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At least 469 records · Page 26

Biomolecular and Characterization Imaging Science Program: 2023 Principal Investigator Meeting Proceedings

The 2023 U.S. Department of Energy (DOE) Biological and Environmental Research (BER) program’s Biomolecular Characterization and Imaging Science (BCIS) Principal Investigator Meeting expanded in scope from previous Bioimaging Science Program (BSP) meetings to include BER Structural Biology and Imaging Resources, which are located largely at DOE Office of Science national laboratories. The BCIS meeting was part of BER’s Biological Systems Science Division (BSSD) annual PI meeting, which was held April 17–19, 2023, and featured parallel meetings of the BCIS and Genomic Science programs (GSP). The meetings were held together to encourage networking and idea exchange across technologies and biological application areas, forging new multidisciplinary collaborations among researchers from adjacent BSSD programmatic areas. Two joint BCIS-GSP sessions were held: “BCIS Technologies for Investigating the Rhizosphere” and “Joint Emerging Topics and Technologies.” The rhizosphere session focused on scientific findings from BCIS and GSP PIs, including national laboratory collaborations. The intent was to identify new opportunities to measure and understand the complex community of microbes, roots, and soils that support plant growth under challenging environmental conditions. The emerging technologies session highlighted forward-looking approaches and tools to tackle challenges within the scope of BSSD research on investigating and modifying genomic and molecular function. A final interactive discussion of the BCIS program was led by plenary session chairs.

59 BASIC BIOLOGICAL SCIENCES↗

Summary of Savannah River Site FY23 Salt Waste Qualification Data

The Savannah River National Laboratory (SRNL) analyzed samples from Savannah River Site (SRS) Waste Tanks 41H and 21H to support qualification of Salt Waste Processing Facility (SWPF) Waste Batches 8 and 9 for processing (the FY23 Salt Batch Qualification samples). These Tanks (i.e. 41H and 21H) are blend tanks for feed to SWPF. None of the samples displayed any unusual or unexpected characteristics such as large amounts of solids, floating solids, or unusual color. Characterization of these samples confirmed similar chemical composition and characteristics to previous salt waste batches. The results for Batches 8 and 9 were provided by SRNL to Savannah River Mission Completion (SRMC), the Liquid Waste Operations subcontractor at SRS, as External Sample Results (Laboratory Information Management System (LIMS)) Reports. Additionally, a separate technical memo was issued by SRNL to report re-test data for Batch 8 for Cs-137 for filtered samples only which were run at the request of SWPF. For Batch 9, a set of samples was also analyzed in parallel by the SWPF-Analytical Laboratory (SWPF-AL). The SWPF-AL data is included herein for comparison with the SRNL data where applicable. The analytical results (both rapid, typically 4 weeks, and long term, typically 8 weeks) for Batches 8 and 9 are now summarized and discussed in this technical report.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

GASNet-EX RMA Communication Performance on Recent Supercomputing Systems

Partitioned Global Address Space (PGAS) programming models, typified by systems such as Unified Parallel C (UPC) and Fortran coarrays, expose one-sided Remote Memory Access (RMA) communication as a key building block for High Performance Computing (HPC) applications. Architectural trends in supercomputing make such programming models increasingly attractive, and newer, more sophisticated models such as UPC++, Legion and Chapel that rely upon similar communication paradigms are gaining popularity. GASNet-EX is a portable, open-source, high-performance communication library designed to efficiently support the networking requirements of PGAS runtime systems and other alternative models in emerging exascale machines. The library is an evolution of the popular GASNet communication system, building upon 20 years of lessons learned. We present microbenchmark results which demonstrate the RMA performance of GASNet-EX is competitive with MPI implementations on four recent, high-impact, production HPC systems. These results are an update relative to previously published results on older systems. The networks measured here are representative of hardware currently used in six of the top ten fastest supercomputers in the world, and all of the exascale systems on the U.S. DOE road map.

