DALiuGE: A Graph Execution Framework for Harnessing the Astronomical Data Deluge

The Data Activated Liu Graph Engine - DALiuGE - is an execution framework for processing large astronomical datasets at a scale required by the Square Kilometre Array Phase 1 (SKA1). It includes an interface for expressing complex data reduction pipelines consisting of both data sets and algorithmic components and an implementation run-time to execute such pipelines on distributed resources. By mapping the logical view of a pipeline to its physical realisation, DALiuGE separates the concerns of multiple stakeholders, allowing them to collectively optimise large-scale data processing solutions in a coherent manner. The execution in DALiuGE is data-activated, where each individual data item autonomously triggers the processing on itself. Such decentralisation also makes the execution framework very scalable and flexible, supporting pipeline sizes ranging from less than ten tasks running on a laptop to tens of millions of concurrent tasks on the second fastest supercomputer in the world. DALiuGE has been used in production for reducing interferometry data sets from the Karl E. Jansky Very Large Array and the Mingantu Ultrawide Spectral Radioheliograph; and is being developed as the execution framework prototype for the Science Data Processor (SDP) consortium of the Square Kilometre Array (SKA) telescope. This paper presents a technical overview of DALiuGE and discusses case studies from the CHILES and MUSER projects that use DALiuGE to execute production pipelines. In a companion paper, we provide in-depth analysis of DALiuGE's scalability to very large numbers of tasks on two supercomputing facilities.Comment: 31 pages, 12 figures, currently under review by Astronomy and Computin

Characterizing Deep-Learning I/O Workloads in TensorFlow

The performance of Deep-Learning (DL) computing frameworks rely on the performance of data ingestion and checkpointing. In fact, during the training, a considerable high number of relatively small files are first loaded and pre-processed on CPUs and then moved to accelerator for computation. In addition, checkpointing and restart operations are carried out to allow DL computing frameworks to restart quickly from a checkpoint. Because of this, I/O affects the performance of DL applications. In this work, we characterize the I/O performance and scaling of TensorFlow, an open-source programming framework developed by Google and specifically designed for solving DL problems. To measure TensorFlow I/O performance, we first design a micro-benchmark to measure TensorFlow reads, and then use a TensorFlow mini-application based on AlexNet to measure the performance cost of I/O and checkpointing in TensorFlow. To improve the checkpointing performance, we design and implement a burst buffer. We find that increasing the number of threads increases TensorFlow bandwidth by a maximum of 2.3x and 7.8x on our benchmark environments. The use of the tensorFlow prefetcher results in a complete overlap of computation on accelerator and input pipeline on CPU eliminating the effective cost of I/O on the overall performance. The use of a burst buffer to checkpoint to a fast small capacity storage and copy asynchronously the checkpoints to a slower large capacity storage resulted in a performance improvement of 2.6x with respect to checkpointing directly to slower storage on our benchmark environment.Comment: Accepted for publication at pdsw-DISCS 201

The medical science DMZ: a network design pattern for data-intensive medical science

Abstract: Objective We describe a detailed solution for maintaining high-capacity, data-intensive network flows (eg, 10, 40, 100 Gbps+) in a scientific, medical context while still adhering to security and privacy laws and regulations. Materials and Methods High-end networking, packet-filter firewalls, network intrusion-detection systems. Results We describe a “Medical Science DMZ” concept as an option for secure, high-volume transport of large, sensitive datasets between research institutions over national research networks, and give 3 detailed descriptions of implemented Medical Science DMZs. Discussion The exponentially increasing amounts of “omics” data, high-quality imaging, and other rapidly growing clinical datasets have resulted in the rise of biomedical research “Big Data.” The storage, analysis, and network resources required to process these data and integrate them into patient diagnoses and treatments have grown to scales that strain the capabilities of academic health centers. Some data are not generated locally and cannot be sustained locally, and shared data repositories such as those provided by the National Library of Medicine, the National Cancer Institute, and international partners such as the European Bioinformatics Institute are rapidly growing. The ability to store and compute using these data must therefore be addressed by a combination of local, national, and industry resources that exchange large datasets. Maintaining data-intensive flows that comply with the Health Insurance Portability and Accountability Act (HIPAA) and other regulations presents a new challenge for biomedical research. We describe a strategy that marries performance and security by borrowing from and redefining the concept of a Science DMZ, a framework that is used in physical sciences and engineering research to manage high-capacity data flows. Conclusion By implementing a Medical Science DMZ architecture, biomedical researchers can leverage the scale provided by high-performance computer and cloud storage facilities and national high-speed research networks while preserving privacy and meeting regulatory requirements

