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In this thesis, parallel computing on installed local area networks (LAN) is focused, analyzing problems and possible solutions taking into account the main factors of computing and communications. More specifically, LAN...

In order to measure the performance of a parallel machine, a set of application kernels as benchmarks have often been used. However, it is not always possible to characterize the performance using only benchmarks, given ...

GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis too...

Materias / palabras clave: Parallel computing; Computer science; Benchmark (surveying); Parallel algorithm; Intel iPSC; Algorithm; Range (aeronautics); Molecular dynamics; Supercomputer; Node (physics); Computational science; Physics

Materias / palabras clave: Message passing; Computer science; Parallel computing; Message Passing Interface; Dynamics (music); Computational science; Molecular dynamics; Physics; Acoustics; Quantum mechanics

The parallel computing model used in this paper, the Collective Computing Model (CCM), is a variant of the well-known Bulk Synchronous Parallel (BSP) model. The synchronicity imposed by the BSP model restricts the set of...

The book Using OpenMP: Portable Shared Memory Parallel Programming, presents OpenMP more than appropriately, from the perspective of high performance computing, which traditionally has provided most (if not all) the para...

Migration of individuals allows a fruitful interaction between subpopulations in the island model, a well known distributed approach for evolutionary computing, where separate subpopulations evolve in parallel. This mode...

Parallel computing on networks of workstations are intensively used in some application areas such as linear algebra operations. Topics such as processing as well as communication hardware heterogeneity are considered so...

Fast response, storage efficiency, fault tolerance and graceful degradation in face of scarce or spurious inputs make neural networks appropiate tools for Intelligent Computer Systems. But on the other hand, learning alg...

UNLABELLED: RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML). Low-level technical...

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on lo...

Our efforts are directed towards the understanding of the coscheduling mechanism in a NOW system when a parallel job is executed jointly with local workloads, balancing parallel perfor-mance against the local interactive...

AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed-up compared with the molecular docking software previously dev...

SUMMARY: CD-HIT is a widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses. In response to the rapid increase in the amount of sequen...

Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS whi...

This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, origi...

Since the classical molecular dynamics simulator LAMMPS was released as an open source code in 2004, it has become a widely-used tool for particle-based modeling of materials at length scales ranging from atomic to mesos...

In this article, we present a new LINear Constraint Solver (LINCS) for molecular simulations with bond constraints. The algorithm is inherently stable, as the constraints themselves are reset instead of derivatives of th...

MapReduce is a programming model and an associated implementation for processing and generating large datasets that is amenable to a broad variety of real-world tasks. Users specify the computation in terms of a map and ...

Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version ...

An account is given of the development of the SHELX system of computer programs from SHELX-76 to the present day. In addition to identifying useful innovations that have come into general use through their implementation...

A new software suite, called Crystallography & NMR System (CNS), has been developed for macromolecular structure determination by X-ray crystallography or solution nuclear magnetic resonance (NMR) spectroscopy. In contra...

Materias / palabras clave: Bottleneck; Metagenomics; Computer science; Diamond; Sensitivity (control systems); Software; Search engine indexing; Speedup; Computational biology; Data mining; Bioinformatics; Parallel computing