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DOE OSTI2024

ECP libraries and tools: An overview

The Exascale Computing Project (ECP) Software Technology and Co-Design teams addressed the growing complexities in high-performance computing (HPC) by developing scalable software libraries and tools that leverage exascale system capabilities. As we enter the exascale era, the need for reusable, optimized software solutions that can handle the unique challenges posed by these systems becomes increasingly important. The primary challenges the ECP teams faced were to create software libraries and tools that are performant on exascale architectures and portable and usable across diverse hardware platforms. Efforts addressed issues related to concurrent execution, memory management, and the integration of heterogeneous computing resources, such as GPUs from multiple vendors. The ECP’s strategy involved a structured development process encompassing the creation, optimization, and deployment of software in collaboration with industry, academia, and national laboratories. The project was organized into several technical areas: co-design of domain-specific suites with target applications, programming models and runtimes, development tools, mathematical libraries, data and visualization tools, and software ecosystem and delivery mechanisms. ECP has successfully developed a large portfolio of software libraries and tools that demonstrate significant improvements in performance and scalability on exascale systems. These products have been integrated into the Department of Energy’s computing facilities, supporting various scientific applications and ensuring robust performance across different hardware setups. ECP advancements in software development for exascale computing highlight the importance of a collaborative and adaptive approach to handling next-generation HPC systems complexities. The lessons learned emphasize the need for continuous engagement with end-users and vendors, and the importance of maintaining a balance between innovation and practical implementation. Future efforts will focus on ensuring scalability, keeping pace with rapid hardware advancements, and further enhancing the interoperability and usability of the software ecosystem. In conclusion, subsequent articles in this special issue provide in-depth discussions and case studies into specific library and tool efforts.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

Instantaneous and cycle optimization of fuel usage on a dual fuel vehicle leveraging gasoline and natural gas

Recent increases in natural gas supply have led to a desire to leverage this fuel in the transportation sector. Dual fuel engines provide a platform on which to use natural gas efficiently; these engines, however, require new hardware and new control strategies to properly utilize two fuels simultaneously. This paper explores the impact of implementing dual fuel capabilities on a sedan and demonstrates that a dual fuel E10 and compressed natural gas engine is able to improve the average engine efficiency by up to 6.5% compared to a single fuel engine on standard drive cycles. An optimal control technique is also developed, and the proposed approach allows factors including fuel cost and fuel availability to be taken into account. Optimization at each time instant is investigated and contrasted with optimization over the entire cycle. Cycle optimization is shown to have particular value for cases in which the level in one fuel tank is low.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2024

Distributed Multi-GPU Community Detection on Exascale Computing Platforms

Community detection is a fundamental operation in graph mining, and by uncovering hidden structures and patterns within complex systems it helps solve fundamental problems pertaining to social networks, such as information diffusion, epidemics, and recommender systems. Scaling graph algorithms for massive networks becomes challenging on modern distributed-memory multi-GPU (Graphics Processing Unit) systems due to limitations such as irregular memory access patterns, load imbalances, higher communication-computation ratios, and cross-platform support. We present a novel algorithm HiPDPL-GPU (distributed parallel Louvain) to address these challenges. We conduct experiments involving different partitioning techniques to achieve optimized performance of HiPDPL-GPU on the two largest supercomputers: Frontier and Summit. Remarkably, HiPDPL-GPU processes a graph with 4.2 billion edges in less than 3 minutes using 1024 GPUs. Qualitatively performance of HiPDPL-GPU is similar or better compared to other state-of-the-art CPU- and GPU-based implementations. While prior GPU implementations have predominantly employed CUDA, our first-of-its-kind implementation for community detection is cross-platform, accommodating both AMD and NVIDIA GPUs.

graph algorithms, high performance comptuing↗

DOE OSTI2018

Effect of Electrode Geometry on the Classification Performance of Rapid Evaporative Ionization Mass Spectrometric (REIMS) Bacterial Identification

