SDSS IPP Research Review, Jun 12, 2013, 1-6pm





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SDSC IPP Research Review

June 12, 2013 1pm-6pm


SDSC Annual Research Review
Wednesday, June 12, 2013

SDSC Annual Research Review


What can SDSC do for you?
Michael Norman, Ph.D.
Director, San Diego Supercomputer Center
Distinguished Professor, Physics, UC San Diego
Director, Laboratory for Computational Astrophysics, UC San Diego
Computational astrophysics

Michael L. Norman is the Director of the San Diego Supercomputer Center and Distinguished Professor of Physics at UC San Diego where he also directs the Laboratory for Computational Astrophysics. He received his B.S. from Caltech in 1975, and his Ph. D. from UC Davis in 1980. After holding appointments at the Lawrence Livermore and Los Alamos National Laboratories, the Max Planck Institute for Astrophysics, and the National Center for Supercomputing Applications, he joined the faculty at UC San Diego in 2000. His research focus is the computer simulation of astronomical phenomena using supercomputers, and the development of the numerical methods to carry them out. He is the author of over 200 papers on diverse topics including star formation, cosmic jets, and cosmological evolution. His computer visualizations have appeared in numerous educational TV shows and films, including PBS Nova and The Discovery Channel. He is the recipient of the Alexander von Humboldt Research Prize and the IEEE Sidney Fernbach Award. He was elected Fellow of the American Physical Society in 2001, and the American Academy of Arts and Sciences in 2005.

SDSC Data Initiatives
Chaitan Baru, Ph.D.
Associate Director, Data Initiatives, SDSC
Director, Center for Large-scale Data Systems Research (CLDS), SDSC
Expertise: Large-scale data systems, database systems, scientific data management, performance and benchmarking of big data systems, data integration, data analytics.

Chaitan Baru is a Distinguished Scientist and research staff member at the San Diego Supercomputer Center. He has played a leadership role in a number of national-scale cyberinfrastructure R&D initiatives across a wide range of science disciplines from earth sciences to ecology, biomedical informatics, and healthcare. One of his current initiatives is an industry-academia effort to define big data benchmarks and establish a BigData Top100 List (see He also coordinates the SDSC Data Science Institute initiative for education and training in data science. Prior to joining SDSC in 1996, Baru was involved in the development of IBM's early UNIX-based shared-nothing database systems (DB2 Parallel Edition), where he also led a team that produced the industry's first result for a decision support benchmark (TPC-D). Baru has also served on the faculty of Computer Science and Engineering at the University of Michigan, Ann Arbor. He has a B.Tech. from the Indian Institute of Technology, Madras; and ME and PhD from the University of Florida, all in Electrical Engineering.

Around SDSC -- A Series of 'Lightning Talks'
Workflows for Distributed Analysis of Biological Big Data
Ilkay Altintas, Ph.D
Deputy Coordinator for Research, SDSC
Lab Director, Scientific Workflow Automation Technologies
Expertise: Scientific Workflows, Provenance, Distributed Computing, Observatory Systems

Ilkay Altintas, Ph.D. is the Director for the Scientific Workflow Automation Technologies Lab at the San Diego Supercomputer Center (SDSC), UC San Diego where she also is the Deputy Coordinator for Research. Since joining SDSC in 2001, she has worked on different aspects of scientific workflows as a principal investigator and in other leadership roles across a wide range of cross-disciplinary NSF, DOE and Moore Foundation projects. She is a co-initiator of and an active contributor to the open-source Kepler Scientific Workflow System, and the co-author of publications related to eScience at the intersection of scientific workflows, provenance, distributed computing, bioinformatics, observatory systems, conceptual data querying, and software modeling. Ilkay Altintas received her Ph.D. degree from the University of Amsterdam in the Netherlands with an emphasis on provenance of workflow-driven collaborative science and she is currently an assistant research scientist at UC San Diego.

