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A performance study of the time-varying cache behavior: a study on APEX, Mantevo, NAS, and PARSEC

Cache has long been used to minimize the latency of main memory accesses by storing frequently used data near the processor. Processor performance depends on the underlying cache performance. Therefore, significant research has been done to identify the most crucial metrics of cache performance. Although the majority of research focuses on measuring cache hit rates and data movement as the primary cache performance metrics, cache utilization is significantly important. We investigate the application’s locality using cache utilization metrics. In addition, we present cache utilization and traditional cache performance metrics as the program progresses providing detailed insights into the dynamic application behavior on parallel applications from four benchmark suites running on multiple cores. We explore cache utilization for APEX, Mantevo, NAS, and PARSEC, mostly scientific benchmark suites. Our results indicate that 40% of the data bytes in a cache line are accessed at least once before line eviction. Also, on average a byte is accessed two times before the cache line is evicted for these applications. Moreover, we present runtime cache utilization, as well as, conventional performance metrics that illustrate a holistic understanding of cache behavior. To facilitate this research, we build a memory simulator incorporated into the Structural Simulation Toolkit (Rodrigues et al. in SIGMETRICS Perform Eval Rev 38(4):37–42, 2011). Finally, our results suggest that variable cache line size can result in better performance and can also conserve power.

97 MATHEMATICS AND COMPUTING↗

Sensor to User - NASA/EOS Data for Coastal Zone Management Applications Developed from Integrated Analyses: Verification, Validation and Benchmark Report

The NASA Applied Sciences Program seeks to transfer NASA data, models, and knowledge into the hands of end-users by forming links with partner agencies and associated decision support tools (DSTs). Through the NASA REASoN (Research, Education and Applications Solutions Network) Cooperative Agreement, the Oceanography Division of the Naval Research Laboratory (NRLSSC) is developing new products through the integration of data from NASA Earth-Sun System assets with coastal ocean forecast models and other available data to enhance coastal management in the Gulf of Mexico. The recipient federal agency for this research effort is the National Oceanic and Atmospheric Administration (NOAA). The contents of this report detail the effort to further the goals of the NASA Applied Sciences Program by demonstrating the use of NASA satellite products combined with data-assimilating ocean models to provide near real-time information to maritime users and coastal managers of the Gulf of Mexico. This effort provides new and improved capabilities for monitoring, assessing, and predicting the coastal environment. Coastal managers can exploit these capabilities through enhanced DSTs at federal, state and local agencies. The project addresses three major issues facing coastal managers: 1) Harmful Algal Blooms (HABs); 2) hypoxia; and 3) freshwater fluxes to the coastal ocean. A suite of ocean products capable of describing Ocean Weather is assembled on a daily basis as the foundation for this semi-operational multiyear effort. This continuous realtime capability brings decision makers a new ability to monitor both normal and anomalous coastal ocean conditions with a steady flow of satellite and ocean model conditions. Furthermore, as the baseline data sets are used more extensively and the customer list increased, customer feedback is obtained and additional customized products are developed and provided to decision makers. Continual customer feedback and response with new improved products are required between the researcher and customer. This document details the methods by which these coastal ocean products are produced including the data flow, distribution, and verification. Product applications and the degree to which these products are used successfully within NOAA and coordinated with the Mississippi Department of Marine Resources (MDMR) is benchmarked.

Hall, Callie↗

Application of the hybrid approach to the benchmark dose of urinary cadmium as the reference level for renal effects in cadmium polluted and non-polluted areas in Japan

Objectives: The aim of this study was to evaluate the reference level of urinary cadmium (Cd) that caused renal effects. An updated hybrid approach was used to estimate the benchmark doses (BMDs) and their 95% lower confidence limits (BMDL) in subjects with a wide range of exposure to Cd. Methods: The total number of subjects was 1509 (650 men and 859 women) in non-polluted areas and 3103 (1397 men and 1706 women) in the environmentally exposed Kakehashi river basin. We measured urinary cadmium (U-Cd) as a marker of long-term exposure, and {beta}2-microglobulin ({beta}2-MG) as a marker of renal effects. The BMD and BMDL that corresponded to an additional risk (BMR) of 5% were calculated with background risk at zero exposure set at 5%. Results: The U-Cd BMDL for {beta}2-MG was 3.5 {mu}g/g creatinine in men and 3.7 {mu}g/g creatinine in women. Conclusions: The BMDL values for a wide range of U-Cd were generally within the range of values measured in non-polluted areas in Japan. This indicated that the hybrid approach is a robust method for different ranges of cadmium exposure. The present results may contribute further to recent discussions on health risk assessment of Cd exposure.

