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DOE OSTI2020

Persistent Memory Object Storage and Indexing for Scientific Computing

This paper presents Mosiqs, a persistent memory object storage framework with metadata indexing and querying for scientific computing. We design Mosiqs based on the key idea that memory objects on shared PM pool can live beyond the application lifetime and can become the sharing currency for applications and scientists. Mosiqs provides an aggregate memory pool atop an array of persistent memory devices to store and access memory objects. Mosiqs uses a lightweight persistent memory key-value store to manage the metadata of memory objects such as persistent pointer mappings, which enables memory object sharing for effective scientific collaborations. Mosiqs is implemented atop PMDK. We evaluate the proposed approach on many-core server with an array of real PM devices. The preliminary evaluation confirms a 100% improvement for write and 30% in read performance against a PM-aware file system approach.

Khan, Awais↗

DOE OSTI2026

MAGIC: M arching Cubes Isosurface Uncertainty Visualization for G auss i an Uncertain Data With Spatial C orrelation

Here, in this paper, we study the propagation of data uncertainty through the marching cubes algorithm for isosurface visualization for correlated uncertain data. Consideration of correlation has been shown paramount for avoiding errors in uncertainty quantification and visualization in multiple prior studies. Although the problem of isosurface uncertainty with spatial data correlation has been previously addressed, there are two major limitations to prior treatments. First, there are no analytical formulations for uncertainty quantification of isosurfaces when the data uncertainty is characterized by a Gaussian distribution with spatial correlation. Second, as a consequence of the lack of analytical formulations,existing techniques resort to a Monte Carlo sampling approach, which is expensive and difficult to integrate into visualization tools. To address these limitations, we present a closed-form framework to efficiently derive uncertainty in marching cubes level-sets for Gaussian uncertain data with spatial correlation (MAGIC). To derive closed-form solutions, we leverage the Hinkley's derivation on the ratio of Gaussian distributions. With our analytical framework, we achieve a significant speed-up and enhanced accuracy of uncertainty quantification over classical Monte Carlo methods. We further accelerate our analytical solutions using many-core processors to achieve speed-ups up to 585× and integrability with production visualization tools for broader impact. We demonstrate the effectiveness of our correlation-aware uncertainty framework through experiments on meteorology, urban flow, and astrophysics simulation datasets.

Gaussian↗

DOE OSTI2026

Memory-Aware External Facelist Calculation: A Data-Parallel Atomic Hash Counting Approach

Unstructured volumetric meshes serve as fundamental data representations in various scientific simulations and analyses. They play a crucial role in representing complex computational domains and are essential for important numerical techniques, such as finite element analysis. Whenever such a mesh is read from a file, streamed in-situ, or generated by algorithms, scientific visualization libraries rely on calculating the external surface of a geometry, named “external facelist”, to produce a polygonal mesh for rendering. Consequently, external facelist calculation has become one of the most widely used algorithms in the scientific visualization domain, necessitating optimal performance. In this paper, we explore relevant work on external facelist calculation algorithms in two common visualization libraries, VTK and Viskores, assess their performance and memory constraints, and introduce a novel memory-aware external facelist calculation algorithm employing an atomic hash counting approach. This algorithm fully leverages Viskores' data-parallel primitive operations, facilitating its execution across diverse many-core architectures. Our algorithm features the lowest memory footprint on the GPU and the second-lowest on the CPU among all evaluated methods, and it also delivers the fastest performance on both CPU and GPU. It has been made available under an open-source license in the VTK and Viskores visualization systems.

