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DOE OSTI2019

Scalable Performance Awareness for In Situ Scientific Applications

Part of the promise of exascale computing and the next generation of scientific simulation codes is the ability to bring together time and spatial scales that have traditionally been treated separately. This enables creating complex coupled simulations and in situ analysis pipelines, encompassing such things as "whole device" fusion models or the simulation of cities from sewers to rooftops. Unfortunately, the HPC analysis tools that have been built up over the preceding decades are ill suited to the debugging and performance analysis of such computational ensembles. In this paper, we present a new vision for performance measurement and understanding of HPC codes, MonitoringAnalytics (MONA). MONA is designed to be a flexible, high performance monitoring infrastructure that can perform monitoring analysis in place or in transit by embedding analytics and characterization directly into the data stream, without relying upon delivering all monitoring information to a central database for post-processing. It addresses the trade-offs between the prohibitively expensive capture of all performance characteristics and not capturing enough to detect the features of interest. We demonstrate several uses of MONA; capturing and indexing multi-executable performance profiles to enable later processing, extraction of performance primitives to enable the generation of customizable benchmarks and performance skeletons, and extracting communication and application behaviors to enable better control and placement for the current and future runs of the science ensemble. Relevant performance information based on a system for MONA built from ADIOS and SOSflow technologies is provided for DOE science applications and leadership machines.

Wolf, Matthew D.↗

DOE OSTI2023

Improved Fast Reactor Capability of Griffin in FY23

Griffin is a MOOSE based reactor multiphysics analysis application jointly developed by Idaho National Laboratory and Argonne National Laboratory under the DOE-NE NEAMS program. In FY23, we enhanced capabilities required for fast reactor analysis. This effort included primarily updating the cross-section generation workflow using MC2-3 for various reactor configurations, such as homogeneous, duct-heterogeneous, ring-heterogeneous, and fully-heterogeneous geometries. In addition, we initiated the implementation of a multi-cycle depletion and shuffling capability. To support fast reactor simulation capabilities, we significantly improved the performance of the DFEM-SN-based R-Z transport solver to efficiently solve ultrafine group (over 1000 groups) transport problems. Additionally, the performance of HFEM-PN was improved by introducing red-black iteration, the cmfd acceleration technique, and various optimizations. We also completed the pin power reconstruction capability to support multiphysics simulations while identifying and addressing issues associated with SPH equivalence parameter approach. These enhanced capabilities for fast reactor core simulations, specially HFEM-PN and pin power reconstruction features, were applied to benchmark problems involving ABTR and ABR-1000. These applications showcased excellent agreement with Monte Carlo and other code solutions in terms of eigenvalue, control rod worth, and assembly and pin powers.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2021

Enhanced relaxed physical factorization preconditioner for coupled poromechanics

The relaxed physical factorization (RPF) preconditioner is a recent algorithm allowing for the efficient and robust solution to the block linear systems arising from the three-field displacement-velocity-pressure formulation of coupled poromechanics. For its application, however, it is necessary to invert blocks with the algebraic form C^ = (C + βFF T ), where C is a symmetric positive definite matrix, FF T a rank-deficient term, and β a real non-negative coefficient. The inversion of C^, performed in an inexact way, can become unstable for large values of β, as it usually occurs at some stages of a full poromechanical simulation. In this work, we propose a family of algebraic techniques to stabilize the inexact solve with C^. This strategy can prove useful in other problems as well where such an issue might arise, such as augmented Lagrangian preconditioning techniques for Navier-Stokes or incompressible elasticity. First, we introduce an iterative scheme obtained by a natural splitting of matrix C^. Second, we develop a technique based on the use of a proper projection operator annihilating the near-kernel modes of C^. Both approaches give rise to a novel class of preconditioners denoted as Enhanced RPF (ERPF). Furthermore, effectiveness and robustness of the proposed algorithms are demonstrated in both theoretical benchmarks and real-world large-size applications, outperforming the native RPF preconditioner.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

A comparison of Amazon Web Services and Microsoft Azure cloud platforms for high performance computing

Advances in commercial cloud computing necessitate continual evaluation of the cloud's performance on a variety of applications. This work looks at compute oriented instances from Amazon Web Services and Microsoft Azure cloud platforms and evaluates them with several high-performance computing benchmarks, including HPCC and HPCG. These benchmarks illustrate that the most cost competitive solution depends on the application to be run.

