Pub Date : 2009-12-09DOI: 10.1109/e-Science.2009.50
Jefferson Tan, D. Abramson, C. Enticott
Computational grids are now mainstream facilities for e-research worldwide. While enterprise grids exist within organizations, national grids have become common, usually consisting of government as well as academic facilities. Such facilities are not uncommonly lenient with blanket policies to allow inbound and outbound grid traffic. This is far from ideal, from a security perspective, but given the dynamic nature of grid use, it is impractical to keep restrictive firewalls and manually keep up with on-demand firewall reconfiguration. Other solutions are necessary, where security is not sacrificed. Apart from first generation solutions that were mostly not sufficiently generic, standardization work is now ongoing, but exclusively aimed at firewall virtualization. We argue for an architectural solution that encompasses firewall virtualization as well as other methods that can be more appropriate in many environments. This paper describes our notion of the missing layer between grid and fabric, which we refer to as the virtual connectivity layer. We have developed two implementations within this layer and discuss how they fit into a complete and well-defined architectural solution.
{"title":"A Virtual Connectivity Layer for Grids","authors":"Jefferson Tan, D. Abramson, C. Enticott","doi":"10.1109/e-Science.2009.50","DOIUrl":"https://doi.org/10.1109/e-Science.2009.50","url":null,"abstract":"Computational grids are now mainstream facilities for e-research worldwide. While enterprise grids exist within organizations, national grids have become common, usually consisting of government as well as academic facilities. Such facilities are not uncommonly lenient with blanket policies to allow inbound and outbound grid traffic. This is far from ideal, from a security perspective, but given the dynamic nature of grid use, it is impractical to keep restrictive firewalls and manually keep up with on-demand firewall reconfiguration. Other solutions are necessary, where security is not sacrificed. Apart from first generation solutions that were mostly not sufficiently generic, standardization work is now ongoing, but exclusively aimed at firewall virtualization. We argue for an architectural solution that encompasses firewall virtualization as well as other methods that can be more appropriate in many environments. This paper describes our notion of the missing layer between grid and fabric, which we refer to as the virtual connectivity layer. We have developed two implementations within this layer and discuss how they fit into a complete and well-defined architectural solution.","PeriodicalId":325840,"journal":{"name":"2009 Fifth IEEE International Conference on e-Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2009-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121637294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2009-12-09DOI: 10.1109/e-Science.2009.10
S. Tarte, D. Wallom, Pin Hu, Kang Tang, Tiejun Ma
Linking up two projects that are dedicated to facilitate the work of documentary scholars, this paper presents image processing algorithms tailored to the study of ancient documents and how they have been made available to the users through a portal that calls upon a web-service exploiting grid computational power. To that end, image processing algorithms were wrapped to fit into the National Grid Service (NGS) Uniform Execution Environment; the data model of an existing Virtual Research Environment (VRE-SDM) was extended; JSR-168 compliant portlets were developed to facilitate secure and seamless distributed image analysis; and a GridSAM interface between the portal and the NGS-installed algorithms was developed. The outcomes of the project include: a web-based application, a proof of concept for the usability of the VRE-SDM platform, an opportunity for wider dissemination for the image processing algorithms, and a proof of feasibility for the use of the NGS for Humanities applications.
{"title":"An Image Processing Portal and Web-Service for the Study of Ancient Documents","authors":"S. Tarte, D. Wallom, Pin Hu, Kang Tang, Tiejun Ma","doi":"10.1109/e-Science.2009.10","DOIUrl":"https://doi.org/10.1109/e-Science.2009.10","url":null,"abstract":"Linking up two projects that are dedicated to facilitate the work of documentary scholars, this paper presents image processing algorithms tailored to the study of ancient documents and how they have been made available to the users through a portal that calls upon a web-service exploiting grid computational power. To that end, image processing algorithms were wrapped to fit into the National Grid Service (NGS) Uniform Execution Environment; the data model of an existing Virtual Research Environment (VRE-SDM) was extended; JSR-168 compliant portlets were developed to facilitate secure and seamless distributed image analysis; and a GridSAM interface between the portal and the NGS-installed algorithms was developed. The outcomes of the project include: a web-based application, a proof of concept for the usability of the VRE-SDM platform, an opportunity for wider dissemination for the image processing algorithms, and a proof of feasibility for the use of the NGS for Humanities applications.","PeriodicalId":325840,"journal":{"name":"2009 Fifth IEEE International Conference on e-Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2009-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131627609","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2009-12-09DOI: 10.1109/E-SCIENCE.2009.32
B. Matthews, Alastair Duncan, C. Jones, C. Neylon, Mark Borkum, S. Coles, Philip Hunter
Data and publications are major outputs of science, but are typically managed in different ways in data archives and institutional repositories. In this paper we discuss a protocol for exchanging cross-citations between data and publications, so that the links between can be tracked and used. We describe a simple instance of such a protocol based on the well-known Trackback protocol, and give an example of how the protocol can be used to exchange citations between a data archive and a publication repository. We conclude by discussing the generalisation of the protocol and its implications for scholarly discourse.
