Numerical simulation of density-driven flow and heat transport processes in porous media using the network method

Density-driven flow and heat transport processes in 2-D porous media scenarios are governed by coupled, non-linear, partial differential equations that normally have to be solved numerically. In the present work, a model based on the network method simulation is designed and applied to simulate these processes, providing steady state patterns that demonstrate its computational power and reliability. The design is relatively simple and needs very few rules. Two applications in which heat is transported by natural convection in confined and saturated media are studied: slender boxes heated from below (a kind of Bénard problem) and partially heated horizontal plates in rectangular domains (the Elder problem). The streamfunction and temperature patterns show that the results are coherent with those of other authors: steady state patterns and heat transfer depend both on the Rayleigh number and on the characteristic Darcy velocity derived from the values of the hydrological, thermal and geometrical parameters of the problems.The first author acknowledges the support of the Universidad Politécnica de Cartagena through a pre-doctoral scholarship and the economic support of the Universidad Católica del Norte to cover the costs to publish in open access

On Designing Multicore-aware Simulators for Biological Systems

The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to speed it up on multi-core platforms, which pose new challenges for parallelisation techniques. These opportunities are developed in two general families of solutions involving both the single simulation and a bulk of independent simulations (either replicas of derived from parameter sweep). Proposed solutions are tested on the parallelisation of the CWC simulator (Calculus of Wrapped Compartments) that is carried out according to proposed solutions by way of the FastFlow programming framework making possible fast development and efficient execution on multi-cores.Comment: 19 pages + cover pag

Modelling and Analysis Using GROOVE

In this paper we present case studies that describe how the graph transformation tool GROOVE has been used to model problems from a wide variety of domains. These case studies highlight the wide applicability of GROOVE in particular, and of graph transformation in general. They also give concrete templates for using GROOVE in practice. Furthermore, we use the case studies to analyse the main strong and weak points of GROOVE

High-Performance Cloud Computing: A View of Scientific Applications

Scientific computing often requires the availability of a massive number of computers for performing large scale experiments. Traditionally, these needs have been addressed by using high-performance computing solutions and installed facilities such as clusters and super computers, which are difficult to setup, maintain, and operate. Cloud computing provides scientists with a completely new model of utilizing the computing infrastructure. Compute resources, storage resources, as well as applications, can be dynamically provisioned (and integrated within the existing infrastructure) on a pay per use basis. These resources can be released when they are no more needed. Such services are often offered within the context of a Service Level Agreement (SLA), which ensure the desired Quality of Service (QoS). Aneka, an enterprise Cloud computing solution, harnesses the power of compute resources by relying on private and public Clouds and delivers to users the desired QoS. Its flexible and service based infrastructure supports multiple programming paradigms that make Aneka address a variety of different scenarios: from finance applications to computational science. As examples of scientific computing in the Cloud, we present a preliminary case study on using Aneka for the classification of gene expression data and the execution of fMRI brain imaging workflow.Comment: 13 pages, 9 figures, conference pape

Modeling adaptation with a tuple-based coordination language

In recent years, it has been argued that systems and applications, in order to deal with their increasing complexity, should be able to adapt their behavior according to new requirements or environment conditions. In this paper, we present a preliminary investigation aiming at studying how coordination languages and formal methods can contribute to a better understanding, implementation and usage of the mechanisms and techniques for adaptation currently proposed in the literature. Our study relies on the formal coordination language Klaim as a common framework for modeling some adaptation techniques, namely the MAPE-K loop, aspect- and context-oriented programming

Teaching Parallel Programming Using Java

This paper presents an overview of the "Applied Parallel Computing" course taught to final year Software Engineering undergraduate students in Spring 2014 at NUST, Pakistan. The main objective of the course was to introduce practical parallel programming tools and techniques for shared and distributed memory concurrent systems. A unique aspect of the course was that Java was used as the principle programming language. The course was divided into three sections. The first section covered parallel programming techniques for shared memory systems that include multicore and Symmetric Multi-Processor (SMP) systems. In this section, Java threads was taught as a viable programming API for such systems. The second section was dedicated to parallel programming tools meant for distributed memory systems including clusters and network of computers. We used MPJ Express-a Java MPI library-for conducting programming assignments and lab work for this section. The third and the final section covered advanced topics including the MapReduce programming model using Hadoop and the General Purpose Computing on Graphics Processing Units (GPGPU).Comment: 8 Pages, 6 figures, MPJ Express, MPI Java, Teaching Parallel Programmin

Computing an Optimal Control Policy for an Energy Storage

We introduce StoDynProg, a small library created to solve Optimal Control problems arising in the management of Renewable Power Sources, in particular when coupled with an Energy Storage System. The library implements generic Stochastic Dynamic Programming (SDP) numerical methods which can solve a large class of Dynamic Optimization problems. We demonstrate the library capabilities with a prototype problem: smoothing the power of an Ocean Wave Energy Converter. First we use time series analysis to derive a stochastic Markovian model of this system since it is required by Dynamic Programming. Then, we briefly describe the "policy iteration" algorithm we have implemented and the numerical tools being used. We show how the API design of the library is generic enough to address Dynamic Optimization problems outside the field of Energy Management. Finally, we solve the power smoothing problem and compare the optimal control with a simpler heuristic control.Comment: Part of the Proceedings of the 6th European Conference on Python in Science (EuroSciPy 2013), Pierre de Buyl and Nelle Varoquaux editors, (2014

Evaluation of Kermeta for Solving Graph-based Problems

Kermeta is a meta-language for specifying the structure and behavior of graphs of interconnected objects called models. In this paper,\ud we show that Kermeta is relatively suitable for solving three graph-based\ud problems. First, Kermeta allows the specification of generic model\ud transformations such as refactorings that we apply to different metamodels\ud including Ecore, Java, and Uml. Second, we demonstrate the extensibility\ud of Kermeta to the formal language Alloy using an inter-language model\ud transformation. Kermeta uses Alloy to generate recommendations for\ud completing partially specified models. Third, we show that the Kermeta\ud compiler achieves better execution time and memory performance compared\ud to similar graph-based approaches using a common case study. The\ud three solutions proposed for those graph-based problems and their\ud evaluation with Kermeta according to the criteria of genericity,\ud extensibility, and performance are the main contribution of the paper.\ud Another contribution is the comparison of these solutions with those\ud proposed by other graph-based tools