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DOE OSTI2022

Agile Acceleration of LLVM Flang Support for Fortran 2018 Parallel Programming

The LLVM Flang compiler ("Flang") is currently Fortran 95 compliant, and the frontend can parse Fortran 2018. However, Flang does not have a comprehensive 2018 test suite and does not fully implement the static semantics of the 2018 standard. We are investigating whether agile software development techniques, such as pair programming and test-driven development (TDD), can help Flang to rapidly progress to Fortran 2018 compliance. Because of the paramount importance of parallelism in high-performance computing, we are focusing on Fortran’s parallel features, commonly denoted “Coarray Fortran.” We are developing what we believe are the first exhaustive, open-source tests for the static semantics of Fortran 2018 parallel features, and contributing them to the LLVM project. A related effort involves writing runtime tests for parallel 2018 features and supporting those tests by developing a new parallel runtime library: the CoArray Fortran Framework of Efficient Interfaces to Network Environments (Caffeine).

Rasmussen, Katherine↗

DOE OSTI2025

VA EDH Advanced Software Pipeline Framework Report: Enhancing Automation and Scalability

The VA Environmental Determinants of Health (EDH) Advanced Software Pipeline Framework is designed to enhance the efficiency, scalability, and security of geospatial data processing workflows. This framework integrates modern data orchestration and containerization technologies, including Prefect for workflow automation, Docker for containerization, and PostgreSQL/PostGIS for geospatial data storage and analysis. It ensures standardized, reproducible, and automated data processing, supporting VA objectives related to substance use risk assessment and recovery research. The pipeline addresses key scalability and performance challenges through horizontal and vertical scaling, high-performance computing (HPC) integration, parallel processing, task caching, and dynamic resource allocation. These optimizations improve throughput and reduce latency, allowing the system to efficiently manage large and complex datasets. Additionally, security and compliance measures—such as data encryption (SSL), Role-Based Access Control (RBAC), and adherence to GDPR and HIPAA standards—safeguard sensitive information throughout data transmission and storage. A key implementation of this framework includes the automation of shelter list geolocation workflows, ensuring that up-to-date data is readily available for VA decision-making. Lessons learned from this project include the transition from in-memory processing to incremental storage writes, improving resource management and reliability. Future enhancements aim to expand automation, integrate AI-driven anomaly detection, and incorporate high-performance computing resources. This framework provides a scalable, secure, and adaptable solution for managing geospatial datasets, reinforcing the VA’s ability to support clinical and strategic initiatives through data-driven decision-making.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

An Orthogonal Recursive Bisection (ORB) Based Time Advancement Algorithm for CFD-DEM Solvers

The time integration of the granular phase in coupled computational fluid dynamics (CFD) – discrete element method (DEM) simulations presents a unique computational challenge brought about by the large variations in particle collisional time scales. Particles in the dilute regions of the computational domain can be advanced with large time steps while dense regions require much smaller time increments. However, the time step size in most solvers is globally set as the limit for accuracy and stability imposed by the collisions and is typically orders of magnitude less than that required away from collisions. This work addresses this precise issue and provides a strategy to avoid the use of a global conservative small time step size for the entire set of particles.A novel time stepping algorithm for CFD-DEM solvers using a partitioning approach using orthogonal recursive bisection (ORB) that allows for variable time steps among particles is described and its computational performance is compared against baseline explicit methods, typically used in several CFD-DEM solvers. ORB has advantages of being relatively quick and easy to update incrementally and has the required heuristic behavior (i.e., it will split the region in half with a cluster on each side) when groups of particles are well separated (clustered). The algorithm presented in this work uses a local time stepping approach to resolve collisional time scales for subsets of particles that are present at the leaves of the ORB, thereby resulting in substantial reduction of computational cost. The parallel implementation of this method where a ``knapsack” algorithm is used in tandem with ORB for effective load-balancing is also presented, where a best possible partitioning is obtained based on number of particles and local time-stepping costs. The algorithm is tested against benchmark problems with varying particle distributions that include fluidized bed and riser flow scenarios. Preliminary results indicate that the approach is 2-3X faster than traditional explicit methods for problems that involve both dense and dilute regions, while maintaining the same level of accuracy.