60 APPLIED LIFE SCIENCES↗

Searching for 'Unknown Unknowns'

The NASA Engineering and Safety Center (NESC) was established to improve safety through engineering excellence within NASA programs and projects. As part of this goal, methods are being investigated to enable the NESC to become proactive in identifying areas that may be precursors to future problems. The goal is to find unknown indicators of future problems, not to duplicate the program-specific trending efforts. The data that is critical for detecting these indicators exist in a plethora of dissimilar non-conformance and other databases (without a common format or taxonomy). In fact, much of the data is unstructured text. However, one common database is not required if the right standards and electronic tools are employed. Electronic data mining is a particularly promising tool for this effort into unsupervised learning of common factors. This work in progress began with a systematic evaluation of available data mining software packages, based on documented decision techniques using weighted criteria. The four packages, which were perceived to have the most promise for NASA applications, are being benchmarked and evaluated by independent contractors. Preliminary recommendations for "best practices" in data mining and trending are provided. Final results and recommendations should be available in the Fall 2005. This critical first step in identifying "unknown unknowns" before they become problems is applicable to any set of engineering or programmatic data.

Parsons, Vickie S.↗

Benchmarking and Testing of Qualcomm Snapdragon System-on-Chip for JPL Space Applications and Missions

As some space missions become more challenging due to new environments, greater distances, or more limited size, weight, and power (SWaP) constraints, spacecraft avionics must adapt to allow the spacecraft to be more autonomous and agile---eliminating the Spacecraft-Earth-Spacecraft feedback loop whenever possible. Prime examples of such missions include Aerobots (such as Ingenuity with extremely low SWaP constraints and demanding signal/image processing during flight) and landers in possibly hostile environments (such as a Europa lander mission, with limited communication capacity, high latency, and constrained power budget). To address these challenges, JPL worked with Qualcomm to demonstrate the use of their Snapdragon 801 system-on-chip (SoC) onboard the Ingenuity Helicopter on Mars. The Qualcomm Snapdragon SoC contains various subsystems, including an ARM cluster, a Graphics processing unit, a Digital Signal Processing subsystem, a Neural Processing Engine, Image Signal Processing subsystem, among others. Since the success of Ingenuity, JPL is continuing to work with Qualcomm to address other applications of the Snapdragon SoC technology. This includes the deployment of two 855 Snapdragon development boards onboard the International Space Station (ISS) for successful in-situ benchmarking of applications in space (beyond those tested on Ingenuity). In this paper, we will examine the performance of various applications that have been identified to benefit from greater onboard computational capability. These applications include (among others): machine vision algorithms that are expected to be critical in autonomous entry-descent-and-landing scenarios and real-time Aerobot flight navigation; Hyperspectral compression algorithms; Synthetic Aperture Radar Processing along with various instrument processing algorithms. We discuss how the infusion of Qualcomm's Snapdragon SoC is capable of enabling missions that may not have been able to achieve their goals with traditional flight computing. In addition, we also show that for some algorithms, the software implementation on the Snapdragon SoC outperforms traditional FPGA implementations.

