𝔖 Bobbio Scriptorium
✦   LIBER   ✦

Parallel implementation of DNAml program on message-passing architectures

✍ Scribed by C Ceron; J Dopazo; E.L Zapata; J.M Carazo; O Trelles

Publisher
Elsevier Science
Year
1998
Tongue
English
Weight
361 KB
Volume
24
Category
Article
ISSN
0167-8191

No coin nor oath required. For personal study only.

✦ Synopsis

We present a new computing approach for the parallelization on message-passing computer architectures of the DNAml algorithm, one of the most powerful tools available for constructing phylogenetic trees from DNA sequences. An analysis of the data dependencies of the method gave little chances to develop an efficient parallel approach. However, a careful run-time analysis of the behaviour of the algorithm allowed us to propose a very efficient parallel implementation based on the combination of advanced dynamic scheduling strategies, speculative running-time execution decisions and IrO buffering. In this work, we discuss specific Parallel Virtual Machine Ε½ . PVM -based implementations for a cluster of workstations and for Distributed Memory multiprocessors, with high performance results. The code can be obtained from our public-domain sites.

πŸ“œ SIMILAR VOLUMES

A highly portable parallel implementatio
A highly portable parallel implementation of AMBER4 using the message passing interface standard
✍ James J. Vincent; Kenneth M. Merz Jr. πŸ“‚ Article πŸ“… 1995 πŸ› John Wiley and Sons 🌐 English βš– 673 KB

We have implemented a portable parallel version of the macromolecular modeling package AMBER4. The message passing paradigm was used. All message passing constructs are compliant with the Message Passing Interface (MPI) standard. The molecular dynamics/minimization module MINMD and the free-energy p

Trace reduction for performance improvem
Trace reduction for performance improvement assessment of message passing parallel programs
✍ Fumihiko Ino; Yuki Kanbe; Masao Okita; Kenichi Hagihara πŸ“‚ Article πŸ“… 2006 πŸ› John Wiley and Sons 🌐 English βš– 794 KB

## Abstract This paper proposes a trace reduction method for assessing the improvability of the performance of message passing parallel programs. This assessment is based on a what‐if prediction approach that forecasts future program performance, for example, the execution time if the target progra

Pipeline implementation of cellular auto
Pipeline implementation of cellular automata for structural design on message-passing multiprocessors
✍ Shahriar Setoodeh; David B. Adams; Zafer GΓΌrdal; Layne T. Watson πŸ“‚ Article πŸ“… 2006 πŸ› Elsevier Science 🌐 English βš– 853 KB

The inherent structure of cellular automata is trivially parallelizable and can directly benefit from massively parallel machines in computationally intensive problems. This paper presents both block synchronous and block pipeline (with asynchronous message passing) parallel implementations of cellu