Multiple biological sequence alignment in heterogeneous multicore clusters with user-selectable task allocation policies

Multiple Sequence Alignment (MSA) is an important problem in Bioinformatics that aims to align more than two sequences in order to emphasize similarity regions. This problem is known to be NP-Hard, so heuristic methods are used to solve it. DIALIGN-TX is an iterative heuristic method for MSA that generates alignments by concatenating ungapped regions with high similarity. Usually, the first phase of MSA algorithms is parallelized by distributing several independent tasks among the nodes. Even though heterogeneous multicore clusters are becoming very common nowadays, very few task allocation policies were proposed for this type of architecture. This paper proposes an MPI/OpenMP master/slave parallel strategy to run DIALIGN-TX in heterogeneous multicore clusters, with several allocation policies. We show that an appropriate choice of the master node has great impact on the overall system performance. Also, the results obtained in a heterogeneous multicore cluster composed of 4 nodes (30 cores), with real sequence sets show that the execution time can be drastically reduced when the appropriate allocation policy is used.     

A surrogate model to assess the whole body SAR induced by multiple plane waves at 2.4?GHz

The assessment of the exposure to electromagnetic waves is nowadays a key question. Dealing with the relationship between exposure and incident field, most of previous investigations have been performed with a single plane wave. Realistic exposure in the far field can be modeled as multiple plane waves with random direction of arrival, random amplitude, and random phase. This paper, based on numerical investigations, studies the whole body specific absorption rate (SAR) linked to the exposure induced by five random plane waves having uniformly distributed angles of arrival in the horizontal plane, log-normal distributed amplitudes, and uniformly distributed phases. A first result shows that this random heterogeneous exposure generates maximal variations of ??25% for the whole body specific absorption. An important observation is that the exposure to a single plane wave arriving face to the body, used for the guidelines, does not constitute the worst case. We propose a surrogate model to assess the distribution of the whole body SAR in the case of an exposure to multiple plane waves. For a sample of 30 values of whole body SAR induced by five plane waves at 2.4?GHz, this simple approach, considering the resulting SAR as the sum of the SAR induced by each isolated plane wave, leads to an estimated distribution of whole body SAR following the real distribution with a p value of 76% according to the Kolmogorov statistical test.     

Performance analysis of a novel hybrid push–pull algorithm with QoS adaptations in wireless networks

In this paper, we present a novel hybrid push–pull algorithm which combines broadcasting of push data items, with dissemination upon request of pull items in asymmetric communication environments. These environments are made up only of one database server and many clients. Requests made by the clients are queued up for the pull items. The (pull) item with the number of pending requests is the one selected to be pulled. We present a performance analysis of our scheme, and determine the individual response time for each item disseminated and the overall time for the pull queue to be flushed. Next, we extend our algorithm by incorporating quality of service (QoS) factors, and then, study its performance analytically.     

Parallel simulation on the hypercube multiprocessor

Summary This paper focuses upon a particular conservative algorithm for parallel simulation, the Time of Next Event (TNE) suite of algorithms [13]. TNE relies upon a shortest path algorithm which is independently executed on each processor in order to unblock LPs in the processor and to increase the parallelism of the simulation. TNE differs fundamentally from other conservative approaches in that it takes advantage of having several LPs assigned to each processor, and does not rely upon message passing to provide lookahead. Instead, it relies upon a shortest path algorithm executed independently in each processor. A deadlock resolution algorithm is employed for interprocessor deadlocks. We describe an empirical investigation of the performance of TNE on the iPSC/i860 hypercube multiprocessor. Several factors which play an important role in TNE's behavior are identified, and the speedup relative to a fast uniprocessor-based event list algorithm is reported. Our results indicate that TNE yields good speedups and out-performs an optimized version of the Chandy&Misra-null message (CMB) algorithm. TNE was 2–5 times as fast as the CM approach for less than 10 processors (and 1.5–3 times as fast when more than 10 processors were used for the same population of processes.) Azzedine Boukerche received the State Engineer degree in Software Engineering from Oran University, Oran, Algeria, and the M.Sc. degree in Computer Science from McGill University, Montreal, Canada. He is a Ph.D. candidate at the School of Computer Science, McGill University. During 1991–1992, he was a visiting doctoral student at the California Institute of Technology. He is employed as a Faculty Lecturer of computer Science at McGill University since 1993. His research interests include parallel simulation, distributed algorithms, and system performance analysis. He is a student member of the IEEE and ACM. Carl Tropper is an Associate Professor of Computer Science at McGill University. His primary area of research is parallel discrete event simulation. His general area of interest is in parallel computing and distributed algorithms in particular. Previously, he has done research in the performance modeling of computer networks, having written a book,Local Computer Network Technologies, while active in the area. Before coming to university life, he worked for the BBN Corporation and the Mitre Corporation, both located in the Boston area. He spent the 1991–92 academic year on a sabbatical leave at the Jet Propulsion Laboratories of the California Institute of Technology where he contributed to a project centered about the verification of flight control software. As part of this project he developed algorithms for the parallel simulation of communicating finite state machines. During winters he may be found hurtling down mountains on skis.This work has been completed while the author was a visiting doctoral student at the California Institute of TechnologyWas on sabbatical leave at the Jet Propulsion laboratories, California Institute of Technology     

