Allen D. Malony malony@cs.uoregon cs.uoregon/research/tau

1. IBM Collaboration Opportunities Allen D. Malony malony@cs.uoregon.edu http://www.cs.uoregon.edu/research/tau Performance Research Laboratory (PRL) Neuroinformatics Center (NIC) Department of Computer and Information Science University of Oregon

2. 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

3. 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

4. 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

5. 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

6. 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.

7. 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

8. 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

9. 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

10. 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

11. 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

12. Building Computational Brain Models • MRI segmentation of brain tissues • Conductivity model • Measure head tissue conductivity • Electrical impedance tomography • small currents are injectedbetween electrode pair • resulting potential measuredat remaining electrodes • Finite element forward solution • Source inverse modeling • Explicit and implicit methods • Bayesian methodology

13. UO ICONIC Grid • NSF Major Research Instrumentation (MRI) proposal “Acquisition of the Oregon ICONIC Grid for IntegratedCOgnitive Neuroscience Informatics and Computation”

14. GEMINI • “Grid-based Environmentsand Methods for IntegratedNeuroimaging” • Dynamic neuroimagingalgorithms and visualization • Grid-based integration(processing and data sharing) • High-end tool integrationand environments • Neuroinformatics dataontologies

15. 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