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DOE OSTI2019

Snippet Open-Source Specification Synopsis

Snippet is a collaborative source code auditing tool developed by Sandia National Laboratories, in conjunction with researchers from other government agencies and partners. As a tool for use by groups of auditors, Snippet showed the value of providing in-line annotations that captured the thoughts of auditors in such a way that teams of auditors could share their insights. Snippet users found that the annotation mechanisms improved the auditing process but were frustrated at having to learn another environment. To address this issue, collaborators made extensions to existing Integrated Development Environments (IDEs) to incorporate functionality that mimics Snippet's behaviors. This document is one of a pair of documents. The other document, "Snippet Open-Source Specification", goes into details about the history and reasoning behind the requirements made in this document. That document provides for a broader understanding of the motivations backing this document. This document provides the complete specification for collaborative annotation, and a characterization of each specification as required or recommended. Tools that implement these specifications will be considered Snippet compliant. The intent is that complete implementation of these specifications will enable seamless sharing of annotation information between disjoint tools.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Developing and Distributing HEP Software Stacks with Spack

The Computational Science and AI Directorate at Fermilab is using Spack to support the development efforts of a large number of scientific programmers, in many independent projects and experiments. While independent, these projects share many dependencies. They are typically under continuous and fairly rapid development. They have to support deployment on diverse hardware. This is a different context than is typical for the management of HPC software, where Spack was born. To support our community, we have created a model that enables users to develop code with greater efficiency than is possible with Spack’s current development facilities. In this talk we will present: - a brief introduction to the science we support (particle physics) - how the code we work with is naturally organized into several layers of packages - how we are using Spack to manage those layers - how we leverage the layering to provide efficient support for developers, using our Spack extension “MPD”. - some suggestions for changes or additions to Spack to make such work easier.

Knoepfel, Kyle J. [Fermilab]↗

NASA NTRS1981

Common data buffer

Time-shared interface speeds data processing in distributed computer network. Two-level high-speed scanning approach routes information to buffer, portion of which is reserved for series of "first-in, first-out" memory stacks. Buffer address structure and memory are protected from noise or failed components by error correcting code. System is applicable to any computer or processing language.

Byrne, F.↗

DOE OSTI2015

Genetic algorithm based task reordering to improve the performance of batch scheduled massively parallel scientific applications

The growth in size of networked high performance computers along with novel accelerator-based node architectures has further emphasized the importance of communication efficiency in high performance computing. The world's largest high performance computers are usually operated as shared user facilities due to the costs of acquisition and operation. Applications are scheduled for execution in a shared environment and are placed on nodes that are not necessarily contiguous on the interconnect. Furthermore, the placement of tasks on the nodes allocated by the scheduler is sub-optimal, leading to performance loss and variability. Here, we investigate the impact of task placement on the performance of two massively parallel application codes on the Titan supercomputer, a turbulent combustion flow solver (S3D) and a molecular dynamics code (LAMMPS). Benchmark studies show a significant deviation from ideal weak scaling and variability in performance. The inter-task communication distance was determined to be one of the significant contributors to the performance degradation and variability. A genetic algorithm-based parallel optimization technique was used to optimize the task ordering. This technique provides an improved placement of the tasks on the nodes, taking into account the application's communication topology and the system interconnect topology. As a result, application benchmarks after task reordering through genetic algorithm show a significant improvement in performance and reduction in variability, therefore enabling the applications to achieve better time to solution and scalability on Titan during production.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