{"title":"A Protocol for Exchanging Scientific Citations","authors":"B. Matthews, Alastair Duncan, C. Jones, C. Neylon, Mark Borkum, S. Coles, Philip Hunter","doi":"10.1109/E-SCIENCE.2009.32","DOIUrl":"https://doi.org/10.1109/E-SCIENCE.2009.32","url":null,"abstract":"Data and publications are major outputs of science, but are typically managed in different ways in data archives and institutional repositories. In this paper we discuss a protocol for exchanging cross-citations between data and publications, so that the links between can be tracked and used. We describe a simple instance of such a protocol based on the well-known Trackback protocol, and give an example of how the protocol can be used to exchange citations between a data archive and a publication repository. We conclude by discussing the generalisation of the protocol and its implications for scholarly discourse.","PeriodicalId":325840,"journal":{"name":"2009 Fifth IEEE International Conference on e-Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2009-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114398106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2009-12-09DOI: 10.1109/e-Science.2009.43
Al Costanzo, C. Jin, Carlos A. Varela, R. Buyya
In this paper, we present a framework that enables scientists to steer computations executing over large-scale grid computing environments. By using computational steering, users can dynamically control their simulations or computations to reach expected results more efficiently. The framework supports steerable applications by introducing an asynchronous iterative MapReduce programming model that is deployed using Hadoop over a set of virtual machines executing on a multi-cluster grid. To tolerate the heterogeneity between different sites, results are collected asynchronously and users can dynamically interact with their computations to adjust the area of interest. According to users' dynamic interaction, the framework can redistribute the computational overload between the heterogeneous sites and explore the user's interest area by using more powerful sites when possible. With our framework, the bottleneck induced by synchronisation between different sites is considerably avoided, and therefore the response to users' interaction is satisfied more efficiently. We illustrate and evaluate this framework with a scientific application that aims to fit models of the Milky Way galaxy structure to stars observed by the Sloan Digital Sky Survey.
{"title":"Enabling Computational Steering with an Asynchronous-Iterative Computation Framework","authors":"Al Costanzo, C. Jin, Carlos A. Varela, R. Buyya","doi":"10.1109/e-Science.2009.43","DOIUrl":"https://doi.org/10.1109/e-Science.2009.43","url":null,"abstract":"In this paper, we present a framework that enables scientists to steer computations executing over large-scale grid computing environments. By using computational steering, users can dynamically control their simulations or computations to reach expected results more efficiently. The framework supports steerable applications by introducing an asynchronous iterative MapReduce programming model that is deployed using Hadoop over a set of virtual machines executing on a multi-cluster grid. To tolerate the heterogeneity between different sites, results are collected asynchronously and users can dynamically interact with their computations to adjust the area of interest. According to users' dynamic interaction, the framework can redistribute the computational overload between the heterogeneous sites and explore the user's interest area by using more powerful sites when possible. With our framework, the bottleneck induced by synchronisation between different sites is considerably avoided, and therefore the response to users' interaction is satisfied more efficiently. We illustrate and evaluate this framework with a scientific application that aims to fit models of the Milky Way galaxy structure to stars observed by the Sloan Digital Sky Survey.","PeriodicalId":325840,"journal":{"name":"2009 Fifth IEEE International Conference on e-Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2009-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114617575","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2009-12-09DOI: 10.1109/e-Science.2009.23
Nayden Markatchev, Roger Curry, C. Kiddle, Andrey Mirtchovski, R. Simmonds, Tingxi Tan
Accessing, running and sharing applications and data presents researchers with many challenges. Cloud computing and social networking technologies have the potential to simplify or eliminate many of these challenges. Cloud computing technologies can provide scientists with transparent and on-demand access to applications served over the Internet in a dynamic and scalable manner. Social networking technologies provide a means for easily sharing applications and data. In this paper we present an on-line/on-demand interactive application service. The service is built on a cloud computing infrastructure that dynamically provisions virtualized application servers based on user demand. An open source social networking platform is leveraged to establish a portal front end that enables applications and results to be easily shared between researchers. Furthermore, the service works with existing/legacy applications without requiring any modifications.
