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At least 1,297 records · Page 72

Open‐Source Anaerobic Digestion Modeling Platform, Anaerobic Digestion Model No. 1 Fast (ADM1F)

An open‐source modeling platform, called Anaerobic Digestion Model No. 1 Fast (ADM1F), is introduced to achieve fast and numerically stable simulations of anaerobic digestion processes. ADM1F is compatible with an iPython interface to facilitate model configuration, simulation, data analysis, and visualization. Faster simulations and more stable results are accomplished by implementing an advanced open‐source library of numerical methods called Portable Extensive Toolkit for Scientific Computation (PETSc) to solve the ADM1 system of equations. Leveraging PETSc, ADM1F can consistently complete a steady‐state simulation under 0.2 s, over 99% faster than a benchmark ADM1 model implemented with MATLAB while achieving agreement of model outputs within 1% of those obtained with the benchmark model. For dynamic simulations, however, ADM1F has a computational speed advantage only when the influent characteristics update more frequently than every 4 h. The ability of ADM1F to be useful as a tool to study anaerobic digestion systems is demonstrated through two example implementations of ADM1F: (1) a two‐phase co‐digestion scenario evaluating the impact of the organic loading rate and the substrate composition on reactor performance and stability, and (2) a conventional digester scenario assessing the effectiveness of recovery strategies after disruptions that led to instability. These examples demonstrate how the high simulation speed and the convenience of the iPython interface allow ADM1F to complete complex analyses within minutes, much faster than computational strategies currently reported in the literature.

anaerobic co-digestion↗

Sparse matrix‐vector and matrix‐multivector products for the truncated SVD on graphics processors

Summary Many practical algorithms for numerical rank computations implement an iterative procedure that involves repeated multiplications of a vector, or a collection of vectors, with both a sparse matrix and its transpose. Unfortunately, the realization of these sparse products on current high performance libraries often deliver much lower arithmetic throughput when the matrix involved in the product is transposed. In this work, we propose a hybrid sparse matrix layout, named CSRC, that combines the flexibility of some well‐known sparse formats to offer a number of appealing properties: (1) CSRC can be obtained at low cost from the popular CSR (compressed sparse row) format; (2) CSRC has similar storage requirements as CSR; and especially, (3) the implementation of the sparse product kernels delivers high performance for both the direct product and its transposed variant on modern graphics accelerators thanks to a significant reduction of atomic operations compared to a conventional implementation based on CSR. This solution thus renders considerably higher performance when integrated into an iterative algorithm for the truncated singular value decomposition (SVD), such as the randomized SVD or, as demonstrated in the experimental results, the block Golub–Kahan–Lanczos algorithm.

Aliaga, José I.↗

Toward efficient polynomial preconditioning for GMRES

Here, we present a polynomial preconditioner for solving large systems of linear equations. The polynomial is derived from the minimum residual polynomial (the GMRES polynomial) and is more straightforward to compute and implement than many previous polynomial preconditioners. Our current implementation of this polynomial using its roots is naturally more stable than previous methods of computing the same polynomial. We implement further stability control using added roots, and this allows for high degree polynomials. We discuss the effectiveness and challenges of root-adding and give an additional check for stability. In this article, we study the polynomial preconditioner applied to GMRES; however it could be used with any Krylov solver. This polynomial preconditioning algorithm can dramatically improve convergence for some problems, especially for difficult problems, and can reduce dot products by an even greater margin.

97 MATHEMATICS AND COMPUTING↗

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↗

Target–decoy false discovery rate estimation using Crema

Assigning statistical confidence estimates to discoveries produced by a tandem mass spectrometry proteomics experiment is critical to enabling principled interpretation of the results and assessing the cost/benefit ratio of experimental follow-up. The most common technique for computing such estimates is to use target-decoy competition (TDC), in which observed spectra are searched against a database of real (target) peptides and a database of shuffled or reversed (decoy) peptides. TDC procedures for estimating the false discovery rate (FDR) at a given score threshold have been developed for application at the level of spectra, peptides, or proteins. Although these techniques are relatively straightforward to implement, it is common in the literature to skip over the implementation details or even to make mistakes in how the TDC procedures are applied in practice. Here we present Crema, an open-source Python tool that implements several TDC methods of spectrum-, peptide- and protein-level FDR estimation. Crema is compatible with a variety of existing database search tools and provides a straightforward way to obtain robust FDR estimates.

