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Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

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Published on: April 8, 2020

An improved distance matrix computation algorithm for multicore clusters.

Mohammed W Al-Neama¹, Naglaa M Reda², Fayed F M Ghaleb²

¹Department of Mathematics, Faculty of Science, Al-Azhar University, Cairo, Egypt ; Education College for Girls, Mosul University, Mosul, Iraq.

Biomed Research International

|July 12, 2014

Summary

This study introduces DistVect1, a parallel algorithm for accelerating distance matrix computation in bioinformatics. It achieves significant speedups on multicore clusters, outperforming previous methods.

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Area of Science:

Bioinformatics
Computational Biology
High-Performance Computing

Background:

Distance matrix computation is crucial for bioinformatics, particularly in multiple sequence alignment.
The rapid growth of biological sequence databases necessitates faster computation methods.
Existing algorithms like DistVect show promise but can be further optimized for modern hardware.

Purpose of the Study:

To propose DistVect1, a highly efficient parallel vectorized algorithm for computing distance matrices on multicore clusters.
To adapt the DistVect algorithm for cluster architectures using MPI and OpenMP.
To optimize partitioning and scheduling for efficient computation on multicore clusters.

Main Methods:

Reformulating the DistVect algorithm for cluster primitives.
Implementing efficient partitioning and scheduling strategies for multicore clusters.
Utilizing Message Passing Interface (MPI) and OpenMP for parallel implementation.

Main Results:

DistVect1 achieves a 3-fold speedup compared to SSE2.
The algorithm demonstrates speedups exceeding 9 orders of magnitude over the parallel implementation in ClustalW-MPI.
Experimental results confirm the high performance and efficiency of DistVect1 on multicore clusters.

Conclusions:

DistVect1 offers a significant performance improvement for distance matrix computation on multicore clusters.
The proposed algorithm addresses the need for accelerated computations in large-scale bioinformatics.
DistVect1 represents a substantial advancement over existing parallel implementations for bioinformatics tasks.