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Optimizing the Energy Usage and Cognitive Value of Extreme-Scale Data-Analysis Approaches

This report serves as a record that we have successfully completed work on the proposal Optimizing the Energy Usage and Cognitive Value of Extreme Scale Analysis Approaches, or, more succinctly, ECX. This includes successful completion of all three phases of the project, findings as summarized below, strong publications across the fields represented in the proposal, and a set of artifacts (code, websites, and other documentation) available to the public. In total, the results of this project represent significant findings in each domain, and a toolkit that will allow the community to engage with this work, advancing it and contributing to it in the years ahead. They also form the basis for a successfully funded follow-on project.

97 MATHEMATICS AND COMPUTING↗

Using XR for Improving Scientific Discovery With Numerical Weather Models

Earth science (ES) digital twins will help us understand the complex interactions and interrelationships that make up our Earth system and the impacts of earth science phenomena on it. Our work addresses two underdeveloped areas in current ES digital twin work: improving the understanding and interaction with ES model outputs by using Virtual and Mixed Reality (XR) tools and improving the non-intuitive mapping of continuous ES natural phenomena to gridded reference frames in current numerical models. Traditionally, scientists working on ES view and analyze the results of calculated or measured observables with static 1-dimensional (1D), 2D or 3D plots displayed on flat computer screens or paper. Using such limited mediums, it can be very difficult to identify, track and understand the evolution of key features due to poor viewing angles and the nature of flat computer screens. In addition, numerical models, such as the NASA Goddard Earth Observing System (GEOS) ES model, are almost exclusively formulated, visualized and analyzed in an Eulerian reference frame with fixed grid points in space and time. However, ES phenomena such as convective clouds, hurricanes and wildfire smoke plumes are visualized and analyzed in a Lagrangian reference frame: therefore it is often difficult and unnatural to understand these phenomena in relation to each other, visualized either in an Eulerian or Lagrangian context. In 3D visualizations, data generally takes one of three forms: gridded (e.g., voxelized) data, where space is divided into regions; point clouds, where data is represented as a set of points; and meshes, where objects are rendered as surfaces composed of small polygons (usually triangles). A gridded, Eulerian reference frame has been the default representation for the 2D visual analysis of atmospheric data in part because the numerical methods used to generate atmospheric model data in the first place use a gridded approach, with equations defining the relationships between the physical variables in each of a grid's cells across successive timesteps. In our work, we are particularly interested in data from GEOS. Another reason why gridded representations tend to be used for visualizing data from such models is because trajectories are difficult to interpret from representations on 2D surfaces, due to line-of-sight ambiguity. Instead of a fixed grid from GEOS, we embed a trajectory model to simulate particles' movement throughout a GEOS run. We then ingest these particle trajectories as animated point clouds with a NASA open source XR toolkit, the Mixed Reality Exploration Toolkit (MRET), and merge GEOS data with ES phenomena data onto one combined visualization that the user can intuitively interact with. Efficient rendering of arbitrarily large point clouds is an ongoing challenge being addressed by the computer science community, with the GPU-based optimizations and efficient GPU memory utilization a common theme of recent advances, especially for XR, where sustained high frame rate is mandatory to save the user from suffering due to simulation sickness. In this work, we describe and evaluate our progress in choosing and implementing appropriate methods for rendering arbitrarily large point clouds within MRET for XR. While tracking the XR headset enables the immersion of a user within a 3D scene of a data visualization, tracking of XR handheld controllers or user’s hands enables us to implement intuitive user interactions with the visualized datasets. Conventional tools require a user working with an ES visualization to conduct many interactions to commit their intended selections or manipulations with a visualized dataset; for example to specify a set of points in 3D space. Doing so in a 2D flat screen interface has traditionally required specifying a set of points in three distinct 2D coordinate systems (XY, XZ, and YZ), which is cumbersome. In other scientific domains, it has been shown that specifying or selecting a location or volume in XR using handheld controllers or tracked hands allows for greater speed and accuracy. We anticipate the same will hold true for atmospheric data, and we will share initial results of measuring the utility of such an interface. Notably, as the data being visualized is generated by GEOS as a prediction based on initial conditions, an intended application of our tool is to serve as part of an iterative feedback loop. Through XR, a scientist will review and manipulate a GEOS model run, modifying the conditions as needed to do subsequent runs of GEOS. Thereby, XR-based improvements to speed and accuracy of 3D tagging of points minimizes the effort required by both the scientist and the computer cluster conducting the necessary calculations.

