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At least 379 records · Page 21

All sources NASA NTRS DOE OSTI

DOE OSTI2015

HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales

HackaMol is an open source, object-oriented toolkit written in Modern Perl that organizes atoms within molecules and provides chemically intuitive attributes and methods. The library consists of two components: HackaMol, the core that contains classes for storing and manipulating molecular information, and HackaMol::X, the extensions that use the core. We tested the core; it is well-documented and easy to install across computational platforms. Our goal for the extensions is to provide a more flexible space for researchers to develop and share new methods. In this application note, we provide a description of the core classes and two extensions: HackaMol::X::Calculator, an abstract calculator that uses code references to generalize interfaces with external programs, and HackaMol::X::Vina, a structured class that provides an interface with the AutoDock Vina docking program.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2014

Simulation for Wind Turbine Generators: With FAST and MATLAB-Simulink Modules

This report presents the work done to develop generator and gearbox models in the Matrix Laboratory (MATLAB) environment and couple them to the National Renewable Energy Laboratory's Fatigue, Aerodynamics, Structures, and Turbulence (FAST) program. The goal of this project was to interface the superior aerodynamic and mechanical models of FAST to the excellent electrical generator models found in various Simulink libraries and applications. The scope was limited to Type 1, Type 2, and Type 3 generators and fairly basic gear-train models. Future work will include models of Type 4 generators and more-advanced gear-train models with increased degrees of freedom. As described in this study, implementation of the developed drivetrain model enables the software tool to be used in many ways. Several case studies are presented as examples of the many types of studies that can be performed using this tool.

17 WIND ENERGY↗

DOE OSTI2023

TeraChem protocol buffers ( TCPB ): Accelerating QM and QM/MM simulations with a client–server model

The routine use of electronic structures in many chemical simulation applications calls for efficient and easy ways to access electronic structure programs. Here, we describe how the graphics processing unit (GPU) accelerated electronic structure program TeraChem can be set up as an electronic structure server, to be easily accessed by third-party client programs. We exploit Google’s protocol buffer framework for data serialization and communication. The client interface, called TeraChem protocol buffers (TCPB), has been designed for ease of use and compatibility with multiple programming languages, such as C++, Fortran, and Python. To demonstrate the ease of coupling third-party programs with electronic structures using TCPB, we have incorporated the TCPB client into Amber for quantum mechanics/molecular mechanics (QM/MM) simulations. The TCPB interface saves time with GPU initialization and I/O operations, achieving a speedup of more than 2× compared to a prior file-based implementation for a QM region with ~250 basis functions. We demonstrate the practical application of TCPB by computing the free energy profile of p-hydroxybenzylidene-2,3-dimethylimidazolinone (p-HBDI - )—a model chromophore in green fluorescent proteins—on the first excited singlet state using Hamiltonian replica exchange for enhanced sampling. All calculations in this work have been performed with the non-commercial freely-available version of TeraChem, which is sufficient for many QM region sizes in common use.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

ASC ATDM Level 2 Milestone #5325: Asynchronous Many-Task Runtime System Analysis and Assessment for Next Generation Platforms

This report provides in-depth information and analysis to help create a technical road map for developing next-generation programming models and runtime systems that support Advanced Simulation and Computing (ASC) work- load requirements. The focus herein is on asynchronous many-task (AMT) model and runtime systems, which are of great interest in the context of "Oriascale7 computing, as they hold the promise to address key issues associated with future extreme-scale computer architectures. This report includes a thorough qualitative and quantitative examination of three best-of-class AIM] runtime systems – Charm-++, Legion, and Uintah, all of which are in use as part of the Centers. The studies focus on each of the runtimes' programmability , performance , and mutability . Through the experiments and analysis presented, several overarching Predictive Science Academic Alliance Program II (PSAAP-II) Asc findings emerge. From a performance perspective, AIV runtimes show tremendous potential for addressing extreme- scale challenges. Empirical studies show an AM runtime can mitigate performance heterogeneity inherent to the machine itself and that Message Passing Interface (MP1) and AM11runtimes perform comparably under balanced conditions. From a programmability and mutability perspective however, none of the runtimes in this study are currently ready for use in developing production-ready Sandia ASC applications. The report concludes by recommending a co- design path forward, wherein application, programming model, and runtime system developers work together to define requirements and solutions. Such a requirements-driven co-design approach benefits the community as a whole, with widespread community engagement mitigating risk for both application developers developers. and high-performance computing runtime systein

