Center for Computational Research FSEC Status Report 2 2003

Center for Computational Research FSEC Status Report 2/2003 Russ Miller, Director “Top 10 Worldwide Supercomputing Center” - www. gapcon. com University at Buffalo The State University of New York

Center for Computational Research n High-Performance Computing and High-End Visualization q 70 (40+ active) Research Groups in 27 Depts q 13 Local Companies q 10 Local Institutions q External Funds: $108 M q Vendor Contributions: $41 M n Deliverables q 350 Publications and Presentations q Hardware, Software, Algorithms, etc n Training q Workshops q Courses q Degree Programs University at Buffalo The State University of New York Center for Computational Research CCR

Computational Resources n Dell Linux Cluster - #22 in World q 600 P 4 Processors (2. 4 GHz) q 600 GB RAM; 40 TB Disk n Dell Linux Cluster - #187 in World q 4036 Processors (PIII 1. 2 GHz) q 2 TB RAM; 160 TB Disk; 16 TB RD q Private Use n SGI Origin 3800 q 64 Processors (400 MHz) q 32 GB RAM; 400 GB Disk n IBM RS/6000 SP q 78 Processors q 26 GB RAM; 640 GB Disk n Sun Microsystems Cluster q 48 Sun Ultra 5 s (333 MHz) q 16 Dual Sunblades (750 MHz) q 30 GB RAM, Myrinet n SGI Intel Linux Cluster q 150 PIII Processors (1 GHz) q 75 GB RAM, 2. 5 TB Disk Storage n Apex Bioinformatics System q Sun V 880 (3), 6800, 280 R (2), PIIIs q Sun 3960: 7 TB Disk Storage n HP/Compaq SAN (3/2003) q 25 TB Disk; 250 TB Tape University at Buffalo The State University of New York Center for Computational Research CCR

Sample Computational Research n Computational Chemistry (King, Kofke, Coppens, Furlani, Tilson, Lund, Swihart, Ruckenstein, Garvey) q Algorithm development & simulations n Groundwater Flow Modeling (Rabideau, Jankovic, Becker, Flewelling) q Predict contaminant flow in groundwater & possible migration into streams and lakes n Geophysical Mass Flows (Patra, Sheridan, Pitman, Bursik, Jones, Winer) q Study of geophysical mass flows for risk assessment of lava flows and mudslides n Bioinformatics (Zhou, Miller, Hu, Szyperski – NIH Consortium, HWI) q Protein Folding: computer simulations to understand the 3 D structure of proteins q Structural Biology; Pharmacology n Computational Fluid Dynamics (Madnia, Des. Jardin, Lordi, Taulbee) q Modeling turbulent flows and combustion to improve design of chemical reactors, turbine engines, and airplanes n Physics (Jones, Sen) q Many-body phenomena in condensed matter physics n Chemical Reactions (Mountziaris) n Molecular Simulation (Errington) University at Buffalo The State University of New York Center for Computational Research CCR

Visualization Resources n Fakespace Immersa. Desk R 2 q Portable 3 D Device n Tiled-Display Wall q 20 NEC projectors: 15. 7 M pixels q Screen is 11’ 7’ q Dell PCs with Myrinet 2000 n Access Grid Node q Group-to-Group Communication q Commodity components n SGI Reality Center 3300 W q Dual Barco’s on 8’ 4’ screen n VREX VR-4200 Stereo Imaging Projector q Portable projector works with PC University at Buffalo The State University of New York Center for Computational Research CCR

Sample Visualization Areas n Computational Science (Patra, Sheridan, Becker, Flewelling, Baker, Miller, Pitman) q Simulation and modeling n Urban Visualization and Simulation (CCR) q Public projects involving urban planning n Medical Imaging (Hoffmann, Bakshi, Glick, Miletich, Baker) q Tools for pre-operative planning; predictive disease analysis n Geographic Information Systems (CCR, Bisantz, Llinas, Kesavadas, Green) q Parallel data sourcing software n Historical Reenactments (Paley, Kesavadas, More) q Faithful representations of previously existing scenarios n Multimedia Presentations (Anstey, Pape) q Networked, interactive, 3 D activities University at Buffalo The State University of New York Center for Computational Research CCR

Groundwater Flow Modeling n Regional-scale modeling of groundwater flow and contaminant transport (Great Lakes Region) n Ability to include all hydrogeologic features as independent objects n Current work is based on Analytic Method n Key features: q q q Element High precision Highly parallel Object-oriented programming Intelligent user interface GIS facilitates large-scale regional applications n Utilized 10, 661 CPU days (32 CPU years) of computing in past year on CCR’s commodity clusters University at Buffalo The State University of New York Center for Computational Research CCR

Risk Mitigation n Integrate information from several sources q Simulation results q Remote sensing q GIS data n Develop realistic 3 D models of geophysical mass flows n Present information at user appropriate resolutions University at Buffalo The State University of New York Center for Computational Research CCR

