Grid Computing: Application Development - Computer …johnsson/Talks/NGSSC_Grid_Computing_2_2003-0… · Grid Computing: Application Development. ... – Designing and constructing

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August 19, 2003 NGSSC School on Grid Computing Lennart Johnsson

Grid Computing:Application Development

Lennart JohnssonDepartment of Computer Science and

the Texas Learning and Computation CenterUniversity of Houston

Houston, TXDepartment of Numerical Analysis and Computer Science and PDC

Royal Institute of TechnologyStockholm, Sweden

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Grids are “Hot”

Courtesy Ken Kennedy

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Grids: Application Development


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Grids: Middleware Development


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Grids: Administration


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Grid Application Development


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Grid Application Development: A Software Grand Challenge

• Goal: Reliable performance on heterogeneous platforms, under varying load on computation nodes and on communications links

• Challenges:– Presenting a high-level application development interface

• If programming is hard, its useless

– Designing and constructing applications for adaptability– Mapping applications to dynamically changing configurations– Determining when to interrupt execution and remap

• Application monitors• Performance estimators

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What is Needed• Execution infrastructure for reliable performance

– Automatic resource location and execution initiation – dynamic configuration to available resources

• Performance monitoring and control strategies– deep integration across compilers, tools, and runtime systems– performance contracts and dynamic reconfiguration

• Abstract Grid programming models and easy-to-use programming interfaces– design of an implementation strategy for those models– problem-solving environments

• Robust reliable numerical and data-structure libraries– predictability and robustness of accuracy and performance– reproducibility, fault tolerance, and auditability

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GrADSoft Architecture• Goal: reliable performance under varying load

Whole-ProgramCompiler

Libraries

DynamicOptimizer

Real-timePerformance

MonitorPerformance

Problem

ServiceNegotiator

Scheduler

GridRuntimeSystem

SourceAppli-cation

Config-urableObject

Program

SoftwareComponents

Performance Feedback

Negotiation

GrADS Project (NSF NGS): Berman, Chien, Cooper, Dongarra, Foster, Gannon Johnsson, Kennedy, Kesselman, Mellor-Crummey, Reed, Torczon, Wolski

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GrADSoft ArchitectureProgram Preparation System Execution Environment


Libraries

DynamicOptimizer


MonitorPerformance

Problem

ServiceNegotiator

Scheduler

GridRuntimeSystem

SourceAppli-cation

Config-urableObject

Program

SoftwareComponents


Negotiation

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High Level Programming System• Built on Libraries Coded by Professionals

– Included mapping strategies and cost models– High level knowledge of integration strategies

• Integration Produces Configurable Object Program– Integrated mapping strategy and cost model– Performance enhanced through context-dependent variants– Context includes potential execution platform

• Dynamic Optimizer Performs Final Binding– Implements mapping strategy– Chooses machine-specific variants– Inserts monitoring probes

• Strategy: move compilation overhead to PSE-generation time

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Configurable Object Program• Representation of the Application

– Supporting dynamic reconfiguration and optimization for distributed targets, may include

• Program intermediate code• Annotations from the compiler

– mapping strategy and performance model• Historical information (run profile to now)

• Mapping strategies– Aggregation of data regions (submeshes) or tasks– Definition of parameters for algorithm selection

• Challenge: synthesis of performance models– User input, especially associated with libraries– Synthesize different components, scale models to problem size

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Execution Cycle• Configurable Object Program is presented

– Space of feasible resources must be defined– Mapping strategy and performance model provided

• Service Negotiator solicits acceptable resource collections– Performance model is used to evaluate each– Best match is selected and contracted for

• Execution begins– Dynamic optimizer tailors program to resources

• Selects mapping strategy• Inserts sensors

• Contract monitoring is conducted during execution– Soft violation detection based on fuzzy logic

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Performance Contracts• At the Heart of the GrADS Model

– Fundamental mechanism for managing mapping and execution

• What are they?– Mappings from resources to performance – Mechanisms for determining when to interrupt and reschedule

• Abstract Definition– Random Variable: r(A,I,C,t0) with a probability distribution

• A = app, I = input, C = configuration, t0 = time of initiation• Important statistics: lower and upper bounds (95% confidence)

• Challenge– When should a contract be (viewed as) violated?