Thomas Grubb↗

Evaluation of Portable Programming Models to Accelerate LArTPC Detector Simulations

The Liquid Argon Time Projection Chamber (LArTPC) technology is widely used in high energy physics experiments, including the upcoming Deep Underground Neutrino Experiment (DUNE). Accurately simulating LArTPC detector responses is essential for analysis algorithm development and physics model interpretations. Accurate LArTPC detector response simulations are computationally demanding, and can become a bottleneck in the analysis workflow. Compute devices such as General-Purpose Graphics Processing Units (GPGPUs) have the potential to substantially accelerate simulations compared to traditional CPU-only processing. The software development for these compute accelerators often carries the cost of specialized code refactorization and porting to match the target hardware architecture. With the rapid evolution and increased diversity of the computer architecture landscape, it is highly desirable to have a portable solution that also maintains reasonable performance. We report our ongoing effort in evaluating Kokkos as a basis for this portable programming model using LArTPC simulations in the context of the Wire-Cell Toolkit, a C++ library for LArTPC simulations, data analysis, reconstruction and visualization.

47 OTHER INSTRUMENTATION↗

Fat Crayon Toolkit

The Fat Crayon Toolkit (FCT) provides python modules for assisting in the design and visualization of boreholes and tunnels and their relationship with natural features such as fractures. Distances of closest approach among the boreholes can be calculated, along with other key design metrics. Additionally, the shear propensity of natural fractures (either deterministic or stochastic) can be visualized in either 3D (as VTK files) or in 2D (stereonets). The example provided demonstrates a test bed developed for the Enhanced Geothermal Systems (EGS) Collab project. This material is based upon work supported by the Geothermal Office of the Department of Energy and the Sanford Underground Research Facility and was prepared by LLNL under Contract DE-AC52-07NA27344.

Morris, JosephP.↗

Remote Visualization and Remote Collaboration On Computational Fluid Dynamics

A new technology has been developed for remote visualization that provides remote, 3D, high resolution, dynamic, interactive viewing of scientific data (such as fluid dynamics simulations or measurements). Based on this technology, some World Wide Web sites on the Internet are providing fluid dynamics data for educational or testing purposes. This technology is also being used for remote collaboration in joint university, industry, and NASA projects in computational fluid dynamics and wind tunnel testing. Previously, remote visualization of dynamic data was done using video format (transmitting pixel information) such as video conferencing or MPEG movies on the Internet. The concept for this new technology is to send the raw data (e.g., grids, vectors, and scalars) along with viewing scripts over the Internet and have the pixels generated by a visualization tool running on the viewer's local workstation. The visualization tool that is currently used is FAST (Flow Analysis Software Toolkit).

Watson, Val↗

Evaluation of Portable Programming Models to Accelerate LArTPC Detector Simulations

The Liquid Argon Time Projection Chamber (LArTPC) technology is widely used in high energy physics experiments, including the upcoming Deep Underground Neutrino Experiment (DUNE). Accurately simulating LArTPC detector responses is essential for analysis algorithm development and physics model interpretations. Accurate LArTPC detector response simulations are computationally demanding, and can become a bottleneck in the analysis workflow. Compute devices such as General-Purpose Graphics Processing Units (GPGPUs) have the potential to substantially accelerate simulations compared to traditional CPU-only processing. The software development that requires often carries the cost of specialized code refactorization and porting to match the target hardware architecture. With the rapid evolution and increased diversity of the computer architecture landscape, it is highly desirable to have a portable solution that also maintains reasonable performance. We report our ongoing effort in evaluating Kokkos as a basis for this portable programming model using LArTPC simulations in the context of the Wire-Cell Toolkit, a C++ library for LArTPC simulations, data analysis, reconstruction and visualization.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Visualization techniques to aid in the analysis of multispectral astrophysical data sets