{"title":"A Cloud-Based Interactive Application Service","authors":"Nayden Markatchev, Roger Curry, C. Kiddle, Andrey Mirtchovski, R. Simmonds, Tingxi Tan","doi":"10.1109/e-Science.2009.23","DOIUrl":"https://doi.org/10.1109/e-Science.2009.23","url":null,"abstract":"Accessing, running and sharing applications and data presents researchers with many challenges. Cloud computing and social networking technologies have the potential to simplify or eliminate many of these challenges. Cloud computing technologies can provide scientists with transparent and on-demand access to applications served over the Internet in a dynamic and scalable manner. Social networking technologies provide a means for easily sharing applications and data. In this paper we present an on-line/on-demand interactive application service. The service is built on a cloud computing infrastructure that dynamically provisions virtualized application servers based on user demand. An open source social networking platform is leveraged to establish a portal front end that enables applications and results to be easily shared between researchers. Furthermore, the service works with existing/legacy applications without requiring any modifications.","PeriodicalId":325840,"journal":{"name":"2009 Fifth IEEE International Conference on e-Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2009-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123869731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2009-12-09DOI: 10.1109/E-SCIENCE.2009.38
Chris Morris, J. Segal
It is apparent that the challenges facing scientific software developers are quite different from those facing their commercial counterparts. Among these differences are the challenges posed by the complex and uncertain nature of the science. There is also the fact that many scientists have experience of developing their own software, albeit in a very restricted setting, leading them to have unrealistic expectations about software development in a different setting. In this paper, we explore the challenges facing scientific software developers focusing especially on molecular biology. We claim that the nature and practice of molecular biology is quite different from that of the physical sciences and pose different problems to software developers. We do not claim that this paper is the last word on the topic but hope that it serves as the inspiration for further debate.
{"title":"Some Challenges Facing Scientific Software Developers: The Case of Molecular Biology","authors":"Chris Morris, J. Segal","doi":"10.1109/E-SCIENCE.2009.38","DOIUrl":"https://doi.org/10.1109/E-SCIENCE.2009.38","url":null,"abstract":"It is apparent that the challenges facing scientific software developers are quite different from those facing their commercial counterparts. Among these differences are the challenges posed by the complex and uncertain nature of the science. There is also the fact that many scientists have experience of developing their own software, albeit in a very restricted setting, leading them to have unrealistic expectations about software development in a different setting. In this paper, we explore the challenges facing scientific software developers focusing especially on molecular biology. We claim that the nature and practice of molecular biology is quite different from that of the physical sciences and pose different problems to software developers. We do not claim that this paper is the last word on the topic but hope that it serves as the inspiration for further debate.","PeriodicalId":325840,"journal":{"name":"2009 Fifth IEEE International Conference on e-Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2009-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121345443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2009-12-09DOI: 10.1109/e-Science.2009.45
R. Ferreiro, N. Seoane, M. Aldegunde, A. García-Loureiro
The next substitution of the XDEnabling Grids for E-sciencE project (EGEE) in 2010 by the European Grid Initiative (EGI), where grid infrastructure of each country will be run by National Grid Initiatives (NGI), is giving a boost to the NGI development. In this context, the Spanish National Grid Initiative (es-NGI) is being developed by the escience Spanish network. The es-NGI is developing virtual organizations where common area applications are associated. In this context, the MOSFET virtual organisation (VO-MOSFET) was born in 2009 to perform semiconductor device simulations using the es-NGI infrastructure. This virtual organization is supported by the es-NGI resource centres and it is developing a job submission and monitoring system independent of the grid middleware. In this paper a general description of the VO-MOSFET and some application level utilities of the job submission system are presented. Furthermore, a gridification example of a nanoelectronic simulation is presented proving the grid benefits for the field of nanoelectronic simulation.
