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At least 685 records · Page 38

On Stable Marriages and Greedy Matchings

Research on stable marriage problems has a long and mathematically rigorous history, while that of exploiting greedy matchings in combinatorial scientific computing is a younger and less developed research field. In this paper we consider the relationships between these two areas. In particular we show that several problems related to computing greedy matchings can be formulated as stable marriage problems and as a consequence several recently proposed algorithms for computing greedy matchings are in fact special cases of well known algorithms for the stable marriage problem. However, in terms of implementations and practical scalable solutions on modern hardware, the greedy matching community has made considerable progress. We show that due to the strong relationship between these two fields many of these results are also applicable for solving stable marriage problems.

matching↗

Modifying the Asynchronous Jacobi Method for Data Corruption Resilience

Moving scientific computation from high-performance computing (HPC) and cloud computing (CC) environments to devices on the edge, i.e., physically near instruments of interest, has received tremendous interest in recent years. Such edge computing environments can operate on data in situ, offering enticing benefits over data aggregation to HPC and CC facilities that include avoiding costs of transmission, increased data privacy, and real-time data analysis. Because of the inherent unreliability of edge computing environments, new fault-tolerant approaches must be developed before the benefits of edge computing can be realized. Motivated by algorithm-based fault tolerance, a variant of the asynchronous Jacobi (ASJ) method is developed that achieves resilience to data corruption by rejecting solution approximations from neighbor devices according to a bound derived from convergence theory. Numerical results on a two-dimensional Poisson problem show that the new rejection criterion, along with a novel approximation to the shortest path length on which the criterion depends, restores convergence for the ASJ variant in the presence of certain types data corruption. Numerical results are obtained for when the singular values in the analytic bound are approximated. Additional linear systems are also explored, one with a more dense sparsity pattern and one that includes advection. All results indicate that successful resilience to data corruption depends on whether the bound tightens fast enough to reject corrupted data before the iteration evolution deviates significantly from that predicted by the convergence theory defining the bound. This observation generalizes to future work on algorithm-based fault tolerance for other asynchronous algorithms, including upcoming approaches that leverage Krylov subspaces.

97 MATHEMATICS AND COMPUTING↗

Bias-Variance Trade-Off in Physics-Informed Neural Networks with Randomized Smoothing for High-Dimensional PDEs

Physics-Informed Neural Networks (PINNs) have triggered a paradigm shift in scientific computing, leveraging mesh-free properties and robust approximation capabilities. While proving effective for low-dimensional partial differential equations (PDEs), the computational cost of PINNs remains a hurdle in high-dimensional scenarios. This is particularly pronounced when computing high-order and high-dimensional derivatives in the physics-informed loss. Randomized Smoothing PINN (RS-PINN) introduces Gaussian noise for stochastic smoothing of the original neural net model, enabling the use of Monte Carlo methods for derivative approximation, which eliminates the need for costly automatic differentiation. Despite its computational efficiency, especially in the approximation of high-dimensional derivatives, RS-PINN introduces biases in both loss and gradients, negatively impacting convergence, especially when coupled with stochastic gradient descent (SGD) algorithms. We present a comprehensive analysis of biases in RS-PINN, attributing them to the nonlinearity of the Mean Squared Error (MSE) loss as well as the intrinsic nonlinearity of the PDE itself. We propose tailored bias correction techniques, delineating their application based on the order of PDE nonlinearity. The derivation of an unbiased RS-PINN allows for a detailed examination of its advantages and disadvantages compared to the biased version. Specifically, the biased version has a lower variance and runs faster than the unbiased version, but it is less accurate due to the bias. To optimize the bias-variance trade-off, we combine the two approaches in a hybrid method that balances the rapid convergence of the biased version with the high accuracy of the unbiased version. In addition to methodological contributions, we present an enhanced implementation of RS-PINN. Extensive experiments on diverse high-dimensional PDEs, including Fokker-Planck, Hamilton-Jacobi-Bellman (HJB), viscous Burgers’, Allen-Cahn, and Sine-Gordon equations, illustrate the bias-variance trade-off and highlight the effectiveness of the hybrid RS-PINN. Empirical guidelines are provided for selecting biased, unbiased, or hybrid versions, depending on the dimensionality and nonlinearity of the specific PDE problem.

