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At least 379 records · Page 21

Parallel peak pruning for scalable SMP contour tree computation

As data sets grow to exascale, automated data analysis and visualisation are increasingly important, to intermediate human understanding and to reduce demands on disk storage via in situ analysis. Trends in architecture of high performance computing systems necessitate analysis algorithms to make effective use of combinations of massively multicore and distributed systems. One of the principal analytic tools is the contour tree, which analyses relationships between contours to identify features of more than local importance. Unfortunately, the predominant algorithms for computing the contour tree are explicitly serial, and founded on serial metaphors, which has limited the scalability of this form of analysis. While there is some work on distributed contour tree computation, and separately on hybrid GPU-CPU computation, there is no efficient algorithm with strong formal guarantees on performance allied with fast practical performance. Here in this paper, we report the first shared SMP algorithm for fully parallel contour tree computation, withfor-mal guarantees of O(lgnlgt) parallel steps and O(n lgn) work, and implementations with up to 10x parallel speed up in OpenMP and up to 50x speed up in NVIDIA Thrust.

97 MATHEMATICS AND COMPUTING↗

Asynchronous distributed-memory task-parallel algorithm for compressible flows on unstructured 3D Eulerian grids

Here, we discuss the implementation of a finite element method, used to numerically solve the Euler equations of compressible flows, using an asynchronous runtime system (RTS). The algorithm is implemented for distributed-memory machines, using stationary unstructured 3D meshes, combining data-, and task-parallelism on top of the Charm++ RTS. Charm++’s execution model is asynchronous by default, allowing arbitrary overlap of computation and communication. Task-parallelism allows scheduling parts of an algorithm independently of, or dependent on, each other. Built-in automatic load balancing enables continuous redistribution of computational load by migration of work units based on real-time CPU load measurement. The RTS also features automatic checkpointing, fault tolerance, resilience against hardware failure, and supports power-, and energy-aware computation. We demonstrate scalability up to 25 x 10 9 cells at $\mathscr{O}$10 4 compute cores and the benefits of automatic load balancing for irregular workloads. The full source code with documentation is available at https://quinoacomputing.org.

42 ENGINEERING↗

The GEWEX LandFlux project: Evaluation of model evaporation using tower-based and globally gridded forcing data

Determining the spatial distribution and temporal development of evaporation at regional and global scales is required to improve our understanding of the coupled water and energy cycles and to better monitor any changes in observed trends and variability of linked hydrological processes. With recent international efforts guiding the development of long-term and globally distributed flux estimates, continued product assessments are required to inform upon the selection of suitable model structures and also to establish the appropriateness of these multi-model simulations for global application. In support of the objectives of the Global Energy and Water Cycle Exchanges (GEWEX) LandFlux project, four commonly used evaporation models are evaluated against data from tower-based eddy-covariance observations, distributed across a range of biomes and climate zones. The selected schemes include the Surface Energy Balance System (SEBS) approach, the Priestley–Taylor Jet Propulsion Laboratory (PT-JPL) model, the Penman–Monteith-based Mu model (PM-Mu) and the Global Land Evaporation Amsterdam Model (GLEAM). Here we seek to examine the fidelity of global evaporation simulations by examining the multi-model response to varying sources of forcing data. To do this, we perform parallel and collocated model simulations using tower-based data together with a global-scale grid-based forcing product. Through quantifying the multi-model response to high-quality tower data, a better understanding of the subsequent model response to the coarse-scale globally gridded data that underlies the LandFlux product can be obtained, while also providing a relative evaluation and assessment of model performance. Using surface flux observations from 45 globally distributed eddy-covariance stations as independent metrics of performance, the tower-based analysis indicated that PT-JPL provided the highest overall statistical performance (0.72; 61 W m –2 ; 0.65), followed closely by GLEAM (0.68; 64 W m –2 ; 0.62), with values in parentheses representing the R 2 , RMSD and Nash–Sutcliffe efficiency (NSE), respectively. PM-Mu (0.51; 78 W m –2 ; 0.45) tended to underestimate fluxes, while SEBS (0.72; 101 W m –2 ; 0.24) overestimated values relative to observations. A focused analysis across specific biome types and climate zones showed considerable variability in the performance of all models, with no single model consistently able to outperform any other. Results also indicated that the global gridded data tended to reduce the performance for all of the studied models when compared to the tower data, likely a response to scale mismatch and issues related to forcing quality. Rather than relying on any single model simulation, the spatial and temporal variability at both the tower- and grid-scale highlighted the potential benefits of developing an ensemble or blended evaporation product for global-scale LandFlux applications. Hence, challenges related to the robust assessment of the LandFlux product are also discussed.