59 BASIC BIOLOGICAL SCIENCES↗

Impact of genotype‐calling methodologies on genome‐wide association and genomic prediction in polyploids

Abstract Discovery and analysis of genetic variants underlying agriculturally important traits are key to molecular breeding of crops. Reduced representation approaches have provided cost‐efficient genotyping using next‐generation sequencing. However, accurate genotype calling from next‐generation sequencing data is challenging, particularly in polyploid species due to their genome complexity. Recently developed Bayesian statistical methods implemented in available software packages, polyRAD, EBG, and updog, incorporate error rates and population parameters to accurately estimate allelic dosage across any ploidy. We used empirical and simulated data to evaluate the three Bayesian algorithms and demonstrated their impact on the power of genome‐wide association study (GWAS) analysis and the accuracy of genomic prediction. We further incorporated uncertainty in allelic dosage estimation by testing continuous genotype calls and comparing their performance to discrete genotypes in GWAS and genomic prediction. We tested the genotype‐calling methods using data from two autotetraploid species, Miscanthus sacchariflorus and Vaccinium corymbosum , and performed GWAS and genomic prediction. In the empirical study, the tested Bayesian genotype‐calling algorithms differed in their downstream effects on GWAS and genomic prediction, with some showing advantages over others. Through subsequent simulation studies, we observed that at low read depth, polyRAD was advantageous in its effect on GWAS power and limit of false positives. Additionally, we found that continuous genotypes increased the accuracy of genomic prediction, by reducing genotyping error, particularly at low sequencing depth. Our results indicate that by using the Bayesian algorithm implemented in polyRAD and continuous genotypes, we can accurately and cost‐efficiently implement GWAS and genomic prediction in polyploid crops.

59 BASIC BIOLOGICAL SCIENCES↗

Identifying preferential flow from soil moisture time series: Review of methodologies

Abstract Identifying and quantifying preferential flow (PF) through soil—the rapid movement of water through spatially distinct pathways in the subsurface—is vital to understanding how the hydrologic cycle responds to climate, land cover, and anthropogenic changes. In recent decades, methods have been developed that use measured soil moisture time series to identify PF. Because they allow for continuous monitoring and are relatively easy to implement, these methods have become an important tool for recognizing when, where, and under what conditions PF occurs. The methods seek to identify a pattern or quantification that indicates the occurrence of PF. Most commonly, the chosen signature is either (1) a nonsequential response to infiltrated water, in which soil moisture responses do not occur in order of shallowest to deepest, or (2) a velocity criterion, in which newly infiltrated water is detected at depth earlier than is possible by nonpreferential flow processes. Alternative signatures have also been developed that have certain advantages but are less commonly utilized. Choosing among these possible signatures requires attention to their pertinent characteristics, including susceptibility to errors, possible bias toward false negatives or false positives, reliance on subjective judgments, and possible requirements for additional types of data. We review 77 studies that have applied such methods to highlight important information for readers who want to identify PF from soil moisture data and to inform those who aim to develop new methods or improve existing ones. Core Ideas Soil moisture data can be used to identify the occurrence of preferential flow (PF) and its initiating conditions. Various data‐analysis methods to identify PF differ in susceptibility to error, bias, and subjectivity. These methods can utilize vast amounts of data from soil moisture monitoring networks to develop understanding of when, where, and under what conditions PF occurs. Newly developed methods may lead to better accuracy and reliability, and reduce the need for subjective judgments. Plain Language Summary Preferential flow through soil occurs when a large amount of water is suddenly available, as during an intense storm. This type of flow moves rapidly through the soil in distinct narrow pathways rather than moving evenly throughout the body of soil, with major consequences for groundwater resources, ecosystems, spreading of contaminants, and other vital concerns. Methods of detecting preferential flow have been developed that utilize measurements of soil water content made by sensors installed at various depths. This measurement technology has been widely implemented, many locations now having datasets years in length, and various methods have been developed for using these to identify preferential flow. The various methods are based on different features in the soil moisture records and vary in their advantages and shortcomings. In this review, we explain and evaluate these methods, highlighting important information for their implementation to identify preferential flow from soil moisture data and for efforts to develop new methods or improve existing ones.

