TY - CHAP A1 - Gorlatch, Sergei A1 - Dünnweber, Jan ED - Getov, Vladimir ED - Laforenza, Domenico ED - Reinefeld, Alexander T1 - From Grid Middleware to Grid Applications BT - Bridging the Gap with HOCs T2 - Future Generation Grids N2 - This paper deals with the problem of application programming for grid systems that combine heterogeneous data and computational resources via the Internet. We argue that grid programming is still too complex because of the big gap between the currently used and anticipated grid middleware, (e.g., Globus or WSRF) and the application level. We suggest that this gap needs to be closed in future-generation grids and propose a novel approach to bridging the gap by using Higher-Order Components (HOCs) — recurring patterns of parallel behaviour that are provided to the user as program building blocks with pre-packaged implementation and middleware setup. The presentation is illustrated with a simple case study of computing fractal images. Our experiments demonstrate that HOCs can simplify grid application programming significantly, without serious performance loss. KW - components KW - Grid services KW - Globus toolkit KW - mobile code Y1 - 2005 SN - 978-0-387-27935-0 U6 - https://doi.org/10.1007/978-0-387-29445-2_13 SP - 241 EP - 261 PB - Springer Verlag CY - Berlin ER - TY - CHAP A1 - Dünnweber, Jan A1 - Tomasoni, Johannes A1 - Gorlatch, Sergei A1 - Claßen, Michael A1 - Claßen, Philipp A1 - Lengauer, Christian ED - Gorlatch, Sergei ED - Fragopoulou, Paraskevi ED - Priol, Thierry T1 - A Grid Component with Embedded Loop Parallelization T2 - Grid Computing N2 - This work integrates two distinct research areas of parallel and distributed computing, (1) automatic loop parallelization, and (2) component-based Grid programming. The latter includes technologies developed within CoreGRID for simplifying Grid programming: the Grid ComponentModel (GCM) and Higher- Order Components (HOCs). Components support developing applications on the Grid without taking all the technical details of the particular platform type into account (network communication, heterogeneity, etc.). The GCMenables a hierarchical composition of programpieces and HOCs enable the reuse of component code in the development of new applications by specifying application-specific operations in a program via code parameters. When a programmer is provided, e. g., with a compute farm HOC, only the independent worker tasks must be described. But, once an application exhibits data or control dependences, the trivial farm is no longer sufficient. Here, the power of loop parallelization tools, like LooPo, comes into play: by embedding LooPo into a HOC, we show that these two technologies in combination facilitate the automatic transformation of a sequential loop nest with complex dependences (supplied by the user as a HOC parameter) into an ordered task graph, which can be processed on the Grid in parallel. This technique can significantly simplify GCM-based systems which combine multiple HOCs and other components. We use an equation system solver based on the successive overrelaxation method (SOR) as our motivating application example and for performance experiments. KW - Higher-Order Components (HOCs) KW - Loop Parallelization KW - GCM KW - Grid Programming Y1 - 2007 SN - 978-0-387-09456-4 U6 - https://doi.org/10.1007/978-0-387-09457-1_22 SP - 261 EP - 273 PB - Springer CY - Berlin ER - TY - CHAP A1 - Dünnweber, Jan A1 - Parlavatzas, Nikos A1 - Gorlatch, Sergei A1 - Baude, Francoise A1 - Legrand, Virginie ED - Gorlatch, Sergei ED - Danelutto, Marco T1 - Automatic Creation of Web Services for Grid Components T2 - Integrated Research in GRID Computing N2 - While high-level software components simplify the programming of grid applications and Web services increase their interoperability, developing such components and configuring the interconnecting services is a demanding task. In this paper, we consider the combination of Higher-Order Components (HOCs) with the Fractal component model and the ProActive library. HOCs are parallel programming components, made accessible on the grid via Web services that use a special class loader enabling code mobility: executable code can be uploaded to a HOC, allowing one to customize the HOC. Fractal simplifies