The recently developed automated, high-throughput monopolar REIMS platform is suited for the identification of clinically important microorganisms. Although already comparable to the previously reported bipolar forceps method, optimization of the geometry of monopolar electrodes, at the heart of the system, holds the most scope for further improvements to be made. For this, sharp tip and round shaped electrodes were optimized to maximize species-level classification accuracy. Following optimization of the distance between the sample contact point and tube inlet with the sharp tip electrodes, the overall cross-validation accuracy improved from 77% to 93% in negative and from 33% to 63% in positive ion detection modes, compared with the original 4 mm distance electrode. As an alternative geometry, round tube shaped electrodes were developed. Geometry optimization of these included hole size, number, and position, which were also required to prevent plate pick-up due to vacuum formation. Additional features, namely a metal “X”-shaped insert and a pin in the middle were included to increase the contact surface with a microbial biomass to maximize aerosol production. Following optimization, cross-validation scores showed improvement in classification accuracy from 77% to 93% in negative and from 33% to 91% in positive ion detection modes. Supervised models were also built, and after the leave 20% out cross-validation, the overall classification accuracy was 98.5% in negative and 99% in positive ion detection modes. This suggests that the new generation of monopolar REIMS electrodes could provide substantially improved species level identification accuracies in both polarity detection modes. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2022

A scalable and tunable thermoreversible polymer for 3D human pluripotent stem cell biomanufacturing

Human pluripotent stem cells (hPSCs) are an exciting and promising source to enable cell replacement therapies for a variety of unmet medical needs. Though hPSCs can be successfully derived into numerous physiologically relevant cell types, effective translation to the clinic is limited by challenges in scalable production of high-quality cells, cellular immaturity following the differentiation process, and the use of animal-derived components in culture. To address these limitations, we have developed a fully defined, reproducible, and tunable thermoreversible polymer for high-quality, scalable 3D cell production. Our reproducible synthesis method enables precise control of gelation temperature (24°C–32°C), hydrogel stiffness (100–4000 Pa), and the prevention of any unintended covalent crosslinking. After material optimization, we demonstrated hPSC expansion, pluripotency maintenance, and differentiation into numerous lineages within the hydrogel. Overall, this 3D thermoreversible hydrogel platform has broad applications in scalable, high-quality cell production to overcome the biomanufacturing burden of stem cell therapy.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Parallel accelerated Custom Correlation Coefficient calculations for genomics applications

The massive quantities of genomic data being made available through gene sequencing techniques are enabling breakthroughs in genomic science in many areas such as medical advances in the diagnosis and treatment of diseases. Analyzing this data, however, is a computational challenge insofar as the computational costs of the relevant algorithms can grow with quadratic, cubic or higher complexity—leading to the need for leadership scale computing. In this paper we describe a new approach to calculations of the Custom Correlation Coefficient (CCC) between Single Nucleotide Polymorphisms (SNPs) across a population, suitable for parallel systems equipped with graphics processing units (GPUs) or Intel Xeon Phi processors. We describe the mapping of the algorithms to accelerated processors, techniques used for eliminating redundant calculations due to symmetries, and strategies for efficient mapping of the calculations to many-node parallel systems. Results are presented demonstrating high per-node performance and near-ideal parallel scalability with rates of more than nine quadrillion (9 × 10 15 ) elementwise comparisons achieved per second with the latest optimized code on the ORNL Titan system, this being orders of magnitude faster than rates achieved using other codes and platforms as reported in the literature. Also it is estimated that as many as 90 quadrillion (90 × 10 15 ) comparisons per second may be achievable on the upcoming ORNL Summit system, an additional 10X performance increase. Finally, in a companion paper we describe corresponding techniques applied to calculations of the Proportional Similarity metric for comparative genomics applications.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Engineering Rhodosporidium toruloides for production of 3-hydroxypropionic acid from lignocellulosic hydrolysate

