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At least 937 records · Page 52

ADEPT: a domain independent sequence alignment strategy for gpu architectures

Bioinformatic workflows frequently make use of automated genome assembly and protein clustering tools. At the core of most of these tools, a significant portion of execution time is spent in determining optimal local alignment between two sequences. This task is performed with the Smith-Waterman algorithm, which is a dynamic programming based method. With the advent of modern sequencing technologies and increasing size of both genome and protein databases, a need for faster Smith-Waterman implementations has emerged. Multiple SIMD strategies for the Smith-Waterman algorithm are available for CPUs. However, with the move of HPC facilities towards accelerator based architectures, a need for an efficient GPU accelerated strategy has emerged. Existing GPU based strategies have either been optimized for a specific type of characters (Nucleotides or Amino Acids) or for only a handful of application use-cases. In this paper, we present ADEPT, a new sequence alignment strategy for GPU architectures that is domain independent, supporting alignment of sequences from both genomes and proteins. Our proposed strategy uses GPU specific optimizations that do not rely on the nature of sequence. We demonstrate the feasibility of this strategy by implementing the Smith-Waterman algorithm and comparing it to similar CPU strategies as well as the fastest known GPU methods for each domain. ADEPT’s driver enables it to scale across multiple GPUs and allows easy integration into software pipelines which utilize large scale computational systems. We have shown that the ADEPT based Smith-Waterman algorithm demonstrates a peak performance of 360 GCUPS and 497 GCUPs for protein based and DNA based datasets respectively on a single GPU node (8 GPUs) of the Cori Supercomputer. Overall ADEPT shows 10x faster performance in a node-to-node comparison against a corresponding SIMD CPU implementation. ADEPT demonstrates a performance that is either comparable or better than existing GPU strategies. We demonstrated the efficacy of ADEPT in supporting existing bionformatics software pipelines by integrating ADEPT in MetaHipMer a high-performance denovo metagenome assembler and PASTIS a high-performance protein similarity graph construction pipeline. Our results show 10% and 30% boost of performance in MetaHipMer and PASTIS respectively.

59 BASIC BIOLOGICAL SCIENCES↗

In-Situ Resource Utilization Modeling of a Lunar Water Processing System

A key element of achieving a sustained surface presence, such as defined in NASA’s Artemis plan, is In-Situ Resource Utilization (ISRU). ISRU is the practice of using local resources to provide mission consumables that reduce system launch mass requirements, and regenerate resources (chiefly, water and oxygen) for propulsion and life support supporting both Lunar and Martian missions. ISRU systems require multiple complex processes, such as excavation, chemical reactors, and electrolysis subsystems that must operate in harmony to optimize the overall system process from beginning to end. The Mission Analysis and Integration Tool (MAIT) was previously developed with MATLAB in FY22 to connect individual subsystem models into a customized, flexible framework for the purpose of technology downselect, optimization, and end-to-end process planning. Beginning in FY24, MAIT was updated and became the capital program in the Systems Engineering and Integration (SE&I) ISRU Modeling and Analysis (SIMA) project. Prior work was leveraged and evolved using MATLAB/Simulink due to its ability to communicate with a vast number of other programming languages and makes up the backbone of data flow between inputs and outputs to the subsystem models. MAIT initially evaluated a suite of ISRU-related technologies, including the water processing Lunar Auger Dryer for ISRU (LADI) system with integrated upstream excavation and downstream electrolysis subsystems. With individual models consolidated, the MAIT tool generated over 5,000 cases during its first round of parametric sweeps on the water processing architecture at multiple production targets; the system analysis produced valuable insight into the optimal LADI geometry that minimized energy demands, estimated effects to cold trap size and radiator requirements, and calculated the power dynamics of the electrolysis unit and liquid oxygen storage volume. Additional efforts are being made to demonstrate the ability to scale ISRU technologies supporting the Space Technology Mission Directorate’s (STMD) commercialization strategy and increase the MAIT software capability. Work is ongoing to handle a wide array of ISRU system models beyond the Lunar environment, e.g. production of propellant for a Martian lander.

