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At least 829 records · Page 46

Scalable deep learning for watershed model calibration

Watershed models such as the Soil and Water Assessment Tool (SWAT) consist of high-dimensional physical and empirical parameters. These parameters often need to be estimated/calibrated through inverse modeling to produce reliable predictions on hydrological fluxes and states. Existing parameter estimation methods can be time consuming, inefficient, and computationally expensive for high-dimensional problems. In this paper, we present an accurate and robust method to calibrate the SWAT model (i.e., 20 parameters) using scalable deep learning (DL). We developed inverse models based on convolutional neural networks (CNN) to assimilate observed streamflow data and estimate the SWAT model parameters. Scalable hyperparameter tuning is performed using high-performance computing resources to identify the top 50 optimal neural network architectures. We used ensemble SWAT simulations to train, validate, and test the CNN models. We estimated the parameters of the SWAT model using observed streamflow data and assessed the impact of measurement errors on SWAT model calibration. We tested and validated the proposed scalable DL methodology on the American River Watershed, located in the Pacific Northwest-based Yakima River basin. Our results show that the CNN-based calibration is better than two popular parameter estimation methods (i.e., the generalized likelihood uncertainty estimation [GLUE] and the dynamically dimensioned search [DDS], which is a global optimization algorithm). For the set of parameters that are sensitive to the observations, our proposed method yields narrower ranges than the GLUE method but broader ranges than values produced using the DDS method within the sampling range even under high relative observational errors. The SWAT model calibration performance using the CNNs, GLUE, and DDS methods are compared using R 2 and a set of efficiency metrics, including Nash-Sutcliffe, logarithmic Nash-Sutcliffe, Kling-Gupta, modified Kling-Gupta, and non-parametric Kling-Gupta scores, computed on the observed and simulated watershed responses. The best CNN-based calibrated set has scores of 0.71, 0.75, 0.85, 0.85, 0.86, and 0.91. The best DDS-based calibrated set has scores of 0.62, 0.69, 0.8, 0.77, 0.79, and 0.82. The best GLUE-based calibrated set has scores of 0.56, 0.58, 0.71, 0.7, 0.71, and 0.8. The scores above show that the CNN-based calibration leads to more accurate low and high streamflow predictions than the GLUE and DDS sets. Our research demonstrates that the proposed method has high potential to improve our current practice in calibrating large-scale integrated hydrologic models.

54 ENVIRONMENTAL SCIENCES↗

Dynamic Load Balancing for Adaptive Computations on Distributed-Memory Machines

Dynamic load balancing is central to adaptive mesh-based computations on large-scale parallel computers. The principal investigator has investigated various issues on the dynamic load balancing problem under NASA JOVE and JAG rants. The major accomplishments of the project are two graph partitioning algorithms and a load balancing framework. The S-HARP dynamic graph partitioner is known to be the fastest among the known dynamic graph partitioners to date. It can partition a graph of over 100,000 vertices in 0.25 seconds on a 64- processor Cray T3E distributed-memory multiprocessor while maintaining the scalability of over 16-fold speedup. Other known and widely used dynamic graph partitioners take over a second or two while giving low scalability of a few fold speedup on 64 processors. These results have been published in journals and peer-reviewed flagship conferences.

Source record↗

MetaStrider: Architectures for Scalable Memory-centric Reduction of Sparse Data Streams

Reduction is an operation performed on the values of two or more key-value pairs that share the same key. Reduction of sparse data streams finds application in a wide variety of domains such as data and graph analytics, cybersecurity, machine learning, and HPC applications. However, these applications exhibit low locality of reference, rendering traditional architectures and data representations inefficient. This article presents MetaStrider, a significant algorithmic and architectural enhancement to the state-of-the-art, SuperStrider. Furthermore, these enhancements enable a variety of parallel, memory-centric architectures that we propose, resulting in demonstrated performance that scales near-linearly with available memory-level parallelism.

