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All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Plant science decadal vision 2020–2030: Reimagining the potential of plants for a healthy and sustainable future

Abstract Plants, and the biological systems around them, are key to the future health of the planet and its inhabitants. The Plant Science Decadal Vision 2020–2030 frames our ability to perform vital and far‐reaching research in plant systems sciences, essential to how we value participants and apply emerging technologies. We outline a comprehensive vision for addressing some of our most pressing global problems through discovery, practical applications, and education. The Decadal Vision was developed by the participants at the Plant Summit 2019, a community event organized by the Plant Science Research Network. The Decadal Vision describes a holistic vision for the next decade of plant science that blends recommendations for research, people, and technology. Going beyond discoveries and applications, we, the plant science community, must implement bold, innovative changes to research cultures and training paradigms in this era of automation, virtualization, and the looming shadow of climate change. Our vision and hopes for the next decade are encapsulated in the phrase reimagining the potential of plants for a healthy and sustainable future. The Decadal Vision recognizes the vital intersection of human and scientific elements and demands an integrated implementation of strategies for research (Goals 1–4), people (Goals 5 and 6), and technology (Goals 7 and 8). This report is intended to help inspire and guide the research community, scientific societies, federal funding agencies, private philanthropies, corporations, educators, entrepreneurs, and early career researchers over the next 10 years. The research encompass experimental and computational approaches to understanding and predicting ecosystem behavior; novel production systems for food, feed, and fiber with greater crop diversity, efficiency, productivity, and resilience that improve ecosystem health; approaches to realize the potential for advances in nutrition, discovery and engineering of plant‐based medicines, and "green infrastructure." Launching the Transparent Plant will use experimental and computational approaches to break down the phytobiome into a "parts store" that supports tinkering and supports query, prediction, and rapid‐response problem solving. Equity, diversity, and inclusion are indispensable cornerstones of realizing our vision. We make recommendations around funding and systems that support customized professional development. Plant systems are frequently taken for granted therefore we make recommendations to improve plant awareness and community science programs to increase understanding of scientific research. We prioritize emerging technologies, focusing on non‐invasive imaging, sensors, and plug‐and‐play portable lab technologies, coupled with enabling computational advances. Plant systems science will benefit from data management and future advances in automation, machine learning, natural language processing, and artificial intelligence‐assisted data integration, pattern identification, and decision making. Implementation of this vision will transform plant systems science and ripple outwards through society and across the globe. Beyond deepening our biological understanding, we envision entirely new applications. We further anticipate a wave of diversification of plant systems practitioners while stimulating community engagement, underpinning increasing entrepreneurship. This surge of engagement and knowledge will help satisfy and stoke people's natural curiosity about the future, and their desire to prepare for it, as they seek fuller information about food, health, climate and ecological systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Evaluating Performance Portability of Accelerator Programming Models using SPEC ACCEL 1.2 Benchmarks

As heterogeneous architectures are becoming mainstream for HPC systems, application programmers are looking for programming model implementations that offer both performance and portability across platforms. Two directive-based programming models for accelerator programming that aim at doing this are OpenMP 4/4.5 and OpenACC. Many users want to know the difference between these two programming models, the state of their implementations, how to use them, and evaluate how suitable they are for their applications.The Standard Performance Evaluation Corporation (SPEC) ACCEL benchmarks, developed by the SPEC High Performance Group (HPG), recently released SPEC ACCEL 1.2 benchmark suite to help the evaluation of OpenCL, OpenMP 4.5 and OpenACC on different platforms. Inthis paper we present our preliminary results that evaluates OpenMP4.5 and OpenACC on a variety of accelerator-based systems: POWER9with NVIDIA V100 GPUs (Summit), Intel Xeon Phi 7230 (Percival), and AMD Bulldozer Opteron with NVIDIA K20x (Titan). Comparing these benchmarks on different systems gives us insight into the support for OpenMP and OpenACC and their execution times provide insights about their quality of implementations provided by different vendors. We also compare best of OpenMP and OpenACC to see if a particular programming model favors a particular type of benchmark kernel.

