Parallel Computing for Power System Climate Resiliency: Solving a Large-Scale Stochastic Capacity Expansion Problem with mpi-sppy
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Integrated System and Application Continuous Performance Monitoring and Analysis Capability
Scientific applications run on high-performance computing (HPC) systems are critical for many national security missions within Sandia and the NNSA complex. However, these applications often face performance degradation and even failures that are challenging to diagnose. To provide unprecedented insight into these issues, the HPC Development, HPC Systems, Computational Science, and Plasma Theory & Simulation departments at Sandia crafted and completed their FY21 ASC Level 2 milestone entitled "Integrated System and Application Continuous Performance Monitoring and Analysis Capability." The milestone created a novel integrated HPC system and application monitoring and analysis capability by extending Sandia's Kokkos application portability framework, Lightweight Distributed Metric Service (LDMS) monitoring tool, and scalable storage, analysis, and visualization pipeline. The extensions to Kokkos and LDMS enable collection and storage of application data during run time, as it is generated, with negligible overhead. This data is combined with HPC system data within the extended analysis pipeline to present relevant visualizations of derived system and application metrics that can be viewed at run time or post run. This new capability was evaluated using several week-long, 290-node runs of Sandia's ElectroMagnetic Plasma In Realistic Environments ( EMPIRE ) modeling and design tool and resulted in 1TB of application data and 50TB of system data. EMPIRE developers remarked this capability was incredibly helpful for quickly assessing application health and performance alongside system state. In short, this milestone work built the foundation for expansive HPC system and application data collection, storage, analysis, visualization, and feedback framework that will increase total scientific output of Sandia's HPC users.
97 MATHEMATICS AND COMPUTING↗
Trends in data locality abstractions for HPC systems
The cost of data movement has always been an important concern in high performance computing (HPC) systems. It has now become the dominant factor in terms of both energy consumption and performance. Support for expression of data locality has been explored in the past, but those efforts have had only modest success in being adopted in HPC applications for various reasons. However, with the increasing complexity of the memory hierarchy and higher parallelism in emerging HPC systems, locality management has acquired a new urgency. Developers can no longer limit themselves to low-level solutions and ignore the potential for productivity and performance portability obtained by using locality abstractions. Fortunately, the trend emerging in recent literature on the topic alleviates many of the concerns that got in the way of their adoption by application developers. Data locality abstractions are available in the forms of libraries, data structures, languages and runtime systems; a common theme is increasing productivity without sacrificing performance. Furthermore, this paper examines these trends and identifies commonalities that can combine various locality concepts to develop a comprehensive approach to expressing and managing data locality on future large-scale high-performance computing systems.
97 MATHEMATICS AND COMPUTING↗
Human Factors and Technical Considerations for a Computerized Operator Support System Prototype
A prototype computerized operator support system (COSS) has been developed in order to demonstrate the concept and provide a test bed for further research. The prototype is based on four underlying elements consisting of a digital alarm system, computer-based procedures, PI&D system representations, and a recommender module for mitigation actions. At this point, the prototype simulates an interface to a sensor validation module and a fault diagnosis module. These two modules will be fully integrated in the next version of the prototype. The initial version of the prototype is now operational at the Idaho National Laboratory using the U.S. Department of Energy’s Light Water Reactor Sustainability (LWRS) Human Systems Simulation Laboratory (HSSL). The HSSL is a full-scope, full-scale glass top simulator capable of simulating existing and future nuclear power plant main control rooms. The COSS is interfaced to the Generic Pressurized Water Reactor (gPWR) simulator with industry-typical control board layouts. The glass top panels display realistic images of the control boards that can be operated by touch gestures. A section of the simulated control board was dedicated to the COSS human-system interface (HSI), which resulted in a seamless integration of the COSS into the normal control room environment. A COSS demonstration scenario has been developed for the prototype involving the Chemical & Volume Control System (CVCS) of the PWR simulator. It involves a primary coolant leak outside of containment that would require tripping the reactor if not mitigated in a very short timeframe. The COSS prototype presents a series of operator screens that provide the needed information and soft controls to successfully mitigate the event.
