Search results for "Parallelism"

Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters

2016

Computing alignments between two or more sequences are common operations frequently performed in computational molecular biology. The continuing growth of biological sequence databases establishes the need for their efficient parallel implementation on modern accelerators. This paper presents new approaches to high performance biological sequence database scanning with the Smith-Waterman algorithm and the first stage of progressive multiple sequence alignment based on the ClustalW heuristic on a Xeon Phi-based compute cluster. Our approach uses a three-level parallelization scheme to take full advantage of the compute power available on this type of architecture; i.e. cluster-level data par…

Ein Axiomensystem f�r partielle affine R�ume

1994

A partial linear space with parallelism is called partial affine space if it is embeddable in an affine space with the same pointset preserving the parallelism. These partial affine spaces will be characterized by a system of three axioms for partial linear spaces with parallelism.

Mixed Parallelism for Single Alternating Group Explicit Method

1991

The paper deals with parallel implementation policies for D.J. Evans S_AGE (Single Alternating Group Explicit) unconditionally stable methods concerning the solution of parabolic problems in two space dimensions.

One, Two, Three,…, Infinity

1999

As concluding remarks to the European Few-Body Conference, the author presents a parallelism between the Few-Body and the Many-Body theories along the last years.

The Jurassic ammonite Coelocerus: an atypical example of dimorphic progenesis elucidated by cladistics

1994

Instances of convergence or parallelism among unrelated Lower Carixian ammonites are not uncommon. The case of polymorphitid-like ammonites is considered here, and the example of Coeloceras is investigated in detail. The small sexual dimorph (microconch) of Coeloceras pettos (Quensitedt) (Coeloceratidae), a progenetic species, provides a remarkable example of complex convergence with the microconch of Uptonia (Polymorphitidae). Homeomorphic morphology is here an amalgam of juvenile traits, of maturation-related transformations, and of completely new features bearing no obvious relation with either progenesis or maturation. A stratophenetic approach is hardly adequate for unravelling such an…

Many-body perturbation theory calculations using the yambo code

2019

Abstract yambo is an open source project aimed at studying excited state properties of condensed matter systems from first principles using many-body methods. As input, yambo requires ground state electronic structure data as computed by density functional theory codes such as Quantum ESPRESSO and Abinit. yambo’s capabilities include the calculation of linear response quantities (both independent-particle and including electron–hole interactions), quasi-particle corrections based on the GW formalism, optical absorption, and other spectroscopic quantities. Here we describe recent developments ranging from the inclusion of important but oft-neglected physical effects such as electron–phonon i…

CUSHAW2-GPU: Empowering Faster Gapped Short-Read Alignment Using GPU Computing

2014

We present CUSHAW2-GPU to accelerate the CUSHAW2 algorithm using compute unified device architecture (CUDA)-enabled GPUs. Two critical GPU computing techniques, namely intertask hybrid CPU-GPU parallelism and tile-based Smith-Waterman map backtracking using CUDA, are investigated to facilitate fast alignments. By aligning both simulated and real reads to the human genome, our aligner yields comparable or better performance compared to BWA-SW, Bowtie2, and GEM. Furthermore, CUSHAW2-GPU with a Tesla K20c GPU achieves significant speedups over the multithreaded CUSHAW2, BWA-SW, Bowtie2, and GEM on the 12 cores of a high-end CPU for both single-end and paired-end alignment.

Quantum Queries on Permutations

2015

K. Iwama and R. Freivalds considered query algorithms where the black box contains a permutation. Since then several authors have compared quantum and deterministic query algorithms for permutations. It turns out that the case of \(n\)-permutations where \(n\) is an odd number is difficult. There was no example of a permutation problem where quantization can save half of the queries for \((2m+1)\)-permutations if \(m\ge 2\). Even for \((2m)\)-permutations with \(m\ge 2\), the best proved advantage of quantum query algorithms is the result by Iwama/Freivalds where the quantum query complexity is \(m\) but the deterministic query complexity is \((2m-1)\). We present a group of \(5\)-permutati…

On the systolic calculation of all-pairs interactions using transputer arrays

1991

SoC-Based Implementation of the Backpropagation Algorithm for MLP

2008

The backpropagation algorithm used for the training of multilayer perceptrons (MLPs) has a high degree of parallelism and is therefore well-suited for hardware implementation on an ASIC or FPGA. However, most implementations are lacking in generality of application, either by limiting the range of trainable network topologies or by resorting to fixed-point arithmetic to increase processing speed. We propose a parallel backpropagation implementation on a multiprocessor system-on-chip (SoC) with a large number of independent floating-point processing units, controlled by software running on embedded processors in order to allow flexibility in the selection of the network topology to be traine…