Science Pipelines for the Square Kilometre Array

The Square Kilometre Array (SKA) will be both the largest radio telescope ever constructed and the largest Big Data project in the known Universe. The first phase of the project will generate on the order of 5 zettabytes of data per year. A critical task for the SKA will be its ability to process data for science, which will need to be conducted by science pipelines. Together with polarization data from the LOFAR Multifrequency Snapshot Sky Survey (MSSS), we have been developing a realistic SKA-like science pipeline that can handle the large data volumes generated by LOFAR at 150 MHz. The pipeline uses task-based parallelism to image, detect sources, and perform Faraday Tomography across the entire LOFAR sky. The project thereby provides a unique opportunity to contribute to the technological development of the SKA telescope, while simultaneously enabling cutting-edge scientific results. In this paper, we provide an update on current efforts to develop a science pipeline that can enable tight constraints on the magnetised large-scale structure of the Universe.Comment: Published in Galaxies, as part of a Special Issue on The Power of Faraday Tomograph

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

Energy Measurements of High Performance Computing Systems: From Instrumentation to Analysis

Energy efficiency is a major criterion for computing in general and High Performance Computing in particular. When optimizing for energy efficiency, it is essential to measure the underlying metric: energy consumption. To fully leverage energy measurements, their quality needs to be well-understood. To that end, this thesis provides a rigorous evaluation of various energy measurement techniques. I demonstrate how the deliberate selection of instrumentation points, sensors, and analog processing schemes can enhance the temporal and spatial resolution while preserving a well-known accuracy. Further, I evaluate a scalable energy measurement solution for production HPC systems and address its shortcomings. Such high-resolution and large-scale measurements present challenges regarding the management of large volumes of generated metric data. I address these challenges with a scalable infrastructure for collecting, storing, and analyzing metric data. With this infrastructure, I also introduce a novel persistent storage scheme for metric time series data, which allows efficient queries for aggregate timelines. To ensure that it satisfies the demanding requirements for scalable power measurements, I conduct an extensive performance evaluation and describe a productive deployment of the infrastructure. Finally, I describe different approaches and practical examples of analyses based on energy measurement data. In particular, I focus on the combination of energy measurements and application performance traces. However, interweaving fine-grained power recordings and application events requires accurately synchronized timestamps on both sides. To overcome this obstacle, I develop a resilient and automated technique for time synchronization, which utilizes crosscorrelation of a specifically influenced power measurement signal. Ultimately, this careful combination of sophisticated energy measurements and application performance traces yields a detailed insight into application and system energy efficiency at full-scale HPC systems and down to millisecond-range regions.:1 Introduction 2 Background and Related Work 2.1 Basic Concepts of Energy Measurements 2.1.1 Basics of Metrology 2.1.2 Measuring Voltage, Current, and Power 2.1.3 Measurement Signal Conditioning and Analog-to-Digital Conversion 2.2 Power Measurements for Computing Systems 2.2.1 Measuring Compute Nodes using External Power Meters 2.2.2 Custom Solutions for Measuring Compute Node Power 2.2.3 Measurement Solutions of System Integrators 2.2.4 CPU Energy Counters 2.2.5 Using Models to Determine Energy Consumption 2.3 Processing of Power Measurement Data 2.3.1 Time Series Databases 2.3.2 Data Center Monitoring Systems 2.4 Influences on the Energy Consumption of Computing Systems 2.4.1 Processor Power Consumption Breakdown 2.4.2 Energy-Efficient Hardware Configuration 2.5 HPC Performance and Energy Analysis 2.5.1 Performance Analysis Techniques 