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Summer Proceedings 2019

The Computer Science Research Institute (CSRI) brings university faculty and students to Sandia for focused collaborative research on Department of Energy (DOE) computer and computational science problems. The institute provides an opportunity for university researchers to learn about problems in computer and computational science at DOE laboratories. Participants conduct leading-edge research, interact with scientists and engineers at the laboratories, and help transfer results of their research to programs at the labs. Some specific CSRI research interest areas are: scalable solvers, optimization, adaptivity and mesh refinement, graph-based, discrete, and combinatorial algorithms, uncertainty estimation, mesh generation, dynamic load-balancing, virus and other malicious-code defense, visualization, scalable cluster computers and heterogeneous computers, data-intensive computing, environments for scalable computing, parallel input/output, advanced architectures, and theoretical computer science. The CSRI Summer Program includes the organization of a weekly seminar series and the publication of this summer proceedings.

97 MATHEMATICS AND COMPUTING↗

Utilizing waste heat in wastewater treatment plants for water desalination: Modeling and Multi-Objective optimization of a Multi-Effect desalination system using Decision Tree Regression and Pelican optimization algorithm

This paper examines the feasibility of using waste heat from wastewater treatment plants (WWTPs) for water desalination. A model was developed to utilize waste heat from the gensets at As Samra WWTP in Jordan, using real data and TRNSYS® software to calculate available waste heat. The desalination process was then modeled with ASPEN PLUS® software, focusing on multi-effect desalination (MED). Both series and parallel configurations for the MED system were compared. The study investigated the effects of system feeding flow rate, feeding pressure, and heat input on productivity, performance ratio, and recovery ratio. The study also introduces a novel optimization technique combining machine learning and modern optimization algorithms to maximize system productivity and performance. Initially, a decision tree regression (DTR) model is developed to establish relationships between key independent variables (flow rate, feed pressure, and heat input) and dependent variables (productivity, performance ratio, and recovery ratio). The Pelican Optimization Algorithm (POA) is then used to identify the optimal values of the independent variables for maximum productivity and performance. The results show that using a series configuration yields a system productivity of 3984.2 kg/hr, a performance ratio of 3.78, and a recovery ratio of 0.991 at a feed flow rate of 4000 kg/hr, feed pressure of 3 bars, and heat input of 719 kW. Optimal productivity (4421 kg/hr), performance ratio (3.81), and recovery ratio (0.851) are achieved at a feed flow rate of 5166 kg/hr, feed pressure of 3.2 bars, and heat input of 794 kW. In conclusion, the techno-economic assessment indicates a levelized cost of water of 1.63 USD/m 3 for parallel configurations and 1.65 USD/m 3 for series configurations, with a payback period of less than two years.

42 ENGINEERING↗

Scalable All-pairs Shortest Paths for Huge Graphs on Multi-GPU Clusters

We present an optimized Floyd-Warshall (Floyd-Warshall) algorithm that computes the All-pairs shortest path (APSP) for GPU accelerated clusters. The Floyd-Warshall algorithm due to its structural similarities to matrix-multiplication is well suited for highly parallel GPU architectures. To achieve high parallel efficiency, we address two key algorithmic challenges: reducing high communication overhead and addressing limited GPU memory. To reduce high communication costs, we redesign the parallel (a) to expose more parallelism, (b) aggressively overlap communication and computation with pipelined and asynchronous scheduling of operations, and (c) tailored MPI-collective. To cope with limited GPU memory, we employ an offload model, where the data resides on the host and is transferred to GPU on-demand. The proposed optimizations are supported with detailed performance models for tuning. Our optimized parallel Floyd-Warshall implementation is up to 5x faster than a strong baseline and achieves 8.1 PetaFLOPS/sec on 256~nodes of the Summit supercomputer at Oak Ridge National Laboratory. This performance represents 70% of the theoretical peak and 80% parallel efficiency. The offload algorithm can handle 2.5x larger graphs with a 20% increase in overall running time.

