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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 379 records · Page 21

Design-Technology Co-Optimization for NVM-based Neuromorphic Processing Elements

An emerging use-case of machine learning (ML) is to train a model on a high-performance system and deploy the trained model on energy-constrained embedded systems. Neuromorphic hardware platforms, which operate on principles of the biological brain, can significantly lower the energy overhead of a machine learning inference task, making these platforms an attractive solution for embedded ML systems. In this paper, we present a design-technology tradeoff analysis to implement such inference tasks on the processing elements (PEs) of a Non-Volatile Memory (NVM)-based neuromorphic hardware. Through detailed circuit-level simulations at scaled process technology nodes, we show the negative impact of technology scaling on the information-processing latency, which impacts the quality-of-service (QoS) of an embedded ML system. At a finer granularity, the latency inside a PE depends on 1) the delay introduced by parasitic components on its current paths, and 2) the varying delay to sense different resistance states of its NVM cells. Based on these two observations, we make the following three contributions. First, on the technology front, we propose an optimization scheme where the NVM resistance state that takes the longest time to sense is set on current paths having the least delay, and vice versa, reducing the average PE latency, which improves the QoS. Second, on the architecture front, we introduce isolation transistors within each PE to partition it into regions that can be individually power-gated, reducing both latency and energy. Finally, on the system-software front, we propose a mechanism to leverage the proposed technological and architectural enhancements when implementing a machine-learning inference task on neuromorphic PEs of the hardware. Evaluations with a recent neuromorphic hardware architecture show that our proposed design-technology co-optimization approach improves both performance and energy efficiency of machine-learning inference tasks without incurring high cost-per-bit.

42 ENGINEERING↗

Automatic Qubit Characterization and Gate Optimization with QubiC

As the size and complexity of a quantum computer increases, quantum bit (qubit) characterization and gate optimization become complex and time-consuming tasks. Current calibration techniques require complicated and verbose measurements to tune up qubits and gates, which cannot easily expand to the large-scale quantum systems. We develop a concise and automatic calibration protocol to characterize qubits and optimize gates using QubiC, which is an open source FPGA (field-programmable gate array) based control and measurement system for superconducting quantum information processors. We propose multi-dimensional loss-based optimization of single-qubit gates and full XY-plane measurement method for the two-qubit CNOT gate calibration. We demonstrate the QubiC automatic calibration protocols are capable of delivering high-fidelity gates on the state-of-the-art transmon-type processor operating at the Advanced Quantum Testbed at Lawrence Berkeley National Laboratory. Finally, the single-qubit and two-qubit Clifford gate infidelities measured by randomized benchmarking are of 4.9(1.1) × 10 -4 and 1.4(3) × 10 -2 , respectively.

97 MATHEMATICS AND COMPUTING↗

Performance portability study of epistasis detection using SYCL on NVIDIA GPU

We describe the experience of converting a CUDA implementation of a high-order epistasis detection algorithm to SYCL. The goals are for our work to be useful to application and compiler developers with a detailed description of migration paths between CUDA and SYCL. Evaluating the CUDA and SYCL applications on an NVIDIA V100 GPU, we find that the optimization of loop unrolling needs to be applied manually to the SYCL kernel for obtaining comparable performance. The performance of the SYCL group reduce function, an alternative to the CUDA warp-based reduction, depends on the problem and work group sizes. The 64-bit popcount operation implemented with tree of adders is slightly faster than the built-in popcount operation. When the number of OpenMP threads is four, the highest performance of the SYCL and CUDA applications are comparable.

Jin, Zheming↗

A Verified Optimizer for Quantum Circuits

We present VOQC, the first verified optimizer for quantum circuits, written using the Coq proof assistant. Quantum circuits are expressed as programs in a simple, low-level language called SQIR, a small quantum intermediate representation, which is deeply embedded in Coq. Optimizations and other transformations are expressed as Coq functions, which are proved correct with respect to a semantics of SQIR programs. SQIR programs denote complex-valued matrices, as is standard in quantum computation, but we treat matrices symbolically to reason about programs that use an arbitrary number of quantum bits. SQIR’s careful design and our provided automation make it possible to write and verify a broad range of optimizations in VOQC, including full-circuit transformations from cutting-edge optimizers.