58 GEOSCIENCES↗

Coupling Big Data Analytics and Reactive Transport Modeling for Cost-effective Groundwater Monitoring - 17163

This study presents an innovative approach for sustainable and cost-effective groundwater monitoring. This approach takes advantage of recent advances in various technologies: (1) in situ autonomous sensors, (2) big data analytics, and (3) parallel high-performance computing for flow and reactive transport modeling. In situ sensors are used to periodically measure the key variables (such as pH, redox potential, electrical conductivity, and groundwater level), which control contaminant mobility and the plume spatial and temporal distribution. Based on a limited number of groundwater sampling, the data analytics methods-data mining and machine learning-allow us to identify and quantify the correlations between the in situ-measured variables and contaminant concentrations, and also to detect significant changes associated with the plume mobility. In addition, a state-of-the-art parallel numerical flow and reactive transport simulator Amanzi, and uncertainty quantification software Agni are used to provide an improved physical and mechanistic understanding of the contaminated groundwater system behavior, and to predict the long-term plume distribution for optimizing and adapting the monitoring strategy. Amanzi and Agni were developed as part of the Advanced Simulation Capability for Environmental Management (ASCEM) program of the DOE Office of Environmental Management. Such modeling is critical, particularly, for assessing the impact of climate change and associated hydrological shifts. The developed approach is expected to significantly reduce the groundwater sampling frequency and associated cost. In addition, the real-time information on plume mobility serves as an early warning system, improving the resiliency of contaminated or potentially contaminated sites. We demonstrate this approach using as an example the Savannah River Site (SRS) F-Area, where groundwater is contaminated by various radionuclides, including uranium, tritium and technetium. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Dark Energy Survey Year 3 Results: Measuring the Survey Transfer Function with Balrog

Abstract We describe an updated calibration and diagnostic framework, Balrog , used to directly sample the selection and photometric biases of the Dark Energy Survey (DES) Year 3 (Y3) data set. We systematically inject onto the single-epoch images of a random 20% subset of the DES footprint an ensemble of nearly 30 million realistic galaxy models derived from DES Deep Field observations. These augmented images are analyzed in parallel with the original data to automatically inherit measurement systematics that are often too difficult to capture with generative models. The resulting object catalog is a Monte Carlo sampling of the DES transfer function and is used as a powerful diagnostic and calibration tool for a variety of DES Y3 science, particularly for the calibration of the photometric redshifts of distant “source” galaxies and magnification biases of nearer “lens” galaxies. The recovered Balrog injections are shown to closely match the photometric property distributions of the Y3 GOLD catalog, particularly in color, and capture the number density fluctuations from observing conditions of the real data within 1% for a typical galaxy sample. We find that Y3 colors are extremely well calibrated, typically within ∼1–8 mmag, but for a small subset of objects, we detect significant magnitude biases correlated with large overestimates of the injected object size due to proximity effects and blending. We discuss approaches to extend the current methodology to capture more aspects of the transfer function and reach full coverage of the survey footprint for future analyses.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