Boehm, Swen↗
DOE OSTI2019

Highly interactive, steered scientific workflows on HPC systems: optimizing design solutions

Scientific workflows are becoming increasingly important in high performance computing (HPC) settings, as the feasibility and appeal of many simultaneous heterogeneous tasks increases with increasing hardware capabilities. Currently no HPC-based workflow platform supports a dynamically adaptable workflow with interactive steering and analysis at run-time. Furthermore, for most workflow programs, compute resources are fixed for a given instance, resulting in a possible waste of expensive allocation resources when tasks are spawned and killed. Here we describe the design and testing of a run-time-interactive, adaptable, steered workflow tool capable of executing thousands of parallel tasks without an MPI programming model, using a database management system to facilitate task management through multiple live connections. We find that on the Oak Ridge Leadership Computing Facility pre-exascale Summit supercomputer it is possible to launch and interactively steer workflows with thousands of simultaneous tasks with negligible latency. For the case of particle simulation and analysis tasks that run for minutes to hours, this paradigm offers the prospect of a robust and efficient means to perform simulation-space exploration with on-the-fly analysis and adaptation.

Ossyra, John R↗
DOE OSTI2020

Toward Real-Time Analysis of Synchrotron Micro-Tomography Data: Accelerating Experimental Workflows with AI and HPC

ynchrotron light sources are routinely used to perform imaging experiments. In this paper, we review the relevant computational stages, identify bottlenecks, and highlight future opportunities to streamline data acquisition for experimental microscopy workflows. We demonstrate our preliminary exploration with an end-to-end scientific workflow on Summit based on micro-computed tomography data. Computational elements include: 1) reconstruction of volumetric image data; 2) denoising with deep neural networks; and 3) non-local means based segmentation and quantitative analysis.

Mcclure, James↗
DOE OSTI2021

Enabling AI-Accelerated Multiscale Modeling of Thrombogenesis at Millisecond and Molecular Resolutions on Supercomputers

We report the first congruent integration of HPC, AI, and multiscale modeling (MSM) for solving a mainstream biomechanical problem of thrombogenesis involving 6 million particles at record molecular-scale resolutions in space and at simulation rates of milliseconds per day. The two supercomputers, the IBM Summit-like AiMOS and our University’s SeaWulf, are used for scalability analysis of, and production runs with, the LAMMPS with our customization and AI augmentation and they attained optimal simulation speeds of 3,077 µs/day and 266 µs/day respectively. The long-time and large scales simulations enable the first study of the integrated platelet flowing, flipping, aggregating dynamics in one dynamically-coupled production run. The platelets’ angular and translational speeds, membrane particles’ speeds, and the membrane stress distributions are presented for the analysis of platelets’ aggregations.

Zhu, Yicong↗
DOE OSTI2022

Fast and Accurate Predictions of Total Energy for Solid Solution Alloys with Graph Convolutional Neural Networks

We use graph convolutional neural networks (GCNNs) to produce fast and accurate predictions of the total energy of solid solution binary alloys. GCNNs allow us to abstract the lattice structure of a solid material as a graph, whereby atoms are modeled as nodes and metallic bonds as edges. This representation naturally incorporates information about the structure of the material, thereby eliminating the need for computationally expensive data pre-processing which would be required with standard neural network (NN) approaches. We train GCNNs on ab-initio density functional theory (DFT) for copper-gold (CuAu) and iron-platinum (FePt) data that has been generated by running the LSMS-3 code, which implements a locally self-consistent multiple scattering method, on OLCF supercomputers Titan and Summit. GCNN outperforms the ab-initio DFT simulation by orders of magnitude in terms of computational time to produce the estimate of the total energy for a given atomic configuration of the lattice structure. We compare the predictive performance of GCNN models against a standard NN such as dense feedforward multi-layer perceptron (MLP) by using the root-mean-squared errors to quantify the predictive quality of the deep learning (DL) models. We find that the attainable accuracy of GCNNs is at least an order of magnitude better than that of the MLP.

