Final documentation of the LUNAR program and emendations to scientific report no. 9
Computer program checkout programming with complete printout of corrected program
Newell, J. B.↗
SEARCH · Engineering Papers
Results for “Scientific Computing.”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Distributed management of scientific projects - An analysis of two computer-conferencing experiments at NASA
Between August 1975 and March 1976, two NASA projects with geographically separated participants used a computer-conferencing system developed by the Institute for the Future for portions of their work. Monthly usage statistics for the system were collected in order to examine the group and individual participation figures for all conferences. The conference transcripts were analysed to derive observations about the use of the medium. In addition to the results of these analyses, the attitudes of users and the major components of the costs of computer conferencing are discussed.
Vallee, J.↗
HYPPO: A Surrogate-Based Multi-Level Parallelism Tool for Hyperparameter Optimization
We present a new software, HYPPO, that enables the automatic tuning of hyperparameters of various deep learning (DL) models. Unlike other hyperparameter optimization (HPO) methods, HYPPO uses adaptive surrogate models and directly accounts for uncertainty in model predictions to find accurate and reliable models that make robust predictions. Using asynchronous nested parallelism, we are able to significantly alleviate the computational burden of training complex architectures and quantifying the uncertainty. HYPPO is implemented in Python and can be used with both TensorFlow and PyTorch libraries. We demonstrate various software features on time-series prediction and image classification problems as well as a scientific application in computed tomography image reconstruction. Finally, we show that (1) we can reduce by an order of magnitude the number of evaluations necessary to find the most optimal region in the hyperparameter space and (2) we can reduce by two orders of magnitude the throughput for such HPO process to complete.
adaptation models↗
BEAM: A Computational Workflow System for Managing and Modeling Material Characterization Data in HPC Environments
Improvements in scientific instrumentation allow imaging at mesoscopic to atomic length scales, many spectroscopic modes, and now—with the rise of multimodal acquisition systems and the associated processing capability—the era of multidimensional, informationally dense data sets has arrived. Technical issues in these combinatorial scientific fields are exacerbated by computational challenges best summarized as a necessity for drastic improvement in the capability to transfer, store, and analyze large volumes of data. The Bellerophon Environment for Analysis of Materials (BEAM) platform provides material scientists the capability to directly leverage the integrated computational and analytical power of High Performance Computing (HPC) to perform scalable data analysis and simulation via an intuitive, cross-platform client user interface. This framework delivers authenticated, “push-button” execution of complex user workflows that deploy data analysis algorithms and computational simulations utilizing the converged compute-and-data infrastructure at Oak Ridge National Laboratory's (ORNL) Compute and Data Environment for Science (CADES) and HPC environments like Titan at the Oak Ridge Leadership Computing Facility (OLCF). In this work we address the underlying HPC needs for characterization in the material science community, elaborate how BEAM's design and infrastructure tackle those needs, and present a small sub-set of user cases where scientists utilized BEAM across a broad range of analytical techniques and analysis modes.
96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
Performance Understanding and Analysis for Exascale Data Management Workflows
The goal of the Exascale Data Management Workflows project is to create tools to support techniques for in-situ data analysis and data management. Online data management co-running with simulations accelerates the scientific processes being carried out, provides rapid and timely scientific insights, and can help avoid unnecessary and scientifically invalid simulation computations, particularly when combined with or able to utilize data from experimental instrument and/or from past simulation runs. The University of Oregon team is contributing to the performance instrumentation and analysis aspect of this project. Our focus has been on efficient performance monitoring of data management at scale. The general approach of the MONA project is depicted in Figure 1 below. The figure shows performance monitoring applied to an I/O workflow associated with a scientific simulation, with online measurements captured from this workflow informing methods for workflow reconfiguration and dynamic adjustment. The goal is to maintain suitable levels of Quality of Service for workflow execution, by understanding the under lying causes of workflow performance and behavior. One outcome is workflow performance models able to characterize realistic workflows. Another outcome is performance ’mini-apps’ implementing such workflow behavior. Out of scope for this project are advanced methods for online workflow control.
