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125 records · Page 7

Speeding Up Hartree–Fock in JuliaChem with Density Fitting

In this work, the density fitting (DF) approximation is added to the restricted Hartree–Fock (RHF) implementation in the JuliaChem computational chemistry code. Utilizing a DF algorithm that uses symmetry and integral screening, a significant reduction in time to compute the Fock matrix is achieved. The symmetry and screening DF-RHF techniques were adapted to be performed on graphics processing units (GPUs), which are well suited to perform the matrix multiplications that comprise the bulk of the Fock build time in DF-RHF. The JuliaChem DF-RHF GPU algorithm employs a novel approach that automatically switches between two DF-RHF algorithms depending on the number of basis functions in the calculation. The JuliaChem GPU DF-RHF implementation demonstrates up to 2× speedup for Fock build times compared to the existing best-in-class GPU DF-RHF implementation by operating directly on screened intermediate matrices. Due to the high portability of the Julia language code, the JuliaChem CPU and GPU DF-RHF implementations could be benchmarked on a variety of CPU and GPU architectures from multiple hardware vendors.

Hayes, John J. [Ames Laboratory, and Iowa State Un

Importance of Ice Nucleation and Precipitation on Climate With the Parameterization of Unified Microphysics Across Scales Version 1 (PUMASv1)

Cloud microphysics is critical for weather and climate prediction. In this work, we document updates and corrections to the cloud microphysical scheme used in the Community Earth System Model (CESM) and other models. These updates include a new nomenclature for the scheme, now called Parameterization of Unified Microphysics Across Scales (PUMAS), and the ability to run the scheme on graphics processing units (GPUs). The main science changes include refactoring an ice number limiter and associated changes to ice nucleation, adding vapor deposition onto snow, and introducing an implicit numerical treatment for sedimentation. We also detail the improvements in computational performance that can be achieved with GPU acceleration. We then show the impact of these scheme changes on the (a) mean state climate, (b) cloud feedback response to warming, and (c) aerosol forcing. We find that corrections are needed to the immersion freezing parameterization and that ice nucleation has important impacts on climate. We also find that the revised scheme produces less cloud liquid and ice but that this can be adjusted by changing the loss process for cloud liquid (autoconversion). Furthermore, there are few discernible effects of the PUMAS changes on cloud feedbacks but some reductions in the magnitude of aerosol–cloud interactions (ACIs). Small cloud feedback changes appear to be related to the implicit sedimentation scheme, with a number of factors affecting ACIs.

Clouds

Utilizing GPUs to Accelerate Turbomachinery CFD Codes

GPU computing has established itself as a way to accelerate parallel codes in the high performance computing world. This work focuses on speeding up APNASA, a legacy CFD code used at NASA Glenn Research Center, while also drawing conclusions about the nature of GPU computing and the requirements to make GPGPU worthwhile on legacy codes. Rewriting and restructuring of the source code was avoided to limit the introduction of new bugs. The code was profiled and investigated for parallelization potential, then OpenACC directives were used to indicate parallel parts of the code. The use of OpenACC directives was not able to reduce the runtime of APNASA on either the NVIDIA Tesla discrete graphics card, or the AMD accelerated processing unit. Additionally, it was found that in order to justify the use of GPGPU, the amount of parallel work being done within a kernel would have to greatly exceed the work being done by any one portion of the APNASA code. It was determined that in order for an application like APNASA to be accelerated on the GPU, it should not be modular in nature, and the parallel portions of the code must contain a large portion of the code's computation time.