An Inter-cluster Communication based Energy Aware and Fault Tolerant Protocol for Wireless Sensor Networks

The ambient intelligence paradigm is built upon Ubiquitous Computing (UC), in which the computing devices are embedded in the environment with the purpose of enhancing the human experience at home, workplace/office, learning, health care etc. The UC applications aim at providing services to the users anywhere, anytime in an unobtrusive, seemingly invisible way. Wireless sensor networks (WSNs) have great potential for UC applications and are envisioned to revolutionize them. This paper presents a clustering routing protocol for event-driven, query-based and periodic WSNs. The protocol aims at optimizing energy dissipation in the network as well as providing network’s fault tolerance and connectivity. Message propagation is accomplished by using short distance transmissions by employing nearest neighbor nodes between neighboring clusters. Moreover, the algorithm proposes using an energy efficient approach by alternating the nodes responsible for inter-cluster communication inside one cluster. The algorithm also aims at even energy dissipation among the nodes in the network by alternating the possible routes to the Sink. This helps to balance the load on sensor nodes and increases the network lifetime, while avoiding congested links at the same time. We discuss the implementation of our protocol, present its proof of correctness as well as the performance evaluation through an extensive set of simulation experiments. This work is partially sponsored by Grants from the NSERC, Canada Research Chairs Program, ORNEC, the Ontario Distinguished Researcher Award and the EAR Award.     

A Practical Approach to Representation of Real-time Building Control Applications in Simulation

Machine Intelligence Research - Computer based automation and control systems are becoming increasingly important in smart sustainable buildings, of- ten referred to as automated buildings (ABs),...     

A performance evaluation of a fault-tolerant path recommendation protocol for smart transportation system

Recommending traveling vehicles to take a certain path towards their targeted destinations have received great interest recently. At the downtown area several paths can lead to the same located destination, this is due to the grid-layout architecture of modern downtowns. Drivers always wish to reach their destinations as fast as possible and without traveling drastically long distance or without consuming extra fuel. The best path towards any destination is determined based on the relative location of the vehicle from its destination and based on other vehicles traffic distribution on the road network. Although numerous studies have investigated this issue over the road network, the communication failures and their effects on the obtained path have been neglected in those previous studies. In this paper, we investigate these potential faults and their effects on the correctness of the selected paths. We then proposed a new protocol to tackle these potential failures while selecting the best path towards each destination over the road network, fault tolerant path recommendation protocol (FT-PR). From the experimental results, we can see that the FT-PR protocol has a higher success ratio than previous path recommendation protocols, such as ICOD. This is demonstrated by obtaining paths with shorter traveling time and shorter traveling distance. The FT-PR protocol also eliminates extra loops over the road network in each selected path.     

Heat Capacity and Thermal Damping Properties of Spin-Crossover Molecules: A New Look at an Old Topic

The thermally induced spin-crossover (SCO) phenomenon in transition metal complexes is an entropy-driven process, which has been extensively studied through calorimetric methods. Yet, the excess heat capacity associated with the molecular spin-state switching has never been explored for practical applications. Herein, the thermal damping effect of an SCO film is experimentally assessed by monitoring the transient heating response of SCO-coated metallic microwires, Joule-heated by current pulses. A damping of the wire temperature, up to 10%, is evidenced on a time scale of tens of microseconds due to the spin-state switching of the molecular film. Fast heat-charging dynamics and negligible fatigability are demonstrated, which, together with the solid-solid nature of the spin transition, appear as promising features for achieving thermal energy management applications in functional devices.