97 MATHEMATICS AND COMPUTING↗

Understanding GPU Memory Corruption at Extreme Scale: The Summit Case Study

GPU memory corruption and in particular double-bit errors (DBEs) remain one of the least understood aspects of HPC system reliability. Albeit rare, their occurrences always lead to job termination and can potentially cost thousands of node-hours, either from wasted computations or as the overhead from regular checkpointing needed to minimize the losses. As supercomputers and their components simultaneously grow in scale, density, failure rates, and environmental footprint, the efficiency of HPC operations becomes both an imperative and a challenge. We examine DBEs using system telemetry data and logs collected from the Summit supercomputer, equipped with 27,648 Tesla V100 GPUs with 2nd-generation high-bandwidth memory (HBM2). Using exploratory data analysis and statistical learning, we extract several insights about memory reliability in such GPUs. We find that GPUs with prior DBE occurrences are prone to experience them again due to otherwise harmless factors, correlate this phenomenon with GPU placement, and suggest manufacturing variability as a factor. On the general population of GPUs, we link DBEs to short- and long-term high power consumption modes while finding no significant correlation with higher temperatures. We also show that the workload type can be a factor in memory’s propensity to corruption.

Oles, Vlad↗

LCLS RF Station Anomaly Candidates, SLAC, Nov 2020 to Dec 2020, Version 1

The data consists of radio-frequency (RF) station process variables (amplitude and amplitude-mean-out-of-tolerance bit) and beam position monitor (BPM) values for about a month of Linac Coherent Light Source (LCLS) time. The data is all from normal conducting hard X-ray operation. The dataset contains roughly 5000 anomaly “candidates.” For each candidate, we include 3.5 minutes of data from the 82 RF stations and ~20 seconds of data from 4 BPMs. We also include several CSV files with additional information and labels for each candidate.

43 PARTICLE ACCELERATORS↗

Integrase-On-Demand-Pipeline Data Set

Files needed to run the Integrase-On-Demand-Pipeline, a program designed to provide users with a list of putative attachment site and integrase pairs for a prokaryotic genome of interest. isles.pkl: Serialized python-object file, containing a dictionary of attachment site sequences and reference genomic island information extracted from the Genomic island database ints.gff: Gene format file containing annotations for all integrases referenced in isles.pkl. The source genome, gene coordinates, integrase name, protein IDs and amino acid sequence included. reps.msh: Binary file containing 1000 128-bit MurmurHash3 hashes for >80,000 genomes

McClain, Hannah Marie [Sandia National Laboratorie↗

Outbreak analysis from case count and survey data

This code enables fitting a model of an infectious disease outbreak, customized for when available data is a combination of case counts and symptom survey responses. This is just a small bit of code being used only for a publication; we need to release it to fulfill a journal's requirement that our work be reproducible.

Goldberg, Emma↗

Generic Multi-Layer Perceptron Inference Accelerator on FPGA (vneuron) v1.0

We have designed and implemented a neural network inference compute engine (vneuron) that can be deployed in the fabric of any FPGA without using special hardware accelerator primitive. The "vneuron" is purely written in verilog, and supports scalable neural network structure with fully connected layers and ReLU activation ( Multi-Layer Perceptron architecture) with 16 bits of precision. We have demonstrated it on an Xilinx Artix 7 FPGA for a 16-input, 8-output MLP with 3 layer, 1600 parameters. It takes 40 DSP48E and 40 BRAM18, and takes 131 clock cycles for computing (1048 ns when clocked at 125MHz). We include PyTorch quantization from a given floating point model, and provide behavioral verification simulation in the disclosed software package.

Du, Qiang↗

CIGEN

CIGEN is a tool that finds input ranges that cause high compiler-induced numerical inconsistencies in numerical programs written in a compiled language. Numerical program behavior may diverge when they are compiled and ran differently. Many factors, such as different hardware architectures (for example, the x87 FPU with its 80-bit registers), different compilers, or different optimization flags may cause the results of floating-point computations to become inconsistent. This kind of inconsistencies are known as compiler-induced numerical inconsistencies. Given a program with floating-point inputs and an output,

Laguna Peralta, Ignacio↗

Microcontroller-based aerosol jet printer control software

This software is used with a microcontroller to control an aerosol jet printing system. It was written for a 32-bit ARM microcontroller, providing greater processing speed and complexity relative to more conventional low-cost printer controllers. The microcontroller software was written using a real-time operating system (FreeRTOS), which simplifies parallel operation of multiple functions and further customization. It supports simultaneous motion planning, pulse generation for stepper motors, reading encoder feedback, communicating with multiple mass flow controllers, controlling solid state relays, handling a software-based emergency stop, and sending data to the client PC. The program is written in C and communicates with the client PC via USB connection. Sandia National Laboratories is a multi-mission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525. SAND2021-0436 O

Secor, EthanBenjamin↗

FTTN: Feature-Targeted Testing for Numerical Properties of NVIDIA & AMD Matrix Accelerators

FTTN is a test suite to evaluate the numerical behaviors of matrix accelerators of GPUs (NVIDIA Tensor Cores and AMD Matrix Cores) in a quick and simple setting. Matrix accelerators are heavily used in today's computationally intense applications to speed up matrix multiplications. This test suite provides a comprehensive study on the numerical behaviors of these accelerators, including support for subnormals, rounding modes, extra precision bits and FMA features. Is there