• Strict adherence balanced against cost of reconfiguration

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Grids - Performance

Courtesy Dan Reed

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Grids - Performance

Courtesy Dan Reed

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Performance Signatures

Courtesy Dan Reed

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Contract Monitoring

• Input:– Performance model

• Integrated from a variety of sources: user, compiler, application experience, application signatures

– Resources contracted for

• Trigger– Registration information from sensors installed in applications

• Inserted by dynamic optimizer or user

• Output– Rule based contract monitor that decides when contract violation

is serious enough to merit reconfiguration• Based on information from sensors

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Grid Computing – Core Library

Courtesy Jack Dongarra

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Grid Computing – Core Library


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Grid Computing – Library Use


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Grid Computing – Library Use


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GrADS Library SequenceLibraryRoutineUser

User makes a sequential callto a numerical library routine.The Library Routine has “crafted code”which invoke other components.

Slide courtesy Jack Dongarra

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GrADS Library SequenceLibraryRoutineUser Resource

Selector

Library Routine calls a grid based routine to determine which resources are possible for use. The Resource Selector returns a “bag of processors” (coarse grid) that are available.


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LibraryRoutineUser Resource

Selector

PerformanceModel

The Library Routinecalls the Performance Modeler to determine thebest set of processors to usefor the given problem. May be done by evaluating aformula or running a simulation.May assign a number of processes toa processor. At this point have a fine grid.

GrADS Library Sequence


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LibraryRoutineUser Resource

Selector

PerformanceModel

ContractDevelopment

The Library Routine calls theContract Development routineto commit the fine grid for this call. A performance guarantee is generated.



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LibraryRoutineUser

ResourceSelector

PerformanceModel

ContractDevelopment

AppLauncher


“mpirun –machinefile fine_grid grid_linear_solve”


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Grids – Library Evaluation


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Arrays of Values Generated by

Resource Selector

x x x x x xx x x x x xx x x x x xx x x x x xx x x x x xx x x x x x

x x x

xx x x x x x x x x x x x x x x x

x x

x

x

x x x x x x x x x x x x x x x x x x x x x x x x x

x

xx x x x x x x x

x x x x x xx x x x x xx x x x x xx x x x x xx x x x x x

• Clique based– 2 @ UT, UCSD, UIUC – Full at the cluster level

and the connections (clique leaders)

– Bandwidth and Latency information looks like this.

– Linear arrays for CPU and Memory Courtesy Jack Dongarra

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Grids – Performance Models


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Grids – Library EvaluationCourtesy Jack Dongarra

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Sample Application - Cactus

Courtesy Ed Seidel

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Cactus on the Grid

Courtesy Ed Seidel

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Cactus on the Grid

Courtesy Ed Seidel

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Cactus – Migration basis

Courtesy Ed Seidel, Ian Foster

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Cactus – Job Migration


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Cactus – Migration Architecture


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Cactus - Migration exampleCourtesy Ed Seidel, Ian Foster

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Bioimaging

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SynchrotronsSynchrotrons

MacromolecularMacromolecularComplexes, Complexes, Organelles, CellsOrganelles, Cells

Organs, Organ Organs, Organ Systems, OrganismsSystems, Organisms

MicroscopesMicroscopes

Magnetic Resonance Magnetic Resonance ImagersImagers

Imaging InstrumentsMolecules

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500 Å

JEOL3000-FEGLiquid He stageNSF support

No. of Particles Needed for 3-D Reconstruction

8.5 Å 4.5 Å6,000 5,000,000

3,000 150,0008.5 Å Structure of the

HSV-1 Capsid

ResolutionB = 100 Å2

B = 50 Å2

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EMEN Database•Archival•Data Mining•Management

VitrificationRobot Particle Selection

Power SpectrumAnalysis

Initial3D Model

ClassifyParticles

Reproject3D Model

AlignAverageDeconvolute

Build New3D Model

EMAN

Micrographs

• 4 - 64 Mpixels, 16-bit (8 – 128 MB)

• 100 – 200/day per lab

• 10 – 1,000 particles per micrograph

• Several TB/yr

Project

• 200 – 10,000+ micrographs

• 10,000 – 10,000,00 particles

• 10k – 1,000k pixels/particle

• Up to hundreds of PFlops

EM imaging

http://ncmi/ncmi/facilities/<img src=

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EMAN

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GrADSoft

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Grid Application Software

• Managing Data, Codes and Resources Securely

• Performance

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SimDB: A Grid Based Problem Solving Environment

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Molecular Dynamics

Jim Briggs

University of Houston

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Molecular Dynamics Simulations

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Trajectory PropertiesFunction Result

