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DOE OSTI2022

Autonomous continuous flow reactor synthesis for scalable atom-precision

With new instrumentation design, robotics, and in-operando hyphenated analytical tool automation, the intelligent discovery of synthesis pathways is becoming feasible. It can potentially bridge the gap for the scale-up of new materials. In this article, we review current progress and describe a new system that uses an autonomous continuous flow chemistry framework to translate high-quality lead molecules and materials to quantities that can meet scalability demands. At the core is a continuous flow synthesis platform that can design its viable synthesis pathway to a particular molecule or material and then autonomously carry it out. This is realized by integrating: (1) A workflow/architecture for multimode chemical/materials characterization in-line. The in-line characterization modes are NMR, ESR, IR, Raman, UV-Vis, GC-MS, and HPLC, along with ex-situ modes for X-Ray and neutron scattering; (2) Integration for feedback/analysis/data storage of the control variables; (3) A core software stack that includes deep learning and reinforcement learning alongside quantum chemistry and molecular dynamics; (4) On-demand compute architectures that parse calculations to compute resources needed which include light-weight edge, mid-level edge (NVIDA DGX-2), and high-performance computing. We demonstrate preliminary results on how this autonomous reactor system can enhance our ability to deliver deuterated materials, copolymers, and site-substituted molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Improving Gas Reactor Design with Complex Non-Standard Reaction Mechanisms in a Reactive Flow Model

Fluorinated gases are critical to a number of high-technology industries including semiconductor manufacturing and related processes such as flat panel display, LED, and photovoltaic manufacturing. These fluorinated gases have very high global warming potentials (GWPs) and, unfortunately are chemically very stable, in some cases lasting for thousands of years in the atmosphere. For environmental reasons, it is imperative that the release of these gases be minimized, but existing methods to destroy them requires a significant amount of energy. The goal of this project was to develop a more energy efficient method of destroying these high GWP gases using computational fluid dynamics, but the computational requirements are significant. In this project, we bring together resources available at the national labs, including high-performance computing hardware and modern computational methods, in order to explore an industrially important problem with key environmental and economic impact. In this project, we examined the state-of-the-art models for the physical processes involved, and made subtle changes to arrive at alternative formulations considerably better suited for computation and study. We examined several representative scenarios and developed a set of analyses techniques and tools that could be used to explore the systems in much greater detail. This exploratory project has demonstrated to ALZETA that HPC can indeed provide a unique view into their complex engineering problem - one that is simply inaccessible by any other means. The tools allow us to explore the details of the chemical process, and allow one to construct "what-if" scenarios to address shortcomings of the physical device in its current operating modes. However, as with many sources of completely new information, many new questions are illuminated with this capability. It will take considerable time, effort and experience before we learn to probe the solutions, pose operating scenarios and confirm modifications to the device that lead to real engineering advances.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Computational Math Problems for a Clean Energy Future

Cutting edge computational mathematics are ubiquitous in renewable energy research. Problems in resilient and reliable electric grid operations, infrastructure planning, wind farm yaw control, and more demand sophisticated and scalable computational tools that enable the transition of renewable energy technologies from proof of concept to deployment into our energy system. The mission of the Computational Science Center at NREL is to lead the lab's efforts to solve energy challenges using high-performance computing (HPC), computational science, applied mathematics, scientific data management, visualization, and informatics. In this poster, we provide a short overview of three areas of computational mathematics research at NREL: wind power scenario generation for stochastic grid operations and infrastructure planning, improved rational function approximations for electromagnetic transients codes, and wind farm yaw control using a combination of the Alternating Direction Method of Multipliers (ADMM) and reinforcement learning (RL). Increasing penetrations of renewable energy into power grids motivate the investigation of new approaches to characterizing uncertainty for five-minute economic dispatch problems. Similarly, as the penetration of distributed energy resources on power grids increases, it becomes important to revisit our methods of modelling transient phenomena, i.e. electromagnetic transients programs. Finally, the combination of ADMM and RL for wind farm yaw control presented here can potentially increase the efficiency of the deployed distributed controllers by orders of magnitude.

