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At least 505 records · Page 28

Optimizing Irregular Communication with Neighborhood Collectives and Locality-Aware Parallelism

Irregular communication often limits both the performance and scalability of parallel applications. Typically, applications individually implement irregular communication as point-to-point, and any optimizations are integrated directly into the application. As a result, these optimizations lack portability. It is difficult to optimize point-to-point messages within MPI, as the interface for single messages provides no information on the collection of all communication to be performed. However, the persistent neighbor collective API, released in the MPI 4 standard, provides an interface for portable optimizations of irregular communication within MPI libraries. This paper presents methods for implementing existing optimizations for irregular communication within neighborhood collectives, analyzes the impact of replacing point-to-point communication in existing codebases such as Hypre BoomerAMG with neighborhood collectives, and finally shows up to a 1.38x speedup on sparse matrix-vector multiplication communication within a BoomerAMG solve through the use of our optimized neighbor collectives. Here, the authors analyze three implementations of persistent neighborhood collectives for Alltoallv: an unoptimized wrapper of standard point-to-point communication, and two locality-aware aggregating methods. The second locality-aware implementation exposes an non-standard interface to perform additional optimization, and the authors present the additional 0.07x speedup from the extended interface. All optimizations are available in an open-source codebase, MPI Advance, which sits on top of MPI, allowing for optimizations to be added into existing codebases regardless of the system MPI install.

AMG↗

PANDORA: A Parallel Dendrogram Construction Algorithm for Single Linkage Clustering on GPU

This paper introduces Pandora, a parallel algorithm for computing dendrograms, the hierarchical cluster trees for single linkage clustering (SLC). Current parallel approaches construct dendrograms by partitioning a minimum spanning tree and removing edges. However, they struggle with skewed, hard-to-parallelize real-world dendrograms. Consequently, computing dendrograms is the sequential bottleneck in HDBSCAN*[21], a popular SLC variant. Pandora uses recursive tree contraction to address this limitation. Pandora contracts nodes to construct progressively smaller trees. It computes the smallest contracted dendrogram and expands it by inserting contracted edges. This recursive strategy is highly parallel, skew-independent, work-optimal, and well-suited for GPUs and multicores. We develop a performance portable implementation of Pandora in Kokkos[31] and evaluate its performance on multicore CPUs and multi-vendor GPUs (e.g., Nvidia, AMD) for dendrogram construction in HDBSCAN*. Multithreaded Pandora is 2.2x faster than the current best-multithreaded implementation. Our GPU version achieves 6-20x speedup on AMD GPUs and 10-37x on NVIDIA GPUs over multithreaded Pandora. Pandora removes HDBSCAN*’s sequential bottleneck, greatly boosting efficiency, particularly with GPUs.

Sao, Piyush↗

ORNL/grit

Grit is a software library designed specifically for conducting particle-based Lagrangian simulations with CPU/GPUperformance portability. This library allows researchers and engineers to perform a wide range of simulations, including multiphase flow, and more. Grit employs Message Passing Interface (MPI) for distributed memory parallelism and Kokkos programming model for on-node shared memory parallelism with performance portability across different architectures of GPUs and multi-core/manycore CPUs.

Ge, Wenjun [Oak Ridge National Laboratory (ORNL), ↗

Julienne v1.0.0

Julienne is a compiler-portable unit-testing framework for Fortran software projects, including those that use the parallel/accelerator-programming features of Fortran 2023. Julienne achieves portability across compilers through minimalism and isolation. The minimal design ensures that Julienne uses only features supported by the majority of Fortran compilers. The isolation through zero dependencies ensures that no other projects block Julienne from building with a particular compiler. Julienne also contains with additional services that support its unit-testing code. These include functions for manipulating strings, command lines and input/output format strings; and a user-defined collective subroutine for verifying that all processes pass a test in parallel testing. Julienne's name derives from the term for vegetables sliced into thin strings: julienne vegetables. Julienne captures the authors' most frequently used thin slice of the Veggies and Sourcery software repositories while avoiding certain compiler limitations of the those two packages.

