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All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Snorri Version 1.0

The software decomposes n-component time-series data into persistence vectors and provide visualizations of various summaries of this information. Persistence vectors are a type of vector, based on multidimensional persistent homology theory, which have magnitudes and directions that reflect dominant trends in the multi-component data. The software is a collection of MATLAB scripts, and thus MATLAB runs the scripts. The master script that calls other scripts is called Snorri. The purpose is thus analysis of time-series data to extract dominant trends or events and to classify the type of event. The software produces characteristic vectors (an average of the persistence vectors), which can have directions that reflect the overall dominant trend in a time-series data set. The MATLAB scripts have been partially converted to the PYTHON language and no do not have the full functionality of the MATLAB and are not fully tested; the python scripts are to be covered under this copyright assertion. Two versions of the PYTHON scripts are included, called: mph25.py and mph38.py, each with their own main.py file.

Callor, Nickolas↗
DOE OSTI2017

Tensor Toolbox for MATLAB v. 3.0

Tensors (also known as multidimensional arrays or N-way arrays) are used in a variety of applications ranging from chemometrics to network analysis. The Tensor Toolbox provides classes for manipulating dense, sparse, and structured tensors using MATLAB's object-oriented features. It also provides algorithms for tensor decomposition and factorization, algorithms for computing tensor eigenvalues, and methods for visualization of results.

Kolda, Tamara↗
DOE OSTI2017

Genten: Software for Generalized Tensor Decompositions v. 1.0.0

Tensors, or multidimensional arrays, are a powerful mathematical means of describing multiway data. This software provides computational means for decomposing or approximating a given tensor in terms of smaller tensors of lower dimension, focusing on decomposition of large, sparse tensors. These techniques have applications in many scientific areas, including signal processing, linear algebra, computer vision, numerical analysis, data mining, graph analysis, neuroscience and more. The software is designed to take advantage of parallelism present emerging computer architectures such has multi-core CPUs, many-core accelerators such as the Intel Xeon Phi, and computation-oriented GPUs to enable efficient processing of large tensors.

Phipps, EricT.↗
DOE OSTI2020

ENSIGN

ENSIGN is a data analytics software package offering a modern unsupervised machine learning solution for scalable discovery in Big Data. The analytics in ENSIGN are based on an advanced mathematical tool called tensor decomposition and they are optimized to run efficiently on a range of computing platforms (from small multicore Desktop platforms to large Supercomputing clusters and novel high-end memory-driven computing platforms such as HPE Superdome Flex). ENSIGN enables the user to extract deep insights from the entirety of massive-scale (100s of Gigabytes or Terabytes scale) multidimensional data. ENSIGN uncovers latent patterns in data without the user having to specify or describe what the patterns are; the user, in the first place, may not even know such patterns existed and that they have to look for such patterns. The insights gained from ENSIGN could be trailheads that can be used as starting points for deeper forensic investigation.

Baskaran, Muthu↗
DOE OSTI2017

Parallel k-means++

A parallelization of the k-means++ seed selection algorithm on three distinct hardware platforms: GPU, multicore CPU, and multithreaded architecture. K-means++ was developed by David Arthur and Sergei Vassilvitskii in 2007 as an extension of the k-means data clustering technique. These algorithms allow people to cluster multidimensional data, by attempting to minimize the mean distance of data points within a cluster. K-means++ improved upon traditional k-means by using a more intelligent approach to selecting the initial seeds for the clustering process. While k-means++ has become a popular alternative to traditional k-means clustering, little work has been done to parallelize this technique. We have developed original C++ code for parallelizing the algorithm on three unique hardware architectures: GPU using NVidia's CUDA/Thrust framework, multicore CPU using OpenMP, and the Cray XMT multithreaded architecture. By parallelizing the process for these platforms, we are able to perform k-means++ clustering much more quickly than it could be done before.

Source record↗
DOE OSTI2015

TabVar: Tabulated Variables

TabVar: A Python library for manipulating datasets in the form of tabulated variables. Tables in tabvar contain many columns representing independent variables, but exactly one distinguished column for the dependent variable. Having a single distinguished column allows a natural lifting of arithmetic operators to tables, much (and in fact fully generalizing) multidimensional array arithmetic. The convenient syntax of whole-table arithmetic, along with the usual operations of filtering and aggregation, and all in the setting of python's interactive REPL allows for rapid exploration of datasets.