Laguna Peralta, Ignacio↗

Code Generators for Floating-Point Unit Design in Integrated Circuits (OpenFloat) v1.0

This IP provides a comprehensive set of code generators for various floating-point units (FPUs) essential for integrated circuit design and integration, targeting a broad spectrum of applications, including machine learning and scientific computing. The suite includes FP adders, multipliers, subtractors, dividers, reciprocals, exponentials, square roots, trigonometric functions (sine, cosine, arctangent), and more. It supports customizable hardware design parameters, such as precision (16, 32, 64, and 128 bits) and pipeline depths, offering users enhanced flexibility and productivity. The generated code is in an industry-standard hardware description language, ensuring compatibility with standard design flows, including simulation, verification, synthesis, and implementation on both field-programmable gate arrays (FPGAs) and application-specific integrated circuits (ASICs).

Shalf, JohnM. [Lawrence Berkeley National Laborato↗

areaDetector/ADTimePix3

ADTimePix3 is an open‑source EPICS areaDetector driver for TimePix3 pixel detectors from Advanced Scientific Instruments (ASI). It provides a complete control and data‑acquisition interface between EPICS and the Serval server, supporting both real detectors (single‑chip and 2×2 quad configurations) and the TimePix3 emulator. The driver configures measurements via an HTTP/JSON REST API and acquires data through high‑rate TCP streams for raw events, images, and histograms. It offers real‑time preview and accumulated images, Time‑of‑Flight histogram processing, pixel masking (including Binary Pixel Configuration files and hot‑pixel tools), extensive health and status monitoring, and integration with standard areaDetector plugins for file saving and downstream analysis. ADTimePix3 is designed for Linux 64‑bit systems (tested on Ubuntu and RHEL) and is distributed under an MIT license with additional institutional disclaimers, enabling reuse and extension in photon science beamlines and other TimePix3‑based experimental facilities.

Gofron, Kaz↗

Evaluating the Lagrangian Evolution of Subtropical Low Clouds in GCMs Using Observations: Mean Evolution, Time Scales, and Responses to Predictors

In this work, a Lagrangian framework is developed to show the daily-scale time evolution of low clouds over the eastern subtropical oceans. An identical framework is applied to two general circulation models (GCMs): the CAM5 and UKMET and a set of satellite observations. This approach follows thousands of parcels as they advect downwind in the subtropical trade winds, comparing cloud evolution in time and space. This study tracks cloud cover, in-cloud liquid water path (CLWP), droplet concentration $N_d$, planetary boundary layer (PBL) depth, and rain rate as clouds transition from regions with predominately stratiform clouds to regions containing mostly trade cumulus. The two models generate fewer clouds with greater $N_d$ relative to observations. Models show stronger Lagrangian cloud cover decline and greater PBL deepening when compared with observations. In comparing frequency distributions of cloud variables over time, it is seen that models generate increasing frequencies of nearly clear conditions at the expense of overcast conditions, whereas observations show transitions from overcast to cloud amounts between 50% and 90%. Lagrangian decorrelation time scales ($\mathcal{e}$-folding time $\tau$) of cloud cover and CLWP are between 11 and 19 h for models and observations, although they are a bit shorter for models. A Lagrangian framework applied here resolves and compares the time evolution of cloud systems as they adjust to environmental perturbations in models and observations. Increasing subsidence in the overlying troposphere leads to declining cloud cover, CLWP, PBL depth, and rain rates in models and observations. Modeled cloud responses to other meteorological variables are less consistent with observations, suggesting a need for continuing mechanical improvements in GCMs.

