Center for Computational
Research
FSEC Status Report 2/2003
| Russ Miller, Director |
Center for Computational Research
| High-Performance Computing and High-End Visualization | ||
| 70 (40+ active) Research Groups in 27 Depts | ||
| 13 Local Companies | ||
| 10 Local Institutions | ||
| External Funds: $108M | ||
| Vendor Contributions: $41M | ||
| Deliverables | ||
| 350 Publications and Presentations | ||
| Hardware, Software, Algorithms, etc | ||
| Training | ||
| Workshops | ||
| Courses | ||
| Degree Programs | ||
| Dell Linux Cluster - #22 in World | ||
| 600 P4 Processors (2.4 GHz) | ||
| 600 GB RAM; 40 TB Disk | ||
| Dell Linux Cluster - #187 in World | ||
| 4036 Processors (PIII 1.2 GHz) | ||
| 2TB RAM; 160TB Disk; 16TB RD | ||
| Private Use | ||
| Computational Chemistry (King, Kofke, Coppens, Furlani, Tilson, Lund, Swihart, Ruckenstein, Garvey) | ||
| Algorithm development & simulations | ||
| Groundwater Flow Modeling (Rabideau, Jankovic, Becker, Flewelling) | ||
| Predict contaminant flow in groundwater & possible migration into streams and lakes | ||
| Geophysical Mass Flows (Patra, Sheridan, Pitman, Bursik, Jones, Winer) | ||
| Study of geophysical mass flows for risk assessment of lava flows and mudslides | ||
| Bioinformatics (Zhou, Miller, Hu, Szyperski – NIH Consortium, HWI) | ||
| Protein Folding: computer simulations to understand the 3D structure of proteins | ||
| Structural Biology; Pharmacology | ||
| Computational Fluid Dynamics (Madnia, DesJardin, Lordi, Taulbee) | ||
| Modeling turbulent flows and combustion to improve design of chemical reactors, turbine engines, and airplanes | ||
| Physics (Jones, Sen) | ||
| Many-body phenomena in condensed matter physics | ||
| Chemical Reactions (Mountziaris) | ||
| Molecular Simulation (Errington) | ||
| Fakespace ImmersaDesk R2 | ||
| Portable 3D Device | ||
| Tiled-Display Wall | ||
| 20 NEC projectors: 15.7M pixels | ||
| Screen is 11’´7’ | ||
| Dell PCs with Myrinet2000 | ||
| Access Grid Node | ||
| Group-to-Group Communication | ||
| Commodity components | ||
| SGI Reality Center 3300W | ||
| Dual Barco’s on 8’´4’ screen | ||
| VREX VR-4200 Stereo Imaging Projector | ||
| Portable projector works with PC | ||
| Computational Science (Patra, Sheridan, Becker, Flewelling, Baker, Miller, Pitman) | ||
| Simulation and modeling | ||
| Urban Visualization and Simulation (CCR) | ||
| Public projects involving urban planning | ||
| Medical Imaging (Hoffmann, Bakshi, Glick, Miletich, Baker) | ||
| Tools for pre-operative planning; predictive disease analysis | ||
| Geographic Information Systems (CCR, Bisantz, Llinas, Kesavadas, Green) | ||
| Parallel data sourcing software | ||
| Historical Reenactments (Paley, Kesavadas, More) | ||
| Faithful representations of previously existing scenarios | ||
| Multimedia Presentations (Anstey, Pape) | ||
| Networked, interactive, 3D activities | ||
| Regional-scale modeling of groundwater flow and contaminant transport (Great Lakes Region) | ||
| Ability to include all hydrogeologic features as independent objects | ||
| Current work is based on Analytic Element Method | ||
| Key features: | ||
| High precision | ||
| Highly parallel | ||
| Object-oriented programming | ||
| Intelligent user interface | ||
| GIS facilitates large-scale regional applications | ||
| Utilized 10,661 CPU days (32 CPU years) of computing in past year on CCR’s commodity clusters | ||
| Integrate information from several sources | ||
| Simulation results | ||
| Remote sensing | ||
| GIS data | ||
| Develop realistic 3D models of geophysical mass flows | ||
| Present information at user appropriate resolutions | ||
| Dynamics of Hemoglobin (Example) | ||
| 50 Days of Processing on 16 Processors (800 CPU Days) | ||
| Key | ||
| White – Heme Groups | ||
| Red – Phe97 | ||
| Red – Oxygen (in the subunit at bottom) | ||
| Green – His 69 and 101 | ||
| Blue – Tyr 72 | ||
| Cyan (Ball) – Water Molecules | ||