Big Data meets High Performance Computing: Genomics and Natural Language Processing as case studies

The main objective of this thesis is to clarify a way to the convergence between the Big Data and the High Performance Computing world. In order to do this, a study of the application of this kind of technologies to two real world scientific problems is performed. These two problems are the sequence alignment in genomics and the natural language processing. These problems have a very big input and output size, and are computationally intensive, requiring a very high execution time. By facing these problems, also new tools that can be used by professionals in the areas are developed. Conclusions about convergence between these two worlds are presented, taking into account results from this study

Heterogeneity-aware scheduling and data partitioning for system performance acceleration

Over the past decade, heterogeneous processors and accelerators have become increasingly prevalent in modern computing systems. Compared with previous homogeneous parallel machines, the hardware heterogeneity in modern systems provides new opportunities and challenges for performance acceleration. Classic operating systems optimisation problems such as task scheduling, and application-specific optimisation techniques such as the adaptive data partitioning of parallel algorithms, are both required to work together to address hardware heterogeneity. Significant effort has been invested in this problem, but either focuses on a specific type of heterogeneous systems or algorithm, or a high-level framework without insight into the difference in heterogeneity between different types of system. A general software framework is required, which can not only be adapted to multiple types of systems and workloads, but is also equipped with the techniques to address a variety of hardware heterogeneity. This thesis presents approaches to design general heterogeneity-aware software frameworks for system performance acceleration. It covers a wide variety of systems, including an OS scheduler targeting on-chip asymmetric multi-core processors (AMPs) on mobile devices, a hierarchical many-core supercomputer and multi-FPGA systems for high performance computing (HPC) centers. Considering heterogeneity from on-chip AMPs, such as thread criticality, core sensitivity, and relative fairness, it suggests a collaborative based approach to co-design the task selector and core allocator on OS scheduler. Considering the typical sources of heterogeneity in HPC systems, such as the memory hierarchy, bandwidth limitations and asymmetric physical connection, it proposes an application-specific automatic data partitioning method for a modern supercomputer, and a topological-ranking heuristic based schedule for a multi-FPGA based reconfigurable cluster. Experiments on both a full system simulator (GEM5) and real systems (Sunway Taihulight Supercomputer and Xilinx Multi-FPGA based clusters) demonstrate the significant advantages of the suggested approaches compared against the state-of-the-art on variety of workloads."This work is supported by St Leonards 7th Century Scholarship and Computer Science PhD funding from University of St Andrews; by UK EPSRC grant Discovery: Pattern Discovery and Program Shaping for Manycore Systems (EP/P020631/1)." -- Acknowledgement

Technologies and Applications for Big Data Value

This open access book explores cutting-edge solutions and best practices for big data and data-driven AI applications for the data-driven economy. It provides the reader with a basis for understanding how technical issues can be overcome to offer real-world solutions to major industrial areas. The book starts with an introductory chapter that provides an overview of the book by positioning the following chapters in terms of their contributions to technology frameworks which are key elements of the Big Data Value Public-Private Partnership and the upcoming Partnership on AI, Data and Robotics. The remainder of the book is then arranged in two parts. The first part “Technologies and Methods” contains horizontal contributions of technologies and methods that enable data value chains to be applied in any sector. The second part “Processes and Applications” details experience reports and lessons from using big data and data-driven approaches in processes and applications. Its chapters are co-authored with industry experts and cover domains including health, law, finance, retail, manufacturing, mobility, and smart cities. Contributions emanate from the Big Data Value Public-Private Partnership and the Big Data Value Association, which have acted as the European data community's nucleus to bring together businesses with leading researchers to harness the value of data to benefit society, business, science, and industry. The book is of interest to two primary audiences, first, undergraduate and postgraduate students and researchers in various fields, including big data, data science, data engineering, and machine learning and AI. Second, practitioners and industry experts engaged in data-driven systems, software design and deployment projects who are interested in employing these advanced methods to address real-world problems

Advancement of Computing on Large Datasets via Parallel Computing and Cyberinfrastructure