97 MATHEMATICS AND COMPUTING↗

Modeling Mesoscale Processes of Scalable Synthesis Final Scientific/Technical Report

This is the final scientific and technical report for this award. Molecular dynamics (MD) is a powerful tool to study biomolecules at the nanoscale. One of its main limitations however is that such simulations typically require a timestep of 1 femtosecond while reactions and conformational changes typically happen on the time scale of 1 microsecond or more. This discrepancy severely restricts the impact of this method. We have developed a series of algorithms to mitigate this problem and allow predicting long-time scale events using much shorter simulations. The method is based on the concurrent adaptive sampling method. It consists in using probabilistic weights for trajectories and biasing the sampling such that rare but important trajectories, e.g., those that go over energy barriers and lead to relevant conformational changes in the molecule, are observed with much higher frequency that in a standard MD simulation. We will demonstrate below that this approach has been very successful. In collaboration with Jay Grate at PNNL we have applied this novel method to the study the triazine polymers, which can be con gured using different types of side chains in order to adopt different 3-dimensional structures. We have found novel stable con- formations and have analyzed the impact of side chain modifcations on the native folded shape of the polymer. Direct MD simulations would have been untractable for this problem. The method of replica exchange was also used successfully to calculate free energy profiles, in particular for cis-trans torsional angle changes with high energy barriers. Studying molecules at the atomistic scale is essential to design new molecules in chemical engineering, such as the triazine polymers developed by Grate, in material science to study the strength of metals for examples (e.g., dislocation dynamics), or in biochemistry to understand how proteins fold and how they interact with ligands (a key step in designing drugs). Although new hardware makes these simulations increasingly faster (e.g., GPU, Anton from DE Shaw Research), new algorithms are key to making these methods more tractable and increase their impact. At this point, because of limitations in modeling, one of the main techniques for advancing science remains to a large extent numerous and costly experiments. For exam- ple, when designing drug, where multiple variants must be screened, the ability to run tests on a computer rather than experimentally testing with high throughput methods thousands of compounds would represent a signi cant advance with broad benefits for the public at large.

36 MATERIALS SCIENCE↗

ExaTN: Scalable GPU-Accelerated High-Performance Processing of General Tensor Networks at Exascale

We present ExaTN (Exascale Tensor Networks), a scalable GPU-accelerated C++ library which can express and process tensor networks on shared- as well as distributed-memory high-performance computing platforms, including those equipped with GPU accelerators. Specifically, ExaTN provides the ability to build, transform, and numerically evaluate tensor networks with arbitrary graph structures and complexity. It also provides algorithmic primitives for the optimization of tensor factors inside a given tensor network in order to find an extremum of a chosen tensor network functional, which is one of the key numerical procedures in quantum many-body theory and quantum-inspired machine learning. Numerical primitives exposed by ExaTN provide the foundation for composing rather complex tensor network algorithms. We enumerate multiple application domains which can benefit from the capabilities of our library, including condensed matter physics, quantum chemistry, quantum circuit simulations, as well as quantum and classical machine learning, for some of which we provide preliminary demonstrations and performance benchmarks just to emphasize a broad utility of our library.

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↗

State Dependent Optimization with Quantum Circuit Cutting

Quantum circuits can be reduced through optimization to better fit the constraints of quantum hardware. One such method, initial-state dependent optimization (ISDO), reduces gate count by leveraging knowledge of the input quantum states. Surprisingly, we found that ISDO is broadly applicable to the downstream circuits produced by circuit cutting. Circuit cutting also requires measuring upstream qubits and has some flexibility of selection observables to do reconstruction. Therefore, we propose a state-dependent optimization (SDO) framework that incorporates ISDO, our newly proposed measure-state dependent optimization (MSDO), and a biased observable selection strategy. Building on the strengths of the SDO framework and recognizing the scalability challenges of circuit cutting, we propose nonseparate circuit cutting-a more flexible approach that enables optimizing gates without fully separating them. We validate our methods on noisy simulations of QAOA, QFT, and BV circuits. Results show that our approach consistently mitigates noise and improves overall circuit performance, demonstrating its promise for enhancing quantum algorithm execution on near-term hardware.

