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DOE Allocates Massive Supercomputer Resources to Drive Advances in Combustion, Astrophysics and Protein Structure Research

December 22, 2004

Media Contacts: Jeff Sherwood, 202/586-5806, or Jon Bashor, 510/486-5849

WASHINGTON, DC – Secretary of Energy Spencer Abraham announced today that 6.5 million hours of supercomputing time have been awarded to three scientific research projects aimed at increasing our understanding of ways to reduce pollution, gaining greater insight into how stars and solar systems form, and advancing our knowledge about how proteins express genetic information.

“As one of the nation’s leading agencies for advancing scientific research, the Energy Department is proud to be able to award these major allocations for studying complex scientific problems that can transform our energy future and boost scientific research,” Secretary Abraham said. “The quantity and quality of proposals for this year’s INCITE program clearly shows the need for increased supercomputing resources to address issues that affect all of us.”

The researchers will use their awards to compute on the IBM supercomputer at the Department of Energy’s (DOE) National Energy Research Scientific Computing (NERSC) Center in Berkeley, Calif. NERSC is the DOE Office of Science’s flagship facility for unclassified supercomputing. The three awards amount to 10 percent of NERSC’s annual computing resources.

The awards are made under the second year of the competitive program, Innovative and Novel Computational Impact on Theory and Experiment (INCITE), announced July 2003 by Secretary Abraham. The program’s goal is to select a small number of computationally intensive, large-scale research projects that can make high-impact scientific advances through the use of a substantial allocation of computer time and data storage at the NERSC Center. The INCITE program specifically encourages proposals from universities and other research institutions.

Two of the projects received two million processor-hours, while the third was awarded 2.5 million processor-hours. Running a calculation on a single-processor PC for two million hours would take about 228 years. Running the same job on 2,000 processors of NERSC’s IBM supercomputer would take just over 41 days. Scaling the job to run on more processors not only is faster, but also allows scientists to study more complex problems.

All three INCITE projects were also awarded significant amounts of data storage at NERSC. Additionally, NERSC’s User Services Group will provide specialized technical support to help the researchers make the most efficient use of their computing resources.

Descriptions of the three projects selected follow.

Chemical Sciences

“Direct Numerical Simulation of Turbulent Non-Premixed Combustion – Fundamental Insights towards Predictive Modeling,” by Jacqueline Chen and Evatt Hawkes of Sandia National Laboratories in Livermore, Calif. This project was awarded 2.5 million processor-hours. The researchers will perform detailed three-dimensional combustion simulations of flames in which fuel and oxygen are not premixed. By better understanding the details of such flames, the researchers hope to gain insight into reducing pollutants and increasing efficiency in combustion devices. This research could have applications in such areas as jet aircraft engines, where fuel and oxidizers are not premixed for safety reasons, and in direct-injection internal combustion engines. These simulations would be the first-ever 3D direct numerical simulations with detailed chemistry of a fully developed turbulent, non-premixed flame.

Under certain conditions, this type of combustion can be extinguished, and this project will also try to gain a better understanding of this problem, as well as re-ignition of extinguished flames.

“We are thrilled at the unique opportunity that the INCITE award provides us,” Chen said. “This vast award will enable us to make significant contributions to the challenging problem of understanding and modeling the interactions of turbulence and finite-rate chemical effects in non-premixed combustion. Ultimately, our plan is to share the resulting data with the turbulent combustion modeling community at large.”


“Magneto-Rotational Instability and Turbulent Angular Momentum Transport,” by Fausto Cattaneo, University of Chicago. This project was awarded 2 million processor-hours and will study the forces that help newly born stars and black holes increase in size. In space, gases and other matter often form swirling disks around attracting central objects such as newly formed stars. The presence of magnetic fields can cause the disks to become unstable and develop turbulence, thereby causing the disk material to fall onto the central object. This project will carry out large-scale simulations to test theories on how turbulence can develop in such disks.

In recent years, laboratory experiments have been developed to test many aspects of this magnetically caused instability, but on a much smaller scale. The INCITE researchers plan to collaborate with the experimentalists in the field and to develop simulations that can extend the lab experiments by several orders of magnitude.

“What we are hoping to achieve is a simulation that matches the experimental work being done at Princeton,” Cattaneo said. “If you can do the research both computationally and experimentally, you are much better off than just using one approach. With these INCITE resources, we should be able to do a very good job on the simulations.”

Life Sciences

“Molecular Dynameomics” by Valerie Daggett of the University of Washington was awarded 2 million processor-hours. The project will combine molecular dynamics and proteomics to create an extensive repository of the molecular dynamics structures for protein folds, including the unfolding pathways. According to Daggett, there are approximately 1,130 known, non-redundant protein folds, of which her group has simulated about 30. She plans to use the information from these simulations to improve algorithms for predicting protein structure.

“Structure prediction remains one of the elusive goals of protein chemistry,” Daggett wrote in her INCITE proposal. “It is necessary to successfully predict native states of proteins, in order to translate the current deluge of genomic information into a form appropriate for better functional identification of proteins and drug design.”

After hearing that her proposal was one of three to receive an INCITE allocation, Daggett said, “We are excited about the massive resources we will have access to now. Our project will run literally hundreds and hundreds of simulations, each a little different, so we will be running a lot of smaller jobs all at once, using up to 1,000 processors at a time.”

Under the first year of the INCITE program, three research groups achieved some of the most extensive simulations ever as they modeled exploding stars, investigated turbulent flows and modeled the chemistry of photosynthesis.

Of the 23 proposals submitted to the 2005 INCITE program:

  • A total of 28,422,000 processor-hours were requested
  • 65 percent of the proposals were from U.S. universities
  • Projects covered 11 different scientific disciplines
  • 48 percent of the projects were supported by research agencies other than DOE.

“This level of pent-up demand for dedicated time on supercomputers highlights the fact computational science is playing an increasingly important role in advancing scientific and technical research at national laboratories and universities,” Abraham said. “While much of the talk about supercomputers often focuses on speed, DOE is a leader in helping turn teraflops into knowledge, and INCITE is a key component of that effort.”

DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the nation and ensures U.S. world leadership across a broad range of scientific disciplines. For more information about the Office of Science, go to

About NERSC and Berkeley Lab
The National Energy Research Scientific Computing Center (NERSC) is a U.S. Department of Energy Office of Science User Facility that serves as the primary high-performance computing center for scientific research sponsored by the Office of Science. Located at Lawrence Berkeley National Laboratory, the NERSC Center serves more than 7,000 scientists at national laboratories and universities researching a wide range of problems in combustion, climate modeling, fusion energy, materials science, physics, chemistry, computational biology, and other disciplines. Berkeley Lab is a DOE national laboratory located in Berkeley, California. It conducts unclassified scientific research and is managed by the University of California for the U.S. Department of Energy. »Learn more about computing sciences at Berkeley Lab.