A Full-Stack Exploration of Language-Based Parallelism in Fortran 2023

This poster explores native parallel features in Fortran 2023 through the lens of supporting applications with libraries, compilers, and parallel runtimes. The language revision informally named Fortran 2008 introduced parallelism in the form of Single Program Multiple Data (SPMD) execution with two broad feature sets: (1) loop-level parallelism via do concurrent and (2) a Partitioned Global Address Space (PGAS) comprised of distributed “coarray” data structures. Fortran’s native parallelism has demonstrated high performance [1] and reduced the burden of inserting what sometimes amounts to more directives than code. Several compilers support both feature sets, typically by translating do concurrent into serial do loops annotated by parallel directives and by translating SPMD/PGAS features into direct calls to a communication library. Our research focuses primarily on two questions: (1) can the compiler’s parallel runtime library be developed in the language being compiled (Fortran) and (2) can we define an interface to the runtime that liberates compilers from being hardwired to one runtime and vice versa. We are answering these questions by developing the Parallel Runtime Interface for Fortran (PRIF) [2] and the Co-Array Fortran Framework of Efficient Interfaces to Network Environments (Caffeine) [3]. Caffeine is initially targeting adoption by LLVM Flang, a new open-source Fortran compiler developed by a broad community in industry, academia, and government labs. We are also exploring the use of these features in Inference-Engine, a deep learning library designed to facilitate neural network training and inference for high-performance computing applications written in modern Fortran.

Rasmussen, Katherine↗

Asynchronous In Situ Connected-Components Analysis for Complex Fluid flows, In: ISAV '16 Proceedings of the 2nd Workshop on In Situ Infrastructures for Enabling Extreme-scale Analysis and Visualization

The simulation of multiscale physics is an important challenge for scientific computing. For this class of problem, large three-dimensional simulations are performed to advance scientific inquiry. On massively parallel computing systems, the volume of data generated by such approaches can become a productivity bottleneck if the raw data generated from the simulation is analyzed in a post-processing step. To address this, we present a physics-based framework for in situ data reduction that is theoretically grounded in multiscale averaging theory. We show how task parallelism can be exploited to concurrently perform a variety of analysis tasks with data-dependent costs, including the generation of iso-surfaces, morphological analyses, and connected components analysis. All analyses are performed in parallel using distributed memory and use the same domain decomposition as the simulation. A task management framework is constructed to leverage available parallelism within a node for analysis. The capabilities of the framework are to launch asynchronous analysis threads, manage dependencies between different tasks, promote data locality and minimize the impact of data transfers. The framework is applied to analyze GPU-based simulations of two-fluid-phase flow in porous media, generating a set of averaged measures that represents the overall system behavior. We demonstrate how the approach can be applied to perform physically-consistent analysis over fluid sub-regions determined from connected components analysis. Simulations performed on Oak Ridge National Lab's Titan supercomputer are profiled to demonstrate the performance of the associated multi-threaded in situ analysis approach for typical production simulation of two-fluid-phase flow.

Computer Science↗

Antiferromagnetic spin correlations and pseudogaplike behavior in Ca(Fe 1-x Co x ) 2 As 2 studied by 75 As nuclear magnetic resonance and anisotropic resistivity

We report 75 As nuclear magnetic resonance (NMR) measurements of single-crystalline Ca(Fe 1–x Co x ) 2 As 2 (x=0.023, 0.028, 0.033, and 0.059) annealed at 350°C for 7 days. From the observation of a characteristic shape of 75 As NMR spectra in the stripe-type antiferromagnetic (AFM) state, as in the case of x=0 (T N =170 K), clear evidence for the commensurate AFM phase transition with the concomitant structural phase transition is observed in x=0.023 (T N =106 K) and x=0.028 (T N =53 K). Through the temperature dependence of the Knight shifts and the nuclear spin lattice relaxation rates (1/T 1 ), although stripe-type AFM spin fluctuations are realized in the paramagnetic state as in the case of other iron pnictide superconductors, we found a gradual decrease of the AFM spin fluctuations below a crossover temperature T* that was nearly independent of Co-substitution concentration, and it is attributed to a pseudogaplike behavior in the spin excitation spectra of these systems. The T* feature finds correlation with features in the temperature-dependent interplane resistivity, ρ c (T), but not with the in-plane resistivity ρ a (T). The temperature evolution of anisotropic stripe-type AFM spin fluctuations is tracked in the paramagnetic and pseudogap phases by the 1/T 1 data measured under magnetic fields parallel and perpendicular to the c axis. As a result, based on our NMR data, we have added a pseudogaplike phase to the magnetic and electronic phase diagram of Ca(Fe 1–x Co x ) 2 As 2 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