computer programming

Acceleration of the particle-in-cell code Osiris with graphics processing units

Fully relativistic particle-in-cell (PIC) simulations are crucial for advancing our knowledge of plasma physics. Modern supercomputers based on graphics processing units (GPUs) offer the potential to perform PIC simulations of unprecedented scale, but require robust and feature-rich codes that can fully leverage their computational resources. In this work, this demand is addressed by adding GPU acceleration to the PIC code Osiris. An overview of the algorithm, which features a CUDA extension to the underlying Fortran architecture, is given. Detailed performance benchmarks for thermal plasmas are presented, which demonstrate excellent weak scaling on NERSC's Perlmutter supercomputer and high levels of absolute performance. The robustness of the code to model a variety of physical systems is demonstrated via simulations of Weibel filamentation and laser-wakefield acceleration run with dynamic load balancing. Finally, measurements and analysis of energy consumption are provided that indicate that the GPU algorithm is up to ~14 times faster and ~7 times more energy efficient than the optimized CPU algorithm on a node-to-node basis. The described development addresses the PIC simulation community's computational demands both by contributing a robust and performant GPU-accelerated PIC code and by providing insight into efficient use of GPU hardware.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY

Iterative methods in GPU-resident linear solvers for nonlinear constrained optimization

Linear solvers are major computational bottlenecks in a wide range of decision support and optimization computations. The challenges become even more pronounced on heterogeneous hardware, where traditional sparse numerical linear algebra methods are often inefficient. For example, methods for solving ill-conditioned linear systems have relied on conditional branching, which degrades performance on hardware accelerators such as graphical processing units (GPUs). To improve the efficiency of solving ill-conditioned systems, our computational strategy separates computations that are efficient on GPUs from those that need to run on traditional central processing units (CPUs). Our strategy maximizes the reuse of expensive CPU computations. Iterative methods, which thus far have not been broadly used for ill-conditioned linear systems, play an important role in our approach. In particular, we extend ideas from Arioli et al., (2007) to implement iterative refinement using inexact LU factors and flexible generalized minimal residual (FGMRES), with the aim of efficient performance on GPUs. In conclusion, we focus on solutions that are effective within broader application contexts, and discuss how early performance tests could be improved to be more predictive of the performance in a realistic environment.

97 MATHEMATICS AND COMPUTING

Graphics Processing Unit Assisted Thermographic Compositing

Objective Develop a software application utilizing high performance computing techniques, including general purpose graphics processing units (GPGPUs), for the analysis and visualization of large thermographic data sets. Over the past several years, an increasing effort among scientists and engineers to utilize graphics processing units (GPUs) in a more general purpose fashion is allowing for previously unobtainable levels of computation by individual workstations. As data sets grow, the methods to work them grow at an equal, and often greater, pace. Certain common computations can take advantage of the massively parallel and optimized hardware constructs of the GPU which yield significant increases in performance. These common computations have high degrees of data parallelism, that is, they are the same computation applied to a large set of data where the result does not depend on other data elements. Image processing is one area were GPUs are being used to greatly increase the performance of certain analysis and visualization techniques.

Ragasa, Scott

Evolution of the ATLAS event data model for the HL-LHC

The upcoming high-luminosity run of the CERN Large Hadron Collider (HL-LHC) will yield an unprecedented volume of data. In order to process this data, the ATLAS collaboration is evolving its offline software to be able to use heterogeneous resources such as graphical processing units (GPUs) and field-programmable gate arrays (FPGAs). To reduce conversion overheads, the event data model (EDM) should be compatible with the requirements of these resources. While the ATLAS EDM has long allowed representing data as a structure of arrays, further evolution of the EDM can enable more efficient sharing of data between CPU and GPU resources. Some of this work will be summarized here, including extensions to allow controlling how memory for event data is allocated and the implementation of jagged vectors.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS

Hardware acceleration for HPS algorithms in two and three dimensions

We provide a flexible, open-source framework for hardware acceleration, namely massively-parallel execution on general-purpose graphics processing units (GPUs), applied to the hierarchical Poincaré–Steklov (HPS) family of algorithms for building fast direct solvers for linear elliptic partial differential equations. To take full advantage of the power of hardware acceleration, we propose two variants of HPS algorithms to improve performance on two- and three-dimensional problems. In the two-dimensional setting, we introduce a novel recomputation strategy that minimizes costly data transfers to and from the GPU; in three dimensions, we modify and extend the adaptive discretization technique of Geldermans and Gillman [1] to greatly reduce peak memory usage. We provide an open-source implementation of these methods written in JAX, a high-level accelerated linear algebra package, which allows for the first integration of a high-order fast direct solver with automatic differentiation tools. We conclude with extensive numerical examples showing our methods are fast and accurate on two- and three-dimensional problems.