Rouson, Damian↗

SPADES (Scalable Parallel Discrete Events Simulation) [SWR-24-99]

SPADES (Solver for PArallel Discrete Event Simulation) is an open-source parallel discrete event simulation (PDES) package built on the AMReX library. Targeted at solving discrete event systems in parallel, this software package aims to be performance portable and scalable on heterogeneous computing architectures, e.g., graphic processing units (GPU). SPADES implements optimistic synchronization with rollback through an implementation of the Time Warp algorithm. An alternative conservative synchronization approach is also implemented using the Lower Bound on Incoming Time Stamp. In our implementation, logical processes are represented as cells in a grid and event messages are represented as particles. SPADES supports various parallel decomposition strategies, including the use of the Message Passing Interface (MPI) and OpenMP threading. All major GPU architectures (e.g., Intel, AMD, NVIDIA) are supported through the use of performance portability functionalities implemented in AMReX. The SPADES software is released in NREL Software Record SWR-24-99 “SPADES (Scalable Parallel Discrete Events Simulation)”.

Henry de Frahan, Marc [National Renewable Energy L↗

HydraGNN v4.0

The new version of HydraGNN v4.0 provides additional core capabilities, such as: Inclusion of multi-body atomistic cluster expansion MACE, polarizable atom interaction neural network PAINN, and equivariant principal neighborhood aggregation (PNAEq) among the message passing layers supported -Inclusion of graph transformers to directly model long-range interactions between nodes that are distant in the graph topology Integration of graph transformers with message passing layers by combining the graph embedding generated by the two mechanisms, which allows for an improved expressivity of the HydraGNN architecture Improved re-implementation of multi-task learning (MTL) to allow its use for stabilized training across imbalanced, multi-source, multi-fidelity data Introduction of multi-task parallelism, a newly proposed type of model parallelism specifically for MTL architectures, which allows to dispatch different output decoding heads to different GPU devices Integration of multi-task parallelism with pre-existing distributed data parallelism to enable a 2D parallelization for distributed training Improved portability of the distributed training across Intel GPUs, which has been testes on ALCF exascale supercomputer Aurora Inclusion of 2-level fine-grained energy profilers portable across NVIDIA, AMD, and Intel GPUs to monitor the power and energy consumption associated with different functions executed by the HydraGNN code during data pre-load and training Restructuring of previous examples and inclusion of new sets of examples to illustrate the download, preprocess, and training of HydraGNN models on new large-scale open-source datasets for atomistic materials modeling (e.g., Alexandria, Transition1x, OMat24, OMol25)