The goal of this project was to support the scientific analysis of multi-spectral astrophysical data by means of scientific visualization. Scientific visualization offers its greatest value if it is not used as a method separate or alternative to other data analysis methods but rather in addition to these methods. Together with quantitative analysis of data, such as offered by statistical analysis, image or signal processing, visualization attempts to explore all information inherent in astrophysical data in the most effective way. Data visualization is one aspect of data analysis. Our taxonomy as developed in Section 2 includes identification and access to existing information, preprocessing and quantitative analysis of data, visual representation and the user interface as major components to the software environment of astrophysical data analysis. In pursuing our goal to provide methods and tools for scientific visualization of multi-spectral astrophysical data, we therefore looked at scientific data analysis as one whole process, adding visualization tools to an already existing environment and integrating the various components that define a scientific data analysis environment. As long as the software development process of each component is separate from all other components, users of data analysis software are constantly interrupted in their scientific work in order to convert from one data format to another, or to move from one storage medium to another, or to switch from one user interface to another. We also took an in-depth look at scientific visualization and its underlying concepts, current visualization systems, their contributions and their shortcomings. The role of data visualization is to stimulate mental processes different from quantitative data analysis, such as the perception of spatial relationships or the discovery of patterns or anomalies while browsing through large data sets. Visualization often leads to an intuitive understanding of the meaning of data values and their relationships by sacrificing accuracy in interpreting the data values. In order to be accurate in the interpretation, data values need to be measured, computed on, and compared to theoretical or empirical models (quantitative analysis). If visualization software hampers quantitative analysis (which happens with some commercial visualization products), its use is greatly diminished for astrophysical data analysis. The software system STAR (Scientific Toolkit for Astrophysical Research) was developed as a prototype during the course of the project to better understand the pragmatic concerns raised in the project. STAR led to a better understanding on the importance of collaboration between astrophysicists and computer scientists. Twenty-one examples of the use of visualization for astrophysical data are included with this report. Sixteen publications related to efforts performed during or initiated through work on this project are listed at the end of this report.

Brugel, E. W.↗

Automated electrosynthesis reaction mining with multimodal large language models (MLLMs)

Leveraging the chemical data available in legacy formats such as publications and patents is a significant challenge for the community. Automated reaction mining offers a promising solution to unleash this knowledge into a learnable digital form and therefore help expedite materials and reaction discovery. However, existing reaction mining toolkits are limited to single input modalities (text or images) and cannot effectively integrate heterogeneous data that is scattered across text, tables, and figures. In this work, we go beyond single input modalities and explore multimodal large language models (MLLMs) for the analysis of diverse data inputs for automated electrosynthesis reaction mining. We compiled a test dataset of 65 articles (MERMES-T24 set) and employed it to benchmark five prominent MLLMs against two critical tasks: (i) reaction diagram parsing and (ii) resolving cross-modality data interdependencies. The frontrunner MLLM achieved ≥96% accuracy in both tasks, with the strategic integration of single-shot visual prompts and image pre-processing techniques. We integrate this capability into a toolkit named MERMES (multimodal reaction mining pipeline for electrosynthesis). Our toolkit functions as an end-to-end MLLM-powered pipeline that integrates article retrieval, information extraction and multimodal analysis for streamlining and automating knowledge extraction. This work lays the groundwork for the increased utilization of MLLMs to accelerate the digitization of chemistry knowledge for data-driven research.

