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High Performance Computing Center Advances MSU’s Research Capabilities
March 2, 2006
Study the Sun's weather patterns. Analyze the behavior of the human immunodeficiency virus (HIV). Examine millions and billions of plant genomes in order to understand how plant biology works at the most basic level. MSU researchers are using the new High Performance Computer Center (HPCC) to further these inquiries into basic science – and many more.
Scientists using the HPCC are able to conduct research in hours or days that previously would have required weeks or months. For example:
- Dr. Leo Kempel serves as director of the HPCC; he is also one of the scientists whose research benefits from the facility. He says "I am using the system to understand the fundamental properties of a class of conformal antennas that has not been widely studied in the past. The advantage of using the high performance computing systems here at MSU is that I can calculate the impedance spectrum of each realization of the antenna in less than three hours whereas previously running in serial mode it would take approximately two days of continuous running. Hence, I can experiment in a virtual environment much more efficiently."
- Dr. Robert Stein, professor of Physics/Astronomy, uses MSU's HPCC as well as similar facilities at NASA to study weather patterns on the Sun. Stein is able to analyze solar weather data in a fraction of the time it took to do so previously. Dr. Stein recalls that in the days of the Cray 2 it took about a month of real time to simulate one hour of solar weather. Now he is able to process one hour of solar simulation in little more than an hour of real time.
- Dr. Robert Cukier, professor of Chemistry, uses the HPCC to understand the behavior of multi-drug-resistant (MDR) variants of HIV. He says "We are using computational methods to study the differences between normal and MDR HIV protease. The Molecular Dynamics (MD) method solves Newton's equations on a computer for the motion of all the atoms of the protein. MD is a complete atomistic description. A very small time step is needed to numerically integrate Newton's equations and many millions of steps are required to generate a sufficiently long run to obtain useful information. Consequently, MD is very computer intensive. The HPC Center has permitted us to carry out long runs on normal and MDR HIV protease and test hypothesis as to why some mutants are MDR resistant."
- MSU doctoral candidate and plant biology researcher Omid Paul Zehtab says "We are trying to turn the As, Ts, Gs, and Cs of plant DNA into a clear picture of how the plant actually works. A smaller plant genome can be a few hundred million base pairs, the larger ones have billions. Without the ability to split our data-mining task up among many CPUs we just couldn't do the science."
HPCC director Kempel observes, "The HPC systems at MSU allow researchers to become more efficient and active in their efforts. Their research will bear fruit in the short term (for example in designing more flood-tolerant structures) as well as offering the potential for long-term benefits (for example designing new materials and drugs). By investing in high performance computing, MSU is providing the tools needed by our world-class researchers as they create knowledge and transform lives in the 21st century."
David Gift, Vice-Provost for Libraries, Computing & Technology, says “We are very pleased by the breadth of research that the HPCC is serving and promises to serve, across a broad span of University disciplines. More rapid analysis not only speeds the delivery of analytical results, but also facilitates more complete and precise analysis, deeper explorations, and generally more productive scientific work. And when MSU's research faculty use the best tools, their students also gain experience with the best tools and with the kinds of leading-edge approaches to scholarship and problem-solving those tools enable.”
Officially launched at a ribbon-cutting in August 2005, the HPCC began serving the needs of MSU scientists soon after its first computer arrived in May 2005. The Center offers an SGI Altix 3700 Bx2 shared memory computer with 64 processors, 256 gigabytes of RAM (over 500 times the memory on a typical personal computer) and 6.4 terabytes of fiber-channel attached storage, providing approximately 333 gigaflops (billion floating-point operations per second) of computing power. The HPCC also provides a Western Scientific AMD cluster with 512 (dual-processor) cores, 1 terabyte (1000 gigabytes) of aggregate RAM, Infiniband connective fabric, and 8 TB of fast attached storage. The cluster is estimated to provide 2.4 teraflops of distributed computing power.
ACNS staff member Andy Keen helps administer HPCC computers. He says that since the HPCC’s inception its computers have handled over 50,000 user jobs, representing over 32 years of CPU time. Almost 200 researchers are using the HPCC, representing some 18 MSU departments.
The HPCC is a collaboration of the College of Engineering, College of Natural Science, National Superconducting Cyclotron Laboratory, and Libraries, Computing & Technology, with substantial financial support from the Vice President for Research and Graduate Studies. It supports computationally-intensive research in all fields practiced by MSU faculty University-wide. The Center's Web site provides information regarding its resources and governance, how to become a user, and other topics. See http://www.hpc.msu.edu.
by Richard Wiggins, Academic Computing and Network Services