Lupo Pasini, Massimiliano [Oak Ridge National Labo↗

matsim-agents v1.0

matsim-agents is a multi-agent AI framework for atomistic materials simulation and discovery. It orchestrates large language models (LLMs), machine-learned interatomic potentials (MLIPs), and DFT codes into a single agentic loop running on laptops and DOE leadership-class supercomputers. MULTI-AGENT ORCHESTRATION A LangGraph state machine with three nodes: a Planner that converts a natural-language research objective into structured tasks; an Executor that dispatches atomistic tools and loops until the queue is empty; and an Analyst that summarizes results into a human-readable report. State is checkpointed after every step and human-in-the-loop gates can be inserted at any edge. HYPOTHESIS-DRIVEN DISCOVERY CHAT An interactive REPL (matsim-agents chat) that couples LLM dialogue with atomistic simulation. Chemical formulas are automatically detected in conversation turns and trigger a full crystal-phase exploration: structure generation → relaxation → stability scoring → result injection back into the conversation, creating a closed hypothesis-refinement loop. CRYSTAL PHASE ENUMERATION Given a composition, the phase explorer enumerates prototypes by stoichiometry: elemental (fcc/bcc/hcp/sc/diamond), binary 1:1 (rocksalt/CsCl/zincblende/ wurtzite/fluorite/rutile), ternary 1:1:3 (cubic perovskite), ternary 1:2:4 (perovskite + spinel), quaternary 1:1:2:6 (Fm-3m double perovskite). 2-D prototypes (graphene, h-BN, MoS2 2H/1T) and multilayer stacking are also supported via --include-2d and --num-layers. SUPERCELL GENERATION AND SITE DECORATION Auto-tiling to a minimum atom count (--min-atoms), explicit NxNxN tiling (--supercell), symmetry-distinct site decorations (--n-orderings), and isotropic lattice-scale sweeps (--lattice-scales) for volume bracketing. MLFF RELAXATION AND STABILITY SCORING HydraGNN (multi-headed GNN) drives structure relaxation via ASE with FIRE, BFGS, or BFGSLineSearch. Stability output: delta-E/atom ranking across phases and a max-residual-force dynamical-stability proxy. Other MLIPs (MACE, NequIP, Orb) can be plugged in through the same interface. DFT BACKENDS Quantum ESPRESSO pw.x and VASP 6.6 are first-class labellers. Both have validated GPU builds and SLURM/PBS launchers for three DOE platforms: Frontier (AMD MI250X, ROCm), Aurora (Intel PVC, oneAPI), Perlmutter (NVIDIA A100, CUDA). QE produces ~100 binaries (pw.x, ph.x, epw.x, ...). VASP supports scf, relax, vc-relax, and vc-relax-shape run types. ACTIVE-LEARNING LOOP matsim-agents al run CONFIG.yaml drives an iterative HydraGNN-DFT loop: MD generates candidates → ensemble/MC-dropout uncertainty selects the most informative → DFT labels them in parallel inside one allocation → dataset grows → HydraGNN retrains → repeat. DFT backend is a single YAML toggle (dft.backend: vasp | qe). LLM-generated seed structures are supported (no curated POSCAR library needed). Config uses ${VAR}, ${VAR:-default}, ${VAR:?msg} shell-style substitution for cross-user/cross-site portability. LLM BACKENDS Ollama (local, default), vLLM (HPC multi-GPU serving), OpenAI, Anthropic, HuggingFace Transformers+Accelerate. Selected at runtime via flag or env var with no code changes. HPC PORTABILITY Same Python entry points run on Frontier (ROCm 7.2), Aurora (oneAPI), and Perlmutter (CUDA 12). DFT and ML stacks are never co-loaded in the same shell; they couple through the scheduler and filesystem. Advanced multi-node launchers (serve, discovery-chat, single-relaxation, active-learning, QE warm-start) are provided for all three platforms. CODABENCH COMPETITION BUNDLE A self-contained benchmark: 159 atomistic test structures across 11 material classes, 5 tasks (formation energy, forces, ML relaxation, AI-DFT relaxation, phase stability ranking), public/private leaderboard split (30/70), and four ready-to-run baselines: MACE-MP-0, HydraGNN, UMA, AllScAIP.

Lupo Pasini, Massimiliano [Oak Ridge National Labo↗

Advances in ArborX to support exascale applications

ArborX is a performance portable geometric search library developed as part of the Exascale Computing Project (ECP). In this paper, we explore a collaboration between ArborX and a cosmological simulation code HACC. Large cosmological simulations on exascale platforms encounter a bottleneck due to the in-situ analysis requirements of halo finding, a problem of identifying dense clusters of dark matter (halos). This problem is solved by using a density-based DBSCAN clustering algorithm. With each MPI rank handling hundreds of millions of particles, it is imperative for the DBSCAN implementation to be efficient. In addition, the requirement to support exascale supercomputers from different vendors necessitates performance portability of the algorithm. We describe how this challenge problem guided ArborX development, and enhanced the performance and the scope of the library. We explore the improvements in the basic algorithms for the underlying search index to improve the performance, and describe several implementations of DBSCAN in ArborX. Further, we report the history of the changes in ArborX and their effect on the time to solve a representative benchmark problem, as well as demonstrate the real world impact on production end-to-end cosmology simulations.

97 MATHEMATICS AND COMPUTING↗

Asynchronous-many-task systems: Challenges and opportunities - Scaling an AMR astrophysics code on exascale machines using Kokkos and HPX

Dynamic and adaptive mesh refinement is pivotal in high-resolution, multi-physics, multi-model simulations, necessitating precise physics resolution in localized areas across expansive domains. Today’s supercomputers’ extreme heterogeneity presents a significant challenge for dynamically adaptive codes, highlighting the importance of achieving performance portability at scale. Our research focuses on astrophysical simulations, particularly stellar mergers, to elucidate early universe dynamics. Here, we present Octo-Tiger, leveraging Kokkos, HPX, and SIMD for portable performance at scale in complex, massively parallel adaptive multi-physics simulations. Octo-Tiger supports diverse processors, accelerators, and network backends. Experiments demonstrate exceptional scalability across several heterogeneous supercomputers including Perlmutter, Frontier, and Fugaku, encompassing major GPU architectures and x86, ARM, and RISC-V CPUs. Parallel efficiency of 47.59% (110,080 cores and 6880 hybrid A100 GPUs) on a full-system run on Perlmutter (26% HPCG peak performance) and 51.37% (using 32,768 cores and 2048 MI250X) on Frontier are achieved.