SU-E-T-255: Development of a Michigan Quality Assurance (MQA) Database for Clinical Machine Operations

Purpose: A unified database system was developed to allow accumulation, review and analysis of quality assurance (QA) data for measurement, treatment, imaging and simulation equipment in our department. Recording these data in a database allows a unified and structured approach to review and analysis of data gathered using commercial database tools. Methods: A clinical database was developed to track records of quality assurance operations on linear accelerators, a computed tomography (CT) scanner, high dose rate (HDR) afterloader and imaging systems such as on-board imaging (OBI) and Calypso in our department. The database was developed using Microsoft Access database and visual basic for applications (VBA) programming interface. Separate modules were written for accumulation, review and analysis of daily, monthly and annual QA data. All modules were designed to use structured query language (SQL) as the basis of data accumulation and review. The SQL strings are dynamically re-written at run time. The database also features embedded documentation, storage of documents produced during QA activities and the ability to annotate all data within the database. Tests are defined in a set of tables that define test type, specific value, and schedule. Results: Daily, Monthly and Annual QA data has been taken in parallel with established procedures to test MQA. The database has been used to aggregate data across machines to examine the consistency of machine parameters and operations within the clinic for several months. Conclusion: The MQA application has been developed as an interface to a commercially available SQL engine (JET 5.0) and a standard database back-end. The MQA system has been used for several months for routine data collection.. The system is robust, relatively simple to extend and can be migrated to a commercial SQL server.

60 APPLIED LIFE SCIENCES↗

Visualization and Data Analysis for High-Performance Computing

This is a set of slides from a guest lecture for a class at the University of Texas, El Paso on visualization and data analysis for high-performance computing. The topics covered are the following: trends in high-performance computing; scientific visualization, such as OpenGL, ray tracing and volume rendering, VTK, and ParaView; data science at scale, such as in-situ visualization, image databases, distributed memory parallelism, shared memory parallelism, VTK-m, "big data", and then an analysis example.

97 MATHEMATICS AND COMPUTING↗

Characterization of bandwidth requirements of algorithms for extreme scale science

Technology trends have resulted in widely different rates of improvement in computational throughput as compared to data movement rates in computer systems. With future systems, the cost of data movement through the memory hierarchy is expected to become even more dominant relative to the cost of performing arithmetic operations, both in terms of time and energy. Therefore, optimizing data access costs will become ever more critical in the coming years. However, unlike the well understood model of computational complexity in terms of the number of elementary operations to execute an algorithm, the inherent data-movement complexity of computations is unknown for most algorithms. Given the crucial importance of optimizing data access costs in scalable parallel systems, it is of great interest to develop techniques for understanding the inherent data movement complexity of an algorithm. In this project, we focus on this fundamental and significant problem.

97 MATHEMATICS AND COMPUTING↗

Workflow-based automatic processing for Internet of Floating Things crowdsourced data

Data from sensors incorporated into mobile devices, such as networked navigational sensors, can be used to capture detailed environmental information. We describe here a workflow and framework for using sensors on boats to construct unique new datasets of underwater topography (bathymetry). Starting with a large number of measurements of position, depth, etc., obtained from such an Internet of Floating Things, we illustrate how, with a specialized protocol, data can be communicated to cloud resources, even when using delayed, intermittent, or disconnected networks. We then propose a method for automatic sensor calibration based on a novel reputation approach. Sampled depth data are interpolated efficiently on a cloud computing platform in order to provide a continuously updated bathymetric database. Our prototype implementation uses the FACE-IT Galaxy workflow engine to manage network communication and exploits the computational power of GPGPUs in a virtualized cloud environment, working with a CUDA-parallel algorithm, for efficient data processing. We report on an initial evaluation involving data from a sailing vessel in Italian coastal waters.

