High Performance Computing Systems and Applications

Front Matter....Pages i-xiii
Front Matter....Pages 1-1
Making Computer Design a Science Instead of an Art....Pages 3-14
Scalable Shared Memory and Shared Memory Clustering....Pages 15-15
High-Performance Computational Grids....Pages 17-18
High Performance Computing and Computational Chemistry in Canada—Quo Vadis....Pages 19-19
Scalable Shared-Memory Multiprocessing: The Future of High-Performance Computing....Pages 21-21
Challenges of Future High-End Computing....Pages 23-33
Front Matter....Pages 35-35
Parallel Performance of a Code Using Multidimensional FFTs....Pages 37-45
Object-Oriented Scientific Programming with Fortran 90....Pages 47-58
Alternating Direction Implicit Methods on Distributed and Shared Memory Parallel Computers....Pages 59-69
Simulating Galaxy Formation on SMPS....Pages 71-82
Front Matter....Pages 83-83
Data Parallelism in Java....Pages 85-99
A Comparative Study of Soft Real-Time Transaction Scheduling Policies in Parallel Database Systems....Pages 101-117
An Age-Threshold Algorithm for Garbage Collection in Log-Structured Arrays and File Systems....Pages 119-132
Thinking Big in a Small World — Efficient Query Execution on Small-Scale SMPs....Pages 133-146
Front Matter....Pages 147-147
Speeding up Automatic Parallel I/O Performance Optimization in Panda....Pages 149-162
Software Caching in a Parallel I/O Runtime System to Support Irregular Applications....Pages 163-175
HIPPI-6400-Designing for Speed....Pages 177-190
Front Matter....Pages 191-191
RSD — Resource and Service Description....Pages 193-206
An Examination of the Performance of Two Electromagnetic Simulations on a Beowulf-Class Computer....Pages 207-216
Managing Divisible Load on Partitionable Networks....Pages 217-228
Front Matter....Pages 229-229
NWChem Molecular Dynamics Simulation....Pages 231-239
Using Gaussian Geminal Functions in Molecular Calculations: Integral Evaluation....Pages 241-241
The Development of Parallel GAMESS....Pages 243-244
Applications/Technology Push/Pull: Building Computational Infrastructure....Pages 245-245
Front Matter....Pages 247-247
A Virtual Cache Scheme for Improving Cache-Affinity on Multiprogrammed Shared Memory Multiprocessors....Pages 249-249
Stable Performance for CC-NUMA Using First-Touch Page Placement and Reactive Proxies....Pages 251-266
A Comparative Study of Cache-Coherent Nonuniform Memory Access Systems....Pages 267-282
Parallel Computation of the Diameter of a Graph....Pages 283-296
Front Matter....Pages 297-297
Calculation of Solvation Free Energies....Pages 299-307
Molecular Docking with a View: The Integration of a Monte Carlo Docking Program into a Virtual Reality Environment....Pages 309-322
Structural Ribonucleic Acid Motifs Identification and Classification....Pages 323-331
Computational Protein Folding....Pages 333-343
Front Matter....Pages 345-345
Distributed Computing Over High-Speed Local Area Networks....Pages 347-362
Fast and Efficient Parallel Matrix Computations on a Linear Array with a Reconfigurable Pipelined Optical Bus System....Pages 363-380
Development of Parallel, Adaptive Finite Element Implementations for Modeling Two-Phase Oil/Water Flow....Pages 381-390
Parallel Solution Alternatives for Sparse Triangular Systems in Interior Point Methods....Pages 391-404
Front Matter....Pages 405-405
Managing Long Linked Lists Using Lock-Free Techniques....Pages 407-422
Single Stepping in Concurrent Executions: Dealing With Partial Orders and Clustering....Pages 423-437
Adaptive Parallelism on a Network of Workstations....Pages 439-452
A New Family of Ring-Bisection Networks and Routing Algorithms....Pages 453-462
Back Matter....Pages 463-464