97 MATHEMATICS AND COMPUTING↗
Scalable Performance Awareness for In Situ Scientific Applications
Part of the promise of exascale computing and the next generation of scientific simulation codes is the ability to bring together time and spatial scales that have traditionally been treated separately. This enables creating complex coupled simulations and in situ analysis pipelines, encompassing such things as "whole device" fusion models or the simulation of cities from sewers to rooftops. Unfortunately, the HPC analysis tools that have been built up over the preceding decades are ill suited to the debugging and performance analysis of such computational ensembles. In this paper, we present a new vision for performance measurement and understanding of HPC codes, MonitoringAnalytics (MONA). MONA is designed to be a flexible, high performance monitoring infrastructure that can perform monitoring analysis in place or in transit by embedding analytics and characterization directly into the data stream, without relying upon delivering all monitoring information to a central database for post-processing. It addresses the trade-offs between the prohibitively expensive capture of all performance characteristics and not capturing enough to detect the features of interest. We demonstrate several uses of MONA; capturing and indexing multi-executable performance profiles to enable later processing, extraction of performance primitives to enable the generation of customizable benchmarks and performance skeletons, and extracting communication and application behaviors to enable better control and placement for the current and future runs of the science ensemble. Relevant performance information based on a system for MONA built from ADIOS and SOSflow technologies is provided for DOE science applications and leadership machines.
Wolf, Matthew D.↗
Software Reuse Methods to Improve Technological Infrastructure for e-Science
Social computing has the potential to contribute to scientific research. Ongoing developments in information and communications technology improve capabilities for enabling scientific research, including research fostered by social computing capabilities. The recent emergence of e-Science practices has demonstrated the benefits from improvements in the technological infrastructure, or cyber-infrastructure, that has been developed to support science. Cloud computing is one example of this e-Science trend. Our own work in the area of software reuse offers methods that can be used to improve new technological development, including cloud computing capabilities, to support scientific research practices. In this paper, we focus on software reuse and its potential to contribute to the development and evaluation of information systems and related services designed to support new capabilities for conducting scientific research.
Marshall, James J.↗
Exploring Memory Hierarchy to Improve Scientific Data Read Performance, In: 2015 IEEE International Conference on Cluster Computing
Improving read performance is one of the major challenges with speeding up scientific data analytic applications. Utilizing the memory hierarchy is one major line of researches to address the read performance bottleneck. Related methods usually combine solide-state-drives(SSDs) with dynamic random-access memory(DRAM) and/or parallel file system(PFS) to mitigate the speed and space gap between DRAM and PFS. However, these methods are unable to handle key performance issues plaguing SSDs, namely read contention that may cause up to 50% performance reduction. In this paper, we propose a framework that exploits the memory hierarchy resource to address the read contention issues involved with SSDs. The framework employs a general purpose online read algorithm that able to detect and utilize memory hierarchy resource to relieve the problem. To maintain a near optimal operating environment for SSDs, the framework is able to orchastrate data chunks across different memory layers to facilitate the read algorithm. Compared to existing tools, our framework achieves up to 50% read performance improvement when tested on datasets from real-world scientific simulations.
Computer Science↗
Modular HPC I/O characterization with Darshan
Contemporary high-performance computing (HPC) applications encompass a broad range of distinct I/O strategies and are often executed on a number of different compute platforms in their lifetime. These large-scale HPC platforms employ increasingly complex I/O subsystems to provide a suitable level of I/O performance to applications. Tuning I/O workloads for such a system is nontrivial, and the results generally are not portable to other HPC systems. I/O profiling tools can help to address this challenge, but most existing tools only instrument specific components within the I/O subsystem that provide a limited perspective on I/O performance. The increasing diversity of scientific applications and computing platforms calls for greater flexibililty and scope in I/O characterization.
Snyder, Shane↗
The U.S. Department of Energy Computational Science Graduate Fellowship, 1991-2021: Follow-Up Study Shows Major Impact on Recipients and the Scientific Workforce
Since 1991, the U.S. Department of Energy Computational Science Graduate Fellowship (DOE CSGF) has addressed DOE National Laboratory needs as well as demands in the national workforce for trained professionals in computational science and engineering. Sponsored by the Department of Energy's Office of Science and the National Nuclear Security Administration, the DOE CSGF supports doctoral students in the pursuit of novel scientific or engineering discoveries using high-performance computing (HPC) resources. To meet the program’s core requirements, recipients participate in multidisciplinary studies, carry out at least one 12-week DOE laboratory research practicum, and contribute to an annual program review where the fellows present their research for sponsor review. The Krell Institute, which as managed the fellowship on behalf of the DOE since 1997, has commissioned several follow-up studies to examine the DOE CSGF recipients’ characteristics, fellows’ outcomes and professional accomplishments, alumni’s career paths and achievements, and recipients’ impact on national priorities through research and education.