97 MATHEMATICS AND COMPUTING↗

iDDS: intelligent distributed dispatch and scheduling for workflow orchestration

The intelligent distributed dispatch and scheduling (iDDS) service is a versatile workflow orchestration system designed for large-scale, distributed scientific computing. iDDS extends traditional workload and data management by integrating data-aware execution, conditional logic, and programmable workflows, enabling automation of complex and dynamic processing pipelines. Originally developed for the ATLAS experiment at the large hadron collider, iDDS has evolved into an experiment-agnostic platform that supports both template-driven workflows and a Function-as-a-Task model for Python-based orchestration. This paper presents the architecture and core components of iDDS, highlighting its scalability, modular message-driven design, and integration with systems such as PanDA and Rucio. We demonstrate its versatility through real-world use cases: fine-grained tape resource optimization for ATLAS, orchestration of large Directed Acyclic Graph (DAG) workflows for the Rubin Observatory, distributed hyperparameter optimization for machine learning applications, active learning for physics analyses, and AI-assisted detector design at the electron–ion collider. By unifying workload scheduling, data movement, and adaptive decision-making, iDDS reduces operational overhead and enables reproducible, high-throughput workflows across heterogeneous infrastructures. We conclude with current challenges and future directions, including interactive, cloud-native, and serverless workflow support.

97 MATHEMATICS AND COMPUTING↗

Optimizing Irregular Applications for Energy and Performance on the Tilera Many-core Architecture

Optimizing applications simultaneously for energy and performance is a complex problem. High performance, parallel, irregular applications are notoriously hard to optimize due to their data-dependent memory accesses, lack of structured locality and complex data structures and code patterns. Irregular kernels are growing in importance in applications such as machine learning, graph analytics and combinatorial scientific computing. Performance- and energy-efficient implementation of these kernels on modern, energy efficient, multicore and many-core platforms is therefore an important and challenging problem. We present results from optimizing two irregular applications { the Louvain method for community detection (Grappolo), and high-performance conjugate gradient (HPCCG) { on the Tilera many-core system. We have significantly extended MIT's OpenTuner auto-tuning framework to conduct a detailed study of platform-independent and platform-specific optimizations to improve performance as well as reduce total energy consumption. We explore the optimization design space along three dimensions: memory layout schemes, compiler-based code transformations, and optimization of parallel loop schedules. Using auto-tuning, we demonstrate whole node energy savings of up to 41% relative to a baseline instantiation, and up to 31% relative to manually optimized variants.

irregular applications, energy opttimization, many↗

CPU Volume Rendering of Adaptive Mesh Refinement Data

Adaptive Mesh Refinement (AMR) methods are widespread in scientific computing, and visualizing the resulting data with efficient and accurate rendering methods can be vital for enabling interactive data exploration. In this work, we detail a comprehensive solution for directly volume rendering block-structured (Berger-Colella) AMR data in the OSPRay interactive CPU ray tracing framework. In particular, we contribute a general method for representing and traversing AMR data using a kd-tree structure, and four different reconstruction options, one of which in particular (the basis function approach) is novel compared to existing methods. Here, we demonstrate our system on two types of block-structured AMR data and compressed scalar field data, and show how it can be easily used in existing production-ready applications through a prototypical integration in the widely used visualization program ParaView.

97 MATHEMATICS AND COMPUTING↗

Improved unconstrained energy functional method for eigensolvers in electronic structure calculations

This paper reports on the performance of a preconditioned conjugate gradient based iterative eigensolver using an unconstrained energy functional minimization scheme. In contrast to standard implementations, this scheme avoids an explicit reorthogonalization of the trial eigenvectors and becomes an attractive alternative for the solution of very large problems. The unconstrained formulation is implemented in the first-principles materials and chemistry CP2K code, which performs electronic structure calculations based on a density functional theory approximation to the solution of the many-body Schrödinger equation. We study the convergence of the unconstrained formulation, as well as its parallel scaling, on a Cray XC40 at the National Energy Research Scientific Computing Center (NERSC). The systems we use in our studies are bulk liquid water, a supramolecular catalyst gold(III)-complex, a bilayer of MoS2-WSe2 and a divacancy point defect in silicon, with the number of atoms ranging from 2,247 to 12,288. We show that the unconstrained formulation with an appropriate preconditioner has good convergence properties and scales well to 230k cores, roughly 38% of the full machine.