Leong, Shi Xuan↗

The Marine and Hydrokinetic ToolKit (MHKiT) for Data Quality Control and Analysis [Slides]

The ability to collect, ingest, condition, reduce, quality control, process, visualize, and store data in a standardized way is critical at all stages of Marine Energy (ME) research and technology/project development. MHKiT is an open-source, standardized suite of ME data processing functions that provides the ability to ingest, condition, reduce, quality control, process, visualize and store ME data. MHKiT is developed in both Python and Matlab.

16 TIDAL AND WAVE POWER↗

Development of an Extended Reality (XR) Tool for Earth Science Visualization

In this presentation, we will discuss our work in adapting the NASA open source XR software, the Mixed Reality Exploration Toolkit (MRET), to an earth science domain. MRET is a NASA open source XR software for rapidly building extended reality (XR) environments for NASA domain problems, e.g., pulling in CAD models of thermal vac chamber and Roman Space Telescope to do fit checks. Primarily used for hardware integration & test, we have been adapting and extending MRET for science problems. Traditionally, scientists view and analyze the result of calculated or measured observables with static 1-D, 2-D or 3-D plots. It can be difficult to identify, track and understand the evolution of key features due to poor viewing angles and the nature of flat computer screens. Additionally, numerical models, such as the NASA GEOS climate model, are almost exclusively formulated and analyzed on Eulerian grids with points fixed in space and time. However, atmospheric phenomena such as convective clouds, hurricanes and wildfire smoke plumes move with the 3-D flow field, and it is often difficult and unnatural to understand these phenomena in an Eulerian reference frame as opposed to the Lagrangian reference frame in which nature operates. As part of an Earth Science Technology Office (ESTO) proposal, we have been adapting MRET to be a scientific exploration and analysis XR tool with integrated Lagrangian Dynamics (LD) for the Goddard Earth Observing System (GEOS) numerical weather prediction model. We believe this will help scientists identify, track, and understand the evolution of Earth Science phenomena. This presentation will discuss current results in our work in developing this XR tool for Earth Science.

Thomas G Grubb↗

Development of an Extended Reality (XR) Tool for Earth Science Visualization

In this presentation, we will discuss our work in adapting the NASA open source XR software, the Mixed Reality Exploration Toolkit (MRET), to an earth science domain. MRET is a NASA open source XR software for rapidly building extended reality (XR) environments for NASA domain problems, e.g., pulling in CAD models of thermal vac chamber and Roman Space Telescope to do fit checks. Primarily used for hardware integration & test, we have been adapting and extending MRET for science problems. Traditionally, scientists view and analyze the result of calculated or measured observables with static 1-D, 2-D or 3-D plots. It can be difficult to identify, track and understand the evolution of key features due to poor viewing angles and the nature of flat computer screens. Additionally, numerical models, such as the NASA GEOS climate model, are almost exclusively formulated and analyzed on Eulerian grids with points fixed in space and time. However, atmospheric phenomena such as convective clouds, hurricanes and wildfire smoke plumes move with the 3-D flow field, and it is often difficult and unnatural to understand these phenomena in an Eulerian reference frame as opposed to the Lagrangian reference frame in which nature operates. As part of an Earth Science Technology Office (ESTO) proposal, we have been adapting MRET to be a scientific exploration and analysis XR tool with integrated Lagrangian Dynamics (LD) for the Goddard Earth Observing System (GEOS) numerical weather prediction model. We believe this will help scientists identify, track, and understand the evolution of Earth Science phenomena. This presentation will discuss current results in our work in developing this XR tool for Earth Science.

