ASCR Monthly Computing News Report - April 2011

In this issue...


Scientists Produce Promising Drug Candidates to Halt Parkinson's Disease
By leveraging the high-end power of the Blue Gene/P supercomputer at the Argonne Leadership Computing Facility, a research team from the University of California at San Diego (UCSD) is performing computational simulations of aggregation of the alpha-synuclein protein responsible for Parkinson's disease. These simulations and further modeling helped to develop drug candidates with high potential for treating the disease by stopping or preventing pore formation. Each theoretical design was tested in the laboratory and led to further design of active compounds. Patents for these drug candidates are pending. The team continues to identify additional compounds for drugs that are high performers in inhibiting protein aggregation and confirm this quality through biomedical experimentation.
Contact: Igor Tsigelny (itsigeln@ucsd.edu)
NERSC Helps Solve LED Efficiency Puzzle
Despite being cool, ultra-efficient and long lasting, the light-emitting diode (LED) has yet to conquer the general lighting market due to a problem called "efficiency droop." New findings from simulations carried out at the National Energy Research Scientific Computer Center (NERSC) have unearthed droop's elusive cause, researchers say, paving the way for wider LED use. Published online April 19 in Applied Physics Letters, the research relies on detailed, quantum-mechanical simulations of the inner workings of nitride-based LEDs to finger the culprit.
At low power, the nitride-based LEDs used to generate white light are astoundingly efficient; but pump up the current to room-illuminating levels and efficiency takes a nosedive. "If you use more electricity, you do get more light, but the efficiency isn't as good, and that adds to the higher cost of LED-based lighting," says Emmanouil Kioupakis, a researcher at the University of California Santa Barbara (UCSB) and lead author of the study. The new study doesn't solve the problem of droop, but it does set researchers and engineers on the right path to do so, says Chris Van de Walle, head of the UCSB research group that carried out the work.
BNL Team Simulates Fuel Pellet Ablation for ITER Fueling
Roman Samulyak of Stony Brook University and the Computational Science Center at Brookhaven National Laboratory (BNL), Tianshi Lu of Witchita State University, and Paul Parks of General Atomics have developed novel mathematical models, numerical algorithms, and computational software for the numerical simulation of free surface magnetohydrodynamic (MHD) flows of conducting liquids and flows of partially ionized plasmas in the presence of phase transitions and high power particle beams. The research is an important part of ITER, a joint international research and development project that aims to demonstrate the scientific and technical feasibility of fusion power. In order to generate fusion energy, ITER must be constantly fueled by the injection of small, frozen deuterium/tritium pellets.
The software was applied for the numerical simulation of the pellet ablation for tokamak fueling. In their recent work, the pellet ablation rate and lifetime in magnetic fields were systematically studied for the first time and compared with theory and existing experimental databases. Simulations revealed several new features of the pellet ablation. Simulations are important because they contribute to the optimization of the ITER fueling efficiency through the study of the detailed physics of the pellet ablation in magnetic fields and the pellet ablation rate. Simulations revealed new features of the pellet ablations, suggesting ways to increase the fueling efficiency. The developed software is also applicable to the study of plasma disruption mitigation in ITER through the injection of pellets and liquid jets.
Contact: Bill Cannon,  william.cannon@pnl.gov
LBNL's David Bailey Helps Supercomputer Crack "Impossible" Calculation