Del Ben, M↗

Adaptive Learning for Concept Drift in Application Performance Modeling

Supervised learning is a promising approach for modeling the performance of applications running on large HPC systems. A key assumption in supervised learning is that the training and testing data are obtained under the same conditions. However, in production HPC systems these conditions might not hold because the conditions of the platform can change over time as a result of hardware degradation, hardware replacement, software upgrade, and configuration updates. These changes could alter the data distribution in a way that affects the accuracy of the predictive performance models and render them less useful; this phenomenon is referred to as concept drift. Ignoring concept drift can lead to suboptimal resource usage and decreased efficiency when those performance models are deployed for tuning and job scheduling in production systems. To address this issue, we propose a concept-drift-aware predictive modeling approach that comprises two components: (1) an online Bayesian changepoint detection method that can automatically identify the location of events that lead to concept drift in near-real time and (2) a moment-matching transformation inspired by transfer learning that converts the training data collected before the drift to be useful for retraining. We use application input/output performance data collected on Cori, a production supercomputing system at the National Energy Research Scientific Computing Center, to demonstrate the effectiveness of our approach. The results show that concept-drift-aware models obtain significant improvement in accuracy; the median absolute error of the best-performing Gaussian process regression improved by 58.8% when the proposed approaches were used.

adaptive learning↗

Evaluating HPC Scheduling Strategies for Urgent Workloads

Scientific computing centers increasingly face workloads with diverse urgency requirements, driven by applications that demand rapid or even immediate execution. Appropriately configured scheduling policies can significantly improve both user satisfaction and overall cluster utilization. In this work, we present a systematic analysis of scheduler configurations under scenarios where a fraction of jobs have urgent computing needs. We evaluate multiple job scheduling simulators, develop a lightweight job-submission emulation framework, and create tools to analyze and visualize the resulting scheduling data. Our study identifies key trade-offs between responsiveness, fairness, and efficiency, and offers a set of practical scheduling configurations (particularly for Slurm) that can be tailored to HPC environments supporting mixed-urgency workloads.

Maheshwari, Ketan [ORNL] (ORCID:000000033800662X)↗

brulilo, Version 0.x

brulilo is a Python package for building and evolving thermonuclear reaction networks, such as those used in astrophysical explosion calculations. It is very much a current work in progress, and much of the intended functionality is still under development. The main goal of brulilo is an easy-to-use code for quick calculations or post-processing, as well as a learning tool to test various implementations of solvers on both CPUs and GPUs. Currently, brulilo parses an input text file that specifies the reactions to be included in the network. The notation of the inputs are in the typical astrophysical notation; i.e. hydrogen burning to deuterium in the sun, "p + p + e --> d + neutrino", is given as "p(p,)d." Each reaction is added to a list comprising the reaction network, and once completed, the network contains a list of all isotopes and reactions involved. brulilo then parses publicly available nuclear data (binding energy, spin, partition function data, etc.) for each isotope from the WebNucleo group's data at nucleo.ces.clemson.edu. Fits to reaction rate data for each reaction are obtained from the publicly available data provided by the Joint Institute for Nuclear Astrophysics' Reaclib database. Reverse reactions are calculated from detailed balance. The reaction network then consists of a sparse system of mathematically stiff ordinary differential equations (ODEs). Physically, "stiffness" here means that there are some reaction rates that are occurring much faster than others; the ratio of the fast to slow often being greater than 10^15 in astrophysics. Numerical integration of such systems typically involves implicit integration schemes, which brulilo will leverage from the scientific computing Python package, Numpy, as well as implement its own. There has recently been work from researchers at Oak Ridge National Lab who have found good results from applying quasi-equilibrium and quasi-asymptotic conditions to the stiff system of ODEs, which effectively remove some of the stiffness and allow for efficient explicit integration techniques to be used. The original intent of brulilo was to implement these stiffness-alleviating techniques with explicit integrators and compare the performance to traditional implicit integrations of the full stiff system. This is still underway, as the code is very much in an alpha-release state. Furthermore, explicit integrators are often much easier to parallelize than their implicit counterparts. brulilo will implement parallelization of these techniques, leveraging both the Python implementation of MPI, mpi4py, as well as highly parallelized versions targeted at GPUs with PyOpenCL and/or PyCUDA.

