Re: [Beowulf] Beowulf Application in the Sciences (fwd from rgb=at=phy.duke.edu)

----- Forwarded message from "Robert G. Brown"
 <rgb=at=phy.duke.edu> -----
 From: "Robert G. Brown" <rgb=at=phy.duke.edu>
 Date: Thu, 23 Sep 2004 08:04:17 -0400 (EDT)
 To: Timo Mechler <mechti01=at=luther.edu>
 Cc: beowulf=at=beowulf.org
 Subject: Re: [Beowulf] Beowulf Application in the Sciences
 On Wed, 22 Sep 2004, Timo Mechler wrote:
 > Hello all,
 >
 > Through my studies of computer clusters so far, it has become apparent to
 > me that a lot of applications exist in both the Math and Physics fields
 > (e.g. different types modeling, for instance in high energy physics,
 > etc.).  I'm now really wondering what kind of applications exist in the
 > other physical sciences such as biology and chemistry.  How would clusters
 > be benefical in these areas?  I would greatly appreciate if someone could
 > provide me with a few examples and some insight.
 Curiously enough, Cluster World Magazine devoted an issue quite recently
 to computational chemistry.  Cluster computing is alive and well there,
 especially in areas that overlap in various ways with physics, e.g.
 quantum chemistry and molecular dynamics, as well as structural
 modelling and more.
 Biology, too, has many clusters serving many purposes.  There are
 "biogrid" projects that range from departmental to national in scope;
 see e.g. http://www.ncbiogrid.org/ for North Carolina's biogrid
 project
 home page.  These projects typically focus on e.g. genomics and
 bioinformatics, but there are also clusters that I'm aware of at Duke
 that study e.g. conduction patterns in heart tissue (solving the poisson
 equation in inhomogeneous media in a distributed way), biomolecular
 folding, and a lot of other things in smaller projects more like what
 one would typically find in math or physics or chemistry.
 If you google a bit, see if you can scare up a copy of the relevant CWM,
 and ask around at area universities or ask the contacts at things like
 biogrid or chemstry grid projects, you can doubtless refine you
 knowledge of this as much as you like.  Clusters and their larger
 multidisciplinary variants the grids are firmly established in pretty
 much all the hard sciences and engineering these days, to the point
 where many campuses (like Duke) are experiencing explosive growth in the
 number and type of clusters.
 Duke has its own internal grid project and a center that has recently
 been set up to coordinate and house and permit sharing of clusters
 purchased by individual groups across the sciences, engineering and
 medicine (see www.csem.duke.edu).  This center can barely keep up with
 the growth as groups all over campus are getting twenty nodes here, a
 hundred nodes there.  It coordinates cluster management and facilitates
 computational science work done on grids and ways of managing
 distributed resources -- most of its toplevel staff have graduate
 experience and/or degrees in a variety of sciences and have some decades
 of cluser experience between them.  Many of them are frequent
 contributors to and familiar names on this list.
 This is actually a very exciting time for cluster computing -- it is
 undergoing something of a paradigm shift from the "beowulf" model that
 has somewhat dominated the last eight years back into a model that is
 both older (distributed parallel computing and compute farms of various
 sorts predated beowulf per se by many years) and newer (they never had
 to cope with authentication, security, batch job coordination over a
 wide range of projects with a wide range of resource constraints being
 run on a heterogeneous collection of resources contributed AND OWNED by
 many individuals with their own agendas and usage priorities;-).
 It is amusing to contemplate where this is going.  In ten years will
 there just be "the Grid" as there is now the Internet, where we
 install
 a toplevel application to join our computer(s) to the grid and
 transparently offer up idle cycles to others in exchange for
 transparently picking up their idle cycles in return (all nice and
 secure and sandboxed)?  Will we start to see a Gibsonesque turn, where
 rogue/viral programs released into this grid become a strange form of
 virtual "life"?
 Stay tuned to this channel...
 (Damn, I need to just put these replies straight into my CWM column.
 Kill two birds with one stone, so to speak;-).
 >
 > My other question is in regards to parallel programming.  Are there some
 > free parallel programs out there that one can download to run on a
 > cluster, or are most of the programs run on clusters "homegrown"?
 There are plenty of free parallel programs you can run for fun or
 specific purposes, some commercial parallel programs ditto, and yes,
 there are lots of homegrown ones.  PVM and MPI sites will typically come
 with some of the former or contain links to them, big projects (like
 biogrid stuff) attract some commercial effort although there are also
 frequently GPL tools available as well.  Homebrew abounds mostly because
 a topically focussed physics computation (for example) is almost always
 a one-off -- you code your particular bit of science in competition with
 everybody else.  There are exceptions to this, of course, where groups
 use the same basic tool to look at different things, but it's pretty
 common to write or port your own code.
    rgb
 >
 > Thanks in advance for your help.
 >
 > -Timo Mechler
 >
 > --
 > Timo R. Mechler
 > mechti01=at=luther.edu
 >
 >
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 >
 Robert G. Brown	                       http://www.phy.duke.edu/~rgb/
 Duke University Dept. of Physics, Box 90305
 Durham, N.C. 27708-0305
 Phone: 1-919-660-2567  Fax: 919-660-2525     email:rgb=at=phy.duke.edu
 _______________________________________________
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 To change your subscription (digest mode or unsubscribe) visit http://www.b=
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