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SDSC Cyberinfrastructure Research Seminar Series

The SDSC Cyberinfrastructure Research Seminar Series is a set of presentations on Cyberinfrastructure and e-Science related research.

If you have any questions about the seminars or would like to participate as a speaker, please contact Ilkay Altintas at

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Past Seminars

June 2, 2011 10-11 am

Speaker:Ross Walker

Title: Development and application of structure-based potentials for parallel simulation of a key transcriptional module

Abstract: This talk will provide an overview of the various research projects within the Walker group at SDSC and will then highlight the progress that has been made on the TRO project between Ross Walker at SDSC and the group of Peter Wolynes in the Department of Chemistry and Biochemistry. This work has focused on both adapting and improving the performance of the structure based potential, termed Associate Memory Hamiltonian (AMH) developed by the Wolynes group. The background behind AMH will be provided along with details of the implementation and the improvements that have been made both to the overall structure of the code and its performance. The improved performance has made it possible to extend the AMH approach beyond a protein folding simulation to a method by which the dynamics (on an accelerated timescale) of protein complexes can be simulated. In this talk recent results on the key NF-kappaB transcriptional factor and it inhibitor IkappaB, key targets for understanding a number of disease mechanisms, including cancer, will be presented along with planned future work to incorporate AMH into the DOE Lammps code.

June 16, 2011 10-11 am SDSC Auditorium
Speakers: Amit Majumdar, SDSC
Mahidhar Tatineni, SDSC
Kenneth A. Benner, Graduate Student, Dept. of Structural Engr. UCSD
Collaborators: Yuri Bazilevs, Dept of Structural Engr, UCSD
Alison L. Marsden, Dept of Mechanical and Aerospace Engr, UCSD

Title: HPC Based CI for Patient-Specific Cardiovascular Simulations - An SDSC TRO Project

Abstract: Currently available detailed patient-specific imaging combined with finite element models has created the opportunity for a patient-specific computational framework for cardiovascular surgical procedures. Currently, surgeons predominantly use intuition and geometric guidelines to perform surgeries such as the Fontan surgery, bypass graft, aorto-pulmonary shunts, etc. Post-surgery, blood flow profiles are altered and quantities such as blood flow energy efficiency, regions prone to risk of plaque deposition, pressure loss, etc., are affected. It is impossible to predict the complex hemodynamics and the aforementioned quantities without a detailed computational study. Research is under way at UCSD Structural Engineering and Aerospace and Mechanical Engineering to develop a framework for performing computations on models derived from MRI images that includes (a) fluid structure interaction (FSI) simulations coupling the Navier-stokes (for blood flow) and stress-equilibrium (for arterial motion) equations, (b) uncertainty quantification in cardiovascular simulations by identifying and incorporating multiple sources of input uncertainties, and (c) shape optimization of cardiovascular surgeries to minimize adverse flow conditions. Meaningful patient-specific simulations can be large and complex, thus incurring an extensive computational cost, both in setting up the models and simulations, and in the simulation solutions themselves. The SDSC-funded TRO project is looking into parallel implementation and scaling studies of the computational environment, on the Triton machine, so that in the future patient-specific simulations can be feasible. We will present the overall workflow and performance results on the Triton machine of this ongoing collaboration between researchers and students from UCSD and SDSC. This TRO-funded initial collaboration has also lead to multiple external proposal activities and those will also be mentioned.

May 19th, 2011 10-11 am SDSC Auditorium

Speaker: Sriram Krishnan

Download Slides: myHadoop-SDSC.pdf. Right-click the link (or Control-click on a Mac) and choose "Save Link As..." to save the document to your computer.

Title: myHadoop - Hadoop-on-Demand on Traditional HPC Resources

Abstract: Traditional High Performance Computing (HPC) resources, such as those available on the TeraGrid, support batch job submissions using Distributed Resource Management Systems (DRMS) like TORQUE or the Sun Grid Engine (SGE). For large-scale data intensive computing, programming paradigms such as MapReduce are becoming popular. A growing number of codes in such scientific domains as Bioinformatics and Geosciences are being written using open source MapReduce tools such as Apache Hadoop. It has proven to be a challenge for Hadoop to co-exist with existing HPC resource management systems, since both provide their own job submissions and management, and because each system is designed to have complete control over its resources. Furthermore, Hadoop uses a shared-nothing style architecture, whereas most HPC resources employ a shared-disk setup. In this talk, we describe myHadoop, a framework for configuring Hadoop on-demand on traditional HPC resources, using standard batch scheduling systems. With myHadoop, users can develop and run Hadoop codes on HPC resources, without requiring root-level privileges. Here, we describe the architecture of myHadoop, and evaluate its performance for a few sample, scientific use-case scenarios. myHadoop is open source, and available for download on SourceForge.

May 5th, 2011, 10-11 am SDSC Auditorium

Speaker: Wayne Pfeiffer

Title: Compute- and Data-Intensive Analyses in Bioinformatics

Abstract: The advent of high-throughput DNA sequencers has produced a flood of genomic data. How big is this flood, and what are the computational requirements for analyzing the data? These questions will be addressed for three common types of bioinformatics analyses: read mapping (including pairwise alignment), de novo assembly, and phylogenetic tree inference. Use of the TeraGrid for phylogenetic analyses via the CIPRES gateway will also be summarized.


HPCwire is a weekly electronic magazine for high-performance computing that includes news, information and analysis related to engineering, scientific and commercial applications. Supercomputing Online is an electronic magazine for high-performance computing that covers high-end computing, communications, networking issues, applications, and research. Both publications also include employment opportunity and conference listings. They offer great introductions to the high-performance computing community.

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