2010年，欧洲电网计划(EGI)将取代XDEnabling Grid for E-sciencE项目(EGEE)，其中每个国家的电网基础设施将由国家电网计划(NGI)运营，这将推动NGI的发展。在这种背景下，西班牙国家电网倡议(es-NGI)正在由escience西班牙网络开发。es-NGI正在开发虚拟组织，其中公共区域应用程序相关联。在这种背景下，MOSFET虚拟组织(VO-MOSFET)于2009年诞生，用于使用es-NGI基础架构执行半导体器件模拟。这个虚拟组织得到es-NGI资源中心的支持，它正在开发一个独立于网格中间件的作业提交和监控系统。本文介绍了VO-MOSFET的总体结构和作业提交系统的一些应用层实用程序。最后，给出了一个纳米电子仿真的网格化实例，证明了网格化在纳米电子仿真领域的优势。
{"title":"The MOSFET Virtual Organisation: Grid Computing for Simulation in Nanoelectronics","authors":"R. Ferreiro, N. Seoane, M. Aldegunde, A. García-Loureiro","doi":"10.1109/e-Science.2009.45","DOIUrl":"https://doi.org/10.1109/e-Science.2009.45","url":null,"abstract":"The next substitution of the XDEnabling Grids for E-sciencE project (EGEE) in 2010 by the European Grid Initiative (EGI), where grid infrastructure of each country will be run by National Grid Initiatives (NGI), is giving a boost to the NGI development. In this context, the Spanish National Grid Initiative (es-NGI) is being developed by the escience Spanish network. The es-NGI is developing virtual organizations where common area applications are associated. In this context, the MOSFET virtual organisation (VO-MOSFET) was born in 2009 to perform semiconductor device simulations using the es-NGI infrastructure. This virtual organization is supported by the es-NGI resource centres and it is developing a job submission and monitoring system independent of the grid middleware. In this paper a general description of the VO-MOSFET and some application level utilities of the job submission system are presented. Furthermore, a gridification example of a nanoelectronic simulation is presented proving the grid benefits for the field of nanoelectronic simulation.","PeriodicalId":325840,"journal":{"name":"2009 Fifth IEEE International Conference on e-Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2009-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125977261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2009-12-09DOI: 10.1109/e-Science.2009.18
N. Beagley, Chad Scherrer, Yan Shi, B. Clowers, W. Danielson, A. Shah
The massive data sets produced by the high- throughput, multidimensional mass spectrometry instruments used in proteomics create challenges in data acquisition, storage and analysis. Data compression can help mitigate some of these problems but at the cost of less efficient data access, which directly impacts the computational time of data analysis. We have developed a compression methodology that 1) is optimized for a targeted mass spectrometry proteomics data set and 2) provides the benefits of size and speed from compression while increasing analysis efficiency by allowing extraction of segments of uncompressed data from a file without having to uncompress the entire file. This paper describes our compression algorithm, presents comparative metrics of compression size and speed, and explores approaches for applying the algorithm to a generalized data set.
{"title":"Increasing the Efficiency of Data Storage and Analysis Using Indexed Compression","authors":"N. Beagley, Chad Scherrer, Yan Shi, B. Clowers, W. Danielson, A. Shah","doi":"10.1109/e-Science.2009.18","DOIUrl":"https://doi.org/10.1109/e-Science.2009.18","url":null,"abstract":"The massive data sets produced by the high- throughput, multidimensional mass spectrometry instruments used in proteomics create challenges in data acquisition, storage and analysis. Data compression can help mitigate some of these problems but at the cost of less efficient data access, which directly impacts the computational time of data analysis. We have developed a compression methodology that 1) is optimized for a targeted mass spectrometry proteomics data set and 2) provides the benefits of size and speed from compression while increasing analysis efficiency by allowing extraction of segments of uncompressed data from a file without having to uncompress the entire file. This paper describes our compression algorithm, presents comparative metrics of compression size and speed, and explores approaches for applying the algorithm to a generalized data set.","PeriodicalId":325840,"journal":{"name":"2009 Fifth IEEE International Conference on e-Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2009-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132938694","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2009-12-09DOI: 10.1109/e-Science.2009.28
Kenton McHenry, R. Kooper, P. Bajcsy
This paper addresses the problem of designing a universal file format converter. File format conversion is a necessary part of data dissemination and curation. Complete and robust converters however are hard to find and build due to the abundance of file formats, the fact that many formats are closed, and the complexities within individual format specifications. On the other hand many software applications exist that are capable of performing some degree of data conversion between a subset of the available formats. To take advantage of this we introduce a data structure called an I/O-Graph to store the available input and output formats of these applications. Based on a concept of textit{textbf{imposed code reuse}} we use this to develop a service, NCSA Polyglot, which through this graph is capable of performing the larger union of conversions supported by the underlying software. The Polyglot system is designed to be easily extensible, scalable with the number of conversion requests, and inclusive of all available third party software. Given a data set of files from a particular domain, we are able to assign weights to the edges within the I/O-Graph indicating the amount of information retained during a conversion. These edge weights allow the system to then choose conversion paths with the least amount of information loss.
