A. J. Rubio-Montero

Management of Virtual Machines on Globus Grids Using GridWay

Virtual machines are a promising technology to overcome some of the problems found in current grid infrastructures, like heterogeneity, performance partitioning or application isolation. In this work, we present straightforward deployment of virtual machines in globus grids. This solution is based on standard services and does not require additional middleware to be installed. Also, we assess the suitability of this deployment in the execution of a high throughput scientific application, the XMM-Newton scientific analysis system.

Improvements on the Fusion Code FAFNER2

FAFNER2, which is a 3-D code adapted to the TJ-II helical axis stellarator from the original one developed by Lister at Max Planck IPP, simulates by Monte Carlo methods the neutral beam injection technology (a key heating method for most of the fusion experiments worldwide). To date, FAFNER2 has been usually run at CIEMAT by means of a batch mode on a shared memory computer with MIPS processors. This paper describes how the application has ben updated to employ MPI and run on standard Linux clusters. As in Grid infrastructures, not every site has MPI installed on their nodes; a serial version has also been developed, together with a Java Distributed Resource Management Application API program able to run FAFNER2 on distributed resource platforms, such as Grid infrastructures. In addition, and with new improvements in the code for maximizing its performance, the metascheduler GridWay has also been incorporated for maximizing the executions on the Grid. Scalability, fault tolerance, and correctness of the result have been proved employing a significant number of particles and nodes within a local cluster and the EGEE infrastructure.

More Efficient Executions of Monte Carlo Fusion Codes by Means of Montera: The ISDEP Use Case

ISDEP (Integrator of Stochastic Differential Equations for Plasmas) is a Monte Carlo code that solves the plasma dynamics in a fusion device and perfectly scales on distributed computing platforms. Montera is a recent framework developed for achieving Grid efficient executions of Monte Carlo applications, as ISDEP is. In this work, the improvement of performing the calculations of ISDEP with Montera, which rise up to 34.9%, is shown as well as an analysis on the implications it could have, which aim to show to the fusion research community the benefits of using Montera.

Drift Kinetic Equation Solver for Grid (DKEsG)

Neoclassical (NC) transport calculations are necessary for the complete simulation cycle of the behavior of plasmas inside both tokamaks and stellarators, which are more complex to be performed on the latest. In addition, due to the fact that the NC transport is mainly determined by the magnetic properties of the device (mathematically designed by the number of Fourier harmonics needed to describe the confining magnetic field), its study is mandatory to ensure the efficiency of a certain coil configuration before it is implemented in a fusion reactor. Thus, improvements to the already constructed devices and certain design decisions for the new ones, such as W7-X, NCSX, or QPS, have been made based on the estimations of the NC transport, among other criteria. In this sense, a compromise between the number of modes and polynomials to describe the distribution function and the required computing time to obtain reliable estimates is a must. This paper presents the porting process to the Grid and the computational optimization of the Drift Kinetic Equation Solver code, devoted to obtain the monoenergetic diffusion coefficients of the NC transport as well as the first coupled prototype for estimating the transport coefficients with such a new code release. The advantage of this code over the Monte Carlo applications already in production on the Grid is that it allows the estimation of all the transport coefficients, not only the diagonal ones. The tests and results obtained have been applied to the TJ-II Flexible Heliac, a stellarator in operation at National Fusion Laboratory (Spain), by using the EELA-2 Project infrastructure.

Computational Challenges on Grid Computing for Workflows Applied to Phylogeny

PhyloGrid is a new tool continuously in progress whose aim is two-fold: to reduce the technological divide that a partial scientific community with low computational skills has for accessing new powerful computational platforms such as Grid; and, to develop a user-friendly interface by means of a workflow integrated in a web-portal. MrBayes software has been selected for calculating the evolutionary history of the species which is being integrated into new tools that performs the execution of jobs. Finally, this new application has been tested on the Human Papillomavirus.