Li, Xinpeng↗

Learning Sequential Distribution System Restoration via Graph-Reinforcement Learning

We report a distribution service restoration algorithm as a fundamental resilient paradigm for system operators provides an optimally coordinated, resilient solution to enhance the restoration performance. The restoration problem is formulated to coordinate distribution generators and controllable switches optimally. A model-based control scheme is usually designed to solve this problem, relying on a precise model and resulting in low scalability. To tackle these limitations, this work proposes a graph-reinforcement learning framework for the restoration problem. We link the power system topology with a graph convolutional network, which captures the complex mechanism of network restoration in power networks and understands the mutual interactions among controllable devices. Latent features over graphical power networks produced by graph convolutional layers are exploited to learn the control policy for network restoration using deep reinforcement learning. The solution scalability is guaranteed by modeling distributed generators as agents in a multi-agent environment and a proper pre-training paradigm. Comparative studies on IEEE 123-node and 8500-node test systems demonstrate the performance of the proposed solution.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Trigger-DAQ and Slow Controls Systems in the Mu2e Experiment

The muon campus program at Fermilab includes the Mu2e experiment that will search for a charged-lepton flavor violating processes where a negative muon converts into an electron in the field of an aluminum nucleus, improving by four orders of magnitude the search sensitivity reached so far. Mu2e's Trigger and Data Acquisition System (TDAQ) uses otsdaq as its solution. Developed at Fermilab, otsdaq uses the artdaq DAQ framework and art analysis framework, under the-hood, for event transfer, filtering, and processing. otsdaq is an online DAQ software suite with a focus on flexibility and scalability, while providing a multi-user, web-based, interface accessible through the Chrome or Firefox web browser. The detector Read Out Controller (ROC), from the tracker and calorimeter, stream out zero-suppressed data continuously to the Data Transfer Controller (DTC). Data is then read over the PCIe bus to a software filter algorithm that selects events which are finally combined with the data flux that comes froma Cosmic Ray Ve to System (CRV). A Detector Control System (DCS) for monitoring, controlling, alarming, and archiving has been developed using the Experimental Physics and Industrial Control System (EPICS) Open Source Platform. The DCS System has also been itegrated into otsdaq. The installation of the TDAQ and the DCS systems in the Mu2e building is planned for 2021-2022, and a prototype has been built at Fermilab's Feynman Computing Center. We report here on the developments and achievements of the integration of Mu2e's DCS system into the online otsdaq software.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Scalable Static and Dynamic Community Detection Using Grappolo

Graph clustering, popularly known as community detection, is a fundamental kernel for several applications of relevance to the Defense Advanced Research Projects Agency’s (DARPA) Hierarchical Identify Verify Exploit (HIVE) Pro- gram. Clusters or communities represent natural divisions within a network that are densely connected within a cluster and sparsely connected to the rest of the network. The need to compute clustering on large scale data necessitates the development of efficient algorithms that can exploit modern architectures that are fundamentally parallel in nature. How- ever, due to their irregular and inherently sequential nature, many of the current algorithms for community detection are challenging to parallelize. In response to the HIVE Graph Challenge, we present several parallelization heuristics for fast community detection using the Louvain method as the serial template. We implement all the heuristics in a software library called Grappolo. Using the inputs from the HIVE Challenge, we demonstrate superior performance and high quality solutions based on four parallelization heuristics. We use Grappolo on static graphs as the first step towards community detection on streaming graphs.

Community Detection↗

MPI + OpenACC: Accelerating radiation transport mini-application, minisweep, on heterogeneous systems

According to the article, architectures are rapidly evolving, and exascale machines are expected to offer billion-way concurrency. We need to rethink algorithms, languages and programming models among other components in order to migrate large scale applications and explore parallelism on these machines. Although directive-based programming models allow programmers to worry less about programming and more about science, expressing complex parallel patterns in these models can be a daunting task especially when the goal is to match the performance that the hardware platforms can offer. One such pattern is wavefront. This paper extensively studies a wavefront-based miniapplication for Denovo, a production code for nuclear reactor modeling. We parallelize the Koch–Baker–Alcouffe (KBA) parallel-wavefront sweep algorithm in the main kernel of Minisweep (the miniapplication) using CUDA 9.0, OpenMP 4.0 (SIMD) and OpenACC 2.6. Our OpenACC implementation running on NVIDIA’s next-generation Volta GPU boasts an 85.06x speedup over serial code, which is larger than CUDA’s 83.72x speedup over the same serial implementation. We also explore the scalability of our solution using MPI to decompose our simulation domain, allowing us to run on many nodes and accelerators present in state-of-the-art HPC systems. Our parallelization effort across platforms also motivated us to define an abstract parallelism model that is architecture independent, with a goal of creating software abstractions that can be used by applications employing the wavefront sweep motif.