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2015

Slope Extensions to ASL Library

Extensions to the AMPL/solver interface library (http://netlib.sandia.gov/ampl/solvers) to compute bounds on algebraic expressions, plus a test program. use in uncertainty quantification and global optimization algorithms. This software is not primarily for military applications.

Gay, David↗

DOE OSTI2023

Software Defined Architectures for Portability and Performance

The Software Defined Architectures for Portability and Performance (SODAPOP) project developed a co-design framework to partition and map converged applications on specialized heterogeneous architectures. We started from key domain applications that combine scientific simulation with data analytics and machine learning as drivers to integrate our framework. The framework includes high-level compilers that interfaces with high-level programming frameworks, domain-specific optimization passes, and hardware-oriented optimizations. The framework leverages hardware generators to enable specialization and facilitate exploration of custom system designs.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

HIPLZ: Enabling performance portability for exascale systems

While heterogeneous computing has emerged as a dominant trend in current and future High-Performance Computing (HPC) systems, it is also widely recognized that this shift has led to increased software complexity due to a proliferation of programming systems for different heterogeneous processors. One such example is the Heterogeneous-Compute Interface for Portability from AMD (HIP ), which is composed of a C Runtime API and C++ Kernel Language. Many HPC applications will likely use HIP on future exascale systems (e.g., Frontier and El Capitan), but HIP currently only targets AMD and NVIDIA processors. This limitation creates challenges for users who would also like to run their applications on exascale systems based on other architectures (e.g., Aurora, which is based on Intel hardware) that are currently not targeted by HIP . In this paper, we introduce the design and implementation of HIPLZ , a compiler and runtime system that uses the Intel Level Zero API to support HIP on Intel GPU architectures. We discuss the design of HIPLZ , derived from HIPCL (an implementation of HIP on top of OpenCL ), and portability issues that occur from using the Level Zero runtime as a backend. We evaluate our implementation by running several performance benchmarks and mini-apps written in HIP on Intel architectures using HIPLZ . Our results show that this approach provides competitive performance relative to Intel's OpenCL implementations on Intel Gen9 and UHD Graphics 770 GPUs, while providing good coverage of features needed by HPC applications. Overall, this approach is a promising demonstration of enabling performance portability for exascale systems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

RBDMS, FracFocus, and Gateway Initiatives for FY15/16

Award DE-FE-0000880 from the Department of Energy to the Ground Water Protection Council (GWPC) focuses on state and federal priorities in the areas of state RBDMS development, connectivity between state systems and FracFocus.org, and data sharing initiatives across agencies. The overarching goals of these projects are to: upgrade the Risk Based Data Management System (RBDMS) to a web based application; upgrade the RBDMS user interface to make it more intuitive and easier to use increase connectivity between state RBDMS systems and FracFocus; provide outreach to states and agencies through training programs, special meetings, and state by state outreach on all deliverables; provide greater functionality for non-IT users; update and install RBDMS modules in additional state programs (IL, CA, WY, WV); and; help make data access more transparent. The primary objective is to enhance the Risk Based Data Management System (RBDMS) by adding new components relevant to current environmental topics such as hydraulic fracturing, increasing field inspection capabilities, creating linkages between FracFocus and state programs, upgrading eForm capabilities, and analyzing potential for data sharing. The GWPC will work with state agencies to develop an RBDMS module(s) that meets these needs.