ADMM↗

DOE OSTI2018

GASNet-EX: A High-Performance, Portable Communication Library for Exascale

Partitioned Global Address Space (PGAS) models, typified by such languages as Unified Parallel C (UPC) and Co-Array Fortran, expose one-sided communication as a key building block for High Performance Computing (HPC) applications. Architectural trends in supercomputing make such programming models increasingly attractive, and newer, more sophisticated models such as UPC++, Legion and Chapel that rely upon similar communication paradigms are gaining popularity. GASNet-EX is a portable, open-source, high-performance communication library designed to efficiently support the networking requirements of PGAS runtime systems and other alternative models in future exascale machines. The library is an evolution of the popular GASNet communication system, building upon over 15 years of lessons learned. We describe and evaluate several features and enhancements that have been introduced to address the needs of modern client systems. Microbenchmark results demonstrate the RMA performance of GASNet-EX is competitive with several MPI-3 implementations on current HPC systems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

Final Technical Report: Integrated Distribution-Transmission Analysis for Very High Penetration Solar PV

Transmission and distribution simulations have historically been conducted separately, echoing their division in grid operations and planning while avoiding inherent computational challenges. Today, however, rapid growth in distributed energy resources (DERs)--including distributed generation from solar photovoltaics (DGPV)--requires understanding the unprecedented interactions between distribution and transmission. To capture these interactions, especially for high-penetration DGPV scenarios, this research project developed a first-of-its-kind, high performance computer (HPC) based, integrated transmission-distribution tool, the Integrated Grid Modeling System (IGMS). The tool was then used in initial explorations of system-wide operational interactions of high-penetration DGPV.

14 SOLAR ENERGY↗

NASA NTRS1992

Future directions in computing and CFD

In recent years CFD on massively parallel machines has become a reality. This paper summarizes some recent trends both in high performance computing, and in CFD using parallel machines. The long term computational requirements for accomplishing some of the large scale problems in computational aerosciences, and current hardware and architecture trends are discussed. Performance results obtained from the implementation of some CFD applications on the Connection Machine CM-2 and the Intel iPSC/860 at NASA Ames Research Center are presented. It is argued that only massively parallel machines will be able to meet these grand challenge requirements.

Bailey, F. R.↗

DOE OSTI2025

Generic Discretization Library

The GenDiL library is a collection of C++ software abstractions designed to discretize and solve partial differential equations (PDEs) for high-performance computing (HPC) applications. Its primary focus is on modern C++ generic programming, which helps ensure portability across various hardware architectures. The central idea behind the library is to provide building blocks for numerical algorithms-such as discretization methods and iteration patterns-so that domain experts can focus on the math, rather than the low-level details of hardware or implementation. By defining abstractions for data types, iteration over computational grids, and scheduling of operations, the library isolates the high-level PDE algorithms from the platform-specific optimizations needed to achieve efficient performance.

Dudouit, Yohann [Lawrence Livermore National Labor↗

DOE OSTI2013

OpenMSI: A High-Performance Web-Based Platform for Mass Spectrometry Imaging

Mass spectrometry imaging (MSI) enables researchers to directly probe endogenous molecules directly within the architecture of the biological matrix. Unfortunately, efficient access, management, and analysis of the data generated by MSI approaches remain major challenges to this rapidly developing field. Despite the availability of numerous dedicated file formats and software packages, it is a widely held viewpoint that the biggest challenge is simply opening, sharing, and analyzing a file without loss of information. Here we present OpenMSI, a software framework and platform that addresses these challenges via an advanced, high-performance, extensible file format and Web API for remote data access (http://openmsi.nersc.gov). The OpenMSI file format supports storage of raw MSI data, metadata, and derived analyses in a single, self-describing format based on HDF5 and is supported by a large range of analysis software (e.g., Matlab and R) and programming languages (e.g., C++, Fortran, and Python). Careful optimization of the storage layout of MSI data sets using chunking, compression, and data replication accelerates common, selective data access operations while minimizing data storage requirements and are critical enablers of rapid data I/O. The OpenMSI file format has shown to provide >2000-fold improvement for image access operations, enabling spectrum and image retrieval in less than 0.3 s across the Internet even for 50 GB MSI data sets. To make remote high-performance compute resources accessible for analysis and to facilitate data sharing and collaboration, we describe an easy-to-use yet powerful Web API, enabling fast and convenient access to MSI data, metadata, and derived analysis results stored remotely to facilitate high-performance data analysis and enable implementation of Web based data sharing, visualization, and analysis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Scaling Ensembles of Data-Intensive Quantum Chemical Calculations for Millions of Molecules

Deep learning models are efficient computational tools that can accelerate the inverse design of molecules with desired functional properties by generating predictions at a fraction of the time required by traditional quantum chemical approaches. To ensure that a model maintains accuracy and transferability across broad regions of the chemical space explored during the inverse design, it must be trained on massively large volumes of simulation data. This requires running large-scale ensemble quantum chemical calculations on high-performance computing (HPC) systems for data collection. However, the efficient execution of such large ensemble calculations and the management of large volumes of output data require tools that can judiciously utilize computational resources and manage metadata overhead on the file system. Therefore, we present a high-performance, scalable, ensemble management framework for performing data-intensive quantum chemical electronic structure calculations for organic molecules. This framework provides abstractions to plug different ab initio, first principles, and first principles-based semi-empirical methods and executes them efficiently at large scale on HPC systems. It dynamically distributes tasks to resources and uses tiered storage for managing large collections of files. We employed this framework to process over ten million organic molecules and generate open-source datasets that provide UV-vis absorption spectra by running time-dependent density-functional tight-binding calculations. It is the largest database containing molecular optical spectra that were simulated with quantum chemical methods in a consistent manner.

