The fast Fourier transform (FFT) is the cornerstone of many supercomputer applications and therefore needs careful performance tuning. Most often, however, the real performance of the FFT implementations is far below the acceptable figures. In this paper, we explore several strategies for performance optimisations of the FFT computation, such as enhancing instruction-level parallelism, loop mer...

The human genome project depends intensively on electronic collection and dissemination of information. In this respect, it arguably foreshadows much future scientific research. Its dependence on electronic collection and dissemination of information also poses strenuous challenges to current databaseand workflow-management technology. We discuss these challenges as they arise in community data...

We present a novel algorithm and a new understanding of reasoning about a sequence of deterministic actions with a probabilistic prior. When the initial state of a dynamic system is unknown, a probability distribution can be still specified over the initial states. Estimating the posterior distribution over states (filtering) after some deterministic actions occurred is a problem relevant to AI...

Genomic evaluations can be calculated using a unified procedure that combines phenotypic, pedigree and genomic information. Implementation of such a procedure requires the inverse of the relationship matrix based on pedigree and genomic relationships. The objective of this study was to investigate efficient computing options to create relationship matrices based on genomic markers and pedigree ...

This document is intended to provide helpful information to anyone wishing to adapt IDENT for use on a computer other than an LSI-11, or on an operating system other than RT-11 version 4, or with different data structures. An overall picture of IDENT is provided by Tables 1-7, in which the common variables and the overlay structure are outlined. The function of each subroutine is noted briefly....

We show that given oracle access to a subroutine which returns approximate closest vectors in a lattice, one may find in polynomial time approximate shortest vectors in a lattice. The level of approximation is maintained; that is, for any function f , the following holds: Suppose that the subroutine, on input a lattice L and a target vector w (not necessarily in the lattice), outputs v ∈ L such...

Numerical solutions to partial differential equations form the backbone of mathematical models that simulate the behavior of various electrochemical systems, specifically, batteries and fuel cells. In this paper, we present a set of numerical algorithms applied to efficiently solve this system of equations. These fast algorithms are identified by fully understanding the physics of the problem a...

This project focussed on speeding up the cyclic Jacobi algorithm of the Singular Value Decomposition for DLX architecture. Using the performance monitor, it is shown that over 96% of the time is spent in a subroutine calculates Jacobi rotations. To speed up the subroutine, the improvement are performed on two aspects. From the algorithm point of view, we rst implemented the fast Jacobi matrix m...

This report describes the optimization implemented in hpfc, our prototype hpf compiler, to remove useless remappings. This optimization is performed on the remapping graph. The construction of this graph from the control ow graph is rst presented. Then the optimization is formalized as a may data-ow problem on this graph. Finally the results are discussed. 1 Remapping Graph Useless remappings m...

The fast Fourier transform (FFT) is the cornerstone of many supercomputer applications and therefore needs careful performance tuning. Most often, however, the real performance of the FFT implementations is far below the acceptable gures. In this paper, we explore several strategies for performance optimisations of the FFT computation , such as enhancing instruction-level parallelism, loop merg...