2.5.2 HPC Performance Analysis Tools 2.5.3 Combining Application and Power Measurements 2.6 Conclusion 3 Evaluating and Improving Energy Measurements 3.1 Description of the Systems Under Test 3.2 Instrumentation Points and Measurement Sensors 3.2.1 Analog Measurement at Voltage Regulators 3.2.2 Instrumentation with Hall Effect Transducers 3.2.3 Modular Instrumentation of DC Consumers 3.2.4 Optimal Wiring for Shunt-Based Measurements 3.2.5 Node-Level Instrumentation for HPC Systems 3.3 Analog Signal Conditioning and Analog-to-Digital Conversion 3.3.1 Signal Amplification 3.3.2 Analog Filtering and Analog-To-Digital Conversion 3.3.3 Integrated Solutions for High-Resolution Measurement 3.4 Accuracy Evaluation and Calibration 3.4.1 Synthetic Workloads for Evaluating Power Measurements 3.4.2 Improving and Evaluating the Accuracy of a Single-Node Measuring System 3.4.3 Absolute Accuracy Evaluation of a Many-Node Measuring System 3.5 Evaluating Temporal Granularity and Energy Correctness 3.5.1 Measurement Signal Bandwidth at Different Instrumentation Points 3.5.2 Retaining Energy Correctness During Digital Processing 3.6 Evaluating CPU Energy Counters 3.6.1 Energy Readouts with RAPL 3.6.2 Methodology 3.6.3 RAPL on Intel Sandy Bridge-EP 3.6.4 RAPL on Intel Haswell-EP and Skylake-SP 3.7 Conclusion 4 A Scalable Infrastructure for Processing Power Measurement Data 4.1 Requirements for Power Measurement Data Processing 4.2 Concepts and Implementation of Measurement Data Management 4.2.1 Message-Based Communication between Agents 4.2.2 Protocols 4.2.3 Application Programming Interfaces 4.2.4 Efficient Metric Time Series Storage and Retrieval 4.2.5 Hierarchical Timeline Aggregation 4.3 Performance Evaluation 4.3.1 Benchmark Hardware Specifications 4.3.2 Throughput in Symmetric Configuration with Replication 4.3.3 Throughput with Many Data Sources and Single Consumers 4.3.4 Temporary Storage in Message Queues 4.3.5 Persistent Metric Time Series Request Performance 4.3.6 Performance Comparison with Contemporary Time Series Storage Solutions 4.3.7 Practical Usage of MetricQ 4.4 Conclusion 5 Energy Efficiency Analysis 5.1 General Energy Efficiency Analysis Scenarios 5.1.1 Live Visualization of Power Measurements 5.1.2 Visualization of Long-Term Measurements 5.1.3 Integration in Application Performance Traces 5.1.4 Graphical Analysis of Application Power Traces 5.2 Correlating Power Measurements with Application Events 5.2.1 Challenges for Time Synchronization of Power Measurements 5.2.2 Reliable Automatic Time Synchronization with Correlation Sequences 5.2.3 Creating a Correlation Signal on a Power Measurement Channel 5.2.4 Processing the Correlation Signal and Measured Power Values 5.2.5 Common Oversampling of the Correlation Signals at Different Rates 5.2.6 Evaluation of Correlation and Time Synchronization 5.3 Use Cases for Application Power Traces 5.3.1 Analyzing Complex Power Anomalies 5.3.2 Quantifying C-State Transitions 5.3.3 Measuring the Dynamic Power Consumption of HPC Applications 5.4 Conclusion 6 Summary and Outloo

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

From Facility to Application Sensor Data: Modular, Continuous and Holistic Monitoring with DCDB

Today's HPC installations are highly-complex systems, and their complexity will only increase as we move to exascale and beyond. At each layer, from facilities to systems, from runtimes to applications, a wide range of tuning decisions must be made in order to achieve efficient operation. This, however, requires systematic and continuous monitoring of system and user data. While many insular solutions exist, a system for holistic and facility-wide monitoring is still lacking in the current HPC ecosystem. In this paper we introduce DCDB, a comprehensive monitoring system capable of integrating data from all system levels. It is designed as a modular and highly-scalable framework based on a plugin infrastructure. All monitored data is aggregated at a distributed noSQL data store for analysis and cross-system correlation. We demonstrate the performance and scalability of DCDB, and describe two use cases in the area of energy management and characterization.Comment: Accepted at the The International Conference for High Performance Computing, Networking, Storage, and Analysis (SC) 201