{"title":"Towards a Universal, Quantifiable, and Scalable File Format Converter","authors":"Kenton McHenry, R. Kooper, P. Bajcsy","doi":"10.1109/e-Science.2009.28","DOIUrl":"https://doi.org/10.1109/e-Science.2009.28","url":null,"abstract":"This paper addresses the problem of designing a universal file format converter. File format conversion is a necessary part of data dissemination and curation. Complete and robust converters however are hard to find and build due to the abundance of file formats, the fact that many formats are closed, and the complexities within individual format specifications. On the other hand many software applications exist that are capable of performing some degree of data conversion between a subset of the available formats. To take advantage of this we introduce a data structure called an I/O-Graph to store the available input and output formats of these applications. Based on a concept of textit{textbf{imposed code reuse}} we use this to develop a service, NCSA Polyglot, which through this graph is capable of performing the larger union of conversions supported by the underlying software. The Polyglot system is designed to be easily extensible, scalable with the number of conversion requests, and inclusive of all available third party software. Given a data set of files from a particular domain, we are able to assign weights to the edges within the I/O-Graph indicating the amount of information retained during a conversion. These edge weights allow the system to then choose conversion paths with the least amount of information loss.","PeriodicalId":325840,"journal":{"name":"2009 Fifth IEEE International Conference on e-Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2009-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131606349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2009-12-09DOI: 10.1109/e-Science.2009.48
P. Bar, Camille Coti, D. Groen, T. Hérault, Valentin Kravtsov, A. Schuster, M. Swain
The concept of topology-aware grid applications is derived from parallelized computational models of complex systems that are executed on heterogeneous resources, either because they require specialized hardware for certain calculations, or because their parallelization is flexible enough to exploit such resources. Here we describe two such applications, a multi-body simulation of stellar evolution, and an evolutionary algorithm that is used for reverse-engineering gene regulatory networks. We then describe the topology-aware middleware we have developed to facilitate the ``modeling-implementing-executing'' cycle of complex systems applications. The developed middleware allows topology-aware simulations to run on geographically distributed clusters with or without firewalls between them. Additionally, we describe advanced coallocation and scheduling techniques that take into account the applications topologies. Results are given based on running the topology-aware applications on the Grid'5000 infrastructure.
{"title":"Running Parallel Applications with Topology-Aware Grid Middleware","authors":"P. Bar, Camille Coti, D. Groen, T. Hérault, Valentin Kravtsov, A. Schuster, M. Swain","doi":"10.1109/e-Science.2009.48","DOIUrl":"https://doi.org/10.1109/e-Science.2009.48","url":null,"abstract":"The concept of topology-aware grid applications is derived from parallelized computational models of complex systems that are executed on heterogeneous resources, either because they require specialized hardware for certain calculations, or because their parallelization is flexible enough to exploit such resources. Here we describe two such applications, a multi-body simulation of stellar evolution, and an evolutionary algorithm that is used for reverse-engineering gene regulatory networks. We then describe the topology-aware middleware we have developed to facilitate the ``modeling-implementing-executing'' cycle of complex systems applications. The developed middleware allows topology-aware simulations to run on geographically distributed clusters with or without firewalls between them. Additionally, we describe advanced coallocation and scheduling techniques that take into account the applications topologies. Results are given based on running the topology-aware applications on the Grid'5000 infrastructure.","PeriodicalId":325840,"journal":{"name":"2009 Fifth IEEE International Conference on e-Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2009-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"117179644","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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