Cretu, Vlad↗

Sensitivity Studies, Gap Analysis, and Benchmark Experiment Optimization for Reactor Physics and Criticality Safety Applications

Many new reactor designs, such as advanced reactors and micro reactors, have materials that lack nuclear data validation. This is also true for many other applications in criticality safety and global security. Both differential and integral experiments are needed to validate cross-section data. Without this, a user cannot have confidence in the predicted results of a radiation-transport code. This work describes an approach called ARCHIMEDES (Application Relevant Critical/Subcritical HEU/Pu-based Integral Measurements for Enhancing Data and Evaluating Sensitivities) to design new criticality experiments that have similar k eff cross-section sensitivities to an application of interest. This process involves simulations to generate cross-section sensitivities to a parameter of interest (such as k eff ), a gap analysis to determine which existing benchmarks are most similar to the application, and an experiment optimization. Recently, there has been a great deal of interest in the reactor physics community on advanced reactors, micro reactors, and accelerator driven systems (ADS). This work will apply the described method to specific examples in this area. The focus of this work will be on the sensitivity study and gap analysis, while future work will include experiment design.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Solving a trillion unknowns per second with HPGMG on Sunway TaihuLight

Benchmarks for supercomputers are important tools, not only for evaluating and ranking modern supercomputers, but also for providing hints for future architecture design. As a new benchmark, HPGMG (high performance geometric multigrid) solves a linear equation set with a full geometric multi-grid algorithm. It involves computation on different scales, data movement with various volumes, global communication and neighbor communication with both large and small messages, etc., and is more correlated to real world applications than traditional benchmarks such as LINPACK. Therefore, it is desirable to examine how well HPGMG can perform on leadership supercomputers such as Sunway Taihulight. Sunway Taihulight, the No. 1 supercomputer in the Top 500 list from June 2016 to June 2018, which uses a specially designed many-core architecture SW26010, is of great interest to the community of high performance computing. With careful analysis and code design, we came up with an efficient implementation of HPGMG on SW26010 processors. We not only employed traditional optimization techniques such as 2.5D partitioning, double buffering, and collective data load, but also introduced a micro-benchmark to help with the choice of optimization direction and parameter tuning. Another contribution is that we proposed a new procedure for the major operations, by granulating and reordering the smooth function and the ghost exchange operation, leading to reduced memory copy and accelerated communication process. Our optimized implementation of HPGMG on Sunway TaihuLight achieved a ground-breaking performance of 1.036 × 10 12 Degrees of Freedom per second at the finest level, which is No. 1 on the HPGMG list of Nov 2017.

97 MATHEMATICS AND COMPUTING↗

Benchmarking exchange-correlation functionals for hydrogen at high pressures using quantum Monte Carlo

The ab initio phase diagram of dense hydrogen is very sensitive to errors in the treatment of electronic correlation. Recently, it has been shown that the choice of the density functional has a large effect on the predicted location of both the liquid-liquid phase transition and the solid insulator-to-metal transition in dense hydrogen. To identify the most accurate functional for dense hydrogen applications, we systematically benchmark some of the most commonly used functionals using quantum Monte Carlo. By considering several measures of functional accuracy, we conclude that the van der Waals and hybrid functionals significantly outperform local density approximation and Perdew-Burke-Ernzerhof. We support these conclusions by analyzing the impact of functional choice on structural optimization in the molecular solid, and on the location of the liquid-liquid phase transition.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Parameterized Micro-benchmarking: An Auto-tuning Approach for Complex Applications

Auto-tuning has emerged as an important practical method for creating highly optimized implementations of key computational kernels and applications. However, the growing complexity of architectures and applications is creating new challenges for auto-tuning. Complex applications can involve a prohibitively large search space that precludes empirical auto-tuning. Similarly, architectures are becoming increasingly complicated, making it hard to model performance. In this paper, we focus on the challenge to auto-tuning presented by applications with a large number of kernels and kernel instantiations. While these kernels may share a somewhat similar pattern, they differ considerably in problem sizes and the exact computation performed. We propose and evaluate a new approach to auto-tuning which we refer to as parameterized micro-benchmarking. It is an alternative to the two existing classes of approaches to auto-tuning: analytical model-based and empirical search-based. Particularly, we argue that the former may not be able to capture all the architectural features that impact performance, whereas the latter might be too expensive for an application that has several different kernels. In our approach, different expressions in the application, different possible implementations of each expression, and the key architectural features, are used to derive a simple micro-benchmark and a small parameter space. This allows us to learn the most significant features of the architecture that can impact the choice of implementation for each kernel. We have evaluated our approach in the context of GPU implementations of tensor contraction expressions encountered in excited state calculations in quantum chemistry. We have focused on two aspects of GPUs that affect tensor contraction execution: memory access patterns and kernel consolidation. Using our parameterized micro-benchmarking approach, we obtain a speedup of up to 2 over the version that used default optimizations, but no auto-tuning. We demonstrate that observations made from microbenchmarks match the behavior seen from real expressions. In the process, we make important observations about the memory hierarchy of two of the most recent NVIDIA GPUs, which can be used in other optimization frameworks as well.