97 MATHEMATICS AND COMPUTING↗

Enabling kilometer-scale E3SM land model simulation over North America: A new integrated framework solution

This study introduces a novel framework designed to enhance the performance, scalability, and portability of the kilometer-scale E3SM Land Model (km-ELM) within the E3SM modeling infrastructure. By seamlessly integrating cutting-edge data tools, we address existing challenges such as slow performance, limited scalability, and difficulties in software integration in current data-driven ELM simulation over large geographic areas. Our innovative approach leverages the KiloCraft data toolkit to generate unified inputs for simulations ranging from a single-cite case, to a 72,083-cell regional case to a continental configuration encompassing 21.6 million land grid cells at a 1 km × 1 km resolution. We conduct extensive strong- and weak-scaling experiments on three state-of-the-art supercomputers, utilizing up to 100,800 CPU cores across 2400 compute nodes to evaluate end-to-end metrics including wall-clock time, simulation-years-per-day (SYPD), initialization costs, and I/O throughput. Our results reveal the land (LND) component’s efficient scaling, demonstrating near-ideal weak scaling and strong-scaling parallel efficiencies reaching up to 87% at 50,400 cores. We confirm portability and reproducibility through bitwise-equivalent outputs across different machines using identical inputs over supported machines. Notably, at extreme scales, we identify I/O as a critical bottleneck and that leads to effective solution with the SCORPIO/ADIOS stack. Collectively, these findings validate the deployment of km-ELM at a continental scale with high parallel efficiency and provide essential guidance on configuration, decomposition, and I/O settings for optimized kilometer-scale land simulations in E3SM. This work emphasizes the innovative design and practical solutions that enhance the operational capabilities of km-ELM, focusing on software performance and scalability while leaving detailed scientific evaluations of simulated land processes for future investigations.

E3SM land model (ELM), km-ELM, scalability, perfor↗

Single-pixel reconstructive mid-infrared micro-spectrometer

Miniaturized spectrometers in the mid-infrared (MIR) are critical in developing next-generation portable electronics for advanced sensing and analysis. The bulky gratings or detector/filter arrays in conventional micro-spectrometers set a physical limitation to their miniaturization. In this work, we demonstrate a single-pixel MIR micro-spectrometer that reconstructs the sample transmission spectrum by a spectrally dispersed light source instead of spatially grated light beams. The spectrally tunable MIR light source is realized based on the thermal emissivity engineered via the metal-insulator phase transition of vanadium dioxide (VO 2 ). We validate the performance by showing that the transmission spectrum of a magnesium fluoride (MgF 2 ) sample can be computationally reconstructed from sensor responses at varied light source temperatures. With potentially minimum footprint due to the array-free design, our work opens the possibility where compact MIR spectrometers are integrated into portable electronic systems for versatile applications.

47 OTHER INSTRUMENTATION↗

Coso Geothermal Spectral Library for Rocks and Minerals

An integrated open mineral spectral library designed to enhance the utility and precision of mineral spectral data for geothermal exploration, developed from a reliable and comprehensive digital dataset for seamless sharing by integrating field data, the USGS spectral library, and pertinent information obtained from Coso geothermal field (Coso) in California. The ASD FieldSpec portable spectrometer was utilized for collecting spectral data, which was subsequently analyzed using the THOR Material Identification tool in ENVI, The Spectral Geologist (TSG) software by CSIRO, and the Fully Constrained Linear Spectral Unmixing algorithm (FCLSU) in MATLAB. Scanning Electron Microscopy (SEM) with a mineralogy-analyzing function was employed to assess the mineral composition of samples, ensuring precise mineralogical analysis. A portable X-ray fluorescence (pXRF) spectrometer was also utilized to gather information on elemental enrichment. A framework for developing spectra data and establishing spectral libraries for various geological cases was proposed within this study. The characteristic spectra of six alteration minerals - alunite, chalcedony, epidote, hematite, kaolinite, and opal - were acquired from Coso samples. The spectral library for the Coso alteration minerals was introduced for further application in academic study or industrial exploration. To browse the Coso Geothermal Spectral data and related figures from spreadsheets: #1 Unzip and store the following items in the same folder. 'Contact Probe Data.zip', 'Sample Photos.zip', and 'Coso spectra of higher-certainity minerals.xlsx'. #2 Open 'Coso spectra of higher-certainity minerals.xlsx'. The hyperlinks in the spreadsheet lead to the folders or figures of: spectra .asd file, spectra ASC II file, spectra plots, and sample photos. The spectra data is raw data without splice correction. Spectra .asd files require particular software to open. (These cannot be opened in GIS software such as ArcGIS.) Spectra ASC II files can be opened in a text editor or spread sheet program.

