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All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

CAASCADE: A System for Static Analysis of HPC Software Application Portfolios

With the increasing complexity of upcoming HPC systems, so-called “co-design” efforts to develop the hardware and applications in concert for these systems also become more challenging. It is currently difficult to gather information about the usage of programming model features, libraries, and data structure considerations in a quantitative way across a variety of applications, and this information is needed to prioritize development efforts in systems software and hardware optimizations. In this paper we propose CAASCADE, a system that can harvest this information in an automatic way in production HPC environments, and we show some early results from a prototype of the system based on GNU compilers and a MySQL database.

Lopez, Graham↗
DOE OSTI2022

MAPredict: Static Analysis Driven Memory Access Prediction Framework for Modern CPUs

Application memory access patterns are crucial in deciding how much traffic is served by the cache and forwarded to the dynamic random-access memory (DRAM). However, predicting such memory traffic is difficult because of the interplay of prefetchers, compilers, parallel execution, and innovations in manufacturer-specific micro-architectures. This research introduced MAPredict, a static analysis-driven framework that addresses these challenges to predict last-level cache (LLC)-DRAM traffic. By exploring and analyzing the behavior of modern Intel processors, MAPredict formulates cache-aware analytical models. MAPredict invokes these models to predict LLC-DRAM traffic by combining the application model, machine model, and user-provided hints to capture dynamic information. MAPredict successfully predicts LLC-DRAM traffic for different regular access patterns and provides the means to combine static and empirical observations for irregular access patterns. Evaluating 130 workloads from six applications on recent Intel micro-architectures, MAPredict yielded an average accuracy of 99% for streaming, 91% for strided, and 92% for stencil patterns. By coupling static and empirical methods, up to 97% average accuracy was obtained for random access patterns on different micro-architectures.

Monil, M. A. H.↗
DOE OSTI2022

Developing an ELM Ecosystem Dynamics Model on GPU with OpenACC

Porting a complex scientific code, such as the E3SM land model (ELM), onto a new computing architecture is challenging. The paper presents design strategies and technical approaches to develop an ELM ecosystem dynamics model with compiler directives (OpenACC) on NVIDIA GPUs. The code has been refactored with advanced OpenACC features (such as deepcopy and routine directives) to reduce memory consumption and to increase the levels of parallelism through parallel loop reconstruction and new data structures. As a result, the optimized parallel implementation achieved more than a 140-time speedup (50 ms vs 7600 ms), compared to a naive implementation that uses OpenACC routine directive and parallelizes the code across existing loops on a single NVIDIA V100. On a fully loaded computing node with 44 CPUs and 6 GPUs, the code achieved over a 3.0-times speedup, compared to the original code on the CPU. Furthermore, the memory footprint of the optimized parallel implementation is 300 MB, which is around 15% of the 2.15 GB of memory consumed by a naive implementation. This study is the first effort to develop the ELM component on GPUs efficiently to support ultra-high-resolution land simulations at continental scales.

Schwartz, Peter↗
DOE OSTI2023

Developing Ultrahigh-Resolution E3SM Land Model for GPU Systems

Designing and refactoring complex scientific code, such as the E3SM land model (ELM), for new computing architectures is challenging. This paper presents design strategies and technical approaches to develop a data-oriented, GPU-ready ELM model using compiler directives (OpenACC/OpenMP). We first analyze the datatypes and processes in the original ELM code. Then we present design considerations for ultrahigh-resolution ELM (uELM) development for massive GPU systems. These techniques include the global data-oriented simulation workflow, domain partition, code porting and data copy, memory reduction, parallel loop restructure and flattening, and race condition detection. We implemented the first version of uELM using OpenACC targeting the NVidia GPUs in the Summit supercomputer at Oak Ridge National Laboratory. During the implementation, we developed a software tool (named SPEL) to facilitate code generation, verification, and performance tuning using these techniques. The first uELM implementation for Nvidia GPUs on Summit delivered promising results: 1) over 98% of the ELM code was automatically generated and tuned by scripts. Most ELM modules had better computational performances than the original ELM code for CPUs. The GPU-ready uELM is more scalable than the CPU code on fully-loaded Summit nodes. Example profiling results from several modules are also presented to illustrate the performance improvements and race condition detection. The lessons learned and toolkit developed in the study are also suitable for further uELM deployment using OpenMP on the first US exascale computer, Frontier, equipped with AMD CPUs and GPUs.