Transport coefficients Scalar

Normal modes Set of scalar values

Solvent residence times Set of scalar values

Average structures 3 x 1D coordinates

Animation 3 x 1D coordinates x N frames

Radial distribution functions 1D histogram

Energy profiles 1D or 2D histogram

Solvent densities 2D or 3D histogram

Angles/distances between solute groups 1D time series

Atom-atom distances 1D time series

Dihedral angles 1D time series

Root mean square deviations 1D time series

Simple thermodynamic properties 1D time series

Time correlation functions 1D time series

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SimDB Workflow

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SimDBArchitecture

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SimDB Data Access

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SimDBData

Generation

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SimDB Administration

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GrADSoft ArchitectureProgram Preparation System Execution Environment


Libraries

DynamicOptimizer


MonitorPerformance

Problem

ServiceNegotiator

Scheduler

GridRuntimeSystem

SourceAppli-cation

Config-urableObject

Program

SoftwareComponents


Negotiation

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Adaptive Software

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Challenges• Algorithmic

– Multiple data structures and their interaction– Unfavorable data access pattern (big 2n strides)

– High efficiency of the algorithm• low floating-point v.s. load/store ratio

– Additions/multiplications unbalance • Version explosion

– Verification– Maintenance

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• Diversity of execution environments– Growing complexity of modern microprocessors.

• Deep memory hierarchies• Out-of-order execution• Instruction level parallelism

– Growing diversity of platform characteristics• SMPs• Clusters (employing a range of interconnect technologies)• Grids (heterogeneity, wide range of characteristics)

• Wide range of application needs– Dimensionality and sizes– Data structures and data types– Languages and programming paradigms

Challenges

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Opportunities

• Multiple algorithms with comparable numerical properties for many functions

• Improved software techniques and hardware performance

• Integrated performance monitors, models and data bases

• Run-time code construction

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Approach• Automatic algorithm selection – polyalgorithmic

functions– Entirely different algorithms, exploit decomposition of

operations,…• Code generation from high-level descriptions• Extensive application independent compile-time

analysis• Integrated performance modeling and analysis• Run-time application and execution environment

dependent composition • Automated installation process

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Performance TuningMethodology

Input ParametersSystem specifics,

UHFFT Code generator

Library of FFT modules

Performancedatabase

User options

Installation

Input ParametersSize, dim., …

InitializationSelect best plan

ExecutionCalculate one or more FFTs

Run-time

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The UHFFT

• Program preparation at installation (platform dependent)

• Integrated performance models (in progress) and data bases

• Algorithm selection at run-time from set defined at installation

• Automatic multiple precision constant generation• Program construction at run-time based on

application and performance predictions

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The Fast Fourier Transform

n

n

WW

of ionsfactorizat sparse algorithmsFast .operations )( requires ofn Applicatio 2

⇔o

o nO

k21n AAAW K=

. same factor the towaysdifferent Many unique.not ision factorizat Sparse

ops. login evaluated becan ofn Applicatio .log and )operations ( sparse are where

n

n

i

W

WA

o

o

o (n))O(n(n)kO(n) =

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Sparse Factorization Algorithms

• Rader’s Algorithm• Prime Factor Algorithm• Split-radix• Mixed-radix (Cooley-Tukey)

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Notation• Simple way to describe highly structured matrices• Tensor (Kronecker) product

⎟⎟⎟⎟⎟

⎠

⎞

⎜⎜⎜⎜⎜

⎝

⎛

=⊗

−−−−

−

−

BBB

BBBBBB

BA

111110

111110

100100

nnnn

n

n

aaa

aaaaaa

L

MOMM

L

K

matrix blocking matrix, scaling == BA

• Direct sum notation:

⎟⎟⎠

⎞⎜⎜⎝

⎛=⊕

B00A

BA

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Prime Factor Algorithm

tion).multiplicafactor twiddle(noPFA theusingby operations ofnumber thereduce to

possible isit 1gcd and ,When == (r,q) rqn

,

2qr1

2qrqr1n

)ΠW(WΠ

)ΠW)(II(WΠW

⊗=

⊗⊗=

matrices.n permutatio are , where 21 ΠΠ

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Split-radix Algorithm

splitting. 2radix of levels Two algorithm.efficient most the2 When

-n k

o

o =

n,2n/22n/22,n/22n )ΠW(I)DI(WW ⊗⊗=

can write we42 When pqn ==o

n,2q,2qq,2n,

223

pn,pn,qm

p2qq2a

maSR

q,2n,ppqSRn

ΠΠIΠ

WWΩΩIB

)]IW()[II(WB

BBB

)ΠWW(WBW

)(

, )1(~ ,

, ~,

,

⊕=

−⊕=⊕⊕=

⊗⊕⊗=

=

⊕⊕=

i

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Mixed-radix Splittingas written becan ,When nW rqn =