Mehta, Kshitij↗

DOE OSTI2023

Snowmass 2021 Computational Frontier CompF4 Topical Group Report Storage and Processing Resource Access

Computing plays a significant role in all areas of high energy physics. The Snowmass 2021 CompF4 topical group's scope is facilities R&D, where we consider "facilities" as the computing hardware and software infrastructure inside the data centers plus the networking between data centers, irrespective of who owns them, and what policies are applied for using them. In other words, it includes commercial clouds, federally funded High Performance Computing (HPC) systems for all of science, and systems funded explicitly for a given experimental or theoretical program. This topical group report summarizes the findings and recommendations for the storage, processing, networking and associated software service infrastructures for future high energy physics research, based on the discussions organized through the Snowmass 2021 community study.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2015

Evaluating Application Resilience with XRay

The rising count and shrinking feature size of transistors within modern computers is making them increasingly vulnerable to various types of soft faults. This problem is especially acute in high-performance computing (HPC) systems used for scientific computing, because these systems include many thousands of compute cores and nodes, all of which may be utilized in a single large-scale run. The increasing vulnerability of HPC applications to errors induced by soft faults is motivating extensive work on techniques to make these applications more resilient to such faults, ranging from generic techniques such as replication or checkpoint/restart to algorithm-specific error detection and tolerance techniques. Effective use of such techniques requires a detailed understanding of how a given application is affected by soft faults to ensure that (i) efforts to improve application resilience are spent in the code regions most vulnerable to faults and (ii) the appropriate resilience technique is applied to each code region. This paper presents XRay, a tool to view the application vulnerability to soft errors, and illustrates how XRay can be used in the context of a representative application. In addition to providing actionable insights into application behavior XRay automatically selects the number of fault injection experiments required to provide an informative view of application behavior, ensuring that the information is statistically well-grounded without performing unnecessary experiments.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Advancing Science Through Computation at NDSU (Final Report)

The Center for Computationally Assisted Science and Technology (CCAST), a research unit within the Office for the Vice President for Research and Creative Activity, is in its build-out phase at North Dakota State University (NDSU). CCAST is developing high-performance computing (HPC) capabilities, designed to support existing HPC-oriented NDSU programs as well as to support its own research program which will initially concentrate, but not be limited to, application of theory and computation toward development of high-value functional materials and systems for renewable energy and energy efficiency. The following initial priorities for the Center were established: (1) reconstruct the NDSU HPC hardware and software infrastructure, (2) define CCAST research focus, (3) hire research and HPC support staff, (4) fit-out CCAST computer rooms to ensure continuation and growth of the Center’s HPC activities and, (5) support the NDSU existing thrust in chemo- and bio-informatics (as applied to the high-throughput combinatorial chemistry, biology, and genomics). These priorities are subject to change as the Center grows and evolves.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

Variable Precision Computing

This report summarizes the activities and major accomplishments of the Variable Precision Computing Strategic Initiative project. The overarching goal of this project was to initiate and promote a new paradigm in High Performance Computing (HPC) that would fundamentally change how we represent and make use of representations of real numbers in finite precision and that would establish Lawrence Livermore National Laboratory (LLNL) as a leader in precision-related research for HPC. We pursued three integrated and concurrent research thrusts: new, more dynamic data representations to address data motion and capacity limitations; improved mixed precision algorithms to accelerate computation and to leverage new hardware; and new tools to help developers reason about precision and to automate code transformations. Within these thrust areas, we made significant advances in the use of compressed array data types in numerical calculations, in the theoretical justification, in improved performance, and in the prospects of hardware implementation; in the development of metrics to significantly reduce the storage needs of molecular dynamics simulations; in the development and analysis of efficient mixed-precision algorithms for time-dependent partial differential equations and for orthogonal factorization; and in the capability of tools that can analyze sensitivity of computed results to choices in precision and that can make automated code transformations based on such analysis. We established that there are definite opportunities to realize significant improvements in HPC above and beyond the 2x limits of traditional mixed precision using the technologies we have developed. The project produced numerous papers, presentations, and posters in important venues as well as open-source software contributions to the community, and many of the new capabilities have initiated or are being leveraged in ongoing projects.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Portable Software Environment for Ultrahigh-Resolution ELM Development on GPUs