Bachan, John↗
DOE OSTI2021

MACAW v1.0

The ability to embed molecules in a numeric space is essential in order to build mathematical and machine-learning models describing molecular properties or other processes affected by molecules. MACAW is a cheminformatic tool that allows embedding small molecules into a multidimensional numeric space. In the embedding, each molecule is assigned a numeric vector that captures information of the molecule in relation to other molecules, and that vector can be used as input to mathematical models. Molecules that are more similar to each other are embedded closer in this numeric space, whereas molecules that are more different are embedded further away. One advantage of the MACAW embedding technology compared to established alterantives is that it is fast and does not require extensive computational resources or expertise. In particular, MACAW embeddings can be used as input to mathematical models without the need for variable cleaning or feature selection, saving time and simplifying their use. On the other hand, MACAW also contains methods to generate new molecules and to recommend new molecules satisfying a desired molecular property. The generation of new molecules can be biased based on an input set of molecules, effectively generating molecular diversity around it. In its turn, MACAW's molecular recommendation tool is a novel method for evolving molecules in silico towards a desired molecular specification. In this method, the biased molecular generator tool is applied iteratively in combination with a molecular selection step. As a result, in each iteration the molecules selected by the software are increasingly closer to the desired specification. Both the molecular generation and the molecular recommendation tools are very fast, efficient, and intuitive to use.

Roger, VincentBlay↗
DOE OSTI2022

ENSIGN

ENSIGN is a data analytics software package offering a modern unsupervised machine learning solution for scalable discovery in Big Data. The analytics in ENSIGN are based on an advanced mathematical tool called tensor decomposition and they are optimized to run efficiently on a range of computing platforms (from small multicore Desktop platforms to large Supercomputing clusters and novel high-end memory-driven computing platforms such as HPE Superdome Flex). ENSIGN enables the user to extract deep insights from the entirety of massive-scale (100s of Gigabytes or Terabytes scale) multidimensional data. ENSIGN uncovers latent patterns in data without the user having to specify or describe what the patterns are; the user, in the first place, may not even know such patterns existed and that they have to look for such patterns. The insights gained from ENSIGN could be trailheads that can be used as starting points for deeper forensic investigation.

Baskaran, Muthu↗
DOE OSTI2023

pnnl/deimos_gui

The DEIMoS Graphical User Interface was created as an interface for DEIMoS: Data Extraction for Integrated Multidimensional Spectrometry. DEIMoS is a Python package to process data from mass spectrometry instrument developed at PNNL.

Oostrom, Marjolein↗
DOE OSTI2022

EMSL-Computing/PeakDecoder

PeakDecoder is a machine learning (ML)-based metabolite identification algorithm for multidimensional mass spectrometry measurements incorporating liquid chromatography (LC) and ion mobility spectrometry (IM) separations, and collecting extensive fragmentation spectra with data-independent acquisition (DIA) methods: LC-IM-DIA-MS. The algorithm learns to distinguish true co-elution and co-mobility from raw data and calculates metabolite identification error rates.

Bilbao Pena, Aivett↗
DOE OSTI2025

pnnl/idpp_rtp

IdPP is a Python package that provides a framework for the curation and analysis of molecular properties from multidimensional mass spectrometry (MS) measurements. The main components of the package are organized around a molecular property database and identification probability analysis

Ross, Dylan [Pacific Northwest National Laboratory↗
DOE OSTI2020

Greenhouse gases, Regulated Emissions, and Energy use in Technologies Model ® (2020 Excel)

To fully evaluate energy and emission impacts of advanced vehicle technologies and new transportation fuels, the fuel cycle from wells to wheels and the vehicle cycle through material recovery and vehicle disposal need to be considered. Sponsored by the U.S. Department of Energy's Office of Energy Efficiency and Renewable Energy (EERE), Argonne has developed a full life-cycle model called GREET (Greenhouse gases, Regulated Emissions, and Energy use in Technologies). It allows researchers and analysts to evaluate various vehicle and fuel combinations on a full fuel-cycle/vehicle-cycle basis. The first version of GREET was released in 1996. Since then, Argonne has continued to update and expand the model. GREET is developed as a multidimensional spreadsheet model in Microsoft Excel. It provides a comprehensive, life-cycle-based approach to compare the energy use and emissions of conventional and advanced vehicle technologies. It includes two sub-models named Fuel-Cycle Model (GREET 1, contains data on fuel cycles and vehicle operations) and Vehicle-Cycle Model (GREET 2, evaluates the energy and emission effects associated with vehicle material recovery and production, vehicle component fabrication, vehicle assembly, and vehicle disposal/recycling). This public domain model is available free of charge for anyone to use.