Performance improvements for the neoclassical transport calculation on Grid by means of pilot jobs

The neoclassical transport is a lower limit of the whole transport in plasmas confined in fusion devices, either stellarators or tokamaks. Even more, the determination of a vast database compiling monoenergetic and transport coefficients is very useful for coupling different codes, which can use those values as input data. The DKEsG application is able to obtain such parameters on Grid infrastructures. Since a large number of regular jobs are needed for filling the aforementioned database, a fast and robust execution scheme is necessary. For this purpose, a new DRMAA-enabled DKEsG version that makes use of a new generic pilot-job platform is used, avoiding the most significant overheads related to standard Grid middleware. This new developed mechanism is suitable for many other scientific applications involving high-throughput calculations.

FAFNER2: A comparison between the Grid and the MPI versions of the code

FAFNER2 is a 3D code that simulates by Monte Carlo methods the Neutral Beam Injection (NBI) technology. The original version was implemented for shared memory computers with MIPS proccesors, so an update to be executed by means of MPI on standard Linux clusters has been carried out as well as a new version to be run on Grid. To do the latest, a serial version has also been developed, together with a Java DRMAA program that is submitted by the GridWay metascheduler. As a result, two new improved versions of the code (HPC and Grid) are available.

A Fault Tolerant Workflow for Reproducible Research

In this work, the authors present a set of tools to overcome the problem of creating and executing distributed applications on dynamic environments in a resilient way, also ensuring the reproducibility of the performed experiments. The objective is to provide a portable, unattended and fault-tolerant set of tools, encapsulating the infrastructure-dependent operations away from the application developers and users, allowing to perform experiments based on open access data repositories. In this way, users can seamlessly search and lately access datasets that can be automatically retrieved as input data into a code already integrated in the proposed workflow. Such a search is based on metadata standards and relies on Persistent Identifiers (PID) to assign specific repositories. The applications profit from Distributed Toolbox, a newly created framework devoted to the creation and execution of distributed applications and includes tools for unattended Cluster and Grid execution, where a total fault tolerance is provided. By decoupling the definition of the remote tasks from its execution and control, the development, execution and maintenance of distributed applications is significantly simplified with respect to previous solutions, increasing their robustness and allowing running them on different computational platforms with little effort. The integration with open access databases and employment of PIDs for long-lasting references ensures that the data related to the experiments will persist, closing a complete research circle of data access / processing/ storage / dissemination of results.

Adapting Reproducible Research Capabilities to Resilient Distributed Calculations

Nowadays, computing calculations are becoming more and more demanding due to the huge pool of resources available. This demand must be satisfied in terms of computational efficiency and resilience, which is compromised in distributed and heterogeneous platforms. Not only this, data obtained are often either reused by other researchers or recalculated. In this work, a set of tools to overcome the problem of creating and executing fault tolerant distributed applications on dynamic environments is presented. Such a set also ensures the reproducibility of the performed experiments providing a portable, unattended and resilient framework that encapsulates the infrastructure-dependent operations away from the application developers and users, allowing performing experiments based on Open Access data repositories. In this way, users can seamlessly search and lately access datasets that can be automatically retrieved as input data into a code already integrated in the proposed workflow. Such a search is based on metadata standards and relies on Persistent Identifiers PID to assign specific repositories. The applications profit from Distributed Toolbox, a framework devoted to the creation and execution of distributed applications and includes tools for unattended cluster and grid execution, where a total fault tolerance is provided. By decoupling the definition of the remote tasks from its execution and control, the development, execution and maintenance of distributed applications is significantly simplified with respect to previous solutions, increasing their robustness and allowing running them on different computational platforms with little effort. The integration with Open Access databases and employment of PIDs for long-lasting references ensures that the data related to the experiments will persist, closing a complete research circle of data access/processing/storage/dissemination of results.

State-of-Art with PhyloGrid: Grid Computing Phylogenetic Studies on the EELA-2 Project Infrastructure

PhyloGrid is an application developed in the framework of the EELA-2 project devoted to the calculation of Phylogenies by means of the MrBayes software, that is, Bayesian statistics. To the moment, it has been used to perform studies on the Human Immunodeficiency Virus (HIV), the Human Papillomavirus (HPV), and the DENgue Virus (DENV). PhyloGrid aims to offer an easy interface for the bioinformatics community, which abstracts the final user from the ICT (Information and Communications Technology) underneath, so only the definition of the parameters for doing the Bayesian calculation should be set, including the model of evolution as well as a multiple alignment of the sequences previously to the final result. This chapter provides a description of the application and some new results related to the aforementioned diseases is also shown.