Frontiers in Scientific Workflows: Pervasive Integration With High-Performance Computing

Research into risky decision making (RDM) has become a multidisciplinary effort. Conversations cut across fields such as psychology, economics, insurance, and marketing. This broad interest highlights the necessity for collaborative investigation of RDM to understand and manipulate the situations within which it manifests. A holistic understanding of RDM has been impeded by the independent development of diverse RDM research methodologies across different fields. There is no software specific to RDM that combines paradigms and analytical tools based on recent developments in high-performance computing technologies. This paper presents a toolkit called RDMTk, developed specifically for the study of risky decision making. RDMTk provides a free environment that can be used to manage globally-based experiments while fostering collaborative research. The incorporation of machine learning and high-performance computing (HPC) technologies in the toolkit further open additional possibilities such as scalable algorithms and big data problems arising from global scale experiments.

High performance computing (HPC) is, today, a key technology to solve large problems in science, engineering, and business by utilizing tremendous computing power which has been evolving to the future. HPC Asia, which is an international conference series on HPC technologies in Asia Pacific region, and was held in the past several times in several countries in Asia regional sites to discuss the issues on high performance computing and to exchange information of research and development results in HPC.

Workflow technology has been adopted in scientific domains to orchestrate and automate scientific processes in order to facilitate experimentation. Such scientific workflows often involve large data sets and intensive computation that necessitate the use of the Grid, which offers supercomputing power through shared distributed resources. To execute a scientific workflow in the Grid, tasks within the workflow that represent steps in the scientific process are assigned to Grid resources for execution. To ensure efficient execution of the workflow, Grid workflow scheduling is required to manage the allocation of Grid resources. Although many Grid workflow scheduling techniques exist, they are mainly designed for the execution of a single workflow. This is not the case with parameter sweep workflows which focus on parametric study and parameter optimisation. A parameter sweep workflow is executed numerous times with different input parameters in order to determine the effect of each parameter combination on the experiment. While executing multiple instances of a parameter sweep workflow in parallel can reduce the time required for the overall execution, this execution introduces new challenges to Grid workflow scheduling. Not only is a scheduling algorithm that is able to manage multiple workflow instances required, but this algorithm also needs the ability to schedule tasks across multiple workflow instances judiciously, as tasks may require the same set of Grid resources. Without appropriate resource allocation, resource competition problem could arise. In the thesis, we propose a new Grid workflow scheduling technique for parameter sweep workflow called the Besom scheduling algorithm. The scheduling decision of our algorithm is based on the resource dependencies of tasks in the workflow, as well as conventional Grid resource-performance metrics. In addition, the proposed technique is extended to handle loop structures in scientific workflows without using existing loop-unrolling techniques. We evaluate the Besom algorithm under a variety of conditions. A comparison between the simulation results of the Besom algorithm and of the three existing Grid workflow scheduling algorithms shows that the Besom algorithm is able to perform better than the existing algorithms for workflows that have complex structures and that involve overlapping resource dependencies of tasks. The Besom scheduling algorithm advances the ability to schedule parallel execution of parameter sweep workflows in the Grid. The outcomes of this thesis justify continuing research in this area to increase our understanding of scheduling multiple Grid workflow instances and to provide support to those involved in parametric study and scientific workflow management.

Towards a model-driven transformation framework for scientific workflows

Modern High Performance Computing (HPC) applications, such as Earth science simulations, produce large amounts of data due to the surging of computing power, while big data applications have become more compute-intensive due to increasingly sophisticated analysis algorithms. The needs of both HPC and big data technologies for advanced HPC and big data applications create a demand for integrated system support. In this study, we introduce Scientific Data Processing (SciDP) to support both HPC and big data applications via integrated scientific data processing. SciDP can directly process scientific data stored on a Parallel File System (PFS), which is typically deployed in an HPC environment, in a big data programming environment running atop Hadoop Distributed File System (HDFS). SciDP seamlessly integrates PFS, HDFS, and the widely-used R data analysis system to support highly efficient processing of scientific data. It utilizes the merits of both PFS and HDFS for fast data transfer, overlaps computing with data accessing, and integrates R into the data transfer process. Experimental results show that SciDP accelerates analysis and visualization of a production NASA Center for Climate Simulation (NCCS) climate and weather application by 6x to 8x when compared to existing solutions.

Combinatorial Scientific Computing explores the latest research on creating algorithms and software tools to solve key combinatorial problems on large-scale high-performance computing architectures. It includes contributions from international researchers who are pioneers in designing software and applications for high-performance computing systems. The book offers a state-of-the-art overview of the latest research, tool development, and applications. It focuses on load balancing and parallelization on high-performance computers, large-scale optimization, algorithmic differentiation of numerical simulation code, sparse matrix software tools, and combinatorial challenges and applications in large-scale social networks. The authors unify these seemingly disparate areas through a common set of abstractions and algorithms based on combinatorics, graphs, and hypergraphs. Combinatorial algorithms have long played a crucial enabling role in scientific and engineering computations and their importance continues to grow with the demands of new applications and advanced architectures. By addressing current challenges in the field, this volume sets the stage for the accelerated development and deployment of fundamental enabling technologies in high-performance scientific computing.