02 PETROLEUM↗

DOE OSTI2014

Embedding Agile Practices within a Plan-Driven Hierarchical Project Life Cycle

Organizations use structured, plan-driven approaches to provide continuity, direction, and control to large, multi-year programs. Projects within these programs vary greatly in size, complexity, level of maturity, technical risk, and clarity of the development objectives. Organizations that perform exploratory research, evolutionary development, and other R&D activities can obtain the benefits of Agile practices without losing the benefits of their program’s overarching plan-driven structure. This paper describes application of Agile development methods on a large plan-driven sensor integration program. While the client employed plan-driven, requirements flow-down methodologies, tight project schedules and complex interfaces called for frequent end-to-end demonstrations to provide feedback during system development. The development process maintained the many benefits of plan-driven project execution with the rapid prototyping, integration, demonstration, and client feedback possible through Agile development methods. This paper also describes some of the tools and implementing mechanisms used to transition between and take advantage of each methodology, and presents lessons learned from the project management, system engineering, and developer’s perspectives.

Agile Development↗

DOE OSTI2024

Complete Demonstration of a Prototype Version of FORCE User Interface and Conduct Analyst Survey Collecting Feedback on Interface Features and Usability

In 2024 the US Department of Energy (DOE) Office of Nuclear Energy (NE) Integrated Energy System (IES) program continued to develop the Framework for Optimization of Resources and Economics (FORCE) analysis ecosystem into a more traditional toolset with simplified software installation, automated workflows, and interactive results visualization. The DOE-NE Nuclear Energy Advanced Modeling and Simulation (NEAMS) Workbench continued to be leveraged for user input, application workflow and runtime environment, and interactive results visualization capabilities. This report documents the demonstration of a FORCE User Interface (UI) prototype and the results of a survey of analysts’ using the Holistic Energy Resource Optimization Network (HERON) tool in FORCE with the prototype UI.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2015

A generalized reconstruction framework for unconventional PET systems

Purpose: Quantitative estimation of the radionuclide activity concentration in positron emission tomography (PET) requires precise modeling of PET physics. The authors are focused on designing unconventional PET geometries for specific applications. This work reports the creation of a generalized reconstruction framework, capable of reconstructing tomographic PET data for systems that use right cuboidal detector elements positioned at arbitrary geometry using a regular Cartesian grid of image voxels. Methods: The authors report on a variety of design choices and optimization for the creation of the generalized framework. The image reconstruction algorithm is maximum likelihood-expectation–maximization. System geometry can be specified using a simple script. Given the geometry, a symmetry seeking algorithm finds existing symmetry in the geometry with respect to the image grid to improve the memory usage/speed. Normalization is approached from a geometry independent perspective. The system matrix is computed using the Siddon’s algorithm and subcrystal approach. The program is parallelized through open multiprocessing and message passing interface libraries. A wide variety of systems can be modeled using the framework. This is made possible by modeling the underlying physics and data correction, while generalizing the geometry dependent features. Results: Application of the framework for three novel PET systems, each designed for a specific application, is presented to demonstrate the robustness of the framework in modeling PET systems of unconventional geometry. Three PET systems of unconventional geometry are studied. (1) Virtual-pinhole half-ring insert integrated into Biograph-40: although the insert device improves image quality over conventional whole-body scanner, the image quality varies depending on the position of the insert and the object. (2) Virtual-pinhole flat-panel insert integrated into Biograph-40: preliminary results from an investigation into a modular flat-panel insert are presented. (3) Plant PET system: a reconfigurable PET system for imaging plants, with resolution of greater than 3.3 mm, is shown. Using the automated symmetry seeking algorithm, the authors achieved a compression ratio of the storage and memory requirement by a factor of approximately 50 for the half-ring and flat-panel systems. For plant PET system, the compression ratio is approximately five. The ratio depends on the level of symmetry that exists in different geometries. Conclusions: This work brings the field closer to arbitrary geometry reconstruction. A generalized reconstruction framework can be used to validate multiple hypotheses and the effort required to investigate each system is reduced. Memory usage/speed can be improved with certain optimizations.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Catalytic oxidative coupling of arenes and alkanes: applications for efficient chemical synthesis and for hydrocarbon oligomerization. Progress Report 2016-7. Final report