Fast direct solvers

Track reconstruction as a service for collider physics

Optimizing charged-particle track reconstruction algorithms is crucial for efficient event reconstruction in Large Hadron Collider (LHC) experiments due to their significant computational demands. Existing track reconstruction algorithms have been adapted to run on massively parallel coprocessors, such as graphics processing units (GPUs), to reduce processing time. Nevertheless, challenges remain in fully harnessing the computational capacity of coprocessors in a scalable and non-disruptive manner. This paper proposes an inference-as-a-service approach for particle tracking in high energy physics experiments. To evaluate the efficacy of this approach, two distinct tracking algorithms are tested: Patatrack, a rule-based algorithm, and Exa.TrkX, a machine learning-based algorithm. The as-a-service implementations show enhanced GPU utilization and can process requests from multiple CPU cores concurrently without increasing per-request latency. The impact of data transfer is minimal and insignificant compared to running on local coprocessors. This approach greatly improves the computational efficiency of charged particle tracking, providing a solution to the computing challenges anticipated in the High-Luminosity LHC era.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND

Automated Hybrid Variance Reduction on Advanced Architectures in the Shift Monte Carlo Code

Monte Carlo transport methods are the most accurate schemes for solving problems with complex energy and spatial features, but they come with a high computational cost. Although hybrid methods have enabled the use of Monte Carlo transport for a large class of problems, they still require significant computing resources. Modern multicore CPUs with large numbers of compute cores and graphical processing units (GPUs) provide opportunities to optimize the memory and run-time costs of hybrid Monte Carlo methods. This paper documents the development and analysis of three Monte Carlo transport algorithms that support hybrid transport using the consistent adjoint-driven importance sampling (CADIS) and forward-weighted CADIS methods in the Shift Monte Carlo code: history-based transport using static and dynamic threading on multicore CPUs and event-based transport enabling weight window tracking on GPUs. The results are shown for two challenging hybrid problems on the Frontier supercomputer at the Oak Ridge Leadership Computing Facility. The results show that all three methods yield good performance and enable solutions of difficult fixed-source transport problems in less than 2 min on 20 nodes of Frontier. Dynamic threading was observed to give up to 20% better scaling behavior than static threading. Moreover, the AMD Instinct 250X GPU was found to give 9 to 11 times greater throughput per graphics compute die than the best CPU performance. In conclusion, additional opportunities for optimization of hybrid transport on GPUs are discussed.

Denovo

Full event interpretation with machine-learning-based particle-flow reconstruction in the CMS detector

The particle-flow (PF) algorithm constructs a global description of each particle collision by producing a comprehensive list of final-state particles, and is central to event reconstruction in the CMS experiment at the CERN LHC. The existing PF implementation relies on physics-motivated heuristics and assumptions that can be replaced by machine-learning (ML) models trained directly on simulated data and naturally suited to modern graphics processing units (GPUs). A state-of-the-art ML-based PF (MLPF) reconstruction algorithm, implemented within the CMS software framework, is presented. The MLPF algorithm performs a learnable full-event reconstruction on GPUs, generalizes across detector conditions and collision energies, and replaces multiple modular reconstruction steps with a single unified model. Physics performance comparable to standard PF reconstruction is achieved in both simulation and data, with improved jet energy resolution and inference time. In simulated top quark-antiquark events under LHC Run-3 (2023-2024) conditions, the jet energy resolution improves by 10-20% for jets with transverse momentum between 30-100 GeV. Inference time is evaluated using simulated multijet events, with a median of $20\,\hbox {ms}$ per event on an Nvidia L4 GPU, compared to approximately $110\,\hbox {ms}$ for the standard CMS PF reconstruction.

Hayrapetyan, Aram [Yerevan Phys. Inst.]

