AMBER Archive (2006)

Subject: Re: AMBER: Parallelization method

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Tue Dec 19 2006 - 12:58:07 CST

Hi,

For sander, see the description on page 9 of the Amber 9 manual.
See also the top of page 102.
I recall that references 19 and 75 cover the Amber specific literature.

In general, a lot has been published; much of it is from allied
scientific fields. Here are some references that I happen to have
recorded, but there are many good ones I didnt:

%
% journal abbreviations
@string{jacs = "J. Am. Chem. Soc."}
@string{jcc = "J. Comput. Chem."}
@string{jcomputp = "J. Comput. Phys."}
@string{jcp = "J. Chem. Phys."}
@string{jpc = "J. Phys. Chem."}
@string{jpca = "J. Phys. Chem. A"}
@string{sapa = "Spectrochim. Acta Part A"}

@article{darden93,
  note = "First PME with Lagrangian interpolation and FFT.",
  author = "{Tom Darden, Darrin York, and Lee Pedersen}",
  title = "Particle Mesh {Ewald: An $N \cdot log(N)$} Method for {Ewald} Sums in Large Systems",
  journal = jcp,
  volume = 98,
  pages = {10089--10092},
  year = 1993 }

@article{essmann95,
  note = "PME with B-spline interpolation and FFT.",
  author = "{Ulrich Essmann, Lalith Perera, Max L. Berkowitz, Tom Darden, Hsing Lee, and Lee G. Pedersen"},
  title = "A Smooth Particle Mesh Ewald Method",
  journal = jcp,
  volume = 103,
  pages = {8577--8593},
  year = 1995 }

@article{feller96,
  note = "Note appendices on parallelization, erfc, and ewald parameters.",
  author = "{Scott E. Feller, Richard W. Pastor, Atipat Rojnuckarin, Stephen Bogusz, and Bernard R. Brooks}",
  title = "Effect of Electrostatic Force Truncation on Interfacial and Transport Properties of Water",
  journal = jpc,
  volume = 100,
  pages = {17011--17020},
  year = 1996 }

@article{kale99,
  author = "{Laxmikant Kal\'e, Robert Skeel, Milind Bhandarkar, Robert Brunner, Attila Gursoy, Neal Krawetz, James Phillips, Aritomo Shinozaki, Krishnan Varadarajan, and Klaus Schulten}",
  title = "{NAMD2}: Greater Scalability for Parallel Molecular Dynamics",
  journal = jcomputp,
  volume = 151,
  pages = {283--312},
  year = 1999 }

@article{mertz91,
  note = "Note the profiling data table on amber and charmm",
  author = "{John E. Mertz, Douglas J. Tobias, Charles L. Brooks, and U. C. Singh}",
  title = "Vector and Parallel Algorithms for the Molecular Dynamics Simulation of Macromolecules on Shared-Memory Computers",
  journal = jcc,
  volume = 12,
  pages = {1270--1277},
  year = 1991 }

@article{plimpton95,
  note = "Excellent article that classifies algorithms.",
  author = "{Steve Plimpton}",
  title = "Fast Parallel Algorithms for Short-Range Molecular Dynamics",
  journal = jcomputp,
  volume = 117,
  pages = {1--19},
  year = 1995 }

@article{steinbach94,
  author = "{Peter J. Steinbach and Bernard R. Brooks}",
  title = "New Spherical-Cutoff Methods for Long-Range Forces in Macromolecular Simulation",
  journal = jcc,
  volume = 15,
  pages = {667--683},
  year = 1994 }

@article{vincent95,
  author = "{James J. Vincent and Kenneth M. Merz, Jr.}",
  title = "A Highly Portable Parallel Implementation of {AMBER4} Using the Message Passing Interface Standard",
  journal = jcc,
  volume = 16,
  pages = {1420--1427},
  year = 1995 }

On Tue, 19 Dec 2006, Robert Duke wrote:

> Jordi -
> I should be putting out a paper on pmemd in the next few months. - Regards -
> Bob Duke
>
> ----- Original Message -----
> From: "Jordi Camps" <jcamps_at_lsi.upc.edu>
> To: <amber_at_scripps.edu>
> Sent: Tuesday, December 19, 2006 1:19 PM
> Subject: AMBER: Parallelization method
>
>
> > Hello,
> >
> > I'm looking for information about the way sander/pmemd are parallelized.
> > How
> > data are distributed, how the algorithm works... Is it described anywhere?
> > I've searched in the manual, but it seems to be any chapter talking about
> > this subject.
> >
> > Thank you very much,
> >
> > --
> > Jordi Camps Puchades
> > jcamps_at_lsi.upc.edu
> > Supercomputing research, support and development
> >
> > Barcelona Supercomputing Center | Instituto Nacional de Bioinformática
> > | GNHC-2 UPC-CIRI
> > (http://inb.lsi.upc.edu)
> > http://www.bsc.es | http://www.inab.org
> > Tel. : 934 137 602 | Tel. : 934 037 155
> > Fax : 934 137 721 | Fax : 934 037 157
> > c/ Jordi Girona, 29 | c/ Josep Samitier, 1-5
> > Edifici Nexus II, despatx 1B | PCB, Edifici Modular, PBC32
> > E-08034 Barcelona | E-08028 Barcelona
> > Catalunya (Spain) | Catalunya (Spain)
> >
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