Kotas, Charlotte↗

DOE OSTI2020

Hydrodynamic conditions in laser irradiated buried layer experiments

The calculation of open shell ionization level and radiative properties of materials in Non-Local Thermal Equilibrium (NLTE) is currently still a major challenge for any atomic model. The predictions of various NLTE atomic codes at these conditions still differ significantly. In recent years, a new buried layer platform was developed at the Lawrence Livermore National Laboratory and the Laboratory for Laser Energetics. This platform is used to measure ionization distribution and emission of open L-shell, mid-Z ions and open M-shell, high-Z ions at NLTE conditions that are relevant in many laser plasma applications. These experiments offer a unique chance for benchmarking the atomic models. In order to perform these experiments, a uniform well characterized plasma source is required. In this work, we present one-dimensional (1D) and two-dimensional simulations of the experimental platform. These simulations were used for both the design and the analysis of the experiments. The simulations demonstrate the different phases of hydrodynamic evolution of the target and identify the time windows in which uniform conditions can be achieved. A 1D expansion of the target was found to be adequate to describe the target's evolution for most of the experiment duration. The fast 1D simulations were compared with recent experimental results from the Omega laser facility. The sensitivity of the results to several modeling parameters such as the electron flux limiter and laser resonant absorption is reported.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Uncertainty Quantification for Smooth Functional Data with Application to Material Properties

This document outlines a method for processing functional output (i.e., curves) for the ultimate purpose of sampling curves under specified input conditions for use in modeling and simulation uncertainty quantification (UQ) studies. A set of benchmark curves sufficiently representative of the relevant scenario(s) being simulated are provided to the process and formatted as described in Section 1. Principal Component Analysis (PCA) is utilized to discover the components of uncertainty in the benchmark curves and is outlined in Section 2. Section 3 describes the application of uncertainty quantification to the PCA results for the purpose of sampling curves to be used in UQ analysis. Section 4 applies these techniques to an example benchmark dataset. Concluding remarks are provided in the final section.

36 MATERIALS SCIENCE↗

NASA NTRS2017

JANNAF "Test and Evaluation Guidelines for Liquid Rocket Engines": Status and Application

For many decades, the U.S. rocket propulsion industrial base has performed remarkably in developing complex liquid rocket engines that can propel critical payloads into service for the nation, as well as transport people and hardware for missions that open the frontiers of space exploration for humanity. This has been possible only at considerable expense given the lack of detailed guidance that captures the essence of successful practices and knowledge accumulated over five decades of liquid rocket engine development. In an effort to provide benchmarks and guidance for the next generation of rocket engineers, the Joint Army Navy NASA Air Force (JANNAF) Interagency Propulsion Committee published a liquid rocket engine (LRE) test and evaluation (T&E) guideline document in 2012 focusing on the development challenges and test verification considerations for liquid rocket engine systems. This document has been well received and applied by many current LRE developers as a benchmark and guidance tool, both for government-driven applications as well as for fully commercial ventures. The USAF Space and Missile Systems Center (SMC) has taken an additional near-term step and is directing activity to adapt and augment the content from the JANNAF LRE T&E guideline into a standard for potential application to future USAF requests for proposals for LRE development initiatives and launch vehicles for national security missions. A draft of this standard was already sent out for review and comment, and is intended to be formally approved and released towards the end of 2017. The acceptance and use of the LRE T&E guideline is possible through broad government and industry participation in the JANNAF liquid propulsion committee and associated panels. The sponsoring JANNAF community is expanding upon this initial baseline version and delving into further critical development aspects of liquid rocket propulsion testing at the integrated stage level as well as engine component level, in order to advance the state of the practice. The full participation of the entire U.S. rocket propulsion industrial base is invited and expected at this opportune moment in the continuing advancement of spaceflight technology.

Parkinson, Douglas↗

NASA NTRS1990

Role of CFD in propulsion design - Government perspective

Various aspects of computational fluid dynamics (CFD), as it relates to design applications in rocket propulsion activities from the government perspective, are discussed. Specific examples are given that demonstrate the application of CFD to support hardware development activities, such as Space Shuttle Main Engine flight issues, and the associated teaming strategy used for solving such problems. In addition, select examples that delineate the motivation, methods of approach, goals and key milestones for several space flight progams are cited. An approach is described toward applying CFD in the design environment from the government perspective. A discussion of benchmark validation, advanced technology hardware concepts, accomplishments, needs, future applications, and near-term expectations from the flight-center perspective is presented.