The main focus of this article is the design of embedded signal processing (ESP) application software. We identify the characteristics of such applications in terms of their computational requirements, data layouts, and latency and throughput constraints. We describe an ESP application, an adaptive sonar beamformer. Then, we briefly survey the state-of-the-art in high performance computing (HPC) technology and address the advantages and challenges in using HPC technology for implementing ESP applications. To describe the software design issues in this context, we define a task model to capture the features of ESP applications. This model specifies the independent activities in each processing stage. We also identify various optimization problems in parallelizing ESP applications. We address the key issues in developing scalable and portable algorithms for ESP applications. We focus on the algorithmic issues in exploiting coarse-grain parallelism. These issues include data layout design and task mapping. We show a task mapping methodology for application software development based on our execution model (Lee et al., 1998). This uses a novel stage partitioning technique to exploit the independent activities in a processing stage. We use our methodology to maximize the throughput of an ESP application for a given platform size. The resulting application software using this methodology is called a software task pipeline. An adaptive sonar beamformer has been implemented using this design methodology.

To reproduce eScience, several challenges need to be solved: scientific workflows need to be automated; the involved software versions need to be provided in an unambiguous way; input data needs to be easily accessible; High-Performance Computing (HPC) clusters are often involved and to achieve bit-to-bit reproducibility, it might be even necessary to execute the code on a particular cluster to avoid differences caused by different HPC platforms (and unless this is a scientist's local cluster, it needs to be accessed across (administrative) borders). Preferably, to allow even inexperienced users to (re-)produce results, all should be user-friendly. While some easy-to-use web-based scientific portals support already to access HPC resources, this typically only refers to computing and data resources that are local. By the example of two community-specific portals in the fields of biodiversity and climate research, we present a solution for accessing remote HPC (and cloud) compute and data resources from scientific portals across borders, involving rigorous container-based packaging of the software version and setup automation, thus enhancing reproducibility.

High performance computing has entered the Exascale Age. Capable of performing over 1018 floating point operations per second, exascale computers, such as El Capitan, the National Nuclear Security Administration's first, have the potential to revolutionize the detailed in-depth study of highly complex science and engineering systems. However, in addition to these kind of whole machine “hero” simulations, exascale systems could also enable new paradigms in digital design by making petascale hero runs routine. Currently, untenable problems in complex system design, optimization, model exploration, and scientific discovery could all become possible. Motivated by the challenge of uncovering the next generation of robust high-yield inertial confinement fusion (ICF) designs, project ICECap (Inertial Confinement on El Capitan) attempts to integrate multiple advances in machine learning (ML), scientific workflows, high performance computing, GPU-acceleration, and numerical optimization to prototype such a future. Built on a general framework, ICECap is exploring how these technologies could broadly accelerate scientific discovery on El Capitan. In addition to our requirements, system-level design, and challenges, we describe some of the key technologies in ICECap, including ML replacements for multiphysics packages, tools for human-machine teaming, and algorithms for multifidelity design optimization under uncertainty. As a test of our prototype pre-El Capitan system, we advance the state-of-the art for ICF hohlraum design by demonstrating the optimization of a 17-parameter National Ignition Facility experiment and show that our ML-assisted workflow makes design choices that are consistent with physics intuition, but in an automated, efficient, and mathematically rigorous fashion.

Scientific workflows are models composed of activities, data and dependencies whose objective is to represent a computer simulation. Workflows are managed by Scientific Workflow Management System (SWfMS). Such workflows commonly demand for many computational resources once their executions may involve a number of different programs processing a huge volume of data. Thus, the use of High Performance Computing (HPC) environments allied to parallelization techniques provides the support for the execution of such experiments. Some resources provided by clouds can be used to build HPC environments. Although clouds offer advantages such as elasticity and availability, failures are a reality rather than a possibility. Thus, SWfMS must be fault-tolerant. There are several types of fault tolerance techniques used in SWfMS such as checkpoint-restart and replication, but which fault tolerance technique best fits with a specific workflow? This work aims at analyzing several fault tolerance techniques in SWfMSs and recommending the suitable one for the user’s workflow using machine learning techniques and provenance data, thus improving resiliency.