Sao, Piyush↗

Empirical validation and comparison of methodologies to simulate micro and macro-encapsulated PCMs in the building envelope

Thermal Energy Storage (TES) has the potential to shift peak electricity demand. Passive TES is usually implemented in building envelope as micro and macro encapsulated phase change materials (PCM) to shift electric energy demand and therefore requires careful heat transfer analysis. Whole building energy modelling with simplified heat transfer analysis has become extremely important for designers, architects, engineers, and researchers to predict energy performance of buildings. It is important to validate PCM modelling algorithms used in building energy programs to quantify their error and prove their capacity to model different PCM encapsulation types. This study uses data from a microencapsulated PCM and two macroencapsulated PCMs (Bio based PCM and hydrate salts) tested in full-scale using the Advanced Multiscale Building Energy Research (AMBER) Lab located at the Colorado School of Mines and is used to validate a numerical algorithm written in MATLAB language. To approximate the heat transfer through a wall assembly with macroencapsulated PCM pouches, several modelling techniques that can reduce 3D heat transfer characteristics to 1D are explored in this research. A parallel path heat transfer modelling approach is found to give the closest agreement with the experimental data for the pouched PCMs in building envelope applications.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

ECP ST Capability Assessment Report (CAR) for VTK-m (FY20)

The ECP/VTK-m project is providing the core capabilities to perform scientific visualization on Exascale architectures. The ECP/VTK-m project fills the critical feature gap of performing visualization and analysis on processors like graphics-based processors. The results of this project will be delivered in tools like ParaView, Vislt, and Ascent as well as in stand-alone form. Moreover, these projects are depending on this ECP effort to be able to make effective use of ECP architectures. One of the biggest recent changes in high-performance computing is the increasing use of accelerators. Accelerators contain processing cores that independently are inferior to a core in a typical CPU, but these cores are replicated and grouped such that their aggregate execution provides a very high computation rate at a much lower power. Current and future CPU processors also require much more explicit parallelism. Each successive version of the hardware packs more cores into each processor, and technologies like hyper threading and vector operations require even more parallel processing to leverage each core's full potential. VTK-m is a toolkit of scientific visualization algorithms for emerging processor architectures. VTK-m supports the fine-grained concurrency for data analysis and visualization algorithms required to drive extreme scale computing by providing abstract models for data and execution that can be applied to a variety of algorithms across many different processor architectures. The ECP/VTK-m project is building up the VTK-m codebase with the necessary visualization algorithm implementations that run across the varied hardware platforms to be leveraged at the Exascale. We will be working with other ECP projects, such as ALPINE, to integrate the new VTK-m code into production software to enable visualization on our HPC systems.

97 MATHEMATICS AND COMPUTING↗

A GPU‐Accelerated Generative Adversarial Model for Causal Inference

We develop a GPU-accelerated machine learning generative adversarial model designed to facilitate causal inferences from observational data. Our model's theoretical framework is conceptualized in a manner that is amenable to being operable and scalable for high-performance computing platforms. We leverage GPU acceleration to develop a parallel evolutionary algorithm to achieve large-scale parallel computation of the model within a now widely accessible computing platform. This capability both enhances computational speedup and efficiency and also extends the use of the model to a broader range of substantive research domains while maintaining the underlying theoretical properties of the model.

GPU↗

cuAlign: Scalable Network Alignment on GPU Accelerators

Given two graphs, the objective of network alignment is to find the best one-to-one mapping of vertices in one graph (??) to vertices in the other (??), such that the number of overlaps is maximized. We say that edges(??, ??) ???and(??', ??') ??? are overlapped if ?? is mapped to ??' and ?? is mapped to??'. Network alignment is an important optimization problem with several applications in bioinformatics, computer vision and ontology matching. Since it is an NP-hard problem, efficient heuristics and scalable implementations are necessary. In this work, we introduce a new framework that combines the concepts of intra-network proximity using vertex embedding,Belief Propagation (BP) and approximate weighted matching, and provides qualitative improvements up to22%over state-of-the-art approaches. We also provide scalable implementations on GPU accelerators, demonstrating up to19×speedup for Belief Propagation and 3× speedup for approximate weighted matching relative to previous multithreaded implementation. A combination of combinatorial and algebraic kernels within the network alignment algorithm poses significant hurdles for parallelization. Load imbalance and irregular DRAM traffic limit achievable performance on GPUs. Our novel approach identifies and exploits unique structural proper-ties of the BP-based algorithm and employs code fusion to reduce data movement between different steps of the algorithm. Using a diverse set of inputs, we demonstrate qualitative improvements of our algorithms, and performance gains of our GPU-accelerated implementation. We believe that our work will enable algorithmic improvements and practical applications of network alignment.