Avery Carlson↗

In-Situ Resource Utilization Modeling of a Lunar Water Processing System

A key element of achieving a sustained surface presence, such as defined in NASA’s Artemis plan, is In-Situ Resource Utilization (ISRU). ISRU is the practice of using local resources to provide mission consumables that reduce system launch mass requirements, and regenerate resources (chiefly, water and oxygen) for propulsion and life support supporting both Lunar and Martian missions. ISRU systems require multiple complex processes, such as excavation, chemical reactors, and electrolysis subsystems that must operate in harmony to optimize the overall system process from beginning to end. The Mission Analysis and Integration Tool (MAIT) was previously developed with MATLAB in FY22 to connect individual subsystem models into a customized, flexible framework for the purpose of technology downselect, optimization, and end-to-end process planning. Beginning in FY24, MAIT was updated and became the capital program in the Systems Engineering and Integration (SE&I) ISRU Modeling and Analysis (SIMA) project. Prior work was leveraged and evolved using MATLAB/Simulink due to its ability to communicate with a vast number of other programming languages and makes up the backbone of data flow between inputs and outputs to the subsystem models. MAIT initially evaluated a suite of ISRU-related technologies, including the water processing Lunar Auger Dryer for ISRU (LADI) system with integrated upstream excavation and downstream electrolysis subsystems. With individual models consolidated, the MAIT tool generated over 5,000 cases during its first round of parametric sweeps on the water processing architecture at multiple production targets; the system analysis produced valuable insight into the optimal LADI geometry that minimized energy demands, estimated effects to cold trap size and radiator requirements, and calculated the power dynamics of the electrolysis unit and liquid oxygen storage volume. Additional efforts are being made to demonstrate the ability to scale ISRU technologies supporting the Space Technology Mission Directorate’s (STMD) commercialization strategy and increase the MAIT software capability. Work is ongoing to handle a wide array of ISRU system models beyond the Lunar environment, e.g. production of propellant for a Martian lander.

Avery Carlson↗

A Near-Term, High-Confidence Heavy Lift Launch Vehicle

The use of well understood, legacy elements of the Space Shuttle system could yield a near-term, high-confidence Heavy Lift Launch Vehicle that offers significant performance, reliability, schedule, risk, cost, and work force transition benefits. A side-mount Shuttle-Derived Vehicle (SDV) concept has been defined that has major improvements over previous Shuttle-C concepts. This SDV is shown to carry crew plus large logistics payloads to the ISS, support an operationally efficient and cost effective program of lunar exploration, and offer the potential to support commercial launch operations. This paper provides the latest data and estimates on the configurations, performance, concept of operations, reliability and safety, development schedule, risks, costs, and work force transition opportunities for this optimized side-mount SDV concept. The results presented in this paper have been based on established models and fully validated analysis tools used by the Space Shuttle Program, and are consistent with similar analysis tools commonly used throughout the aerospace industry. While these results serve as a factual basis for comparisons with other launch system architectures, no such comparisons are presented in this paper. The authors welcome comparisons between this optimized SDV and other Heavy Lift Launch Vehicle concepts.

Rothschild, William J.↗

xesn: Echo state networks powered by Xarray and Dask

Xesn is a Python package that allows scientists to easily design Echo State Networks (ESNs) for forecasting problems. ESNs are a Recurrent Neural Network architecture introduced by Jaeger (2001) that are part of a class of techniques termed Reservoir Computing. One defining characteristic of these techniques is that all internal weights are determined by a handful of global, scalar parameters, thereby avoiding problems during backpropagation and reducing training time significantly. Because this architecture is conceptually simple, many scientists implement ESNs from scratch, leading to questions about computational performance. Xesn offers a straightforward, standard implementation of ESNs that operates efficiently on CPU and GPU hardware. The package leverages optimization tools to automate the parameter selection process, so that scientists can reduce the time finding a good architecture and focus on using ESNs for their domain application. Importantly, the package flexibly handles forecasting tasks for out-of-core, multi-dimensional datasets, eliminating the need to write parallel programming code. Xesn was initially developed to handle the problem of forecasting weather dynamics, and so it integrates naturally with Python packages that have become familiar to weather and climate scientists such as Xarray (Hoyer & Hamman, 2017). However, the software is ultimately general enough to be utilized in other domains where ESNs have been useful, such as in signal processing (Jaeger & Haas, 2004).