97 MATHEMATICS AND COMPUTING↗
The U.S. Department of Energy Computational Science Graduate Fellowship, 1991-2021: Follow-Up Study Shows Major Impact on Recipients and the Scientific Workforce
Since 1991, the U.S. Department of Energy Computational Science Graduate Fellowship (DOE CSGF) has addressed DOE National Laboratory needs as well as demands in the national workforce for trained professionals in computational science and engineering. Sponsored by the Department of Energy's Office of Science and the National Nuclear Security Administration, the DOE CSGF supports doctoral students in the pursuit of novel scientific or engineering discoveries using high-performance computing (HPC) resources. To meet the program’s core requirements, recipients participate in multidisciplinary studies, carry out at least one 12-week DOE laboratory research practicum, and contribute to an annual program review where the fellows present their research for sponsor review. The Krell Institute, which as managed the fellowship on behalf of the DOE since 1997, has commissioned several follow-up studies to examine the DOE CSGF recipients’ characteristics, fellows’ outcomes and professional accomplishments, alumni’s career paths and achievements, and recipients’ impact on national priorities through research and education.
97 MATHEMATICS AND COMPUTING↗
Better together: Elements of successful scientific software development in a distributed collaborative community
Many scientific disciplines rely on computational methods for data analysis, model generation, and prediction. Implementing these methods is often accomplished by researchers with domain expertise but without formal training in software engineering or computer science. This arrangement has led to underappreciation of sustainability and maintainability of scientific software tools developed in academic environments. Some software tools have avoided this fate, including the scientific library Rosetta. We use this software and its community as a case study to show how modern software development can be accomplished successfully, irrespective of subject area. Rosetta is one of the largest software suites for macromolecular modeling, with 3.1 million lines of code and many state-of-the-art applications. Since the mid 1990s, the software has been developed collaboratively by the RosettaCommons, a community of academics from over 60 institutions worldwide with diverse backgrounds including chemistry, biology, physiology, physics, engineering, mathematics, and computer science. Developing this software suite has provided us with more than two decades of experience in how to effectively develop advanced scientific software in a global community with hundreds of contributors. Here we illustrate the functioning of this development community by addressing technical aspects (like version control, testing, and maintenance), community-building strategies, diversity efforts, software dissemination, and user support. We demonstrate how modern computational research can thrive in a distributed collaborative community. The practices described here are independent of subject area and can be readily adopted by other software development communities
97 MATHEMATICS AND COMPUTING↗
PyGDH: Python Grid Discretization Helper
Mathematical models expressed in the form of discretized equations play an important role inmany scientific disciplines. In our experience, few domain scientists have sufficient backgroundin numerical computing (or the time required to acquire such a background) to use manyflexible and powerful but complex open source packages, such as FEniCS (Alnæs et al., 2015)and OpenFOAM (The OpenFOAM Foundation Ltd, n.d.). Many user-friendly open sourcepackages, such as FiPy (J. E. Guyer & Warren, 2009), and many commercial packages, suchas COMSOL Multiphysics (COMSOL AB, n.d.) and Simcenter STAR-CCM+ (Siemens DigitalIndustries Software, n.d.), provide limited flexibility in the equations that users can express.Additionally, the use of commercial packages, which by nature do not perform calculationstransparently, can hinder reproducibility, which is vital to the scientific process. PyGDH(“pigged”) is a Python 2 / Python 3 (Python Software Foundation, 1991–2020) package thatis meant to be accessible to scientists who might not be specialists in scientific computing,while approaching the level of flexibility associated with writing dedicated programs tailoredto solving specific problems. The PyGDH User’s Guide provides detailed instructions forcreating numerical models, including a brief introduction to necessary command line andPython (Python Software Foundation, 1991–2020) skills, and discussions of discretization andvalidation. Note that PyGDH emphasizes flexibility and simplicity over performance, and wasnot designed for high-performance applications or models describing complex spatial domains.