Xiang, Lizhi↗

Machine Committee Framework for Power Grid Disturbances Analysis Using Synchrophasors Data

Events detection is a key challenge in power grid frequency disturbances analysis. Accurate detection of events is crucial for situational awareness of the power system. In this paper, we study the problem of events detection in power grid frequency disturbance analysis using synchrophasors data streams. Current events detection approaches for power grid rely on individual detection algorithm. This study integrates some of the existing detection algorithms using the concept of machine committee to develop improved detection approaches for grid disturbance analysis. Specifically, we propose two algorithms—an Event Detection Machine Committee (EDMC) algorithm and a Change-Point Detection Machine Committee (CPDMC) algorithm. Both algorithms use parallel architecture to fuse detection knowledge of its individual methods to arrive at an overall output. The EDMC algorithm combines five individual event detection methods, while the CPDMC algorithm combines two change-point detection methods. Each method performs the detection task separately. The overall output of each algorithm is then computed using a voting strategy. The proposed algorithms are evaluated using three case studies of actual power grid disturbances. Compared with the individual results of the various detection methods, we found that the EDMC algorithm is a better fit for analyzing synchrophasors data; it improves the detection accuracy; and it is suitable for practical scenarios.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Computational Strategies for Scalable Genomics Analysis

The revolution in next-generation DNA sequencing technologies is leading to explosive data growth in genomics, posing a significant challenge to the computing infrastructure and software algorithms for genomics analysis. Various big data technologies have been explored to scale up/out current bioinformatics solutions to mine the big genomics data. In this review, we survey some of these exciting developments in the applications of parallel distributed computing and special hardware to genomics. We comment on the pros and cons of each strategy in the context of ease of development, robustness, scalability, and efficiency. Although this review is written for an audience from the genomics and bioinformatics fields, it may also be informative for the audience of computer science with interests in genomics applications.

59 BASIC BIOLOGICAL SCIENCES↗

Fast and Accurate Intersections on a Sphere

We introduce a fast, high-precision algorithm for calculating intersections between great circle arcs and lines of constant latitude on the unit sphere. We first propose a simplified intersection point formula with improved speed and numerical robustness over the ones traditionally implemented in geoscience software. We then show how algorithms based on the concept of error-free transformations (EFT) can be applied to evaluate this formula within a relative error bound that is on the order of machine precision. Here, we demonstrate that, with a vectorized and parallelized implementation, this enhanced accuracy is achieved with no compute time overhead compared to a direct calculation in hardware floating point, making our algorithm suitable for performance-sensitive applications like regridding of high-resolution climate data. In contrast, evaluating our formula using high-precision data types like quadruple precision and arbitrary precision, or using the robust intersection computation routines from the Computational Geometry Algorithms Library, leads to significant computational overhead, especially since these alternatives inhibit vectorization. More generally, our work demonstrates how EFT techniques can be combined and extended to implement nontrivial geometric calculations with high accuracy and speed.

Environmental sciences↗

Avoiding Communication in Primal and Dual Block Coordinate Descent Methods

Primal and dual block coordinate descent methods are iterative methods for solving regularized and unregularized optimization problems. Distributed-memory parallel implementations of these methods have become popular in analyzing large machine learning datasets. However, existing implementations communicate at every iteration, which, on modern data center and supercomputing architectures, often dominates the cost of floating-point computation. Recent results on communication-avoiding Krylov subspace methods suggest that large speedups are possible by re-organizing iterative algorithms to avoid communication. We show how applying similar algorithmic transformations can lead to primal and dual block coordinate descent methods that only communicate every $s$ iterations---where $s$ is a tuning parameter---instead of every iteration for the regularized least-squares problem. We show that the communication-avoiding variants reduce the number of synchronizations by a factor of $s$ on distributed-memory parallel machines without altering the convergence rate and attain strong scaling speedups of up to $6.1\times$ over the “standard algorithm" on a Cray XC30 supercomputer.

97 MATHEMATICS AND COMPUTING↗

Efficient First-Order Algorithms for Large-Scale, Non-Smooth Maximum Entropy Models with Application to Wildfire Science

Maximum entropy (MaxEnt) models are a class of statistical models that use the maximum entropy principle to estimate probability distributions from data. Due to the size of modern data sets, MaxEnt models need efficient optimization algorithms to scale well for big data applications. State-of-the-art algorithms for MaxEnt models, however, were not originally designed to handle big data sets; these algorithms either rely on technical devices that may yield unreliable numerical results, scale poorly, or require smoothness assumptions that many practical MaxEnt models lack. In this paper, we present novel optimization algorithms that overcome the shortcomings of state-of-the-art algorithms for training large-scale, non-smooth MaxEnt models. Our proposed first-order algorithms leverage the Kullback–Leibler divergence to train large-scale and non-smooth MaxEnt models efficiently. For MaxEnt models with discrete probability distribution of n elements built from samples, each containing m features, the stepsize parameter estimation and iterations in our algorithms scale on the order of O(mn) operations and can be trivially parallelized. Moreover, the strong ℓ1 convexity of the Kullback–Leibler divergence allows for larger stepsize parameters, thereby speeding up the convergence rate of our algorithms. To illustrate the efficiency of our novel algorithms, we consider the problem of estimating probabilities of fire occurrences as a function of ecological features in the Western US MTBS-Interagency wildfire data set. Our numerical results show that our algorithms outperform the state of the art by one order of magnitude and yield results that agree with physical models of wildfire occurrence and previous statistical analyses of wildfire drivers.

