Supercomputing and Visualization Russ Miller Director Center for

Supercomputing and Visualization Russ Miller, Director Center for Computational Research “Top 10 Worldwide Supercomputing Center” - www. gapcon. com University at Buffalo The State University of New York

Outline n Pervasive Computing n Computer Trends n Definition of Supercomputer n Overview of Center for Computational Research n Sample CCR Projects n Center of Excellence in Bioinformatics n H. S. Workshop University at Buffalo The State University of New York Center for Computational Research CCR

Take-Home Message n Computers play an important role in your life n Currently ~10 processors person n Working with computers can be fun and exciting University at Buffalo The State University of New York Center for Computational Research CCR

Computers Touch Every Aspect of Our Life…. University at Buffalo The State University of New York Center for Computational Research CCR

…. including entertainment University at Buffalo The State University of New York Center for Computational Research CCR

Computers are used in Many Professions n Science and Engineering q. Physics, Chemistry, Biology q. Aerospace, Mechanical, Civil, Environmental n Architecture q. Building and Bridge Design n Computer Animation q. Cartoons, Movies, Advertising q. Games (Playstation, Nintendo, PC games, etc) n Graphic Arts/Design n Computer programmers University at Buffalo The State University of New York Center for Computational Research CCR

What is a CPU? It’s the computer’s brain it’s the main processor CPU stands for Central Processing Unit University at Buffalo The State University of New York Center for Computational Research CCR

Gordon E. Moore n Co-Founder of Intel n Predicted (1965/75) that transistor density would double every 12/18 months n Processing speed doubling every 18 mos. n Disk storage doubling every 12 mos. n Aggregate bandwidth doubling every 9 mos. Gordon E. Moore n A computation that took 1 year to run on a PC in 1985 would only take 5 mins to run on a PC today! n A computation that runs in 2 hours on a PC today would have taken 24 years to run on a PC in 1985! University at Buffalo The State University of New York Center for Computational Research CCR

What is a Parallel Computer? A computer that contains more than 1 processor (CPU) Why are they used? To solve problems faster than they could be solved using only 1 processor University at Buffalo The State University of New York Center for Computational Research CCR

Parallel Computing Architectures P P M P P Shared Memory Distributed Memory University at Buffalo The State University of New York Distributed-Shared Memory Center for Computational Research CCR

What is a (Beowulf) Cluster? n Industry Standard Hardware and Software q PC-Based Components (Intel or AMD) q Ethernet or Myrinet q Linux, PBS, MPI q “Commodity Off-The-Shelf” (COTS) Thomas Sterling Caltech n Operates as a Single System n Rivals Performance of Traditional Supercomputer at a Fraction of the Price University at Buffalo The State University of New York Center for Computational Research CCR

What is a Supercomputer? n Fastest computers at any point in time n Used to solve large and complex problems n Machines 1000 times faster than a PC n Machines 10 times slower than what you need to solve the most challenging problems Cray 1 - 1976 “Seymour Cray is the Thomas Edison of the supercomputing industry” Seymour Cray - Larry L. Smarr 1925 -1996 University at Buffalo The State University of New York Center for Computational Research CCR

Example If you wanted to know what the weather will be like tomorrow, you could. . . Solve the problem at home on your PC and wait one month to get the answer or Solve the problem on a supercomputer and have the answer in one hour! University at Buffalo The State University of New York Center for Computational Research CCR

Fastest Computers Year Mach Procs GFlops 1976 Cray 1 1 0. 1 1993 1982 Cray XMP 4 0. 9 1986 Cray 2 4 1989 Cray YMP 8 1989 1992 Year Mach Procs GFlops Cray T 3 D 1024 152 1994 Fujitsu VPP 140 236 2 1996 Hitachi SR 2 2048 368 2. 7 1997 Intel 9152 1830 6144 3072 8192 12, 288 5120 40, 960 ASCI-R TMC CM-2 8192 TMC CM-5 1024 28 1999 SGI ASCI-BM 131 A 1 -year calc in 1980 = 5. 4 sec today A 1990 HPC = a laptop today University at Buffalo The State University of New York 2000 IBM ASCI-W 2002 NEC E. S. Center for Computational Research CCR

Earth Simulator in Japan (NEC Vector Supercomputer) University at Buffalo The State University of New York Center for Computational Research CCR

Earth Simulator n 40 TFlops Peak n Homogeneous, Centralized, Proprietary, Vector n Expensive! n CFD-Weather, Climate, Earthquake n 640 NEC SX/6 Nodes (5120 CPUs) n Footprint = 4 tennis courts n $6 M/year in power University at Buffalo The State University of New York Center for Computational Research CCR

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 Folding n Ability of proteins to perform biological function is attributed to their 3 -D structure. n Protein folding problem refers to the challenge of predicting 3 -D structure from amino-acid sequence. n Solving the protein folding problem will impact drug design. 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

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

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

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

WNY Biomedical Advances n PSA Test (screen for Prostate Cancer) n Avonex: Interferon Treatment for Multiple Sclerosis n Artificial Blood n Nicorette Gum n Fetal Viability Test n Implantable Pacemaker n Edible Vaccine for Hepatitis C n Timed-Release Insulin Therapy n Anti-Arrythmia Therapy q Tarantula venom n Direct Methods Structure Determination q Listed on “Top Ten Algorithms of the 20 th Century” q Vancomycin q Gramacidin A n High Throughput Crystallization Method: Patented n NIH National Genomics Center: Northeast Consortium n Howard Hughes Medical Institute: Center for Genomics & Proteomics University at Buffalo The State University of New York Center for Computational Research CCR

Bioinformatics in Buffalo n UB Center for Advanced Bioengineering & Biomedical Technologies q $1 M/yr NYS q Med Tech for Product Dev & Commer. n Center Disease Modeling & Therapy Discovery q UB, HWI, RPCI, Kaleida q $15. 3 M NYS q Software, device development, and drug therapies n Buffalo Center of Excellence in Bioinformatics q UB, HWI, RPCI q $61 M NYS q $10. 6 M Federal Government q $151 Corporate Funding q Significant Local Foundation Support University at Buffalo The State University of New York Center for Computational Research CCR

Buffalo Center of Excellence in Bioinformatics n Act as a research, development, education, and economic resource for industries based on bioinformatics, including information technology, biotech, and pharmaceuticals. n Combine state-of-the-art computational facilities with high -throughput experimental facilities to enable the development of new medical treatments. n Develop and exploit new algorithms for data acquisition, storage, management, and transmission. 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

2003 H. S. Summer Workshop Bioinformatics n June 30 – July 11 n Perl Scripts n Public Databases n Filtering Results n Graphics & Visualization n Contact q Dr. Bruce Pitman (pitman@buffalo. edu) University at Buffalo The State University of New York Center for Computational Research CCR

Lunch & Exhibition miller@buffalo. edu www. ccr. buffalo. edu H. S. Program pitman@buffalo. edu University at Buffalo The State University of New York Center for Computational Research CCR