Allen D. Malony Performance Research Laboratory (PRL) Neuroinformatics Center (NIC) Department of Computer and Information Science University of Oregon IBM Collaboration Opportunities

IBM Visit Outline  TAU parallel performance system  Overview  Projects  IBM involvement  UO Neuroinformatics Center  Overview  Projects  ICONIC Grid  Computational science  Oregon high-performance computing and data grid

IBM Collaboration OpportunitiesIBM Visit TAU Performance System  Tuning and Analysis Utilities (14+ year project effort)  Performance system framework for HPC systems  Integrated, scalable, flexible, and parallel  Open source toolkit for performance problem solving  Instrumentation, measurement, analysis, and visualization  All computing platforms, processor architectures, OSs  IBM, HP, Sun, Linux, SGI, Cray, Apple, Windows, …  Many programming languages and compilers  C, C++, Fortran 90/95, UPC, HPF, Java, OpenMP, Python  IBM, Intel, PGI, GNU, Sun, Microsoft, SGI, Cray, HP, …  Partners: LLNL, ANL, Research Center Jülich, LANL

IBM Collaboration OpportunitiesIBM Visit TAU Projects  TAU performance system  ParaProf: parallel profile analysis and visualization  PerfDMF: performance data management  PerfExplorer: performance data mining  KTAU: Linux kernel performance monitoring  Integration with the Eclipse Platform  Open Trace Format (OTF) for scalable parallel tracing  Performance analysis of large-scale application  CCSM / ESMF / WRF climate/earth/weather simulation  National laboratory applications  DOE SciDAC and DoD PET

IBM Collaboration OpportunitiesIBM Visit IBM Involvement  TAU runs on all IBM platforms and processors  pSeries, xSeries, BG/L (64K system at LLNL)  All national laboratory IBM systems run TAU  Porting to Cell processor  IBM Petascale Tools Workshop (‘05 and ‘06)  IBM T.J. Watson Research Center (David Klepacki)  Student participation (K. Huck, A. Nataraj)  IBM HPCS project  TAU integration in Eclipse Parallel Tools Platform (PTP)  Open Software Development Lab  University of Oregon membership

IBM Collaboration OpportunitiesIBM Visit Support Acknowledgements  Department of Energy (DOE)  Office of Science  MICS, Argonne National Lab  ASC/NNSA  University of Utah ASC/NNSA Level 1  ASC/NNSA, Lawrence Livermore National Lab  Department of Defense (DoD)  HPC Modernization Office (HPCMO)  Programming Environment and Training (PET)  NSF Software and Tools for High-End Computing  Research Centre Juelich  Los Alamos National Laboratory  ParaTools, Inc.

IBM Collaboration OpportunitiesIBM Visit Acknowledgements  Dr. Sameer Shende, Senior Scientist  Alan Morris, Senior Software Engineer  Wyatt Spear, PRL staff  Scott Biersdorff, PRL staff  Robert Yelle, PRL staff  Kevin Huck, Ph.D. student  Aroon Nataraj, Ph.D. student  Kai Li, Ph.D. student  Li Li, Ph.D. student  Suravee Suthikulpanit, M.S. student

IBM Collaboration OpportunitiesIBM Visit Neuroinformatics Center (NIC)  UO Brain, Biology, and Machine Initiative (BBMI)  Interdisciplinary research in cognitive neuroscience, biology, physics, and computer science  Human neuroscience focus  Computational science applied to human neuroscience  Tools to help understand dynamic brain function  Tools to help diagnosis brain-related disorders  HPC simulation, large-scale data analysis, visualization  Integration of neuroimaging methods and technology  Interaction with Electrical Geodesics, Inc.  Technology transfer to Cerebral Data Systems

IBM Collaboration OpportunitiesIBM Visit NIC Projects  Advanced statistical signal analysis (PCA, ICA)  HiPerSAT  High-performance signal analysis toolkit  Parallelize ICA, wavelet, and other algorithms  APECS  Automated protocol for EEG component separation  Computational human head / brain modeling  Conductivity modeling  Source localization modeling  Image segmentation and brain structure extraction  GEMINI

IBM Collaboration OpportunitiesIBM Visit Electrical Geodesics Inc. (EGI)  EGI Geodesics Sensor Net  Dense-array sensor technology  64/128/256 channels  256-channel geodesics sensor net  AgCl plastic electrodes  Carbon fiber leads  Net Station  Advanced EEG/ERP data analysis  Stereotactic EEG sensor registration  Research and medical services  Epilepsy diagnosis, pre-surgical planning

IBM Collaboration OpportunitiesIBM Visit Dipole Sources in the Cortex  Scalp EEG is generated in the cortex  Interested in dipole location, orientation, and magnitude  Cortical sheet gives possible dipole locations  Orientation is normal to cortical surface  Need to capture convoluted geometry in 3D mesh  From segmented MRI/CT  Linear superposition

IBM Collaboration OpportunitiesIBM Visit Building Computational Brain Models  MRI segmentation of brain tissues  Conductivity model  Measure head tissue conductivity  Electrical impedance tomography  small currents are injected between electrode pair  resulting potential measured at remaining electrodes  Finite element forward solution  Source inverse modeling  Explicit and implicit methods  Bayesian methodology

IBM Collaboration OpportunitiesIBM Visit UO ICONIC Grid  NSF Major Research Instrumentation (MRI) proposal “Acquisition of the Oregon ICONIC Grid for Integrated COgnitive Neuroscience Informatics and Computation”

IBM Collaboration OpportunitiesIBM Visit GEMINI  “Grid-based Environments and Methods for Integrated Neuroimaging”  Dynamic neuroimaging algorithms and visualization  Grid-based integration (processing and data sharing)  High-end tool integration and environments  Neuroinformatics data ontologies

IBM Collaboration OpportunitiesIBM Visit Leveraging Internet, HPC, and Grid Computing  Telemedicine imaging and neurology  Distributed EEG and MRI measurement and analysis  Neurological medical services  Shared brain data repositories  Remote and rural imaging capabilities  Build on emerging web services and grid technology  Leverage HPC compute and data centers  Create institutional and industry partnerships  Electrical Geodesics, Inc.  Cerebral Data Systems (UO partnership with EGI)  Looking for other industrial partnerships