AutoMap and AutoLink tools for communicating complex and dynamic data-structures using MPI

Goujon, Delphine Stéphanie; Michel, Martial; Peeters, Jasper; Devaney, J E.

doi:10.1007/bfb0052210

Cited by 13 publications

(12 citation statements)

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“…However, a comparison of our work with other directly related approaches, such as MPI Pre-Processor [28], AutoMap/AutoLink [11], or C++2MPI [14], is impossible due to their lack of support for C++ language features or even C++ itself.…”

Section: Case Studies and Performance Resultsmentioning

confidence: 99%

“…These approaches include both automatic tools and special purpose libraries. The automatic tools that we consider closely related work include AutoMap/AutoLink [11], C++2MPI [14], and MPI Pre-Processor [28]. In addition, Boost.MPI and Boost.Serialization [17] provide library support for seamless marshaling and unmarshaling.…”

Section: Directly Related Workmentioning

confidence: 99%

“…AutoMap/AutoLink [11] provides automatic marshaling of C structures by enabling the user to annotate fields to be marshaled. While the annotations provide a level of abstraction, its granularity might be too low-level particularly for non-expert users, possibly violating objective one.…”

Section: Directly Related Workmentioning

confidence: 99%

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Efficient automated marshaling of C++ data structures for MPI applications

Tansey

Tilevich

2008

2008 IEEE International Symposium on Parallel and Distributed Processing

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Section: Case Studies and Performance Resultsmentioning

confidence: 99%

Section: Directly Related Workmentioning

confidence: 99%

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Efficient automated marshaling of C++ data structures for MPI applications

Tansey

Tilevich

2008

2008 IEEE International Symposium on Parallel and Distributed Processing

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“…AutoMap [6] is a high level tool that facilitate the use of data-structures in MPI. This piece of software generates new MPI derived datatypes from a user-defined file provided by the user.…”

Section: Related Workmentioning

confidence: 99%

MPI Pre-Processor: Generating MPI Derived Datatypes from C Datatypes Automatically

Renault

Parrot

2006 International Conference on Parallel Processing Workshops (ICPPW'06)

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The grid usage is facing the problem that consists in running existing sequential code for parallel execution transparently (ie. using source code without modification). AIPE is a middleware that deals with this problem. MPIPP is the software component we have developed to allow the generation of MPI derived datatypes from C datatype definitions automatically. The goal of this new tool is to make the building of complex messages easier for the end-user. Moreover, this paper shows that MPIPP goes farther in the complexity level of C datatypes that can be taken into account than any other similar tools have ever gone to.

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“…El tejido está internamente representado en el simulador como un vector de estructuras en C. El vector tiene un tamaño igual al número total de células del tejido y cada estructura almacena el estado de una célula cardiaca, es decir, todos los atributos definidos por el modelo celular al que pertenece dicha célula. Para poder diseñar un método de grabación genérico que permita guardar cualquier tipo de célula, independientemente del modelo celular, se utiliza una herramienta llamada AutoMap [113], que permite la generación automática de un tipo de datos MPI (MPI Datatype) [114] a partir de cualquier estructura en lenguaje C. Este tipo de datos MPI posteriormente se utiliza para especificar la información que debe ser guardada en disco.…”

Section: Persistencia En Las Simulaciones: Copias De Seguridadunclassified

Computación de altas prestaciones sobre entornos grid en aplicaciones biomédicas: simulación de la actividad eléctrica cardiaca y diseño de proteínas

Martínez¹

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The important research advances, in many scientific areas, have been fostered by an improvement of the computational strategies employed. As an example, High Performance Computing enables the collaborative usage of multiple processors to accelerate the resolution of scientific problems, and even to face large problems.However, there are several scientific applications whose computational requirements can exceed the computing capacities of a single organisation. This way, the recent advances in the bandwidth of the communication networks have leveraged the idea of joining geographically distributed resources, creating a global computing infrastructure known as the Grid.This thesis combines High Performance Computing and Grid Computing in order to accelerate the execution of scientific applications, and to allow solving problems that can not be solved, in a reasonable time, with the resources of a single organisation.For that purpose, a system that offers an abstraction layer to simplify the execution of general scientific applications, in Grid infrastructures, has been developed. This system, called GMarte, provides metascheduling functionality for the concurrent execution of parallel applications on resources based on the Globus Toolkit, the standard software in computational Grids. Later, and according to the current trend towards service-oriented architectures, a metascheduler Grid service has been created, featuring interoperability and based on standard technologies. This Grid service offers metascheduling functionality to multiple clients, which use high-level graphical applications to interact with it, using security mechanisms for data protection. This way, it is possible to simplify and foster the usage of Grid technologies for the efficient execution of scientific applications.The proposed computational approach has been applied to two biomedical applications: the cardiac electrical activity simulation and the protein design with targeted properties. First of all, a parallel simulation system of the action potential propagation on cardiac tissues has been developed.Secondly, an efficient system has been implemented for the design of proteins. In both cases, the usage of High Performance Computing has enabled to accelerate the executions as well as to face larger dimension problems.Finally, executions of both applications have been performed over different Grid deployments, in order to evaluate the advantages of a strategy that combines both computationally advanced techniques. 3 Títol Computació d'Altes Prestacions en Entorns Grid en Aplicacions Biomèdiques: Simulació de l'Activitat Elèctrica Cardiaca i Disseny de Proteines ResumEls importants avanços en la investigació, de nombrosesàrees de coneixement, han vingut propiciats per una millora en les estratègies de computació emprades. A mode d'exemple, la Computació d'Altes Prestacions permet la utilització col·laborativa de múltiples processadors per a accelerar la resolució de problemes científics, i fins i tot abordar problemes de major dimens...

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AutoMap and AutoLink tools for communicating complex and dynamic data-structures using MPI

Cited by 13 publications

References 1 publication

Efficient automated marshaling of C++ data structures for MPI applications

Efficient automated marshaling of C++ data structures for MPI applications

MPI Pre-Processor: Generating MPI Derived Datatypes from C Datatypes Automatically

Computación de altas prestaciones sobre entornos grid en aplicaciones biomédicas: simulación de la actividad eléctrica cardiaca y diseño de proteínas

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