Center for Computational Research
University at Buffalo

Russ Miller, Director

Professor of Computer Science & Engineering

Senior Research Scientist @ Hauptman-Woodward Inst.

CCR Overview

Supercomputing Center

High-Performance Computing (9TF; 250TB)

High-End Visualization

$42M New Grants

Support ~100 Groups in ~25 Depts + 12 Industry

Bioinformatics Center

$61M NYS; $3M Feds; $53M New Grants;

$3.5 Foundation; $135M Corporate

Degree Programs

Education/Outreach/Training

H.S. Summer Program

Hosts Meetings/Provides Tours

Work with Local Industry & Local Colleges

M.S. Certificate Program in Compt’l Sci

CCR Computing

Dell Linux Cluster

5.8TF Peak; 4036 Processors (PIII 1.2GHz + P4 2.4GHz)

2TB RAM; 160TB Disk

16TB RAID

Dell Linux Cluster

2.9TF Peak; 304 Processors (P4 2.4GHz)

Myrinet2000

600GB RAM; 40TB Disk

HP/Compaq SAN (Oct, 2002)

25TB Disk

250TB Tape

HP/Compaq 1TF EV7 Alpha System (3/03)

CCR Visualization

Urban Planning

Manufacturing

Medical Imaging

Computational Science

Simulation & Modeling

Historical Reenactments

Multimedia Presentations

Sample CCR-Supported Research

Groundwater Modeling

Predict contaminant flow in groundwater & possible migration into streams and lakes.

Geophysical Mass Flows

Study of geophysical mass flows for risk assessment of lava flows and mudslides.

Astrophysics

Determine whether interacting astrophysical jets in dense star environments can generate turbulence in surrounding medium

Bioinformatics

Protein Folding (Computer simulations determine the 3D structure of proteins.)

Pharmacology

Computational Chemistry

Algorithm Development & Simulations

Fluid Dynamics

Modeling turbulent flows and combustion to improve design of chemical reactors, turbine engines, and airplanes.

Groundwater Flow Modeling

Regional-scale modeling of groundwater flow and contaminant transport (Great Lakes Region)

Ability to include all hydrogeologic features as independent objects

Analytic Element Method

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

Computational Geophysical Mass Flows

Risk Mitigation

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

Computational Astrophysics

Applications:

Star Formation

Winds from Evolved Stars

Astrophysical Magnetohydrodynamics

Plasma Physics

Computational Methods and Requirements

Developing 3-D Adaptive Mesh Refinement Code

Ionization dynamics and chemistry

Radiation transfer

Magnetic fields

Code parallelized via MPI

Moderate sized runs require parallel machines (> 32 PE)

Interacting Astrophysical Jets

Unresolved Issue: Can interacting jets in a dense star environment generate turbulence in surrounding medium?

Molecular Structure Determination

SnB Software by UB/HWI

“Top Algorithms of the Century”

Critical to Rational Drug Design

Important Link in Structural Biology

Vancomycin - Antibiotic of Last Resort

Current Research

Grid Computing

Data Mining

Collaboratory

Children’s Hospital CT

3D Reconstruction of CT Dataset

Created with the Visualization Toolkit (VTK) on a Linux Workstation

3D Isosurface Clearly Shows Structure that is Nearly Impossible to Determine from 2D Slices

Recent Viz Acquisitions

Hardware

Portable Systems

Additional Workbench

SGI 3300W

Access Grid Node

Tiled Display Wall

Onyx3 with IR4 graphics

Contact Information

miller@buffalo.edu

www.ccr.buffalo.edu

www.bioinformatics.buffalo.edu


	Russ Miller, Director
	Professor of Computer Science & Engineering
	Senior Research Scientist @ Hauptman-Woodward Inst.


	Supercomputing Center
		High-Performance Computing (9TF; 250TB)
		High-End Visualization
		$42M New Grants
	Support ~100 Groups in ~25 Depts + 12 Industry
		Bioinformatics Center
		$61M NYS; $3M Feds; $53M New Grants;
		$3.5 Foundation; $135M Corporate
		Degree Programs
	Education/Outreach/Training
		H.S. Summer Program
		Hosts Meetings/Provides Tours
		Work with Local Industry & Local Colleges
		M.S. Certificate Program in Compt’l Sci


	Dell Linux Cluster
		5.8TF Peak; 4036 Processors (PIII 1.2GHz + P4 2.4GHz)
		2TB RAM; 160TB Disk
		16TB RAID
	Dell Linux Cluster
		2.9TF Peak; 304 Processors (P4 2.4GHz)
		Myrinet2000
		600GB RAM; 40TB Disk
	HP/Compaq SAN (Oct, 2002)
		25TB Disk
		250TB Tape
	HP/Compaq 1TF EV7 Alpha System (3/03)


	Urban Planning
	Manufacturing
	Medical Imaging
	Computational Science
	Simulation & Modeling
	Historical Reenactments
	Multimedia Presentations


	Groundwater Modeling
		Predict contaminant flow in groundwater & possible migration into streams and lakes.
	Geophysical Mass Flows
		Study of geophysical mass flows for risk assessment of lava flows and mudslides.
	Astrophysics
		Determine whether interacting astrophysical jets in dense star environments can generate turbulence in surrounding medium
	Bioinformatics
		Protein Folding (Computer simulations determine the 3D structure of proteins.)
		Pharmacology
	Computational Chemistry
		Algorithm Development & Simulations
	Fluid Dynamics
		Modeling turbulent flows and combustion to improve design of chemical reactors, turbine engines, and airplanes.


	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


	Applications:
	Star Formation
	Winds from Evolved Stars
	Astrophysical Magnetohydrodynamics
	Plasma Physics


	Developing 3-D Adaptive Mesh Refinement Code
		Ionization dynamics and chemistry
		Radiation transfer
		Magnetic fields
	Code parallelized via MPI
	Moderate sized runs require parallel machines (> 32 PE)


	Unresolved Issue: Can interacting jets in a dense star environment generate turbulence in surrounding medium?


	SnB Software by UB/HWI
		“Top Algorithms of the Century”
	Critical to Rational Drug Design
	Important Link in Structural Biology
	Vancomycin - Antibiotic of Last Resort
	Current Research
		Grid Computing
		Data Mining
		Collaboratory


	3D Reconstruction of CT Dataset
	Created with the Visualization Toolkit (VTK) on a Linux Workstation
	3D Isosurface Clearly Shows Structure that is Nearly Impossible to Determine from 2D Slices


Hardware
	Portable Systems
	Additional Workbench
		SGI 3300W
	Access Grid Node
	Tiled Display Wall
	Onyx3 with IR4 graphics


	miller@buffalo.edu
	www.ccr.buffalo.edu
	www.bioinformatics.buffalo.edu