21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
Integrated System and Application Continuous Performance Monitoring and Analysis Capability (Final)
Scientific applications run on high-performance computing (HPC) systems are critical for many national security missions within Sandia and the NNSA complex. However, these applications often face performance degradation and even failures that are challenging to diagnose. To provide unprecedented insight into these issues, the HPC Development, HPC Systems, Computational Science, and Plasma Theory & Simulation departments at Sandia crafted and completed their FY21 ASC Level 2 milestone entitled "Integrated System and Application Continuous Performance Monitoring and Analysis Capability." The milestone created a novel integrated HPC system and application monitoring and analysis capability by extending Sandia’s Kokkos application portability framework, Lightweight Distributed Metric Service (LDMS) monitoring tool, and scalable storage, analysis, and visualization pipeline. The extensions to Kokkos and LDMS enable collection and storage of application data during run time, as it is generated, with negligible overhead. This data is combined with HPC system data within the extended analysis pipeline to present relevant visualizations of derived system and application metrics that can be viewed at run time or post run. This new capability was evaluated using several week-long, 290-node runs of Sandia’s ElectroMagnetic Plasma In Realistic Environments (EMPIRE) modeling and design tool and resulted in 1TB of application data and 50TB of system data. EMPIRE developers remarked this capability was incredibly helpful for quickly assessing application health and performance alongside system state. In short, this milestone work built the foundation for expansive HPC system and application data collection, storage, analysis, visualization, and feedback framework that will increase total scientific output of Sandia’s HPC users.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Evaluation of Revised Computer-Based Procedure System Prototype
The nuclear power industry is very procedure driven, i.e. almost all activities that take place at a nuclear power plant are conducted by following procedures. The paper-based procedures (PBPs) currently used by the industry do a good job at keeping the industry safe. However, these procedures are most often paired with methods and tools put in place to anticipate, prevent, and catch errors related to hands-on work. These tools are commonly called human performance tools. The drawback with the current implementation of these tools is that the task of performing one procedure becomes time and labor intensive. For example, concurrent and independent verification of procedure steps are required at times, which essentially means that at least two people have to be actively involved in the task. Even though the current use of PBPs and human performance tools are keeping the industry safe, there is room for improvement. The industry could potentially increase their efficiency and safety by replacing their existing PBPs with CBPs. If implemented correctly, the CBP system could reduce the time and focus spent on using the human performance tools. Some of the tools can be completely incorporated in the CBP system in a manner that the performer does not think about the fact that these tools are being used. Examples of these tools are procedure use and adherence, placekeeping, and peer checks. Other tools can be partly integrated in a fashion that reduce the time and labor they require, such as concurrent and independent verification. The incorporation of advanced technology, such as CBP systems, may help to manage the effects of aging systems, structures, and components. The introduction of advanced technology may also make the existing LWR fleet more attractive to the future workforce, which will be of importance when the future workforce will chose between existing fleet and the newly built nuclear power plants.
97 MATHEMATICS AND COMPUTING↗
File I/O for MPI Applications in Redundant Execution Scenarios
As multi-petascale and exa-scale high-performance computing (HPC) systems inevitably have to deal with a number of resilience challenges, such as a significant growth in component count and smaller circuit sizes with lower circuit voltages, redundancy may offer an acceptable level of resilience that traditional fault tolerance techniques, such as checkpoint/restart, do not. Although redundancy in HPC is quite controversial due to the associated cost for redundant components, the constantly increasing number of cores-per-processor is tilting this cost calculation toward a system design where computation, such as for redundancy, is much cheaper and communication, needed for checkpoint/restart, is much more expensive. Recent research and development activities in redundancy for Message Passing Interface (MPI) applications focused on availability/reliability models and replication algorithms. This paper takes a first step toward solving an open research problem associated with running a parallel application redundantly, which is file I/O under redundancy. The approach intercepts file I/O calls made by a redundant application to employ coordination protocols that execute file I/O operations in a redundancy-oblivious fashion when accessing a node-local file system, or in a redundancy-aware fashion when accessing a shared networked file system. A proof-of concept prototype is presented and a number of coordination protocols are described and evaluated. The results show the performance impact for redundantly accessing a shared networked file system, but also demonstrate the capability to regain performance by utilizing MPI communication between replicas and parallel file I/O.