This paper presents our endeavors in developing the large-scale, ultra-high-resolution E3SM Land Model (uELM), specifically designed for exascale computers furnished with accelerators such as Nvidia GPUs. The uELM is a sophisticated code that substantially relies on High-Performance Computing (HPC) environments, necessitating particular machine and software configurations. To facilitate community-based uELM developments employing GPUs, we have created a portable, standalone software environment preconfigured with uELM input datasets, simulation cases, and source code. This environment, utilizing Docker, encompasses all essential code, libraries, and system software for uELM development on GPUs. It also features a functional unit test framework and an offline model testbed for comprehensive numerical experiments. From a technical perspective, the paper discusses GPU-ready container generations, uELM code management, and input data distribution across computational platforms. Lastly, the paper demonstrates the use of environment for functional unit testing, end-to-end simulation on CPUs and GPUs, and collaborative code development.

E3SM Land Model↗

NASA NTRSDate not supplied

Assessment of Edge-Based Viscous Method for Corner-Flow Solutions on Graphics Processing Units

A highly efficient, edge-based viscous (EBV) discretization method has been recently implemented in a practical, unstructured-grid, node-centered, finite-volume flow solver and evaluated for Reynolds-averaged Navier-Stokes (RANS) formulations. In comparison to a well-established cell-based viscous (CBV) method, the EBV method has demonstrated multifold acceleration of all viscous-kernel computations on general unstructured mixed-element grids. The viscous kernels include evaluation of viscous fluxes, diffusion terms in turbulence models, and the corresponding Jacobian terms. In this paper, an EBV implementation of a nonlinear extension of the Spalart-Allmaras turbulence model, SA-neg-QCR2000, is presented and verified. The SA-neg-QCR2000 model is used for simulating turbulent corner flows. Previously reported EBV computations have been conducted on traditional computing architectures based on central processing units (CPU). This paper assesses benefits of the EBV method on modern high-performance computing architectures based on graphics processing units (GPU). The GPU implementations of the CBV and EBV methods are verified by comparing solutions and iterative convergence with those observed in CPU computations on the same grids. A comprehensive assessment of the EBV speedup on CPU and GPU architectures is presented for established benchmark corner flows, namely, a supersonic flow through a long square duct and a subsonic flow around a NASA juncture flow model.

CFD↗

NASA NTRSDate not supplied

Assessment of Edge-Based Viscous Method for Corner-Flow Solutions on Graphics Processing Units

CFD↗

NASA NTRSDate not supplied

Enabling Open and Interoperable Science: Multi-Omics Data Processing Platform with NASA GeneLab Standardized Bioinformatics Workflows for Space and Earth Research

Multi-omics biological data continues to be generated at an astounding pace. Genomics, transcriptomics, metabolomics, and proteomics, or collectively known as multi-omics data, are used to assess biological functions, and provide invaluable insights into human, animal, plant, and environmental health both on Earth and in Space. Despite the abundance of these valuable data, the need for bioinformatics expertise, particularly as it relates to the niche filed of space biology, and a lack of accessible resources for processing these data limit their usefulness in deriving biological insights. The NASA Open Science Data Repository (OSDR) provides access to omics data from various spaceflight and analog studies. To enhance the accessibility and reusability of these data, GeneLab (part of OSDR) designs and implements standardized, community-driven, open-source bioinformatics workflows to transform raw omics data into standardized processed data. Currently, GeneLab-processed data from hundreds of space studies have been reused for meta-analyses. This has led to new insights and scientific publications that extend beyond the initial research, thereby enriching our understanding of molecular-scale biological responses to the space environment. To make these bioinformatics workflows open and accessible, GeneLab teamed up with DOE-funded initiatives, including the National Microbiome Data Collaborative (NMDC), to create the NASA EDGE [Empowering the Development of Genomics Expertise] Bioinformatics web-based platform. NASA EDGE utilizes shared compute resources to run the GeneLab standardized bioinformatics workflows, which eliminates the need for researchers to have their own high performance computing cluster. The web-based platform makes complicated biological analyses incredibly easy to perform, thus expanding the reach of these analyses to bioinformatics novices, students, and even citizen scientists enabling them to contribute to scientific discoveries and progress. The authors will demonstrate how the NASA EDGE platform can be used to process microbial omics data hosted on OSDR as well as user-generated omics datasets using GeneLab’s standard workflows.

Amanda M. Saravia-Butler↗

DOE OSTI2014

Argonne Out Loud: Computation, Big Data, and the Future of Cities

Charlie Catlett, a Senior Computer Scientist at Argonne and Director of the Urban Center for Computation and Data at the Computation Institute of the University of Chicago and Argonne, talks about how he and his colleagues are using high-performance computing, data analytics, and embedded systems to better understand and design cities.

97 MATHEMATICS AND COMPUTING↗