Nimmo, John R↗

Developing Ultrahigh-Resolution E3SM Land Model for GPU Systems

Designing and refactoring complex scientific code, such as the E3SM land model (ELM), for new computing architectures is challenging. This paper presents design strategies and technical approaches to develop a data-oriented, GPU-ready ELM model using compiler directives (OpenACC/OpenMP). We first analyze the datatypes and processes in the original ELM code. Then we present design considerations for ultrahigh-resolution ELM (uELM) development for massive GPU systems. These techniques include the global data-oriented simulation workflow, domain partition, code porting and data copy, memory reduction, parallel loop restructure and flattening, and race condition detection. We implemented the first version of uELM using OpenACC targeting the NVidia GPUs in the Summit supercomputer at Oak Ridge National Laboratory. During the implementation, we developed a software tool (named SPEL) to facilitate code generation, verification, and performance tuning using these techniques. The first uELM implementation for Nvidia GPUs on Summit delivered promising results: 1) over 98% of the ELM code was automatically generated and tuned by scripts. Most ELM modules had better computational performances than the original ELM code for CPUs. The GPU-ready uELM is more scalable than the CPU code on fully-loaded Summit nodes. Example profiling results from several modules are also presented to illustrate the performance improvements and race condition detection. The lessons learned and toolkit developed in the study are also suitable for further uELM deployment using OpenMP on the first US exascale computer, Frontier, equipped with AMD CPUs and GPUs.

Schwartz, Peter↗

Entanglement Renormalization for Quantum Field Theories with Discrete Wavelet Transforms

We propose an adaptation of Entanglement Renormalization for quantum field theories that, through the use of discrete wavelet transforms, strongly parallels the tensor network architecture of the Multiscale Entanglement Renormalization Ansatz (a.k.a. MERA). Our approach, called wMERA, has several advantages of over previous attempts to adapt MERA to continuum systems. In particular, (i) wMERA is formulated directly in position space, hence preserving the quasi-locality and sparsity of entanglers; and (ii) it enables a built-in RG flow in the implementation of real-time evolution and in computations of correlation functions, which is key for efficient numerical implementations. As examples, we describe in detail two concrete implementations of our wMERA algorithm for free scalar and fermionic theories in (1+1) spacetime dimensions. Possible avenues for constructing wMERAs for interacting field theories are also discussed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Efficient Quantum Gibbs Samplers with Kubo–Martin–Schwinger Detailed Balance Condition

Lindblad dynamics and other open-system dynamics provide a promising path towards efficient Gibbs sampling on quantum computers. In these proposals, the Lindbladian is obtained via an algorithmic construction akin to designing an artificial thermostat in classical Monte Carlo or molecular dynamics methods, rather than being treated as an approximation to weakly coupled system-bath unitary dynamics. Recently, Chen, Kastoryano, and Gilyén (arXiv:2311.09207) introduced the first efficiently implementable Lindbladian satisfying the Kubo–Martin–Schwinger (KMS) detailed balance condition, which ensures that the Gibbs state is a fixed point of the dynamics and is applicable to non-commuting Hamiltonians. This Gibbs sampler uses a continuously parameterized set of jump operators, and the energy resolution required for implementing each jump operator depends only logarithmically on the precision and the mixing time. In this work, we build upon the structural characterization of KMS detailed balanced Lindbladians by Fagnola and Umanità, and develop a family of efficient quantum Gibbs samplers using a finite set of jump operators (the number can be as few as one), akin to the classical Markov chain-based sampling algorithm. Compared to the existing works, our quantum Gibbs samplers have a comparable quantum simulation cost but with greater design flexibility and a much simpler implementation and error analysis. Moreover, it encompasses the construction of Chen, Kastoryano, and Gilyén as a special instance.

97 MATHEMATICS AND COMPUTING↗

Spatiotemporal pattern detection, generation, and computation with circuits

Abstract Implementations of neurons, delays, and synapse circuits are presented with simulations. These neural elements are used to create two small spiking neural networks, the Rate-Window and Order-Biased clusters, which are capable of detecting simple two-spike spatiotemporal patterns. A simple pattern detecting network (SPDN) is created by combining the Rate-Window and Order-Biased clusters, where clusters are small spiking neural networks, and its simple pattern detection ability is demonstrated in simulation. The SPDN is used to implement a complex pattern detecting network (CPDN) and its complex pattern detection ability is demonstrated in simulation. Methods for generating arbitrary spatiotemporal patterns are presented. The CPDN and spatiotemporal pattern generation methods are then used to implement a novel spatiotemporal computing paradigm based on detecting and responding to spatiotemporal symbols. A simulation of a spatiotemporal half adder is presented to demonstrate the computing paradigm.