The Earth System Prediction Suite: Toward a Coordinated U.S. Modeling Capability

The Earth System Prediction Suite (ESPS) is a collection of flagship U.S. weather and climate models and model components that are being instrumented to conform to interoperability conventions, documented to follow metadata standards, and made available either under open-source terms or to credentialed users. Furthermore, the ESPS represents a culmination of efforts to create a common Earth system model architecture, and the advent of increasingly coordinated model development activities in the United States. ESPS component interfaces are based on the Earth System Modeling Framework (ESMF), community-developed software for building and coupling models, and the National Unified Operational Prediction Capability (NUOPC) Layer, a set of ESMF-based component templates and interoperability conventions. Our shared infrastructure simplifies the process of model coupling by guaranteeing that components conform to a set of technical and semantic behaviors. The ESPS encourages distributed, multiagency development of coupled modeling systems; controlled experimentation and testing; and exploration of novel model configurations, such as those motivated by research involving managed and interactive ensembles. ESPS codes include the Navy Global Environmental Model (NAVGEM), the Hybrid Coordinate Ocean Model (HYCOM), and the Coupled Ocean–Atmosphere Mesoscale Prediction System (COAMPS); the NOAA Environmental Modeling System (NEMS) and the Modular Ocean Model (MOM); the Community Earth System Model (CESM); and the NASA ModelE climate model and the Goddard Earth Observing System Model, version 5 (GEOS-5), atmospheric general circulation model.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2000

Towards Flange-to-Flange Turbopump Simulations for Liquid Rocket Engines

The primary objective of this research is to support the design of liquid rocket systems for the Advanced Space Transportation System. Since the space launch systems in the near future are likely to rely on liquid rocket engines, increasing the efficiency and reliability of the engine components is an important task. One of the major problems in the liquid rocket engine is to understand fluid dynamics of fuel and oxidizer flows from the fuel tank to plume. Understanding the flow through the entire turbopump geometry through numerical simulation will be of significant value toward design. This will help to improve safety of future space missions. One of the milestones of this effort is to develop, apply and demonstrate the capability and accuracy of 3D CFD methods as efficient design analysis tools on high performance computer platforms. The development of the MPI and MLP versions of the INS3D code is currently underway. The serial version of INS3D code is a multidimensional incompressible Navier-Stokes solver based on overset grid technology. INS3D-MPI is based on the explicit massage-passing interface across processors and is primarily suited for distributed memory systems. INS3D-MLP is based on multi-level parallel method and is suitable for distributed-shared memory systems. For the entire turbopump simulations, moving boundary capability and an efficient time-accurate integration methods are build in the flow solver. To handle the geometric complexity and moving boundary problems, overset grid scheme is incorporated with the solver that new connectivity data will be obtained at each time step. The Chimera overlapped grid scheme allows subdomains move relative to each other, and provides a great flexibility when the boundary movement creates large displacements. The performance of the two time integration schemes for time-accurate computations is investigated. For an unsteady flow which requires small physical time step, the pressure projection method was found to be computationally efficient since it does not require any subiterations procedure. It was observed that the artificial compressibility method requires a fast convergence scheme at each physical time step in order to satisfy incompressibility condition. This was obtained by using a GMRES-ILU(0) solver in our computations. When a line-relaxation scheme was used, the time accuracy was degraded and time-accurate computations became very expensive. The current geometry for the LOX boost turbopump has various rotating and stationary components, such as inducer, stators, kicker, hydrolic turbine, where the flow is extremely unsteady. Figure 1 shows the geometry and computed surface pressure of the inducer. The inducer and the hydrolic turbine rotate in different rotational speed.