97 MATHEMATICS AND COMPUTING↗

Stanford Hardware Development Program

Architectures for high performance, digital signal processing, particularly for high resolution, wide band spectrum analysis were developed. These developments are intended to provide instrumentation for NASA's Search for Extraterrestrial Intelligence (SETI) program. The real time signal processing is both formal and experimental. The efficient organization and optimal scheduling of signal processing algorithms were investigated. The work is complemented by efforts in processor architecture design and implementation. A high resolution, multichannel spectrometer that incorporates special purpose microcoded signal processors is being tested. A general purpose signal processor for the data from the multichannel spectrometer was designed to function as the processing element in a highly concurrent machine. The processor performance required for the spectrometer is in the range of 1000 to 10,000 million instructions per second (MIPS). Multiple node processor configurations, where each node performs at 100 MIPS, are sought. The nodes are microprogrammable and are interconnected through a network with high bandwidth for neighboring nodes, and medium bandwidth for nodes at larger distance. The implementation of both the current mutlichannel spectrometer and the signal processor as Very Large Scale Integration CMOS chip sets was commenced.

Peterson, A.↗

Efficient Quantum Gate Discovery with Optimal Control

Optimal control theory provides a framework for numerical discovery of device controls that implement quantum logic gates, but common objective functions used for optimization often assign arbitrarily high costs to otherwise useful controls. We propose a framework for designing objective functions that permit novel gate designs such as echo pulses or locally-equivalent gates. We use numerical simulations to demonstrate the efficacy of the new objective functions by designing microwave-only pulses that act as entangling gates for superconducting transmon architectures. We observe that the proposed objective functions lead to higher fidelity controls in fewer optimization iterations than obtainable by traditional objective functions.

Kairys, Paul↗

A Scalable Readout for Microwave SQUID Multiplexing of Transition-Edge Sensors

The readout requirements for instruments based on transition-edge sensors (TESs) have dramatically increased over the last decade as demand for systems with larger arrays and faster sensors has grown. Emerging systems are expected to contain many thousands of sensors and/or sensors with time constants as short as 100 ms. These requirements must be satisfied while maintaining low noise, high dynamic range, and low crosstalk. A promising readout candidate for future TES arrays is the microwave SQUID multiplexer, which offers several gigahertz of readout bandwidth per pair of coaxial cables. In microwave SQUID multiplexing, sensor signals are coupled to RF-SQUIDs embedded in superconducting microwave resonators, which are probed via a common microwave feedline and read out using gigahertz signals. This form of SQUID multiplexing moves complexity from the cryogenic stages to room temperature hardware and digital signal processing firmware which must synthesize the microwave tones and process the information contained within them. To demultiplex signals from the microwave SQUID multiplexer, we have implemented an FPGA-based firmware architecture that is flexible enough to read out a variety of differently optimized TESs. A gamma-ray spectrometer targeted at nuclear materials accounting applications, known as SLEDGEHAMMER, is an early adopter of microwave SQUID multiplexing and is driving our current firmware development effort. This instrument utilizes 300 kHz full-width half-maximum resonators with 256 channels in a one gigahertz wide band. We have recently demonstrated undegraded readout of 128 channels using two ROACH2s on a single pair of coaxial cables. This manuscript describes the firmware implementation for the readout electronics of these early array-scale demonstrations.

42 ENGINEERING↗

End-to-end online performance data capture and analysis for scientific workflows

With the increased prevalence of employing workflows for scientific computing and a push towards exascale computing, it has become paramount that we are able to analyze characteristics of scientific applications to better understand their impact on the underlying infrastructure and vice-versa. Such analysis can help drive the design, development, and optimization of these next generation systems and solutions. Here, we present the architecture, integrated with existing well-established and newly developed tools, to collect online performance statistics of workflow executions from various, heterogeneous sources and publish them in a distributed database (Elasticsearch). Using this architecture, we are able to correlate online workflow performance data, with data from the underlying infrastructure, and present them in a useful and intuitive way via an online dashboard. We have validated our approach by executing two classes of real-world workflows, both under normal and anomalous conditions. The first is an I/O-intensive genome analysis workflow; the second, a CPU- and memory-intensive material science workflow. Based on the data collected in Elasticsearch, we are able to demonstrate that we can correctly identify anomalies that we injected. The resulting end-to-end data collection of workflow performance data is an important resource of training data for automated machine learning analysis.