Tsalikis, Spiros [Kitware] (ORCID:0000000151137195↗

DOE OSTI2024

FunM2C: A Filter for Uncertainty Visualization of Multivariate Data on Multi-Core Devices

Uncertainty visualization is an emerging research topic in data visualization because neglecting uncertainty in visualization can lead to inaccurate assessments. In this paper, we study the propagation of multivariate data uncertainty in visualization. Although there have been a few advancements in probabilistic uncertainty visualization of multivariate data, three critical challenges remain to be addressed. First, the state-of-the-art probabilistic uncertainty visualization framework is limited to bivariate data (two variables). Second, existing uncertainty visualization algorithms use computationally intensive techniques and lack support for cross-platform portability. Third, as a consequence of the computational expense, integration into production visualization tools is impractical. In this work, we address all three issues and make a threefold contribution. First, we take a step to generalize the state-of-the-art probabilistic framework for bivariate data to multivariate data with an arbitrary number of variables. Second, through utilization of VTK-m’s shared-memory parallelism and cross-platform compatibility features, we demonstrate acceleration of multivariate uncertainty visualization on different many-core architectures, including OpenMP and AMD GPUs. Third, we demonstrate the integration of our algorithms with the ParaView software. We demonstrate the utility of our algorithms through experiments on multivariate simulation data with three and four variables.

Hari, Gautam↗

DOE OSTI2021

PAGANI: a parallel adaptive GPU algorithm for numerical integration

We present a new adaptive parallel algorithm for the challenging problem of multi-dimensional numerical integration on massively parallel architectures. Adaptive algorithms have demonstrated the best performance, but efficient many-core utilization is difficult to achieve because the adaptive work-load can vary greatly across the integration space and is impossible to predict a priori. Existing parallel algorithms utilize sequential computations on independent processors, which results in bottlenecks due to the need for data redistribution and processor synchronization. Our algorithm employs a high-throughput approach in which all existing sub-regions are processed and sub-divided in parallel. Repeated sub-region classification and filtering improves upon a brute-force approach and allows the algorithm to make efficient use of computation and memory resources. A CUDA implementation shows orders of magnitude speedup over the fastest open-source CPU method and extends the achievable accuracy for difficult integrands. Our algorithm typically outperforms other existing deterministic parallel methods.

Sakiotis, Ioannis↗

DOE OSTI2023

Graph Contractions for Calculating Correlation Functions in Lattice QCD

Computing correlation functions for many-particle systems in Lattice QCD is vital to extract nuclear physics observables like the energy spectrum of hadrons such as protons. However, this type of calculation has long been considered to be very challenging and computing-resource intensive because of the complex nature of a hadron composed of quarks with many degrees of freedom. In particular, a correlation function can be calculated through a sum of all possible pairs of quark contractions, each of which is a batched tensor contraction, dictated by Wick's theorem. Because the number of terms of this sum can be very large for any hadronic system of interest, fast evaluation of the sum faces several challenges: an extremely large number of contractions, a huge memory footprint at runtime, and the speed of tensor contractions. In this paper, we present a Lattice QCD analysis software suite, Redstar, which addresses these challenges by utilizing novel algorithmic and software engineering methods targeting modern computing platforms such as many-core CPUs and GPUs. In particular, Redstar represents every term in the sum of a correlation function by a graph, applies efficient graph algorithms to reduce the number of contractions to lower the cost of computations, and minimizes the total memory footprint. Moreover, Redstar carries out the contractions on either CPUs or GPUs utilizing an internal and highly efficient Hadron contraction library. Specifically, we illustrate some important algorithmic optimizations of Redstar, show various key design features of Hadron library, and present the speedup values due to the optimizations along with performance figures for calculating six correlations functions on four computing platforms.

Chen, Jie↗

DOE OSTI2020

TChem 2.0

The TChem toolkit is an object-oriented C++ software library that enables numerical simulations using complex chemistry and facilitates the analysis of detailed kinetic models. The toolkit provides capabilities for thermodynamic properties and gas-phase and surface chemistry. The computations rely on the Kokkos framework for parallel execution on many-core and GPU-based platforms. 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. SAND2021-2752 O