| Yellow – Helix E/F | ||
| Interest | ||
| Flip of the Phe97 ring at top | ||
| Water movement around Phe97 | ||
| Heme-heme relative movement | ||
| Collaboration with Children’s Hospital | ||
| Leading miniature access surgery center | ||
| Application reads data output from a CT Scan | ||
| Visualize multiple surfaces and volumes | ||
| Export images, movies or CAD representation of model | ||
| Collaboration with Buffalo Neuroimaging Analysis Center (BNAC) | ||
| Developers of Avonex, drug of choice for treatment of MS | ||
| MS Project examines patients and compares scans to healthy volunteers | ||
| Compare caudate nuclei between MS patients and healthy controls | ||
| Looking for size as well as structure changes | ||
| Localized deformities | ||
| Spacing between halves | ||
| Able to see correlation between disease progression and physical structure changes | ||
| StreetScenes® is a Virtual Reality (VR) software solution for 3D visualization of surface traffic | |
| 3D model of proposed soccer stadium in Rochester | |
| Used StreetScenes® to import output file from Synchro traffic simulation | |
| International Crossing | ||
| The Problem | ||
| 75 year old bridge | ||
| 3 lanes – poor capacity | ||
| Existing US plaza: small and poor design | ||
| Media Study (Anstey, More) | |||
| Donation of PCs | |||
| Courses, Students, UB Grant | |||
| “Alive on the Grid” | |||
| NSF ITR Grant | |||
| AVID Software | |||
| MAE (Kesavadas) | |||
| Gov. Pataki Visit | |||
| Peace Bridge (Early) | |||
| Commodity Projection | |||
| Classics/MAE (Paley, Kesavadas) | |||
| Virtual Site Museum, BBC2 | |||
| H.S. Bioinformatics Program (Pitman) | |||
| Verizon/Compaq | |||
| Buffalo Neuroimaging Analysis Center (Bakshi) | |||
| MS Visualization | |||
| Children’s Hospital (Glick) | |||
| CT 3D Viz | |||
| Dent Neurologic Institute (Miletich) | |||
| PET Imaging | |||
| Computer Science & Engineering | |||
| Crash Lab | |||
| Library (Dilandro, Bertholf) | |||
| Darwin Martin House | |||
| James Joyce Novel On-Line | |||
| Anthropology (Zubrow) | |||
| Solar Powered Cluster | |||
| Management (Jain) & Math (Pitman) | |||
| Tops Friendly Markets | |||
| M&T Bank | |||
| Access Grid Node (too numerous) | |||
| Campus-Wide Outreach for Conf. | |||
| Center for Americas | |||
| Human Rights (China/Sweden) | |||
| IBC Digital | ||
| Gov. Pataki Visit | ||
| Peace Bridge (Early & Current) | ||
| Buffalo-Niagara Medical Campus | ||
| Compute Cycles for Animation | ||
| Bergmann Associates | ||
| Peace Bridge (Current) | ||
| NYS Thruway Toll Plaza | ||
| Azar & More | ||
| Reenactment of 1901 Pan Am Exhibition | ||
| PHSCologram & Courses | ||
| Avid Digital Editing | ||
| Niagara College | ||
| Start up | ||
| Peace Bridge (Current) | ||
| Hauptman-Woodward Medical Research Institute | ||
| Computing | ||
| Collaboratory | ||
| The Children’s Hospital of Buffalo | ||
| Medical Visualization | ||
| Veridian | ||
| Battlespace Management | ||
| Leadership | ||
| Director & Associate Director | ||
| Clerical | ||
| Office Manager; Budget; Receptionist; | ||
| Computational Scientists | ||
| Comptutational Chemistry, Comptutational Physics | ||
| Bioinformatics, Scientific Visualization | ||
| Programmers | ||
| Bioinformatics, Database, MultiMedia | ||
| System Administrators | ||
| Sysadmins (5), SAN admin, Web/Help Desk | ||
| Soft Money | ||
| Post-Docs (4) | ||
| Bachelor’s & Master’s Program in Bioinformatics | ||
| Related Disciplines | ||
| Chemical Biology | ||
| Computational Chemistry | ||
| Environmental Analysis (Sloan Support) | ||
| Medical Informatics (Sloan Support) | ||
| Advanced Degrees under Development | ||
| Pharmacometrics, Biophotonics | ||
| UB-HWI Department of Structural Biology | ||
| Complementary Degrees | ||
| Canisius College | ||
| Niagara University | ||
| “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 |
| miller@buffalo.edu | |
| www.ccr.buffalo.edu | |