97 MATHEMATICS AND COMPUTING↗

NSFnets (Navier-Stokes flow nets): Physics-informed neural networks for the incompressible Navier-Stokes equations

In the last 50 years there has been a tremendous progress in solving numerically the Navier-Stokes equations using finite differences, finite elements, spectral, and even meshless methods. Yet, in many real cases, we still cannot incorporate seamlessly (multi-fidelity) data into existing algorithms, and for industrial-complexity applications the mesh generation is time consuming and still an art. Moreover, solving ill-posed problems (e.g., lacking boundary conditions) or inverse problems is often prohibitively expensive and requires different formulations and new computer codes. Here, we employ physics-informed neural networks (PINNs), encoding the governing equations directly into the deep neural network via automatic differentiation, to overcome some of the aforementioned limitations for simulating incompressible laminar and turbulent flows. We develop the Navier-Stokes flow nets (NSFnets) by considering two different mathematical formulations of the Navier-Stokes equations: the velocity-pressure (VP) formulation and the vorticity-velocity (VV) formulation. Since this is a new approach, we first select some standard benchmark problems to assess the accuracy, convergence rate, computational cost and flexibility of NSFnets; analytical solutions and direct numerical simulation (DNS) databases provide proper initial and boundary conditions for the NSFnet simulations. The spatial and temporal coordinates are the inputs of the NSFnets, while the instantaneous velocity and pressure fields are the outputs for the VP-NSFnet, and the instantaneous velocity and vorticity fields are the outputs for the VV-NSFnet. This is unsupervised learning and, hence, no labeled data are required beyond boundary and initial conditions and the fluid properties. The residuals of the VP or VV governing equations, together with the initial and boundary conditions, are embedded into the loss function of the NSFnets. No data is provided for the pressure to the VP-NSFnet, which is a hidden state and is obtained via the incompressibility constraint without extra computational cost. Unlike the traditional numerical methods, NSFnets inherit the properties of neural networks (NNs), hence the total error is composed of the approximation, the optimization, and the generalization errors. Here, we empirically attempt to quantify these errors by varying the sampling (“residual”) points, the iterative solvers, and the size of the NN architecture. For the laminar flow solutions, we show that both the VP and the VV formulations are comparable in accuracy but their best performance corresponds to different NN architectures. The initial convergence rate is fast but the error eventually saturates to a plateau due to the dominance of the optimization error. For the turbulent channel flow, we show that NSFnets can sustain turbulence at , but due to expensive training we only consider part of the channel domain and enforce velocity boundary conditions on the subdomain boundaries provided by the DNS data base. We also perform a systematic study on the weights used in the loss function for balancing the data and physics components, and investigate a new way of computing the weights dynamically to accelerate training and enhance accuracy. In the last part, we demonstrate how NSFnets should be used in practice, namely for ill-posed problems with incomplete or noisy boundary conditions as well as for inverse problems. We obtain reasonably accurate solutions for such cases as well without the need to change the NSFnets and at the same computational cost as in the forward well-posed problems. As a result, we also present a simple example of transfer learning that will aid in accelerating the training of NSFnets for different parameter settings.

97 MATHEMATICS AND COMPUTING↗

An End-To-End Earthquake Detection Method for Joint Phase Picking and Association Using Deep Learning

Earthquake monitoring by seismic networks typically involves a workflow consisting of phase detection/picking, association, and location tasks. In recent years, the accuracy of these individual stages has been improved through the use of machine learning techniques. Here, in this study, we introduce a new end-to-end approach that improves overall earthquake detection accuracy by jointly optimizing each stage of the detection pipeline. We propose a neural network architecture for the task of multi-station processing of seismic waveforms recorded over a seismic network. This end-to-end architecture consists of three sub-networks: a backbone network that extracts features from raw waveforms, a phase picking sub-network that picks P- and S-wave arrivals based on these features, and an event detection sub-network that aggregates the features from multiple stations to associate and detect earthquakes across a seismic network. We use these sub-networks together with a shift-and-stack module based on back-projection that introduces kinematic constraints on arrival times, allowing the neural network model to generalize to different velocity models and to variable station geometry in seismic networks. We evaluate our proposed method on the STanford EArthquake Dataset (STEAD) and on the 2019 Ridgecrest, CA earthquake sequence. The results demonstrate that our end-to-end approach can effectively pick P- and S-wave arrivals and achieve earthquake detection accuracy rivaling that of other state-of-the-art approaches. Because our approach preserves information across tasks in the detection pipeline, it has the potential to outperform approaches that do not.