Wang, Michael↗
DOE OSTI2021

Greenhouse gases, Regulated Emissions, and Energy use in Technologies Model ® (2021 Excel)

To fully evaluate energy and emission impacts of advanced vehicle technologies and new transportation fuels, the fuel cycle from wells to wheels and the vehicle cycle through material recovery and vehicle disposal need to be considered. Sponsored by the U.S. Department of Energy's Office of Energy Efficiency and Renewable Energy (EERE), Argonne has developed a full life-cycle model called GREET (Greenhouse gases, Regulated Emissions, and Energy use in Technologies). It allows researchers and analysts to evaluate various vehicle and fuel combinations on a full fuel-cycle/vehicle-cycle basis. The first version of GREET was released in 1996. Since then, Argonne has continued to update and expand the model. GREET is developed as a multidimensional spreadsheet model in Microsoft Excel. It provides a comprehensive, life-cycle-based approach to compare the energy use and emissions of conventional and advanced vehicle technologies. It includes two sub-models named Fuel-Cycle Model (GREET 1, contains data on fuel cycles and vehicle operations) and Vehicle-Cycle Model (GREET 2, evaluates the energy and emission effects associated with vehicle material recovery and production, vehicle component fabrication, vehicle assembly, and vehicle disposal/recycling). This public domain model is available free of charge for anyone to use.

Wang, Michael↗
DOE OSTI2022

Greenhouse gases, Regulated Emissions, and Energy use in Technologies Model ® (2022 Excel)

To fully evaluate energy and emission impacts of advanced vehicle technologies and new transportation fuels, the fuel cycle from wells to wheels and the vehicle cycle through material recovery and vehicle disposal need to be considered. Sponsored by the U.S. Department of Energy's Office of Energy Efficiency and Renewable Energy (EERE), Argonne has developed a full life-cycle model called GREET (Greenhouse gases, Regulated Emissions, and Energy use in Technologies). It allows researchers and analysts to evaluate various vehicle and fuel combinations on a full fuel-cycle/vehicle-cycle basis. The first version of GREET was released in 1996. Since then, Argonne has continued to update and expand the model. GREET is developed as a multidimensional spreadsheet model in Microsoft Excel. It provides a comprehensive, life-cycle-based approach to compare the energy use and emissions of conventional and advanced vehicle technologies. It includes two sub-models named Fuel-Cycle Model (GREET 1, contains data on fuel cycles and vehicle operations) and Vehicle-Cycle Model (GREET 2, evaluates the energy and emission effects associated with vehicle material recovery and production, vehicle component fabrication, vehicle assembly, and vehicle disposal/recycling). This public domain model is available free of charge for anyone to use.

Wang, Michael↗
DOE OSTI2023

Greenhouse gases, Regulated Emissions, and Energy use in Technologies Model ® (2023 Excel)

To fully evaluate energy and emission impacts of advanced vehicle technologies and new transportation fuels, the fuel cycle from wells to wheels and the vehicle cycle through material recovery and vehicle disposal need to be considered. Sponsored by the U.S. Department of Energy's Office of Energy Efficiency and Renewable Energy (EERE), Argonne has developed a full life-cycle model called GREET (Greenhouse gases, Regulated Emissions, and Energy use in Technologies). It allows researchers and analysts to evaluate various vehicle and fuel combinations on a full fuel-cycle/vehicle-cycle basis. The first version of GREET was released in 1996. Since then, Argonne has continued to update and expand the model. GREET is developed as a multidimensional spreadsheet model in Microsoft Excel. It provides a comprehensive, life-cycle-based approach to compare the energy use and emissions of conventional and advanced vehicle technologies. It includes two sub-models named Fuel-Cycle Model (GREET 1, contains data on fuel cycles and vehicle operations) and Vehicle-Cycle Model (GREET 2, evaluates the energy and emission effects associated with vehicle material recovery and production, vehicle component fabrication, vehicle assembly, and vehicle disposal/recycling). This public domain model is available free of charge for anyone to use.

