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Nature
Model
Experiments
Computer Simulations
ApproximateTheories
NumericalResults
TheoreticalPredictions
Data
TestModel
TestTheory
UNL Computer Science & Engineering
RCF : Research Computing Facility
Provide Local HPC Resources Provide Training and Support Facilitate Production of Scalable Code
UNL Computer Science & Engineering
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
UNL Computer Science & Engineering
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
UNL Computer Science & Engineering
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
UNL Computer Science & Engineering
Scavenger SCAlable Varied Environment for Graduate Education and Research
UNL Computer Science & Engineering
Bugeater Prototype number-crunching Beowulf
Dual PIII 800MHz
512 MB RAM
20 GB HDD
RedHat LINUX
Fast Ethernet
UNL Computer Science & Engineering
Atomistic Simulation
Molecular Dynamics 3N 2nd order differential equations Simulation stores and updates positions and
velocities
ii
i
ji rmfr
rr
,...,
UNL Computer Science & Engineering
Predictor-Corrector Method
Predicted values are easily calculated
tbttb
tbttatta
tbttattvttv
tbttattvttrttr
p
p
p
p
2
21
3612
21
UNL Computer Science & Engineering
Predictor-Corrector Correction
ttacttbttb
ttacttatta
ttacttvttv
ttacttrttr
ttattatta
pc
pc
pc
pc
pc
3
2
1
0
UNL Computer Science & Engineering
Distributed Cell Algorithm
Divide system into cells and distribute
Calculate within cells Potential range
determines communication
UNL Computer Science & Engineering
Ozone Detonation Detonation proceeds left to right
Density: low (blue), medium (white), high (red)
UNL Computer Science & Engineering
Summary
Simulations link Mathematical Theory to Natural Phenomena
Beowulf technology is cost-effective HPC
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