Large datasets require efficient processing, storage and management to efficiently extract useful information for innovation and decision-making. This dissertation demonstrates novel approaches and algorithms using virtual memory approach, parallel computing and cyberinfrastructure. First, we introduce a tailored user-level virtual memory system for parallel algorithms that can process large raster data files in a desktop computer environment with limited memory. The application area for this portion of the study is to develop parallel terrain analysis algorithms that use multi-threading to take advantage of common multi-core processors for greater efficiency. Second, we present two novel parallel WaveCluster algorithms that perform cluster analysis by taking advantage of discrete wavelet transform to reduce large data to coarser representations so data is smaller and more easily managed than the original data in size and complexity. Finally, this dissertation demonstrates an HPC gateway service that abstracts away many details and complexities involved in the use of HPC systems including authentication, authorization, and data and job management

PROFET: modeling system performance and energy without simulating the CPU

The approaching end of DRAM scaling and expansion of emerging memory technologies is motivating a lot of research in future memory systems. Novel memory systems are typically explored by hardware simulators that are slow and often have a simplified or obsolete abstraction of the CPU. This study presents PROFET, an analytical model that predicts how an application's performance and energy consumption changes when it is executed on different memory systems. The model is based on instrumentation of an application execution on actual hardware, so it already takes into account CPU microarchitectural details such as the data prefetcher and out-of-order engine. PROFET is evaluated on two real platforms: Sandy Bridge-EP E5-2670 and Knights Landing Xeon Phi platforms with various memory configurations. The evaluation results show that PROFET's predictions are accurate, typically with only 2% difference from the values measured on actual hardware. We release the PROFET source code and all input data required for memory system and application profiling. The released package can be seamlessly installed and used on high-end Intel platforms.Peer ReviewedPostprint (author's final draft

Design considerations for workflow management systems use in production genomics research and the clinic

Abstract The changing landscape of genomics research and clinical practice has created a need for computational pipelines capable of efficiently orchestrating complex analysis stages while handling large volumes of data across heterogeneous computational environments. Workflow Management Systems (WfMSs) are the software components employed to fill this gap. This work provides an approach and systematic evaluation of key features of popular bioinformatics WfMSs in use today: Nextflow, CWL, and WDL and some of their executors, along with Swift/T, a workflow manager commonly used in high-scale physics applications. We employed two use cases: a variant-calling genomic pipeline and a scalability-testing framework, where both were run locally, on an HPC cluster, and in the cloud. This allowed for evaluation of those four WfMSs in terms of language expressiveness, modularity, scalability, robustness, reproducibility, interoperability, ease of development, along with adoption and usage in research labs and healthcare settings. This article is trying to answer, which WfMS should be chosen for a given bioinformatics application regardless of analysis type?. The choice of a given WfMS is a function of both its intrinsic language and engine features. Within bioinformatics, where analysts are a mix of dry and wet lab scientists, the choice is also governed by collaborations and adoption within large consortia and technical support provided by the WfMS team/community. As the community and its needs continue to evolve along with computational infrastructure, WfMSs will also evolve, especially those with permissive licenses that allow commercial use. In much the same way as the dataflow paradigm and containerization are now well understood to be very useful in bioinformatics applications, we will continue to see innovations of tools and utilities for other purposes, like big data technologies, interoperability, and provenance

Technologies and Applications for Big Data Value

This open access book explores cutting-edge solutions and best practices for big data and data-driven AI applications for the data-driven economy. It provides the reader with a basis for understanding how technical issues can be overcome to offer real-world solutions to major industrial areas. The book starts with an introductory chapter that provides an overview of the book by positioning the following chapters in terms of their contributions to technology frameworks which are key elements of the Big Data Value Public-Private Partnership and the upcoming Partnership on AI, Data and Robotics. The remainder of the book is then arranged in two parts. The first part “Technologies and Methods” contains horizontal contributions of technologies and methods that enable data value chains to be applied in any sector. The second part “Processes and Applications” details experience reports and lessons from using big data and data-driven approaches in processes and applications. Its chapters are co-authored with industry experts and cover domains including health, law, finance, retail, manufacturing, mobility, and smart cities. Contributions emanate from the Big Data Value Public-Private Partnership and the Big Data Value Association, which have acted as the European data community's nucleus to bring together businesses with leading researchers to harness the value of data to benefit society, business, science, and industry. The book is of interest to two primary audiences, first, undergraduate and postgraduate students and researchers in various fields, including big data, data science, data engineering, and machine learning and AI. Second, practitioners and industry experts engaged in data-driven systems, software design and deployment projects who are interested in employing these advanced methods to address real-world problems