auto-tuning↗

Creation of a Benchmark Suite for SNL Nuclear Criticality Safety Code Validation (Volume 1 - MCNP)

The Nuclear Criticality Safety Program at Sandia National Laboratories has developed a suite of benchmark problems to be utilized for validation of MCNP6 Version 1.0 with ENDF/B-VII Release 1 cross sections. The benchmark suite covers a broad range of fissile material types, material forms, moderators, reflectors, and neutron energy spectra. It is anticipated that this benchmark suite will cover the vast majority of critical safety applications at SNL. The benchmark suite establishes a Bias and Bias Uncertainty for use in criticality safety analyses. In addition, the Bias and Bias Uncertainty value derived from the benchmark suite using the traditional SNL NCS methodology is demonstrated to be equivalent to the more robust statistical techniques used at many DOE sites.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

The Need for a New LLNL Pulsed Sphere Neutron Leakage Spectra Series

Here, it is shown that spectra measured as part of the Lawrence Livermore National Laboratory Pulsed Sphere (LPS) program offer decisive information to locate formatting or physics issues in nuclear data of key interest for fusion reactor simulations. However, experiments from this measurement series are not benchmarks. For instance, their uncertainties are incomplete. There are also many open questions—e.g., on the setup, the detector response, and whether LPS are accurately modeled—that cannot be answered anymore given the limited documentation and that many of the experimenters are no longer actively working. This limited knowledge has implications when one tries to adjust nuclear data to LPS spectra. Usually, one adjusts to benchmarks representing an application with the hope to get more precise nuclear data for the application of interest where differential data might be scarce and/or to reduce nuclear data uncertainties in the application simulations. However, it is demonstrated that adjustment with LPS spectra without accounting for missing uncertainties and modeling potential biases in the experimental data leads to adjusted data that are highly unphysical. That means adjusted data differ significantly from evaluated data based on information from differential experiments; also, application quantities predicted with the adjusted data deviate distinctly from experimental ones. While we can approximate our limited knowledge on these experiments with Gaussian processes in the adjustment process, this modeling of bias is arbitrary rather than based on a physics explanation, calling into doubt the validity of resulting adjusted data. Thus, we discuss here the need for a new measurement series, learning from the strengths and weaknesses of the LPS program, to yield decisive and well-benchmarked integral experiments to support fusion reactor research.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

D and D knowledge management information tool feasibility study for cross-platform mobile applications - 15704

The D and D Knowledge Management Information tool (D and D KM- IT) is a web-based knowledge management information tool built for the D and D user community. A feasibility study is being conducted on cross-platform application frameworks for their viability to the D and D KM-IT mobile needs. Currently, three main Operating Systems comprise the majority of the mobile market IOS, Android, and Windows, requiring a separate application for each device. Cross-development software allows the development of one application using one language, that can be ported or deployed on multiple devices with little effort. Using Xamarin, a native cross-platform framework, create a shared mobile application using Visual Studio. Build a D and D KMIT mobile application designed for the three major mobile platforms. Use Xamarin to compile the application into native applications for the three target platforms. Build and deploy the application on all three mobile platforms. Perform benchmark tests of the developed applications to analyze the performance on the three platforms. A large portion of the business logic of the application has been shared, eliminating development redundancy and minimizing planning, design, and validation time. The user interface development could not fully be shared cross-platform and some platform specific code must be individually implemented for each device. Maintenance, testing and design phases of the software engineering process were reduced from one for each device to having just one shared cycle processes. A less diverse skill-set for developers is required with cross-platform development. Some processes within the development cycle still require redundant activities.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space