ERF: Energy Research and Forecasting Model

High performance computing (HPC) architectures have undergone rapid development in recent years. As a result, established software suites face an ever increasing challenge to remain performant on and portable across modern systems. Many of the widely adopted atmospheric modeling codes cannot fully (or in some cases, at all) leverage the acceleration provided by General-Purpose Graphics Processing Units, leaving users of those codes constrained to increasingly limited HPC resources. Energy Research and Forecasting (ERF) is a regional atmospheric modeling code that leverages the latest HPC architectures, whether composed of only Central Processing Units (CPUs) or incorporating GPUs. ERF contains many of the standard discretizations and basic features needed to model general atmospheric dynamics. The modular design of ERF provides a flexible platform for exploring different physics parameterizations and numerical strategies. ERF is built on a state-of-the-art, well-supported, software framework (AMReX) that provides a performance portable interface and ensures ERF's long-term sustainability on next generation computing systems. This paper details the numerical methodology of ERF, presents results for a series of verification/validation cases, and documents ERF's performance on current HPC systems. The roughly 5× speed up of ERF (using GPUs) over Weather Research and Forecasting (CPUs only) for a 3D squall line test case highlights the significance of leveraging GPU acceleration.

17 WIND ENERGY

Real-Time Wavefront Control for the PALM-3000 High Order Adaptive Optics System

We present a cost-effective scalable real-time wavefront control architecture based on off-the-shelf graphics processing units hosted in an ultra-low latency, high-bandwidth interconnect PC cluster environment composed of modules written in the component-oriented language of nesC. The architecture enables full-matrix reconstruction of the wavefront at up to 2 KHz with latency under 250 us for the PALM-3000 adaptive optics systems, a state-of-the-art upgrade on the 5.1 meter Hale Telescope that consists of a 64 x 64 subaperture Shack-Hartmann wavefront sensor and a 3368 active actuator high order deformable mirror in series with a 241 active actuator tweeter DM. The architecture can easily scale up to support much larger AO systems at higher rates and lower latency.

GPU

Parallelization of a Six Degree of Freedom Entry Vehicle Trajectory Simulation Using OpenMP and OpenACC

The art and science of writing parallelized software, using methods such as Open Multi-Processing (OpenMP) and Open Accelerators (OpenACC), is dominated by computer scientists. Engineers and non-computer scientists looking to apply these techniques to their project applications face a steep learning curve, especially when looking to adapt their original single threaded software to run multi-threaded on graphics processing units (GPUs). There are significant changes in mindset that must occur; such as how to manage memory, the organization of instructions, and the use of if statements (also known as branching). The purpose of this work is twofold: 1) to demonstrate the applicability of parallelized coding methodologies, OpenMP and OpenACC, to tasks outside of the typical large scale matrix mathematics; and 2) to discuss, from an engineer’s perspective, the lessons learned from parallelizing software using these computer science techniques. This work applies OpenMP, on both multi-core central processing units (CPUs) and Intel® Xeon Phi™ 7210, and OpenACC on GPUs. These parallelization techniques are used to tackle the simulation of thousands of entry vehicle trajectories through the integration of six degree of freedom (DoF) equations of motion (EoM). The forces and moments acting on the entry vehicle, and used by the EoM, are estimated using multiple models of varying levels of complexity. Several benchmark comparisons are made on the execution of six DoF trajectory simulation: single thread Intel® Xeon® E5-2670 CPU, multi-thread CPU using OpenMP, multi-thread Xeon Phi™ 7210 using OpenMP, and multi-thread NVIDIA® Tesla® K40 GPU using OpenACC. These benchmarks are run on the Pleiades Supercomputer Cluster at the National Aeronautics and Space Administration (NASA) Ames Research Center (ARC), and a Xeon Phi™ 7210 node at NASA Langley Research Center (LaRC).

Green, Justin S.