99 GENERAL AND MISCELLANEOUS↗
Implementation of Parallel Dynamic Simulation on Shared-Memory vs. Distributed-Memory Environments
Power system dynamic simulation computes the system response to a sequence of large disturbance, such as sudden changes in generation or load, or a network short circuit followed by protective branch switching operation. It consists of a large set of differential and algebraic equations, which is computational intensive and challenging to solve using single-processor based dynamic simulation solution. High-performance computing (HPC) based parallel computing is a very promising technology to speed up the computation and facilitate the simulation process. This paper presents two different parallel implementations of power grid dynamic simulation using Open Multi-processing (OpenMP) on shared-memory platform, and Message Passing Interface (MPI) on distributed-memory clusters, respectively. The difference of the parallel simulation algorithms and architectures of the two HPC technologies are illustrated, and their performances for running parallel dynamic simulation are compared and demonstrated.
dynamic simulation↗
Network support for system initiated checkpoints
A system, method and computer program product for supporting system initiated checkpoints in parallel computing systems. The system and method generates selective control signals to perform checkpointing of system related data in presence of messaging activity associated with a user application running at the node. The checkpointing is initiated by the system such that checkpoint data of a plurality of network nodes may be obtained even in the presence of user applications running on highly parallel computers that include ongoing user messaging activity.
97 MATHEMATICS AND COMPUTING↗
Network support for system initiated checkpoints
A system, method and computer program product for supporting system initiated checkpoints in parallel computing systems. The system and method generates selective control signals to perform checkpointing of system related data in presence of messaging activity associated with a user application running at the node. The checkpointing is initiated by the system such that checkpoint data of a plurality of network nodes may be obtained even in the presence of user applications running on highly parallel computers that include ongoing user messaging activity.
Chen, Dong↗
Understanding and Analyzing Interconnect Errors and Network Congestion on a Large Scale HPC System
Today's High Performance Computing (HPC) systems are capable of delivering performance in the order of petaflops due to the fast computing devices, network interconnect, and back-end storage systems. In particular, interconnect resilience and congestion resolution methods have a major impact on the overall interconnect and application performance. This is especially true for scientific applications running multiple processes on different compute nodes as they rely on fast network messages to communicate and synchronize frequently. Unfortunately, the HPC community lacks state-of-practice experience reports that detail how different interconnect errors and congestion events occur on large-scale HPC systems. Therefore, in this paper, we process and analyze interconnect data of the Titan supercomputer to develop a thorough understanding of interconnects faults, errors and congestion events. We also study the interaction between interconnect, errors, network congestion and application characteristics.
Kumar, Mohit↗
A Review of Edge Computing Technology and Its Applications in Power Systems
Recent advancements in network-connected devices have led to a rapid increase in the deployment of smart devices and enhanced grid connectivity, resulting in a surge in data generation and expanded deployment to the edge of systems. Classic cloud computing infrastructures are increasingly challenged by the demands for large bandwidth, low latency, fast response speed, and strong security. Therefore, edge computing has emerged as a critical technology to address these challenges, gaining widespread adoption across various sectors. This paper introduces the advent and capabilities of edge computing, reviews its state-of-the-art architectural advancements, and explores its communication techniques. A comprehensive analysis of edge computing technologies is also presented. Furthermore, this paper highlights the transformative role of edge computing in various areas, particularly emphasizing its role in power systems. It summarizes edge computing applications in power systems that are oriented from the architectures, such as power system monitoring, smart meter management, data collection and analysis, resource management, etc. Additionally, the paper discusses the future opportunities of edge computing in enhancing power system applications.