Schwartz, Peter↗
DOE OSTI2015

Roofline model toolkit: A practical tool for architectural and program analysis

We present preliminary results of the Roofline Toolkit for multicore, many core, and accelerated architectures. This paper focuses on the processor architecture characterization engine, a collection of portable instrumented micro benchmarks implemented with Message Passing Interface (MPI), and OpenMP used to express thread-level parallelism. These benchmarks are specialized to quantify the behavior of different architectural features. Compared to previous work on performance characterization, these microbenchmarks focus on capturing the performance of each level of the memory hierarchy, along with thread-level parallelism, instruction-level parallelism and explicit SIMD parallelism, measured in the context of the compilers and run-time environments. We also measure sustained PCIe throughput with four GPU memory managed mechanisms. By combining results from the architecture characterization with the Roofline model based solely on architectural specifications, this work offers insights for performance prediction of current and future architectures and their software systems. To that end, we instrument three applications and plot their resultant performance on the corresponding Roofline model when run on a Blue Gene/Q architecture.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms, In: ISC High Performance 2016: High Performance Computing

All-atom molecular dynamics simulations of biomolecules provide a powerful tool for exploring the structure and dynamics of large protein complexes within realistic cellular environments. Unfortunately, such simulations are extremely demanding in terms of their computational requirements, and they present many challenges in terms of preparation, simulation methodology, and analysis and visualization of results. We describe our early experiences porting the popular molecular dynamics simulation program NAMD and the simulation preparation, analysis, and visualization tool VMD to GPU-accelerated OpenPOWER hardware platforms. We report our experiences with compiler-provided autovectorization and compare with hand-coded vector intrinsics for the POWER8 CPU. We explore the performance benefits obtained from unique POWER8 architectural features such as 8-way SMT and its value for particular molecular modeling tasks. Finally, we evaluate the performance of several GPU-accelerated molecular modeling kernels and relate them to other hardware platforms.

Computer Science↗
DOE OSTI2016

Profiling Production OpenSHMEM Applications, In: OpenSHMEM 2016: OpenSHMEM and Related Technologies. Enhancing OpenSHMEM for Hybrid Environments

Developing high performance OpenSHMEM applications routinely involves gaining a deeper understanding of software execution, yet there are numerous hurdles to gathering performance metrics in a production environment. Most OpenSHMEM performance profilers rely on the PSHMEM interface but PSHMEM is an optional and often unavailable feature. We present a tool that generates direct measurement performance profiles of OpenSHMEM applications even when PSHMEM is unavailable. The tool operates on dynamically linked and statically linked application binaries, does not require debugging symbols, and functions regardless of compiler optimization level. Integrated in the TAU Performance System, the tool uses automatically-generated wrapper libraries that intercept OpenSHMEM API calls to gather performance metrics with minimal overhead. Dynamically linked applications may use the tool without modifying the application binary in any way.

Computer Science↗
DOE OSTI2018

An Event Detection Framework for Virtual Observation System: Anomaly Identification for an ACME Land Simulation

Based on previous work on in-situ data transfer infrastructure and compiler-based software analysis, we have designed a virtual observation system for real time computer simulations. This paper presents an event detection framework for a virtual observation system. By using signal processing and detection approaches to the memory-based data streams, this framework can be reconfigured to capture high-frequency events and low-frequency events. These approaches used in the framework can dramatically reduce the data transfer needed for in-situ data analysis (between distributed computing nodes or between the CPU/GPU nodes). In the paper, we also use a terrestrial ecosystem system simulation within the Earth System Model to demonstrate the practical values of this effort.

