Search results for "SPEED"
showing 10 items of 876 documents
Faster GPU-Accelerated Smith-Waterman Algorithm with Alignment Backtracking for Short DNA Sequences
2014
In this paper, we present a GPU-accelerated Smith-Waterman (SW) algorithm with Alignment Backtracking, called GSWAB, for short DNA sequences. This algorithm performs all-to-all pairwise alignments and retrieves optimal local alignments on CUDA-enabled GPUs. To facilitate fast alignment backtracking, we have investigated a tile-based SW implementation using the CUDA programming model. This tiled computing pattern enables us to more deeply explore the powerful compute capability of GPUs. We have evaluated the performance of GSWAB on a Kepler-based GeForce GTX Titan graphics card. The results show that GSWAB can achieve a performance of up to 56.8 GCUPS on large-scale datasets. Furthermore, ou…
SWAPHI: Smith-Waterman Protein Database Search on Xeon Phi Coprocessors
2014
The maximal sensitivity of the Smith-Waterman (SW) algorithm has enabled its wide use in biological sequence database search. Unfortunately, the high sensitivity comes at the expense of quadratic time complexity, which makes the algorithm computationally demanding for big databases. In this paper, we present SWAPHI, the first parallelized algorithm employing Xeon Phi coprocessors to accelerate SW protein database search. SWAPHI is designed based on the scale-and-vectorize approach, i.e. it boosts alignment speed by effectively utilizing both the coarse-grained parallelism from the many co-processing cores (scale) and the fine-grained parallelism from the 512-bit wide single instruction, mul…
GSWABE: faster GPU-accelerated sequence alignment with optimal alignment retrieval for short DNA sequences
2014
In this paper, we present GSWABE, a graphics processing unit GPU-accelerated pairwise sequence alignment algorithm for a collection of short DNA sequences. This algorithm supports all-to-all pairwise global, semi-global and local alignment, and retrieves optimal alignments on Compute Unified Device Architecture CUDA-enabled GPUs. All of the three alignment types are based on dynamic programming and share almost the same computational pattern. Thus, we have investigated a general tile-based approach to facilitating fast alignment by deeply exploring the powerful compute capability of CUDA-enabled GPUs. The performance of GSWABE has been evaluated on a Kepler-based Tesla K40 GPU using a varie…
Gravitational Lensing of Supernova Neutrinos
2006
The black hole at the center of the galaxy is a powerful lens for supernova neutrinos. In the very special circumstance of a supernova near the extended line of sight from Earth to the galactic center, lensing could dramatically enhance the neutrino flux at Earth and stretch the neutrino pulse.
Mechanical and neural stretch responses of the human soleus muscle at different walking speeds
2009
During human walking, a sudden trip may elicit a Ia afferent fibre mediated short latency stretch reflex. The aim of this study was to investigate soleus (SOL) muscle mechanical behaviour in response to dorsiflexion perturbations, and to relate this behaviour to short latency stretch reflex responses. Twelve healthy subjects walked on a treadmill with the left leg attached to an actuator capable of rapidly dorsiflexing the ankle joint. Ultrasound was used to measure fascicle lengths in SOL during walking, and surface electromyography (EMG) was used to record muscle activation. Dorsiflexion perturbations of 6 deg were applied during mid-stance at walking speeds of 3, 4 and 5 km h(-1). At eac…
A Problem Based Approach to Sound Propagation in Different Materials
2010
In this paper we present a problem-based approach to the study of sound propagation devoted to pre-service physics teacher education at University of Palermo, Italy. Small groups of trainee teachers are proposed with real life situations and must organize themselves, define objectives, conduct researches, analyze results, and present conclusions. In particular, the problem of wave propagation in different materials is discussed, by starting from the real life situation of soundproofing a house. Examples of experiments performed by the trainee teachers with Real Time Laboratory (RTL) equipment and of interpretative models built and tested by using computer simulation environments are reporte…
La rete ferroviaria ad Alta Velocità in Corea del Sud [The High-Speed Rail network in South Korea]
2012
LA RETE FERROVIARIA AD ALTA VELOCITA’ IN COREA DEL SUD High speed rail in South Korea
A comparative empirical assessment of roundabouts operations in rural areas: impacts on congestion-specific vehicle speed profiles, pollutant and noi…
2020
Increasing concern about global warming and air quality has meant an increasing use of energetic and environmental indicators in roundabout design. The main objective of this paper is to compare different rural roundabouts in terms of traffic performance, pollutant and noise emissions through an integrated empirical assessment. Field measurements were carried out with a light duty vehicle in single-lane (SL), compact two-lane (CTL) and multi-lane (ML) roundabouts using Portable Emission Measurements Systems, OBD scan tool and Sound Level Meter, to measure real-world exhaust emissions, engine activity and acoustic data, respectively. Road traffic scene at roundabouts were obtained from video…
Reconstruction of Low Energy Neutrino Events with GPUs at IceCube
2020
IceCube is a cubic kilometer neutrino observatory located at the South Pole that produces massive amounts of data by measuring individual Cherenkov photons from neutrino interaction events in the energy range from few GeV to several PeV. The actual reconstruction of neutrino events in the GeV range is computationally challenging due to the scarcity of data produced by single events. This can lead to run times of several weeks for the state-of-the-art reconstruction method – Pegleg – on CPUs for typical workloads of many ten-thousand events. We propose a GPU version of Pegleg that probes the likelihood space with several hypotheses in parallel while adapting the amount of parallel sampled hy…
The Dynamical Kernel Scheduler - Part 1
2015
Emerging processor architectures such as GPUs and Intel MICs provide a huge performance potential for high performance computing. However developing software using these hardware accelerators introduces additional challenges for the developer such as exposing additional parallelism, dealing with different hardware designs and using multiple development frameworks in order to use devices from different vendors. The Dynamic Kernel Scheduler (DKS) is being developed in order to provide a software layer between host application and different hardware accelerators. DKS handles the communication between the host and device, schedules task execution, and provides a library of built-in algorithms. …