Thomas Grubb↗

LIVVkit 2.1: automated and extensible ice sheet model validation

A collection of scientific analyses, metrics, and visualizations for robustvalidation of ice sheet models is presented using the Land Ice Verificationand Validation toolkit (LIVVkit), version 2.1, and the LIVVkit Extensionsrepository (LEX), version 0.1. This software collection targets stand-aloneice sheet or coupled Earth system models, and handles datasets and analysesthat require high-performance computing and storage. LIVVkit aims to enableefficient and fully reproducible workflows for postprocessing, analysis, andvisualization of observational and model-derived datasets in a shareableformat, whereby all data, methodologies, and output are distributed to usersfor evaluation. Extending from the initial LIVVkit software framework, wedemonstrate Greenland ice sheet simulation validation metrics using thecoupled Community Earth System Model (CESM) as well as an idealizedstand-alone high-resolution Community Ice Sheet Model, version 2 (CISM2),coupled to the Albany/FELIX velocity solver (CISM-Albany or CISM-A). As oneexample of the capability, LIVVkit analyzes the degree to which modelscapture the surface mass balance (SMB) and identifies potential sources ofbias, using recently available in situ and remotely sensed data ascomparison. Related fields within atmosphere and land surface models, e.g.,surface temperature, radiation, and cloud cover, are also diagnosed. Appliedto the CESM1.0, LIVVkit identifies a positive SMB bias that is focusedlargely around Greenland's southwest region that is due to insufficientablation.

58 GEOSCIENCES↗

Feature Learning for Multispectral Satellite Imagery Classification Using Neural Architecture Search

Automated classification of remote sensing data is an integral tool for earth scientists, and deep learning has proven very successful at solving such problems. However, building deep learning models to process the data requires expert knowledge of machine learning. We introduce DELTA, a software toolkit to bridge this technical gap and make deep learning easily accessible to earth scientists. Visual feature engineering is a critical part of the machine learning lifecycle, and hence is a key area that will be automated by DELTA. Hand-engineered features can perform well, but require a cross functional team with expertise in both machine learning and the specific problem domain, which is costly in both researcher time and labor. The problem is more acute with multispectral satellite imagery, which requires considerable computational resources to process. In order to automate the feature learning process, a neural architecture search samples the space of asymmetric and symmetric autoencoders using evolutionary algorithms. Since denoising autoencoders have been shown to perform well for feature learning, the autoencoders are trained on various levels of noise and the features generated by the best performing autoencoders evaluated according to their performance on image classification tasks. The resulting features are demonstrated to be effective for Landsat-8 flood mapping, as well as benchmark datasets CIFAR10 and SVHN.

Robert Campbell↗

Visualization techniques to aid in the analysis of multi-spectral astrophysical data sets

The goal of this project was to support the scientific analysis of multi-spectral astrophysical data by means of scientific visualization. Scientific visualization offers its greatest value if it is not used as a method separate or alternative to other data analysis methods but rather in addition to these methods. Together with quantitative analysis of data, such as offered by statistical analysis, image or signal processing, visualization attempts to explore all information inherent in astrophysical data in the most effective way. Data visualization is one aspect of data analysis. Our taxonomy as developed in Section 2 includes identification and access to existing information, preprocessing and quantitative analysis of data, visual representation and the user interface as major components to the software environment of astrophysical data analysis. In pursuing our goal to provide methods and tools for scientific visualization of multi-spectral astrophysical data, we therefore looked at scientific data analysis as one whole process, adding visualization tools to an already existing environment and integrating the various components that define a scientific data analysis environment. As long as the software development process of each component is separate from all other components, users of data analysis software are constantly interrupted in their scientific work in order to convert from one data format to another, or to move from one storage medium to another, or to switch from one user interface to another. We also took an in-depth look at scientific visualization and its underlying concepts, current visualization systems, their contributions, and their shortcomings. The role of data visualization is to stimulate mental processes different from quantitative data analysis, such as the perception of spatial relationships or the discovery of patterns or anomalies while browsing through large data sets. Visualization often leads to an intuitive understanding of the meaning of data values and their relationships by sacrificing accuracy in interpreting the data values. In order to be accurate in the interpretation, data values need to be measured, computed on, and compared to theoretical or empirical models (quantitative analysis). If visualization software hampers quantitative analysis (which happens with some commercial visualization products), its use is greatly diminished for astrophysical data analysis. The software system STAR (Scientific Toolkit for Astrophysical Research) was developed as a prototype during the course of the project to better understand the pragmatic concerns raised in the project. STAR led to a better understanding on the importance of collaboration between astrophysicists and computer scientists.