58 GEOSCIENCES↗

Sub-nanosecond signal propagation in anisotropy-engineered nanomagnetic logic chains

Energy efficient nanomagnetic logic (NML) computing architectures propagate binary information by relying on dipolar field coupling to reorient closely spaced nanoscale magnets. In the past, signal propagation in nanomagnet chains were characterized by static magnetic imaging experiments; however, the mechanisms that determine the final state and their reproducibility over millions of cycles in high-speed operation have yet to be experimentally investigated. Here we present a study of NML operation in a high-speed regime. We perform direct imaging of digital signal propagation in permalloy nanomagnet chains with varying degrees of shape-engineered biaxial anisotropy using full-field magnetic X-ray transmission microscopy and time-resolved photoemission electron microscopy after applying nanosecond magnetic field pulses. Moreover, an intrinsic switching time of 100 ps per magnet is observed. In conclusion these experiments, and accompanying macrospin and micromagnetic simulations, reveal the underlying physics of NML architectures repetitively operated on nanosecond timescales and identify relevant engineering parameters to optimize performance and reliability.

97 MATHEMATICS AND COMPUTING↗

Multi-objective optimization of root phenotypes for nutrient capture using evolutionary algorithms

Root phenotypes are avenues to the development of crop cultivars with improved nutrient capture, which is an important goal for global agriculture. The fitness landscape of root phenotypes is highly complex and multidimensional. It is difficult to predict which combinations of traits (phene states) will create the best performing integrated phenotypes in various environments. Brute force methods to map the fitness landscape by simulating millions of phenotypes in multiple environments are computationally challenging. Evolutionary optimization algorithms may provide more efficient avenues to explore high dimensional domains such as the root phenotypic space. We coupled the three-dimensional functional–structural plant model, SimRoot, to the Borg Multi-Objective Evolutionary Algorithm (MOEA) and the evolutionary search over several generations facilitated the identification of optimal root phenotypes balancing trade-offs across nutrient uptake, biomass accumulation, and root carbon costs in environments varying in nutrient availability. Our results show that several combinations of root phenes generate optimal integrated phenotypes where performance in one objective comes at the cost of reduced performance in one or more of the remaining objectives, and such combinations differed for mobile and non-mobile nutrients and for maize (a monocot) and bean (a dicot). Functional–structural plant models can be used with multi-objective optimization to identify optimal root phenotypes under various environments, including future climate scenarios, which will be useful in developing the more resilient, efficient crops urgently needed in global agriculture.

59 BASIC BIOLOGICAL SCIENCES↗

PetaVision version 2.0

PetaVision is an open source, object oriented neural simulation toolbox optimized for high-performance multi-core, multi-node computer architectures. PetaVision is intended for computational neuroscientists who seek to apply neuromorphic models to hard signal processing problems; both to improve on the performance of existing algorithms and/or to gain insight into the computational mechanisms underlying biological neural processing. Please note that this assertion and ESTSC deposit are only for the portions of PetaVision which have been funded and written by LANL developers.

Lundquist, Sheng↗

CReST-VCT System Integration Framework

In this paper, we propose a system integration framework for deploying the Coordinated Real-time Sub-Transmission Volt-var Control Tool (CReST VCT) functionality between the transmission system, the distribution system, and DERs. This represents one possible set of design choices to implement the coordinated optimization capabilities in an operating environment. The framework provides the following: An architectural reference model that describes how the CReST VCT solution maps into a broader grid architecture that accommodates and enables higher levels of DER penetration and utilization: A system integration reference model that defines a possible allocation of CReST VCT functionality within a utility’s operational environment. This includes one possible system design approach for allocation of functionality within software and protocol selections across the various interfaces; A list of potential performance and security issues that should be considered during an implementation. This framework does not represent a specific implementation of the CReST VCT algorithm or integration into a specific utility environment. It is intended to serve as a reference for those who plan to implement such a solution into their environment. The general model provided by the framework can be tailored to a specific environment based on its specific constraints and requirements.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Understanding HPC Benchmark Performance on Intel Broadwell and Cascade Lake Processors