58 GEOSCIENCES↗

Resiliency in numerical algorithm design for extreme scale simulations

Here this work is based on the seminar titled ‘Resiliency in Numerical Algorithm Design for Extreme Scale Simulations’ held March 1–6, 2020, at Schloss Dagstuhl, that was attended by all the authors. Advanced supercomputing is characterized by very high computation speeds at the cost of involving an enormous amount of resources and costs. A typical large-scale computation running for 48 h on a system consuming 20 MW, as predicted for exascale systems, would consume a million kWh, corresponding to about 100k Euro in energy cost for executing 10 23 floating-point operations. It is clearly unacceptable to lose the whole computation if any of the several million parallel processes fails during the execution. Moreover, if a single operation suffers from a bit-flip error, should the whole computation be declared invalid? What about the notion of reproducibility itself: should this core paradigm of science be revised and refined for results that are obtained by large-scale simulation? Naive versions of conventional resilience techniques will not scale to the exascale regime: with a main memory footprint of tens of Petabytes, synchronously writing checkpoint data all the way to background storage at frequent intervals will create intolerable overheads in runtime and energy consumption. Forecasts show that the mean time between failures could be lower than the time to recover from such a checkpoint, so that large calculations at scale might not make any progress if robust alternatives are not investigated. More advanced resilience techniques must be devised. The key may lie in exploiting both advanced system features as well as specific application knowledge. Research will face two essential questions: (1) what are the reliability requirements for a particular computation and (2) how do we best design the algorithms and software to meet these requirements? While the analysis of use cases can help understand the particular reliability requirements, the construction of remedies is currently wide open. One avenue would be to refine and improve on system- or application-level checkpointing and rollback strategies in the case an error is detected. Developers might use fault notification interfaces and flexible runtime systems to respond to node failures in an application-dependent fashion. Novel numerical algorithms or more stochastic computational approaches may be required to meet accuracy requirements in the face of undetectable soft errors. These ideas constituted an essential topic of the seminar. The goal of this Dagstuhl Seminar was to bring together a diverse group of scientists with expertise in exascale computing to discuss novel ways to make applications resilient against detected and undetected faults. In particular, participants explored the role that algorithms and applications play in the holistic approach needed to tackle this challenge. This article gathers a broad range of perspectives on the role of algorithms, applications and systems in achieving resilience for extreme scale simulations. The ultimate goal is to spark novel ideas and encourage the development of concrete solutions for achieving such resilience holistically.

79 ASTRONOMY AND ASTROPHYSICS↗

Compressed basis GMRES on high-performance graphics processing units

Krylov methods provide a fast and highly parallel numerical tool for the iterative solution of many large-scale sparse linear systems. To a large extent, the performance of practical realizations of these methods is constrained by the communication bandwidth in current computer architectures, motivating the investigation of sophisticated techniques to avoid, reduce, and/or hide the message-passing costs (in distributed platforms) and the memory accesses (in all architectures). This article leverages Ginkgo’s memory accessor in order to integrate a communication-reduction strategy into the (Krylov) GMRES solver that decouples the storage format (i.e., the data representation in memory) of the orthogonal basis from the arithmetic precision that is employed during the operations with that basis. Given that the execution time of the GMRES solver is largely determined by the memory accesses, the cost of the datatype transforms can be mostly hidden, resulting in the acceleration of the iterative step via a decrease in the volume of bits being retrieved from memory. Together with the special properties of the orthonormal basis (whose elements are all bounded by 1), this paves the road toward the aggressive customization of the storage format, which includes some floating-point as well as fixed-point formats with mild impact on the convergence of the iterative process. We develop a high-performance implementation of the “compressed basis GMRES” solver in the Ginkgo sparse linear algebra library using a large set of test problems from the SuiteSparse Matrix Collection. We demonstrate robustness and performance advantages on a modern NVIDIA V100 graphics processing unit (GPU) of up to 50% over the standard GMRES solver that stores all data in IEEE double-precision.

97 MATHEMATICS AND COMPUTING↗

P finder: genomic and metagenomic annotation of RNase P RNA gene (rnpB)

Abstract Background The rnpB gene encodes for an essential catalytic RNA (RNase P). Like other essential RNAs, RNase P’s sequence is highly variable. However, unlike other essential RNAs (i.e. tRNA, 16 S, 6 S,...) its structure is also variable with at least 5 distinct structure types observed in prokaryotes. This structural variability makes it labor intensive and challenging to create and maintain covariance models for the detection of RNase P RNA in genomic and metagenomic sequences. The lack of a facile and rapid annotation algorithm has led to the rnpB gene being the most grossly under annotated essential gene in completed prokaryotic genomes with only a 24% annotation rate. Here we describe the coupling of the largest RNase P RNA database with the local alignment scoring algorithm to create the most sensitive and rapid prokaryote rnpB gene identification and annotation algorithm to date. Results Of the 2772 completed microbial genomes downloaded from GenBank only 665 genomes had an annotated rnpB gene. We applied P Finder to these genomes and were able to identify 2733 or nearly 99% of the 2772 microbial genomes examined. From these results four new rnpB genes that encode the minimal T-type P RNase P RNAs were identified computationally for the first time. In addition, only the second C-type RNase P RNA was identified in Sphaerobacter thermophilus . Of special note, no RNase P RNAs were detected in several obligate endosymbionts of sap sucking insects suggesting a novel evolutionary adaptation. Conclusions The coupling of the largest RNase P RNA database and associated structure class identification with the P Finder algorithm is both sensitive and rapid, yielding high quality results to aid researchers annotating either genomic or metagenomic data. It is the only algorithm to date that can identify challenging RNAse P classes such as C-type and the minimal T-type RNase P RNAs. P Finder is written in C# and has a user-friendly GUI that can run on multiple 64-bit windows platforms (Windows Vista/7/8/10). P Finder is free available for download at https://github.com/JChristopherEllis/P-Finder as well as a small sample RNase P RNA file for testing.

59 BASIC BIOLOGICAL SCIENCES↗