HPCwire: TeraGrid '09: How HPC and Therapeutic Drug Design Have Grown Up Together

The Leading Source for Global News and Information Covering the Ecosystem of High Productivity Computing

HPCwire >> Industry >> Academia & Research

July 06, 2009

TeraGrid '09: How HPC and Therapeutic Drug Design Have Grown Up Together

by Michael Schneider, Pittsburgh Supercomputing Center, for TeraGrid & HPCwire

When it comes to a take-home from Tom Cheatham's keynote speech on Thursday morning two weeks ago at the TeraGrid '09 conference in Arlington, Va., the subtitle says it all: "Chronicling the growth of a student to tenured professor in the NSF supercomputing center microcosm."

Cheatham has been involved in biomolecular simulations at the NSF supercomputing centers since the beginning of his career, which as a grad student was in the early years of the supercomputing centers. Nearly 20 years later, Cheatham (as of July 1) is an associate professor of medicinal chemistry and of pharmaceutics and pharmaceutical chemistry in the University of Utah's College of Pharmacy, one of the highest ranked pharmaceutical schools in the country (receiving $23 million a year in funding for pharmaceutical research). In his talk, he acknowledged how his career -- he's an international leader in the art and science of simulating proteins and nucleic acids, particularly as it relates to the development of drugs -- has tracked the evolution of the NSF centers, now TeraGrid, and would not have been possible without it.

Cheatham highlighted how the TeraGrid and its progenitors enabled the field of biomolecular simulation. "In my case," he said, "this started with exposure to education and training workshops at the various centers as a graduate student, successful collaboration with vendors and the centers to improve our codes and methods, exposing and fixing lots of problems, to now my continued extensive use and development of, and strong advocating for, HPC resources."
Tom Cheatham at TeraGrid '09

He briefly sketched the complexities involved in understanding how drugs interact with proteins and nucleic acids, such as RNA, which has been a focus of some of Cheatham's recent work. As a drug molecule associates with its target protein or RNA, it can alter structure, and the goal is to use biomolecular simulations, codes and methods developed over the past 40 years by various groups and centers, to track the atom-to-atom interactions and thereby to help improve understanding of the structural changes.

In his recent work, Cheatham has learned more about RNA and its roles in regulating gene expression and synthesizing of peptides. While there are some drugs that bind to RNA in the ribosome, he notes, there are few that bind to the many other RNAs molecules present, which are a potentially effective target for therapeutics. Cheatham has begun a research effort with potential for treatment of Hepatitis C. This viral infection is the major cause of liver transplants, and Cheatham's work aims at direct therapeutic intervention with the viral RNA.

Cheatham sketched a brief history of biomolecular simulations, from the first protein simulation in 1975 to the present. More powerful resources and software advances have made it possible for simulations to extend over longer (more biologically realistic) time scales -- from nanoseconds to microseconds (first achieved by Cheatham's colleague Peter Kollman at PSC in 1998) and now milliseconds.

Inevitably, however, longer simulations have revealed flaws that weren't apparent in shorter periods. "I'm known in our field as the guy who breaks things," said Cheatham. "The longer we run, the more problems we find, and without pushing the simulations, we wouldn't find the problems." These breakdowns in methods lead to back-to-the-drawing-board efforts -- often involving improvement to the force-fields that describe the atom-to-atom interactions -- and result in new, better simulations and deeper understanding.

Cheatham also reinforced themes from other TeraGrid '09 sessions. One of them, from a Wednesday (June 24) session on federal agencies, is the disproportion between the reliance of biomolecular simulation on TeraGrid resources and NIH support for HPC. "If we didn't have TeraGrid," said Cheatham, "my field would stagnate, and perhaps die." Cheatham advocated for collaboration among federal agencies to support HPC.

Cheatham also fortified the message from Ed Seidel, director of the NSF Office of Cyberinfrastructure, Wednesday's keynote speaker (June 24), about the need for HPC education at the undergrad and grad student level. New grad students in his research group, Cheatham said, have little if any HPC experience and training. "Most students who come into my lab don't know Unix." As a result, they experience a steep learning curve that discourages them from using TeraGrid. Cheatham often sends these students to TeraGrid tutorials, and stressed the need for more of such training resources.