Microbial production of valuable bioproducts is a promising route towards green and sustainable manufacturing. The oleaginous yeast, Rhodosporidium toruloides, has emerged as an attractive host for the production of biofuels and bioproducts from lignocellulosic hydrolysates. 3-hydroxypropionic acid (3HP) is an attractive platform molecule that can be used to produce a wide range of commodity chemicals. This study focuses on establishing and optimizing the production of 3HP in R. toruloides. As R. toruloides naturally has a high metabolic flux towards malonyl-CoA, we exploited this pathway to produce 3HP. Upon finding the yeast capable of catabolizing 3HP, we then implemented functional genomics and metabolomic analysis to identify the catabolic pathways. Deletion of a putative malonate semialdehyde dehydrogenase gene encoding an oxidative 3HP pathway was found to significantly reduce 3HP degradation. We further explored monocarboxylate transporters to promote 3HP transport and identified a novel 3HP transporter in Aspergillus pseudoterreus by RNA-seq and proteomics. Combining these engineering efforts with media optimization in a fed-batch fermentation resulted in 45.4 g/L 3HP production. This represents one of the highest 3HP titers reported, and the highest titer produced from lignocellulosic hydrolysate to the best of our knowledge. This work demonstrates microbial production of 3HP in R. toruloides from lignocellulosic hydrolysate at high titers, and it represents a significant step toward enabling industrial production of 3HP in the future.

3-Hydroxypropionic acid↗

DOE OSTI2022

WfBench: Automated Generation of Scientific Workflow Benchmarks

The prevalence of scientific workflows with high computational demands calls for their execution on various distributed computing platforms, including large-scale leadership-class high-performance computing (HPC) clusters. To handle the deployment, monitoring, and optimization of workflow executions, many workflow systems have been developed over the past decade. There is a need for workflow benchmarks that can be used to evaluate the performance of workflow systems on current and future software stacks and hardware platforms.We present a generator of realistic workflow benchmark specifications that can be translated into benchmark code to be executed with current workflow systems. Our approach generates workflow tasks with arbitrary performance characteristics (CPU, memory, and I/O usage) and with realistic task dependency structures based on those seen in production workflows. We present experimental results that show that our approach generates benchmarks that are representative of production workflows, and conduct a case study to demonstrate the use and usefulness of our generated benchmarks to evaluate the performance of workflow systems under different configuration scenarios.

Coleman, Taina↗

DOE OSTI2017

Volumetric Additive Manufacturing of Polymer Structures by Holographically Projected Light Fields

As additive manufacturing technologies proliferate and mature, overcoming some of their process limitations becomes increasingly important for the continued expansion of practical applications. Two such limitations that arise from layer-based fabrication are slow speed and geometric constraints (which include poor surface quality and challenges fabricating span, cantilever, and overhang elements). Moving beyond point-by-point and layer-by-layer approaches, the ability to generate a complex 3D volume as a unit operation has the potential to overcome these limitations. Since holography has been extensively studied as a means for storage and retrieval of 3D geometrical information, this dissertation explores the use of holographically-shaped light fields for producing three-dimensional structures in a “volume at once” approach. Leveraging advances in spatial light modulator (SLM) technology, phase-controlled light fields are projected into photopolymer resin to cure a desired geometry. By overlapping multiple sub-regions of a single light field within the target volume, the successful fabrication of non-periodic complex 3D geometries is demonstrated by single exposures on timescales of seconds. This dissertation presents a complete prototype platform that makes this approach possible, comprising a suitable hardware configuration along with the computational algorithms necessary to calculate and optimize the required optical fields. A study of the photopolymerization kinetics is also carried out, to determine the boundaries of usable process parameters such as resin absorbance and available light intensity. The results indicate that low-absorbing resins containing ~0.1% photoinitiator, illuminated at modest powers (~10-100 mW) may be used to produce full 3D structures from 1-10 second exposures, with volume build rates exceeding 100 cm3/hr, without layering and with no need for a substrate or support material.

