SimMillenniumSimMillennium: Computer Systems, Computational Science and Engineering in the Large Jim...

SimMillennium:Computer Systems,

Computational Science and Engineering in the Large

Jim Demmel, David Culler

E. Brewer, J. Canny, A. Joseph, J. Landay, S. McCanne

A. Neureuther, C. Papadimitrou, C. Sequin, K. YelickEECS, UC Berkeley

www.millennium.berkeley.edu

NSF CISE EIA RI and MII PI’s Workshop

Aug 7-9 1999

Millennium 2

Project Goals

• Enable major advances in Computational Science and Engineering

– Simulation, Modeling, and Information Processing becoming ubiquitous

– Many participants outside CS

• Explore novel design techniques for large, complex systems

– Fundamental Computer Science problems ahead are problems of scale

– Use Capitalism, not Socialism (i.e. not Computer Center)

• Develop fundamentally better ways of assimilating and interacting with large volumes of information

– and with each other

• Explore emerging technologies– networking, OS, devices

Millennium 3

Outline

• Background on UC Berkeley

• Millennium infrastructure description

• Other infrastructure contributions

• Systems research– Networking

– Computational Economy

• Applications– List of all participants

– A few highlights

• Conclusions

Millennium 4

Background at UC Berkeley

• Mammoth NSF RI (1988-1993)– CM-5

• Titan NSF RI (1994-1999)– Culler, spoke yesterday

– NOW = Network of Workstations

• Curriculum– CS 267 - Applications of Parallel Computing

– MS in Comp Sci & Eng Curriculum

– Proposed Comp Eng Sci undergrad program

• NERSC at LBNL– National Energy Research Scientific Computing Center

– Supercomputer center next to campus

• SimMillennium (1998-2003)

Millennium 5

Planned Millennium Infrastructure

Millennium 6

The Community

School of Info. Mgmt and Sys.

Computer Science

Electrical Eng.

Mechanical Eng.

BMRC

Nuclear Eng.

IEORCivil Eng.

Inst. OfTransport

Business

Chemistry

Astro

Physics

Biology

EconomyMath

Geo

Millennium 7

NT Workstations for Sci. & Eng.

SIMS

C.S.

E.E.

M.E.

BMRC

N.E.

IEORCivil Eng

Transport

Business

Chemistry

Astro

Physics

Biology

EconomyMath

Geo

Millennium 8

SMP => storage, small-scale parallelism

SIMS

C.S.

E.E.

M.E.

BMRC

N.E.

IEORCivil Eng

Transport

Business

Chemistry

Astro

Physics

Biology

EconomyMath

Geo

Millennium 9

Group Cluster of SMPs => Parallelism

SIMS

C.S.

E.E.

M.E.

BMRC

N.E.

IEORCivil Eng

NERSC

Transport

Business

Chemistry

Astro

Physics

Biology

EconomyMath

Geo

Millennium 10

Campus Cluster => large-scale Parallelism

SIMS

C.S.

E.E.

M.E.

BMRC

N.E.

IEORCivil Eng

NERSC

Transport

Business

Chemistry

Astro

Physics

Biology

EconomyMath

Geo

Millennium 11

Gigabit Ethernet Connectivity

Gigabit Ethernet

SIMS

C.S.

E.E.

M.E.

BMRC

N.E.

IEORCivil Eng

NERSC

Transport

Business

Chemistry

Astro

Physics

Biology

EconomyMath

Geo

Millennium 12

Physical Connectivity

Millennium 13

Visualization and Novel User Interfaces

Millennium 14

Current Infrastructure (by end of 8/99)

• All 195 desktops and 20 SMPs delivered

• All 18 16-(or smaller)-processor clusters (8 dual SMPs)

– Mostly running Myrinet interconnects, some 100Mb Ethernet

• NOW functioning as large central cluster

• Cluster build service

• Millennium wide services– .5 Tbyte file server

– distributed system services and software for UNIX and NT

• Optical fiber for Gigabit in place

• 10 Gigabit switches purchased

• 2 Vision Maker Digital Desks purchased

Millennium 15

A Millennium Cluster

• 16x2 Processor

• 400 MHz Pentium II

• 100 MHz Memory Bus

• 33 MHz 32-Bit PCI

• 100BaseTX Ethernet

• Myrinet M2F

• Windows NT 4.0 or LINUX– Terminal Server Edition

Millennium 16

Industrial / Academic Collaboration

• Computers via Intel Technology 2000 grant– 200 NT desktops

– 16 department 4-way SMPs

– 10+ 8x2 Group Clusters,

– 1 ~200x2 Campus Cluster

– PPro => Pentium II => Pentium III

• Additional storage via IBM SUR grant– 0.5 TB this year => 4 TB

• NT tools via Microsoft grant

• Solaris x86 tools via SMCC grant

• Nortel discounts the gigabit Ethernet 70%

• Campus provides 3 technical staff, fiber

• Research provides the prog. and system support

200 Gflop/s

150 GB memory

8 TB disk

Millennium 17

What NSF is paying for

• Fast internal networks for clusters

• Gigabit ethernet switches

• Interesting I/O devices– Large displays

– 3D glasses

– Haptic mice

– Position sensors

• One staff person

Millennium 18

Primary Faculty Participants - 1

• CS – D. Culler, J. Demmel, E. Brewer, J. Canny, A. Joseph, R. Katz, J. Landay, S. McCanne, C.