Kim, Kyungjoo↗

DOE OSTI2021

Exascale models of stellar explosions: Quintessential multi-physics simulation

The ExaStar project aims to deliver an efficient, versatile, and portable software ecosystem for multi-physics astrophysics simulations run on exascale machines. The code suite is a component-based multi-physics toolkit, built on the capabilities of current simulation codes (in particular Flash-X and Castro), and based on the massively parallel adaptive mesh refinement framework AMReX. It includes modules for hydrodynamics, advanced radiation transport, thermonuclear kinetics, and nuclear microphysics. The code will reach exascale efficiency by building upon current multi- and many-core packages integrated into an orchestration system that uses a combination of configuration tools, code translators, and a domain-specific asynchronous runtime to manage performance across a range of platform architectures. The target science includes multi-physics simulations of astrophysical explosions (such as supernovae and neutron star mergers) to understand the cosmic origin of the elements and the fundamental physics of matter and neutrinos under extreme conditions.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Enhancing scalability of a matrix-free eigensolver for studying many-body localization

We propose several techniques to enhance the parallel scalability of a matrix-free eigensolver designed for studying many-body localization (MBL) of quantum spin chain models with nearest-neighbor interactions and on-site disorder. This type of problem is computationally challenging because the dimension of the associated Hamiltonian matrix grows exponentially with respect to the number of spins L, and we need to average over different realizations of the random disorder to obtain relevant statistical behavior. For each disorder realization, we need to compute eigenvalues from different regions of the spectrum and their corresponding eigenvectors. In previous work, the interior eigenstates for a single eigenvalue problem are computed via the shift-and-invert Lanczos algorithm. Due to the extremely high memory footprint of the LU factorizations, this technique is not well suited for large L’s. For example, we need thousands of compute nodes on modern high performance computing infrastructures to go beyond L = 24. The matrix-free approach does not suffer from this memory bottleneck, however, its scalability is limited by a computation and communication load imbalance. To reduce this imbalance and to significantly enhance the scalability of the matrix-free eigensolver, we reorder the matrix and leverage the consistent space runtime, CSPACER. We also show its efficiency in managing irregular communication patterns at scale compared to optimized MPI non-blocking two-sided and one-sided RMA implementation variants. This effort enables us to study MBL for spin chains with a larger number of spins. The efficiency and effectiveness of the proposed algorithm is demonstrated by computing eigenstates on a massively parallel many-core high performance computer.

METIS↗

DOE OSTI2020

The Kokkos Ecosystem [Brief]

In 2016/2017, the field of High-Performance Computing (HPC) entered a new era driven by fundamental physics challenges to produce ever more energy and cost-efficient processors. Since the convergence on the Message-Passing Interface (MPI) standard in the mid-1990s, application developers enjoyed a seemingly static view of the underlying machine — that of a distributed collection of homogeneous nodes executing in collaboration. However, after almost two decades of dominance, the sole use of MPI to derive parallelism acted as a limiter to improved future performance. While MPI is widely expected to continue to function as the basic mechanism for communication between compute nodes for the immediate future, additional parallelism is required on the computing node itself if high performance and efficiency goals are to be realized. When reviewing the architectures of the top HPC systems today, the change in paradigm is clear: the compute nodes of the leading machines in the world are either powered by many-core chips with a few dozen cores each, or use heterogeneous designs, where traditional CPUs marshal work to massively parallel compute accelerators which has as many as 200,000 processing threads in flight simultaneously. Complicating matters further for application developers, each processor vendor has its own preferred way of writing code for their architecture.The Kokkos EcoSystem was released by Sandia in 2017 to address this new era in HPC system design by providing a vendor independent performance portable programming system for scientific, engineering, and mathematical software applications written in the C++ programming language. Using Kokkos, application developers can be more productive because they will not have to create and maintain separate versions of their software for each architecture, nor will they have to be experts in each architecture's peculiar requirements. Instead, they will have a single method of programming for the diverse set of modern HPC architectures. While Kokkos started in 2011 as a programming model only, it soon became clear that complex applications needed more. It is also critical to have a portable mathematical functions and developers need tools to debug their applications, gain insight into the performance characteristics of their codes and tune algorithm performance parameters through automated processes. The Kokkos EcoSystem addresses those needs through its three main components: the Kokkos Core programming model, the Kokkos Kernels math library, and the Kokkos Tools project.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Fixing Amdahl's Law within the Limits of Accelerated Systems: FALLACY