Hargrove, Paul H↗

m-CUBES An efficient and portable implementation of multi-dimensional integration for gpus

The task of multi-dimensional numerical integration is frequently encountered in physics and other scientific fields, e.g., in modeling the effects of systematic uncertainties in physical systems and in Bayesian parameter estimation. Multi-dimensional integration is often time-prohibitive on CPUs. Efficient implementation on many-core architectures is challenging as the workload across the integration space cannot be predicted a priori. We propose m-Cubes, a novel implementation of the well-known Vegas algorithm for execution on GPUs. Vegas transforms integration variables followed by calculation of a Monte Carlo integral estimate using adaptive partitioning of the resulting space. m-Cubes improves performance on GPUs by maintaining relatively uniform workload across the processors. As a result, our optimized Cuda implementation for Nvidia GPUs outperforms parallelization approaches proposed in past literature. We further demonstrate the efficiency of m-Cubes by evaluating a six-dimensional integral from a cosmology application, achieving significant speedup and greater precision than the CUBA library's CPU implementation of VEGAS. We also evaluate m-Cubes on a standard integrand test suite. m-Cubes outperforms the serial implementations of the Cuba and GSL libraries by orders of magnitude speedup while maintaining comparable accuracy. Our approach yields a speedup of at least 10 when compared against publicly available Monte Carlo based GPU implementations. In summary, m-Cubes can solve integrals that are prohibitively expensive using standard libraries and custom implementations. A modern C++ interface header-only implementation makes m-Cubes portable, allowing its utilization in complicated pipelines with easy to define stateful integrals. Compatibility with non-Nvidia GPUs is achieved with our initial implementation of m-Cubes using the Kokkos framework.

Sakiotis, Ioannis↗

A parallel-plate avalanche counter for the prompt fission neutron spectrum measurement

Neutrons, gamma’s, and fission fragments are among the prompt fission observables. Their precision measurements are fundamental to advance our understanding of fission and any application of fission. For our programmatic need, the χ matrix, which defines as the outgoing neutron spectrum as a function of incoming neutron energy, is sparsely populated and poorly measured for 233,235,238 U and 239,240 Pu. To improve the quality of those χ matrices, a joint LANLLLNL project was undertaken to measure their prompt fission neutron spectra at the LANSCE/WNR facility using neutron detector arrays and a charged-particle detector for the fission-fragment detection. A typical setup is shown in Fig. 1, where one of neutron detector array with a charged-particle detector is given.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

In-depth analysis on parallel processing patterns for high-performance Dataframes

The Data Science domain has expanded monumentally in both research and industry communities during the past decade, predominantly owing to the Big Data revolution. Artificial Intelligence (AI) and Machine Learning (ML) are bringing more complexities to data engineering applications, which are now integrated into data processing pipelines to process terabytes of data. Typically, a significant amount of time is spent on data preprocessing in these pipelines, and hence improving its efficiency directly impacts the overall pipeline performance. The community has recently embraced the concept of Dataframes as the de-facto data structure for data representation and manipulation. However, the most widely used serial Dataframes today (R, pandas) experience performance limitations while working on even moderately large data sets. We believe that there is plenty of room for improvement by taking a look at this problem from a high-performance computing point of view. In a prior publication, we presented a set of parallel processing patterns for distributed dataframe operators and the reference runtime implementation, Cylon. In this paper, we are expanding on the initial concept by introducing a cost model for evaluating the said patterns. Furthermore, we evaluate the performance of Cylon on the ORNL Summit supercomputer.