Wang, Michael↗
DOE OSTI2022

The Influence of Shear on Deep Convection Initiation. Part II: Simulations

Abstract This study evaluates a hypothesis for the role of vertical wind shear in deep convection initiation (DCI) that was introduced in Part I by examining behavior of a series of numerical simulations. The hypothesis states, “Initial moist updrafts that exceed a width and shear threshold will ‘root’ within a progressively deeper steering current with time, increase their low-level cloud-relative flow and inflow, widen, and subsequently reduce their susceptibility to entrainment-driven dilution, evolving toward a quasi-steady self-sustaining state.” A theoretical model that embodied key elements of the hypothesis was developed in Part I, and the behavior of this model was explored within a multidimensional environmental parameter space. Remarkably similar behavior is evident in the simulations studied here to that of the theoretical model, both in terms of the temporal evolution of DCI and in the sensitivity of DCI to environmental parameters. Notably, both the simulations and theoretical model experience a bifurcation in outcomes, whereby nascent clouds that are narrower than a given initial radius R 0 threshold quickly decay and those above the R 0 threshold undergo DCI. An important assumption in the theoretical model, which states that the cloud-relative flow of the background environment V CR determines cloud radius R , is scrutinized in the simulations. It is shown that storm-induced inflow is small relative to V CR beyond a few kilometers from the updraft edge, and V CR therefore plays a predominant role in transporting conditionally unstable air to the updraft. Thus, the critical role of V CR in determining R is validated.

58 GEOSCIENCES↗
DOE OSTI2020

Combining Emergent Constraints for Climate Sensitivity

A method is proposed for combining information from several emergent constraints into a probabilistic estimate for a climate sensitivity proxy Y such as equilibrium climate sensitivity (ECS). The method is based on fitting a multivariate Gaussian PDF for Y and the emergent constraints using an ensemble of global climate models (GCMs); it can be viewed as a form of multiple linear regression of Y on the constraints. The method accounts for uncertainties in sampling this multidimensional PDF with a small number of models, for observational uncertainties in the constraints, and for overconfidence about the correlation of the constraints with the climate sensitivity. Its general form (Method C) accounts for correlations between the constraints. Method C becomes less robust when some constraints are too strongly related to each other; this can be mitigated using regularization approaches such as ridge regression. An illuminating special case, Method U, neglects any correlations between constraints except through their mutual relationship to the climate proxy; it is more robust to small GCM sample size and is appealingly interpretable. These methods are applied to ECS and the climate feedback parameter using a previously published set of 11 possible emergent constraints derived from climate models in the Coupled Model Intercomparison Project (CMIP). The ±2σ posterior range of ECS for Method C with no overconfidence adjustment is 4.3 ± 0.7 K. For Method U with a large overconfidence adjustment, it is 4.0 ± 1.3 K. This study adds confidence to past findings that most constraints predict higher climate sensitivity than the CMIP mean.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Parthenon—a performance portable block-structured adaptive mesh refinement framework

On the path to exascale the landscape of computer device architectures and corresponding programming models has become much more diverse. While various low-level performance portable programming models are available, support at the application level lacks behind. To address this issue, we present the performance portable block-structured adaptive mesh refinement (AMR) framework Parthenon, derived from the well-tested and widely used Athena++ astrophysical magnetohydrodynamics code, but generalized to serve as the foundation for a variety of downstream multi-physics codes. Parthenon adopts the Kokkos programming model, and provides various levels of abstractions from multidimensional variables, to packages defining and separating components, to launching of parallel compute kernels. Parthenon allocates all data in device memory to reduce data movement, supports the logical packing of variables and mesh blocks to reduce kernel launch overhead, and employs one-sided, asynchronous MPI calls to reduce communication overhead in multi-node simulations. Using a hydrodynamics miniapp, we demonstrate weak and strong scaling on various architectures including AMD and NVIDIA GPUs, Intel and AMD x86 CPUs, IBM Power9 CPUs, as well as Fujitsu A64FX CPUs. At the largest scale on Frontier (the first TOP500 exascale machine), the miniapp reaches a total of 1.7 × 10 13 zone-cycles/s on 9216 nodes (73,728 logical GPUs) at [Formula: see text] weak scaling parallel efficiency (starting from a single node). In combination with being an open, collaborative project, this makes Parthenon an ideal framework to target exascale simulations in which the downstream developers can focus on their specific application rather than on the complexity of handling massively-parallel, device-accelerated AMR.

97 MATHEMATICS AND COMPUTING↗