Computer Science↗

Prototype Data Acquisition and Slow Control Systems for the Mu2e Experiment

The Mu2e experiment at the Fermilab Muon Campus will search for the coherent neutrinoless conversion of a muon into an electron in the field of an aluminum nucleus with a sensitivity improvement by a factor of 10 000 over existing limits. Such a charged lepton flavor-violating reaction probes new physics at a scale unavailable with direct searches at either present or planned high-energy colliders. The Mu2e Trigger and Data Acquisition (TDAQ) system exploits otsdaq as its online Data Acquisition System (DAQ) solution. Furthermore, developed at Fermilab, otsdaq integrates both the artdaq DAQ and the art analysis frameworks for event transfer, filtering, and processing. otsdaq is an online DAQ software suite with a focus on flexibility and scalability and provides a multi-user, web-based, interface accessible through a web browser. The read out controllers (ROCs) stream out zero-suppressed data continuously from the detector subsystems to the data transfer controllers (DTCs). The data stream is then read over the peripheral component interconnect express (PCIe) bus to a software filter algorithm that selects events which are combined with the data flux coming from a cosmic-ray veto (CRV) system. The detector control system (DCS) has been developed using the experimental physics and industrial control system (EPICS) open source platform for monitoring, controlling, alarming, and archiving. The DCS has been integrated into otsdaq. A prototype of the TDAQ system and the DCS has been built at Fermilab's Feynman Computing Center. In this article, we report on the progress of the integration of this prototype in the online otsdaq software.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Scalable Computation of Topological Abstractions for Scalar Data

Topological data analysis has become an important tool for large scale scalar data analysis and visualization, efficiently extracting the inherent structure and features of interest of the data. However, with growing dataset sizes and complexity, it is increasingly becoming infeasible to compute topological abstractions of interest in serial and on single machines. This paper presents the state of the art in the scalable computation of topological abstractions on scalar data, in shared memory parallel on single machines, and in distributed memory parallel on multiple machines. We highlight results for set‐based, graph‐based and complex‐based abstractions and organize the state of the art based on this taxonomy. The paper identifies parallelization and distribution techniques common in topological algorithms and highlights further areas of interest with underdeveloped efforts.

97 MATHEMATICS AND COMPUTING↗

Exploration of structure-activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment linking and active learning

The macrodomain of severe acute respiratory syndrome coronavirus 2 nonstructural protein 3 is required for viral pathogenesis and is an emerging antiviral target. We previously performed an x-ray crystallography–based fragment screen and found submicromolar inhibitors by fragment linking. However, these compounds had poor membrane permeability and liabilities that complicated optimization. Here, we developed a shape-based virtual screening pipeline—FrankenROCS. We screened the Enamine high-throughput collection of 2.1 million compounds, selecting 39 compounds for testing, with the most potent binding with a 130 μM median inhibitory concentration (IC 50 ). We then paired FrankenROCS with an active learning algorithm (Thompson sampling) to efficiently search the Enamine REAL database of 22 billion molecules, testing 32 compounds with the most potent binding with a 220 μM IC 50 . Further optimization led to analogs with IC 50 values better than 10 μM. This lead series has improved membrane permeability and is poised for optimization. FrankenROCS is a scalable method for fragment linking to exploit synthesis-on-demand libraries.

Science & Technology - Other Topics↗

Single-shot Quantum Signal Processing Interferometry

Quantum systems of infinite dimension, such as bosonic oscillators, provide vast resources for quantum sensing. Yet, a general theory on how to manipulate such bosonic modes for sensing beyond parameter estimation is unknown. We present a general algorithmic framework, quantum signal processing interferometry (QSPI), for quantum sensing at the fundamental limits of quantum mechanics by generalizing Ramsey-type interferometry. Our QSPI sensing protocol relies on performing nonlinear polynomial transformations on the oscillator's quadrature operators by generalizing quantum signal processing (QSP) from qubits to hybrid qubit-oscillator systems. We use our QSPI sensing framework to make efficient binary decisions on a displacement channel in the single-shot limit. Theoretical analysis suggests the sensing accuracy, given a single-shot qubit measurement, scales inversely with the sensing time or circuit depth of the algorithm. We further concatenate a series of such binary decisions to perform parameter estimation in a bit-by-bit fashion. Numerical simulations are performed to support these statements. Our QSPI protocol offers a unified framework for quantum sensing using continuous-variable bosonic systems beyond parameter estimation and establishes a promising avenue toward efficient and scalable quantum control and quantum sensing schemes beyond the NISQ era.