Brugel, Edward W.↗

User's manual for the two-dimensional transputer graphics toolkit

The user manual for the 2-D graphics toolkit for a transputer based parallel processor is presented. The toolkit consists of a package of 2-D display routines that can be used for the simulation visualizations. It supports multiple windows, double buffered screens for animations, and simple graphics transformations such as translation, rotation, and scaling. The display routines are written in occam to take advantage of the multiprocessing features available on transputers. The package is designed to run on a transputer separate from the graphics board.

Ellis, Graham K.↗

py4DSTEM: A Software Package for Four-Dimensional Scanning Transmission Electron Microscopy Data Analysis

Scanning transmission electron microscopy (STEM) allows for imaging, diffraction, and spectroscopy of materials on length scales ranging from microns to atoms. By using a high-speed, direct electron detector, it is now possible to record a full two-dimensional (2D) image of the diffracted electron beam at each probe position, typically a 2D grid of probe positions. These 4D-STEM datasets are rich in information, including signatures of the local structure, orientation, deformation, electromagnetic fields, and other sample-dependent properties. However, extracting this information requires complex analysis pipelines that include data wrangling, calibration, analysis, and visualization, all while maintaining robustness against imaging distortions and artifacts. In this paper, we present py4DSTEM, an analysis toolkit for measuring material properties from 4D-STEM datasets, written in the Python language and released with an open-source license. We describe the algorithmic steps for dataset calibration and various 4D-STEM property measurements in detail and present results from several experimental datasets. We also implement a simple and universal file format appropriate for electron microscopy data in py4DSTEM, which uses the open-source HDF5 standard. We hope this tool will benefit the research community and help improve the standards for data and computational methods in electron microscopy, and we invite the community to contribute to this ongoing project.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Hardening DOE R&D Software Tools for Web-based Visualization SBIR Phase I Final Report

Ubiquitous web-based visualization is essential to delivering large-scale data visualization to various stakeholders, from the scientist to the board member. These stakeholders will not tolerate a stalled application or a pop-up window asking them to wait for the processing to complete. They require a responsive and interactive visualization environment with high-quality imagery suitable for detailed analysis and boardroom presentations. At Kitware, Inc., we have accomplished web visualization to this point, leveraging state-of-the-art tools like HTML5, CSS3, SVG, Canvas, and WebGL. Solutions that leverage a combination of these technologies are necessary to handle workloads that vary significantly in data size efficiently. However, it is not always practical to move large data to the web client for visualization. Kitware's ParaView as a Service combines client-side visualization using both distributed processing and remote rendering on big data impractical to move. Existing distributed processing and remote rendering solution's interactivity is below the expectations of web-based applications. Our project examined proposed solutions to the areas outlined above in ParaView as a Service. We have investigated concurrent pipelines, streaming images, progressive rendering, and optimization of algorithms and data movement to address these concerns. For the Phase I project, we completed the proposed work plan. As a result, the project produced three prototypes of essential importance for web visualization and the ParaView as a Service community. We created a simple desktop application for an interactive streamline placement prototype, a web-based interactive streamline placement prototype, and a web-based progressive rendering utilizing raytracing prototype. These prototypes relied on the hardening of emerging software toolkits funded by the Department of Energy (DOE) Advanced Scientific Computing Research (ASCR) program (such as ParaView, VTK-m, and Mochi). We blended these components into web-based visualization prototypes that meet the industry's expectations for interactivity and responsiveness. The Phase I project had four essential focus areas: 1. Develop prototype ParaView as a Service backend server using asynchronous, non-blocking design principles. 2. Develop a prototype web application that uses the ParaView as a Service backend server for remote data visualization. 3. Implement image streaming with encoding/compression and progressive rendering capabilities in the proposed platform. 4. Evaluate the prototype developed and summarize observations, including the challenges and pitfalls of our approach. After our successful completion of Phase I, we are strongly positioned to propose a successful Phase II project.

Geveci, Berk↗