Closeout report for FALLACY project. The performance of Data Model Convergence Initiative (DMC) applications on parallel machines is far below the limit set by Amdahl’s law. Whether the machine is based on many-core, GPUs, FPGAs, or a heterogeneous combination, usually the most significant bottleneck is accessing data from the memory system. Aligning with DMC’s HW/architecture thrust, this project developed a set of memory-centric tools called ‘MemGaze’ that inform the HW/SW stack about an application’s memory behavior, including data access latency and diagnosing poor data layout and data composition. Our approach uses architectural modeling and analysis of workload data accesses.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Green's function methods for multiphysics simulations (Final Report)

Green's functions are important tools for analyzing mathematical properties of partial differential equations (PDEs), and for numerically solving PDEs, especially when equations for the same operator but with multiple right hand sides need to be solved simultaneously. This proposal aims at developing efficient and accurate numerical methods for computing Green's functions, which can be used to tackle a challenging question in multiphysics simulation of DOE-mission science problems: how to couple quantum physics with classical physics. The key mathematical difficulty is properly formulate a "boundary condition" for the region described by quantum physics, and conventional approaches often model such boundary conditions in an empirical way. The proposed Green's function methods use the Dirichlet-to-Neumann map to formulate a boundary condition that is non-empirical and can couple the quantum and classical regions in an in principle exact way. The key ingredient of the new methods is to construct the Dirichlet-to-Neumann map in an efficient, accurate and versatile manner. The new methods have provably low complexity and are ideally suited for massively parallel and emerging many-core computational systems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Graph Contractions for Calculating Correlation Functions in Lattice QCD

Chen, Jie↗

DOE OSTI2023

Technical descriptions of the experimental dynamical downscaling simulations over North America by the CAM–MPAS variable-resolution model

Abstract. Comprehensive assessment of climate datasets is important for communicating model projections and associated uncertainties to stakeholders. Uncertainties can arise not only from assumptions and biases within the model but also from external factors such as computational constraint and data processing. To understand sources of uncertainties in global variable-resolution (VR) dynamical downscaling, we produced a regional climate dataset using the Model for Prediction Across Scales (MPAS; dynamical core version 4.0) coupled to the Community Atmosphere Model (CAM; version 5.4), which we refer to as CAM–MPAS hereafter. This document provides technical details of the model configuration, simulations, computational requirements, post-processing, and data archive of the experimental CAM–MPAS downscaling data. The CAM–MPAS model is configured with VR meshes featuring higher resolutions over North America as well as quasi-uniform-resolution meshes across the globe. The dataset includes multiple uniform- (240 and 120 km) and variable-resolution (50–200, 25–100, and 12–46 km) simulations for both the present-day (1990–2010) and future (2080–2100) periods, closely following the protocol of the North American Coordinated Regional Climate Downscaling Experiment. A deviation from the protocol is the pseudo-warming experiment for the future period, using the ocean boundary conditions produced by adding the sea surface temperature and sea-ice changes from the low-resolution version of the Max Planck Institute Earth System Model (MPI-ESM-LR) in the Coupled Model Intercomparison Project Phase 5 to the present-day ocean state from a reanalysis product. Some unique aspects of global VR models are evaluated to provide background knowledge to data users and to explore good practices for modelers who use VR models for regional downscaling. In the coarse-resolution domain, strong resolution sensitivity of the hydrological cycles exists over the tropics but does not appear to affect the midlatitude circulations in the Northern Hemisphere, including the downscaling target of North America. The pseudo-warming experiment leads to similar responses of large-scale circulations to the imposed radiative and boundary forcings in the CAM–MPAS and MPI-ESM-LR models, but their climatological states in the historical period differ over various regions, including North America. Such differences are carried to the future period, suggesting the importance of the base state climatology. Within the refined domain, precipitation statistics improve with higher resolutions, and such statistical inference is verified to be negligibly influenced by horizontal remapping during post-processing. Limited (≈50 % slower) throughput of the current code is found on a recent many-core/wide-vector high-performance computing system, which limits the lengths of the 12–46 km simulations and indirectly affects sampling uncertainty. Our experience shows that global and technical aspects of the VR downscaling framework require further investigations to reduce uncertainties for regional climate projection.