, rn,qrqr,qrn )ΠW(I)DI(WW ⊗⊗=

matrix diagonal a is where factor twiddleD qr,

,1

,1r

n nωω −

−

⊕⊕⊕=

⊕⊕⊕=

L

L

qn,

1rqn,qn,qqr,

Ω

ΩΩID

matrix.n permutatiosort mod a is and -rrn,Π

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Algorithm Selection Logic

if n<=2 DFTelse if n is prime use Rader’s algorithmelse

Chose factor r of nif r and n/r are coprime use PFAelse if n is divisible by (r2) and n>r3

use Split-Radix algorithmelse use Mixed-radix algorithm

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Example N = 6FFTPrimeFactor n = 6, r = 3, dir = Forward, rot = 1

FFTRader n = 3, r = 2, dir = Forward, rot = 1DFT n = 2, r = 2, dir = Forward, rot = 1DFT n = 2, r = 2, dir = Inverse, rot = 1

FFTRader n = 3, r = 2, dir = Forward, rot = 1DFT n = 2, r = 2, dir = Forward, rot = 1DFT n = 2, r = 2, dir = Inverse, rot = 1

DFT n = 2, r = 2, dir = Forward, rot = 1DFT n = 2, r = 2, dir = Forward, rot = 1DFT n = 2, r = 2, dir = Forward, rot = 1

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UHFFT Architecture

Key:Fixed library code

Generated code

Code generator

Unparser Scheduler

Optimizer Initializer(Algorithm Abstraction)

FFT CodeGenerator

Library ofFFT Modules

InitializationRoutines

Mixed-Radix(Cooly-Tukey)

Prime FactorAlgorithm

Split-RadixAlgorithm

Rader'sAlgorithm

ExecutionRoutines

Utilities

UHFFTLibrary

Funded in part by the Alliance (NSF) and LACSI (DoE)

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Optimization Strategy• High level (performed at application

initialization)– Selection of the optimal factorization using

preoptimized codelets– Generation of an execution plan

• Low level – Selected set of codelets– Selected codelets automaticly generated and

highly optimized by a special-purpose compiler

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The UHFFT: Code Generation• Structure

• Algorithm abstraction• Optimization• Generation of a DAG• Scheduling of instructions• Unparsing

• Implementation• Code generator is written in C

• Speed, portability and installation tuning• Highly optimized straight line C code• Generates FFT codelets of arbitrary size,

direction, and rotation

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• Basic structure is an Expression– Constant, variable, sum, product, sign change, …

• Basic functions– Expression sum, product, assign, sign change, …

• Derived structures– Expression vectors, matrices and lists

• Higher level functions– Matrix vector operations– FFT specific operations

• Algorithms currently supported• Rader (two versions), PFA, Split-radix, Mixed-radix

The UHFFT: Code Generation (cont’d)

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The UHFFT: Code Generation Mixed-Radix Algorithm

rn,mrmr,mrn )ΠW(I)DI(WW ⊗⊗=

/** FFTMixedRadix() Mixed-radix splitting.* Input:* r radix,* dir, rot direction and rotation of the transform,* u input expression vector.*/ExprVec *FFTMixedRadix(int r, int dir, int rot, ExprVec *u)

int m, n = u->n, *p;

m = n/r;p = ModRSortPermutation(n, r);u = FFTxI(r, m, dir, rot,

TwiddleMult(r, m, dir, rot,IxFFT(r, m, dir, rot, PermuteExprVec(u, p))));

free(p);return u;

Equation:

Is implemented as:

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The UHFFT: Performance Modeling

• Analytic models• Cache influence on library codes• Performance measuring tools (PCL, PAPI)• Prediction of composed code performance• Updated from execution experience

• Data base• Library codes. Recorded at installation time• Composed codes. Recorded and updated for each

execution.

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The UHFFT: Execution Plan Generation

• Optimal plan search options– Exhaustive– Recursive– Empirical

• Algorithms used – Rader (FFTW, UHFFT)– PFA (UHFFT) – Split-radix (UHFFT) – Mixed-radix (FFTW, SPIRAL, UHFFT)

