Table of Contents
Application Performance on Commodity-class and High-end Computers
Outline
Capability and Capacity Computing - Cost and Performance
PNNL’s HPCS2 - 1960 Processor HP Supercluster
DisCo: Technical Progress in 2003-4
Working with the Community
Working with the Community II.
Commodity Systems (CSx) Prototype / Evaluation Hardware
Commodity Systems (CSx) II.
High-End Systems Evaluated
Applications Performance Overview
Performance Metrics: 1999-2001
Commodity Comparisons with High-end Systems
Commodity Comparisons with High-end Systems
SPEC CPU 2000 - SPECfp2000 Values relative to HP RX5670 Itanium2/1.5GHz
The GAMESS-UK Serial Benchmark
Single CPU performance - A Case Study
Interconnects and Networking
Communication Benchmarks PMB: Pallas MPI Benchmark Suite (V2.2) and B_EFF
PingPong Performance
Interconnect Benchmark - EFF_BW
Interconnect Benchmark - Latency
Collective Operations (Time - usec) - as function of no.of CPUs
MPI_allreduce Performance
64-CPU Relative Performance for Allreduce
128-CPU Relative Performance for Allreduce
64-CPU Relative Performance for Allgather
128-CPU Relative Performance for Allgather
64-CPU Performance for all collective operations
Application Codes
Performance Metrics: 2004
Molecular Simulation
DL_POLY: A Parallel MD Package
DL_POLY Parallel Benchmarks (Cray T3E/1200)
DL_POLY V2: Bench 4 - Commodity-based Systems
DL_POLY V2: Bench 5 - Commodity-based Systems
DL_POLY V2: Bench 7 - Commodity-based Systems
Migration from Replicated to Distributed data: DL_POLY-3 : Domain Decomposition
Migration from Replicated to Distributed data DL_POLY-3: Coulomb Energy Evaluation
DL_POLY3 Coulomb Energy Evaluation
DL_POLY3 Macromolecular Simulations
DL_POLY3 Macromolecular Simulations
DLMULTI
DLMULTI: High-end and Commodity-based Systems
DLMULTI: Commodity-based Systems
CHARMM
Parallel CHARMM Benchmark
Molecular Electronic Structure
CCP1: Molecular Electronic Structure
Molecular Electronic Structure
Distributed Data SCF
Global Arrays
Global Array Benchmark I. GET
Global Array Benchmark II. PUT
Global Array Benchmark III. ACCUMULATE
High-End Computational Chemistry The NWChem Software
Case Studies - Zeolite Fragments
DFT Coulomb Fit - NWChem 4.6
DFT Coulomb Fit - NWChem 4.6
Exploiting Global Memory: NWChem
Exploiting HPC: The PNNL Collaboration
GAMESS-UK
GAMESS-UK features 1.
GAMESS-UK features 2.
Parallel Implementation of GAMESS-UK
Parallel Implementation of GAMESS-UK
Parallel Implementations of GAMESS-UK
Parallel Linux Implementations of GAMESS-UK
Parallel Linear Algebra
PeIGS 3.0 Parallel Performance
Eigensolver Performance - “Small” case (IBM p690+)
PDSYEVD – IBM p690+ and SGI Altix 3700
Eigensolver Performance - “Largest” Case (IBM p690+)
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 HCTH on Valinomycin. Impact of Coulomb Fitting
GAMESS-UK - GA-based Implementation
GAMESS-UK - GA-based Implementation
DFT BLYP Gradient: 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 Commodity-based Systems - HCTH functional
MP2 Gradient Algorithms
Performance of MP2 Gradient Module High-end and Commodity-based Systems
Distributed Data Implementation of GAMESS-UK
Coupled QM/MM Calculations
GAMESS-UK Interface with CHARMM
QM/MM Applications
Materials Simulation Codes
Materials Simulation. Plane Wave Methods: CASTEP, CPMD
CPMD - Car-Parrinello Molecular Dynamics
CPMD - Mixed Mode Programming
CPMD 3.7 - C120 Benchmark
CPMD 3.7 - C120 Benchmark
CPMD 3.7 - Si512 Benchmark
Computational Engineering
ANGUS: Combustion modelling (regular grid) High-end and Commodity-based Systems
ANGUS: Combustion modelling (regular grid) High-end and Commodity-based Systems
ANGUS: Combustion modelling (regular grid) Memory Bandwidth Effects: Pentium Xeon and Opteron Systems
ANGUS: Combustion modelling (regular grid) High-end and Commodity-based Systems
Computational Engineering: UK Turbulence Consortium
Direct Numerical Simulation: 3603 benchmark
DNS: 1203 benchmark. High-end and Commodity-based Systems
DNS: 1203 benchmark. High-end and Commodity-based Systems
Commodity Comparisons with High-end Systems
Commodity Comparisons with High-end Systems
Summary
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