Accelerating exhaustive pairwise metagenomic comparisons

In this manuscript, we present an optimized and parallel version of our previous work IMSAME, an exhaustive gapped aligner for the pairwise and accurate comparison of metagenomes. Parallelization strategies are applied to take advantage of modern multiprocessor architectures. In addition, sequential optimizations in CPU time and memory consumption are provided. These algorithmic and computational enhancements enable IMSAME to calculate near optimal alignments which are used to directly assess similarity between metagenomes without requiring reference databases. We show that the overall efficiency of the parallel implementation is superior to 80% while retaining scalability as the number of parallel cores used increases. Moreover, we also show thats equential optimizations yield up to 8x speedup for scenarios with larger data.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tec

Estimating the Potential Speedup of Computer Vision Applications on Embedded Multiprocessors

Computer vision applications constitute one of the key drivers for embedded multicore architectures. Although the number of available cores is increasing in new architectures, designing an application to maximize the utilization of the platform is still a challenge. In this sense, parallel performance prediction tools can aid developers in understanding the characteristics of an application and finding the most adequate parallelization strategy. In this work, we present a method for early parallel performance estimation on embedded multiprocessors from sequential application traces. We describe its implementation in Parana, a fast trace-driven simulator targeting OpenMP applications on the STMicroelectronics' STxP70 Application-Specific Multiprocessor (ASMP). Results for the FAST key point detector application show an error margin of less than 10% compared to the reference cycle-approximate simulator, with lower modeling effort and up to 20x faster execution time.Comment: Presented at DATE Friday Workshop on Heterogeneous Architectures and Design Methods for Embedded Image Systems (HIS 2015) (arXiv:1502.07241

Experimenting with independent and-parallel prolog using standard prolog

This paper presents an approximation to the study of parallel systems using sequential tools. The Independent And-parallelism in Prolog is an example of parallel processing paradigm in the framework of logic programming, and implementations like <fc-Prolog uncover the potential performance of parallel processing. But this potential can also be explored using only sequential systems. Being the spirit of this paper to show how this can be done with a standard system, only standard Prolog will be used in the implementations included. Such implementations include tests for parallelism in And-Prolog, a correctnesschecking meta-interpreter of <fc-Prolog and a simulator of parallel execution for <fc-Prolog

Extending a multi-set relational algebra to a parallel environment

Parallel database systems will very probably be the future for high-performance data-intensive applications. In the past decade, many parallel database systems have been developed, together with many languages and approaches to specify operations in these systems. A common background is still missing, however. This paper proposes an extended relational algebra for this purpose, based on the well-known standard relational algebra. The extended algebra provides both complete database manipulation language features, and data distribution and process allocation primitives to describe parallelism. It is defined in terms of multi-sets of tuples to allow handling of duplicates and to obtain a close connection to the world of high-performance data processing. Due to its algebraic nature, the language is well suited for optimization and parallelization through expression rewriting. The proposed language can be used as a database manipulation language on its own, as has been done in the PRISMA parallel database project, or as a formal basis for other languages, like SQL