15 GEOTHERMAL ENERGY↗

Fifty years of lithium-ion batteries and what is next?

Here, the first rechargeable lithium batteries were built 50 years ago, at the same time as the Materials Research Society was formed. Great strides have been made since then taking a dream to domination of portable energy storage. During the past two decades, the demand for the storage of electrical energy has mushroomed both for portable applications such as for the iPhone and electric vehicles and for more than 1 GWh grid applications. As storage and power demands have increased, the batteries have evolved with their chemistries being pushed to the limits. This has resulted in the energy densities almost doubling and the cost dropping by more than an order of magnitude. However, the present electrochemical systems are still too costly to penetrate major new markets, still higher performance is required, and environmentally acceptable and sustainable materials are required.

25 ENERGY STORAGE↗

Vidyut3d: A Gpu Accelerated Fluid Solver for Non-Equilibrium Plasmas on Adaptive Grids

We present the numerical methods, programming methodology, verification, and performance assessment of a non-equilibrium plasma fluid solver that can effectively utilize current and upcoming central processing and graphics processing unit (CPU+GPU) architectures, in this work. Our plasma fluid model solves the coupled conservation equations for species transport, electrostatic Poisson and electron temperature on adaptive Cartesian grids. Our solver is written using performance portable adaptive-grid/particle management library, AMReX, and is portable over widely available vendor specific GPU architectures. We present verification of our solver using method of manufactured solutions that indicate formal second order accuracy with central diffusion and fifth-order weighted-essentially-non-oscillatory (WENO) advection scheme. We also verify our solver with published literature on capacitive discharges and atmospheric pressure streamer propagation. We demonstrate the use of our solver on two 3D simulation cases: an atmospheric streamer propagation in Ar-H2 mixtures and a low pressure twin electrode radio frequency reactor. Our performance studies on three different CPU+GPU architectures indicate approximately 150-400X speed-up using AMD and NVIDIA GPUs per time step compared to a single CPU core for a 4 million cell simulation with 15 species.

Sitaraman, Hariswaran↗

ECP ST Project 2.3.1.06-STPM08-RAJA (Final Report)

Modern high-performance computing architectures are diverse, with hardware designs that feature multicore CPUs and CPUs plus accelerators, such as GPUs or FPGAs. Achieving good application performance often requires using a programming model and managing application data in ways that are best suited to a particular platform. For large codes that are used daily in production, and are under continual development, architecture-specific ports are untenable. Maintainability requires single-source code that is performance portable across a range of architectures and programming model back-ends. This report describes RAJA, Umpire, and CHAI, three software libraries that provide complementary capabilities to enable application portability for high performance computing (HPC) platforms. In particular, these libraries provide software abstractions that insulate application source code from hardware architecture and programming model-specific implementation details. These development of these libraries was motivated by the needs of multiphysics applications in the Weapons Simulation and Computing Program (WSC) at Lawrence Livermore National Laboratory (LLNL). Funding though the Exascale Computing Project (ECP) Software Technology (ST) project 2.3.1.06 RAJA has fostered outreach and collaboration with the ECP application and software technology development communities. In this report, we describe ECP adoption and integration of these tools to this point. The larger goal of the report is to describe to the ECP community what these projects offer, how they are used, and how to approach adoption and integration of them.