Kiris, Cetin↗

NASA NTRS2000

Supercomputing Aspects for Simulating Incompressible Flow

The primary objective of this research is to support the design of liquid rocket systems for the Advanced Space Transportation System. Since the space launch systems in the near future are likely to rely on liquid rocket engines, increasing the efficiency and reliability of the engine components is an important task. One of the major problems in the liquid rocket engine is to understand fluid dynamics of fuel and oxidizer flows from the fuel tank to plume. Understanding the flow through the entire turbo-pump geometry through numerical simulation will be of significant value toward design. One of the milestones of this effort is to develop, apply and demonstrate the capability and accuracy of 3D CFD methods as efficient design analysis tools on high performance computer platforms. The development of the Message Passage Interface (MPI) and Multi Level Parallel (MLP) versions of the INS3D code is currently underway. The serial version of INS3D code is a multidimensional incompressible Navier-Stokes solver based on overset grid technology, INS3D-MPI is based on the explicit massage-passing interface across processors and is primarily suited for distributed memory systems. INS3D-MLP is based on multi-level parallel method and is suitable for distributed-shared memory systems. For the entire turbo-pump simulations, moving boundary capability and efficient time-accurate integration methods are built in the flow solver, To handle the geometric complexity and moving boundary problems, an overset grid scheme is incorporated with the solver so that new connectivity data will be obtained at each time step. The Chimera overlapped grid scheme allows subdomains move relative to each other, and provides a great flexibility when the boundary movement creates large displacements. Two numerical procedures, one based on artificial compressibility method and the other pressure projection method, are outlined for obtaining time-accurate solutions of the incompressible Navier-Stokes equations. The performance of the two methods is compared by obtaining unsteady solutions for the evolution of twin vortices behind a flat plate. Calculated results are compared with experimental and other numerical results. For an unsteady flow, which requires small physical time step, the pressure projection method was found to be computationally efficient since it does not require any subiteration procedure. It was observed that the artificial compressibility method requires a fast convergence scheme at each physical time step in order to satisfy the incompressibility condition. This was obtained by using a GMRES-ILU(0) solver in present computations. When a line-relaxation scheme was used, the time accuracy was degraded and time-accurate computations became very expensive.

Kwak, Dochan↗

DOE OSTI2021

Development of MCNP Training Modules for Safeguards Practitioners [Abstract]

The Monte-Carlo N-Particle (MCNP) software developed at LANL is the most widely used neutron transport code in the world. It is an essential tool for a variety of applications including detector development and design, nuclear fuel burnup simulation, criticality safety, and nondestructive assay system optimization. For this reason, it is indispensable within the safeguards and materials control & accountability (MC&A) communities. Multiple MCNP training courses have been created and taught over the last several decades by the MCNP development team at LANL, however there are no existing courses that cover specialized topics considered fundamental to NDA and safeguards models. To fill this gap, the MCNP team and Safeguards Science and Technology group at LANL have co-created a set of training modules customized to meet the specialized needs of the safeguards and MC&A communities. The basic modules cover concepts such as NDA system optimization, He-specific and other capture tallies, and tools for improved theoretical understanding. An advanced module was also created to cover topics including variance reduction for active interrogation simulations, use of the LANL MCNPTools post-processor, PTRAC (particle tracking) and list-mode data simulations, and fuel burnup simulations. The training modules teach to the latest and most state-of-the-art MCNP features and tools released by the development team at LANL and are intended to be taught jointly by the developers and safeguards experts. Ultimately, we hope that creation of these modules will serve to capture and convey the safeguards modeling and MCNP expertise at LANL, and that we will be able to share the modules more broadly with the MC&A and safeguards communities.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2019

Computer Modeling and Simulation: Increasing Reliability by Disentangling Verification and Validation

Verification and validation (V&V) of computer codes and models used in simulations are two aspects of the scientific practice of high importance that recently have been discussed widely by philosophers of science. While verification is predominantly associated with the correctness of the way a model is represented by a computer code or algorithm, validation more often refers to the model’s relation to the real world and its intended use. Because complex simulations are generally opaque to a practitioner, the Duhem problem can arise with verification and validation due to their entanglement; such an entanglement makes it impossible to distinguish whether a coding error or the model’s general inadequacy to its target should be blamed in the case of a failure. I argue that a clear distinction between computer modeling and simulation has to be made to disentangle verification and validation. Drawing on that distinction, I suggest to associate modeling with verification and simulation, which shares common epistemic strategies with experimentation, with validation. To explain the reasons for their entanglement in practice, I propose a Weberian ideal–typical model of modeling and simulation as roles in practice. I examine an approach to mitigate the Duhem problem for verification and validation that is generally applicable in practice and is based on differences in epistemic strategies and scopes. Based on this analysis, I suggest two strategies to increase the reliability of simulation results, namely, avoiding alterations of verified models at the validation stage as well as performing simulations of the same target system using two or more different models. In response to Winsberg’s claim that verification and validation are entangled I argue that deploying the methodology proposed in this work it is possible to mitigate inseparability of V&V in many if not all domains where modeling and simulation are used.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

