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Communication avoiding and overlapping for numerical linear algebra
(IEEE Computer Society, 2013-02-25)
[Abstract] To efficiently scale dense linear algebra problems to future exascale systems, communication cost must be avoided or overlapped. Communication-avoiding 2.5D algorithms improve scalability by reducing inter-processor ...
Performance Evaluation of Sparse Matrix Products in UPC
(Springer New York LLC, 2013-04)
[Abstract] Unified Parallel C (UPC) is a Partitioned Global Address Space (PGAS) language whose popularity has increased during the last years owing to its high programmability and reasonable performance through an efficient ...
Parallel Pairwise Epistasis Detection on Heterogeneous Computing Architectures
(Institute of Electrical and Electronics Engineers, 2016-08)
[Abstract] Development of new methods to detect pairwise epistasis, such as SNP-SNP interactions, in Genome-Wide Association Studies is an important task in bioinformatics as they can help to explain genetic influences on ...
The Servet 3.0 benchmark suite: characterization of network performance degradation
(Pergamon Press, 2013-11)
[Abstract] Servet is a suite of benchmarks focused on extracting a set of parameters with high influence on the overall performance of multicore clusters. These parameters can be used to optimize the performance of parallel ...
Automatic mapping of parallel applications on multicore architectures using the Servet benchmark suite
(Pergamon Press, 2012-03)
[Abstract] Servet is a suite of benchmarks focused on detecting a set of parameters with high influence on the overall performance of multicore systems. These parameters can be used for autotuning codes to increase their ...
Analysis of I/O Performance on an Amazon EC2 Cluster Compute and High I/O Platform
(Springer Netherlands, 2013-12)
[Abstract] Cloud computing is currently being explored by the scientific community to assess its suitability for High Performance Computing (HPC) environments. In this novel paradigm, compute and storage resources, as well ...
MarDRe: efficient MapReduce-based removal of duplicate DNA reads in the cloud
(Oxford University Press, 2017)
[Abstract] This article presents MarDRe, a de novo cloud-ready duplicate and near-duplicate removal tool that can process single- and paired-end reads from FASTQ/FASTA datasets. MarDRe takes advantage of the widely adopted ...
Acceleration of a Feature Selection Algorithm Using High Performance Computing
(MDPI AG, 2020-09-01)
[Abstract]
Feature selection is a subfield of data analysis that is on reducing the dimensionality of datasets, so that subsequent analyses over them can be performed in affordable execution times while keeping the same ...
A 2D algorithm with asymmetric workload for the UPC conjugate gradient method
(Springer New York LLC, 2014)
[Abstract] This paper examines four different strategies, each one with its own data distribution, for implementing the parallel conjugate gradient (CG) method and how they impact communication and overall performance. ...
Servet: A Benchmark Suite for Autotuning on Multicore Clusters
(Institute of Electrical and Electronics Engineers, 2010-05-24)
[Abstract] MapReduce is a powerful tool for processing large data sets used by many applications running in distributed environments. However, despite the increasing number of computationally intensive problems that require ...