97 MATHEMATICS AND COMPUTING↗
Ecological risk assessment software for radioactive waste management facilities - 15464
Environmental Risk Assessment (ERA) is a systematic process which can be used to identify, quantify and characterize the risk posed by contaminants and physical stressors in the environment on biological receptors, including human and non-human biota. Human receptors can be addressed through a Human Health Risk Assessment and non-human biota can be addressed through an Ecological Risk Assessment (EcoRA). In 2012 the Canadian Standards Association (CSA) issued a CSA standard N288.6 Environmental Risk Assessment at Class I Nuclear Facilities and Uranium Mines and Mills. The standard applies to radioactive waste management facilities, as well as nuclear power plants. The ERA can also be used retrospectively, to estimate the effect that a contaminant or stressor has already had on the environment; and can be used to assist in determining possible remedial or risk management options to return the quality of the affected environment to a predetermined state. While industry-standard tools for estimating radiological doses to humans are readily available, there is a need for a tool to implement the CSA N288.6 standard for Ecological Risk Assessment. To address this need, AMEC developed a computer code called -Assessment of Impact of Contaminants on Ecological Receptors (AICER)-. The code was developed to be consistent with the CSA standard N288.6, by assessing the impact of radiological contamination on non-human biota for normal operations. The code can also be used to screen for the potential effects of conventional contamination on the environment. In addition, the code is also applicable for abnormal events and accidents with the appropriate modification of some parameters used in the code. The AICER code was qualified in accordance with the requirements of the Canadian quality standard CSA N286.7 -Quality Assurance of Analytical, Scientific, and Design Computer Programs for Nuclear Power Plants-. The functionality of the code is illustrated with screen shots in the paper, following the introduction of the theoretical model for the dose calculation. An inter-comparison with RESRAD-BIOTA and ERICA Assessment tool at the conceptual level was conducted. In addition, the practical application of the code for the assessment of the impacts related to an existing radioactive waste management facility is provided. In particular, analysis was conducted to evaluate radiological doses to non-human biota resulting from a fire accident scenario involving an existing waste storage and processing facility. Analysis included all feasible waterborne and airborne exposure pathways. Doses were evaluated for a range of species representing valued ecological components at various trophic levels and compared with benchmark values for indicator species. (authors)
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
Understanding data motion in the modern HPC data center
The utilization and performance of storage, compute, and network resources within HPC data centers have been studied extensively, but much less work has gone toward characterizing how these resources are used in conjunction to solve larger scientific challenges. To address this gap, we present our work in characterizing workloads and workflows at a data-center-wide level by examining all data transfers that occurred between storage, compute, and the external network at the National Energy Research Scientific Computing Center over a three-month period in 2019. Using a simple abstract representation of data transfers, we analyze over 100 million transfer logs from Darshan, HPSS user interfaces, and Globus to quantify the load on data paths between compute, storage, and the wide-area network based on transfer direction, user, transfer tool, source, destination, and time. We show that parallel I/O from user jobs, while undeniably important, is only one of several major I/O workloads that occurs throughout the execution of scientific workflows. We also show that this approach can be used to connect anomalous data traffic to specific users and file access patterns, and we construct time-resolved user transfer traces to demonstrate that one can systematically identify coupled data motion for individual workflows.