Yao, Cindy↗
DOE OSTI2018

OpenMP 4.5 Validation and Verification Suite for Device Offload

OpenMP has been widely adopted for shared memory systems for over a decade. With the heterogeneity trend in architectures rapidly growing, the programming model needed to evolve such that applications could not only be ported to traditional CPUs but also to accelerators often acting as discrete or integrated devices to CPUs. To that end, OpenMP started to provide support for heterogeneous systems since 2013 when the version 4.0 of the specification was ratified. OpenMP 4.5 is being enhanced to cover major requirements of Exascale Computing Project (ECP) applications. As a result it is time-critical to ensure that the implementations of the 4.5 features are correct and conforming to the specification. This paper focuses on building a Validation and Verification testsuite that will test and present results for several offloading features implemented in compilers such as Clang, IBM XL C/C++, CCE, and GCC. We have results for our testsuite on TITAN, Summitdev and Summit at the Oak Ridge National Lab. We will highlight some of the ambiguities we encountered in the process of validating and verifying feature implementations. We also make the testsuite available for anyone to use and will walk the readers through the infrastructure and the workflow of the testsuite. A website has been built to capture our efforts narrated in this paper https://crpl.cis.udel.edu/ompvvsollve.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2013

A Similarity-Based Analysis Tool for Porting OpenMP Applications. In: Facing the Multicore-Challenge III. Lecture Notes in Computer Science, vol 7686.

Exascale computers are expected to exhibit an unprecedented level of complexity, thereby posing significant challenges for porting applications to these new systems. One of the ways to support this transition is to create tools that allow their users to benefit from prior successful porting experiences. The key to such an approach is the manner in which we define source code similarity, and whether similar codes can be ported in the same way to a given system. In this paper, we propose a novel approach based on the notion of similarity that uses static and dynamic code features to check if two serial subroutines can be ported with the same OpenMP strategy. Our approach creates an annotated family distance tree based on the syntactic structure of subroutines, where subroutines that belong to the same syntactic family and share the similar code features have a greater potential to be optimized in the same way. We describe the design and implementation of a tool, based upon a compiler and performance tool, that is used to gather the data to build this porting planning tree. We then validate our approach by analyzing the similarity in subroutines of the serial version of the NAS benchmarks and comparing how they were ported in the OpenMP version of the suite.

Ding, Wei↗
DOE OSTI2013

Software design space exploration for exascale combustion co-design

The design of hardware for next-generation exascale computing systems will require a deep understanding of how software optimizations impact hardware design trade-offs. In order to characterize how co-tuning hardware and software parameters affects the performance of combustion simulation codes, we created ExaSAT, a compiler-driven static analysis and performance modeling framework. Our framework can evaluate hundreds of hardware/software configurations in seconds, providing an essential speed advantage over simulators and dynamic analysis techniques during the co-design process. Our analytic performance model shows that advanced code transformations, such as cache blocking and loop fusion, can have a significant impact on choices for cache and memory architecture. Our modeling helped us identify tuned configurations that achieve a 90% reduction in memory traffic, which could significantly improve performance and reduce energy consumption. These techniques will also be useful for the development of advanced programming models and runtimes, which must reason about these optimizations to deliver better performance and energy efficiency.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Categorisation and detection of dark matter candidates from string/M-theory hidden sectors

We study well-motivated dark matter candidates arising from weakly-coupled hidden sectors in compactified string/ M -theory. Imposing generic top-down constraints greatly restricts allowed candidates. By considering the possible mechanisms for achieving the correct dark matter relic density, we compile categories of viable dark matter candidates and annihilation mediators. We consider the case where supersymmetry breaking occurs via moduli stabilization and is gravitationally mediated to the visible and other hidden sectors, without assuming sequestering of the sector in which supersymmetry is broken. We find that in this case, weakly-coupled hidden sectors only allow for fermionic dark matter. Additionally, most of the mechanisms for obtaining the full relic density only allow for a gauge boson mediator, such as a dark Z' . Given these considerations, we study the potential for discovering or constraining the allowed parameter space given current and future direct detection experiments, and direct production at the LHC. We also present a model of a hidden sector which would contain a satisfactory dark matter candidate.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Quantifying the Potential of Argon Detection Capabilities for Nuclear Explosion Monitoring