Lightfall v0.0.1

Lightfall is a desktop application for synchrotron beamline instrument control, data acquisition, and live analysis at the Advanced Light Source (ALS). Built on Python and Qt, it provides a native graphical interface for operating beamline hardware, configuring and executing experimental scans, and visualizing results in real time. Key features include direct integration with EPICS control systems, a built-in electronic logbook, remote beamline access over secure tunnels, and an interprocess communication (IPC) architecture that coordinates with external analysis applications via ZMQ and EPICS process variables. This IPC approach allows Lightfall to orchestrate specialized analysis tools—including GPU-accelerated streaming correlators—without embedding them, avoiding the dependency conflicts common in monolithic scientific software platforms. Compared to prior approaches such as Xi-CAM's plugin-based architecture, Lightfall's design cleanly separates instrument control from domain-specific analysis, enabling feedback-driven acquisition where live analysis results can adjust scan parameters during an experiment. Its native Qt interface provides responsive performance for real-time data visualization that web-based alternatives struggle to match. Lightfall is designed for use by beamline scientists and staff operating synchrotron instruments at national user facilities.

Pandolfi, Ronald [Lawrence Berkeley National Labor

High-Performance Data Analysis Tools for Sun-Earth Connection Missions

The data analysis tool of choice for many Sun-Earth Connection missions is the Interactive Data Language (IDL) by ITT VIS. The increasing amount of data produced by these missions and the increasing complexity of image processing algorithms requires access to higher computing power. Parallel computing is a cost-effective way to increase the speed of computation, but algorithms oftentimes have to be modified to take advantage of parallel systems. Enhancing IDL to work on clusters gives scientists access to increased performance in a familiar programming environment. The goal of this project was to enable IDL applications to benefit from both computing clusters as well as graphics processing units (GPUs) for accelerating data analysis tasks. The tool suite developed in this project enables scientists now to solve demanding data analysis problems in IDL that previously required specialized software, and it allows them to be solved orders of magnitude faster than on conventional PCs. The tool suite consists of three components: (1) TaskDL, a software tool that simplifies the creation and management of task farms, collections of tasks that can be processed independently and require only small amounts of data communication; (2) mpiDL, a tool that allows IDL developers to use the Message Passing Interface (MPI) inside IDL for problems that require large amounts of data to be exchanged among multiple processors; and (3) GPULib, a tool that simplifies the use of GPUs as mathematical coprocessors from within IDL. mpiDL is unique in its support for the full MPI standard and its support of a broad range of MPI implementations. GPULib is unique in enabling users to take advantage of an inexpensive piece of hardware, possibly already installed in their computer, and achieve orders of magnitude faster execution time for numerically complex algorithms. TaskDL enables the simple setup and management of task farms on compute clusters. The products developed in this project have the potential to interact, so one can build a cluster of PCs, each equipped with a GPU, and use mpiDL to communicate between the nodes and GPULib to accelerate the computations on each node.

Messmer, Peter

Performance-portable Binary Neutron Star Mergers with AthenaK

We introduce an extension to the AthenaK code for general-relativistic magnetohydrodynamics (GRMHD) in dynamical spacetimes using a 3+1 conservative Eulerian formulation. Like the fixed-spacetime GRMHD solver, we use standard finite-volume methods to evolve the fluid and a constrained-transport scheme to preserve the divergence-free constraint for the magnetic field. We also utilize a first-order flux correction (FOFC) scheme to reduce the need for an artificial atmosphere and optionally enforce a maximum principle to improve robustness. We demonstrate the accuracy of AthenaK using a set of standard tests in flat and curved spacetimes. Using a SANE accretion disk around a Kerr black hole, we compare the new solver to the existing solver for stationary spacetimes using the so-called "HARM-like" formulation. We find that both formulations converge to similar results. We also include the first published binary neutron star (BNS) mergers performed on graphical processing units (GPUs). Thanks to the FOFC scheme, our BNS mergers maintain a relative error of $\mathcal{O}$(10 –11 ) or better in baryon mass conservation up to collapse. Finally, we perform scaling tests of AthenaK on OLCF Frontier, where we show excellent weak scaling of ≥80% efficiency up to 32,768 GPUs and 74% up to 65,536 GPUs for a GRMHD problem in dynamical spacetimes with six levels of mesh refinement. AthenaK achieves an order-of-magnitude speedup using GPUs compared to CPUs, demonstrating that it is suitable for performing numerical relativity problems on modern exascale resources.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS