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The software provides machine learning analysis and visualization to detect patterns in epigenetic data, including conventional machine learning and statistical methods, and open-source packages like pyBigWig (https://github.com/deeptools/pyBigWig) for data processing. The software is written in python, it uses some python libraries.
ReNCAT is a software application that suggests microgrid portfolios that reduce the impact of large-scale disruptions to power, as measured by the Social Burden Metric. ReNCAT examines a power distribution network to identify regions that can be isolated into microgrids that enable critical services to be provided even if the remainder of the study area is left without power. ReNCAT operates on a simplified representation of the power grid, one that aggregates and approximates loads and conductors. Microgrids are formed within the power network by setting switch states to split or join portions of the grid. ReNCAT identifies candidate microgrid portfolios with varying tradeoffs between cost and service availability.
Scientific processes rely on software as an important tool for data acquisition, analysis, and discovery. Over the years, sustainable software development practices have made progress in being considered as an integral component of research. However, management of computation-based scientific studies is often left to individual researchers who design their computational experiments based on personal preferences and the nature of the study. Here, we believe that the quality, efficiency, and reproducibility of computation-based scientific research can be improved by explicitly creating an execution environment that allows researchers to provide a clear record of traceability. This is particularly relevant to complex computational studies in high-performance computing (HPC) environments. In this article, we review the documentation required to maintain a comprehensive record of HPC computational experiments for reproducibility. We also provide an overview of tools and practices that we have developed to perform such studies around Flash-X, a multiphysics scientific software.
Multichannel Analysis of Surface Waves (MASW) is a technique frequently used in geotechnical engineering and engineering geophysics to infer 1D layered models of seismic shear wave velocities in the top tens to hundreds of meters of the subsurface. We aim to accelerate MASW calculations by capitalizing on modern computer hardware available in the workstations of most engineers: multiple cores and graphics processing units (GPUs). We propose new parallel and GPU accelerated algorithms for computing 1D MASW inversion, and provide software implementations in C using Message Passing Interface (MPI) and CUDA. These algorithms take advantage of sparsity that arises in the problem, and the work balance between processes considers typical data trends. We compare our methods to an existing open source Matlab MASW tool. Our serial C implementation achieves a 2x speedup over the Matlab software, and we continue to see improvements by parallelizing the problem with MPI. Here we see nearly perfect strong and weak scaling for uniform data, and improve strong scaling for realistic data by repartitioning the problem to process mapping. By utilizing GPUs available on most modern workstations, we observe an additional 1.3x speedup over the serial C implementation on the first use of the method. We typically repeatedly evaluate theoretical dispersion curves as part of an optimization procedure, and on the GPU the kernel can be cached for faster reuse on later runs. We observe a 3.2x speedup on the cached GPU runs compared to the serial C runs. This work is the first open-source parallel or GPU-accelerated software tool for MASW imaging, and should enable geotechnical engineers to fully utilize all computer hardware at their disposal.
Accessible machine learning algorithms, software, and diagnostic tools for energy-efficient devices and systems are extremely valuable across a broad range of application domains. In scientific domains, real-time near-sensor processing can drastically improve experimental design and accelerate scientific discoveries. To support domain scientists, we have developed hls4ml, an open-source software-hardware codesign workflow to interpret and translate machine learning algorithms for implementation with both FPGA and ASIC technologies. We expand on previous hls4ml work by extending capabilities and techniques towards low-power implementations and increased usability: new Python APIs, quantization-aware pruning, end-to-end FPGA workflows, long pipeline kernels for low power, and new device backends include an ASIC workflow. Taken together, these and continued efforts in hls4ml will arm a new generation of domain scientists with accessible, efficient, and powerful tools for machine-learning-accelerated discovery.
This report is on the Forestry Electric Vehicle Energy Routing (FEVER) Tool, a novel software system developed to support heavy-duty electric vehicle (EV) operations in remote, forested, and mountainous regions. The Phase I project aimed to demonstrate the feasibility of modeling EV energy consumption using terrain elevation, road conditions, and route features specific to forestry logistics. The tool combines geographic information systems (GIS), electric motor physics, and vehicle-specific data to calculate feasible, energy-efficient routes. Collaborations with Oregon State University’s Research Forests and Titan Freight Systems enabled collection and validation of GPS and elevation-based trip data. The FEVER Tool offers substantial opportunities for the efficient management of medium- and heavy-duty electric vehicles in sectors like forestry, agriculture, mining, defense and waste management—areas which are beginning to adopt HDEVs. The project demonstrated technical feasibility and lays the groundwork for commercial development and deployment in other industries and environmental conditions in Phase II.
Virtual Reality (VR) offers the opportunity to display data, instrumentation, and experimental setups in three dimensions and gives the user the ability to interact with the objects. This technology moves visualization beyond two-dimensional projections on a flat screen with a fixed field of view in which a keyboard or another similar controller is needed to change the view. Advances in both hardware and software for VR make it possible for the non-expert to develop visualization tools for scientific applications both for viewing and for sharing data or diagnostic hardware between users in three dimensions. Furthermore, this manuscript describes application development using two VR software tools, Unity gaming engine and A-frame, for visualizing data and high energy physics targets.
The New York State Energy Research and Development Authority (NYSERDA) is the owner of the Western New York Nuclear Service Center (WNYNSC), a 1,351-ha site located approximately 48 km south of Buffalo, New York. In 1962, Nuclear Fuel Services, Inc. (NFS) entered into agreements with the Atomic Energy Commission and New York State to construct the first commercial reprocessing plant of nuclear fuel in the United States at the WNYNSC. NFS built and operated the spent fuel reprocessing plant and waste disposal facilities, processing 640 Mg (640 metric tons) of spent nuclear fuel from 1966 to 1972 under an Atomic Energy Commission license. Nuclear fuel reprocessing operations halted in 1972 and never restarted, leaving behind radioactive and chemical wastes. The U.S. Department of Energy (DOE) was required to complete certain waste management activities under the West Valley Demonstration Project (WVDP) Act of 1980 including decommissioning of WVDP facilities. As collaborating agencies, NYSERDA and the DOE are tasked with making decisions about decommissioning and risk reduction for the West Valley Site. Neptune and Company, Inc. (Neptune) was contracted to develop a probabilistic performance assessment (PPA) model to assist the agencies in their decision making process for decommissioning the WVDP and WNYNSC. One important tool that is needed in order to inform the decision-making process is a science-based model of the West Valley Site that evaluates potential future consequences for human health and the environment. This forms the core of the spatial domain of the West Valley PPA Model. The PPA Model, developed using the GoldSim system modeling software, is a tool intended to provide support for decision making that evaluates uncertainty, in a manner that is transparent, defensible, and robust. The PPA Model includes contaminant transport and health effects components, and is organized around geographically-grouped contaminated facilities. These include the waste disposal areas licensed by the U.S. Nuclear Regulatory Commission and the State of New York, a waste tank farm for storage of high level radioactive waste resulting from reprocessing operations, and several areas contaminated with radioactive and chemical constituents. The PPA Model evaluates contaminant transport from these sources to points of exposure across the site and into receiving surface waters and sediments. Hypothetical people and wildlife could be exposed to contamination at these locations, and the effects of these exposures are evaluated. Contaminant transport processes to be evaluated in the PPA Model include groundwater and surface water transport, contaminant translocation by plants and animals, diffusion, and erosion. The evaluation of exposures to people in this preliminary model is limited to a resident farmer scenario, and ecological assessment is performed at the level of a screening analysis. The results of these preliminary evaluations inform future model developments. PPA Model results are subjected to sensitivity analysis in order to determine those pathways and parameters that are most significant in influencing the results. This information allows analysts and decision makers to focus on those aspects of Site behavior and processes. With this information, the decision makers can drive informed, defensible decisions regarding decommissioning of the Site. This paper includes an update of the information presented at WM2019 [1]. (authors)
This was a collaborative effort between Lawrence Livermore National Security, LLC as manager and operator of Lawrence Livermore National Laboratory (LLNL) and Siemens Energy, Inc. (Siemens) to develop a wind resource forecasting tool. LLNL was to develop an independent high-resolution mesoscale modeling capability forecasting tool that could be implemented in conjunction with existing wind farm control and monitoring software to provide forecasting of wind resources using local observations of winds and temperature. Research with LLNL’s state-of-the-art large-eddy simulation meteorological prediction model, based on the community WRF model and innovative turbulence parameterizations, would improve that model’s applicability to large wind farms offshore and in complex terrain. The modeling capability would include uncertainty quantification. Finally, the application of the modeling tool and existing global climate change predictions would enable the delineation of the likely effects of climate change on wind resources. Siemens was to provide high time resolution hub-height wind speed and other meteorological data streams, including temperature profiles from wind farms, for LLNL to incorporate into the modeling system, to validate and tune this forecasting model for their locations of interest. These data streams would also be used for longer-term studies of correlations of wind resources to climate oscillations to indicate how long-term climate change trends may affect the available wind resource. Siemens would also provide information and observations of turbine wakes for incorporation into the modeling tool. By implementing state-of-the-art turbulence parameterizations into a simulation model and/or ensembles of simulation models, and by integrating real-time hub height wind speed and other meteorological datastreams from wind farms into that model or ensemble of models, LLNL would develop a forecasting tool that could be implemented by Siemens as an add-on to existing wind farm control and monitoring software to provide owners with useful resource forecasting. The desired outcome was that the accuracy level of the output would be sufficient to substantiate power output commitments. The final deliverable for this work would consist of a document outlining the algorithms and software tools that could be integrated into Siemens Wind Park Supervisor.
The Building Efficiency Targeting Tool for Energy Retrofits (BETTER) V.1.0 web application identifies cost-saving energy and emissions reductions in buildings and portfolios, without site visits or complex modeling. With minimal data entry, BETTER benchmarks a building's or portfolio's energy use against peers; quantifies energy, cost, and greenhouse gas (GHG) reduction potential; and recommends energy efficiency measures for individual buildings or portfolios, targeting specific energy savings levels. The source code of BETTER's modular, cross-platform analytical engine has previously been disclosed (2019-001) and is available on GitHub and can be adopted, redeveloped, and redistributed freely under an open-source license, allowing users to incorporate BETTER's analytical capabilities into their own software platforms and tools. The BETTER V.1.0 web application, developed with the Django web-framework and the Model-View-Controller (MVC) architecture being disclosed here, provides a graphical user interface (GUI) for any user to view the software tutorials, download and upload a data entry template, configure and run the BETTER analyses, and view the final analytical reports.
The Deep Underground Neutrino Experiment (DUNE) will be theworld’s foremost neutrino detector when it begins taking data in the mid-2020s.Two prototype detectors, collectively known as ProtoDUNE, have begun tak-ing data at CERN and have accumulated over 3 PB of raw and reconstructeddata since September 2018. Particle interaction within liquid argon time projec-tion chambers are challenging to reconstruct, and the collaboration has set upa dedicated Production Processing group to perform centralized reconstructionof the large ProtoDUNE datasets as well as to generate large-scale Monte Carlosimulation. Part of the production infrastructure includes workflow manage-ment software and monitoring tools that are necessary to eciently submit andmonitor the large and diverse set of jobs needed to meet the experiment’s goals.We will give a brief overview of DUNE and ProtoDUNE, describe the varioustypes of jobs within the Production Processing group’s purview, and discuss thesoftware and workflow management strategies are currently in place to meetexisting demand. We will conclude with a description of our requirements in aworkflow management software solution and our planned evaluation process.
The project seeks to develop tools and techniques to help software developers verify the correctness and accuracy of their code. The target domain is scientific software of the kind widely used and developed in the Department of Energy research community, with a particular focus on "extreme scale" programs - those that are expected to involve possibly millions of parallel threads of execution. The report covers the University of Delaware contribution to the collaborative project. The project had a number of successful outcomes, especially regarding the development and extension of the CIVL software verification framework. CIVL is a verification tool for C or Fortran programs that use MPI, OpenMP, CUDA, and/or Pthreads for parallelization. CIVL went through vast improvements and extensions, and was successfully applied to a number of challenging codes. It found a subtle bug in the Devito PDE framework. It was able to verify the functional correctness of a conjugate gradient solver using a novel probabilistic technique with vanishingly small chance of error. CIVL was used very successfully in verification competitions, and the CIVL solutions to the competition challenges were presented and published. CIVL was also used successfully by other researchers on a computational chemistry kernel.