This is the final report for DE-FG02-08ER15997 with a grant period of 8/15/2008-8/14/2018 (plus 1 year NCE); Program: Basic Energy Sciences; PI: Melanie S. Sanford; co-PI: Adam J. Matzger. The project resulted in 20 publications, 12 supported entirely by this grant and 8 supported substantially by this grant. The overall goals of this project were design catalysts (both homogeneous catalysts and MOF-supported catalysts) to control reactivity and selectivity in energy relevant C–H bond functionalization reactions. The proposed research led to a variety of new catalysts and catalytic processes which are currently finding application in organic synthesis. These efforts were well aligned with the goals of the DOE BES Catalysis Science Program. C–H functionalization reactions have extensive applications in energy-related industries, including petroleum and biofuels processing. The research activities also matched many of the priority areas identified by the Catalysis Science Program, including: investigating problems at the interface of heterogeneous and homogeneous catalysis as a means to derive new catalysts; incorporating 2° interactions to modulate catalyst stability, reactivity, and selectivity; using these new catalysts to tune molecular-level catalytic activity and selectivity; and studying structure-reactivity relationships of inorganic, organic, or hybrid catalytic materials in solution.

02 PETROLEUM↗

DOE OSTI2015

Parallel Programming Models and Systems for High Performance Computing. In: Emerging Research in Cloud Distributed Computing Systems

A parallel programming model is an abstraction of a parallel system that allows expression of both algorithms and shared data structures. To accommodate the diversity in parallel system architectures and user requirements, there are a variety of programming models including the models providing a shared memory view or a distributed memory view of the system. The programming models are implemented as libraries, language extensions, or compiler directives. This chapter provides a discussion on programming models and its implementations aimed at application developers, system software researchers, and hardware architects. The first part provides an overview of the programming models. The second part is an in-depth discussion on high-performance networking interface to implement the programming model. The last part of the chapter discusses implementation of a programming model with a case study. Each part of the chapter concludes with a discussion on current research trends and its impact on future architectures.

Venkata, Manjunath Gorentia↗

DOE OSTI2024

Designing and prototyping extensions to the Message Passing Interface in MPICH

As HPC system architectures and the applications running on them continue to evolve, the MPI standard itself must evolve. The trend in current and future HPC systems toward powerful nodes with multiple CPU cores and multiple GPU accelerators makes efficient support for hybrid programming critical for applications to achieve high performance. However, the support for hybrid programming in the MPI standard has not kept up with recent trends. The MPICH implementation of MPI provides a platform for implementing and experimenting with new proposals and extensions to fill this gap and to gain valuable experience and feedback before the MPI Forum can consider them for standardization. Here, in this work, we detail six extensions implemented in MPICH to increase MPI interoperability with other runtimes, with a specific focus on heterogeneous architectures. First, the extension to MPI generalized requests lets applications integrate asynchronous tasks into MPI’s progress engine. Second, the iovec extension to datatypes lets applications use MPI datatypes as a general-purpose data layout API beyond just MPI communications. Third, a new MPI object, MPIX_Stream, can be used by applications to identify execution contexts beyond MPI processes, including threads and GPU streams. MPIX stream communicators can be created to make existing MPI functions thread-aware and GPU-aware, thus providing applications with explicit ways to achieve higher performance. Fourth, MPIX Streams are extended to support the enqueue semantics for offloading MPI communications onto a GPU stream context. Fifth, thread communicators allow MPI communicators to be constructed with individual threads, thus providing a new level of interoperability between MPI and on-node runtimes such as OpenMP. Lastly, we present an extension to invoke MPI progress, which lets users spawn progress threads with fine-grained control to adapt the communication performance to their application designs. We describe the design and implementation of these extensions, provide usage examples, and highlight their expected benefits with performance results.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