97 MATHEMATICS AND COMPUTING↗

Asi Nuclear Energy Sensors Data Portal Chatbot And Data Structuring Tool

The Idaho National Laboratory (INL) is advancing the development of an AI-powered chatbot and data structuring tool specifically designed to accelerate data mining processes for sensor-related information and seamlessly integrate the results into the ASI Sensors Data Portal (https://nes.energy.gov/). By doing so, the software aims to enhance the accessibility, usability, and organization of sensor data for nuclear energy applications. The software initial phase focuses on retrieving comprehensive datasets, prioritizing the past five years of publicly available information from the Office of Scientific and Technical Information (OSTI). These datasets will be meticulously processed to ensure compatibility, employing cleaning and preprocessing steps to eliminate irrelevant, incomplete, or corrupted information, thus establishing a robust foundation for subsequent AI use. The data will serve as the backbone for training an AI model and chatbot, which will act as an interactive tool enabling users to ask complex, context-specific questions and receive accurate, validated answers derived from constrained literature. In parallel, the project incorporates a data structuring process supported by AI to organize sensor information from multiple sources into a standardized format. This structured data will include detailed sensor specifications, such as measurement range, applications, accuracy, and operating conditions, generated and documented with AI. These specifications will be systematically integrated into the sensor portal. To maintain the highest levels of accuracy and relevance, all AI-generated outputs will be reviewed and validated by subject matter experts (SMEs), with additional fields or parameters added as needed. Future stages of the project aim to expand the dataset beyond OSTI to include other sources and potentially incorporate unclassified controlled information (UCI) with restricted access protocols to address security and confidentiality requirements.

Mapes, NormanJ. [Idaho National Laboratory (INL), ↗

A 1D coupled transport/cold plasma wave model for parallel ponderomotive density modification near RF actuators

The plasma density profile close to RF actuators plays a vital role in the efficiency of power coupling from the antenna to the core plasma of fusion devices. Nonlinear interactions can be significant when considering the interaction of applied RF power and the tenuous SOL plasma, and the inclusion of this region in computational analysis is essential to providing robust predictive simulations of plasma response to RF application. Of particular interest is the observed density modification during RF operation. Here we present a self consistent description of the nonlinear ponderomotive force in the antenna near field region, via coupling a 1D field aligned transport model with a 1D cold plasma wave model. Results are presented, which show a parallel electric field of 300 Vm -1 drove a density reduction of ~ 20% over 25 RF periods.

Barnett, Rhea↗

Modelling of edge plasma dynamics with active wall boundary conditions

A self-consistent 2D model is presented for transport in boundary plasma and plasma-facing material walls. Plasma dynamics in the domain is represented by a 2D collisional plasma fluid model in the edge-plasma code UEDGE, and transport of hydrogen and heat in the wall is represented by a system of reaction–diffusion equations in the 1D wall code FACE. To account for variation of parameters along the wall, in the coupled model multiple instances of the FACE code run in parallel. Here, the coupled model provides a tool for investigating a range of dynamic plasma–material interactions phenomena in 2D. For demonstration of its capability, one application of particular interest is the role of active wall in tokamak strike point sweeping proposed for mitigation of divertor heat loads. In the present study, the coupled calculations are applied to investigation of the impact of heat and hydrogen transport in the material wall on the divertor plasma and target heat load during sweeping of the target strike point for parameters of a high-power tokamak.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Simulation of 24,000 Electron Dynamics: Real-Time Time-Dependent Density Functional Theory (TDDFT) with the Real-Space Multigrids (RMG)

Here, we present the theory, implementation, and benchmarking of a real-time time-dependent density functional theory (RT-TDDFT) module within the RMG code, designed to simulate the electronic response of molecular systems to external perturbations. Our method offers insights into nonequilibrium dynamics and excited states across a diverse range of systems, from small organic molecules to large metallic nanoparticles. Benchmarking results demonstrate excellent agreement with established TDDFT implementations and showcase the superior stability of our time integration algorithm, enabling long-term simulations with minimal energy drift. The scalability and efficiency of RMG on massively parallel architectures allow for simulations of complex systems, such as plasmonic nanoparticles with thousands of atoms. Future extensions, including nuclear and spin dynamics, will broaden the applicability of this RT-TDDFT implementation, providing a powerful toolset for studies of photoactive materials, nanoscale devices, and other systems where real-time electronic dynamics is essential.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Interfacial Inversion of Stealth Surfactants