36 MATERIALS SCIENCE↗

DOE OSTI2021

TEAM Project Review, Year 2

This report summarizes our research activities within the TEAM project between December 2020 and December 2021, funded by the ASCR Advanced Research in Quantum Computing program. During the reporting period the LLNL-MSU team has made progress on several fronts. An overarching goal of the team is to provide a comprehensive suite of software tools that can be used for the Characterize-Optimize-Compute loop needed to implement and execute algorithms on quantum devices. We are concurrently developing lightweight solvers that can be used on desktop computers to find optimal control pulses and to characterize small quantum systems (consisting of a few transmons and cavities). However, desktop computers are insufficient for simulating and characterizing larger quantum systems. We have therefore also developed parallel, distributed memory, simulators and optimization solvers, both for open and closed quantum systems. These parallel solvers have, for example, been used to study quantum optimal control for pure-state preparation, utilizing 1000’s of cores on a modern high-performance computing (HPC) platform.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

Efficient genetic code expansion tools enable in vivo study of lysine acetylation in non-model bacteria

Recent proteomic advancements have revealed widespread Nε-lysine acetylation in pathways governing pathogenicity, metabolism, and antibiotic resistance in bacteria. The spontaneous, non-specific nature of this modification in prokaryotes obscures its biological role, necessitating prokaryotic specific in vivo interrogation systems. Genetic Code Expansion (GCE) offers a powerful method to investigate the roles and regulation dynamics of acetyl-lysine in vivo with the precise incorporation of a suite of non-canonical amino acids, including acetyl-lysine analogs. However, its use has been largely restricted to E. coli strains due to challenges associated with implementation and optimization of the technology in more diverse bacterial strains. Here, we present a bacterial host-agnostic, readily optimizable GCE platform designed to site-specifically incorporate non-canonical amino acids into target proteins within living bacteria. We further demonstrate the versatility of this technology by showcasing, for the first time, the successful incorporation of acetyl-lysine in a non- E. coli bacterium.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Clean Water Production in Cooling Towers

This project developed and demonstrated a novel technology that produces clean water from cooling tower recirculating water by using the natural evaporation and condensation cycle inside cooling towers. The system captures the escaping plume and converts blowdown quality water into high purity water suitable for on-site reuse such as boiler feed. The technology uses electric fields to ionize exhaust plumes, charge the entrained droplets, and direct them toward collection electrodes where they coalesce and flow downward. This allows water recovery at a low energy cost while reducing visible plume emissions. In addition, we developed a complementary software platform that improves overall cooling tower performance. The system uses wireless sensors and physics-based machine learning algorithms to optimize key parameters of the cooling process. For power generation facilities, this increases the thermal efficiency of the cooling loop and condenser, resulting in measurable cycle efficiency gains. Improvements of one percent or more can deliver significant increases in electricity production for the same fuel input.

01 COAL, LIGNITE, AND PEAT↗

DOE OSTI2024

Distributed Multi-GPU Community Detection on Exascale Computing Platforms

Community detection is a fundamental operation in graph mining, and by uncovering hidden structures and patterns within complex systems it helps solve fundamental problems pertaining to social networks, such as information diffusion, epidemics, and recommender systems. Scaling graph algorithms for massive networks becomes challenging on modern distributed-memory multi-GPU (Graphics Processing Unit) systems due to limitations such as irregular memory access patterns, load imbalances, higher communication-computation ratios, and cross-platform support. We present a novel algorithm HiPDPL-GPU (Distributed Parallel Louvain) to address these challenges. We conduct experiments involving different partitioning techniques to achieve an optimized performance of HiPDPL-GPU on the two largest supercomputers: Frontier and Summit. Remarkably, HiPDPL-GPU processes a graph with 4.2 billion edges in less than 3 minutes using 1024 GPUs. Qualitatively, the performance of HiPDPL-GPU is similar or better compared to other state-of-the-art CPU- and GPU-based implementations. While prior GPU implementations have predominantly employed CUDA, our first-of-its-kind implementation for community detection is cross-platform, accommodating both AMD and NVIDIA GPUs.