Protein Dynamics of Hemoglobin (Example) n 50 Days of Processing on 16 Processors (800 CPU Days) n Key q q q q White – Heme Groups Red – Phe 97 Red – Oxygen (in the subunit at bottom) Green – His 69 and 101 Blue – Tyr 72 Cyan (Ball) – Water Molecules Yellow – Helix E/F n Interest q Flip of the Phe 97 ring at top q Water movement around Phe 97 q Heme-heme relative movement University at Buffalo The State University of New York Center for Computational Research CCR

3 D Medical Visualization App n Collaboration with Children’s Hospital q. Leading miniature access surgery center n Application reads data output from a CT Scan n Visualize multiple surfaces and volumes n Export images, movies or CAD representation of model University at Buffalo The State University of New York Center for Computational Research CCR

Multiple Sclerosis Project n Collaboration with Buffalo Neuroimaging Analysis Center (BNAC) q Developers of Avonex, drug of choice for treatment of MS n MS Project examines patients and compares scans to healthy volunteers University at Buffalo The State University of New York Center for Computational Research CCR

Multiple Sclerosis Project n Compare caudate nuclei between MS patients and healthy controls n Looking for size as well as structure changes q. Localized deformities q. Spacing between halves n Able to see correlation between disease progression and physical structure changes University at Buffalo The State University of New York Center for Computational Research CCR

® Street. Scenes Demo n Street. Scenes® is a Virtual Reality (VR) software solution for 3 D visualization of surface traffic n 3 D model of proposed soccer stadium in Rochester n Used Street. Scenes® to import output file from Synchro traffic simulation University at Buffalo The State University of New York Center for Computational Research CCR

Peace Bridge Visualization n International Crossing n The Problem q 75 year old bridge q 3 lanes – poor capacity q Existing US plaza: small and poor design n. Proposed Options q Relocate US plaza q Build a 3 -lane companion span, rehab existing bridge q Build a six lane signature span University at Buffalo The State University of New York Center for Computational Research CCR

Sample UB Synergies n Media Study (Anstey, More) q q q Donation of PCs Courses, Students, UB Grant “Alive on the Grid” NSF ITR Grant AVID Software n MAE (Kesavadas) q Gov. Pataki Visit q Peace Bridge (Early) q Commodity Projection n Classics/MAE (Paley, Kesavadas) q Virtual Site Museum, BBC 2 n H. S. Bioinformatics Program (Pitman) n Children’s Hospital (Glick) q CT 3 D Viz n Dent Neurologic Institute (Miletich) q PET Imaging n Computer Science & Engineering q Crash Lab n Library (Dilandro, Bertholf) q Darwin Martin House q James Joyce Novel On-Line n Anthropology (Zubrow) q Solar Powered Cluster n Management (Jain) & Math (Pitman) q Tops Friendly Markets q M&T Bank q Verizon/Compaq n Buffalo Neuroimaging Analysis Center (Bakshi) n Access Grid Node (too numerous) q MS Visualization q Campus-Wide Outreach for Conf. q Center for Americas m Human Rights (China/Sweden) University at Buffalo The State University of New York Center for Computational Research CCR

Select WNY Synergies n IBC Digital n Niagara College q Gov. Pataki Visit q Start up q Peace Bridge (Early & Current) q Peace Bridge (Current) q Buffalo-Niagara Medical Campus n Hauptman-Woodward q Compute Cycles for Animation Medical Research Institute n Bergmann Associates q Peace Bridge (Current) q NYS Thruway Toll Plaza n Azar & More q Reenactment of 1901 Pan Am Exhibition q PHSCologram & Courses q Avid Digital Editing q Computing q Collaboratory n The Children’s Hospital of Buffalo q Medical Visualization n Veridian University at Buffalo The State University of New York q Battlespace Management Center for Computational Research CCR

Personnel n Leadership q Director & Associate Director n Clerical q Office Manager; Budget; Receptionist; n Computational Scientists q Comptutational Chemistry, Comptutational Physics q Bioinformatics, Scientific Visualization n Programmers q Bioinformatics, Database, Multi. Media n System Administrators q Sysadmins (5), SAN admin, Web/Help Desk n Soft Money q Post-Docs (4) University at Buffalo The State University of New York Center for Computational Research CCR

Academic Programs n Bachelor’s & Master’s Program in Bioinformatics n Related Disciplines q Chemical Biology q Computational Chemistry q Environmental Analysis (Sloan Support) q Medical Informatics (Sloan Support) n Advanced Degrees under Development q Pharmacometrics, Biophotonics n UB-HWI Department of Structural Biology n Complementary Degrees q Canisius College q Niagara University at Buffalo The State University of New York Center for Computational Research CCR

Outreach University at Buffalo The State University of New York Center for Computational Research CCR

Bioinformatics in Buffalo “This Center [of Excellence in Bioinformatics] will, through the University of Buffalo’s Center for Computational Research, create academic and industrial partnerships …” - NYS Gov. George S. Pataki, January 2001 Gov. Pataki Congressman Reynolds Senator Clinton University at Buffalo The State University of New York Center for Computational Research CCR

Contact Information miller@buffalo. edu www. ccr. buffalo. edu University at Buffalo The State University of New York Center for Computational Research CCR