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.

Skyalert delivers events in real time via email, Twitter, instant message, and other protocols to observatories that can do rapid follow-up — some completely automatically with no human in the loop. Other event-driven actions can include fetching data to build a data portfolio, and running machine-learning algorithms and classification rules to make better automatic decisions. The intention is for automated systems to make real-time intelligent decisions. Skyalert uses an international standard, VOEvent, enabling participation in the global event infrastructure, exchanging events with other event brokers, such as NASA’s GCN.

As of Sept 8, 2009, SHC has been transitioned to the new sw stack (RHEL+OpenIB). There are currently 115 core4 nodes and 65 core8 nodes, in production. For more information, please visit the SHC Getting Started / System Guide.

Melaine Stefan
Computational Neurobiology Group
European Bioinformatics Institute (EBI)
Cambridge UK

Over the next couple of days, more backend nodes from shc-a will be transitioned to shc-[c,new]’s cluster of backend nodes, running the new software stack. By Sept 4, there will be just 24 shc-a backend nodes, all the rest of the compute nodes will be running the new software stack, seen from shc-[new,c].

• Please port your codes to the new software environment if you’ve not already done so!
• Please report any porting problems you’re having; we’ll help asap.
• Details on how to rebuild your code for the new SHC environment can be found here
• Your MPI based code must be rebuilt for the new and improved shc software stack.

Preventive Maintenance on Sept 8 from 0800 to 1400 will encompass testing the complete transition of SHC compute and head node resources to the upgraded software stack environment. The fully upgraded production SHC cluster configuration will be two head nodes (shc-[a,b]) and 1180 Opteron compute node cores (163 dual cpu/dual core + 66 dual cpu/quad core).

Questions or concerns about the upgrade? Just let us know.

Read more in the Caltech Press Release

A bright supernova discovered by CRTS within the interacting Antennae galaxies. Click for larger images.

CACR is pleased to announce that an award of $890,000 from the National Science Foundation Astronomy & Astrophysics Research Grants Program was made to the Catalina Real-Time Transient Survey (CRTS) project. The CRTS is based on the special processing and analysis of a data stream from the ongoing NASA-funded Catalina Sky Survey (CSS), which is cataloging near-earth objects and potential planetary hazard asteroids.  The CRTS leverages this existing data stream to discover and study objects and phenomena outside the solar system, opening a new discovery space for time-domain astrophysics at a greatly reduced cost. This project will provide a steady open stream of astronomical events, available to the entire community in real-time. This will be the first and only fully open synoptic sky survey data and event stream.

Exploration of the time domain – discovery and study of objects and phenomena changing on time scales ranging from seconds to years – is now one of the most exciting and rapidly growing fields of astronomy, touching on a broad and diverse spectrum of research areas, from the solar system and discoveries of extra-solar planets to the distant quasars, and from stellar astrophysics to cosmology and extreme relativistic astrophysics. Time domain information is essential for understanding some of the most interesting phenomena we observe. For example, we could not learn anything from a single picture of a supernova, or a single snapshot of a gamma-ray burst: the variability of stars aids to our understanding of their structure and evolution, motions of stars tell us about the structure of our galaxy, and so on.

The CRTS project is already making significant scientific discoveries. For example, CRTS recently found the most energetic supernova ever seen. This event appears to be an example of an extremely rare pair-instabilty supernova. The survey will aid the entire astronomical community in developing new scientific strategies and procedures in the area of large synoptic sky surveys, and develop further and exercise time-domain astronomy cyber-infrastructure within existing Virtual Observatory (VO) environment and framework.

Representing CACR’s expertise in time-domain astronomy, research scientist Andrew Drake created and manages the process for real-time data filtering and analysis, mining through the CSS data for astrophysical transients. Scientific areas of interest include beamed active galactic nuclei (blazars), unusual types of supernovae, fast transients, and an organized serendipitous approach to the discovery of new types of objects and phenomena. More information about the project can be found on the CRTS website.

Jing Qiang Goh, Caltech & National University of Singapore Undergraduate Research Exchange Program
Mentor: Dr. Mark Stalzer Co-mentor: Dr. Ufuk Topcu

We have developed a Matlab-based prototyping toolbox for uncertainty quantification. The underlying uncertainty quantification framework is based on the concentration-of-measure inequalities. We implemented two global optimization schemes, Simulated Annealing and Differential Evolution, for uncertainty quantification. The implementation exploits sources of parallelization at the optimization level and within uncertainty quantification. Our toolbox offers a user-friendly interface and a robust optimizer for uncertainty quantification on physical models.

Aviral Shrivastava
Assistant Professor, Department of Computer Science and Engineering,
School of Computing and Informatics, Arizona State University

Unlike design or manufacturing errors, soft errors are much harder to protect against, since they can happen anywhere and anytime. Consequently, soft error protection mechanisms incur extremely high overheads.  Most software schemes against soft errors are based on re-execution of programs or parts thereof, to detect and correct soft errors, and therefore have very high performance (avoidable by adding more resources) power (unavoidable) overheads. In contrast, our research tries to achieve protection without explicit re-execution. Fundamentally, our compiler changes the way application uses microarchitectural components, so that it uses the already protected components to process the vulnerable data, and uses the unprotected components to process the protected data. Towards this philosophy goal, we have developed several compiler techniques to better use caches, and register files (RFs), two sites which most critically need protection. While I’ll gloss over our solutions for the cache, I will concentrate on the RF protection problem.

BIO:
Aviral Shrivastava is an Assistant Professor in the Department of Computer Science and Engineering, at the Arizona State University, where he has established and heads the Compiler and Microarchitecture Lab (CML).   He received his master’s and doctorate in Information and Computer Science from University of California, Irvine. He received his bachelors in Computer Science and Engineering from Indian Institute of Technology, Delhi. His research interests lie at the intersection of compilers and microarchitectures in particular of embedded systems. He studies microarchitecture and compiler techniques for power, performance, temperature, and most recently reliability.  Dr. Shrivastava is a lifetime member of ACM, and serves on organizing and program committees of several premier embedded system conferences, including CODES+ISSS, CASES and LCTES.