The BlueGene/P supercomputer system, used for IBM's benchmarking tests and quality control, has been used to conquer a calculation thought to be unachievable. The result is the paper “The Computation of Previously Inaccessible Digits of π2 and Catalan’s Constant” by David H. Bailey, Chief Technologist in the Computational Research Division at Lawrence Berkeley National Laboratory (LBNL); Jonathan M. Borwein of Newcastle University in Australia; and Andrew Mattingly and Glenn Wightwick of IBM Australia. Bailey said the project came about when IBM Australia was looking to do something related to "Pi Day" (March 14) on a new IBM BlueGene/P computer system. Bailey's colleague Jon Borwein suggested that IBM use one of the formulas (originally discovered in part by Bailey) that permit one to calculate digits of pi squared, beginning at some huge starting point (this has already been done for pi itself, also using formulas discovered in part by Bailey). So beginning with a computer program originally written by Bailey, IBM researchers developed highly efficient parallel code to compute digits of both pi squared and also Catalan's constant, another important number that arises in mathematics and mathematical physics.
In the end, the IBM researchers did three calculations - pi squared in binary (beginning at the 60 trillionth binary digit), pi squared in base-3 (beginning at the 60 trillionth base-3 digit), and Catalan's constant in binary (beginning at the 120 trillionth binary digit). "What is interesting in these computations is that until just a few years ago, it was widely believed that such mathematical objects were forever beyond the reach of human reasoning or machine computation," Bailey said. "Once again we see the utter futility in placing limits on human ingenuity and technology."
Record-Setting Antimatter Particle Detected with NERSC Help
Eighteen examples of the heaviest antiparticle ever found, the nucleus of antihelium-4, have been made in the STAR experiment at the Relativistic Heavy Ion Collider at Brookhaven National Laboratory. The finding wasn't unexpected, but it is a milestone for scientists exploring a fundamental puzzle of physics: Why is there any matter at all? The next possible heavyweight antimatter particle will be thousands of times harder to detect, so this record is likely to stand for years to come.
"The STAR experiment is uniquely capable of finding antihelium 4," says the STAR experiment's spokesperson, Nu Xu, of the Nuclear Science Division (NSD) at Lawrence Berkeley National Laboratory (Berkeley Lab). "STAR already holds the record for massive antiparticles, last year having identified the anti-hypertriton, which contains three constituent antiparticles. With four antinucleons, antihelium-4 is produced at a rate a thousand times lower yet. To identify the 18 examples required sifting through the debris of a billion gold-gold collisions."
That sifting is done on the PDSF high-energy physics computing cluster hosted at the National Energy Research Scientific Computing Center (NERSC) managed by Berkeley Lab. "STAR uses PDSF extensively for analysis and simulation essential to discoveries such as the anti-alpha [antihelium-4] that require good understanding of the detector response," says Hank Crawford, a STAR collaborator at Berkeley Lab's NSD and the University of California Berkeley's Space Sciences Laboratory.
Researchers Use Jaguar to Explore Germanium-72 Isotope
Physicists from ORNL, the University of Tennessee, and Germany's GSI in Darmstadt recently used ORNL's Jaguar supercomputer to explore the pair bonding of neutrons in one uncommon isotope - germanium-72. In doing so they discovered that changes in temperature and rotation take the nucleus through at least two physical phases. Their work, which offers the first realistic description of this kind of phase transition in an atomic nucleus, was featured in the November 19, 2010, edition of Physical Review Letters.
Germanium-72 has 32 protons (like all germanium isotopes) and 40 neutrons. Those 40 neutrons pair off strongly when the nucleus is cold and calm, but pairing weakens as you increase the temperature or rotation. What the team discovered, however, was that the relationship is not straightforward. When rotation is high, the pairing weakens as temperature rises, spikes back up at one small range of temperatures, and then weakens as temperature continues to rise. That spike indicates the transition between phases.
"So what is the physical impact of learning that germanium has a phase change? Well, phase changes are certainly exploited in many engineering practices," said team member Hai Ah Nam of ORNL. "For now, these results get us one step closer to understanding the atomic nucleus."