Background Protein language models (PLMs) have revolutionized protein fitness prediction, yet their application to rapidly evolving viral pathogens is often confounded by extreme sequence homology. This homology leads to “data leakage” in standard random validation splits, yielding inflated performance metrics that fail to translate into real-world biosurveillance utility. Results We present Protein Representation Inference for Mutation Evaluation (PRIME), a framework that integrates domain-specific fine-tuning with a rigorous position-stratified validation protocol to evaluate viral threats. Using a dataset of 347,432 SARS-CoV-2 receptor binding domain (RBD) sequences, we demonstrate that while random training data split yields deceptive R 2 values (> 0.90), they fail to generalize to novel mutational sites. By benchmarking models up to 650 M parameters, we show that domain-specific fine-tuning of the ESM-C 600 M model with correctly stratified data provides an initial demonstration of predictive signal for binding affinity and expression at unseen mutational sites of binding affinity and expression on unseen sites (R 2 ~0.23), a significant advancement over base foundation models which exhibit no predictive power (R 2 <0). PRIME’s embedding-based clustering identified 3.03% of bat coronavirus sequences as candidates for further experimental prioritization based on their functional similarity to human-infective strains in embedding space, offering a perspective complementary to traditional phylogenetic methods. Conclusion PRIME establishes a new benchmark for the application of PLMs in pathogen surveillance. Our findings demonstrate that state-of-the-art models and fine-tuning, when paired with stratified validation, provide biologically meaningful insights into pathogen evolution and zoonotic risk.

59 BASIC BIOLOGICAL SCIENCES↗

Energy-efficient specialization of functional units in a Coarse-Grained Reconfigurable Array

Functional units provide the backbone of any spatial accelerator by providing the computing resources. The desire for having rich and expensive functional units is in tension with producing a regular and energy-efficient computing fabric. This paper explores the design trade-off between complex, universal functional units and simpler, limited functional units. We show that a modest amount of specialization reduces the area-delay-energy product of an optimized architecture to 0.86x a baseline architecture. Furthermore, we provide a design guideline that allows an architect to customize the contents of the computing fabric just by examining the profile of benchmarks within the application domains. Functional units are the core of compute-intensive spatial accelerators. They perform the computation of interest with support from local storage and communication structures. Ideally, the functional units will provide rich functionality, supporting operations ranging from simple addition, to fused multiply-adds, to advanced transcendental functions and domain specific operations like add-compare-select. However, the total opportunity cost to support the more complex operations is a function of the cost of the hardware, the rate of occurrence of the operation in the application domain, and the inefficiency of emulating the operation with simpler operators. Examples of operations that are typically emulated in spatial accelerators are division and trigonometric functions, which can be solved using table-lookup based algorithms and the CORDIC algorithm. One reason to avoid having direct hardware support for complex operations in a tiled architecture like a Coarse-Grained Reconfigurable Array (CGRA) is that the expensive hardware will typically need to be replicated in some or all of the architecture's tiles. Tiled architecture are designed such that their tiles are either homogeneous or heterogeneous. Homogeneous architectures are simpler to design but heterogeneous architectures can be more efficient. Generally, CGRAs try to support a rich set of operations with the smallest possible set of hardware devices.

97 MATHEMATICS AND COMPUTING↗

Impact of Thermal Scattering Law on Similarity Assessment in Light-Water or Polyethylene-Moderated Systems