Amphiphilic macromolecular surfactants segregate to liquid–liquid interfaces, thereby reducing the interfacial tension and free energy. Here, we investigated “stealth surfactants” in the form of core–shell bottlebrush polymers comprised of pH-responsive diblock copolymer side chains forming a hydrophilic core and a hydrophobic shell, enabling solubility in oil. At liquid–liquid interfaces, these polymers undergo a structural “inversion”, with hydrophilic blocks segregating into the aqueous phase and hydrophobic blocks residing in the oil phase. The reconfiguration kinetics and surfactant properties are influenced by multiple factors, including the molecular weights of the backbone and side chain components, the hydrophilic-to-hydrophobic balance of the side chains, and the pH of the aqueous phase. An observed nonmonotonic dependence of interfacial tension with time is attributed to a progressive structural inversion, where the projected area of the macromolecule onto the interface decreases. To validate this inversion hypothesis, interfacial properties were characterized by sum-frequency generation vibrational spectroscopy, which revealed configurational changes of the core–shell bottlebrush polymers at the fluid interface and revealed a pH-dependent interfacial coverage. Coarse-grained molecular dynamics simulations supported these experimental findings, showing that the pH-responsive core and hydrophobic shell assume a time-averaged configuration with orientations parallel and perpendicular to the plane of the interface, respectively. These findings open routes to design multistimuli-responsive polymeric surfactants and compatibilizers, expanding their potential applications in advanced interfacial systems.

Stealth surfactants↗

Neoclassical transport and profile prediction in transport barriers

Strong gradient regions in tokamaks, such as the pedestal or internal transport barriers, are regions of reduced turbulence where neoclassical transport can play a dominant role. However, standard neoclassical transport theory assumes that the gradient length scales of density, temperature, and potential are of the order of the system size. In the pedestal, gradient length scales are much shorter and are measured to be of the order of the ion poloidal gyroradius. We present an extension of neoclassical theory that is applicable in transport barriers of large aspect ratio tokamaks. We show that particle and momentum transport are connected in such a way that a source of parallel momentum can drive a significant neoclassical ion particle flux. In strong gradient regions, density, electric potential, mean parallel flow, and ion temperature are shown to no longer be flux functions. Instead, they have a small but important poloidally varying piece that modifies the transport equations to lowest order. This introduces a nonlinearity in the transport problem through the coupling with quasineutrality that yields multiple co-existing solutions when solving for the plasma profiles. The different solutions could be connected to low and high transport states and jumps between solutions could provide a new neoclassical explanation for H-L back-transitions.

Trinczek, Silvia [Princeton Plasma Physics Laborat↗

Fast neural Poincaré maps for toroidal magnetic fields

Poincaré maps for toroidal magnetic fields are routinely employed to study gross confinement properties in devices built to contain hot plasmas. In most practical applications, evaluating a Poincaré map requires numerical integration of a magnetic field line, a process that can be slow and that cannot be easily accelerated using parallel computations. We propose a novel neural network architecture, the HénonNet, and show that it is capable of accurately learning realistic Poincaré maps from observations of a conventional field-line-following algorithm. After training, such learned Poincaré maps evaluate much faster than the field-line integration method. Moreover, the HénonNet architecture exactly reproduces the primary physics constraint imposed on field-line Poincaré maps: flux preservation. Furthermore, this structure-preserving property is the consequence of each layer in a HénonNet being a symplectic map. We demonstrate empirically that a HénonNet can learn to mock the confinement properties of a large magnetic island by using coiled hyperbolic invariant manifolds to produce a sticky chaotic region at the desired island location. This suggests a novel approach to designing magnetic fields with good confinement properties that may be more flexible than ensuring confinement using KAM tori.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

UPC++ v1.0 Specification, Revision 2020.10.0

UPC++ is a C++11 library providing classes and functions that support Partitioned Global Address Space (PGAS) programming. The key communication facilities in UPC++ are one-sided Remote Memory Access (RMA) and Remote Procedure Call (RPC). All communication operations are syntactically explicit and default to non-blocking; asynchrony is managed through the use of futures, promises and continuation callbacks, enabling the programmer to construct a graph of operations to execute asynchronously as high-latency dependencies are satisfied. A global pointer abstraction provides system-wide addressability of shared memory, including host and accelerator memories. The parallelism model is primarily process-based, but the interface is thread-safe and designed to allow efficient and expressive use in multi-threaded applications. The interface is designed for extreme scalability throughout, and deliberately avoids design features that could inhibit scalability.