Predictive Analytics and Data Mining Research and Applications
Natasha Balac, Ph.D.
Director, Predictive Analytics Center of Excellence, SDSC
Director of Data Application and Service, SDSC
Expertise: Data mining and analysis, Machine learning, Scientific data management, Data-intensive computing

Natasha Balac, Ph.D. is the Director of Predictive Analytics Center of Excellence at the San Diego Supercomputer Center (SDSC) encompassing many data mining projects including collaborations with UC San Diego Medical School and UC San Diego 's Smart Energy Grid. Natasha received her Ph.D. in Computer Science from Vanderbilt University with an emphasis in Machine Learning from large data sets. She has been with SDSC since 2003 leading multiple large projects and collaborations across a wide range of organizations in industry, government and academia including the Centers for Medicare and Medicaid Services (CMS), National Science Foundation (NSF), National Institutes of Health (NIH), and the California Energy Commission (CEC).

PMaC Tools and Methods for Performance and Energy Optimization for HPC
Laura Carrington,
Director of Performance Modeling and Characterization (PMaC) Lab
Expertise: HPC performance and power modeling, application analysis, benchmarking, and energy efficient research

Laura Carrington is an expert in High Performance Computing (HPC). Her work has resulted in over 40 publication in HPC benchmarking, workload analysis, application performance modeling, analysis of accelerators (i.e. FPGAs and GPUs) for scientific workloads, tools in performance analysis (i.e. processor and network simulators), and energy-efficient computing. At UC San Diego, she is the director of the Performance, Modeling, and Characterization (PMaC) Lab. She is also the UC San Diego PI for Institute for Sustained Performance, Energy, and Resilience (SUPER) DoE SciDAC-3 and lead for the energy efficiency thrust for the institute as well as PI on a number other awards that support the lab. She has presented at numerous invited talks, member of various panels and committees, and an active member of DoD HPCMP Performance team involved in their annual HPC system procurement for past 10 years.

Building a Semantic Information Infrastructure
Amarnath Gupta, Ph.D.
Director, Advanced Query Processing Lab, SDSC
Expertise: Information Integration, Semantic Information Infrastructure, Graph Data Management, Event Modeling

Amarnath Gupta received his Ph.D. in Computer Science from Jadavpur University in India. He is currently a full Research Scientist at the San Diego Supercomputer Center of UC San Diego, and directs the Advanced Query Processing Lab. His primary areas of research include semantic information integration, large-scale graph databases, ontology management, event data management and query processing techniques. Before joining UC San Diego, he was the Chief Scientist at Virage, Inc., a startup company in multimedia information systems. Dr. Gupta has authored over 100 papers and a book on Event Modeling, holds 13 patents and is a recipient of the 2011 ACM Distinguished Scientist award.

Benchmarking and Tuning Big Data Software
David Nadeau, Ph.D.
Computer Scientist, SDSC
Expertise: Data mining, Visualization techniques, User interface design, High-dimensionality data sets, Software development, Audio synthesis

David Nadeau is a senior computer scientist specializing in visualization and high-performance computing.  He specializes in very large high-dimensionality data sets for such diverse fields as geoscience, astrophysics, and medical imaging.  His works visualizing nebulae are featured in planetarium shows from the American Museum of Natural History in New York City.  He has taught courses in computer graphics and is the co-author of two books on the subject.

Bioinformatics Meets Big Data
Wayne Pfeiffer, Ph.D.
Distinguished Scientist, SDSC
Expertise: Supercomputer performance analysis, Novel computer architectures, Bioinformatics

Wayne Pfeiffer studied math, physics, and nuclear engineering in college and graduate school. After obtaining a PhD from Caltech, he joined General Atomics where he did research and development related to nuclear fission and fusion. Subsequently he helped found SDSC and served as a department manager and deputy director. In recent years he has been doing research in computer performance analysis and bioinformatics. Besides his work, he enjoys outdoor activities such as running, cycling, mountain climbing, and skiing.

