Toward High-Performance Computing and Big Data Analytics Convergence: The Case of Spark-DIY

Convergence between high-performance computing (HPC) and big data analytics (BDA) is currently an established research area that has spawned new opportunities for unifying the platform layer and data abstractions in these ecosystems. This work presents an architectural model that enables the interoperability of established BDA and HPC execution models, reflecting the key design features that interest both the HPC and BDA communities, and including an abstract data collection and operational model that generates a unified interface for hybrid applications. This architecture can be implemented in different ways depending on the process- and data-centric platforms of choice and the mechanisms put in place to effectively meet the requirements of the architecture. The Spark-DIY platform is introduced in the paper as a prototype implementation of the architecture proposed. It preserves the interfaces and execution environment of the popular BDA platform Apache Spark, making it compatible with any Spark-based application and tool, while providing efficient communication and kernel execution via DIY, a powerful communication pattern library built on top of MPI. Later, Spark-DIY is analyzed in terms of performance by building a representative use case from the hydrogeology domain, EnKF-HGS. This application is a clear example of how current HPC simulations are evolving toward hybrid HPC-BDA applications, integrating HPC simulations within a BDA environment.This work was supported in part by the Spanish Ministry of Economy, Industry and Competitiveness under Grant TIN2016-79637-P(toward Unification of HPC and Big Data Paradigms), in part by the Spanish Ministry of Education under Grant FPU15/00422 TrainingProgram for Academic and Teaching Staff Grant, in part by the Advanced Scientific Computing Research, Office of Science, U.S.Department of Energy, under Contract DE-AC02-06CH11357, and in part by the DOE with under Agreement DE-DC000122495,Program Manager Laura Biven

Systematic Design Space Exploration of Dynamic Dataflow Programs for Multi-core Platforms

The limitations of clock frequency and power dissipation of deep sub-micron CMOS technology have led to the development of massively parallel computing platforms. They consist of dozens or hundreds of processing units and offer a high degree of parallelism. Taking advantage of that parallelism and transforming it into high program performances requires the usage of appropriate parallel programming models and paradigms. Currently, a common practice is to develop parallel applications using methods evolving directly from sequential programming models. However, they lack the abstractions to properly express the concurrency of the processes. An alternative approach is to implement dataflow applications, where the algorithms are described in terms of streams and operators thus their parallelism is directly exposed. Since algorithms are described in an abstract way, they can be easily ported to different types of platforms. Several dataflow models of computation (MoCs) have been formalized so far. They differ in terms of their expressiveness (ability to handle dynamic behavior) and complexity of analysis. So far, most of the research efforts have focused on the simpler cases of static dataflow MoCs, where many analyses are possible at compile-time and several optimization problems are greatly simplified. At the same time, for the most expressive and the most difficult to analyze dynamic dataflow (DDF), there is still a dearth of tools supporting a systematic and automated analysis minimizing the programming efforts of the designer. The objective of this Thesis is to provide a complete framework to analyze, evaluate and refactor DDF applications expressed using the RVC-CAL language. The methodology relies on a systematic design space exploration (DSE) examining different design alternatives in order to optimize the chosen objective function while satisfying the constraints. The research contributions start from a rigorous DSE problem formulation. This provides a basis for the definition of a complete and novel analysis methodology enabling systematic performance improvements of DDF applications. Different stages of the methodology include exploration heuristics, performance estimation and identification of refactoring directions. All of the stages are implemented as appropriate software tools. The contributions are substantiated by several experiments performed with complex dynamic applications on different types of physical platforms

High-Performance Modelling and Simulation for Big Data Applications

This open access book was prepared as a Final Publication of the COST Action IC1406 “High-Performance Modelling and Simulation for Big Data Applications (cHiPSet)“ project. Long considered important pillars of the scientific method, Modelling and Simulation have evolved from traditional discrete numerical methods to complex data-intensive continuous analytical optimisations. Resolution, scale, and accuracy have become essential to predict and analyse natural and complex systems in science and engineering. When their level of abstraction raises to have a better discernment of the domain at hand, their representation gets increasingly demanding for computational and data resources. On the other hand, High Performance Computing typically entails the effective use of parallel and distributed processing units coupled with efficient storage, communication and visualisation systems to underpin complex data-intensive applications in distinct scientific and technical domains. It is then arguably required to have a seamless interaction of High Performance Computing with Modelling and Simulation in order to store, compute, analyse, and visualise large data sets in science and engineering. Funded by the European Commission, cHiPSet has provided a dynamic trans-European forum for their members and distinguished guests to openly discuss novel perspectives and topics of interests for these two communities. This cHiPSet compendium presents a set of selected case studies related to healthcare, biological data, computational advertising, multimedia, finance, bioinformatics, and telecommunications