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Characteristics of Some ProcessorsProcessor Clock

frequencyPeak

PerformanceCache structure

Intel Pentium IV 1.8 GHz 1.8 GFlops L1: 8K+8K, L2: 256K

AMD Athlon 1.4 GHz 1.4 GFlops L1: 64K+64K, L2: 256K

Alpha EV67/68 833 MHz 1.66 GFlops L1: 64K+64K, L2: 4M

PowerPC G4

867 MHz 867 MFlopsL1: 32K+32K

L2: 256K, L3: 1-2M

Intel Itanium 800 Mhz 3.2 GFlopsL1: 16K+16K

L2: 92K, L3: 2-4M

IBM Power3/4 375 MHz 1.5 GFlops L1: 64K+32K, L2: 1-16M

HP PA 8x00 750 MHz 3 GFlops L1: 1.5M + 0.75M

MIPS R1x000 500 MHz 1 GFlop L1: 32K+32K, L2: 4M

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Codelet efficiency

Intel PIV 1.8 GHz AMD Athlon 1.4 GHz

PowerPC G4 867 MHz

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Plan Performance, 32-bit Architectures

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Power3 plan performance

0

50

100

150

200

250

300

350

MFL

OPS

16

2 8

4 4

8 2

2 2

4

2 4

2

4 2

2

2 2

2 2

Plan

222 MHz888 Mflops

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340

350

360

370

380

390

400

410

420

430

"MFL

OPS

"

9 5

8 7

7 9

5 8

5 7

8 9

5 8

7 9

8 9

5 7

8 5

7 9

8 7

9 5

9 7

5 8

5 9

8 7

8 7

5 9

9 5

7 8

9 7

8 5

5 8

9 7

5 7

9 8

7 8

9 5

7 5

8 9

8 5

9 7

9 8

5 7

7 8

5 9

7 5

9 8

8 9

7 5

9 8

7 5

7 9

8 5

5 9

7 8

Plan

n = 2520 (PFA Plan)

IBM Power3 222 MHz Execution Plan Comparison

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HP zx1 Chipset

Features:•2-way and 4-way•Low latency connection to the DDR memory (112 ns)

•Directly (112 ns latency)•Through (up to 12 ) scalable memory expanders (+25 ns latency)

•Up to 64 GB of DDR today (256 in the future)•AGP 4x today (8x in the future versions)•1-8 I/O adapters supporting

•PCI, PCI-X, AGP 2-way block diagram

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Itanium …..Processor Clock frequency

PeakPerformance

Cache structure

Intel Itanium 800 Mhz 3.2 GFlopsL1: 16K+16K

(Data+Instruction)L2: 92K, L3: 2-4M (off-die)

Intel Itanium 2 900 Mhz 3.6 GFlopsL1: 16K+16K

(Data+Instruction)L2: 256K, L3: 1.5M (on-die)

Intel Itanium 2 1000 Mhz 4 GFlopsL1: 16K+16K

(Data+Instruction)L2: 256K, L3: 3M (on-die)

Sun UltraSparc-III 750 Mhz 1.5 GFlopsL1: 64K+32K+2K+2K

(Data+Instruction+Pre-fetch+Write)L2: up to 8M (off-die)

Sun UltraSparc-III 1050 Mhz 2.1 GFlopsL1: 64K+32K+2K+2K

(Data+Instruction+Pre-fetch+Write)L2: up to 8M (off-die)

Tested configuration

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Memory HierarchyItanium-2 (McKinley) Itanium

Size:Line size/Associativity:

Latency:Write Policies:

16KB + 16KB64B/4-way

1 cycleWrite through, No write allocate

16KB + 16KB32B/4-way

1 cycleWrite through, No write allocate


Integer Latency:FP Latency:

Write Policies:

256KB128B/8-wayMin 5 cyclesMin 6 cycles

Write back, write allocate

96K B64B/6-way

Min 6 cyclesMin 9 cycles

Write back, write allocate


Integer Latency:FP Latency:

Bandwith:

3MB or 1.5MB on chip128B/12-wayMin 12 cyclesMin 13 cycles

32B/cycle

4MB or 2MB off chip64B/4-way

Min 21 cyclesMin 24 cycles

16B/cycle

L1I

and

L1D

Unified

L2

Unified

L3

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UHFFT Codelet Performance

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Codelet Performance Radix-2

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GrADS Testbed

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GrADS Testbed

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GrADS Testbed Web Interface

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GrADS Testbed Web Interface

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GrADS Testbed Services

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GrADS team•Ken Kennedy•Ruth Aydt/Celso Mendez•Francine Berman/Henry Cassanova•Andrew Chien•Keith Cooper•Jack Dongarra•Ian Foster•Dennis Gannon•Lennart Johnsson•Carl Kesselman•Dan Reed•Richard Wolski•Linda Torczon•Many students

NSF funded under NGS

Documents

Grid Computing: Application Development - Computer …johnsson/Talks/NGSSC_Grid_Computing_2_2003-0… · Grid Computing: Application Development. ... – Designing and constructing