A generalized massively parallel ultra-high order FFT-based Maxwell solver

Dispersion-free ultra-high order FFT-based Maxwell solvers have recently proven to be paramount to a large range of applications, including the high-fidelity modeling of high-intensity laser–matter interactions with Particle-In-Cell (PIC) codes. To enable a massively parallel scaling of these solvers, a novel parallelization technique was recently proposed, which consists in splitting the simulation domain into several processor sub-domains, with guard regions appended at each sub-domain boundary. Maxwell's equations are advanced independently on each sub-domain using local shared-memory FFTs (instead of a single distributed global FFT). This implies small truncation errors at sub-domain boundaries, the amplitude of which depends on guard regions sizes and order of the Maxwell solver. For moderate guard region sizes, this ’local’ technique proved to be highly scalable on up to a million cores and notably enabled the 3D modeling of so-called plasma mirrors, for which 8 guard cells only were enough to prevent truncation error growth. Yet, for other applications, the required number of guard cells might be much higher, which would severely limit the parallel efficiency of this technique due to the large volume of guard cells to be exchanged between sub-domains. In this context, we propose a novel parallelization technique that ensures very good scaling of FFT-based solvers with an arbitrarily high number of guard cells. Our ’hybrid’ technique consists in performing distributed FFTs on local groups of processors with guard regions now appended to boundaries of each group of processors. It uses a dual domain decomposition method for the Maxwell solver and other parts of the PIC cycle to keep the simulation load-balanced. This ’hybrid’ technique was implemented in the open source exascale library PICSAR. Benchmarks show that for a large number of guard cells (>16), the ’hybrid’ technique offers up to ×3 speed-up and ×8 memory savings compared to the ’local’ one.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2019

Sierra Center of Excellence: Lessons Learned

The introduction of heterogeneous computing via GPUs from the Sierra architecture represented a significant shift in direction for computational science at Lawrence Livermore National Laboratory (LLNL), and therefore required significant preparation. Over the last five years, the Sierra Center of Excellence (CoE) has brought employees with specific expertise from IBM and NVIDIA together with LLNL in a concentrated effort to prepare applications, system software, and tools for the Sierra supercomputer. This article shares the process we applied for the CoE and documents lessons learned during the collaboration, with the hope that others will be able to learn from both our success and intermediate setbacks. We describe what we have found to work for the management of such a collaboration and best practices for algorithms and source code, system configuration and software stack, tools, and application performance.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

“It is amazing what you can accomplish if you do not care who gets the credit”: Creating Alignment between Cities and Utility Energy Efficiency Programs

Cities are significantly acting as market catalysts to encourage and require building owners to improve energy performance. Yet, cities implementing building performance policies that require actions like audits or re-tuning may experience conflicts with their regulated utilities’ efficiency programs, which depend on energy savings being additional—not attributable to market adoption or preexisting laws. These utility programs preclude free ridership, meaning that the energy savings should be achieved by someone who otherwise would not have acted in the absence of the incentive or rebate. Utilities may decline to offer incentives where cities require particular actions, in turn dissuading cities from enacting ordinances that would lead to further efficiency improvements. This regulatory challenge impedes what could otherwise be a shared goal of improving energy efficiency. Finding solutions that allow city ordinances and utility programs to coexist is vital as cities are taking climate and energy matters into their own hands. Cities and utilities have so far navigated this problem informally. One potential approach is to apply established models from the world of energy codes, where some state regulators have permitted utilities to earn energy savings credit from supporting adoption of energy codes, or from improving code compliance. We consider how this approach and other frameworks could be applied to building performance policies. More specifically, this paper lays out a theory for how utilities can collaborate with local partners to drive deeper energy savings, with oversight from regulators, and examines the question of attributing the savings between the city and utility.