adaptive timestepping↗

NASA NTRS1995

RISC Processors and High Performance Computing

In this tutorial, we will discuss top five current RISC microprocessors: The IBM Power2, which is used in the IBM RS6000/590 workstation and in the IBM SP2 parallel supercomputer, the DEC Alpha, which is in the DEC Alpha workstation and in the Cray T3D; the MIPS R8000, which is used in the SGI Power Challenge; the HP PA-RISC 7100, which is used in the HP 700 series workstations and in the Convex Exemplar; and the Cray proprietary processor, which is used in the new Cray J916. The architecture of these microprocessors will first be presented. The effective performance of these processors will then be compared, both by citing standard benchmarks and also in the context of implementing a real applications. In the process, different programming models such as data parallel (CM Fortran and HPF) and message passing (PVM and MPI) will be introduced and compared. The latest NAS Parallel Benchmark (NPB) absolute performance and performance per dollar figures will be presented. The next generation of the NP13 will also be described. The tutorial will conclude with a discussion of general trends in the field of high performance computing, including likely future developments in hardware and software technology, and the relative roles of vector supercomputers tightly coupled parallel computers, and clusters of workstations. This tutorial will provide a unique cross-machine comparison not available elsewhere.

Saini, Subhash↗

NASA NTRS1997

HARP: A Dynamic Inertial Spectral Partitioner

Partitioning unstructured graphs is central to the parallel solution of computational science and engineering problems. Spectral partitioners, such recursive spectral bisection (RSB), have proven effecfive in generating high-quality partitions of realistically-sized meshes. The major problem which hindered their wide-spread use was their long execution times. This paper presents a new inertial spectral partitioner, called HARP. The main objective of the proposed approach is to quickly partition the meshes at runtime in a manner that works efficiently for real applications in the context of distributed-memory machines. The underlying principle of HARP is to find the eigenvectors of the unpartitioned vertices and then project them onto the eigerivectors of the original mesh. Results for various meshes ranging in size from 1000 to 100,000 vertices indicate that HARP can indeed partition meshes rapidly at runtime. Experimental results show that our largest mesh can be partitioned sequentially in only a few seconds on an SP2 which is several times faster than other spectral partitioners while maintaining the solution quality of the proven RSB method. A parallel WI version of HARP has also been implemented on IBM SP2 and Cray T3E. Parallel HARP, running on 64 processors SP2 and T3E, can partition a mesh containing more than 100,000 vertices into 64 subgrids in about half a second. These results indicate that graph partitioning can now be truly embedded in dynamically-changing real-world applications.

Simon, Horst D.↗

DOE OSTI2021

Understanding the Design Space of Sparse/Dense Multiphase Dataflows for Mapping Graph Neural Networks on Spatial Accelerators

Graph Neural Networks (GNNs) have garnered a lot of recent interest because of their success in learning representations from graph-structured data across several critical applications in cloud and HPC. Owing to their unique compute and memory characteristics that come from an interplay between dense and sparse phases of computations, the emergence of reconfigurable dataflow (aka spatial) accelerators offers promise for acceleration by mapping optimized dataflows (i.e., computation order and parallelism) for both phases. The goal of this work is to characterize and understand the design-space of dataflow choices for running GNNs on spatial accelerators in order for the compilers to optimize the dataflow based on the workload. Specifically, we propose a taxonomy to describe all possible choices for mapping the dense and sparse phases of GNNs spatially and temporally over a spatial accelerator, capturing both the intra-phase dataflow and the inter-phase (pipelined) dataflow. Using this taxonomy, we do deep-dives into the cost and benefits of several dataflows and perform case studies on implications of hardware parameters for dataflows and value of flexibility to support pipelined execution.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Uncertainty Visualization of Critical Points of 2D Scalar Fields for Parametric and Nonparametric Probabilistic Models