Software is an increasingly important component in the pursuit of scientific discovery. Both its development and use are essential activities for many scientific teams. At the same time, very little scientific study has been conducted to understand, characterize, and improve the development and use of software for science. Computational science teams have diversified over time to include contributions from domain scientists who provide expertise in scientific and engineering disciplines, applied mathematicians and computer scientists who provide optimal algorithms and data structures, and software and data engineers who provide methodologies and tools adapted and adopted from other software domains. These diverse contributions have enabled tremendous advances in the pursuit of scientific discovery, even as models, computer architectures, and software environments have become more complicated. With this increasing diversity, we believe the next opportunity for qualitative improvement comes from applying the scientific method to understanding, characterizing, and improving how scientific software is developed and used. We believe that this pursuit requires expertise from computational scientists themselves, and from the cognitive and social sciences as well as the software engineering research community. As we look to increase the productivity and sustainability of the scientific-software-development-and-use cycle, a more systematic application of the scientific method to understand processes for software development and use will be a valuable tool to guide future work and result in more usable and sustainable software. This workshop will bring together computer scientists, software engineering researchers, computational scientists, applied mathematicians, social scientists, cognitive scientists, and others, to explore how we can conduct such systematic investigations, what can be learned, and how doing so will benefit the scientific enterprise. The workshop will be structured around a set of breakout sessions, with every attendee expected to participate actively in the discussions. Afterward, workshop attendees — from DOE, industry, and academia — will produce a report for ASCR that summarizes the findings of the workshop.
Functional layered material (LM) architectures will dominate nanomaterials science in this century. We have developed theory, modeling, simulation, and software and data tools that enhance understanding and AI guide synthesis, enable characterization of complex structures, and improve capabilities in the predictive design and growth of LMs. Research at the Center has focused on: Computational synthesis and characterization: AI guided synthesis and experimental synthesis of stacked LMs with tailored properties via optimized chemical vapor deposition (CVD) growth and liquid-phase exfoliation; study defects, edges, grain boundaries, wrinkling of atomic layers and their effects on chemical, mechanical, electrical, and optical properties. Far-from-equilibrium processes: Joint experimental and simulation based probe of electronic processes with NAQMD and ultrafast X-ray free-electron laser (XFEL) and ultrafast electron diffraction (UED) facilities at Stanford. Experimentally validate NAQMD by ultrafast electron diffraction and X-ray spectroscopy studies of structural and excited state dynamics, shape fluctuations, and phonon dynamics. Scalable software: Simulation engines for desktop-to-exascale platforms using low-overhead, linear-scaling QMD algorithms; divide-conquer-recombine NAQMD with electronic excitations; extended-Lagrangian reactive molecular dynamics (RMD), machine learning (ML) based neural-network quantum molecular dynamics (NNQMD), and super-state accelerated molecular dynamics (AMD) and kinetic Monte Carlo codes; thermal and electrical transport software; and design 3D architectures of LMs with desired functionality using scalable software. Distribution of software and data, and training: Software and simulation-experimental data generated within the Center are distributed to the materials science community via Berkeley Materials Project (MP) framework. We have also organized three workshops for software distribution and training at USC (Nov. 2017, Mar. 2018) and Gaithersburg, MD (Nov. 2018) to train researchers, with the last one in focused on underrepresented groups, in collaboration with Howard University which is one of the largest HBCUs. The Center supported a total of 46 personnel and 6 undergraduate students. These include 14 faculty, 11 postdoctoral research associates, 20 graduate research assistants, and mentored 6 undergraduate students. This resulted in the publications of 63 research papers that include 46 publications on Reactive and Quantum Dynamics Simulations, 13 publications on Machine Learning for Quantum Materials, and 4 publications on Quantum Computing.
This SBIR effort was focused on developing a production ready system to address the integration and interoperability challenges with analysis and visualization in fusion simulations. Our overarching technical objective was to minimize the code development simulation scientists incur when coupling their simulation codes with different analysis frameworks. To this end, we developed an open-source software library to make data exchange between application easier and a Web application to manage and display analysis extracts from simulations. We have also augmented existing libraries funded by DOE such as ADIOS and VTK-m. When used together, these make it significantly easier to integrate simulation and analysis capability. We demonstrated the flexibility of our approach using two common simulation codes in the fusion community, XGC1 and GTC.