BNL's Mann, Stony Brook's Shamash to lead NY Center for Computational Sciences
The New York Center for Computational Sciences (NYCCS) has announced that Reinhold Mann, Brookhaven National Laboratory's Associate Director for Environment and Life Sciences, and Yacov Shamash, Stony Brook University's Vice President for Economic Development and Dean of the College of Engineering and Applied Sciences, have been named co-directors of the Center.
NYCCS is a joint venture of Stony Brook University and BNL. The Center was formed in 2007 to foster high performance massively parallel computing on the whole range of science and technology topics.
Berkeley Lab’s Kathy Yelick Gives Distinguished Lecture at USC
Kathy Yelick, LBNL's Associate Laboratory Director for Computing Sciences and Director of the NERSC Division, discussed "Exascale Computing: More and Moore?" on April 6 as part of the Distinguished Lecture Series at the University of Southern California Department of Electrical Engineering. The goal of the lecture series "is to bring internationally recognized researchers known for their contributions in research areas of relevance to USC and the research community at large. DLS speakers are selected for their superior caliber in cutting edge research as well as their ability to convey the complexities of their research to a general audience."


NERSC Honored for Innovative Use of Globus Online
At GlobusWORLD 2011, held April 11-13 at Argonne National Laboratory, NERSC was awarded "Most Innovative Use of Globus Online" for using it to archive data onto HPSS. What makes the NERSC application unique is that Globus Online was originally developed as a reliable and secure tool for moving data between remote sites, but NERSC staff also found that it could be used to easily move data between computing systems and the center's HPSS data archive.
Archiving data has traditionally involved running command-line tools, but several NERSC users have requested a graphical user interface (GUI) to move data between HPSS and compute systems. A GUI makes it easier to back up or restore relevant data. Using Globus Online, NERSC demonstrated a "drag and drop archiving" capability which is currently being tested and will be available to the NERSC user community shortly.


LBNL and ORNL Organize Workshop for Independent Software Developers and Industry Partners
Approximately 60 software experts gathered in Chicago on March 31 for the first Workshop for Independent Software Developers and Industry Partners, sponsored by the Department of Energy's (DOE) Advanced Scientific Computing Research office. Jointly organized by Lawrence Berkeley and Oak Ridge national laboratories, this workshop introduced independent software vendors (ISVs) and industrial software developers to software resources that can help ease the private sector's transition to multicore computer systems. These tools, libraries and applications were developed through DOE's Scientific Discovery through Advanced Computing (SciDAC) program to enable DOE critical codes to run in a multicore environment.
The cost and difficulty of scalably parallelizing legacy codes (codes written for non-operational or outdated operating systems or computer technologies) often are prohibitive to independent software vendors, particularly if they are small businesses. They also hamper many firms that, for proprietary and competitive reasons, maintain their own code in addition to using commercial options. The problem is becoming acute as desktop workstations and small clusters are rapidly being designed and built using multicore processors.
The one-day workshop started a dialogue on cost-effectively addressing these obstacles. It gave participants an overview of the SciDAC program and over 60 SciDAC-developed software packages, and outlined the process to obtain them, often at no cost. In addition, DOE explained its role in providing research grants through the U.S. Small Business Administration's Small Business Innovation and Research (SBIR) grant program. This program ensures that the nation's small, high-tech, innovative businesses are a significant part of the federal government's research and development efforts.
ALCF, NERSC and OLCF Participate in NUFO Science Exhibition
On April 7, the National User Facilities Organization (NUFO) hosted a science exhibition on Capitol Hill for members of Congress, their staff and the public. The exhibit highlighted over 30 national user facilities in areas as diverse as nuclear physics, astronomy, and supercomputing. Among the participating facilities were the Argonne Leadership Computing Facility, the National Energy Research Scientific Computing Center and the Oak Ridge Leadership Computing Facility. Ten members of Congress visited the exhibition, as well as congregational staff, NSF and DOE representatives, and the general public. The exhibition coincided with the Sixteenth Annual Science-Engineering-Technology Congressional Visits Day, and many of the participants stopped by the NUFO exhibition to learn more about user facilities and their critical role in the scientific community.

Contact: Vitali Morozov,  morozov@anl.gov