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jmodeltest.org: selection of nucleotide substitution models on the cloud
(Oxford University Press, 2014)
[Abstract] The selection of models of nucleotide substitution is one of the major steps of modern phylogenetic analysis. Different tools exist to accomplish this task, among which jModelTest 2 (jMT2) is one of the most ...
FastMPJ: a scalable and efficient Java message-passing library
(Springer New York LLC, 2014)
[Abstract] The performance and scalability of communications are key for high performance computing (HPC) applications in the current multi-core era. Despite the significant benefits (e.g., productivity, portability, ...
Interactive Rendering of NURBS Surfaces
(Pergamon Press, 2014)
[Abstract] NURBS (Non-uniform rational B-splines) surfaces are one of the most useful primitives employed for high quality modeling in CAD/CAM tools and graphics software. Since direct evaluation of NURBS surfaces on the ...
Free adaptive tessellation strategy of bézier surfaces
(SciTePress, 2014-01)
[Abstract] Rendering of Bézier surfaces is currently performed by tessellating the model on the GPU and rendering the highly detailed triangle mesh. Whereas non-adaptive strategies apply the same tessellation pattern to ...
High-performance computing selection of models of DNA substitution for multicore clusters
(Sage Publications Ltd., 2014)
[Abstract] This paper presents the high-performance computing (HPC) support of jModelTest2, the most popular bioinformatic tool for the statistical selection of models of DNA substitution. As this can demand vast computational ...
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. ...
Hybrid CPU/GPU Acceleration of Detection of 2-SNP Epistatic Interactions in GWAS
(Springer, 2014-08)
[Abstract] High-throughput genotyping technologies allow the collection of up to a few million genetic markers (such as SNPs) of an individual within a few minutes of time. Detecting epistasis, such as 2-SNP interactions, ...
Scalable PGAS collective operations in NUMA clusters
(Springer New York LLC, 2014-12)
[Abstract] The increasing number of cores per processor is turning manycore-based systems in pervasive. This involves dealing with multiple levels of memory in non uniform memory access (NUMA) systems and processor cores ...
In-memory application-level checkpoint-based migration for MPI programs
(Springer New York LLC, 2014)
[Abstract] Process migration provides many benefits for parallel environments including dynamic load balancing, data access locality or fault tolerance. This paper describes an in-memory application-level checkpoint-based ...
Failure Avoidance in MPI Applications Using an Application-Level Approach
(Oxford University Press, 2014)
[Abstract] Execution times of large-scale computational science and engineering parallel applications are usually longer than the mean-time-between-failures. For this reason, hardware failures must be tolerated by the ...