Navid Azizi, Ian Kuon, Aaron Egier, Ahmad Darabiha and...

FCCM 2004

Reconfigurable Molecular Dynamics Simulator

Navid Azizi, Ian Kuon, Aaron Egier, Ahmad Darabihaand Paul ChowUniversity of Toronto

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FCCM 2004


Why is Molecular Dynamics interesting? Simulates interaction of atoms over time

Many possible applications– Biomolecules

Computationally intensive to handle >1000 atoms

Large computer clusters used in the past

Can a reconfigurable simulation system do this better?

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FCCM 2004


What is Molecular Dynamics?

Simulate using classical Newtonian mechanicsF = m a

Integrate acceleration to get position and velocity changes

Use a very small timestep ~ 1 femtosecond

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FCCM 2004


Molecular Dynamics Background

Simulation Procedure per timestep– Sum force over all interacting atoms

– Calculate acceleration

– Integrate acceleration to update atom position and velocity

– Repeat for all atoms

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FCCM 2004


Background - Forces

Two types of forces–Bonded – O(n)

–No hardware acceleration required–Non Bonded – O(n2)

–Needs hardware acceleration

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FCCM 2004


-2.5E-11

0.0E+00

2.5E-11

5.0E-11

7.5E-11

1.0E-10

Distance

Pote

ntia

lBackground – Force Calculation

Lennard-Jones (LJ) potential models interaction

Force on a atom is the gradient of potential

( )⎥⎥⎦

⎤

⎢⎢⎣

⎡⎟⎠⎞

⎜⎝⎛−⎟

⎠⎞

⎜⎝⎛=

612

4rr

rLJσσεφ

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FCCM 2004


Background – Simulating Large VolumesAny interesting volume has far too many atoms to simulate

Solution – Periodic Boundary Conditions

ReplicatedBox

ReplicatedBox

ReplicatedBox

ReplicatedBox

ReplicatedBox

ReplicatedBox

ReplicatedBox

ReplicatedBox

Box beingsimulated

BA

B’A’

B’A’

B’A’

B’A’

B’A’

B’A’

B’A’

B’A’

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FCCM 2004


Architectural Design – System Overview

PairGen

VerletUpdate

ForceComputer

AccelerationUpdate

SunWorkstation

SystemControl

ParticleMemory

FunctionValue

Memory

SlopeMemory

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FCCM 2004


Architectural Design – Force Computer

r2 from PG used for function lookup

Interpolate to obtain a more accurate force magnitude

PairG

enForce

Computer

AccelerationUpdate

FunctionValue

Memory

SlopeMemory

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FCCM 2004


Architectural Design – Force Computerr2 is larger than 18-bits

–Look up table has a 18-bit address

-1.00E+09

0.00E+00

1.00E+09

2.00E+09

3.00E+09

4.00E+09

5.00E+09

6.00E+09

0 5E-19 1E-18 1.5E-18 2E-18

Separation2

Psue

do-A

ccel

erat

ion

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Architectural Design – Force Computer

r2

FF...FF

low bits

middlebits

highbits

Residual forinterpolation

Address tolookup tables

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FCCM 2004


Precision and Scaling Factors

Architecture uses integer operations to reduce complexity

Precision: number of bits used to represent a valueScaling Factor: the weight of the least significant bit of the value

Precision

ScalingFactor

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FCCM 2004


Calculating the Precision and Scaling FactorsCalculations made with atoms at varying distances

Scaling Factor = the minimum valuePrecision = log2 of the difference between minimum and maximum

372-64Acceleration

512-15Velocity

382-64Position

PrecisionScaling Factor

Quantity

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FCCM 2004


Simulation Environment is ConfigurableSimulation reconfigurability

– Change precision, scaling factors, number of atoms. forces

– No wasted hardware

– No time overhead when precision is reduced

Entire process is automated– One input file controls entire process

– Hardware – C program creates appropriate VHDL

– Software interface, Software initialization– Always match the hardware

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FCCM 2004


ImplementationUsed the Transmogrifier 3

–4 interconnected Virtex-E 2000’s

–2MB memories connected to each Virtex-E

–Slow by today’s standards

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FCCM 2004


VerificationTested accuracy of implementation

–Compared TM3 results with software

0

500

1000

1500

2000

2500

0 100 200 300 400 500 600 700

Timestep

Ener

gy (k

J/m

ol)

TM3 -Total EnergySoftware - Total EnergyTM3 - Kinetic EnergySoftware - Kinetic EnergyTM3 - Potential EnergySoftware - Potential Energy

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FCCM 2004


System Performance

For a 8192 atom MD system running on the TM3

–Frequency: 26 MHz–Timestep Duration: 37 sec

For a 8192 atom software system running on a 2.4GHz Pentium 4

–Timestep Duration: 10.8 sec

MD system is 3.4X slower than software

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FCCM 2004


How to improve this?Memory

New FPGA

Parallelism

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FCCM 2004


Memory Requirements of MD System

Acceleration Array (8192 atom system uses 0.17 MB)

Velocity Array (8192 atom system uses 0.17 MB)

Position Array (8192 atom system uses 0.34 MB)

Lookup Tables: 2 MB

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FCCM 2004


Improving Performance – Memory Organization On TM3 there is only one external SRAM per FPGA

Single SRAM for all atom information causes large slowdowns

– Handshaking

– Serial reads for x, y and z

– Hardware issues

Better memory system

2.1 seconds/timestep (5X faster than software)

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FCCM 2004


Improving Performance – Clock Speed

Run on modern FPGA

All possible improvements for clock speed not explored

Expect a factor of 4 increase to a 100MHz

Better memory system + Faster Clock Speed

0.51 seconds/timestep (21X faster than software)

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FCCM 2004


Improving Performance – Parallel Architecture

Better memory system + Faster Clock Speed + Parallelize

0.51/n seconds/timestep (21n X faster than software)

PairGen

AU(1)AA

AU(0)AA

AU(n-1)AA

VU(1)VA

VU(0)VA

VU(n-1)VA

PAi

PA

iP

AiPA

jPA

jPA

j

LJFC(0)

LJFC(1)

LJFC(n-1)

Slope Mem

Value Mem

Value Mem

Slope Mem

Value Mem

Slope Mem

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FCCM 2004


Cost, Power Benefits

Performance– MD system can deliver a 21X performance benefit over

software

– Assume a conservative 10X performance advantage

Cost– Microprocessor motherboard-sized board can fit 4

FPGAs

– 4 FPGAs (each $200) + board + SRAM + misc. ~ $1500

– Microprocessor Motherboard + CPU + DRAM ~ $1500

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FCCM 2004


Comparison of MD Simulator and Supercomputers

40W106WPower~$1500~$1500Cost40X1XPerformance

4 FPGAs + 24 MB SRAM

1 Pentium + 1 GB DRAM

Per Board

40X ImprovementPerformance/Space40X ImprovementPerformance/Cost

100X ImprovementPerformance/Power

Improvement of MD System

Metric

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FCCM 2004


ConclusionsEasily reconfigurable MD System designed

Molecular dynamics simulation can be done on FPGAs

Simple enhancements will improve speed– Power, Cost and Space savings over software

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FCCM 2004


Future WorkImprove accuracy

Target newer FPGA platform

Support new forces

Funding for the TM3 Project was provided by Micronet and Xilinx

Acknowledgements

Navid Azizi, Ian Kuon, Aaron Egier, Ahmad Darabiha and...

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