Schutzenhofer, L. A.↗

DOE OSTI2019

Balancing Performance and Portability with Containers in HPC: An OpenSHMEM Example

There is a growing interest in using Linux containers to streamline software development and application deployment. A container enables the user to bundle the salient elements of the software stack from an application’s perspective. In this paper, we discuss initial experiences in using the Open MPI implementation of OpenSHMEM with containers on HPC resources. We provide a brief overview of two container runtimes, Docker & Singularity, highlighting elements that are of interest for HPC users. The Docker platform offers a rich set of services that are widely used in enterprise environments, whereas Singularity is an emerging container runtime that is specifically written for use on HPC systems. We describe our procedure for container assembly and deployment that strives to maintain the portability of the container-based application. We show performance results for the Graph500 benchmark running along the typical continuum of development testbed up to full production supercomputer (ORNL’s Titan). The results show consistent performance between the native and Singularity (container) tests. The results also showed an unexplained drop in performance when using the Cray Gemini network with Open MPI’s OpenSHMEM, which was unrelated to the container usage.

Naughton III, Thomas↗

DOE OSTI2017

DINO: Divergent node cloning for sustained redundancy in HPC

Complexity and scale of next generation HPC systems pose significant challenges in fault resilience methods such that contemporary checkpoint/restart (C/R) methods that address fail-stop behavior may be insufficient. Redundant computing has been proposed as an alternative at extreme scale. Triple redundancy has an advantage over C/R in that it can also detect silent data corruption (SDC) and then correct results via voting. However, current redundant computing approaches do not repair failed or corrupted replicas. Consequently, SDCs can no longer be detected after a replica failure since the system has been degraded to dual redundancy without voting capability. Hence, a job may have to be aborted if voting uncovers mismatching results between the remaining two replicas. And while replicas are logically equivalent, they may have divergent runtime states during job execution, which presents a challenge to simply creating new replicas dynamically. This problem is addressed by, DIvergent NOde cloning (DINO), a redundant execution environment that quickly recovers from hard failures. DINO consists of a novel node cloning service integrated into the MPI runtime system that solves the problem of consolidating divergent states among replicas on-the-fly. With DINO, after degradation to dual redundancy, a good replica can be quickly cloned so that triple redundancy is restored. We present experimental results over 9 NAS Parallel Benchmarks (NPB), Sweep3D and LULESH. Results confirm the applicability of the approach and the correctness of the recovery process and indicate that DINO can recover from failures nearly instantly. The cloning overhead depends on the process image size that needs to be transferred between source and destination of the clone operation and varies between 5.60 to 90.48 s. Here, simulation results with our model show that dual redundancy with DINO recovery always outperforms 2x and surpasses 3x redundancy on up to 1 million nodes. To the best of our knowledge, the design and implementation for repairing failed replicas in redundant MPI computing is unprecedented.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Sampling lattices in semi-grand canonical ensemble with autoregressive machine learning

Calculating thermodynamic potentials and observables efficiently and accurately is key for the application of statistical mechanics simulations to materials science. However, naive Monte Carlo approaches, on which such calculations are often dependent, struggle to scale to complex materials in many state-of-the-art disciplines such as the design of high entropy alloys or multi-component catalysts. To address this issue, we adapt sampling tools built upon machine learning-based generative modeling to the materials space by transforming them into the semi-grand canonical ensemble. Furthermore, we show that the resulting models are transferable across wide ranges of thermodynamic conditions and can be implemented with any internal energy model U, allowing integration into many existing materials workflows. We demonstrate the applicability of this approach to the simulation of benchmark systems (AgPd, CuAu) that exhibit diverse thermodynamic behavior in their phase diagrams. Finally, we discuss remaining challenges in model development and promising research directions for future improvements.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Counterpart identification and classification for eRASS1 and characterisation of the active galactic nuclei content

Context. Accurately accounting for the Active Galactic Nucleus (AGN) phase in galaxy evolution requires a large, clean AGN sample. This is now possible with SRG/eROSITA, which completed its first all-sky X-ray survey (eRASS1) on June 12, 2020. The public Data Release 1 (DR1, Jan 31, 2024) includes 930,203 sources from the western Galactic hemisphere. Aims. The data enable the selection of a large AGN sample and the discovery of rare sources. However, scientific return depends on accurate characterisation of the X-ray emitters, requiring high-quality multi-wavelength data. This paper presents the identification and classification of optical and infrared counterparts to eRASS1 sources. Methods. Counterparts to eRASS1 X-ray point sources were identified using Gaia DR3, CatWISE2020, and Legacy Survey DR10 (LS10) with the Bayesian NWAY algorithm and trained priors. Sources were classified as Galactic or extragalactic via a machine-learning model combining optical/IR and X-ray properties, trained on a reference sample. For extragalactic LS10 sources, photometric redshifts were computed using CIRCLEZ. Results. Within the LS10 footprint, all 656,614 eROSITA/DR1 sources have at least one possible optical counterpart; ∼570 000 are extragalactic and likely AGN. Half are new detections compared to AllWISE, Gaia, and Quaia AGN catalogues. Gaia and CatWISE2020 counterparts are less reliable, due to the survey’s shallowness and the limited amount of features available to assess the probability of being an X-ray emitter. In the Galactic plane, where the overdensity of stellar sources also increases the chance of associations, using conservative reliability cuts, we identified approximately 18 000 Gaia and 55 000 CatWISE2020 extragalactic sources. Conclusions. We have released three high-quality counterpart catalogues – plus the training and validation sets – as a benchmark for the field. These datasets have many applications, but in particular, they empower researchers to build AGN samples tailored for completeness and purity, accelerating the hunt for the Universe’s most energetic engines.

