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Berkeley Lab Team Wins Best Paper at CloudCom

Can cloud computing serve as a cost-efficient model for scientific computing?

December 10, 2010

Media Contact: Linda Vu, lvu@lbl.gov, 510-495-2402

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Simulation of a lean hydrogen-air mixture burning in a low-swirl injector. The colors indicate the presence of nitric oxide emissions near the highly wrinkled flame, while the gray structures at the flame base show the turbulent vorticity generated near the breakdown of the swirling flow from the injector.

Cloud computing has proven to be a cost-efficient model for many commercial web applications, but will it work for scientific computing? Not unless the cloud is optimized for it, writes a team from the Lawrence Berkeley National Laboratory.

supernove simulation

Type 1a supernova simulation developed using the CASTRO code. Image by Haitao Ma of UC Santa Cruz.

After running a series of benchmarks designed to represent a typical midrange scientific workload—applications that use less than 1,000 cores—on Amazon's EC2 system, the researchers found that the EC2's interconnect severely limits performance and causes significant variability. Overall, the cloud ran six times slower than a typical mid-range Linux cluster, and 20 times slower than a modern high performance computing system.

The team's paper, "Performance Analysis of High Performance Computing Applications on the Amazon Web Services Cloud," was honored with the Best Paper Award at the IEEE's International Conference on Cloud Computing Technology and Science (CloudCom 2010) held Nov. 30-Dec.1 in Bloomington, Ind.

"We saw that the communication pattern of the application can impact performance, Applications like PARATEC with significant global communication perform relatively worse than those with less global communication," says Keith Jackson, a computer scientist in the Berkeley Lab’s Computational Research Division (CRD) and lead author of the paper.

ZnO nanorods could serve as the foundation of future electronics. But scientists must first understand their many unique qualities. Scientists can do this by running the linear scaling three dimensional fragment method (LS3DF) on a supercomputer. This image is a ZnO nanorod calculated with LS3DF. With this computation, scientists found the structure's large surface dipole momentis, a property that significantly changes the its internal electronic structure.

He also notes that the EC2 cloud performance varied significantly for scientific applications because of the shared nature of the virtualized environment, the network, and differences in the underlying non-virtualized hardware.

The benchmarks and performance monitoring software used in this research were adapted from the large-scale codes used in the National Energy Research Scientific Computing Center's (NERSC) procurement process. NERSC is located at the Berkeley Lab and serves approximately 4,000 Department of Energy (DOE) supported researchers annually in disciplines ranging from cosmology and climate to chemistry and nanoscience.In this study, the researchers essentially cut these benchmarks down to midrange size before running them on the Amazon cloud.

"This set of applications was carefully selected to cover both diversity of science areas and the diversity of algorithms," said John Shalf, who leads NERSC’s Advanced Technologies Group."They provide us with a much more accurate view of the true usefulness of a computing system than ‘peak flops’ measured under ideal computing conditions."

The benchmark modifications and performance analysis in this research were done in collaboration with the DOE’s Magellan project, funded by the American Recovery and Reinvestment Act."The purpose of the Magellan Project is to understand how cloud computing may be used to address the computing needs for the Department of Energy's Office of Science.  Understanding how our applications run in these environments is a critical piece of the equation," says Shane Canon, who leads the Technology Integration Group at NERSC.

In addition to Canon, Jackson and Shalf, Berkeley Lab's Lavanya Ramakrishnan, Krishna Muriki, Shreyas Cholia, Harvey Wasserman and Nicholas Wright are also authors on the paper.

"This was a real collaborative effort between researchers in Berkeley Lab's CRD, Information Technologies and NERSC divisions, with generous support from colleagues at UC Berkeley—it is a great honor to be recognized by our global peers with a Best Paper Award," adds Jackson.

The award is the second such honor for Jackson and Ramakrishnan this year. Along with Berkeley Lab colleagues Karl Runge of the Physics Division and Rollin Thomas of the Computational Cosmology Center, they won the Best Paper Award at the Association for Computing Machinery’s ScienceCloud 2010 workshop for "Seeking Supernovae in the Clouds: A Performance Study."

The Department of Energy's Office of Advanced Scientific Computing Research and the National Science Foundation funded the work; and CITRIS at the University of California, Berkeley donated Amazon EC2 time.

Read the paper here.


About Computing Sciences at Berkeley Lab

The Lawrence Berkeley National Laboratory (Berkeley Lab) Computing Sciences organization provides the computing and networking resources and expertise critical to advancing the Department of Energy's research missions: developing new energy sources, improving energy efficiency, developing new materials and increasing our understanding of ourselves, our world and our universe.

ESnet, the Energy Sciences Network, provides the high-bandwidth, reliable connections that link scientists at 40 DOE research sites to each other and to experimental facilities and supercomputing centers around the country. The National Energy Research Scientific Computing Center (NERSC) powers the discoveries of 6,000 scientists at national laboratories and universities, including those at Berkeley Lab's Computational Research Division (CRD). CRD conducts research and development in mathematical modeling and simulation, algorithm design, data storage, management and analysis, computer system architecture and high-performance software implementation. NERSC and ESnet are DOE Office of Science User Facilities.

Lawrence Berkeley National Laboratory addresses the world's most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab's scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the DOE’s Office of Science.

DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.