Lockwood, GK↗
Anti-Icing Coatings using Ionomer Film Layer Structuring
This research effort examined the application of Nafion polymers in alcohol solvents as an anti-ice surface coating, as a mixture with hydrophilic polymers and freezing point depressant salt systems. Co-soluble systems of Nafion, polymer and salt were applied using dip coating methods to create smooth films for frost observation over a Peltier plate thermal system in ambient laboratory conditions. Cryo-DSC was applied to examine freezing events of the Nafion-surfactant mixtures, but the sensitivity of the measurement was insufficient to determine frost behavior. Collaborations with the Fog Chamber at Sandia-Albuquerque, and in environmental SAXS measurements with CINT-LANL were requested but were not able to be performed under the research duration. Since experimental characterization of these factors is difficult to achieve directly, computational modeling was used to guide the scientific basis for property improvement. Computational modeling was performed to improve understanding of the dynamic association between ionomer side groups and added molecules and deicing salts. The polyacrylic acid in water system was identified at the start of the project as a relevant system for exploring the effect of varying counterions on the properties of fully deprotonated polyacrylic acid (PAA) in the presence of water. Simulations were modeled with four different counterions, two monovalent counterions (K+ and Na+) and two divalent counterions (Ca2+ and Mg2+). The wt% of PAA in these systems was varied from ~10 to 80 wt% PAA for temperatures from 250K to 400K. In the second set of simulations, the interpenetration of water into a dry PAA film was studied for Na+ or Ca2+ counterions for temperatures between 300K and 400K. The result of this project is a sprayable Nafion film composite which resists ice nucleation at -20 °C for periods of greater than three hours. It is composed of Nafion polymer, hydrophilic polyethylene oxide polymer and CaCl2 anti-ice crosslinker. Durability and field performance properties remain to be determined.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
ESnet Requirements Review Program Through the IRI Lens: A Meta-Analysis of Workflow Patterns Across DOE Office of Science Programs (Final Report)
The Department of Energy (DOE) ensures America’s security and prosperity by addressing its energy, environmental, and nuclear challenges through transformative science and technology solutions. The DOE’s Office of Science (SC) delivers groundbreaking scientific discoveries and major scientific tools that transform our understanding of nature and advance the energy, economic, and national security of the United States. The SC’s programs advance DOE mission science across a wide range of disciplines and have developed the research infrastructure needed to remain at the forefront of scientific discovery. The DOE SC’s world-class research infrastructure — exemplified by the 28 SC scientific user facilities — provides the research community with premier observational, experimental, computational, and network capabilities. Each user facility is designed to provide unique capabilities to advance core DOE mission science for its sponsor SC program and to stimulate a rich discovery and innovation ecosystem. Research communities gather and flourish around each user facility, bringing together diverse perspectives. A hallmark of many facilities is the large population of students, postdoctoral researchers, and early-career scientists who contribute as full-fledged users. These facility staff and users collaborate over years to devise new approaches to utilizing the user facility’s core capabilities. The history of the SC user facilities has many examples of wildly inventive researchers challenging operational orthodoxy to pioneer new vistas of discovery; for example, the use of the synchrotron X-ray light sources for study of proteins and other large biological molecules. This continual reinvention of the practice of science — as users and staff forge novel approaches expressed in research workflows — unlocks new discoveries and propels scientific progress. Within this research ecosystem, the high-performance computing (HPC) and networking user facilities stewarded by SC’s Advanced Scientific Computing Research (ASCR) program play a dynamic cross-cutting role, enabling complex workflows demanding high performance data, networking, and computing solutions. The DOE SC’s three HPC user facilities and the Energy Sciences Network (ESnet) high-performance research network serve all of the SC’s programs as well as the global research community. Argonne Leadership Computing Facility (ALCF), the National Energy Research Scientific Computing Center (NERSC), and Oak Ridge Leadership Computing Facility (OLCF) conceive, build, and provide access to a range of supercomputing, advanced computing, and large-scale data-infrastructure platforms, while ESnet interconnects DOE SC research infrastructure and enables seamless exchange of scientific data. All four facilities operate testbeds to expand the frontiers of computing and networking research. Together, the ASCR facilities enterprise seeks to understand and meet the needs and requirements across SC and DOE domain science programs and priority efforts, highlighted by the formal requirements reviews (RRs) methodology. In recent years, the research communities around the SC user facilities have begun experimenting with and demanding solutions integrated with HPC and data infrastructure. This rise of integrated-science approaches is documented in many community and high-level government reports. At the dawn of the era of exascale science and the acceleration of artificial intelligence (AI) innovation, there is a broad need for integrated computational, data, and networking solutions. In response to these drivers, DOE has developed a vision for an Integrated Research Infrastructure (IRI): To empower researchers to meld DOE’s world-class research tools, infrastructure, and user facilities seamlessly and securely in novel ways to radically accelerate discovery and innovation.
42 ENGINEERING↗
Equation solvers for distributed-memory computers
A large number of scientific and engineering problems require the rapid solution of large systems of simultaneous equations. The performance of parallel computers in this area now dwarfs traditional vector computers by nearly an order of magnitude. This talk describes the major issues involved in parallel equation solvers with particular emphasis on the Intel Paragon, IBM SP-1 and SP-2 processors.
Storaasli, Olaf O.↗