the composition of components and the ProActive library offers a generator for automatically creating Web services from components composed with Fractal, as long as all the parameters of these services have primitive types. Taking all the advantages of HOCs, ProActive and Fractal together, the obvious conclusion is that composing HOCs using Fractal and automatically exposing them as Web services on the grid via ProActive minimizes the required efforts for building complex grid systems. In this context, we solved the problem of exchanging code-carrying parameters in automatically generated Web services by integrating the HOC class loading mechanism into the ProActive library. KW - CoreGRID Component Model (GCM) & Fractal KW - Higher-Order Components Y1 - 2006 SN - 978-0-387-47656-8 U6 - https://doi.org/10.1007/978-0-387-47658-2_3 SP - 31 EP - 42 PB - Springer CY - Sophia Antipolis, France ER - TY - CHAP A1 - Dünnweber, Jan A1 - Lüdeking, Philipp A1 - Gorlatch, Sergei ED - Danelutto, Marco ED - Fragopoulou, Paraskevi ED - Getov, Vladimir T1 - A Higher-Order Component for Efficient Genome Processing on the Grid T2 - Making Grids Work N2 - Computational grids combine computers in the Internet for distributed data processing and are an attractive platform for the data-intensive applications of bioinformatics. We present an extensible genome processing software for the grid and evaluate its performance. Our software was able to discover previously unknown circular permutations (CP) in the ProDom database containing more than 70MB of protein data. A specific feature of our software is its design as a component: the Alignment HOC, a Higher-Order Component that makes use of the latest Globus toolkit as grid middleware. Besides genome data, the Alignment HOC accepts plugin code for processing this data as its input, and contains all the required configuration to run the component on top of Globus, thus, freeing the non-grid-expert user from dealing with grid middleware. Instead of writing data distribution procedures and configuring the middleware appropriately for every new algorithm, Alignment HOC users reuse the existing component and only write application-specific plugins. To maintain plugins persistently in a reusable manner, we built a web-accessible plugin database with a comfortable administration GUI. The flexible component-based implementation makes it easy to study CPs in other databases (e.g. UniProt/Swiss-Prot) or to use an alignment algorithm different than the standard Needleman-Wunsch. For the efficient distribution of workload, we developed a library of group communication operations for HOCs. KW - higher-order components KW - genome processing KW - sequence alignment KW - middleware Y1 - 2007 SN - 978-0-387-78447-2 U6 - https://doi.org/10.1007/978-0-387-78448-9_28 SP - 351 EP - 362 PB - Springer CY - Boston, MA ER - TY - CHAP A1 - Dünnweber, Jan A1 - Aldinucci, Marco A1 - Gorlatch, Sergei A1 - Campa, Sonia A1 - Danelutto, Marco ED - Gorlatch, Sergei ED - Danelutto, Marco T1 - Adaptable Parallel Components for Grid Programming T2 - Integrated Research in GRID Computing N2 - We suggest that parallel software components used for grid computing should be adaptable to application-specific requirements, instead of developing new components from scratch for each particular application. As an example, we take a parallel farm component which is “embarrassingly parallel”, i. e., free of dependencies, and adapt it to the wavefront processing pattern with dependencies that impact its behavior. We describe our approach in the context of Higher-Order Components (HOCs), with the Java-based system Lithium as our implementation framework. The adaptation process relies on HOCs’ mobile code parameters that are shipped over the network of the grid. We describe our implementation of the proposed component adaptation method and report first experimental results for a particular grid application — the alignment of DNA sequence pairs, a popular, time-critical problem in computational molecular biology. KW - Grid Components KW - Adaptable Code KW - Wavefront Parallelism KW - Java KW - Web Services Y1 - 2006 SN - 978-0-387-47656-8 U6 - https://doi.org/10.1007/978-0-387-47658-2_4 SP - 43 EP - 57 PB - Springer Verlag CY - Boston, MA ER -