Physics↗

Scalable, Dual-Mode Occupancy Sensing for Commercial Venues

The ability to establish accurate occupancy is a key enabler for improved energy efficiency in human-occupied indoor spaces. The accurate counts can be used to adjust, in real-time, air exchange, heating, and cooling, to closely match the environmental needs of the occupants rather than to use a single setting based on maximum room occupancy. This project focuses on the use of overhead fisheye cameras and artificial intelligence (AI) algorithms as the technology to realize accurate people counting in large commercial spaces. We developed Computational Occupancy Sensing SYstem ("COSSY''), which supports large-scale deployment (thousands of square feet) and straightforward installation (using conventional power over ethernet), while providing high accuracy and low cost. COSSY has been validated at Boston University and by a third party, demonstrating people-counting accuracy of at least 89.5% in large spaces (2,000 sqft). A cost/benefit analysis performed for Boston commercial market indicates that a full payback of COSSY deployment costs due to energy savings would occur within 3-6 months from installation. Applications of COSSY reach far beyond saving energy. The precise people counting in real time could also be useful for emergency response (e.g., fire), in spatial analytics (e.g., office space management) and in some health applications (e.g., social distance assessment during pandemics).

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Scalable molecular dynamics on CPU and GPU architectures with NAMD

NAMD is a molecular dynamics program designed for high-performance simulations of very large biological objects on CPU- and GPU-based architectures. NAMD offers scalable performance on petascale parallel supercomputers consisting of hundreds of thousands of cores, as well as on inexpensive commodity clusters commonly found in academic environments. It is written in C++ and leans on Charm++ parallel objects for optimal performance on low-latency architectures. NAMD is a versatile, multipurpose code that gathers state-of-the-art algorithms to carry out simulations in apt thermodynamic ensembles, using the widely popular CHARMM, AMBER, OPLS, and GROMOS biomolecular force fields. Here, we review the main features of NAMD that allow both equilibrium and enhanced-sampling molecular dynamics simulations with numerical efficiency. We describe the underlying concepts utilized by NAMD and their implementation, most notably for handling long-range electrostatics; controlling the temperature, pressure, and pH; applying external potentials on tailored grids; leveraging massively parallel resources in multiple-copy simulations; and hybrid quantum-mechanical/molecular-mechanical descriptions. We detail the variety of options offered by NAMD for enhanced-sampling simulations aimed at determining free-energy differences of either alchemical or geometrical transformations and outline their applicability to specific problems. Last, we discuss the roadmap for the development of NAMD and our current efforts toward achieving optimal performance on GPU-based architectures, for pushing back the limitations that have prevented biologically realistic billion-atom objects to be fruitfully simulated, and for making large-scale simulations less expensive and easier to set up, run, and analyze. NAMD is distributed free of charge with its source code at www.ks.uiuc.edu.

high-performance computing↗

Flexible machine-learning interatomic potential for simulating structural disordering behavior of Li 7 La 3 Zr 2 O 12 solid electrolytes

Batteries based on solid-state electrolytes, including Li 7 La 3 Zr 2 O 12 (LLZO), promise improved safety and increased energy density; however, atomic disorder at grain boundaries and phase boundaries can severely deteriorate their performance. Machine-learning (ML) interatomic potentials offer a uniquely compelling solution for simulating chemical processes, rare events, and phase transitions associated with these complex interfaces by mixing high scalability with quantum-level accuracy, provided that they can be trained to properly address atomic disorder. To this end, we report the construction and validation of an ML potential that is specifically designed to simulate crystalline, disordered, and amorphous LLZO systems across a wide range of conditions. The ML model is based on a neural network algorithm and is trained using ab initio data. Performance tests prove that the developed ML potential can predict accurate structural and vibrational characteristics, elastic properties, and Li diffusivity of LLZO comparable to ab initio simulations. As a demonstration of its applicability to larger systems, we show that the potential can correctly capture grain boundary effects on diffusivity, as well as the thermal transition behavior of LLZO. Here these examples show that the ML potential enables simulations of transitions between well-defined and disordered structures with quantum-level accuracy at speeds thousands of times faster than ab initio methods.

25 ENERGY STORAGE↗