A collaborative effort between Pacific Northwest National Laboratory (PNNL) and Oak Ridge National Laboratory (ORNL) is underway to provide a technical basis and methodology for the criticality safety community to use the sum of fractions (SoF) method for generating limits for mixtures of “selected actinide nuclides” included in the ANSI/ANS 8.15 standard. The PNNL scope in this project is to define a range of mixtures of 233 U, 235 U, and 239 Pu moderated with either light water or polyethylene and to examine the critical masses for these mixtures. The ORNL scope is primarily to provide validation support for these studies. More complete discussion of the project and its validation aspects will be presented at the upcoming International Conference on Nuclear Criticality Safety (ICNC) this Fall in Sendai, Japan. Clear differences in benchmark similarity to application systems as assessed by the integral parameter ck are noted in the validation studies performed as part of this project as a function of moderator. The c k value is a correlation coefficient that represents that amount of shared uncertainty in k eff due to cross sections between two systems. Individual nuclide-reaction contributions between the two systems can be simply summed to arrive at the total c k value. Specifically, the c k values for light-water–moderated solution experiments are higher for a water-moderated application than for a polyethylene-moderated application. This result is neither totally unexpected nor surprising, but the magnitude of the difference was difficult to anticipate. The TSUNAMI sequence, in the SCALE 6.2.4 code package developed by ORNL, was used to generate eigenvalues and reactivity effects with perturbation-theory based approach through sensitivity coefficients for all nuclides in the system with all reactions and energy groups. The TSUNAMI-Indices and Parameters (IP) sequence then uses the sensitivity data generated through TSUNAMI to generate relational parameters (i.e., c k ) to determine the degree of similarity between systems. One detail of the SCALE material and data implementation must be discussed at this point. Several thermal scattering laws (TSLs) are available for 1 H. SCALE uses a different nuclide ID number for each TSL; essentially, each version of 1 H is treated as a unique nuclide. For example, 1 H bound in water ( 1 H-H2O) is assigned the nuclide ID 1001, whereas 1 H bound in polyethylene (h-poly) is assigned the nuclide ID 9001001. The same cross section data are used for all reactions in 1 H, regardless of TSL, except for scattering below the TSL cutoff energy. TSUNAMI-IP treats different nuclide IDs as different nuclides; thus, no uncertainty is shared between 1 H-H2O and h-poly, despite much of the same data, including covariance data, being used for both nuclides. This presents a question: how much of the difference in assessed similarity between water- and polyethylene-moderated systems is due to the moderators, and how much is caused by the treatment of 1 H-H2O and h poly with cross section and covariance data. The extended edits generated by TSUANMI-IP allow for an investigation of this issue specifically, as well as a demonstration of the general techniques available within TSUNAMI to understand the results of the similarity assessment. This paper presents and analyzes the similarity assessment of both water- and polyethylene-moderated systems for a single benchmark: PST-002-001.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Verification of MCNP6.2 for Nuclear Criticality Safety Applications

Several suites of verification/validation benchmark problems were run in early 2017 to verify that the new production release of MCNP6.2 performs correctly for nuclear criticality safety applications (NCS). MCNP6.2 results for several NCS validation suites were compared to the results from MCNP6.1 [1] and MCNP6.1.1 [2]. MCNP6.1 is the production version of MCNP® released in 2013, and MCNP6.1.1 is the update released in 2014. MCNP6.2 includes all of the standard features for NCS calculations that have been available for the past 15 years, along with new features for sensitivity-uncertainty based methods for NCS validation [3]. Results from the benchmark suites were compared with results from previous verification testing [4-8]. Criticality safety analysts should consider testing MCNP6.2 on their particular problems and validation suites. No further development of MCNP5 is planned. MCNP6.1 is now 4 years old, and MCNP6.1.1 is now 3 years old. In general, released versions of MCNP are supported only for about 5 years, due to resource limitations. All future MCNP improvements, bug fixes, user support, and new capabilities are targeted only to MCNP6.2 and beyond.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

Verification of MCNP6.1, MCNP6.1.1, and MCNP6.2-pre for Criticality Safety Applications

Several suites of verification/validation benchmark problems were run in early 2016 to verify that MCNP6.1, MCNP6.1.1, and MCNP6.2-pre are performing correctly for nuclear criticality safety (NCS) applications. MCNP6.1 is the production version of MCNP{sup R} released in 2013; MCNP6.1.1 is the update released in 2014; MCNP6.2-pre is the pre-release development version of MCNP6.2, which is targeted for release in the near future. All versions of MCNP6 include all of the standard features for NCS calculations that have been available for the past 15 years, along with new features for sensitivity-uncertainty based methods for NCS validation. Results from the benchmark suites were compared with results from previous verification testing. Several standard criticality benchmark suites were used for the verification calculations: - VERIFICATION-KEFF - A suite of criticality problems for which exact analytical results are available, - VALIDATION-CRITICALITY - 31 ICSBEP problems, using ENDF/B-VII.1, - VALIDATION-CRIT-EXPANDED - 119 ICSBEP problems, using ENDF/B-VII.1. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