This paper presents a novel end-to-end framework for closed-form computation and visualization of critical point uncertainty in 2D uncertain scalar fields. Critical points are fundamental topological descriptors used in the visualization and analysis of scalar fields. The uncertainty inherent in data (e.g., observational and experimental data, approximations in simulations, and compression), however, creates uncertainty regarding critical point positions. Uncertainty in critical point positions, therefore, cannot be ignored, given their impact on downstream data analysis tasks. Here, in this work, we study uncertainty in critical points as a function of uncertainty in data modeled with probability distributions. Although Monte Carlo (MC) sampling techniques have been used in prior studies to quantify critical point uncertainty, they are often expensive and are infrequently used in production-quality visualization software. We, therefore, propose a new end-to-end framework to address these challenges that comprises a threefold contribution. First, we derive the critical point uncertainty in closed form, which is more accurate and efficient than the conventional MC sampling methods. Specifically, we provide the closed-form and semianalytical (a mix of closed-form and MC methods) solutions for parametric (e.g., uniform, Epanechnikov) and nonparametric models (e.g., histograms) with finite support. Second, we accelerate critical point probability computations using a parallel implementation with the VTK-m library, which is platform portable. Finally, we demonstrate the integration of our implementation with the ParaView software system to demonstrate near-real-time results for real datasets.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1984

Feasibility of using the Massively Parallel Processor for large eddy simulations and other Computational Fluid Dynamics applications

The results of an investigation into the feasibility of using the MPP for direct and large eddy simulations of the Navier-Stokes equations is presented. A major part of this study was devoted to the implementation of two of the standard numerical algorithms for CFD. These implementations were not run on the Massively Parallel Processor (MPP) since the machine delivered to NASA Goddard does not have sufficient capacity. Instead, a detailed implementation plan was designed and from these were derived estimates of the time and space requirements of the algorithms on a suitably configured MPP. In addition, other issues related to the practical implementation of these algorithms on an MPP-like architecture were considered; namely, adaptive grid generation, zonal boundary conditions, the table lookup problem, and the software interface. Performance estimates show that the architectural components of the MPP, the Staging Memory and the Array Unit, appear to be well suited to the numerical algorithms of CFD. This combined with the prospect of building a faster and larger MMP-like machine holds the promise of achieving sustained gigaflop rates that are required for the numerical simulations in CFD.

Bruno, John↗

NASA NTRS1995

Software For Diagnosis Of Parallel Processing

Ames Instrumentation System (AIMS) computer program package of software tools measuring and analyzing performances of parallel-processing application programs. Helps programmer to debug and refine, and to monitor and visualize execution of, parallel-processing application software for Intel iPSC/860 (or equivalent) multicomputer. Performance data collected displayed graphically on computer workstations supporting X-Windows.

Hontalas, Philip↗

DOE OSTI2018

Scalable deep text comprehension for Cancer surveillance on high-performance computing

Background: Deep Learning (DL) has advanced the state-of-the-art capabilities in bioinformatics applications which has resulted in trends of increasingly sophisticated and computationally demanding models trained by larger and larger data sets. This vastly increased computational demand challenges the feasibility of conducting cutting-edge research. One solution is to distribute the vast computational workload across multiple computing cluster nodes with data parallelism algorithms. In this study, we used a High-Performance Computing environment and implemented the Downpour Stochastic Gradient Descent algorithm for data parallelism to train a Convolutional Neural Network (CNN) for the natural language processing task of information extraction from a massive dataset of cancer pathology reports. We evaluated the scalability improvements using data parallelism training and the Titan supercomputer at Oak Ridge Leadership Computing Facility. To evaluate scalability, we used different numbers of worker nodes and performed a set of experiments comparing the effects of different training batch sizes and optimizer functions.Results: We found that Adadelta would consistently converge at a lower validation loss, though requiring over twice as many training epochs as the fastest converging optimizer, RMSProp. The Adam optimizer consistently achieved a close 2nd place minimum validation loss significantly faster; using a batch size of 16 and 32 allowed the network to converge in only 4.5 training epochs.Conclusions: We demonstrated that the networked training process is scalable across multiple compute nodes communicating with message passing interface while achieving higher classification accuracy compared to a traditional machine learning algorithm.