Sattar, Naw Safrin↗

DOE OSTI2019

An investigation on the impact of halidization on substituted dimethoxybenzenes

Functionalized organic molecules are emerging as charge storage materials in electrochemical technologies as the breadth and diversity of the organic design space offers the possibility of purpose-built materials with property sets optimized for a particular application. First developed as overcharge protection materials in lithium-ion batteries, substituted dialkoxybenzenes represent a potentially promising molecular platform for advancing soluble charge storage materials. In this study, we systematically substitute a series of halide groups at the 2- and 5-positions of the 1,4-dimethoxybenzene core, investigate the impact the halide groups have on molecular properties using electrochemical and spectroscopy methods, and compare these results to those of 2,5-dimethyl-1,4-dimethoxybenzene (25DDB), a previously reported derivative. In general, we observe that introduction of heavy halogen atoms leads to decreased gravimetric capacity as compared to 25DDB, but concomitantly improves solubility and redox potentials. As the halide functional group increases in size, the active material becomes less stable in its oxidized state as evinced by both cyclic voltammetry and bulk electrolysis cycling. None of the halogenated species are as stable as 25DDB indicating that these materials may be better suited for applications with more rapid cycling conditions (e.g., redox shuttling). More broadly, these results may serve as a useful data set for computational methods for materials discovery and optimization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

Surface plasmons and Bloch surface waves: Towards optimized ultra-sensitive optical sensors

In photonics, the field concentration and enhancement have been major objectives for achieving size reduction and device integration. Plasmonics offers resonant field confinement and enhancement, but ultra-sharp optical resonances in all-dielectric multi-layer thin films are emerging as a powerful contestant. Thus, applications capitalizing upon stronger and sharper optical resonances and larger field enhancements could be faced with a choice for the superior platform. Here in this paper, we present a comparison between plasmonic and dielectric multi-layer thin films for their resonance merits. We show that the remarkable characteristics of the resonance behavior of optimized dielectric multi-layers can outweigh those of their metallic counterpart.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2024

Demonstrating the Potential of Adaptive LMS Filtering on FPGA-Based Qubit Control Platforms for Improved Qubit Readout in 2D and 3D Quantum Processing Units

Advancements in quantum computing underscore the critical need for sophisticated qubit readout techniques to accurately discern quantum states. This abstract presents our research intended for optimizing readout pulse fidelity for 2D and 3D Quantum Processing Units (QPUs), the latter coupled with Superconducting Radio Frequency (SRF) cavities. Focusing specifically on the application of the Least Mean Squares (LMS) adaptive filtering algorithm, we explore its integration into the FPGA-based control systems to enhance the accuracy and efficiency of qubit state detection by improving Signal-to-Noise Ratio (SNR). Implementing the LMS algorithm on the Zynq UltraScale+ RFSoC Gen 3 devices (RFSoC 4x2 FPGA and ZCU216 FPGA) using the Quantum Instrumentation Control Kit (QICK) open-source platform, we aim to dynamically test and adjust the filtering parameters in real-time to characterize and adapt to the noise profile presented in quantum computing readout signals. Our preliminary results demonstrate the LMS filter's capability to maintain high readout accuracy while efficiently managing FPGA resources. These findings are expected to contribute to developing more reliable and scalable quantum computing architectures, highlighting the pivotal role of adaptive signal processing in quantum technology advancements.

Johnson, Hans↗

DOE OSTI2024

Demonstrating the Potential of Adaptive LMS Filtering on FPGA-Based Qubit Control Platforms for Improved Qubit Readout in 2D and 3D Quantum Processing Units

Johnson, Hans↗

DOE OSTI2023

Functional Assessment of Shell Recharge Solutions' SKY™ Platform OpenADR Capability

The project’s overall objective is to research, develop, and conduct a wide-scale demonstration of a utility smart charge management (SCM) system to develop optimal managed charging structures for grid value, evaluate the impact of EV charging on local distribution utility operations, and evaluate the utilities’ ability to control electronic vehicle (EV) charging load based on grid conditions. This report covers Argonne’s validation testing in the first period of the project, the objective of which was to determine the current managed charging functionality of the EVSE hardware, the network and the vehicle telematics software solution and understand gaps that need to be addressed prior to a large-scale demonstration.

24 POWER TRANSMISSION AND DISTRIBUTION↗