X-rays: general↗

DOE OSTI2021

A comparison of Raman and pyrometry dynamic temperature measurements of shocked cyclohexane

Optical pyrometry is a well-developed, broadly applicable method to determine temperature in dynamic compression experiments. However, it measures radiation from only the skin depth of the radiant material, is highly susceptible to spurious backgrounds, and requires an often-unmeasurable free parameter—the sample dynamic emissivity. Raman spectroscopy offers a method to determine temperature directly from fundamental theory, but it is practically limited in applications to a small subset of shock experiments. In this work, we describe an experiment allowing simultaneous application of Raman and pyrometric temperature techniques to benchmark a specific instance of pyrometry. We attempted both measurements on multiple experiments and compare the successful temperature results between the separate but highly repeatable shots. Here, we find that dynamic shock temperatures inferred from Raman spectroscopy and pyrometry generally agree within the uncertainties of each measurement, although those uncertainties are larger than typical for a specially designed pyrometry experiment on a shocked metal sample.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2022

Improving Single-Stage Object Detectors for Nighttime Pedestrian Detection

We report Improving the reliability of nighttime pedestrian detection is a crucial challenge towards the design of robust autonomous systems. Not surprisingly, most pedestrian fatalities occur in low-illumination settings, thus emphasizing the need for new algorithmic advances. This work presents a novel pedestrian detection approach that makes a number of crucial modifications to the state-of-the-art YOLOV5-PANet architecture, in order to improve the reliability of features extracted from nighttime images. More specifically, the proposed architecture systematically incorporates powerful shuffle attention mechanisms and a transformer module to improve the feature learning pipeline. Instead of advocating the use of other sensing modalities that are better suited for nighttime detection, our approach relies only on conventional RGB cameras and is hence broadly applicable. Our empirical studies with nighttime pedestrian detection benchmarks show that with only minimal increase in model complexity, our approach provides significant improvements in detection efficacy over existing solutions. Finally, we explore the impact of post-hoc network pruning on the speed-accuracy trade-off of our approach and demonstrate that it is well suited for reduced memory/compute requirements.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Electronic, Ionic, and Mixed Conduction in Polymeric Systems

Polymers that simultaneously transport electrons and ions are paramount to drive the technological advances necessary for next-generation electrochemical devices, including energy storage devices and bioelectronics. However, efforts to describe the motion of ions or electrons separately within polymeric systems become inaccurate when both species are present. In this paper, we highlight the basic transport equations necessary to rationalize mixed transport and the multiscale materials properties that influence their transport coefficients. Potential figures of merit that enable a suitable performance benchmark in mixed conducting systems independent of end application are discussed. Practical design and implementation of mixed conducting polymers require an understanding of the evolving nature of structure and transport with ionic and electronic carrier density to capture the dynamic disorder inherent in polymeric materials.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2011

Enabling High Performance Application I/O

This work provides software that enables scientific applications to more efficiently access available storage resources at different levels of interfaces. We developed scalable techniques and optimizations for PVFS parallel file systems, MPI I/O, and parallel netCDF I/O library. These implementations were evaluated using production application I/O kernels as well as popular I/O benchmarks and demonstrated promising results. The software developed under this work has been made available to the public via MCS, ANL web sites.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Review of Enabling Technologies to Facilitate Secure Compute Customization

