The Leading Source for Global News and Information Covering the Ecosystem of High Productivity Computing
From the Editor | Main Blog Index
June 24, 2008
Fresh from ISC'08 and the associated petaflop-mania, I noticed that the latest issue of Wired magazine has a series of articles on the ramifications of petabyte data. The issue is titled "The End of Science," and the main thesis is that these enormous data sets are forcing us to rethink the way traditional science is performed.
While petabyte-sized data may be relatively new to the HPC world, Google, Amazon and eBay have been wrestling with this for some time. Rather than trying to model the data, these companies use heuristic-based methods to generate useful information -- or at least useful enough so that you can sell products or ads around it. The theory is that given enough data, heuristics is the most practical path to the best results.
In the Wired piece titled "The Data Deluge Makes the Scientific Method Obsolete," the author posits that when data reaches petabyte size, it's not just more of the same. With such a quantity of data to from, researchers no longer need to bother with hypotheses to be tested; in fact, it's often not practical to do so. Instead, statistical magic can be applied so that the data itself shapes the solution. For example, Google doesn't "know" why one Web page is better than another; it just exposes the usage patterns. In a nutshell: correlation is in, models are out.
From the article:
At the petabyte scale, information is not a matter of simple three- and four-dimensional taxonomy and order but of dimensionally agnostic statistics. It calls for an entirely different approach, one that requires us to lose the tether of data as something that can be visualized in its totality. It forces us to view data mathematically first and establish a context for it later. For instance, Google conquered the advertising world with nothing more than applied mathematics. It didn't pretend to know anything about the culture and conventions of advertising — it just assumed that better data, with better analytical tools, would win the day. And Google was right.
A practical example in science is the gene sequencing work Craig Venter is doing in marine microbiology. Instead of separating the individual organisms and sequencing them one by one, he employs "shotgun sequencing" and a supercomputer to derive the likely species based on statistical analysis of the gene fragments collected in a given saltwater sample. This approach doesn't produce a definitive list of species, but does yield a tremendous amount of information about all the possible species encountered and the genetic parameters of the ecosystem.
This new computational approach was also reflected in Dan Reed's presentation at the recent TeraGrid '08 conference, which we report on this week. One area he talked about is the way these big data sets are challenging conventional thinking:
Data models, noted Reed, are in rapid flux because of larger and larger data volumes. This is especially pronounced in some fields, such as biomedical research, where large databases are subject to distributed analysis. A big challenge, probably underappreciated, says Reed, is the scale of the data deluge. "We will be running queries on 100,000 servers," said Reed." And research is moving from being hypothesis driven ("I have an idea, let me verify it.") to exploratory ("What correlations can I glean from everyone's data?"). This kind of exploratory analysis will rely on tools for deep data-mining." Massive, multi-disciplinary data, said Reed, is rising rapidly and at unprecedented scale.
These heuristic computational methods are not exactly new. One that's been around awhile is the genetic algorithm -- a technique that mimics biological evolution as a problem-solving strategy. To make it work, you have to be able to define the general shape of the solution, so it's useless if you don't have some idea of what you're looking for. Like Darwinian evolution, a genetic algorithm makes random changes in the candidate solution and lets the "fitness" of the result determine if it's on the right track.
A 2004 article on genetic algorithms and evolutionary computation describes a real-life example:
[A] genetic algorithm developed jointly by engineers from General Electric and Rensselaer Polytechnic Institute produced a high-performance jet engine turbine design that was three times better than a human-designed configuration and 50% better than a configuration designed by an expert system by successfully navigating a solution space containing more than 10,387 possibilities. Conventional methods for designing such turbines are a central part of engineering projects that can take up to five years and cost over $2 billion; the genetic algorithm discovered this solution after two days on a typical engineering desktop workstation [Holland, John. "Genetic algorithms." Scientific American, July 1992, p. 66-72].
I suppose taking the human element out of problem-solving is the logical end to all science becoming computer science. And it certainly is a capitalist-friendly way of doing business. After all, why bother employing dozens of domain experts when you can just buy or rent some software in the cloud? But even if the petabyte age brings an end to theories and models, humans aren't completely expendable. We still get to ask the interesting questions.
Posted by Michael Feldman - June 24 @ 7:41PM
(Digg, Technorati, more)
PGI Accelerator™ Fortran 95/03 and C99 compilers for x64+NVIDIA
Accelerate applications on x64+GPU platforms by adding OpenMP-like compiler directives to existing Fortran and C programs. Available now for Linux, MacOS and Windows. Download a free 15 day trial.
Platform HPC Workgroup Manager
Platform HPC Workgroup Manager integrates all the cluster productivity tools you need to deploy, run and manage your HPC environment.