Qiu, John X.↗

DOE OSTI2022

Proximity Portability and in Transit , M-to-N Data Partitioning and Movement in SENSEI [Book Chapter]

In high-performance parallel in situ processing, the term in transit processing refers to those configurations where data must move from a producer to a consumer that runs on separate resources. In the context of parallel and distributed computing on an HPC platform one of the central challenges is to determine a mapping of data from producer ranks to consumer ranks. This problem is complicated by the heterogeneity that arises in producer-consumer pairs, such as when producer and consumer codes have different levels of concurrency, different scaling characteristics, or different data models. The resulting mapping and movement of data from M producer to N consumer ranks can have a significant impact on aggregate application performance, particularly when the data consumer requires only a subset of the overall data for its task. This chapter focuses on the design considerations that underlie SENSEI’s implementation to this challenging problem. These design considerations extend the core SENSEI architecture and include ideas like the need to accommodate flexibility in the choice of different partitioning methods, the ability for a data consumer to request and receive only the subset of data needed for its particular operation, and the ability to leverage any of several different data transport tools. The idea of proximity portability, being able to use different data transport methods as part of an in transit workflow, is illustrated through the use of three different transport layers where switching from one transport tool to another is accomplished with only a configuration file change. Here, the chapter also includes a performance analysis summary showing the performance gains that are possible in terms of multiple metrics, such as memory footprint, time to solution, and amount of data moved, when using optimized partitioners in an in transit setting, gains that are made possible by the implementation shaped by specific design considerations.

Bethel, E. Wes↗

DOE OSTI2020

Asynchronous Richardson iterations: theory and practice

We consider asynchronous versions of the first- and second-order Richardson methods for solving linear systems of equations. These methods depend on parameters whose values are chosen a priori. We explore the parameter values that can be proven to give convergence of the asynchronous methods. This is the first such analysis for asynchronous second-order methods. We find that for the first-order method, the optimal parameter value for the synchronous case also gives an asynchronously convergent method. For the second-order method, the parameter ranges for which we can prove asynchronous convergence do not contain the optimal parameter values for the synchronous iteration. In practice, however, the asynchronous second-order iterations may still converge using the optimal parameter values, or parameter values close to the optimal ones, despite this result. We explore this behavior with a multithreaded parallel implementation of the asynchronous methods.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Full spectrum optical constant interface to the Materials Project

Optical constants characterize the interaction of materials with light and are important properties in material design. Here we present a Python-based Corvus workflow for simulations of full spectrum optical constants from the visible and ultraviolet to hard x-ray wavelengths based on the real-space Green’s function code FEFF10 and structural data from the Materials Project (MP). The Corvus workflow manager and its associated tools provide an interface to FEFF10 and the MP database. The workflow parallelizes the FEFF computations of optical constants over all absorption edges for each material in the MP database specified by a unique MP-ID. The workflow tools determine the distribution of computational resources needed for that case. Similarly, the optical constants for selected sets of materials can be computed in a single-shot. Additionally, to illustrate the approach, we present results for several elemental solids in the periodic table, as well as a sample compound, and compare our predictions with experimental results. In addition, we provide a database of calculated results for all elements for which there is a stable elemental solid at standard conditions available in the Materials Project database. As in x-ray absorption spectra, these results are interpreted in terms of an atomic-like background and fine-structure contributions.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Scalable self attraction and loading calculations for unstructured ocean tide models

Self attraction and earth-loading effects are important for accurately modeling global tides. A common approach of handling this forcing is to expand mass anomalies into spherical harmonics, which are scaled by load Love numbers to account for elastic earth deformation. We investigate two different approaches to perform these calculations for ocean models that employ unstructured meshes and distributed memory parallelization. The first approach leverages a highly efficient spherical harmonics library, but requires all-to-one and one-to-all communications and interpolation operations between the unstructured and a structured mesh. This approach is compared to a parallel algorithm that computes the spherical harmonic transformations directly on the unstructured mesh with an all-reduce communication. Here, our results show that although the unstructured mesh calculations are more expensive, the scalability of the unstructured mesh approach allows for more efficient spherical harmonics transforms for high-resolution meshes and large processor counts. This methodology enables the efficient inclusion of tidal dynamics large-scale Earth system model simulations.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Lowering entry barriers to developing custom simulators of distributed applications and platforms with SimGrid