The petascale era presents major challenges for biomolecular simulations, says Cheatham. The programs scale well enough up to 256 processors, but getting to 10,000 processors, he says, is "going to be really, really hard." An approach that to some extent compensates is ensemble simulations -- running many smaller, parallel simulations at the same time. While gaining efficiency in the use of hardware, ensemble runs create serious challenges in management of workflow and data.

In raising concerns about the deluge of data resulting from petascale computations, Cheatham echoed one of the prevalent themes of the TeraGrid '09 gathering. Whereas previously simulations on the nanosecond scale, he said, took months to years, this now happens in hours to days, which presents daunting barriers in data manipulation, analysis and interpretation. "We now run up to 1,000 processors. With storing of data and analyzing it locally, the data is too large, takes too long to transfer, and the analysis has become rate limiting."

One solution, he offered, is to create ways to interact with the simulations -- to "steer" simulations and examine data on the fly. "How can we find hidden correlations in the data?" asked Cheatham. "How can we find things we do not already know?" The goal, he emphasized, is to do less computational science and accomplish more science.

Article Tools

Share Options

(Digg, Technorati, more)

Subscribe

Subscribe to HPCwire

Discussion

There are 0 discussion items posted.

Join the Discussion

You must be a registered user in order to comment on HPCwire stories.

Members enjoy:

	Access to Special Content, including Podcasts, Webcasts, and Whitepapers and more!
	Ability to take an active role in the discussions that are shaping the HPC technology discipline!
	Special offers available only to HPCwire members!

Become a Registered User Today!

Registered Users Log in Here to Comment

Email Address:	Password (case sensitive)

Remember me	Forgot Password?

RSS Feeds

Feeds by Topic

Feeds by Industry

Feeds by Content Type

Feature Articles

The Week in Review

TACC's Ranger supercomputer celebrates its second year of enabling important research; Microsoft partners with NSF to bring cloud services to researchers; and NSF submits its fiscal year 2011 budget request. We recap those stories and more in our weekly wrapup.
Read More...

NASA Looks to Move Science Apps Into the Cloud

It seems only natural that the US space agency would be casting its eyes toward the clouds. Sure enough, NASA is now looking to cloud computing to optimize the operation of the agency's IT infrastructure for some of its science codes. Like many commercial businesses and government organizations, NASA is being asked to do more computing with fewer datacenter resources.
Read More...

Thoughts, Observations, Beliefs & Opinions About the NSF Supercomputer Centers

There is no such thing as an NSF (Supercomputer) Center and there never has been. There should be. What there are, in the words of Ed Hayes, then comptroller of NSF, are "NSF ASSISTED Supercomputer Centers." This is a double edged sword.
Read More...

Read more HPCwire features...

Top Headlines

IBM Releases Energy Efficient Power7 System

Feb 09 | eWeek Europe | Company says new high-end servers will deliver "intelligent performance." Read more...

Inductive Coupling Packs Flash Drive in a Chip

Feb 09 | EE Times | Wireless technology promises energy-efficient chip-to-chip communication. Read more...

IBM, Microsoft Help Create Montana Supercomputer

Feb 08 | eWeek | A new kind of Rocky Mountain high. Read more...

AMD Aims for GPUs in Mainstream Servers Starting 2012

Feb 08 | Computerworld | Chip maker hopes to bring CPU-GPU processors to servers in two years. Read more...

Graphene Transistors That Work at Blistering Speeds

Feb 05 | Technology Review | IBM has created graphene transistors that leave silicon ones in the dust. Read more...

Read more headlines...

Featured Whitepapers

Virtualization for Aggregation And The vSMP Architecture™

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.

Copper Cable Technologies for High Performance Computing

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.

Appro Assists LLNL with Cluster Designed for Extreme Scale Visualization

Jan 11 | | LLNL is home to some of the fastest computers in the world. In 2012, LLNL expects to have the Sequoia supercomputing cluster operational with a projected performance of over 20 PFLOP/s. These systems will focus on strengthening the foundations of predictive simulation through running large suites of complex simulations and then comparing model predictions with experimental data. To visualize this project’s large amount of data, LLNL requested an Appro Supercomputing Cluster specifically designed to support interactive data analysis.

View the White Paper Library

Multimedia

Webcast: Virtualized Data Center Roundtable

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.

Webcast: Watch SC09 Birds of a Feather Video: Scalable Fault-Tolerant HPC Supercomputers

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.

Webcast: High Performance Computing for a Smarter Planet

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