Hardware platforms in high performance computing are constantly getting more complex to handle even when considering multicore CPUs alone. Numerous features and configuration options in the hardware and the software environment that are relevant for performance are not even known to most application users or developers. Microbenchmarks, i.e., simple codes that fathom a particular aspect of the hardware, can help to shed light on such issues, but only if they are well understood and if the results can be reconciled with known facts or performance models. The insight gained from microbenchmarks may then be applied to real applications for performance analysis or optimization. In this paper we investigate two modern Intel x86 server CPU architectures in depth: Broadwell EP and Cascade Lake SP. We highlight relevant hardware configuration settings that can have a decisive impact on code performance and show how to properly measure on-chip and off-chip data transfer bandwidths. The new victim L3 cache of Cascade Lake and its advanced replacement policy receive due attention. Finally we use DGEMM, sparse matrix-vector multiplication, and the HPCG benchmark to make a connection to relevant application scenarios.

97 MATHEMATICS AND COMPUTING↗

Sensor enabled data-driven predictive analytics for modeling and control with high penetration of DERs in distribution systems

The electric power grid is undergoing a tremendous transformation due to the increasing penetration of renewable energy resources beginning with wind and more recently with the distributed energy resources (DERs) such as solar and battery storage. DERs have dramatically changed the role of the distribution systems in the overall power grid, and they are expected to contribute a significant portion of power generation in the future. If current trends for DERs continue, system operation and control will need to change dramatically for improved grid reliability and resiliency. As renewable resources increase in penetration, new and challenging operational, planning, and design problems are expected to emerge. Some of the key challenges that arise in the planning and operation of the future grid are: 1) Quantifying the impact of high DER penetration in distribution systems on bulk grid behavior over multiple time scales. 2) Identifying whether a particular DER configuration/settings have a large impact on the overall grid behavior. These challenges can be addressed in an offline manner using detailed T&D grid models and they can also be addressed in an online manner using sensor measurements. In particular, the advancement and planned growth in sensor technology in power grid over various voltage levels provide us with a unique opportunity to tackle these challenges from a data analytic perspective without needing detailed T&D grid models. A few questions that naturally arise when addressing the challenges from DERs using sensor data are: 1) How can we use limited sensor measurements to monitor & control voltage stability and small signal stability of the bulk system? 2) How can we ensure that the developed data analytic methods are robust to data availability and quality issues? 3) How can we compute the developed analytics in a scalable manner using streaming measurements? In this project, we addressed the aforementioned challenges arising from DERs and answered the questions raised above on how to effectively use the sensor measurements to enhance the reliability and performance of the electric grid. Thus, the overarching goal of this project is to develop effective reduced/representative system models from data that make the computational complexity sufficiently manageable so as to be useful to simulate, analyze, and even control complex non-linear power systems dynamics with large penetrations of DERs. In order to achieve the objective, the project team established a four-fold technical approach 1) Formulated a combined transmission-distribution co-simulation framework for data generation and validation, 2) Derived reduced/representative models of power systems based on data-driven methods for efficient computation and appropriate representation of system behavior, 3) Developed data driven characterization of power system behavior based on transfer operator theory, machine learning and optimization for model estimation, 4) Incorporated a scalable data management and processing architecture using distributed Kafka streaming applications that coordinate input data streams to the developed data analytics. The key accomplishments of the project are: 1) Development of a scalable multi-timescale T&D co-simulation framework (both for steady state and for dynamic co-simulation) using commercial solvers (PSSE and GridLAB-D). The steady-state T&D co-simulation interface is shared with our industry partner (PJM). 2) A structured reduced order dynamic model of distribution systems that can represent partial motor stalling along with a systematic procedure to derive the model parameters. 3) A PMU based online method to monitor, localize and mitigate fault-induced delayed voltage recovery using DER reactive support and load control in distribution systems. 4) Development of linear operator based robust methodologies for dynamic state estimation, uncertainty quantification, system identification and trajectory prediction for power system dynamics. 5) An adaptive damping control for utilizing wind energy resources to provide oscillation damping and system stability. 6) Implementation of Kafka-based framework for efficient processing of streaming data using Linux-based local virtual environment.

DER integration↗