97 MATHEMATICS AND COMPUTING↗

Protein Factory on a Chip for Rapid Therapeutics

The potential for new, re-emerging, or engineered pandemic threats could challenge our nation's biosecurity, requiring rapid and flexible countermeasure development platforms. In healthcare, one of the main hindrances to the timely development of protein-based therapeutics for cancer, infectious disease, and other diseases has been a slow and expensive quality-controlled production stage. We present a protein-based technology that has the potential to address these crucial problems in biosecurity and healthcare by maximizing protein production and system portability, while minimizing production latency and cost. Specifically, we have developed a reusable, portable first-generation platform that leverages the advantages of cell-free protein synthesis (CFPS) and flow cells to create practical amounts of clinically relevant therapeutics. We have demonstrated that this technology is reusable and programmable, enabling a single platform that can synthesize multiple dosages of various therapeutics and vaccine in the field. Implementing this technology could mitigate pandemic threats by providing a rapidly-deployable (just-in-time), versatile (precision medicine) production of biologic therapeutics to the infected patient’s locale (point-of-care). In drug development, once promising drug variations are identified, the platform can be scaled to quickly produce practical amounts of protein for patient testing in the matter of days (vs. months) at a fraction of the cost of existing technology.

59 BASIC BIOLOGICAL SCIENCES↗

Improving the performance of medical imaging applications using SYCL

As opposed to the Open Computing Language (OpenCL) programming model, in which host and device codes are generally written in different programming languages, SYCL can combine host and device codes for an application in a type-safe way to improve development productivity and performance portability. Hence, this report shows the experimental results of applying the SYCL programming model to medical imaging applications for a study on performance portability and programming productivity between OpenCL and SYCL. Rodinia is a widely used open-source benchmark suite for heterogeneous computing. We choose two medical imaging applications (Heart Wall and Particle Filter) in the benchmark suite, migrate the OpenCL implementations of the applications to the SYCL implementations, and evaluate their performance and productivity on Intel® microprocessors that contain a central processing unit (CPU) and an integrated graphics processing unit (GPU). The maturing SYCL compilers, which are based on a conformant implementation of the SYCL 1.2.1 Khronos specification, have been actively optimized for Intel® computing platforms. The experimental results are promising in terms of the raw performance and productivity. Although the SYCL implementation of the Heart Wall application does not execute successfully on a CPU, the SYCL implementations of the application can achieve comparable or better performance than the OpenCL implementation on Intel® integrated GPUs. For the Particle Filter application, the performance difference between the SYCL and OpenCL implementations is comparable on the GPUs for most cases, but the SYCL implementations are on average 4X faster than the OpenCL implementations on Intel® Xeon® CPUs. For programming productivity, we arguably use lines of code as a way to measure programming productivity in software. The SYCL programs reduce the lines of code of the OpenCL programs by 52% and 38% for the Heart Wall and Particle Filter, respectively. The results indicate that SYCL is a promising programming model for heterogeneous computing with the maturing compilers. We organize the remainder of the report as follows. Section II introduces the SYCL programming model, compares the major differences between an OpenCL program and a SYCL program, and describes the characteristics of the two applications. Section III describes the SYCL programming model in more details, and shows the SYCL implementation of a kernel function in the Particle Filter application as an example. In Section IV, we evaluate the performance of the applications on the CPUs and GPUs. Section V concludes the report.

59 BASIC BIOLOGICAL SCIENCES↗

The Rodinia Benchmark Suite in SYCL

As opposed to the Open Computing Language (OpenCL) programming model in which host and device codes are generally written in different programming languages, SYCL can combine host and device codes for an application in a type-safe way to improve development productivity and performance portability. Rodinia is a widely used benchmark suite for heterogeneous computing. Hence, we port the OpenCL implementations of the benchmark suite to SYCL manually. The SYCL benchmark suite is an opensource project for tracking the development of the mainstream SYCL compilers, and for developers and researchers interested in programming productivity, performance analysis, and portability across different computing platforms. We organize the remainder of the report as follows. Section II introduces the SYCL programming model, shows the major differences between an OpenCL program and a SYCL program, and gives a summary of the benchmark suite. In Section III, we describe our SYCL implementations in more details. We evaluate the SYCL benchmarks on the Intel® central processing units (CPUs) and graphics processing units (GPUs) in Section IV. Section V concludes the report.

97 MATHEMATICS AND COMPUTING↗