Lupo Pasini, Massimiliano↗
DOE OSTI2022

Transitioning from File-Based HPC Workflows to Streaming Data Pipelines with openPMD and ADIOS2

This paper aims to create a transition path from file-based IO to streaming-based workflows for scientific applications in an HPC environment. By using the openPMP-api, traditional workflows limited by filesystem bottlenecks can be overcome and flexibly extended for in situ analysis. The openPMD-api is a library for the description of scientific data according to the Open Standard for Particle-Mesh Data (openPMD). Its approach towards recent challenges posed by hardware heterogeneity lies in the decoupling of data description in domain sciences, such as plasma physics simulations, from concrete implementations in hardware and IO. The streaming backend is provided by the ADIOS2 framework, developed at Oak Ridge National Laboratory. This paper surveys two openPMD-based loosely-coupled setups to demonstrate flexible applicability and to evaluate performance. In loose coupling, as opposed to tight coupling, two (or more) applications are executed separately, e.g. in individual MPI contexts, yet cooperate by exchanging data. This way, a streaming-based workflow allows for standalone codes instead of tightly-coupled plugins, using a unified streaming-aware API and leveraging high-speed communication infrastructure available in modern compute clusters for massive data exchange. We determine new challenges in resource allocation and in the need of strategies for a flexible data distribution, demonstrating their influence on efficiency and scaling on the Summit compute system. The presented setups show the potential for a more flexible use of compute resources brought by streaming IO as well as the ability to increase throughput by avoiding filesystem bottlenecks.

Poeschel, Franz↗
DOE OSTI2022

Secure Collaborative Environment for Seamless Sharing of Scientific Knowledge

In a secure collaborative environment, tera-bytes of data generated from powerful scientific instruments are used to train secure machine learning (ML) models on exascale computing systems, which are then securely shared with internal or external collaborators as cloud-based services. Devising such a secure platform is necessary for seamless scientific knowledge sharing without compromising individual, or institute-level, intellectual property and privacy details. By enabling new computing opportunities with sensitive data, we envision a secure collaborative environment that will play a significant role in accelerating scientific discovery. Several recent technological advancements have made it possible to realize these capabilities. In this paper, we present our efforts at ORNL toward developing a secure computation platform. We present a use case where scientific data generated from complex instruments, like those at the Spallation Neutron Source (SNS), are used to train a differential privacy enabled deep learning (DL) network on Summit, which is then hosted as a secure multi-party computation (MPC) service on ORNL’s Compute and Data Environment for Science (CADES) cloud computing platform for third-party inference. In this feasibility study, we discuss the challenges involved, elaborate on leveraged technologies, analyze relevant performance results and present the future vision of our work to establish secure collaboration capabilities within and outside of ORNL.

Yoginath, Srikanth↗
DOE OSTI2022

OpenMP Target Task: Tasking and Target Offloading on Heterogeneous Systems

This work evaluated the use of OpenMP tasking with target GPU offloading as a potential solution for programming productivity and performance on heterogeneous systems. Also, it is proposed a new OpenMP specification to make the implementation of heterogeneous codes simpler by using OpenMP target task, which integrates both OpenMP tasking and target GPU offloading in a single OpenMP pragma. As a test case, the authors used one of the most popular and widely used Basic Linear Algebra Subprogram Level-3 routines: triangular solver (TRSM). To benefit from the heterogeneity of the current high-performance computing systems, the authors propose a different parallelization of the algorithm by using a nonuniform decomposition of the problem. This work used target GPU offloading inside OpenMP tasks to address the heterogeneity found in the hardware. This new approach can outperform the state-of-the-art algorithms, which use a uniform decomposition of the data, on both the CPU-only and hybrid CPU-GPU systems, reaching speedups of up to one order of magnitude. The performance that this approach achieves is faster than the IBM ESSL math library on CPU and competitive relative to a highly optimized heterogeneous CUDA version. One node of Oak Ridge National Laboratory’s supercomputer, Summit, was used for performance analysis.

