Search results for "020203 distributed computing"

On the Use of Binary Trees for DNA Hydroxymethylation Analysis

2017

DNA methylation (mC) and hydroxymethylation (hmC) can have a significant effect on normal human development, health and disease status. Hydroxymethylation studies require specific treatment of DNA, as well as software tools for their analysis. In this paper, we propose a parallel software tool for analyzing the DNA hydroxymethylation data obtained by TAB-seq. The software is based on the use of binary trees for searching the different occurrences of methylation and hydroxymethylation in DNA samples. The binary trees allow to efficiently store and access the information about the methylation of each methylated/hydroxymethylated cytosines in the samples. Evaluation results shows that the perf…

2016

The growth of next-generation sequencing (NGS) datasets poses a challenge to the alignment of reads to reference genomes in terms of alignment quality and execution speed. Some available aligners have been shown to obtain high quality mappings at the expense of long execution times. Finding fast yet accurate software solutions is of high importance to research, since availability and size of NGS datasets continue to increase. In this work we present an efficient parallelization approach for NGS short-read alignment on multi-core clusters. Our approach takes advantage of a distributed shared memory programming model based on the new UPC++ language. Experimental results using the CUSHAW3 alig…

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…

Near field improvements of stochastic collaborative beamforming in wireless sensor networks

2020

Wireless sensor networks (WSN) are groups of small devices that contain a microcontroller in which a large number of sensors can be added. They transmit data and communicate to each other in the ISM band, standard IEEE 802.15.4, exchanging packets using a multi-hop routing. These devices are named motes and are nodes of the WSN. They are very simple and easy to program, powered by batteries of 1.5Volts (AA and AAA). The nodes are autonomous elements that can be deployed implementing any type of network. In a typical deployment the nodes communicate with each other and with a master node or Base Station (BS), which in turn transmits the information to an external server, which collects the e…

Data offloading and task allocation for cloudlet-assisted ad hoc mobile clouds

2016

Nowadays, although the data processing capabilities of the modern mobile devices are developed in a fast speed, the resources are still limited in terms of processing capacity and battery lifetime. Some applications, in particular the computationally intensive ones, such as multimedia and gaming, often require more computational resources than a mobile device can afford. One way to address such a problem is that the mobile device can offload those tasks to the centralized cloud with data centers, the nearby cloudlet or ad hoc mobile cloud. In this paper, we propose a data offloading and task allocation scheme for a cloudlet-assisted ad hoc mobile cloud in which the master device (MD) who ha…

Touch or touchless?:Evaluating usability of interactive displays for persons with autistic spectrum disorders

2019

Interactive public displays have been exploited and studied for engaging interaction in several previous studies. In this context, applications have been focused on supporting learning or entertainment activities, specifically designed for people with special needs. This includes, for example, those with Autism Spectrum Disorders (ASD). In this paper, we present a comparison study aimed at understanding the difference in terms of usability, effectiveness, and enjoyment perceived by users with ASD between two interaction modalities usually supported by interactive displays: touch-based and touchless gestural interaction. We present the outcomes of a within-subject setup involving 8 ASD users…

A Generic Approach to Scheduling and Checkpointing Workflows

2018

This work deals with scheduling and checkpointing strategies to execute scientific workflows on failure-prone large-scale platforms. To the best of our knowledge, this work is the first to target fail-stop errors for arbitrary workflows. Most previous work addresses soft errors, which corrupt the task being executed by a processor but do not cause the entire memory of that processor to be lost, contrarily to fail-stop errors. We revisit classical mapping heuristics such as HEFT and MinMin and complement them with several checkpointing strategies. The objective is to derive an efficient trade-off between checkpointing every task (CkptAll), which is an overkill when failures are rare events, …

Hierarchies of probabilistic and team FIN-learning

2001

AbstractA FIN-learning machine M receives successive values of the function f it is learning and at some moment outputs a conjecture which should be a correct index of f. FIN learning has two extensions: (1) If M flips fair coins and learns a function with certain probability p, we have FIN〈p〉-learning. (2) When n machines simultaneously try to learn the same function f and at least k of these machines output correct indices of f, we have learning by a [k,n]FIN team. Sometimes a team or a probabilistic learner can simulate another one, if their probabilities p1,p2 (or team success ratios k1/n1,k2/n2) are close enough (Daley et al., in: Valiant, Waranth (Eds.), Proc. 5th Annual Workshop on C…

Online Scheduling of Task Graphs on Heterogeneous Platforms

2020

Modern computing platforms commonly include accelerators. We target the problem of scheduling applications modeled as task graphs on hybrid platforms made of two types of resources, such as CPUs and GPUs. We consider that task graphs are uncovered dynamically, and that the scheduler has information only on the available tasks, i.e., tasks whose predecessors have all been completed. Each task can be processed by either a CPU or a GPU, and the corresponding processing times are known. Our study extends a previous $4\sqrt{m/k}$ 4 m / k -competitive online algorithm by Amaris et al. [1] , where $m$ m is the number of CPUs and $k$ k the number of GPUs ( $m\geq k$ m ≥ k ). We prove that no online…

Scheduling on Two Types of Resources: a Survey

2020

International audience; We study the problem of executing an application represented by a precedence task graph on a parallel machine composed of standard computing cores and accelerators. Contrary to most existing approaches, we distinguish the allocation and the scheduling phases and we mainly focus on the allocation part of the problem: choose the most appropriate type of computing unit for each task. We address both off-line and on-line settings and design generic scheduling approaches. In the first case, we establish strong lower bounds on the worst-case performance of a known approach based on Linear Programming for solving the allocation problem. Then, we refine the scheduling phase …