97 MATHEMATICS AND COMPUTING↗

MAUS: the MICE analysis user software

The Muon Ionization Cooling Experiment (MICE) collaboration has developed the MICE Analysis User Software (MAUS) to simulate and analyze experimental data. It serves as the primary codebase for the experiment, providing for offline batch simulation and reconstruction as well as online data quality checks. The software provides both traditional particle-physics functionalities such as track reconstruction and particle identification, and accelerator physics functions, such as calculating transfer matrices and emittances. The code design is object orientated, but has a top-level structure based on the Map-Reduce model. This allows for parallelization to support live data reconstruction during data-taking operations. MAUS allows users to develop in either Python or C++ and provides APIs for both. Various software engineering practices from industry are also used to ensure correct and maintainable code, including style, unit and integration tests, continuous integration and load testing, code reviews, and distributed version control. The software framework and the simulation and reconstruction capabilities are described.

47 OTHER INSTRUMENTATION↗

Strong parallel evidence of selection during switchgrass sward establishment in hybrid and lowland ecotypes

Switchgrass sward establishment results in up to 90% seedling mortality. The degree of selection during sward establishment has not been reported using modern genetic methods. Pooled leaf samples were sequenced from replicated swards of 46 half-sib families from two breeding groups (lowland and hybrid) before and through 3 years of stand establishment. Pooled allele frequencies were then assessed using fixation indices (Fst) and an independent data set was used to predict the polygenic impact of establishment selection on two traits (heading date and winter survivorship). Last, the DNA pools were assigned survival rankings to predict the sward survival genomically estimated breeding values within the training data set. Strong and parallel selection occured in both breeding groups. Five genomic regions exceeded the significant threshold of 99.9% in >10 families, indicating consistent selection across families and breeding groups. Polygenic trait predictions determined that establishment selection was partially associated with winter survivorship but resulted in variable heading date alterations. The genomewide variation is consistent with selection for a small number of related parental lines. This study observed strong selection for a small number of hybrid and coastal ecotype individuals which are promising germplasm sources for improved sward survival. This confirms prior reports of sward selection during grassland establishment and highlights the strength of pooled DNA sequencing for survival traits.

54 ENVIRONMENTAL SCIENCES↗

Reinforcement Learning for Load-balanced Parallel Particle Tracing

We explore an online reinforcement learning (RL) paradigm to dynamically optimize parallel particle tracing performance in distributed-memory systems. Our method combines three novel components: (1) a work donation algorithm, (2) a high-order workload estimation model, and (3) a communication cost model. First, we design an RL-based work donation algorithm. Our algorithm monitors workloads of processes and creates RL agents to donate data blocks and particles from high-workload processes to low-workload processes to minimize program execution time. The agents learn the donation strategy on the fly based on reward and cost functions designed to consider processes' workload changes and data transfer costs of donation actions. Second, we propose a workload estimation model, helping RL agents estimate the workload distribution of processes in future computations. Third, we design a communication cost model that considers both block and particle data exchange costs, helping RL agents make effective decisions with minimized communication costs. We demonstrate that our algorithm adapts to different flow behaviors in large-scale fluid dynamics, ocean, and weather simulation data. Our algorithm improves parallel particle tracing performance in terms of parallel efficiency, load balance, and costs of I/O and communication for evaluations with up to 16,384 processors.

Distributed and parallel particle tracing↗

Big Data Seismology

The discipline of seismology is based on observations of ground motion that are inherently undersampled in space and time. Our basic understanding of earthquake processes and our ability to resolve 4D Earth structure are fundamentally limited by data volume. Currently, Big Data Seismology is an emergent revolution involving the use of large, data-dense inquiries that is providing new opportunities to make fundamental advances in these areas. This article reviews recent scientific advances enabled by Big Data Seismology through the context of three major drivers: the development of new data-dense sensor systems, improvements in computing, and the development of new types of techniques and algorithms. Each driver is explored in the context of both global and exploration seismology, alongside collaborative opportunities that combine the features of long-duration data collections (common to global seismology) with dense networks of sensors (common to exploration seismology). The review explores some of the unique challenges and opportunities that Big Data Seismology presents, drawing on parallels from other fields facing similar issues. Finally, recent scientific findings enabled by dense seismic data sets are discussed, and we assess the opportunities for significant advances made possible with Big Data Seismology. This review is designed to be a primer for seismologists who are interested in getting up-to-speed with how the Big Data revolution is advancing the field of seismology.

58 GEOSCIENCES↗