Parallel Patterns for Adaptive Data Stream Processing

In recent years our ability to produce information has been growing steadily, driven by an ever increasing computing power, communication rates, hardware and software sensors diffusion. This data is often available in the form of continuous streams and the ability to gather and analyze it to extract insights and detect patterns is a valuable opportunity for many businesses and scientific applications. The topic of Data Stream Processing (DaSP) is a recent and highly active research area dealing with the processing of this streaming data. The development of DaSP applications poses several challenges, from efficient algorithms for the computation to programming and runtime systems to support their execution. In this thesis two main problems will be tackled: * need for high performance: high throughput and low latency are critical requirements for DaSP problems. Applications necessitate taking advantage of parallel hardware and distributed systems, such as multi/manycores or cluster of multicores, in an effective way; * dynamicity: due to their long running nature (24hr/7d), DaSP applications are affected by highly variable arrival rates and changes in their workload characteristics. Adaptivity is a fundamental feature in this context: applications must be able to autonomously scale the used resources to accommodate dynamic requirements and workload while maintaining the desired Quality of Service (QoS) in a cost-effective manner. In the current approaches to the development of DaSP applications are still missing efficient exploitation of intra-operator parallelism as well as adaptations strategies with well known properties of stability, QoS assurance and cost awareness. These are the gaps that this research work tries to fill, resorting to well know approaches such as Structured Parallel Programming and Control Theoretic models. The dissertation runs along these two directions. The first part deals with intra-operator parallelism. A DaSP application can be naturally expressed as a set of operators (i.e. intermediate computations) that cooperate to reach a common goal. If QoS requirements are not met by the current implementation, bottleneck operators must be internally parallelized. We will study recurrent computations in window based stateful operators and propose patterns for their parallel implementation. Windowed operators are the most representative class of stateful data stream operators. Here computations are applied on the most recent received data. Windows are dynamic data structures: they evolve over time in terms of content and, possibly, size. Therefore, with respect to traditional patterns, the DaSP domain requires proper specializations and enhanced features concerning data distribution and management policies for different windowing methods. A structured approach to the problem will reduce the effort and complexity of parallel programming. In addition, it simplifies the reasoning about the performance properties of a parallel solution (e.g. throughput and latency). The proposed patterns exhibit different properties in terms of applicability and profitability that will be discussed and experimentally evaluated. The second part of the thesis is devoted to the proposal and study of predictive strategies and reconfiguration mechanisms for autonomic DaSP operators. Reconfiguration activities can be implemented in a transparent way to the application programmer thanks to the exploitation of parallel paradigms with well known structures. Furthermore, adaptation strategies may take advantage of the QoS predictability of the used parallel solution. Autonomous operators will be driven by means of a Model Predictive Control approach, with the intent of giving QoS assurances in terms of throughput or latency in a resource-aware manner. An experimental section will show the effectiveness of the proposed approach in terms of execution costs reduction as well as the stability degree of a system reconfiguration. The experiments will target shared and distributed memory architectures

Proceedings of the First International Workshop on Sustainable Ultrascale Computing Systems (NESUS 2014): Porto, Portugal

Proceedings of: First International Workshop on Sustainable Ultrascale Computing Systems (NESUS 2014). Porto (Portugal), August 27-28, 2014

High-Performance Modelling and Simulation for Big Data Applications

This open access book was prepared as a Final Publication of the COST Action IC1406 “High-Performance Modelling and Simulation for Big Data Applications (cHiPSet)“ project. Long considered important pillars of the scientific method, Modelling and Simulation have evolved from traditional discrete numerical methods to complex data-intensive continuous analytical optimisations. Resolution, scale, and accuracy have become essential to predict and analyse natural and complex systems in science and engineering. When their level of abstraction raises to have a better discernment of the domain at hand, their representation gets increasingly demanding for computational and data resources. On the other hand, High Performance Computing typically entails the effective use of parallel and distributed processing units coupled with efficient storage, communication and visualisation systems to underpin complex data-intensive applications in distinct scientific and technical domains. It is then arguably required to have a seamless interaction of High Performance Computing with Modelling and Simulation in order to store, compute, analyse, and visualise large data sets in science and engineering. Funded by the European Commission, cHiPSet has provided a dynamic trans-European forum for their members and distinguished guests to openly discuss novel perspectives and topics of interests for these two communities. This cHiPSet compendium presents a set of selected case studies related to healthcare, biological data, computational advertising, multimedia, finance, bioinformatics, and telecommunications