Physics↗

Two-dimensional materials for bio-realistic neuronal computing networks

Two-dimensional (2D) van der Waals materials have found broad utility in a diverse range of applications including electronics, optoelectronics, renewable energy, and quantum information technologies. Meanwhile, exponentially growing digital data coupled with the ubiquity of artificial intelligence algorithms have generated significant interest in edge neuromorphic computing as an alternative to centralized cloud computing. The drive to incorporate neuroscience principles into computing hardware is motivated by the low power consumption, parallel processing, and reconfigurability of the human brain. The diverse library of 2D materials with atomic-level thicknesses, exceptional electrostatic tunability, and integration versatility is particularly well-suited for realizing bio-realistic synaptic and neuronal functionality. Here, we summarize past and present work in this field and outline the frontier challenges that have not yet been overcome. Here we also delineate potential solutions and suggest that the neuroscience principles of criticality and synchrony have the potential to inspire breakthrough applications of 2D materials in neuronal computing networks.

36 MATERIALS SCIENCE↗

Novel strategies for modal-based structural material identification

Here, we present modal-based methods for model calibration in structural dynamics, and address several key challenges in the solution of gradient-based optimization problems with eigenvalues and eigenvectors, including the solution of singular Helmholtz problems encountered in sensitivity calculations, non-differentiable objective functions caused by mode swapping during optimization, and cases with repeated eigenvalues. Unlike previous literature that relied on direct solution of the eigenvector adjoint equations, we present a parallel iterative domain decomposition strategy (Adjoint Computation via Modal Superposition with Truncation Augmentation) for the solution of the singular Helmholtz problems. For problems with repeated eigenvalues we present a novel Mode Separation via Projection algorithm, and in order to address mode swapping between inverse iterations we present a novel Injective mode ordering metric. We present the implementation of these methods in a massively parallel finite element framework with the ability to use measured modal data to extract unknown structural model parameters from large complex problems. A series of increasingly complex numerical examples are presented that demonstrate the implementation and performance of the methods in a massively parallel finite element framework [7], [5], using gradient-based optimization techniques in the Rapid Optimization Library (ROL) [21].

36 MATERIALS SCIENCE↗

Scalable Deep Learning via I/O Analysis and Optimization

Scalable deep neural network training has been gaining prominence because of the increasing importance of deep learning in a multitude of scientific and commercial domains. Consequently, a number of researchers have investigated techniques to optimize deep learning systems. Much of the prior work has focused on runtime and algorithmic enhancements to optimize the computation and communication. Despite these enhancements, however, deep learning systems still suffer from scalability limitations, particularly with respect to data I/O. This situation is especially true for training models where the computation can be effectively parallelized, leaving I/O as the major bottleneck. In fact, our analysis shows that I/O can take up to 90% of the total training time. Thus, in this article, we first analyze LMDB, the most widely used I/O subsystem of deep learning frameworks, to understand the causes of this I/O inefficiency. Based on our analysis, we propose LMDBIO—an optimized I/O plugin for scalable deep learning. LMDBIO includes six novel optimizations that together address the various shortcomings in existing I/O for deep learning. Lastly, our experimental results show that LMDBIO significantly outperforms LMDB in all cases and improves overall application performance by up to 65-fold on a 9,216-core system.

97 MATHEMATICS AND COMPUTING↗

Viskores: Integrating Parallel Scientific Visualization Research into Applications

Viskores is a scientific visualization library that is the primary deployment of such algorithms to the parallel accelerated processors of modern DOE supercomputers. In this paper, we review the capabilities provided by Viskores and how these capabilities are leveraged by other software in the high-performance computing ecosystem. We discuss the Viskores data representation and pay particular attention to array management. Through this array management we describe how data is adapted between Viskores and other software along with strategies for converting dynamic, polymorphic objects to static representations better suited to GPU processing. We conclude with several examples of Viskores integrating with high-performance software that is used in production today.

