Regards

Andreas

>Sent to CCL by: "Don  Steiger" [ don.steiger~~gmail.com]
>I am looking for a program that would make a good test case for
>parallelization.  I want to try out some parallelization ideas that uses mpi-2
>for intra-machine message passing, and Globus for inter-machine message passing
>(i.e. over the internet).  In addition, instead of using a passive
>synchronization, which mpi programs normally use, I want to try an approach
>that uses a dedicated processor to coordinate the processing performed by the
>individual processors. I'm hoping that this kind of parallelization scales well
>when the number of processors are large and spread across multiple machines.
>
>There are three key requirements for an appropriate test case:
>
>           1) the algorithm has an underlying parallel structure,
>
>           2) the scalar version of the code is reasonably bug free, and
>
>           3) the code must be either very well documented, or
>              reasonably simple to figure out, or somebody familiar with
>              the source be willing to take some time to provide guidance.
>
>If you have, or know of, a scalar program that you would like to port to a
>parallel environment, and want somebody else to do the work then let me know.
>
>
>Don
>don.steiger- -gmail.com>
>
>
>
>
>


--
Dr. Andreas Bick
Scienomics SARL
Sales and Marketing
mobile: +491621309945



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