UNL Computer Science & Engineering

Cluster Computing

David R. Swanson

Beowulf and Bombs

Nature

Model

Experiments

Computer Simulations

ApproximateTheories

NumericalResults

TheoreticalPredictions

Data

TestModel

TestTheory

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RCF : Research Computing Facility

Provide Local HPC Resources Provide Training and Support Facilitate Production of Scalable Code

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RCF: Hardware

32 CPU SGI Origin 2000 8 GB RAM 300 GB HDD

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Beowulf : Definition

MMCOTS LAN LINUX MPI

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So We Built a Beowulf…

Origin cost half a million dollars PCs are increasingly powerful and

affordable Network hardware is similarly improving Open source success (LINUX) Not many MPP options available

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Beowulf History

6th Century: Beowulf slays Grendel 1994: Wiglaf 74 MFlops74 MFlops

16 486/66, 16 MB RAM, 540 MB HDD, Ethernet

1995: Hrothgar 280 MFlops280 MFlops 16 Pentium 100, 32 MB RAM, 1.2 GB HDD, Fast Ethernet

1996: Beowulfs at JPL and LANL GflopsGflops 1998: Avalon 48 Gflops48 Gflops 2000: Scavenger

16 Pentium 100+, 32 MB RAM, 1 GB HDD, Ethernet

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Beowulf How To

Gather up old Pentiums from Inventory Get them to boot Load RedHat LINUX and MPI Borrow a HUB Warm up the Basement

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Scavenger SCAlable Varied Environment for Graduate Education and Research

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Bugeater Prototype number-crunching Beowulf

Dual PIII 800MHz

512 MB RAM

20 GB HDD

RedHat LINUX

Fast Ethernet

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Atomistic Simulation

Molecular Dynamics 3N 2nd order differential equations Simulation stores and updates positions and

velocities

ii

i

ji rmfr

rr

,...,

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Predictor-Corrector Method

Predicted values are easily calculated

tbttb

tbttatta

tbttattvttv

tbttattvttrttr

p

p

p

p

2

21

3612

21

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Predictor-Corrector Correction

ttacttbttb

ttacttatta

ttacttvttv

ttacttrttr

ttattatta

pc

pc

pc

pc

pc

3

2

1

0

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Distributed Cell Algorithm

Divide system into cells and distribute

Calculate within cells Potential range

determines communication

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Ozone Detonation Detonation proceeds left to right

Density: low (blue), medium (white), high (red)

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Summary

Simulations link Mathematical Theory to Natural Phenomena

Beowulf technology is cost-effective HPC

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Acknowledgements

NSF/EPSCoR UN Foundation NRC/NRL (ONR)