Moreland, Ken [ORNL] (ORCID:0000000270513288)↗

Distributed fiber sensing systems for 3D combustion temperature field monitoring in coal-fired boilers using optically generated acoustic waves (Final Report)

In this project, we have developed and tested three kinds of fiber optic sensing systems for real time monitoring of temperature variations within an industrial scale boiler furnace. The fiber optic sensing systems target spatial and temporal distributions of high temperature profiles in a boiler furnace in fossil power plants. The reconstructed temperature profile will provide critical input for the control mechanisms to optimize the combustion process. This temperature profile will address the essential problem for fossil power plants in achieving higher efficiency and fewer pollutant emissions. Acoustic pyrometer systems have been used to reconstruct temperature field of power plant boilers based on measuring TOF (times-of-flight) of sound waves along some straight paths in a 2D cross-section of the boiler. In this project, optically generated acoustic signals from a fiber optic sensing system have replaced the acoustic signals generated from an electrical transducer. A 3D reconstruction algorithm replaced the previous 2D model. In this project, three kinds of fiber optic sensing systems have been developed and tested. They are fiber optic sensing system I, fiber optic sensing system II (Distributed Sensing System I) and fiber optic sensing system III (Distributed Sensing System II). For fiber optic sensing system I, the fiber optic ultrasound generator acts as a signal generator. A microphone, hydrophone or other electronic devices serve as a signal receiver. In this system, there are one generator and one receiver. Distance test, water temperature test, air temperature test, air temperature reconstruction, and GE ISBF pilot test were performed by Fiber optic sensing system I. The fiber optic sensing system I successfully detected temperature in all these tests. We got 2D temperature reconstruction results by using the fiber optic sensing system I and it matched the reference data. The fiber optic sensing system I successfully survived in GE ISBF boiler environment (480 °F). For fiber optic sensing system II (Distributed Sensing System I), it is an all optical ultrasound system. The fiber optic ultrasound generator acts as a signal generator. Fiber Bragg Grating (FBG) and Fabry-Perot (FP) sensor act as a signal receiver. In this system, there is one generator and one receiver. Aluminum plate temperature test, furnace high temperature test, and GE ISBF pilot test were performed by the fiber optic sensing system II. Fiber optic sensing system II successfully detected the temperature in all these tests. The fiber optic sensing system II successfully survived at up to 700 °C furnace environment and 320 °C GE ISBF boiler environment. For fiber optic sensing system III (Distributed Sensing System II), it is also an all optical ultrasound system. The fiber optic ultrasound generator acts as a signal generator. Multiple FP fiber sensors act as signal receivers. In this system, there is one generator and three receivers. Three GE ISBF pilot tests were performed by fiber optic sensing system III. The fiber optic sensing system III survived in the cold flow tests in GE’s ISBF pilot test facility. However, we didn’t get high temperature data by using this system since the nanosecond laser issues. During the period of the project, test trials, data simulation and algorithm optimization was performed successfully. For real time temperature field construction, the sampling rate must be fast enough to capture the field variations. The technology of Code-division multiple access (CDMA) is well studied which could allow parallel multiplexing, even if signals overlap in time or frequencies. Moreover, it has been known that extending the length of signal significantly improves SNR. For acoustic signals, these multiplexing techniques have also been widely used, mainly for sonar and acoustic communications. The CDMA modulation technique has been proposed and studied to guarantee high network throughput, low channel access delay and low energy consumption. We have studied the temperature field reconstruction using Gaussian Radial Basis Functions (GRBF)-based approximation approach. Reconstruction of 3D temperature field using Neural Networks with measured TOF and known propagation paths is feasible. 2D and 3D temperature field reconstruction simulation results are achieved. The milestone status is shown in Table 1. We finished milestone 1-8 and milestone 10. For milestone 9, we did three pilot tests by using the fiber optic sensing system III (Distributed Sensing System II) at GE Power. However, due to the failure of the ns laser, we did not get the temperature results. We conducted some additional tasks that were not originally proposed: 1) We fabricated a fiber optic sensing system I and did a pilot test based on this system. 2) In the proposal, we proposed two pilot tests at GE Power. In reality, we finished at least seven pilot tests at GE Power. GE Power has made a lot of efforts for supporting the pilot tests. 3) We got a simulation results based on CDMA. In summary, most of the tasks have been accomplished. The outcome of this project removed a few barriers that hinder the achievement of the final product of the distributed sensing systems. With the successful accomplishment of this project, a prototype of the fiber optic sensing system can be fabricated to attract more interests from companies and other funding agencies.

47 OTHER INSTRUMENTATION↗