Crandall, Kelly↗

DOE OSTI2019

ISiCLE: A Quantum Chemistry Pipeline for Establishing in Silico Collision Cross Section Libraries

High throughput, comprehensive, and confident identifications of metabolites and other chemicals in biological and envi-ronmental samples will revolutionize our understanding of the role of these intriguing and chemically diverse molecules in biological systems. Despite recent technological advances, a metabolomics study still results in the detection of a dispropor-tionate number of features than cannot be confidently assigned to a chemical structure. This inadequacy is driven by the sin-gle most significant limitation in metabolomics: the reliance on reference libraries constructed through the analysis of au-thentic reference chemicals and the limited commercial availability of these compounds. To this end, we have developed the in silico chemical library engine (ISiCLE), a high-performance computing-friendly cheminformatics workflow for generating chemical properties. In the instantiation described here, we predict probable three-dimensional molecular conformers (i.e. conformational isomers) using chemical identifiers as input, from which collision cross sections (CCS) are derived. The ap-proach employs state-of-the-art first-principles simulation, distinguished by use of molecular dynamics, quantum chemistry, and ion mobility calculations to generate predictions, all without training data. Importantly, optimization of ISiCLE includ-ed a refactoring of the popular MOBCAL code for trajectory-based mobility calculations, improving its computational effi-ciency by over two orders of magnitude. Calculated CCS values were validated against 1,983 experimental CCS values and compared to previously reported CCS calculation approaches. Average CCS calculation absolute error is 3.2% with standard deviation 3.1%. An online database is introduced for sharing both calculated and experimental CCS values (metabolom-ics.pnnl.gov), initially including a CCS library with over 0.8M entries. Finally, three successful applications of molecule characterization using calculated CCS are described, including the identification of an environmental degradation product, the separation of molecular isomers, and the decoding of complex blinded mixtures of exposure chemicals. This work represents a promising method to address the limitations of small molecule identification, and offers alternatives to standards-based chemical identification amenable to high-performance computation.

metabolomics, standards-free, collision cross sect↗

DOE OSTI2022

Entanglement Purification and Protection in a Superconducting Quantum Network

High-fidelity quantum entanglement is a key resource for quantum communication and distributed quantum computing, enabling quantum state teleportation, dense coding, and quantum encryption. Any sources of decoherence in the communication channel, however, degrade entanglement fidelity, thereby increasing the error rates of entangled state protocols. Entanglement purification provides a method to alleviate these nonidealities by distilling impure states into higher-fidelity entangled states. In this work, we demonstrate the entanglement purification of Bell pairs shared between two remote superconducting quantum nodes connected by a moderately lossy, 1-meter long superconducting communication cable. We use a purification process to correct the dominant amplitude damping errors caused by transmission through the cable, with fractional increases in fidelity as large as 25%, achieved for higher damping errors. The best final fidelity the purification achieves is 94.09 ± 0.98%. In addition, we use both dynamical decoupling and Rabi driving to protect the entangled states from local noise, increasing the effective qubit dephasing time by a factor of 4, from 3 to 12 μs. These methods demonstrate the potential for the generation and preservation of very high-fidelity entanglement in a superconducting quantum communication network.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

ComStock™ 2024 Release 1 [SWR-19-33 and SWR-20-32]