Valero Lara, Pedro↗
DOE OSTI2023

Toward an Autonomous Workflow for Single Crystal Neutron Diffraction

The operation of the neutron facility relies heavily on beamline scientists. Some experiments can take one or two days with experts making decisions along the way. Leveraging the computing power of HPC platforms and AI advances in image analyses, here we demonstrate an autonomous workflow for the single-crystal neutron diffraction experiments. The workflow consists of three components: an inference service that provides real-time AI segmentation on the image stream from the experiments conducted at the neutron facility, a continuous integration service that launches distributed training jobs on Summit to update the AI model on newly collected images, and a frontend web service to display the AI tagged images to the expert. Ultimately, the feedback can be directly fed to the equipment at the edge in deciding the next-step experiment without requiring an expert in the loop. With the analyses of the requirements and benchmarks of the performance for each component, this effort serves as the first step toward an autonomous workflow for real-time experiment steering at ORNL neutron facilities.

Yin, Junqi↗
DOE OSTI2023

Towards a Standard Process Management Infrastructure for Workflows Using Python

Orchestrating the execution of ensembles of processes lies at the core of scientific workflow engines on large scale parallel platforms. This is usually handled using platform-specific command line tools, with limited process management control and potential strain on system resources. The PMIx standard provides a uniform interface to system resources. The low level C implementation of PMIx has hampered its use in workflow engines, leading to the development of Python binding that has yet to gain traction. In this paper, we present our work to harden the PMIx Python client, demonstrating its usability using a prototype Python driver to orchestrate the execution of an ensemble of processes. We present experimental results using the prototype on the Summit supercomputer at Oak Ridge National Laboratory. This work lays the foundation for wider adoption of PMIx for workflow engines, and encourages wider support of more PMIx functionality in vendor provided system software stacks.

Elwasif, Wael↗
DOE OSTI2023

Asynchronous Execution of Heterogeneous Tasks in ML-Driven HPC Workflows

Heterogeneous scientific workflows consist of numerous types of tasks that require execution on heterogeneous resources. Asynchronous execution of those tasks is crucial to improve resource utilization, task throughput and reduce workflows' makespan. Therefore, middleware capable of scheduling and executing different task types across heterogeneous resources must enable asynchronous execution of tasks. In this paper, we investigate the requirements and properties of the asynchronous task execution of machine learning (ML)-driven high-performance computing (HPC) workflows. We model the degree of asynchronicity permitted for arbitrary workflows and propose key metrics that can be used to determine qualitative benefits when employing asynchronous execution. Our experiments represent relevant scientific drivers, we perform them at scale on Summit, and we show that the performance enhancements due to asynchronous execution are consistent with our model.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Experiences Evaluating Functionality and Performance of IBM POWER8+ Systems

In preparation for Summit, Oak Ridge National Laboratory’s next generation supercomputer, two IBM Power-based systems were deployed in late 2016 at the Oak Ridge Leadership Computing Facility (OLCF). This paper presents a detailed description of the acceptance of the first IBM Power-based early access systems installed at the OLCF. The two systems, Summitdev and Tundra, contain IBM POWER8+ processors with NVIDIA Pascal GPUs and were acquired to provide researchers with a platform to optimize codes for the Power architecture. In addition, this paper presents early functional and performance results obtained on Summitdev with the latest software stack available.

Vergara Larrea, Veronica G.↗
DOE OSTI2018

OpenMP 4.5 Validation and Verification Suite for Device Offload

OpenMP has been widely adopted for shared memory systems for over a decade. With the heterogeneity trend in architectures rapidly growing, the programming model needed to evolve such that applications could not only be ported to traditional CPUs but also to accelerators often acting as discrete or integrated devices to CPUs. To that end, OpenMP started to provide support for heterogeneous systems since 2013 when the version 4.0 of the specification was ratified. OpenMP 4.5 is being enhanced to cover major requirements of Exascale Computing Project (ECP) applications. As a result it is time-critical to ensure that the implementations of the 4.5 features are correct and conforming to the specification. This paper focuses on building a Validation and Verification testsuite that will test and present results for several offloading features implemented in compilers such as Clang, IBM XL C/C++, CCE, and GCC. We have results for our testsuite on TITAN, Summitdev and Summit at the Oak Ridge National Lab. We will highlight some of the ambiguities we encountered in the process of validating and verifying feature implementations. We also make the testsuite available for anyone to use and will walk the readers through the infrastructure and the workflow of the testsuite. A website has been built to capture our efforts narrated in this paper https://crpl.cis.udel.edu/ompvvsollve.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2018

Groundwater drainage from fissures as a source for lahars

One mechanism for generating lahars at volcanoes experiencing unrest is the disruption of internal aquifers. These disruptions can trigger releases of large quantities of groundwater. An example of such aquifer disruption occurred at Nevado del Huila Volcano, Colombia, during February and April 2007 when large fractures formed across the summit area of the volcano and lahars were emitted from them. Previous work interpreted that lahar volumes could not be accounted for by melted glacial snow or precipitation, and by elimination suggested that the primary water source was groundwater. Conceptual models have been developed for perched, confined aquifers that have been heated and pressurized by magma intrusions, followed by sudden pressure release and water emission during fracture formation. In this paper, we consider an alternative end member wherein water release from large fissures at volcanoes is driven by simple gravity drainage. We apply numerical modeling to quantify water discharge from the porous medium surrounding a fissure with a low-elevation free exit. If a long fracture with high vertical extent (on the order of hundreds of meters) intersects a highly connected saturated porous medium, large volumes (on order 10 3 m 3 /m of crack length) of water may be released within tens of minutes. The drainage rates from the model may be adequate to account for the Nevado del Huila events if the medium surrounding the crack contains a large volume of water and has high horizontal permeability. Finally, this simple but poorly understood mechanism can present a hazard on its own or compound other processes releasing water from volcanoes.

58 GEOSCIENCES↗
DOE OSTI2022

Controls on the frequency content of near-source infrasound at open-vent volcanoes: a case study from Volcán Villarrica, Chile

Infrasound signals from open-vent volcanoes can contain information related to that volcano’s eruption dynamics and future activity. Studying a specific volcano’s acoustic signature during periods of relative quiescence is thus important for understanding potential warning signs of impending eruptions. Volcán Villarrica, located in southern Chile, has a long-lived active lava lake that produces continuous infrasound with spectral peaks centered around 1 Hz that vary by + / - ~ 0.2 Hz over day-to-week-long time scales. The infrasound frequency content has been shown to illuminate key volcanic properties such as eruption style and crater shape. Leading up to Villarrica’s most recent paroxysm in 2015, for instance, infrasound spectral changes coincided with a rise in Villarrica’s lava lake level. Quantifying and understanding the regular fluctuation in recorded infrasonic frequencies from Villarrica and other open-vent volcanoes is thus imperative during periods of relative calm. Our experiment entailed a week-long period of crater rim infrasound observations associated with stable, open-vent activity and revealed two independent source processes: spatter bursting events (relatively broadband infrasound) and lava lake-induced tremor (sustained signals peaked at 1 Hz). A comparison of these acoustic signals with results from 3-D finite-difference time-domain wave propagation models shows that while sound speed variability can influence Villarrica’s spectrum, it cannot explain the full extent of the observed frequency excursions. We conclude that source spectrum variability is primarily responsible for the frequency excursions. In conclusion, our work highlights the utility of data collected from a dense distribution of twenty infrasound sensors operating at the summit coupled with numerical modeling of sound radiation.