97 - MATHEMATICS AND COMPUTING↗

Zonal-Based Emission Source Term Model for Predicting Particulate Emission Factors in Wildfire Simulations

A physics/chemistry-based numerical model for predicting the emission of fine particles from wildfires is proposed. This model implements the fundamental mechanisms of soot formation in a combustion environment: soot nucleation, surface growth, agglomeration, oxidation, and particle fragmentation. These mechanisms occur on a scale too fine for the discretization of most wildfire models, which need to simulate landscape-scale dynamics. As a result this model implements a zonal approach, where the computed soot particle distribution is partitioned into process zones within a single resolved grid cell. These process zones include: an inception zone (for nucleation), a heating zone (for coagulation, surface growth, and fragmentation), a reaction zone (for oxidation), and a quenched zone (for atmospheric processes). Governing mechanisms are applied to the appropriate zones to predict total particle growth and emission. Additionally, the proposed model is implemented into HIGRAD/FIRETEC, a physics-based wildfire simulation code which couples interactions between fire, fuels, atmosphere, and topography on a landscape scale. Fire simulations among grasslands and conifer forests are performed and compared against experimental data for emission factors.

54 ENVIRONMENTAL SCIENCES↗

Realization of the Werner-Holevo and Landau-Streater Quantum Channels for Qutrits on Quantum Computers.

We realize the Landau-Streater (LS) and Werner-Holevo (WH) quantum channels for qutrits on IBM quantum computers. These channels correspond to the interaction between a qutrit and its environment that results in the globally unitarily covariant qutrit transformation violating the multiplicativity of the maximal p-norm. Our realization of the LS and WH channels is based on embedding the qutrit states into states of two qubits and using the single-qubit and two-qubit CNOT gates to implement the specific interaction. We employ the standard quantum gates, hence the developed algorithm suits any quantum computer. We run our algorithm on a 5-qubit computer and a 20-qubit computer, as well as on a simulator. We quantify the quality of the implemented channels comparing their action on different input states with theoretical predictions. The overall efficiency is quantified by the fidelity between the theoretical and experimental Choi states implemented on the 20-qubit computer.

completely-positive trace-preserving map↗

Pyomo.GDP: an ecosystem for logic based modeling and optimization development

We present three core principles for engineering-oriented integrated modeling and optimization tool sets—intuitive modeling contexts, systematic computer-aided reformulations, and flexible solution strategies—and describe how new developments in Pyomo.GDP for Generalized Disjunctive Programming (GDP) advance this vision. We describe a new logical expression system implementation for Pyomo.GDP allowing for a more intuitive description of logical propositions. The logical expression system supports automated reformulation of these logical constraints to linear constraints. We also describe two new logic-based global optimization solver implementations built on Pyomo.GDP that exploit logical structure to avoid “zero-flow” numerical difficulties that arise in nonlinear network design problems when nodes or streams disappear. These new solvers also demonstrate the capability to link to external libraries for expanded functionality within an integrated implementation. We present these new solvers in the context of a flexible array of solution paths available to GDP models. Finally, we present results on a new library of GDP models demonstrating the value of multiple solution approaches.

42 ENGINEERING↗

Distributed out-of-memory NMF on CPU/GPU architectures

We propose an efficient distributed out-of-memory implementation of the non-negative matrix factorization (NMF) algorithm for heterogeneous high-performance-computing systems. The proposed implementation is based on prior work on NMFk, which can perform automatic model selection and extract latent variables and patterns from data. In this work, we extend NMFk by adding support for dense and sparse matrix operation on multi-node, multi-GPU systems. The resulting algorithm is optimized for out-of-memory problems where the memory required to factorize a given matrix is greater than the available GPU memory. Memory complexity is reduced by batching/tiling strategies, and sparse and dense matrix operations are significantly accelerated with GPU cores (or tensor cores when available). Input/output latency associated with batch copies between host and device is hidden using CUDA streams to overlap data transfers and compute asynchronously, and latency associated with collective communications (both intra-node and inter-node) is reduced using optimized NVIDIA Collective Communication Library (NCCL) based communicators. Benchmark results show significant improvement, from 32X to 76x speedup, with the new implementation using GPUs over the CPU-based NMFk. Good weak scaling was demonstrated on up to 4096 multi-GPU cluster nodes with approximately 25,000 GPUs when decomposing a dense 340 Terabyte-size matrix and an 11 Exabyte-size sparse matrix of density 10 -6 .