58 GEOSCIENCES↗

DOE OSTI2020

Reconstruction of Charged Particle Tracks in Realistic Detector Geometry Using a Vectorized and Parallelized Kalman Filter Algorithm

One of the most computationally challenging problems expected for the High-Luminosity Large Hadron Collider (HL-LHC) is finding and fitting particle tracks during event reconstruction. Algorithms used at the LHC today rely on Kalman filtering, which builds physical trajectories incrementally while incorporating material e ects and error estimation. Recognizing the need for faster computational throughput, we have adapted Kalman-filterbased methods for highly parallel, many-core SIMD and SIMT architectures that are now prevalent in high-performance hardware. Previously we observed significant parallel speedups, with physics performance comparable to CMS standard tracking, on Intel Xeon, Intel Xeon Phi, and (to a limited extent) NVIDIA GPUs. While early tests were based on artificial events occurring inside an idealized barrel detector, we showed subsequently that our mkFit software builds tracks successfully from complex simulated events (including detector pileup) occurring inside a geometrically accurate representation of the CMS-2017 tracker. Here, we report on advances in both the computational and physics performance of mkFit, as well as progress toward integration with CMS production software. Recently we have improved the overall eciency of the algorithm by preserving short track candidates at a relatively early stage rather than attempting to extend them over many layers. Moreover, mkFit formerly produced an excess of duplicate tracks; these are now explicitly removed in an additional processing step. We demonstrate that with these enhancements, mkFit becomes a suitable choice for the first iteration of CMS tracking, and eventually for later iterations as well. We plan to test this capability in the CMS High Level Trigger during Run 3 of the LHC, with an ultimate goal of using it in both the CMS HLT and oine reconstruction for the HL-LHC CMS tracker.

Cerati, Giuseppe↗

DOE OSTI2022

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↗

DOE OSTI2021

A compute-bound formulation of Galerkin model reduction for linear time-invariant dynamical systems

This work aims to advance computational methods for projection-based reduced-order models (ROMs) of linear time-invariant (LTI) dynamical systems. For such systems, current practice relies on ROM formulations expressing the state as a rank-1 tensor (i.e., a vector), leading to computational kernels that are memory bandwidth bound and, therefore, ill-suited for scalable performance on modern architectures. This weakness can be particularly limiting when tackling many-query studies, where one needs to run a large number of simulations. This work introduces a reformulation, called rank-2 Galerkin, of the Galerkin ROM for LTI dynamical systems which converts the nature of the ROM problem from memory bandwidth to compute bound. We present the details of the formulation and its implementation, and demonstrate its utility through numerical experiments using, as a test case, the simulation of elastic seismic shear waves in an axisymmetric domain. We quantify and analyze performance and scaling results for varying numbers of threads and problem sizes. In conclusion, we present an end-to-end demonstration of using the rank-2 Galerkin ROM for a Monte Carlo sampling study. We show that the rank-2 Galerkin ROM is one order of magnitude more efficient than the rank-1 Galerkin ROM (the current practice) and about 970 times more efficient than the full-order model, while maintaining accuracy in both the mean and statistics of the field.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Toward performance-portable PETSc for GPU-based exascale systems

The Portable Extensible Toolkit for Scientific computation (PETSc) library delivers scalable solvers for nonlinear time-dependent differential and algebraic equations and for numerical optimization. The PETSc design for performance portability addresses fundamental GPU accelerator challenges and stresses flexibility and extensibility by separating the programming model used by the application from that used by the library, and it enables application developers to use their preferred programming model, such as Kokkos, RAJA, SYCL, HIP, CUDA, or OpenCL, on upcoming exascale systems. Furthermore, a blueprint for using GPUs from PETSc-based codes is provided, and case studies emphasize the flexibility and high performance achieved on current GPU-based systems.

97 MATHEMATICS AND COMPUTING↗