Papadimitriou, C. Sequin, R. Wilensky, K. Yelick

– Systems, Numerical Methods, Services, HCI, Networking, Computational Economics, Digital libraries, Parallel languages

• EE – A. Neureuther

– Technology CAD for EBEAM Lithography

• Civil Engineering – S. Govindjee, G. Fenves

– Earthquake Engineering, Finite Element Modeling

• Physics – B. Price, J. Wurtele, D. Lowder

– Processing neutrinos and muons at South Pole

• SIMS – H. Varian, R. Larson, M. Hearst– Computational Economics, User Interfaces

Millennium 19

Primary Faculty Participants - 2

• Astronomy – J. Arons, C. McKee. P. Marcus

– Star Formation, Geophysical Turbulence

• Transportation Studies – S. Sastry, A. Kanafani

– Redesign of Nation’s Air Traffic Control System

Millennium 20

Secondary Faculty Participants - 1

• Geology/Geophysics – M. Richards, D. Dreger

– Mantle modeling

• Math – D. Eisenbud, B. Poonen, A. Grunbaum, T. Slaman, B. Sturmfels, P. Vojta

– Crystal growth modeling, tomography, symbolic computing

• Berkeley Multimedia Research Center – L. Rowe

– Video effects processing

• Mechanical Engineering– V. Carey, M. Frenklach, A. Packard, P. Papadopoulos, P. Marcus

– Modeling Automated Highways, Material Processing

• Biology – D. Lindberg, S. Brenner

– Reconstruct Phylogenetic Tree of Life, Genome studies

• Nuclear Engineering – J. Vujic

– Planning radiotherapy for Brain Tumors

Millennium 21

Secondary Faculty Participants - 2

• NERSC – W. Saphir

• Business – N. Hakansson

– Computational Finance Laboratory

• Chemistry – K. Durkin, D. Chandler, D. Harris, W. Lester, W. Miller, R. Stevens, B.

Whaley

– Computational Chemistry, Molecular Dynamics Visualization

• Economics – A. Nevo

– Market Modeling

Millennium 22

The CS Research Agenda

• High Performance Cluster Computing Environment

– Fast communication on Clusters of SMPs

– Compiler Techniques for Performance and Ease of use

– Numerical Techniques and Solvers

» Particles, FFT, AMR, Multigrid, Sparse and Dense Lin. Alg.

• Novel System Design Techniques– Clusters of clusters

– Computational Economy

– Open infrastructure services

• Novel modes of interacting with large amounts of data

– User interfaces, Digital Libraries

Millennium 23

Communication Interface Revolution

• Low Overhead Communication “Happens”

• Academic Research put it on the map– Active Messages (AM), FM, PM, … Unet

– Memory Messaging (Get/Put, Reflective, VMMC, Mem. Chan.)

• Intel / Microsoft / Compaq recognized it

– Virtual Interface Architecture 1.0 released 12/16/97

• Berkeley VIA over Myrinet released on NT and Linux

Millennium 24

World-Record Datamation Sort

0

2

4

6

8

10

2 4 6 8 10 12 14 16Nodes

Tim

e ( m

sec)

WriteSortReadOverhead

VIA

Win

soc

k

OldRecord(NOW)

Millennium 25

Computational Economy Approach

• System has a supply of various resources

• Demand on resources revealed in price– distinct from the cost of acquiring the resources

• User has unique assessment of value

• Client agent negotiates for system resources on user’s behalf

– submits requests, receives bids or participates in auctions

– selects resources of highest value at least cost

Millennium 26

Advantages of the Approach

• Decentralized load balancing– according to user’s perception of what is important, not system’s

own metric

– adapts to system and workload changes

• Creates incentive to adopt efficient modes of use– exploit under-utilized resources

– maximize flexibility (e.g., migratable, restartable applications)

• Establishes user-to-user feedback on resource usage

– basis for exchange rate across resources

• Powerful framework for system design– Natural for client to be watchful, proactive, and wary

– Generalizes from resources to services

• Rich body of theory ready for application

Millennium 27

Current Prototype• Specify #procs p and value on job

– rexec -n 16 -value 20 fft.mpi

• Market-based Proportional Sharing– Bidder i gets fraction bi / k bk of resource