This report describes a tool for three dimensional, high fidelity, coupled electro-chemo-thermo-mechanical modeling of solid-state batteries. A complete version of the tool is available as open source software at https://github.com/hugary1995/eel.git. The theoretical framework of the tool revolves around an inf-sup statement on a total potential, comprising the Helmholtz free energy, the electrical kinetic potential, the chemical potential, the Fourier potential, the chemical reaction potential, and the external power expenditure. The tool uses the finite element framework of Multiphysics Object-Oriented Simulation Environment (MOOSE) and a variational formulation to solve the boundary value problem for solid-state battery incorporating the full set of multiphysics couplings. The variational formulation also enables a modular software architecture for the tool so additional physics can be easily included by specifying the new contribution to the total potential. The report discusses several method of manufactured solutions that were used to verify the implementation of different physics and the Butler-Volmer reaction kinetics at the electrolyte-electrode interface. Finally, the report discusses results from complete charge/discharge simulations of a quasi-1D and a 3D solid-state battery.
Abstract Hydrological models often involve constitutive laws that may not be optimal in every application. We propose to replace such laws with the Kolmogorov‐Arnold networks (KANs), a class of neural networks designed to identify symbolic expressions. We demonstrate KAN's potential on the problem of baseflow identification, a notoriously challenging task plagued by significant uncertainty. KAN‐derived functional dependencies of the baseflow components on the aridity index outperform their original counterparts; they demonstrate that water availability, rather than potential evapotranspiration, drives baseflow by constraining actual evapotranspiration under arid conditions. On a test set, they increase the Nash‐Sutcliffe efficiency (NSE) by 65%, decrease the root mean squared error by 29%, and increase the Kling‐Gupta efficiency by 34%. This superior performance is achieved while reducing the number of fitting parameters from three to two. Next, we use data from 378 catchments across the continental United States to refine the water‐balance equation at the mean‐annual scale. The KAN‐derived equations based on the refined water balance outperform both the current aridity index model, with up to a 105% increase in NSE, and the KAN‐derived equations based on the original water balance. While the performance of our model and tree‐based machine learning methods is similar, KANs offer the advantage of simplicity and transparency and require no specific software or computational tools. This case study focuses on the aridity index formulation, but the approach is flexible and transferable to other hydrological processes. Plain Language Summary Equations used in hydrologic model are often suboptimal, resulting in reduced prediction accuracy and efficiency. We implemented Kolmogorov‐Arnold networks (KAN), a machine learning algorithm for deriving symbolic formulations, to estimate groundwater recharge and showed that it outperforms an existing state‐of‐the‐art semi‐empirical formulation. In hydrology, Nash‐Sutcliffe efficiency (NSE), root mean squared error (RMSE), and Kling‐Gupta efficiency (KGE) are commonly used to evaluate model performance. Higher NSE and KGE values indicate better performance, while lower RMSE values are preferable. Our results show that NSE increased by 71%, RMSE decreased by 32%, and KGE improved by 25%. In addition, KAN identifies an optimal functional form and can be used to derive new analytical formulas using the prior knowledge. The KAN‐inspired equation outperformed the original formulation and reduced the fitting parameters. Furthermore, we refined the water‐balance equation at the mean‐annual scale and showed that, based on the new water‐balance equation, KAN can derive new formulations that are superior to the original aridity index formulations (up to 105% increase in NSE) and KAN‐derived equations based on the original water balance. These findings highlight the significant potential of KAN to advance the scientific understanding of a wide range of hydrologic processes. Key Points Kolmogorov‐Arnold networks (KANs) enhance interpretability of machine‐learned hydrological models KAN‐derived symbolic formulations outperform state‐of‐the‐art semi‐empirical aridity indices KAN‐identified functional form yields an analytical index with fewer fitting parameters and improved performance
This software uses AI tools for enhanced functional imaging using Lorentz transmission electron microscopy by retrieving phase shift at higher spatial resolution, and under noisy conditions. This is a companion code for a publication that is currently being submitted (APT # 164160).