Researchers in parallel and distributed computing (PDC) often resort to simulation because experiments conducted using a simulator can be for arbitrary experimental scenarios, are less resource-, labor-, and time-consuming than their real-world counterparts, and are perfectly repeatable and observable. Many frameworks have been developed to ease the development of PDC simulators, and these frameworks provide different levels of accuracy, scalability, versatility, extensibility, and usability. Further, the SimGrid framework has been used by many PDC researchers to produce a wide range of simulators for over two decades. Its popularity is due to a large emphasis placed on accuracy, scalability, and versatility, and is in spite of shortcomings in terms of extensibility and usability. Although SimGrid provides sensible simulation models for the common case, it was difficult for users to extend these models to meet domain-specific needs. Furthermore, SimGrid only provided relatively low-level simulation abstractions, making the implementation of a simulator of a complex system a labor-intensive undertaking. In this work we describe developments in the last decade that have contributed to vastly improving extensibility and usability, thus lowering or removing entry barriers for users to develop custom SimGrid simulators.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Xcompact3D: An open-source framework for solving turbulence problems on a Cartesian mesh

Xcompact3D is a Fortran 90–95 open-source framework designed for fast and accurate simulations of turbulent flows, targeting CPU-based supercomputers. It is an evolution of the flow solver Incompact3D which was initially designed in France in the mid-90’s for serial processors to solve the incompressible Navier–Stokes equations. Incompact3D was then ported to parallel High Performance Computing (HPC) systems in the early 2010’s. Very recently the capabilities of Incompact3D have been extended so that it can now tackle more flow regimes (from incompressible flows to compressible flows at low Mach numbers), resulting in the design of a new user-friendly framework called Xcompact3D. The present manuscript presents an overview of Xcompact3D with a particular focus on its functionalities, its ready-to-run simulations and a few case studies to demonstrate its impact.

17 WIND ENERGY↗

DOE OSTI2024

Short-Wave Infrared Upconverting Nanoparticles

Optical technologies enable real-time, noninvasive analysis of complex systems but are limited to discrete regions of the optical spectrum. While wavelengths in the short-wave infrared (SWIR) window (typically, 1700-3000 nm) should enable deep subsurface penetration and reduced photodamage, there are few luminescent probes that can be excited in this region. Here, we report the discovery of lanthanide-based upconverting nanoparticles (UCNPs) that efficiently convert 1740 or 1950 nm excitation to wavelengths compatible with conventional silicon detectors. Screening of Ln3+ ion combinations by differential rate equation modeling identifies Ho3+/Tm3+ or Tm3+ dopants with strong visible or NIR-I emission following SWIR excitation. Experimental upconverted photoluminescence excitation (U-PLE) spectra find that 10% Tm3+-doped NaYF4 core/shell UCNPs have the strongest 800 nm emission from SWIR wavelengths, while UCNPs with an added 2% or 10% Ho3+ show the strongest red emission when excited at 1740 or 1950 nm. Mechanistic modeling shows that addition of a low percentage of Ho3+ to Tm3+-doped UCNPs shifts their emission from 800 to 652 nm by acting as a hub of efficient SWIR energy acceptance and redistribution up to visible emission manifolds. Parallel experimental and computational analysis shows rate equation models are able to predict compositions for specific wavelengths of both excitation and emission. These SWIR-responsive probes open a new IR bioimaging window, and are responsive at wavelengths important for vision technologies.

Qi, Xiao↗

DOE OSTI2024

A meshless stochastic method for Poisson–Nernst–Planck equations

A plethora of biological, physical, and chemical phenomena involve transport of charged particles (ions). Its continuum-scale description relies on the Poisson–Nernst–Planck (PNP) system, which encapsulates the conservation of mass and charge. The numerical solution of these coupled partial differential equations is challenging and suffers from both the curse of dimensionality and difficulty in efficiently parallelizing. We present a novel particle-based framework to solve the full PNP system by simulating a drift–diffusion process with time- and space-varying drift. We leverage Green’s functions, kernel-independent fast multipole methods, and kernel density estimation to solve the PNP system in a meshless manner, capable of handling discontinuous initial states. The method is embarrassingly parallel, and the computational cost scales linearly with the number of particles and dimension. We use a series of numerical experiments to demonstrate both the method’s convergence with respect to the number of particles and computational cost vis-à-vis a traditional partial differential equation solver.

Chemistry↗