Computer Architecture

1
CPEG Reseach Activities An Overview
Guang R. Gao Computer Architecture and Parallel
Systems Laboratory Dept. of Electrical and
Computer Engineering University of
Delaware ggao_at_capsl.udel.edu
2
CPEG Faculty

• John Elias
• Guang R. Gao
• Dave Mills
• Fouad Kiamilev
• Kevin Theobald
• Peter Warter (Emeritus)

3
Research Areas

• Traditional Computer Engineering Research Areas
• Computer Networking (Mills)
• VLSI Design for Optical Comm. (Kiamilev)
• Computer Systems, Compilers and Software (Gao)
• Neuromorphic Engineering and User Interfaces
  (Elias)
• Computer Architecture and Hardware (Theobald)
• High-Performance Computing for Biotechnology

4
John Elias Research Interests

• Neuromorphic Engineering
• Silicon neurons
• Neurocomputation
• User Interfaces (collaboration with Prof.
  Westerman)
• Gesture based
• Multi-hand and Multi-finger
• Unified (touch, voice, force, gesture, etc.)

5
Professors Westerman and Elias The FingerBoard

• Integrates typing, mouse, and gesture input.
• Touch sensitive surface images multiple fingers
  and multiple hands.
• Gesture used to control graphics, text, and apps.

Commercialization underway
6
FingerBoard Product Concept
7
FingerBoard Product Concept
8
Kiamilev Active Projects

• Honeywell (DARPA VLSI Photonics)
• Lockheed (DARPA STAB)
• Mayo (DARPA VLSI Photonics)
• GMU (DARPA P-WASSP)
• OE Consortium East Coast (DARPA)
• GORE Photonics (IRD)
• SUN Microsystems (IRD)
• Xilinx (Teaching equipment grant)

9
CVORG CMOS for VLSI Opto-Electronics Group Prof.
Fouad Kiamilev, Jeremy Ekman, Premanand
Chandramani, Ping Gui, Xiaoqing Wang, Muhammad
Fikri, Amitava Bhaduri
12Gbit/sec PCI NIC for workstation clusters.
Demonstrated communication between 2 dell
workstations in Q4/2000. Funding Source Darpa
MTO Partners Honeywell, Sun, Intel
10Gbit/sec SiGe circuits and advanced
communication and power-saving protocols for
parallel optical links. Funding Source Darpa
MTO, ITO Partners Raytheon, Mayo Clinic, BAE
32-port 12Gbit/sec/port router using MCM and
free-space optical interconnect. Funding Darpa
Partners Honeywell
10
Mills Research Projects

• Autonomous Configuration and Authentication in
  Very Large Networks
• Simulation of Very Large Networks
• CAKRD/DARTnet Collaboration
• Network Time Synchronization Project
• Precision Time Synchronization
• Fault-Tolerance Time Synchronization

11
Kevin B. Theobald

• Models for parallel computation based on
  two-level multithreading
• Evolutionary path to effective MPP for irregular
  applications on COTS processors
• Hardware prototype SU being developed for cluster
  of 16 PCs

EARTH (Efficient Architecture for Running
Threads) divides processing between a COTS
"Execution Unit" and a custom "Synchronization
Unit"
12
Gao Research Projects

• Execution model for the HTMT Petaflop
  Architectures
• High-Performance Compiler Infrastructure
• Power-Aware Software Optimization for Embedded
  Architectures
• Architecture/Compiler Design Issues for
  Single-Chip Multiprocessors
• High-Performance Visualization

13
CPEG Bioinformatics Research --Overview

• Introduction
• Research Focus and Infrastracture
• A Profile on Pilot Projects
• Summary

14
Core Intellectual Capacity -- An Overview
Bio/Medical applications
Core Technology/Asset
Discovery Informatics
Embedded System and Applications
HPC System and Applications
15
Computation Biology/Bioinformatics Overview
Data collection Organization

• focus
• Parallelization of
• certain key
• information
• mining and
• discovery
• algorithm
• High-performance
• modeling and
• simulation tools
• - Virual reality visualization tools

Information Mining Discovery
Modeling
Database
Simulation/ Emulator
Result presentation/visualization
16
CAPSL Bioinformatics Portal Service Model
User-1
User-2
User-n
. . .
CAPSL BIOINFOR Web Interface
Public Resources
CAPSL HPC Bioinformatic toolbox
CAPSL internal Database
High-speed Network
External Private Resources
High-Performance Parallel Computing Servers
EARTH Technology
17
High-Performance Bioinformatic Toolset/Testbed
Modeling/Simulation/Emulation
Multiple Sequence Alignment Visualization
Pathway Analysis Visualization
Expression Analysis Visualization
Sequence Database Tools
Array Database tools
Pathway Database tools
A Sketch of CAPSL Bioinformatic Tool Development
18
Pilot Research Projects

• Discovery Informatics
• sequence similarity search
• structure homology search (MSA, SNP, etc.)
• pattern discovery for arrays
• Predictive Modeling and Simulation
• biological pathway modeling and simulation
• protein structure prediction
• Visulaization

19
BIO
Transcript expression Profiles across
perturbation series
Arterial Baroreceptors
Cardiac Ganglion
Heart and Peripheral Vasculature
mRNA in identified cell type
(a) Intercellular Level
Principal Neuron and other homeostatic control
neurons
Inter NA/DMN
NTS
Cardiorespiratory control circuit
(b) Signaling Pathway
Ca2
messenger
MICRO
p3
Threaded programs
p1
p2
p4
receptor
K
BIOMEX Platform
Modeled by ODE dr dt dp dt
(c) Gene Network
Threaded Algorithm for ODE/PDE implementation
BIOMEX Engine
Protein
DNA
mRNA
f(p) - Vr
High-speed net
Protein
DNA
mRNA
Lr - Up
Bioinformatics Server
Visualization Server
BioMEX Model and Testbed
INFO
20
New Bioinformatics Courses

• ELEG 667-13 Discovery Informatics fall 2000
  (with Prof. Javier Garcia-Frias )
• ELEG 667-13 Discovery Informatics II Spring
  2001 (With Prof. Javier Garcia-Frias)
• ECE/DBI Joint Distinguished Seminar IBM Blue
  Gene Project (M. Snir)
• Other ECE/CAPSL seminars (NCBI, Fox Chase, etc.)

21
Industry Connections

• DuPont
• AstroZenica
• Others

22
Summary

• Multi-discipline team for novel algorithms,
  modeling and visualization methods
• In-house high-performance computing capability
  for joint research with collaborators
• New education activities tighted into rigorous
  research programs