Abstract Current noble gas detection systems for nuclear explosion monitoring are based on the detection of four radioxenon isotopes—Xe-131m, -133, -133m and -135. The data provided by radioxenon detection could be enhanced by other radionuclide signatures such as Ar-37. Activation of Ca-40 in rock by neutrons produces Ar-37, and monitoring for this additional nuclide could help distinguish detections of nuclear explosions from background sources, such as medical isotope production. This work studies the capabilities of a hypothetical argon detection network. A 10 kt explosion was modeled using MCNP and SCALE to determine the inventory of Ar-37 created in a representative granite rock layer, assuming either 0.1, 1 or 10% of the total inventory was released. The Ar-37 inventory was combined with atmospheric transport data from HYSPLIT compiled in a previous study, along with the detection limits of standard Ar-37 detection systems, to determine how many hypothetical monitoring stations would detect Ar-37 from an explosion. This method was repeated for 365 HYSPLIT data sets to create a year’s worth of hypothetical explosions, releases, and detections. The study quantified the average number of detections per release, the number of stations detecting Ar-37, and the possibility of detecting Ar-37 in coincidence with xenon.

37Ar↗
DOE OSTI2012

Risk Factors and Complications Associated with Difficult Retrieval of Embolic Protection Devices in Carotid Artery Stenting

Purpose: This study was designed to investigate the risk factors and complications of difficult retrieval (DR) of embolic protection devices (EPDs) in carotid artery stenting (CAS). Methods: A total of 195 consecutive patients who underwent CAS between December 2007 and March 2010 in a general hospital were enrolled and divided into two groups: with DR and without DR. The risk factors of DR were analyzed with univariate and multivariate analyses. The complications of DR were recorded and analyzed. Results: A total of 30 (15.4%) patients with DR of EPDs were observed, of whom EPDs were successfully retrieved in 29, and in 1 was it taken out by surgical treatment. The retrieval time was significantly longer in patients with DR (490.5 {+-} 143.9 s) than in patients without DR (157.2 {+-} 15.7 s, p = 0.000). Vasospasm was observed more frequently in patients with DR than in patients without DR (55.2% vs. 14.5%, p = 0.000). Intracranial compilations were more frequent in patients with DR than in those without DR (17.2% vs. 0.6%, p = 0.000). Calcified plaques, degree of residual stenosis, types of the stents, and tortuosity index (TI > 80 Degree-Sign) were all associated with DR. A logistic regression analysis indicated that calcified plaques (odds ratio (OR) = 6.5; p = 0.000) and TI > 80 Degree-Sign (OR = 18.8; p = 0.000) were independent predictors of DR. Conclusions: Calcified plaques and TI > 80 Degree-Sign may be related to DR in patients with CAS. DR may lengthen the retrieving time and increase the complications of the procedure.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2012

Analysis of the Quality of Information Obtained About Uterine Artery Embolization From the Internet

Purpose: The Internet is widely used by patients to source health care-related information. We sought to analyse the quality of information available on the Internet about uterine artery embolization (UAE). Materials and Methods: We searched three major search engines for the phrase 'uterine artery embolization' and compiled the top 50 results from each engine. After excluding repeated sites, scientific articles, and links to documents, the remaining 50 sites were assessed using the LIDA instrument, which scores sites across the domains of accessibility, usability, and reliability. The Fleisch reading ease score (FRES) was calculated for each of the sites. Finally, we checked the country of origin and the presence of certification by the Health On the Net Foundation (HONcode) as well as their effect on LIDA and FRES scores.ResultsThe following mean scores were obtained: accessibility 48/60 (80%), usability 42/54 (77%), reliability 20/51 (39%), total LIDA 110/165 (67%), and FRES 42/100 (42%). Nine sites had HONcode certification, and this was associated with significantly greater (p < 0.05) reliability and total LIDA and FRES scores. When comparing sites between United Kingdom and United States, there was marked variation in the quality of results obtained when searching for information on UAE (p < 0.05). Conclusion: In general, sites were well designed and easy to use. However, many scored poorly on the reliability of their information either because they were produced in a non-evidence-based way or because they lacking currency. It is important that patients are guided to reputable, location-specific sources of information online, especially because prominent search engine rank does not guarantee reliability of information.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2015