24 POWER TRANSMISSION AND DISTRIBUTION↗
UnigeneFinder: An Automated Pipeline for Gene Calling From Transcriptome Assemblies Without a Reference Genome
ABSTRACT For most species, transcriptome data are much more readily available than genome data. Without a reference genome, gene calling is cumbersome and inaccurate because of the high degree of redundancy in de novo transcriptome assemblies. To simplify and increase the accuracy of de novo transcriptome assembly in the absence of a reference genome, we developed UnigeneFinder. Combining several clustering methods, UnigeneFinder substantially reduces the redundancy typical of raw transcriptome assemblies. This pipeline offers an effective solution to the problem of inflated transcript numbers, achieving a closer representation of the actual underlying genome. UnigeneFinder performs comparably or better, compared with existing tools, on plant species with varying genome complexities. UnigeneFinder is the only available transcriptome redundancy solution that fully automates the generation of primary transcript, coding region, and protein sequences, analogous to those available for high‐quality reference genomes. These features, coupled with the pipeline’s cross‐platform implementation, focus on automation, and an accessible, user‐friendly interface, make UnigeneFinder a useful tool for many downstream sequence‐based analyses in nonmodel organisms lacking a reference genome, including differential gene expression analysis, accurate ortholog identification, functional enrichments, and evolutionary analyses. UnigeneFinder also runs efficiently both on high‐performance computing (HPC) systems and personal computers, further reducing barriers to use.
Xue, Bo [Plant Resilience Institute Michigan State↗
Human Factors Guidance for Building a Computer-Based Procedures System: How to Give the Users Something They Actually Want.
Abstract not provided.
Gilmore, Walter Edgar↗
Improvement of prostate cancer detection combining a computer-aided diagnostic system with TRUS-MRI targeted biopsy
Purpose: To validate a novel consensus method, called target-in-target, combining human analysis of mpMRI with automated CAD system analysis, with the aim to increasing the prostate cancer detection rate of targeted biopsies. Methods: A cohort of 420 patients was enrolled and 253 patients were rolled out, due to exclusion criteria. 167 patients, underwent diagnostic 3T MpMRI. Two expert radiologists evaluated the exams adopting PI-RADSv2 and CAD system. When a CAD target overlapped with a radiologic one, we performed the biopsy in the overlapping area which we defined as target-in-target. Targeted TRUS-MRI fusion biopsy was performed in 63 patients with a total of 212 targets. The MRI data of all targets were quantitatively analyzed, and diagnostic findings were compared to pathologist’s biopsy reports. Results: CAD system diagnostic performance exhibited sensitivity and specificity scores of 55.2% and 74.1% [AUC = 0.63 (0.54 ÷ 0.71)] , respectively. Human readers achieved an AUC value, in ROC analysis, of 0.71 (0.63 ÷ 0.79). The target-in-target method provided a detection rate per targeted biopsy core of 81.8 % vs. a detection rate per targeted biopsy core of 68.6 % for pure PI-RADS based on target definitions. The higher per-core detection rate of the target-in-target approach was achieved irrespective of the presence of technical flaws and artifacts. Conclusions: A novel consensus method combining human reader evaluation with automated CAD system analysis of mpMRI to define prostate biopsy targets was shown to improve the detection rate per biopsy core of TRUS-MRI fusion biopsies. Results suggest that the combination of CAD system analysis and human reader evaluation is a winning strategy to improve targeted biopsy efficiency.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
Molecular Electrostatic Potential and Electron Density of Large Systems in Solution Computed with the Fragment Molecular Orbital Method
A solvent screening model for the molecular electrostatic potential is developed for the fragment molecular orbital method combined with the polarizable continuum model at the Hartree–Fock and density functional theory levels. The accuracy of the generated potentials is established in comparison to calculations without fragmentation. Solvent effects upon the molecular electrostatic potential and electron density of solute are discussed. Finally, the method is applied to two proteins: chignolin (PDB: 1UAO) and ovine prostaglandin H(2) synthase-1 (1EQG).
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