Rendering of a rapidly spinning, gravitational-wave emitting newborn neutron star. Simulation: Ott et al. 2007 Rendering: Ralf Kaehler ZIB/AEI/KIPAC 2007

This month CACR has installed and configured a new cluster in the Powell-Booth Laboratory for Computational Science. This system is specifically configured to meet the applications needs of Caltech’s Theoretical AstroPhysics Including Relativity (TAPIR) group in the Physics, Mathematics, and Astronomy Division.

The MRI2 cluster is funded by an NSF MRI-R2 award with matching funds from the Sherman Fairchild Foundation.The configuration, integrated by Hewlett-Packard and CACR’s operations team, consists of 1536 Intel X5650 compute cores in 128 dual Westmere hex-core nodes equipped with a total of ~3 TB of memory, connected via QDR InfiniBand (IB). It includes 100 TB of high-performance, high-reliability disk space access via IB through a Panasas rack.

The research project using the new cluster, Simulating eXtreme Spacetimes: Facilitating LIGO and Enabling Multi-Messenger Astronomy, is led by Professor Christian Ott. The co-Investigators on the MRI award are Dr. Mark Scheel of TAPIR and CACR’s director, Dr. Mark Stalzer. The research will explore the dynamics of spacetime curvature, matter, and radiation at high energies and densities. Central project aspects are the simulation of black hole binary coalescence, neutron-star — black hole inspiral and merger, and the collapse of massive stars leading to core-collapse supernovae or gamma-ray bursts. Key results will be the prediction of gravitational waveforms from these phenomena to enable LIGO gravitational wave searches and to facilitate the extraction of (astro-)physics from observed signals.

The MRI2 cluster is named Zwicky, in honor of Caltech Astrophysics Professor Fritz Zwicky (1898-1974), who discovered supernovae and who was the first to explain how supernovae can be powered by the collapse of a massive star into a neutron star. Zwicky also discovered the first evidence for dark matter in our universe, proposed to use supernovae as standard candles to measure distances in the universe, and suggested that galaxy clusters could act as gravitational lenses.

Visit us at Booth 2135!

At the 2009 Supercomputing (SC) Conference being held in Portland, Oregon November 14-20, CACR will be highlighting our research in computational biology, computing and networking for high-energy physics, data analysis for neutron scattering experiments, hypervelocity impact simulations, and time-domain astronomy. The SC Conference is the premier international conference for high performance computing (HPC), networking, storage and analysis.

Among the demonstrations at the CACR exhibit will be the Caltech entry in SC’s Bandwidth Challenge. The Bandwidth Challenge is an annual competition for leading-edge network applications developed by teams of researchers from around the globe. The Caltech entry for this year’s challenge is entitled Moving towards Terabit/sec Scientific Dataset Transfers: the LHC Challenge. This entry will demonstrate Storage to Storage physics dataset transfers of up to 100 Gbps sustained in one direction, and well above 100 Gbps in total bidirectionally, using a total of fifteen 10Gbps drops at the Caltech Booth.

Caltech’s PSAAP center will be represented in the NNSA exhibit as one of five centers of excellence focusing on predictive science. A talk entitled, “UQ Pipeline Ballistic Impact Simulations – Methods and Experiences”, will be given by Sharon Brunett in the NNSA exhibit (Booth 735) on Tuesday, November 17 at 5:15PM.

Enabling Computational Plant Development: From Confocal Images to Finite Element Simulations
In Computational Methods in Image Analysis, 10th US National Congress of Computational Mechanics, Columbus, Ohio, USA, July 16 – 19 2009
Alexandre Cunha

Computation for Chip-seq and RNA-seq studies
Nature Methods, to appear.
Shirley Pepke, Barbara Wold, and Ali Mortazavi

Whole-volume integrated gyrokinetic simulation of plasma turbulence in realistic diverted-tokamak geometry
SciDAC 2009, Journal of Physics: Conference Series. J Phys: Conf Ser 180 (2009) 012057.
C S Chang, S Ku, P Diamond, M Adams, R Barreto, Y Chen, J Cummings, E D’Azevedo, G Dif-Pradalier, S Ethier, L Greengard, T S Hahm, F Hinton, D Keyes, S Klasky, Z Lin, J Lofstead, G Park, S Parker, N Podhorszki, K Schwan, A Shoshani, D Silver, M Wolf, P Worley, H Weitzner, E Yoon and D Zorin

Engineering Computational Science and Engineering
Presentation/Lecture (given at Lousiana State University, Caltech, and the Institute for Defense Analysis, MD)
Mark Stalzer

First results from the Catalina Real-time Transient Survey
2009, ApJ, in press (arXiv:0809.1394)
Drake A.J., Djorgovski S.G., Mahabal A., Beshore E., Larson S., Graham M.J., Williams R., Christensen R., Catelan M., Boattini A., Gibbs A., Hill R., Kowalski R.

Many thanks to Chip, Sharon, Michael, Mark, and Santiago for their many years of service to the institute and to CACR!