ComStock™ is an NREL model of the U.S. commercial building stock. The model takes some building characteristics from the U.S. Department of Energy's (DOE's) Commercial Prototype Building Models and Commercial Reference Building. However, unlike many other building stock models, ComStock also combines these with a variety of additional public- and private-sector data sets. Collectively, this information provides high-fidelity building stock representation with a realistic diversity of building characteristics. This repository contains the source code used to build and execute ComStock models, including upgrade scenarios. In addition, the sampling of buildings characteristics used for the initial ComStock (V1.0) release is provided. The ComStock model is under active calibration and development, which is publicly visible on this repository. Execution of the ComStock workflow is managed through the buildstockbatch repository, a shared asset of ResStock™ and ComStock™ , specifically developed to scale to execution of tens of millions of simulations through multiple infrastructure providers. The dataset output from the initial ComStock (V1.0) release can be found at the accompanying ComStock data viewer website and additional information about ComStock found on the NREL Buildings Website. For more details about ongoing model development please consult the End Use Load Profiles website. ComStock is a direct result of the NREL residential stock modeling tool ResStock™ (recipient of a R&D100 award) and was inspired by the high-fidelity solar & storage adoption model dGen™. Additionally, this tool would not be possible without the decades of work undertaken by the OpenStudio® and EnergyPlus® visionaries and contributors, significant funding, feedback and support from the Los Angeles Department of Water and Power, and the Department of Energy's Building Technology Office ongoing support of and investment in building energy modeling software. is an analytic methodology for modeling the energy usage of the commercial building stock within the United States of America. The commercial building stock is represented through a sampling of complex probabilistic distributions of various features of interest for modeling energy usage within commercial buildings. Each sample from these distributions is converted into a building energy model based on the features of that specific sample. Each building energy model can be simulated as is, but additional changes can be made to the model through addition of energy conservation measures, component faults, or other desired alterations. The results of the simulations are then processed to provide insights for various stakeholders, including but not limited to policy makers, engineers, and marketers.

Horsey, Henry↗

DOE OSTI2018

ISiCLE: A Quantum Chemistry Pipeline for Establishing in Silico Collision Cross Section Libraries

Colby, Sean M↗

NASA NTRS1989

Aeronautical mobile TDMA/MCTDMA system

A multiple carrier Time Division Multiple Access (TDMA) system capable of supporting voice, stream data, and packet data traffic between aircraft and ground terminals is presented. Demand assignment permits efficient resource sharing for voice and stream data. The bandwidth efficiency of uncoded A Quadrature Phase Shift Keying (AQPSK) is 1 bps/Hz. High time efficiency (approximately equals 83 percent) is achieved through the use of symbol synchronous TDMA. Demodulation is achieved without loop hang-up while requiring only a 16 symbol preamble each burst. A concatenated coding system provides reliable transmission under multipath conditions.

Magill, Thomas↗

NASA NTRS1992

A transient FETI methodology for large-scale parallel implicit computations in structural mechanics

Explicit codes are often used to simulate the nonlinear dynamics of large-scale structural systems, even for low frequency response, because the storage and CPU requirements entailed by the repeated factorizations traditionally found in implicit codes rapidly overwhelm the available computing resources. With the advent of parallel processing, this trend is accelerating because explicit schemes are also easier to parallelize than implicit ones. However, the time step restriction imposed by the Courant stability condition on all explicit schemes cannot yet -- and perhaps will never -- be offset by the speed of parallel hardware. Therefore, it is essential to develop efficient and robust alternatives to direct methods that are also amenable to massively parallel processing because implicit codes using unconditionally stable time-integration algorithms are computationally more efficient when simulating low-frequency dynamics. Here we present a domain decomposition method for implicit schemes that requires significantly less storage than factorization algorithms, that is several times faster than other popular direct and iterative methods, that can be easily implemented on both shared and local memory parallel processors, and that is both computationally and communication-wise efficient. The proposed transient domain decomposition method is an extension of the method of Finite Element Tearing and Interconnecting (FETI) developed by Farhat and Roux for the solution of static problems. Serial and parallel performance results on the CRAY Y-MP/8 and the iPSC-860/128 systems are reported and analyzed for realistic structural dynamics problems. These results establish the superiority of the FETI method over both the serial/parallel conjugate gradient algorithm with diagonal scaling and the serial/parallel direct method, and contrast the computational power of the iPSC-860/128 parallel processor with that of the CRAY Y-MP/8 system.

Farhat, Charbel↗