97 MATHEMATICS AND COMPUTING↗

Performance evaluations of signed and unsigned noisy approximate quantum Fourier arithmetic

The Quantum Fourier Transform (QFT) grants competitive advantages, especially in resource usage and circuit approximation, for performing arithmetic operations on quantum computers, and offers a potential route toward a numerical quantum-computational paradigm. In this paper, we utilize efficient techniques to implement QFT-based integer addition and multiplications. These operations are fundamental to various quantum applications including Shor’s algorithm, weighted-sum optimization problems in data processing and machine learning, and quantum algorithms requiring inner products. We carry out performance evaluations of these implementations based on IBM’s superconducting-qubit architecture using different compatible noise models. We isolate the sensitivity of the component quantum circuits on both one-/two-qubit gate error rates, and the number of the arithmetic operands’ superposed integer states. We analyze performance and identify the most effective approximation depths for unsigned quantum addition and quantum multiplication within the given context. We then perform a similar analysis of signed addition and compare to the unsigned results. We observe significant dependency of the optimal approximation depth on the degree of machine noise and the number of superposed states in certain performance regimes. Finally, we elaborate on the algorithmic challenges—relevant to signed, unsigned, modular and non-modular versions—that could also be applied to current implementations of QFT-based subtraction, division, exponentiation, and their potential tensor extensions. Here, we analyze the performance trends in our results and speculate on possible future developments within this computational paradigm.

Computational models↗

Organizational and psychological measures for data center energy efficiency: barriers and mitigation strategies

Abstract It was last estimated that in 2020, data centers comprised approximately 2% of total US electricity consumption, with an estimated annual growth rate of 4%. As our country increasingly relies on information technology (IT), our data centers (DCs) will need to increase their energy efficiency (EE) to stabilize their energy consumption. The task of studying EE in DCs is complicated by the interconnected nature of humans and mission-critical technical systems. Moreover, the literature tends to focus on technology solutions such as improvements to IT equipment, cooling infrastructure, and software, without addressing organizational and psychological drivers. Our research demystifies the complex interactions between humans and DCs, by asking What non-technical barriers impede EE investment decision-making and/or implementing energy management strategies? To begin to answer this question, we perform a literature review of 86 resources, ranging from peer-reviewed journal publications to handbooks. We also consider related fields such as organizational behavioral management and energy intensive buildings. We develop a public Zotero library, perform content coding, and complete a rudimentary network analysis. Our findings from the literature review suggest that (1) technological solutions are abundant in the literature but fall short of providing practical guidance on the pitfalls of implementation, (2) making energy efficiency a priority at the executive level of organizations will be largely ineffective if the IT and facilities staff are not directly incentivized to increase EE, and (3) there is minimal current understanding of how the individual psychologies of IT and facilities staff affect EE implementation in DCs. In the next phase of our research, we plan to interview data center operators/experts to ground-truth our literature findings and collaboratively design decarbonization policy solutions that target organizational structure, empower individual staff, and foster a supportive external market.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Pathways to commercial building plug and process load efficiency and control

Abstract To accomplish net-zero carbon emissions in the built environment by 2050, we must equitably decarbonize commercial buildings, including reducing plug and process loads (PPLs). PPLs are plug-in or hardwired electric and gas loads that are not associated with major building end uses like lighting and HVAC. Research shows PPL energy reduction strategies and control technologies have the potential to save energy. But even when implemented, these savings have rarely been achieved and there has not been widespread uptake in U.S. commercial buildings. We investigate why these technologies and strategies have not seen widespread adoption and identify behavior and technology pathways to increase PPL reduction in U.S. commercial buildings. We examined behaviors of commercial building stakeholders through 44 interviews and cross-referenced qualitative analysis findings with in-depth technical knowledge of existing PPL control technologies and reduction strategies. PPL control implementation must be paired with management strategies, such as occupant engagement and training, to achieve optimal savings, and best practices should be disseminated across the industry. We found that increasing access to cost and energy savings data will promote uptake of PPL control technologies and allow designers to better incorporate PPLs into building design. Improving access to funding for PPL energy efficiency projects and addressing the split-incentive problem will increase adoption of PPL efficiency and control. Code bodies should continue to include PPL monitoring and reduction measures in energy codes. Key building stakeholders, including cybersecurity and information technology teams, should be involved in PPL monitoring and reduction strategy processes for successful implementation.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