Malone, Chris↗

Algebraic Multigrid Benchmark

AMG is a parallel algebraic multigrid solver for linear systems arising from problems on unstructured grids. It has been derived directly from the BoomerAMG solver in the hypre library, a large linear solvers library that is being developed in the Center for Applied Scientific Computing (CASC) at LLNL and is very similar to the AMG2013 benchmark with additional optimizations. The driver provided in the benchmark can build various test problems. The default problem is a Laplace type problem with a 27-point stencil, which can be scaled up and is designed to solve a very large problem. A second problem simulates a time dependent problem, in which successively various smnllcr systems are solved.

Yang, Ulrike↗

Framework for Analysis and Visualization of Simulation Data (VizAly)

As supercomputing resources increase, cosmological scientists are able to run more detailed and larger simulations generating massive amounts of data. Analyzing these simulations with an available open-source toolkit is important for collaborative Department of Energy scientific discovery across labs, universities, and other partners. Developed software as a part of this collection include: comparing data with other existing simulations, verifying and validating results with observation databases, new halo finder algorithms, and using analytical tools to get insights into the physics of the cosmological universe. The goal of this software project is to provide a set of open-source libraries, tools, and packages for large-scale cosmology that allows scientists to visualize, analyze, and compare large-scale simulation and observational data sets. Developed software will provide a variety of methods for processing, visualization, and analysis of astronomical observation and cosmological simulation data. These tools are intended for deployment on multiple scientific computing platforms, including but not limited to personal computers, cloud computing, experimental sites (telescopes) and high performance supercomputers.

Wendelberger, Joanne↗

BuildingsPy

BuildingsPy is a Python package that can be used to run Modelica simulations and to process Modelica output files. It can also be used to run unit tests as part of the development of LBNL's Modelica Buildings library. The package provides functions to extract data series from the output file for further use in the python packages matplotlib for plotting and SciPy for scientific computing.

Wetter, Michael↗

Spify Parser of Input Files with YAML syntax

SPIFY is a C++ library for parsing input files to be used in scientific computing applications. The library allows an application developer to define a full set of required and optional input variable of different types and handles all of the parsing and validation.

Whitesides, Russell↗

Quantities need Representation, Unit and Scale

C++ template library to represent quantities in scientific computing. It enables a strong, compile-time, typing of physical quantities. This typing includes information about: - representation: float, double, ... - unit: [ mass, length, time, angle ] - scale: kilo, milli, micro, ... Is

VANDERBRUGGEN, TRISTANL.↗

JPype

JPype is a Python module to provide full access to Java from within Python. It allows Python to make use of Java only libraries, exploring and visualization of Java structures, development and testing of Java libraries, scientific computing, and much more. By gaining the best of both worlds using Python for rapid prototyping and Java for strong typed production code, JPype provides a powerful environment for engineering and code development. This is achieved not through re-implementing Python, as Jython has done, but rather through interfacing at the native level in both virtual machines. This shared memory based approach achieves decent computing performance, while providing the access to the entirety of CPython and Java libraries.

Nelson, KarlE.↗

Consistent Space Runtime (CSPACER) v1.0

This software provides a runtime for communication-bound applications, especially with irregular communication patterns. The target programming abstraction for the runtime is the space consistency model, which defines consistency guarantees at the granularity of memory spaces. This model has relaxed consistency semantics that enables a wide range of runtime optimizations. The runtime leverages threading to accelerate communication primitives, especially collective operations. It also allows efficient pipelining of communication operations and enable constructing a consistent state of multiple unordered communication activities targeting a memory space. The runtime uses a reduced API design that decomposes complex communication primitives in traditional general-purpose runtime into a sequence of simpler steps. To improve the productivity of using this runtime, we provide communication patterns commonly used for regular scientific computing applications and irregular data analytics. These communication patterns offer skeletons for the integration with application computation to allow efficient overlap.

Ibrahim, Khaled↗

P3A

Portably Performant Physical Algebra (P3A) is a C++ library that provides classes representing variables in a physical algebra equation. These equations are the fundamental way that physics models are written ("f = ma" for example). P3A provides a way to write in the C++ programming language similar to how one would do math on paper. P3A provides support tools for rapidly solving equations in a way that is common in scientific computing. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525. SAND2021-3183 O

Ibanez-Granados, Daniel↗