58 GEOSCIENCES↗
DOE OSTI2017

Two early eudicot fossil flowers from the Kamikitaba assemblage (Coniacian, Late Cretaceous) in northeastern Japan

Two new fossil taxa referable to the basal eudicot grade are described from the Kamikitaba locality (ca. 89 MYBP, early Coniacian: Late Cretaceous) in the Ashizawa Formation (Asamigawa Member) of Futaba Group in northeastern Japan. These charcoalified mesofossils exhibit well-preserved three-dimensional structure and were analyzed using synchrotron-radiation X-ray microtomography (SRXTM) at the Advanced Photon Source (APS) to document the composition and internal structure. Cathiaria japonica sp. nov. is represented by infructescence segments that consist of an axis bearing three to four fruits. The capsular fruits are sessile and dehiscent and consist of a gynoecium subtended by a bract. No perianth parts are present. The gynoecium is monocarpellate containing two pendulous seeds. The carpel is ascidiate in the lower half and conduplicate in the upper part, style is deflected abaxially with a dorsiventral suture and a large, obliquely decurrent stigma. Pollen grains are tricolpate with a reticulate exine. The morphological features of Cathiaria are consistent with an assignment to the Buxaceae s. l. (including Didymelaceae). Archaeostella verticillata gen. et sp. nov. is represented by flowers that are small, actinomorphic, pedicellate, bisexual, semi-inferior, and multicarpellate. The floral receptacle is cup shaped with a perigynous perianth consisting of several tepals inserted around the rim. The androecium comprises ca. 120 stamens with clear differentiation into anther and filament. The anthers are basifixed and tetrasporangiate. The gynoecium consists of a whorl of ten conduplicate, laterally connate but distally distinct carpels with a conspicuous dorsal bulge, including a central cavity. The styles are short, becoming recurved with a ventrally decurrent stigma. The fruit type is a follicle. Seeds are ca. 10 per carpel, marginal, pendulous from the broad, oblique summit of the locule. Seeds are small, spindle-shaped, with a chalazal extension, Pollen grains are tricolpate with a reticulate exine pattern, suggesting a relationship to eudicots. The morphological features of Archaeostella indicate a possible relationship to Trochodendraceae in the basal grade of eudicots, although it is uncertain if the anther thecae open by longitudinal slits as in extant Trochodendron. The fossil currently provides the earliest record of the family and documents the presence of Trochodendraceae in eastern Eurasia during the middle part of the Late Cretaceous. Furthermore, the recovery of Cathiaria japonica and Archaeostella verticillata from the Kamikitaba locality suggests that the basal eudicot families Trochodendraceae and Buxaceae s. l. (including Didymelaceae) were differentiated and distributed in eastern Eurasia area during the Late Cretaceous.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Erosional redistribution of topsoil controls soil nitrogen dynamics

In recent years, the role of soil erosion on terrestrial carbon sequestration had been the focus of a growing number of studies. However, relatively little attention has been paid so far to the role of erosion on the lateral distribution of soil nitrogen (N) and the role of geomorphic processes on soil N dynamics. We present primary data on the stock of nitrogen in soil and its rate of erosion at a relatively undisturbed, zero-order watershed in northern California. Erosion transports 0.26–0.47 g N m -2 year -1 from eroding slope positions (Summit and Slope), and about two-thirds of the eroded N enters depositional landform positions (Hollow and Plain). Our results show that depositional-position soil profiles contain up to 3 times more N than soil profiles in the eroding positions. More than 92% of all soil nitrogen was chemically bound to soil minerals in all the landform positions, compared to 2–4% each found in the free light and occluded light fractions. Nitrogen associated with the free light fraction in topsoil is particularly susceptible to loss by soil erosion. By comparison, soil N associated with the aggregate-protected occluded light fractions and the mineral-associated dense fractions is likely to be protected from gaseous and dissolved losses. On average, we found that soil N has mean residence time of 694 years in eroding landform positions, compared to 2951 years in depositional landform positions. Our results also show that microbial processing of organic matter exerts strong control on overall soil N storage and N stabilized through sorptive interactions with soil minerals only in poorly drained depositional landform positions. Finally, soil erosion exerts important control on stock, distribution, and long-term fate of soil N in dynamic landscapes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