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Parallel stochastic simulators in system biology: the evolution of the species
"... Abstract—The stochastic simulation of biological systems is an increasingly popular technique in Bioinformatics. It is often an enlightening technique, especially for multi-stable systems which dynamics can be hardly captured with ordinary differential equations. To be effective, stochastic simulati ..."
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Abstract—The stochastic simulation of biological systems is an increasingly popular technique in Bioinformatics. It is often an enlightening technique, especially for multi-stable systems which dynamics can be hardly captured with ordinary differential equations. To be effective, stochastic simulations should be supported by powerful statistical analysis tools. The simulation-analysis workflow may however result in being computationally expensive, thus compromising the interactivity required in model tuning. In this work we advocate the high-level design of simulators for stochastic systems as a vehicle for building efficient and portable parallel simulators. In particular, the Calculus of Wrapped Components (CWC) simulator, which is designed according to the FastFlow’s pattern-based approach, is presented and discussed in this work. FastFlow has been extended to support also clusters of multi-cores with minimal coding effort, assessing the portability of the approach. Keywords-Parallel patterns; multi-core; distributed computing; stochastic simulation; systems biology. I.
The STAPL skeleton framework
- In Proc. 27th Int. Wkshp. on Langs. and Comps. for Par. Comp. (LCPC
, 2014
"... Abstract. This paper describes the stapl Skeleton Framework, a highlevel skeletal approach for parallel programming. This framework abstracts the underlying details of data distribution and parallelism from programmers and enables them to express parallel programs as a composition of existing eleme ..."
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Abstract. This paper describes the stapl Skeleton Framework, a highlevel skeletal approach for parallel programming. This framework abstracts the underlying details of data distribution and parallelism from programmers and enables them to express parallel programs as a composition of existing elementary skeletons such as map, map-reduce, scan, zip, butterfly, allreduce, alltoall and user-defined custom skeletons. Skeletons in this framework are defined as parametric data flow graphs, and their compositions are defined in terms of data flow graph compositions. Defining the composition in this manner allows dependencies between skeletons to be defined in terms of point-to-point dependencies, avoiding unnecessary global synchronizations. To show the ease of composability and expressivity, we implemented the NAS Integer Sort (IS) and Embarrassingly Parallel (EP) benchmarks using skeletons and demonstrate comparable performance to the hand-optimized reference implementations. To demonstrate scalable performance, we show a transformation which enables applications written in terms of skeletons to run on more than 100,000 cores.
Task number: T8.1/2/3
"... Editor and editor’s address: Todd Wilde Project co-funded by the European Commission within the Seventh Framework Programme PU Public Dissemination Level PP Restricted to other programme participants (including the Commission Services) RE Restricted to a group specified by the consortium (including ..."
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Editor and editor’s address: Todd Wilde Project co-funded by the European Commission within the Seventh Framework Programme PU Public Dissemination Level PP Restricted to other programme participants (including the Commission Services) RE Restricted to a group specified by the consortium (including the Commission Services) CO Confidential, only for members of the consortium (including the Commission Services) Executive Summary This document describes overall plans for the use and dissimination of foreground knowledge in the ParaPhrase project. It describes the dissemination activities that have taken place at each of the consortium partners in the first year of the projects, outlines the general plans for the use and dissmenination of knowledge at each
Dissemination Level
, 2012
"... PP Restricted to other programme participants (including the Commission Services) RE Restricted to a group specified by the consortium (including the Commission Services) CO Confidential, only for members of the consortium (including the Commission Services) Executive Summary This is the second deli ..."
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PP Restricted to other programme participants (including the Commission Services) RE Restricted to a group specified by the consortium (including the Commission Services) CO Confidential, only for members of the consortium (including the Commission Services) Executive Summary This is the second deliverable in Work Package 2: Parallel patterns. It aims at describing the implementation of the initial generic pattern-set defined in deliverable D2.1 [14]. This initial set of parallel patterns has been explicitly designed to be minimal but able to exploit the most common patterns of parallelism in typical parallel applications. The implementation refers to two different frameworks: FastFlow, which is based on a C++ technology, and Erlang, which is instead a functional programming language. Both implementations target homogeneous architectures. With respect to FastFlow, we took advantage of a pre-existing framework already offering pipeline and farm implementations for shared-memory systems. In particular, the FastFlow framework has been enriched with new generic pattern data parallel pattern, providing suitable ways to implement both map and reduce
Memory-Optimised Parallel Processing of Hi-C Data
"... Abstract—This paper presents the optimisation efforts on the creation of a graph-based mapping representation of gene adjacency. The method is based on the Hi-C process, starting from Next Generation Sequencing data, and it analyses a huge amount of static data in order to produce maps for one or mo ..."
