Grid Infrastructure for Domain Decomposition Methods in Computational ElectroMagnetics

The accurate and efficient solution of Maxwell's equation is the problem addressed by the scientific discipline called Computational ElectroMagnetics (CEM). Many macroscopic phenomena in a great number of fields are governed by this set of differential equations: electronic, geophysics, medical and biomedical technologies, virtual EM prototyping, besides the traditional antenna and propagation applications. Therefore, many efforts are focussed on the development of new and more efficient approach to solve Maxwell's equation. The interest in CEM applications is growing on. Several problems, hard to figure out few years ago, can now be easily addressed thanks to the reliability and flexibility of new technologies, together with the increased computational power. This technology evolution opens the possibility to address large and complex tasks. Many of these applications aim to simulate the electromagnetic behavior, for example in terms of input impedance and radiation pattern in antenna problems, or Radar Cross Section for scattering applications. Instead, problems, which solution requires high accuracy, need to implement full wave analysis techniques, e.g., virtual prototyping context, where the objective is to obtain reliable simulations in order to minimize measurement number, and as consequence their cost. Besides, other tasks require the analysis of complete structures (that include an high number of details) by directly simulating a CAD Model. This approach allows to relieve researcher of the burden of removing useless details, while maintaining the original complexity and taking into account all details. Unfortunately, this reduction implies: (a) high computational effort, due to the increased number of degrees of freedom, and (b) worsening of spectral properties of the linear system during complex analysis. The above considerations underline the needs to identify appropriate information technologies that ease solution achievement and fasten required elaborations. The authors analysis and expertise infer that Grid Computing techniques can be very useful to these purposes. Grids appear mainly in high performance computing environments. In this context, hundreds of off-the-shelf nodes are linked together and work in parallel to solve problems, that, previously, could be addressed sequentially or by using supercomputers. Grid Computing is a technique developed to elaborate enormous amounts of data and enables large-scale resource sharing to solve problem by exploiting distributed scenarios. The main advantage of Grid is due to parallel computing, indeed if a problem can be split in smaller tasks, that can be executed independently, its solution calculation fasten up considerably. To exploit this advantage, it is necessary to identify a technique able to split original electromagnetic task into a set of smaller subproblems. The Domain Decomposition (DD) technique, based on the block generation algorithm introduced in Matekovits et al. (2007) and Francavilla et al. (2011), perfectly addresses our requirements (see Section 3.4 for details). In this chapter, a Grid Computing infrastructure is presented. This architecture allows parallel block execution by distributing tasks to nodes that belong to the Grid. The set of nodes is composed by physical machines and virtualized ones. This feature enables great flexibility and increase available computational power. Furthermore, the presence of virtual nodes allows a full and efficient Grid usage, indeed the presented architecture can be used by different users that run different applications

A Cloud Infrastructure for Optimization of a Massive Parallel Sequencing Workflow

Massive Parallel Sequencing is a term used to describe several revolutionary approaches to DNA sequencing, the so-called Next Generation Sequencing technologies. These technologies generate millions of short sequence fragments in a single run and can be used to measure levels of gene expression and to identify novel splice variants of genes allowing more accurate analysis. The proposed solution provides novelty on two fields, firstly an optimization of the read mapping algorithm has been designed, in order to parallelize processes, secondly an implementation of an architecture that consists of a Grid platform, composed of physical nodes, a Virtual platform, composed of virtual nodes set up on demand, and a scheduler that allows to integrate the two platform

Virtual Environment for Next Generation Sequencing Analysis

Next Generation Sequencing technology, on the one hand, allows a more accurate analysis, and, on the other hand, increases the amount of data to process. A new protocol for sequencing the messenger RNA in a cell, known as RNA- Seq, generates millions of short sequence fragments in a single run. These fragments, or reads, can be used to measure levels of gene expression and to identify novel splice variants of genes. The proposed solution is a distributed architecture consisting of a Grid Environment and a Virtual Grid Environment, in order to reduce processing time by making the system scalable and flexibl

Enhancing Job Scheduling of an Atmospheric Intensive Data Application

Nowadays, e-Science applications involve great deal of data to have more accurate analysis. One of its application domains is the Radio Occultation which manages satellite data. Grid Processing Management is a physical infrastructure geographically distributed based on Grid Computing, that is implemented for the overall processing Radio Occultation analysis. After a brief description of algorithms adopted to characterize atmospheric profiles, the paper presents an improvement of job scheduling in order to decrease processing time and optimize resource utilization. Extension of grid computing capacity is implemented by virtual machines in existing physical Grid in order to satisfy temporary job requests. Also scheduling plays an important role in the infrastructure that is handled by a couple of schedulers which are developed to manage data automaticall

Engineering of an Extreme Rainfall Detection System using Grid Computing

This paper describes a new approach for intensive rainfall data analysis. ITHACA's Extreme Rainfall Detection System (ERDS) is conceived to provide near real-time alerts related to potential exceptional rainfalls worldwide, which can be used by WFP or other humanitarian assistance organizations to evaluate the event and understand the potentially floodable areas where their assistance is needed. This system is based on precipitation analysis and it uses rainfall data from satellite at worldwide extent. This project uses the Tropical Rainfall Measuring Mission Multisatellite Precipitation Analysis dataset, a NASA-delivered near real-time product for current rainfall condition monitoring over the world. Considering the great deal of data to process, this paper presents an architectural solution based on Grid Computing techniques. Our focus is on the advantages of using a distributed architecture in terms of performances for this specific purpos

Optimizing Splicing Junction Detection in Next Generation Sequencing Data on a Virtual-GRID Infrastructure

The new protocol for sequencing the messenger RNA in a cell, named RNA-seq produce millions of short sequence fragments. Next Generation Sequencing technology allows more accurate analysis but increase needs in term of computational resources. This paper describes the optimization of a RNA-seq analysis pipeline devoted to splicing variants detection, aimed at reducing computation time and providing a multi-user/multisample environment. This work brings two main contributions. First, we optimized a well-known algorithm called TopHat by parallelizing some sequential mapping steps. Second, we designed and implemented a hybrid virtual GRID infrastructure allowing to efficiently execute multiple instances of TopHat running on different samples or on behalf of different users, thus optimizing the overall execution time and enabling a flexible multi-user environmen

Virtual Environment for Next Generation Sequencing Analysis

Next Generation Sequencing technology, on the one hand, allows a more accurate analysis, and, on the other hand, increases the amount of data to process. A new protocol for sequencing the messenger RNA in a cell, known as RNA- Seq, generates millions of short sequence fragments in a single run. These fragments, or reads, can be used to measure levels of gene expression and to identify novel splice variants of genes. The proposed solution is a distributed architecture consisting of a Grid Environment and a Virtual Grid Environment, in order to reduce processing time by making the system scalable and flexibl