The Management of Cephalic Arch Stenosis in Arteriovenous Fistulas for Hemodialysis: A Systematic Review

AimTo conduct a systematic review of management of current cephalic arch stenosis (CAS) and associated outcomes in the context of dysfunctional hemodialysis access.Materials and MethodsPubMed, Web of Science, and Cochrane Library were searched to retrieve literature on the management of CAS. Studies had to focus on management of access stenosis solely in the cephalic arch. Case reports and literature reviews were excluded. Studies were categorized by intervention, and primary and secondary patency data were compiled. Studies were aggregated, and meta-analyses were performed where possible.ResultsNine papers satisfied the aforementioned criteria: five were retrospective studies and four were prospective studies. CAS management strategies have included percutaneous transluminal balloon angioplasty (PTA), peripheral cutting balloons, surgical cephalic vein transpositions, bare stents, and stent grafts. Reporting strategies varied between studies. Meta-analyses showed that results were variable even within studies using the same modality, particularly for PTA.ConclusionNo singular, definitive management strategy exists for CAS. Current studies are limited by being primarily single-center retrospective trials featuring heterogenous patient populations, interventions, and endpoints. Priorities for future studies should include larger randomized trials, more uniform management strategies and endpoints, and a longer duration of follow-up.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2016

Feasibility of Intraoperative Nerve Monitoring in Preventing Thermal Damage to the “Nerve at Risk” During Image-Guided Ablation of Tumors

PurposeTo assess feasibility of intraoperative neurophysiologic monitoring (IONM) during image-guided, percutaneous thermal ablation of tumors.Materials and MethodsFrom February 2009 to October 2013, a retrospective review of all image-guided percutaneous thermal ablation interventions using IONM was performed and data was compiled using electronic medical records and imaging studies.ResultsTwelve patients were treated in 13 ablation interventions. In 4 patients, real-time feedback from the monitoring neurologist was used to adjust applicator placement and ablation settings. IONM was technically feasible in all procedures and there were no complications related to monitoring or ablation. All nerves at risk remained intact and of the 11 patients who could be followed, none developed new nerve deficit up to a minimum of 2 months after ablation.ConclusionIONM is safe and feasible for use during image-guided thermal ablation of tumors in the vicinity of nerves. Outcomes in this study demonstrate its potential utility in image-guided ablation interventions.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2014

An annotated database of Arabidopsis mutants of acyl lipid metabolism

Mutants have played a fundamental role in gene discovery and in understanding the function of genes involved in plant acyl lipid metabolism. The first mutant in Arabidopsis lipid metabolism ( fad4 ) was described in 1985. Since that time, characterization of mutants in more than 280 genes associated with acyl lipid metabolism has been reported. This review provides a brief background and history on identification of mutants in acyl lipid metabolism, an analysis of the distribution of mutants in different areas of acyl lipid metabolism and presents an annotated database (ARALIPmutantDB) of these mutants. The database provides information on the phenotypes of mutants, pathways and enzymes/proteins associated with the mutants, and allows rapid access via hyperlinks to summaries of information about each mutant and to literature that provides information on the lipid composition of the mutants. Mutants for at least 30 % of the genes in the database have multiple names, which have been compiled here to reduce ambiguities in searches for information. Furthermore, the database should also provide a tool for exploring the relationships between mutants in acyl lipid-related genes and their lipid phenotypes and point to opportunities for further research.

59 BASIC BIOLOGICAL SCIENCES↗