High performance computing environments are often used for a wide variety of workloads ranging from simulation, data transformation and analysis, and complex workflows to name just a few. These systems may process data for a variety of users, often requiring strong separation between job allocations. There are many challenges to establishing these secure enclaves within the shared infrastructure of high-performance computing (HPC) environments. The isolation mechanisms in the system software are the basic building blocks for enabling secure compute enclaves. There are a variety of approaches and the focus of this report is to review the different virtualization technologies that facilitate the creation of secure compute enclaves. The report reviews current operating system (OS) protection mechanisms and modern virtualization technologies to better understand the performance/isolation properties. We also examine the feasibility of running ``virtualized'' computing resources as non-privileged users, and providing controlled administrative permissions for standard users running within a virtualized context. Our examination includes technologies such as Linux containers (LXC [32], Docker [15]) and full virtualization (KVM [26], Xen [5]). We categorize these different approaches to virtualization into two broad groups: OS-level virtualization and system-level virtualization. The OS-level virtualization uses containers to allow a single OS kernel to be partitioned to create Virtual Environments (VE), e.g., LXC. The resources within the host's kernel are only virtualized in the sense of separate namespaces. In contrast, system-level virtualization uses hypervisors to manage multiple OS kernels and virtualize the physical resources (hardware) to create Virtual Machines (VM), e.g., Xen, KVM. This terminology of VE and VM, detailed in Section 2, is used throughout the report to distinguish between the two different approaches to providing virtualized execution environments. As part of our technology review we analyzed several current virtualization solutions to assess their vulnerabilities. This included a review of common vulnerabilities and exposures (CVEs) for Xen, KVM, LXC and Docker to gauge their susceptibility to different attacks. The complete details are provided in Section 5 on page 33. Based on this review we concluded that system-level virtualization solutions have many more vulnerabilities than OS level virtualization solutions. As such, security mechanisms like sVirt (Section 3.3) should be considered when using system-level virtualization solutions in order to protect the host against exploits. The majority of vulnerabilities related to KVM, LXC, and Docker are in specific regions of the system. Therefore, future "zero day attacks" are likely to be in the same regions, which suggests that protecting these areas can simplify the protection of the host and maintain the isolation between users. The evaluations of virtualization technologies done thus far are discussed in Section 4. This includes experiments with 'user' namespaces in VEs, which provides the ability to isolate user privileges and allow a user to run with different UIDs within the container while mapping them to non-privileged UIDs in the host. We have identified Linux namespaces as a promising mechanism to isolate shared resources, while maintaining good performance. In Section 4.1 we describe our tests with LXC as a non-root user and leveraging namespaces to control UID/GID mappings and support controlled sharing of parallel file-systems. We highlight several of these namespace capabilities in Section 6.2.3. The other evaluations that were performed during this initial phase of work provide baseline performance data for comparing VEs and VMs to purely native execution. In Section 4.2 we performed tests using the High-Performance Computing Conjugate Gradient (HPCCG) benchmark to establish baseline performance for a scientific application when run on the Native (host) machine in contrast with execution under Docker and KVM. Our tests verified prior studies showing roughly 2-4% overheads in application execution time & MFlops when running in hypervisor-base environments (VMs) as compared to near native performance with VEs. For more details, see Figures 4.5 (page 28), 4.6 (page 28), and 4.7 (page 29). Additionally, in Section 4.3 we include network measurements for TCP bandwidth performance over the 10GigE interface in our testbed. The Native and Docker based tests achieved >= ~9Gbits/sec, while the KVM configuration only achieved 2.5Gbits/sec (Table 4.6 on page 32). This may be a configuration issue with our KVM installation, and is a point for further testing as we refine the network settings in the testbed. The initial network tests were done using a bridged networking configuration. The report outline is as follows: - Section 1 introduces the report and clarifies the scope of the proj...

Aderholdt, Ferrol↗

DOE OSTI2023

Benchmarking the PCMCI Causal Discovery Algorithm for Spatiotemporal Systems

Causal discovery algorithms construct hypothesized causal graphs that depict causal dependencies among variables in observational data. While powerful, the accuracy of these algorithms is highly sensitive to the underlying dynamics of the system in ways that have not been fully characterized in the literature. In this report, we benchmark the PCMCI causal discovery algorithm in its application to gridded spatiotemporal systems. Effectively computing grid-level causal graphs on large grids will enable analysis of the causal impacts of transient and mobile spatial phenomena in large systems, such as the Earth’s climate. We evaluate the performance of PCMCI with a set of structural causal models, using simulated spatial vector autoregressive processes in one- and two-dimensions. We develop computational and analytical tools for characterizing these processes and their associated causal graphs. Our findings suggest that direct application of PCMCI is not suitable for the analysis of dynamical spatiotemporal gridded systems, such as climatological data, without significant preprocessing and downscaling of the data. PCMCI requires unrealistic sample sizes to achieve acceptable performance on even modestly sized problems and suffers from a notable curse of dimensionality. This work suggests that, even under generous structural assumptions, significant additional algorithmic improvements are needed before causal discovery algorithms can be reliably applied to grid-level outputs of earth system models.

54 ENVIRONMENTAL SCIENCES↗