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Abstract—This paper presents the optimisation efforts on the creation of a graph-based mapping representation of gene adjacency. The method is based on the Hi-C process, starting from Next Generation Sequencing data, and it analyses a huge amount of static data in order to produce maps for one or more genes. Straightforward parallelisation of this scheme does not yield acceptable performance on multicore architectures since the scalability is rather limited due to the memory bound nature of the problem. This work focuses on the memory optimisations that can be applied to the graph construction algorithm and its (complex) data structures to derive a cache-oblivious algorithm and eventually to improve the memory bandwidth utilisation. We used as running example NuChart-II, a tool for annotation and statistic analysis of Hi-C data that creates a gene-centric neigh-borhood graph. The proposed approach, which is exemplified for Hi-C, addresses several common issue in the parallelisation of memory bound algorithms for multicore. Results show that the proposed approach is able to increase the parallel speedup from 7x to 22x (on a 32-core platform). Finally, the proposed C++ implementation outperforms the first R NuChart prototype, by which it was not possible to complete the graph generation because of strong memory-saturation problems. I.
Microgrid- The microthreaded many-core architecture
, 2014
"... Traditional processors use the von Neumann execution model, some other processors in the past have used the dataflow execution model. A combination of von Neuman model and dataflow model is also tried in the past and the resultant model is referred as hybrid dataflow ex-ecution model. We describe a ..."
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Traditional processors use the von Neumann execution model, some other processors in the past have used the dataflow execution model. A combination of von Neuman model and dataflow model is also tried in the past and the resultant model is referred as hybrid dataflow ex-ecution model. We describe a hybrid dataflow model known as the microthreading. It provides constructs for creation, synchronization and communication between threads in an intermedi-ate language. The microthreading model is an abstract programming and machine model for many-core architecture. A particular instance of this model is named as the microthreaded architecture or the Microgrid. This architecture implements all the concurrency constructs of the microthreading model in the hardware with the management of these constructs in the
International Journal of Parallel Programming ISSN 0885-7458
"... Design patterns percolating to parallel programming framework implementation ..."
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Design patterns percolating to parallel programming framework implementation
Message passing on InfiniBand RDMA for parallel
"... Abstract—InfiniBand networks are commonly used in the high performance computing area. They offer RDMA-based opera-tions that help to improve the performance of communication subsystems. In this paper, we propose a minimal message-passing communication layer providing the programmer with a point-to- ..."
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Abstract—InfiniBand networks are commonly used in the high performance computing area. They offer RDMA-based opera-tions that help to improve the performance of communication subsystems. In this paper, we propose a minimal message-passing communication layer providing the programmer with a point-to-point communication channel implemented by way of InfiniBand RDMA features. Differently from other libraries exploiting the InfiniBand features, such as the well-known Message Passing Interface (MPI), the proposed library is a communication layer only rather than a programming model, and can be easily used as building block for high-level parallel programming frameworks. Evaluated on micro-benchmarks, the proposed RDMA-based communication channel implementation achieves a comparable performance with highly optimised MPI/InfiniBand implemen-tations. Eventually, the flexibility of the communication layer is evaluated by integrating it within the FastFlow parallel frame-work, currently supporting TCP/IP networks (via the ZeroMQ communication library). I.
Exercising high-level parallel programming on streams: a systems biology use case
"... Abstract—The stochastic modelling of biological systems, cou-pled with Monte Carlo simulation of models, is an increasingly popular technique in Bioinformatics. The simulation-analysis workflow may result into a computationally expensive task reducing the interactivity required in the model tuning. ..."
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Abstract—The stochastic modelling of biological systems, cou-pled with Monte Carlo simulation of models, is an increasingly popular technique in Bioinformatics. The simulation-analysis workflow may result into a computationally expensive task reducing the interactivity required in the model tuning. In this work, we advocate high-level software design as a vehicle for building efficient and portable parallel simulators for a variety of platforms, ranging from multi-core platforms to GPGPUs to cloud. In particular, the Calculus of Wrapped Compartments (CWC) parallel simulator for systems biology equipped with on-line mining of results, which is designed according to the FastFlow pattern-based approach, is discussed as a running example. In this work, the CWC simulator is used as a paradigmatic example of a complex C++ application where the quality of results is correlated with both computation and I/O bounds, and where high-quality results might turn into big data. The FastFlow parallel programming framework, which advocates C++ pattern-based parallel programming makes it possible to develop portable parallel code without relinquish neither run-time efficiency nor performance tuning opportunities. Performance and effectiveness of the approach are validated on a variety of platforms, inter-alia cache-coherent multi-cores, cluster of multi-core (Ethernet and Infiniband) and the Amazon Elastic Compute Cloud. I.