• Charles “Chip” Chapman (30 years)
• Sharon Brunett (20 years)
• Michael Aivazis (10 years)
• Mark Bartelt (10 years)
  
• Santiago Lombeyda (10 years)

Chip Chapman has been employed at Caltech since 1976. After starting in the physics stockroom and lecture hall in East Bridge, he went on to build several microcomputers from scratch with Prof. Ricardo Gomez for data acquisition and analysis in the physics sophomore lab. The project ended as IBM introduced the personal computer. In 1981 Chip worked in high energy physics with Prof. Geoffrey Fox, supporting the first campus network and DEC VAX computers. Later, he managed the Educational Computing Project, delivering over $5M worth of IBM PCs to the campus. In 1990 Chip helped form the Caltech Concurrent Supercomputing Facility, which later transformed into today’s Center for Advanced Computing Research. He held the position of technical supervisor during the era when the world’s fastest supercomputer was running at Caltech. Chip had a central role as liaison to the architect, contractors, and physical plant in the renovation of the Powell-Booth Laboratory for Computational Science, where he presently serves as facilities manager. He was also a main contributor to the high performance computing (HPC) task force report that is helping to define the future of HPC on campus. Chip has worked with students and scientists on many projects and research programs including the CASA Gigabit Testbed, the Scalable I/O Initiative, the Beowulf Project, and Caltech’s Center for Simulation of Dynamic Response of Materials.

Sharon Brunett came to Caltech in 1989 as a Computing Analyst at the Caltech Concurrent Supercomputing Facility (CCSF). CCSF later transformed into today’s Center for Advanced Computing Research (CACR), where Sharon is currently a senior computational scientist and manager of the CACR operations group. She determines appropriate hardware and software solutions to meet CACR’s resource needs, and serves as a liaison to research groups all over campus, including projects in astronomy, biology, high energy physics, materials science, and geophysics. Sharon played a major role in Caltech’s Center for Simulation of Dynamic Response of Materials, which provided significant funding to Caltech and CACR for ten years. That project’s success helped in the development of Caltech’s current Predictive Science Academic Alliance Program Center, in which Sharon also plays a significant role. Sharon’s dedicated nature and welcoming attitude have made her a key player in the history, and future, of computational science and engineering at Caltech.

“Bayesian Networks as a Scientific Tool”

Dr. David Heckerman (Microsoft Research)

Tuesday, March 10, at 1 pm, in 100 Powell-Booth

About the speaker: Dr. Heckerman is the Manager of the eScience Research Group at Microsoft Research and a world-renowned expert in this field and applications of modern data mining techniques in biomedical
sciences in particular.

This lecture also represents the final one in this term for the “Methods of Computational Science” class (Ay/Bi 199a).

The ASC program has provided significant funding for Caltech and CACR since 1998. Dan Meiron, ASC center director, accepted a Certificate of Service from Dmitry Kusnezov from the NNSA, “for your steadfast dedication and leadership in advancing the field of computational science and engineering by using high-performance computing … to elevate the state of technology of materials design through the Virtual Test Facility’s capability to simulate the dynamic response of materials under intense loading conditions.” The Caltech center’s work included constructing a proof of concept for a Virtual shock physics Test Facility in which the full three-dimensional response of a variety of target materials could be simulated for a wide range of compressive, tensional, and shear loadings, including those produced by detonation of energetic materials.

Caltech’s ASC ASAP center’s success was key in securing a role in the Predictive Science Academic Alliance Program (PSAAP).

The activities of this committee include:

• Market pull strategies (collectively influencing vendors)
• HPC/SC energy performance metrics and benchmarking
• Computer center (infrastructure) energy performance metrics and benchmarking
• Best practices, case studies, and lessons learned in design and operation of super computer centers
• Energy efficient design guidelines and specifications for super computer centers
• Improving software for energy efficiency
• Integrating energy efficiency into SC09’s technical program and HPCC (energy challenge) – subject to organizer’s approval

CACR’s goals in participating in this initiative are to keep our infrastructure as efficient as possible and to help Caltech’s Facility department make informed choices when preparing upgrades or modifications to the existing and future HPC computer rooms on campus.

Tue & Thu, 1-2:30 pm, in 153 Noyes, starting January 8, 2009. (Class Website)

The goal of this class is to introduce students to a number of increasingly important tools and concepts in computationally enabled and data intensive science and engineering. The class is aimed at upper division undergrads and graduate students, who wish to learn the tools that are becoming increasingly important in research in all disciplines. The grading will be P/F only. Postdocs (and anyone else interested) are welcome to attend. Prerequisites: some familiarity with computational science or engineering, programming; a working knowledge of unix; or a consent of the instructors. The class will be in form of topical lectures, and practical exercises associated with them.  Lecturers for both terms include CACR Staff members M. Aivazis, J. Bunn, A. Cunha, M. Graham, S. Lombeyda, S. Pepke, M. Stalzer, E. Upchurch, R. Williams.Topics to be covered in the Winter 2009 term include:

• Scientific communication and collaboration tools (wikis, blogs, etc.)
• Databases, their design, uses, etc.
• Flavors of programming languages, and intro to Python
• Data mining: general principles, supervised & unsupervised classifiers, etc.
• Scientific visualization: principles and practice
• Bayesian data modeling and analysis, Bayesian networks

(Note: we are not covering traditional CS topics, numerical methods, or programming, as these subjects
are already well covered by other classes.)
Other lecturers include G. Djorgovski, C. Donalek, J. Jewell, A. Mahabal, M. Turmon, and other visiting lecturers.  The class is coordinated by Profs. G. Djorgovski (Ay) and M. Kennedy (Bi). For more info, please contact Prof. Djorgovski:  george@astro.caltech.edu

The SC Conference is the premier international conference for high performance computing (HPC), networking, storage and analysis. SC08 marks the 20th anniversary of the first SC Conference, then called Supercomputing, held in Orlando, Florida in 1988. It is also the 20th anniversary of the participation of the group that evolved into CACR. Visit us at Booth 751!