Michael Feldman is the editor of HPCwire.
More Michael Feldman
Compairson to Core i7-980X by rsingle
HPC? not so much by ewahl
Re: IBM and HPC by truly64
HPC = servers but a lot more by lawries
Multi core deployment becomes a memory game by truly64
Re: Venture Capital Drought? Not So Much. by Ron Van Holst
Re: Podcast: Cray Awarded Defense Deal; SGI Makes Storage Buy; IBM Invents New Algorithm by Nastyanna
Painful Truth by jeffrey.mcallister
SGI = graphics + HPC by johnbarr
HPC = servers but a lot more by truly64
Oracle SPARC != Fujitsu SPARC by Alan M. Feldstein
Sun & HPC != Oracle & HPC by Merblich
a third vendor for lossless low latency 10GbE fabric by lee.fisher@hp.com
Response to GAH by KevinButerbaugh
Response to KevinButerbaugh by GAH
Response to KevinButerbaugh by GAH
Response to GAH by KevinButerbaugh
Response to bdrupp by KevinButerbaugh
Climate Crisis and Exaflops by bdrupp
Climate Crisis and Exaflops by John Hules
Climate Crisis and Exaflops by GAH
Climate Crisis by KevinButerbaugh
IBM "Brain Simulation" article is not properly presented. by Merritt
563 out of 1206 by vvolkov
Little Iron by gadunk
At least it's not "cloud" by KevinButerbaugh
Native QPI Interface? by commike
Mmmmmm by hellcats
New transistorized IC chip scales. by symmecon
Itanium at IDF by Alan M. Feldstein
Communication time by jnapper
"The financial meltdown and computing" by donpellegrino
Human Models by mdgabriel
High-End SPARC Chip for Scientific Applications by Alan M. Feldstein
RapidMind by Mr LolO
Rapidmind by dminor
Longer run times by JohnWest
re: Algo trading Angst by jshore
Results of Testing by in_the_crease
C-DAC announces plans for a petaflop system; IBM researchers are working on vertical integration techniques to extend Moore's Law another 15 years. We recap those stories and more in our weekly wrapup.
Read More...
The Moscow State University supercomputer, Lomonosov, has been selected for a high-performance makeover, with the goal of tripling its processing power to achieve petaflop-level performance in 2010. T-Platforms, who developed and manufactured the supercomputer, is the odds-on favorite to lead the project.
Read More...
Right on schedule, Intel has launched its Xeon 5600 processors, codenamed "Westmere EP." The 5600 represents the 32nm sequel to the Xeon 5500 (Nehalem EP) for dual-socket servers. Intel is touting better performance and energy efficiency, along with new security features, as the big selling points of the new Xeons.
Read More...
Mar 19 | OfficialWire | New super to support intelligence work Down Under. Read more...
Mar 18 | ChannelWeb | Westmere parts already showing up in HPC machines. Read more...
Mar 17 | The Register | But what about the tier ones? Read more...
Mar 17 | Cadalyst Magazine | A new generation of workstations is changing the nature of technical computing. Read more...
Mar 17 | Linux Magazine | Latest iteration of Sun Grid Engine able to tap into Cloud. Read more...
Jan 12 | | In-depth look at vSMP Foundation server virtualization technology, technical implementation, use cases and capabilities. The technical whitepaper provides an architectural overview and details on the three vSMP Foundation products: vSMP Foundation for SMP, vSMP Foundation for Cluster and vSMP Foundation for Cloud.
Jan 18 | | This white paper discusses Gore’s copper cable assemblies, and how they continue to exceed the standards for providing reliable, cost-effective solutions for high-performance computer applications.
Join this online panel discussion for live Q&A with leading industry experts, analysts, and end-users to discuss the latest innovations, best practices, barriers to implementation, and measurable benefits of server virtualization with a particular focus on today's real world solutions.
Learn about scalable fault-tolerant architectures and examples of energy efficient and scalable supercomputing clusters using dual QDR InfiniBand to combine capacity computing with network failover capabilities with the help of programming languages such as MPI and a robust Linux cluster management package.
LIVE@SCO9: The IBM team discusses new innovations in hardware, software and services that help clients better understand their workloads and get insight from their R&D efforts. Technology demonstrations include the soon-to-be-released Power7 HPC processor, the DCS990 system with 2.4 petabytes of storage, the xCAT management tool, secure HPC cloud computing and more. Winners of two HPCwire Readers' and Editors’ Choice Awards! Take the IBM virtual tour at SC09 or more information go online to: http://www-03.ibm.com/systems/deepcomputing/sc09.html