Biomedical Data Integration System and Web Search Engine
Julia Ponomarenko, Ph.D.
Principal Investigator, UCSD San Diego Supercomputer Center
Expertise: Bioinformatics, Immunoinformatics, Databases and Software, Protein Structure, Genomics

Julia Ponomarenko, Ph.D., is Principal Investigator for the National Institute of Health. Her research involves the development of the Immune Epitope Database and Analysis Resource (IEDB), computational studies of gene transcriptional regulation in mammals, and protein/DNA structural informatics. Julia is also Director and Instructor of the Bioinformatics courses for the Biomedical and Bioinformatics graduate programs at UCSD and Lecturer at UCSD Extension.  Dr. Ponomarenko obtained her M.Sc. in Physics from Novosibirsk State University (ranked among the top three universities in Russia) and Ph.D. in Biology from the Russian Academy of Science.  During her career in Russia and for the last 11 years at SDSC, she has initiated, lead, and developed several high-profiled bioinformatics resources and did pioneering work on predicting gene regulatory sites and effect of SNPs in eukaryotic genomes, using DNA structural information. 

Gordon, a Data-intensive Supercomputer
Shawn Strande, M.S.
Co-PI and Project Manager for Gordon
Expertise: High performance computing, aerodynamics, computational fluid dynamics, project management.

Shawn Strande is the Co-PI and Project Manager for Gordon: A Data Intensive Computer. He has been involved with high performance computing since 1982 when he started his career at the NASA Ames Research Center doing wind tunnel testing and computational aerodynamics. Since then he has worked as an engineer in the aerospace industry; at a software start-up; and within higher education and research computing. He has been with the San Diego Supercomputer Center for 10 years where he now manages the Gordon project. He holds an MS in Aeronautics and Astronautics from Stanford University.


Managing HPC Systems at the National and Campus Levels
Rick Wagner, Ph.D. Candidate
HPC Systems Manager
Expertise: Linux Clusters, Astrophysics

Rick Wagner is the High Performance Computing Systems Manager at the San Diego Supercomputer Center, and a Ph.D. Candidate in Physics at the University of California, San Diego focusing his research on analyzing simulations of supersonic turbulence. In his managerial role, Rick has technical and operational responsibility for two of the NSF-funded Extreme Science and Engineering Discovery Environment (XSEDE) HPC clusters, Trestles and Gordon, and SDSC's Data Oasis parallel file systems. He has also worked with Argonne National Laboratory on coupling remote large-scale visualization resources to tiled display walls over dynamic circuits networks on the Department of Energy's Energy Sciences Network. Rick's other interests include promoting the sharing of astrophysical simulations through standardized metadata descriptions and access protocols, and he is currently serving as the Vice-Chair of the Theory Interest Group of the International Virtual Astronomical Observatory. His latest side project involves working with undergraduates to develop course materials on parallel programming for middle and high school students using Raspberry Pis.

Ron Hawkins,
Director, Industry Partners Program, SDSC

Ron Hawkins is the director of Industry Relations at the University of California’s San Diego Supercomputer Center, where he is responsible for developing industry partnerships and research collaborations in high performance computing.   He also manages business development for SDSC’s service offerings in high performance computing and cloud storage.  Mr. Hawkins is a technology industry veteran, having held VP-level management, engineering, and product development positions at companies such as SONY, SAIC, and Titan.  Mr. Hawkins’ technology background and interests include high performance and cloud computing, big data, data-intensive systems, microelectronics, embedded and real-time systems, and systems engineering.  Mr. Hawkins volunteers as an entrepreneur-in-residence in the ‘CONNECT’ Springboard entrepreneurship program, is a consultant or advisor to several early stage technology companies, and serves on the advisory board of the engineering school at the University of San Diego.  He received the Master of Information Systems degree from Virginia Tech and the BSEE degree from the U.S. Naval Academy.