An MLIR-based Compiler Flow for System-Level Design and Hardware Acceleration

The generation of custom hardware accelerators for applications implemented within high-level productive programming frameworks requires considerable manual effort. To automate this process, we introduce \sodaopt, a compiler tool that extends the MLIR infrastructure. \sodaopt automatically searches, outlines, tiles, and pre-optimizes relevant code regions to generate high-quality accelerators through high-level synthesis. \sodaopt can support any high-level programming framework and domain-specific language that interface with the MLIR infrastructure. By leveraging MLIR, \sodaopt solves compiler optimization problems with specialized abstractions. Backend synthesis tools connect to \sodaopt through progressive intermediate representation lowerings. \sodaopt interfaces to a design space exploration engine to identify the combination of compiler optimization passes and options that provides high-performance generated designs for different backends and targets. We demonstrate the practical applicability of the compilation flow by exploring the automatic generation of accelerators for deep neural networks operators outlined at arbitrary granularity and by combining outlining with tiling on large convolution layers. Experimental results with kernels from the PolyBench benchmark show that \sodaopt high-level optimizations improve execution delays of synthesized accelerators up to 60x. We also show that for the selected kernels, our solution outperforms the current of state-of-the art in more than 70% of the benchmarks and provides better average speedup in 55% of them.

Bohm Agostini, Nicolas↗

DOE OSTI2015

An introduction to PYTHIA 8.2

The Pythia program is a standard tool for the generation of events in high-energy collisions, comprising a coherent set of physics models for the evolution from a few-body hard process to a complex multiparticle final state. It contains a library of hard processes, models for initial- and final-state parton showers, matching and merging methods between hard processes and parton showers, multiparton interactions, beam remnants, string fragmentation and particle decays. It also has a set of utilities and several interfaces to external programs. Pythia 8.2 is the second main release after the complete rewrite from Fortran to C++, and now has reached such a maturity that it offers a complete replacement for most applications, notably for LHC physics studies. The many new features should allow an improved description of data.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2016

Designing of smart home automation system based on Raspberry Pi

Locally networked or remotely controlled home automation system becomes a popular paradigm because of the numerous advantages and is suitable for academic research. This paper proposes a method for an implementation of Raspberry Pi based home automation system presented with an android phone access interface. The power consumption profile across the connected load is measured accurately through programming. Users can access the graph of total power consumption with respect to time worldwide using their Dropbox account. An android application has been developed to channelize the monitoring and controlling operation of home appliances remotely. This application facilitates controlling of operating pins of Raspberry Pi by pressing the corresponding key for turning “on” and “off” of any desired appliance. Systems can range from the simple room lighting control to smart microcontroller based hybrid systems incorporating several other additional features. Smart home automation systems are being adopted to achieve flexibility, scalability, security in the sense of data protection through the cloud-based data storage protocol, reliability, energy efficiency, etc.

42 ENGINEERING↗

DOE OSTI2014

Endpoint-based parallel data processing with non-blocking collective instructions in a parallel active messaging interface of a parallel computer

Methods, apparatuses, and computer program products for endpoint-based parallel data processing with non-blocking collective instructions in a parallel active messaging interface (`PAMI`) of a parallel computer are provided. Embodiments include establishing by a parallel application a data communications geometry, the geometry specifying a set of endpoints that are used in collective operations of the PAMI, including associating with the geometry a list of collective algorithms valid for use with the endpoints of the geometry. Embodiments also include registering in each endpoint in the geometry a dispatch callback function for a collective operation and executing without blocking, through a single one of the endpoints in the geometry, an instruction for the collective operation.

97 MATHEMATICS AND COMPUTING↗