Message Passing with Communication Structures

Institute for Computing Systems ArchitectureAbstraction concepts based on process groups have largely dominated the design and implementation of communication patterns in message passing systems. Although such an approach seems pragmatic—given that participating processes form a ‘group’—in this dissertation, we discuss subtle issues that affect the qualitative and quantitative aspects of this approach. To address these issues, we introduce the concept of a ‘communication structure,’ which defines a communication pattern as an implicit runtime composition of localised patterns, known as ‘roles.’ During application development, communication structures are derived from the algorithm being implemented. These are then translated to an executable form by defining process specific data structures, known as ‘branching channels.’ The qualitative advantages of the communication structure approach are that the resulting programming model is non-ambiguous, uniform, expressive, and extensible. To use a pattern is to access the corresponding branching channels; to define a new pattern is simply to combine appropriate roles. The communication structure approach therefore allows immediate implementation of ad hoc patterns. Furthermore, it is guaranteed that every newly added role interfaces correctly with all of the existing roles, therefore scaling the benefit of every new addition. Quantitatively, branching channels improve performance by automatically overlapping computations and communications. The runtime system uses a receiver initiated communication protocol that allows senders to continue immediately without waiting for the receivers to respond. The advantage is that, unlike split-phase asynchronous communications, senders need not check whether the send operations were successful. Another property of branching channels is that they allow communications to be grouped, identified, and referenced. Communication structure specific parameters, such as message buffering, can therefore be specified immediately. Furthermore, a ‘commit’ based interface optimisation for send-and-forget type communications—where senders do not reuse sent data—is presented. This uses the referencing property of branching channels, allowing message buffering without incurring performance degradation due to intermediate memory copy

A Structural Approach for Modelling Performance of Systems Using Skeletons

AbstractIn this paper, we discuss a structural approach to automatic performance modelling of skeleton based applications. This uses a synthesis of performance evaluation process algebra (pepa) and a pattern-oriented hierarchical expression scheme. Such approaches are important in parallel and distributed systems where the performance models must be updated regularly based on the current state of the resources

A bioimage informatics platform for high-throughput embryo phenotyping

High-throughput phenotyping is a cornerstone of numerous functional genomics projects. In recent years, imaging screens have become increasingly important in understanding gene–phenotype relationships in studies of cells, tissues and whole organisms. Three-dimensional (3D) imaging has risen to prominence in the field of developmental biology for its ability to capture whole embryo morphology and gene expression, as exemplified by the International Mouse Phenotyping Consortium (IMPC). Large volumes of image data are being acquired by multiple institutions around the world that encompass a range of modalities, proprietary software and metadata. To facilitate robust downstream analysis, images and metadata must be standardized to account for these differences. As an open scientific enterprise, making the data readily accessible is essential so that members of biomedical and clinical research communities can study the images for themselves without the need for highly specialized software or technical expertise. In this article, we present a platform of software tools that facilitate the upload, analysis and dissemination of 3D images for the IMPC. Over 750 reconstructions from 80 embryonic lethal and subviable lines have been captured to date, all of which are openly accessible at mousephenotype.org. Although designed for the IMPC, all software is available under an open-source licence for others to use and develop further. Ongoing developments aim to increase throughput and improve the analysis and dissemination of image data. Furthermore, we aim to ensure that images are searchable so that users can locate relevant images associated with genes, phenotypes or human diseases of interest

A mouse informatics platform for phenotypic and translational discovery

The International Mouse Phenotyping Consortium (IMPC) is providing the world’s first functional catalogue of a mammalian genome by characterising a knockout mouse strain for every gene. A robust and highly structured informatics platform has been developed to systematically collate, analyse and disseminate the data produced by the IMPC. As the first phase of the project, in which 5000 new knockout strains are being broadly phenotyped, nears completion, the informatics platform is extending and adapting to support the increasing volume and complexity of the data produced as well as addressing a large volume of users and emerging user groups. An intuitive interface helps researchers explore IMPC data by giving overviews and the ability to find and visualise data that support a phenotype assertion. Dedicated disease pages allow researchers to find new mouse models of human diseases, and novel viewers provide high-resolution images of embryonic and adult dysmorphologies. With each monthly release, the informatics platform will continue to evolve to support the increased data volume and to maintain its position as the primary route of access to IMPC data and as an invaluable resource for clinical and non-clinical researchers

Message passing with communication structures

Abstraction concepts based on process groups have largely dominated the design and implementation of communication patterns in message passing systems. Although such an approach seems pragmatic—given that participating processes form a ‘group’—in this dissertation, we discuss subtle issues that affect the qualitative and quantitative aspects of this approach. To address these issues, we introduce the concept of a ‘communication structure,’ which defines a communication pattern as an implicit runtime composition of localised patterns, known as ‘roles.’ During application development, communication structures are derived from the algorithm being implemented. These are then translated to an executable form by defining process specific data structures, known as ‘branching channels.’ The qualitative advantages of the communication structure approach are that the resulting programming model is non-ambiguous, uniform, expressive, and extensible. To use a pattern is to access the corresponding branching channels; to define a new pattern is simply to combine appropriate roles. The communication structure approach therefore allows immediate implementation of ad hoc patterns. Furthermore, it is guaranteed that every newly added role interfaces correctly with all of the existing roles, therefore scaling the benefit of every new addition. Quantitatively, branching channels improve performance by automatically overlapping computations and communications. The runtime system uses a receiver initiated communication protocol that allows senders to continue immediately without waiting for the receivers to respond. The advantage is that, unlike split-phase asynchronous communications, senders need not check whether the send operations were successful. Another property of branching channels is that they allow communications to be grouped, identified, and referenced. Communication structure specific parameters, such as message buffering, can therefore be specified immediately. Furthermore, a ‘commit’ based interface optimisation for send-and-forget type communications—where senders do not reuse sent data—is presented. This uses the referencing property of branching channels, allowing message buffering without incurring performance degradation due to intermediate memory copy.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

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High-performance computing for Monte Carlo radiotherapy calculations

We report on the RTGrid project, which investigates approaches for using high-performance computing infrastructures, such as the grid, in order to reduce the turnaround time of Monte Carlo (MC) simulation-based radiotherapy treatment planning. The main aim of this project is to render accurate dose calculations using MC simulations clinically feasible. To this end, we have successfully implemented and deployed the RTGrid distributed simulation framework for MC dose calculations. In this paper, we present the main experimental findings