The advent of large-scale collaborative scientific applications has demonstrated the potential for broad scientific communities to pool globally distributed resources to produce unprecedented data acquisition, movement, and analysis. System resources including supercomputers, data repositories, computing facilities, network infrastructures, storage systems, and display devices have been increasingly deployed at national laboratories and academic institutes. These resources are typically shared by large communities of users over Internet or dedicated networks and hence exhibit an inherent dynamic nature in their availability, accessibility, capacity, and stability. Scientific applications using either experimental facilities or computation-based simulations with various physical, chemical, climatic, and biological models feature diverse scientific workflows as simple as linear pipelines or as complex as a directed acyclic graphs, which must be executed and supported over wide-area networks with massively distributed resources. Application users oftentimes need to manually configure their computing tasks over networks in an ad hoc manner, hence significantly limiting the productivity of scientists and constraining the utilization of resources. The success of these large-scale distributed applications requires a highly adaptive and massively scalable workflow platform that provides automated and optimized computing and networking services. This project is to design and develop a generic Scientific Workflow Automation and Management Platform (SWAMP), which contains a web-based user interface specially tailored for a target application, a set of user libraries, and several easy-to-use computing and networking toolkits for application scientists to conveniently assemble, execute, monitor, and control complex computing workflows in heterogeneous high-performance network environments. SWAMP will enable the automation and management of the entire process of scientific workflows with the convenience of a few mouse clicks while hiding the implementation and technical details from end users. Particularly, we will consider two types of applications with distinct performance requirements: data-centric and service-centric applications. For data-centric applications, the main workflow task involves large-volume data generation, catalog, storage, and movement typically from supercomputers or experimental facilities to a team of geographically distributed users; while for service-centric applications, the main focus of workflow is on data archiving, preprocessing, filtering, synthesis, visualization, and other application-specific analysis. We will conduct a comprehensive comparison of existing workflow systems and choose the best suited one with open-source code, a flexible system structure, and a large user base as the starting point for our development. Based on the chosen system, we will develop and integrate new components including a black box design of computing modules, performance monitoring and prediction, and workflow optimization and reconfiguration, which are missing from existing workflow systems. A modular design for separating specification, execution, and monitoring aspects will be adopted to establish a common generic infrastructure suited for a wide spectrum of science applications. We will further design and develop efficient workflow mapping and scheduling algorithms to optimize the workflow performance in terms of minimum end-to-end delay, maximum frame rate, and highest reliability. We will develop and demonstrate the SWAMP system in a local environment, the grid network, and the 100Gpbs Advanced Network Initiative (ANI) testbed. The demonstration will target scientific applications in climate modeling and high energy physics and the functions to be demonstrated include workflow deployment, execution, steering, and reconfiguration. Throughout the project period, we will work closely with the science communities in the fields of climate modeling and high energy physics including Spallation Neutron Source (SNS) and Large Hadron Collider (LHC) projects to mature the system for production use.

This paper reports on a four-year project that aims to raise the abstraction level through the use of model-driven engineering (MDE) techniques in the development of scientific applications relying on high-performance computing. The development and maintenance of high-performance scientific computing software is reputedly a complex task. This complexity results from the frequent evolutions of supercomputers and the tight coupling between software and hardware aspects. Moreover, current parallel programming approaches result in a mixing of concerns within the source code. Our approach relies on the use of MDE and consists in defining domain-specific modeling languages targeting various domain experts involved in the development of HPC applications, allowing each of them to handle their dedicated model in a both user-friendly and hardware-independent way. The different concerns are separated thanks to the use of several models as well as several modeling viewpoints on these models. Depending on the targeted execution platforms, these abstract models are translated into executable implementations by means of model transformations. To make all of these effective, we have developed a tool chain that is also presented in this paper. The approach is assessed through a multi-dimensional validation that focuses on its applicability, its expressiveness and its efficiency. To capitalize on the gained experience, we analyze some lessons learned during this project.

High performance computing for multidisciplinary design optimization and robustness of vehicle structures

High performance computing promotes the solution of large mathematical models of complex mechanical systems and lays a foundation for the theoretical analysis of complicated and difficult problems in the mechanical field. At the same time, the high reliability transmission of wireless data makes it possible for a variety of motion state mechanical systems to measure and control. In this paper, we present the energy loss model of the wet axle transmission system based on bond graph theory, and obtain the heat source boundary condition of the thermal analysis of the wet axle by calculating the mathematical model of the energy loss. Moreover, thermal network method is proposed to analysis heat accumulation and disequilibrium of multistage closed wet axle, by analyzing heat source distribution and heat transfer characteristics among machine elements, oil and air, finally the mathematic model of thermal analysis is established. The thermal numerical calculation of the thermal network for the complex mechanical system and the verification of the whole vehicle test for the results of the thermal calculation have been realized, then thermal optimization is done for wet axle heat equilibrium. Theory and experiment results indicate that heat accumulation in wet hub and heat disequilibrium of different parts are severe especially under efficient operating condition; thermal network calculation and optimization results verified by real vehicle experiment are true and valid. The research proves that high performance computer and high reliable wireless data transmission technology have promoted the optimization design of complex mechanical system.

Transient stability constrained optimal power flow (TSCOPF) is one the most computational-intensive applications in power systems. Research efforts were made to utilize high performance computing (HPC) technology to parallelize and accelerate TSCOPF solving process, but challenges still exist in performance analysis to identify bottlenecks and improve efficiency on practical HPC platforms such as Beowulf clusters. Based on first two authors' previous work [8, 12] - two-level parallel TSCOPF with reduced-space interior point method (RIPM), a systematic performance analysis approach is demonstrated in this paper. Comprehensive performance analysis procedures - wall time analysis, MPI/OpenMP profiling and tracing - is employed in order to discover performance bottlenecks. State-of-the-art performance analysis software are employed to generate and visualize performance data, providing guidelines for parallel performance enhancement. Numerical results on a 2746-bus system show effectiveness of the proposed approach and relative low overhead in solving large-scale multi-contingency TSCOPF on a Beowulf cluster.