From: Eugene.Leitl@lrz.uni-muenchen.de
Date: Fri Dec 08 2000 - 13:11:56 PST
http://www.sciencemag.org/cgi/content/full/290/5498/1903
Screen Savers of the World Unite!
Michael Shirts and Vijay S. Pande*
Recently, a new computing paradigm has emerged: a worldwide
distributed computing environment consisting of thousands or even
millions of heterogeneous processors, frequently volunteered by
private citizens across the globe (1). This large number of processors
dwarfs even the largest modern supercomputers. In addition to the
scientific possibilities suggested by such enormous computing
resources, the involvement of hundreds of thousands of nonscientists
in research opens the door to new means of science education and
outreach, in which the public becomes an active participant.
A handful of projects have already demonstrated how such large-scale
distributed computing power can be utilized. For example, SETI@home
has totaled over 400,000 years of single-processor CPU time in about 3
years in its search for alien life (2). Similarly, distributed.net has
used the power of this huge computational resource for the brute-force
cracking of DES-56 cryptography codes.
Virtually any other computationally intensive project could be aided
by distributed computing, from the simulation of nuclear reactions or
star clusters to atomic-scale modeling in material science. Perhaps
the most exciting possibility, however, is in the biological realm. In
the last few years, the huge amount of raw scientific data generated
by molecular biology, structural biology, and genomics has outstripped
the analytical capabilities of modern computers. Novel methods,
algorithms, and computational resources are needed to process this
wealth of raw information. For example, we need to compute the
structure, thermodynamics, dynamics, and folding of protein molecules,
the binding ability of drugs, and the causal events in biochemical
pathways. Many of the newest distributed applications have thus
focused on biological systems.
Both SETI@home and distributed.net tackle so-called "embarrassingly
parallel" problems, in which the desired calculation can easily be
divided between many computers. For example, SETI@home looks for alien
life by Fourier-transforming radio telescope data from different parts
of the sky. These chunks can easily be assigned to different computers
to be processed. However, not all problems are so easily broken down
into independent parts ("parallelized"). Just as having 1000
assistants does not necessarily mean that one's work will be done 1000
times faster, the great challenge for distributed computing is the
development of novel algorithms that allow calculations previously
deemed unparallelizable to be performed on hundreds or thousands of
computers with very little communication between the processors.
Even if an algorithm can be parallelized, it may still be poorly
suited for distributed computing. Consider, for example, simulations
of the dynamics of biomolecules at the atomic level. Such simulations
are traditionally limited to the nanosecond time scale. Duan and
Kollman have demonstrated that traditional parallel molecular dynamics
simulations can break the microsecond barrier (3), provided that one
uses many tightly connected processors running on an expensive
supercomputer for many months. This style of calculation requires,
however, that the processors frequently communicate information and is
thus poorly suited for worldwide distributed computing, where computer
communication is thousands of times slower than the interprocessor
communication in today's supercomputers.
Recently, an algorithm has been developed that helps address the
problems of both parallelization and communication by allowing loosely
connected multiple processors to be used for molecular dynamics (4,
5). The Folding@home project (5) has shown that this algorithm can
reach orders of magnitude longer time scales than have previously been
achieved when used for distributed atomistic biomolecular dynamics
simulations. The design of similar algorithms for parallelization will
likely play a major role in adapting other problems in computational
biophysics (such as the design of more effective drugs) and other
fields for distributed computing.
The ability to engage users to run the simulation software is central
to the success of worldwide distributed computing. First, the user
must have some interest in volunteering his or her computer. SETI@home
and distributed.net have had great success in generating excitement
about their projects. Biological and biomedical applications may have
an even greater potential for generating public interest. Some
commercial ventures even plan to expand this resource by paying users
for their excess CPU time (6).
Second, distributed systems must not interfere with the user's
personal use. This is most commonly (and perhaps most elegantly) done
using screen savers (see the figure). The user downloads and installs
the screen saver from the project's Web site. The vast majority of
idle computer cycles will then be used for the project, without
interfering with the user's work. To perform a calculation, the screen
saver downloads some task from the project's server, performs the
required calculation, returns the results to the server, and then
repeats the cycle. To address networking and security issues, many
projects use the same techniques as Web browsers and Web servers,
because these methods of distributing data from client to server are
well developed and secure. The project's server(s) must be carefully
designed to handle the enormous number of clients in distributed
computing.
Merging research and education. The Folding@home screen saver shows a
graphical representation of the protein and its potential energy as it
is folding, making the research more visually accessible to the public
contributing to the project.
There are at least 300 million personal computers on the Internet
(7). Up to 80 to 90% of their CPU power is wasted. If each distributed
computing project involved 500,000 active users, as SETI@home
currently claims, and half of all PCs now connected to the Internet
participated, there would be sufficient capacity for 300 SETI-sized
projects worldwide.
The world's supply of CPU time is very large, growing rapidly, and
essentially untapped. Used to analyze the data generated by recent
genomic and proteomic efforts or conduct other important calculations,
distributed computing could raise biological and other scientific
computation to fundamentally new predictive levels.
References and Notes
1.D. Butler, Nature 402, C67 (1999); Netwatch, Science 289, 503 (2000); Random Samples,
Science 289, 1135 (2000); B. Hayes, Am. Sci. 87, 118 (1998) [American Scientist].
2.J. Kaiser, Science 282, 839 (1998). See also http://setiathome.ssl.berkeley.edu
3.Y. Duan, P. A. Kollman, Science 282, 740 (1998).
4.A. F. Voter, Phys. Rev. B 57, 13985 (1998) [APS].
5.I. Baker et al., in preparation. See also http://foldingathome.stanford.edu
6.D. Cohen, New Sci. 167 (no. 2247), 11 (2000). These ventures could potentially reduce
availability of CPU time for noncommercial projects, although many are scientifically
focused themselves and are operating in conjunction with academic researchers.
7.Number of computers on the internet estimated by using total PCs sold worldwide in the past
3 years (1998-2000), as published by IDC (www.idc.com).
8.The authors acknowledge S. Doniach for useful discussions and thank M. Levitt for a
thorough review of our manuscript. Supported in part by the Fannie and John Hertz
Foundation and the Stanford Graduate Fellowship program.
The authors are in the Department of Chemistry, Stanford University,
Stanford, CA 94305-9450, USA. E-mail: pande@stanford.edu
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