Parallel Computing Technologies
Program of the Conference
Monday, September 5
Tutorials | 9:00–18:00 |
An Introduction to Genomics and Biomedical Applications for Parallel Computing
Thomas L. Casavant,
Center for Bioinformatics, University of Iowa, USA
| 9:00–12:20 |
This will be a half-day tutorial on Parallel Computing-related issues in Bioinformatics and Computational Biology (BCB). The target audience will be scientifically-literate computational researchers who are not currently engaged in BCB. About half of the tutorial will be an overview of a representative collection of basic life science and medical research problems contemporary to this rapidly expanding field. The second half of the tutorial will focus attention on some of the problems in BCB that are most in need of high-performance computing and networking. The tutorial will provide a basic level of introduction to these problems, and is intended to serve to introduce this area of inter-disciplinary research to people interested in becoming partially involved in applying their backgrounds in Parallel Computing to BCB.
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Coffee break | 10:30–10:50 |
Lunch | 12:20–14:00 |
Fine-grained parallelism in spatial dynamics simulation
Olga L. Bandman,
Supercomputer Software Department, ICM&MG SB RAS, RUSSIA
| 14:00–17:20 |
The concept of fine-grained parallelism is considered in the context of its application in simulation of spatially distributed processes. It comprises models, algorithms and computing technologies exhibiting two following properties: 1) spatial parallelism (at any discrete time the next values of the spatial function in all points of the space are allowed to be computed in parallel), and 2) locality (the computation for any point uses as variables the values of the function in its fixed vicinity). The scope of fine-grain spatial dynamics models is classified and illustrated by examples, the domain of application of each class being specified. Theoretical background of fine-grained parallel computations is given in brief. Computational properties (accuracy, stability, coarse-grained parallelization efficiency) are discussed, and methods of fine-grained algorithms synthesis are presented and shown at work by examples.
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Coffee break | 15:30–15:50 |
Welcome party | 19:00 |
Tuesday, September 6
Opening session | 10:00–10:15 |
V. Shaidurov
Director of the Institute of Computational Modeling RAS | 10:00–10:10 |
V. Malyshkin
Program Committee Chairman | 10:10–10:15 |
Invited talk | 10:15–11:00 |
Blue Gene/L and Petascale Computing
Carl G. Tengwall, Blue Gene Solutions Executive IBM Strategic Growth Business EMEA (invited paper) | 10:15–11:00 |
Coffee break | 11:00–11:30 |
Fine-grain computations
Chairman Stefania Bandini | 11:30–13:00 |
Composing Fine-Grained Parallel Algorithms for Spatial Dynamics Simulation
Olga L. Bandman | 11:30–12:00 |
Optimal Behavior of a Moving Creature in the Cellular Automata Model
M. Halbach, R. Hoffmann | 12:00–12:20 |
Associative Parallel Algorithm for Dynamic Reconstruction of a Minimum Spanning Tree after Deletion of a Vertex
A. S. Nepomniaschaya | 12:20–12:40 |
Development of Predictive TFRC with Neural Network
Sung-goo Yoo, Kil To Chong, Hyong-suk Kim | 12:40–13:00 |
Lunch | 13:00–14:30 |
Applications
Chairman Bernard Roux | 14:30–16:00 |
XenoCluster: A Grid Computing Approach to Finding Ancient Evolutionary Genetic Anomalies
J. D. Walters, T. L. Casavant, J. P. Robinson, T. B. Bair, T. A. Braun, T. E. Scheetz | 14:30–15:00 |
RAxML-OMP: An Efficient Program for Phylogenetic Inference on SMPs
A. Stamatakis, M. Ott, T. Ludwig | 15:00–15:30 |
A Parallel Version for the Propagation Algorithm
M. B. Castro, L. Baldo, L. G. Fernandes, M. Raeder, P. Velho | 15:30–16:00 |
Coffee break | 16:00–16:30 |
Programming environment
Chairman M. Raynal | 16:30–18:00 |
OpenTS: An Outline of Dynamic Parallelization approach
S. Abramov, A. Adamovich, A. Inyukhin, A. Moskovsky, V. Roganov, E. Shevchuk, Yu. Shevchuk, A. Vodomerov | 16:30–17:00 |
ParC#: Parallel Computing with C# in. Net
J. F. Ferreira, J. L. Sobral | 17:00–17:30 |
A Model for Designing and Implementing Parallel Applications using Extensible Architectural Skeletons
M. M. Akon, D. Goswami, Hon Fung Li | 17:30–18:00 |
Wednesday, September 7
Theory of programming
Chairman Valeri A. Sokolov | 9:30–11:00 |
Early-Stopping k-set Agreement in Synchronous Systems Prone to any Number of Process Crashes
P. R. Parvedy, M. Raynal, C. Travers | 9:30–10:00 |
Allowing Atomic Objects to Coexist with Sequentially Consistent Objects
