Table of Contents
Application Performance on High-End and Commodity-class Computers
Outline
Capability Computing - Cost Effectiveness & Dependencies
High-end Commodity-based Systems
PNNL’s HPCS2 - 1400 Processor HP Supercluster
High-End Systems Evaluated
Technical Progress in 2003
Commodity Systems (CSx) Prototype / Evaluation Hardware
Commodity Systems (CSx) II. Evaluation Hardware
Applications Performance Overview
SPEC CPU 2000 - SPECfp2000 Values relative to IBM p-series 690/pwr4 1.3 GHz
The GAMESS-UK Serial Benchmark
STREAM: Measured Sustainable Memory Bandwidth in HPC (TRIAD)
Communications Benchmark PMB and EFF_BW
Collective Operations (Time - usec) - as function of no.of CPUs
Communications Benchmark PMB: Pallas MPI Benchmark Suite (V2.2)
PingPong Performance
MPI_allreduce Performance
Interconnect Benchmark - EFF_BW
Interconnect Benchmark - Latency
Application Codes
Performance Metrics: 1999-2001
Beowulf Comparisons with the T3E & O3800/R14k-500
Commodity Comparisons with High-end Systems: Compaq AlphaServer SC ES45/1000 and the SGI O3800/R14k-500
Performance Metrics: 2003
Molecular Simulation
DL_POLY: A Parallel MD Package
DL_POLY Parallel Benchmarks (Cray T3E/1200)
DL_POLY V2: High-end and Commodity-based Systems
DL_POLY V2: High-end and Commodity-based Systems I.
DL_POLY V2: High-end and Commodity-based Systems II.
DL_POLY V2: High-end and Commodity-based Systems III.
DL_POLY V2: Replicated Data
DLMULTI
DLMULTI: High-end and Commodity-based Systems
CHARMM
Parallel CHARMM Benchmark
Parallel CHARMM Benchmark: LAM MPI vs. MPICH
Migration from Replicated to Distributed data DL_POLY-3: Coulomb Energy Evaluation
Migration from Replicated to Distributed data DL_POLY-3: Coulomb Energy Performance
DL_POLY3 Macromolecular Simulations
DL_POLY3 Commodity Performance
Molecular Electronic Structure
Distributed Data SCF
High-End Computational Chemistry: The NWChem Software
Global Arrays
PeIGS 3.0 Parallel Performance
Scalability of Numerical Algorithms I.
Scalability of Numerical Algorithms II.
Parallel Eigensolvers
Case Studies - Zeolite Fragments
DFT Coulomb Fit - NWChem
DFT Coulomb Fit - NWChem
Memory-driven Approaches: NWChem - DFT (LDA): Performance on the IBM SP/p690
2.2 GAMESS-UK
GAMESS-UK features 1.
GAMESS-UK features 2.
Parallel Implementations of GAMESS-UK
GAMESS-UK ?SCF Performance IBM SP/p690, High-end and Commodity-based Systems
GAMESS-UK. DFT B3LYP Performance IBM SP/p690, High-end and Commodity-based Systems
GAMESS-UK. DFT B3LYP Performance The IBM SP/p690 and High-end Systems
GAMESS-UK. DFT HCTH Performance The IBM SP/p690 and High-end Systems
Auxilliary Basis Coulomb Fit (I)
Auxilliary Basis Coulomb Fit (ii)
GAMESS-UK: DFT HCTH on Valinomycin. Impact of Coulomb Fitting: IBM SP/p690, Compaq AlphaServer SC/1000 and SGI Origin R14k/500
GAMESS-UK: DFT HCTH on Valinomycin. Impact of Coulomb Fitting
GAMESS-UK: DFT HCTH on Valinomycin. Impact of Coulomb Fitting
GAMESS-UK. DFT HCTH Performance: Impact of Coulomb Fitting
Memory-driven Approaches - SCF and DFT
DFT BLYP Gradient: High-end and Commodity-based Systems
MP2 Gradient Algorithms
Performance of MP2 Gradient Module Cray T3E/1200, High-end and Commodity- based Systems
SCF and DFT Analytic 2nd Derivatives
SCF Analytic 2nd Derivatives Performance IBM SP/p690, High-end and Commodity-based Systems
DFT Analytic 2nd Derivatives Performance IBM SP/p690, HP/Compaq SC ES45/1000 and SGI Origin 3800
Modelling Complex Systems: The QM/MM Approach
QM/MM Modelling - Challenges
GAMESS-UK Version 6.3 QM/MM Interface with CHARMM
Quantum Simulation in Industry (QUASI)
QUASI Partners and QM/MM Developments
QM/MM Applications
Performance Analysis of GA-based Applications using Vampir
GAMESS-UK / Si8O25H18 : 8 CPUs: One DFT Cycle
GAMESS-UK / Si8O25H18 : 8 CPUs
Materials Simulation Codes
Materials Simulation. Plane Wave Methods
CPMD 3.5 - Car-Parrinello Molecular Dynamics
CPMD 3.7 - C120 Benchmark
CPMD 3.7 - C120 Benchmark
Computational Engineering
ANGUS: Combustion modelling (regular grid) Cray T3E/1200, High-end and Commodity-based Systems
ANGUS: Combustion modelling (regular grid) Memory Bandwidth Effects: Pentium Xeon and Alpha Linux Systems
ANGUS: Combustion modelling (regular grid) High-end and Commodity-based Systems
Computation Engineering: UK Turbulence Consortium
Parallel Implementation and DNS Benchmark
DNS: 3603 benchmark. High End Systems
DNS: 1203 benchmark. High-end and Commodity-based Systems
DNS: 1203 benchmark. High-end and Commodity-based Systems
Commodity Comparisons with High-end Systems: Compaq AlphaServer SC ES45/1000 and the IBM SP/p690
Commodity Comparisons with High-end Systems: The Compaq AlphaServer SC ES45/1000
Summary
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