97 MATHEMATICS AND COMPUTING↗

UPC++ v1.0 Specification, Revision 2021.9.0

UPC++ is a C++ library providing classes and functions that support Partitioned Global Address Space (PGAS) programming. The key communication facilities in UPC++ are one-sided Remote Memory Access (RMA) and Remote Procedure Call (RPC). All communication operations are syntactically explicit and default to non-blocking; asynchrony is managed through the use of futures, promises and continuation callbacks, enabling the programmer to construct a graph of operations to execute asynchronously as high-latency dependencies are satisfied. A global pointer abstraction provides system-wide addressability of shared memory, including host and accelerator memories. The parallelism model is primarily process-based, but the interface is thread-safe and designed to allow efficient and expressive use in multi-threaded applications. The interface is designed for extreme scalability throughout, and deliberately avoids design features that could inhibit scalability.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

UPC++ v1.0 Specification (Rev. 2023.9.0)

UPC++ is a C++ library providing classes and functions that support Partitioned Global Address Space (PGAS) programming. The key communication facilities in UPC++ are one-sided Remote Memory Access (RMA) and Remote Procedure Call (RPC). All communication operations are syntactically explicit and default to non-blocking; asynchrony is managed through the use of futures, promises and continuation callbacks, enabling the programmer to construct a graph of operations to execute asynchronously as high-latency dependencies are satisfied. A global pointer abstraction provides system-wide addressability of shared memory, including host and accelerator memories. The parallelism model is primarily process-based, but the interface is thread-safe and designed to allow efficient and expressive use in multi-threaded applications. The interface is designed for extreme scalability throughout, and deliberately avoids design features that could inhibit scalability.

97 MATHEMATICS AND COMPUTING↗

UPC++ v1.0 Specification (Revision 2022.3.0)

UPC++ is a C++ library providing classes and functions that support Partitioned Global Address Space (PGAS) programming. The key communication facilities in UPC++ are one-sided Remote Memory Access (RMA) and Remote Procedure Call (RPC). All communication operations are syntactically explicit and default to non-blocking; asynchrony is managed through the use of futures, promises and continuation callbacks, enabling the programmer to construct a graph of operations to execute asynchronously as high-latency dependencies are satisfied. A global pointer abstraction provides system-wide addressability of shared memory, including host and accelerator memories. The parallelism model is primarily process-based, but the interface is thread-safe and designed to allow efficient and expressive use in multi-threaded applications. The interface is designed for extreme scalability throughout, and deliberately avoids design features that could inhibit scalability.

97 MATHEMATICS AND COMPUTING↗

UPC++ v1.0 Specification, Revision 2023.3.0

UPC++ is a C++ library providing classes and functions that support Partitioned Global Address Space (PGAS) programming. The key communication facilities in UPC++ are one-sided Remote Memory Access (RMA) and Remote Procedure Call (RPC). All communication operations are syntactically explicit and default to non-blocking; asynchrony is managed through the use of futures, promises and continuation callbacks, enabling the programmer to construct a graph of operations to execute asynchronously as high-latency dependencies are satisfied. A global pointer abstraction provides system-wide addressability of shared memory, including host and accelerator memories. The parallelism model is primarily process-based, but the interface is thread-safe and designed to allow efficient and expressive use in multi-threaded applications. The interface is designed for extreme scalability throughout, and deliberately avoids design features that could inhibit scalability.

97 MATHEMATICS AND COMPUTING↗