M. Raynal, M. Roy | 10:00–10:30 |
Information Flow Analysis for VHDL
T. K. Tolstrup, F. Nielson, H. R. Nielson | 10:30–10:50 |
Coffee break | 10:50–11:30 |
Grid computing
Chairman Thomas Ludwig | 11:30–13:00 |
Performance Analysis of Applying Replica Selection Technology for Data Grid Environments
Chao-Tung Yang, Chun-Hsiang Chen, Kuan-Ching Li, Ching-Hsien Hsu | 11:30–12:00 |
IBM Technologies for High Performance Computing (invited paper)
A. Pershikov | 12:00–12:30 |
Experimenting with a Multi-Agent E-Commerce Environment
C. Badica, M. Ganzha, M. Paprzycki, A. Pirvanescu | 12:30–13:00 |
Lunch | 13:00–14:30 |
Models
Chairman Irina Virbitskaite | 14:30–16:00 |
Situated Agents Interaction: Coordinated Change of State for Adjacent Agents
S. Bandini, S. Manzoni, G. Vizzari | 14:30–15:00 |
Similarity of Generalized Resources in Petri Nets
Vladimir A. Bashkin, Irina A. Lomazova | 15:00–15:30 |
Timed Equivalences for Timed Event Structures
M. V. Andreeva, I. B. Virbitskaite | 15:30–16:00 |
Coffee break | 16:00–16:30 |
Protocols
Chairman Sergey Abramov | 16:30–17:15 |
On Evaluating the Performance of Security Protocols
C. Bodei, M. Buchholtz, M. Curti, P. Degano, F. Nielson, H. R. Nielson, C. Priami | 16:30–17:00 |
An approach to the Implementation of Dynamical Priorities Method
V. A. Sokolov, E. A. Timofeev | 17:00–17:30 |
Short papers & demonstrations | 17:30–18:20 |
Real-Time Event Structures and Scott Domains
R. S. Dubtsov | #1 |
Parallelization Techniques for Multidimensional Hypercomplex Discrete Fourier Transform
M. Chicheva, M. Aliev, A. Yershov | #2 |
The Parallel Implementation of the Algorithm Solution of Model for Two-phase Cluster in Liquids
V. D. Korneev, V. A. Vshivkov, G. G. Lazareva, V. K. Kedrinskii | #4 |
Neural Network Approach for Parallel Construction of Adaptive Meshes
O. Nechaeva | #5 |
Clustering Multiple and Cooperative Instances of Computational Intensive Software Tools
D. Petcu, M. Paprzycki, M. Ganzha | #6 |
NumGrid Middleware: MPI Support for Computational Grids
D. Fougere, M. Gorodnichev, N. Malyshkin, V. Malyshkin, A. Merkulov, B. Roux | #7 |
Thursday, September 8
Social program | 10:00–18:00 |
Conference dinner | 19:00 |
Friday, September 9
Optimization
Chairman Joao Luis Sobral | 9:30–11:00 |
Planning of Parallel Abstract Programs as Boolean Satisfiability
G. A. Oparin, A. P. Novopashin | 9:30–9:55 |
Efficient Communication Scheduling Methods for Irregular Data Redistribution in Parallelizing Compilers
Shih-Chang Chen, Ching-Hsien Hsu, Chao-Yang Lan, Chao-Tung Yang, Kuan-Ching Li | 9:55–10:15 |
Minimizing Hotspot Delay by Fully Utilizing the Link Bandwidth on 2D Mesh with Virtual Cut-Through Switching
MinHwan Ok, Myong-soon Park | 10:15–10:35 |
A Shape Optimizing Load Distribution Heuristic for Parallel Adaptive FEM Computations
S. Schamberger | 10:35–11:00 |
Coffee break | 11:00–11:30 |
Fine-grain applications
Chairman Irina Lomazova | 11:30–13:00 |
Systolic Routing in an Optical Butterfly
R. T. Honkanen | 11:30–11:50 |
Feasibility of the Circularly Connected Analog CNN Cell Array-based Viterbi Decoder
Hongrak Son, Hyunjung Kim, Hyongsuk Kim, and Kil To Chong | 11:50–12:10 |
The Use of Vertical Processing Principle in Parallel Image Processing on Conventional MIMD Computers
E. V. Rusin | 12:10–12:30 |
Parallel Implementation of Back-propagation Neural Network Software on SMP Computers
V. G. Tsaregorodtsev | 12:30–12:50 |
Lunch | 13:00–14:30 |
Tools
Chairman Giancarlo Alfonsi | 14:30–16:00 |
A Practical Tool for Detecting Races in OpenMP Programs
Young-Joo Kim, Mi-Young Park, So-Hee Park, Yong-Kee Jun | 14:30–15:00 |
Comprehensive Cache Inspection with Hardware Monitors
J. Tao, J. Jeitner, C. Trinitis, Wolfgang Karl, J. Weidendorfer | 15:00–15:20 |
A Fast Technique for Constructing Evolutionary Tree with the Application of Compact Sets
Kun-Ming Yu, Yu-Wai Chang, YaoHua Yang, Jiayi Zhou, Chun-Yuan Lin, Chuan Yi Tang | 15:20–15:40 |
Online Virtual Disk Migration with Performance Guarantees in a Shared Storage Environment
Yong Feng, Yan-yuan Zhang, Rui-yong Jia, Xiao Zhang | 15:40–16:00 |
Coffee break | 16:00–16:30 |
Numerical algorithms
Chairman V. Shaidurov | 16:30–17:40 |
A Multigrid Parallel Program for Protoplanetary Disc Simulation
A. Snytnikov, V. Vshivkov | 16:30–17:00 |
An Implementation of the Matrix Multiplication Algorithm SUMMA in mpF
A. Kalinov, I. Ledovskikh, M. Posypkin, Z. Levchenko, V. Chizhov | 17:00–17:20 |
A Parallel Computational Code for the Eduction of Coherent Structures of Turbulence in Fluid Dynamics
G. Alfonsi, L. Primavera | 17:20–17:40 |
Closing of the conference | 17:40 |
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