– If one bidder, no cost to use resource

– Resource may be CPU, Memory, Network, I/O

• Existing OS mechanisms/policies insufficient– New proportional CPU schedule for LINUX

– New page replacement policy

– Game theoretic analysis

• Preliminary experience in CS267– Students trusted system to allocate fairly, so they did not try to flood

system with jobs

• Future work – other mechanisms and analysis (Vikrey auction, batch vs interactive)

– package up and market services (make, popular simulators, DB search)

Millennium 28

Application Highlights

• PEER - NSF Earthquake Engineering Center– FE modeling of Bay Area during Big One

– Need better parallel sparse linear system solvers

• EBEAM - Electron Beam Lithography– Simulate next generation chip manufacturing

– Need better parallel N-body force calculation

• AMANDA – Antarctic Muon and Neutrino Detector Array

– Need to process many detector tracks for events

• Web Page Design– Better human interfaces using novel devices

• Digital Library– Support access to large active document collection

Millennium 29

Earthquake Modeling

• PEER = Pacific Earthquake Engineering Research Center

• UC, Caltech, Stanford, USC, U Washington

• Model behavior of civil infrastructure in Big One

• Improve earthquake resistant designs

• Requires large scale FE models– Buildings, roads, bridges, etc. coupled to ground

– Simulate effects of earthquakes

– Requires solution of very large sparse linear systems

• Collaboration on software– G. Fenves - OO Finite Element Modeling System

– J. Demmel - direct and iterative parallel linear equation solvers

» Prometheus - a multigrid solver for FE problems (M. Adams)

» SuperLU - sparse Gaussian elimination (X. Li)

• Port from Cray T3E to Millennium

Millennium 30

SuperLU Scales well on Millennium

Millennium 31

Millennium sometimes beats a Cray T3E

Millennium 32

EBEAM - Lithography Simulation

• A. Neureuther and J. Demmel

• Simulate future chip manufacturing devices which will use electron beams instead of light

• Computational Bottleneck: computing electrostatic forces on electrons

• Pbody (D. Blackston)– Parallel O(N) or O(N log N) N-Body code

– Incorporates Barnes-Hut / Fast Multipole Method / Anderson in unified framework

– Portable across many platforms

– Easy to tune for accuracy and performance

• Now used in production runs

• Will be packaged as Web service on Millennium, with other TCAD tools

Millennium 33

Performance of Pbody

Timings for Pbody

0

50

100

150

200

250

300

350

1 2 3 4

Number of processors

se

co

nd

s

200K EBEAM

100K Uniform

Parallel Efficiency of Pbody

0

0.2

0.4

0.6

0.8

1

1.2

1.4

1 2 3 4

Number of processors

Eff

icie

nc

y200K EBEAM

100K Uniform

• Over 90% efficient on 4 Millennium procs

• 61 secs for 200K electrons on 1 proc– (vs 46 secs for Cray T3E)

• 500x faster than direct O(N2) method

Millennium 34

AMANDA

• Antarctic Muon And Neutrino Detector Array

• International project to detect particles in 1 km3 of ice at South Pole

• 98 scientists, 15 universities, 4 countries

• Millennium uses– Machine at South Pole for data collection, webcast,

teleconference

– Used in PBS broadcast ``Passport to Knowledge: Live from the Pole” in 1998 linking schoolchildren in Mississippi to South Pole crew

– Simulation of AMANDA events and calculating optical properties of the ice

Millennium 35

Millennium 36

Better Interfaces for Web Site Design

• J. Landay, Raecine Sapien (SUPERB student)

• Most web designers do not like to program, edit

• Provide a more natural user interface that matches their style

• Exploit large displays, position trackers, vision and gesture recognition to make design easier and faster

• Prototype (minus vision) built over summer, evaluated on a group of designers

Millennium 37

Web Site Design Issues

Taken from Contextual Design

Beyer & Holtzblatt

Millennium 38

System Components

• Physical components– Vision system

– CrossPad

– Digital Desk

– Command Area

Millennium 39

Second User Tests

Digital Libraries: Rethinking Scholarly Information

Dissemination and Use

Robert WilenskyPrincipal Investigator

David ForsythCo-principal Investigator

The UC Berkeley Digital Library Team

Millennium 41

Goal: Complete Rethinking of How we Use Information

• Must support – entire “information cycle”: creation, dissemination and collaboration

» in addition to organization, access, presentation and preservation

– non-textual material (photos, video, maps)

» in addition to text-based content

– primary data sources, informal “publication”

» as well as traditional archival product

– radically new modes of use

• Scholarly information use is an especially attractive place to start.

Millennium 42

GIS Viewer: Streetfinder example

Millennium 43

GIS Viewer Example

Millennium 44

Conclusions:What is Millennium About?

• An experiment in large-scale system design

• Advance the state of computational science and engineering

• Exploring novel design techniques

• Exploring important new technologies

• NSF support essential