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At least 811 records · Page 45
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

ZMPY3D: accelerating protein structure volume analysis through vectorized 3D Zernike moments and Python-based GPU integration

Abstract Motivation Volumetric 3D object analyses are being applied in research fields such as structural bioinformatics, biophysics, and structural biology, with potential integration of artificial intelligence/machine learning (AI/ML) techniques. One such method, 3D Zernike moments, has proven valuable in analyzing protein structures (e.g., protein fold classification, protein–protein interaction analysis, and molecular dynamics simulations). Their compactness and efficiency make them amenable to large-scale analyses. Established methods for deriving 3D Zernike moments, however, can be inefficient, particularly when higher order terms are required, hindering broader applications. As the volume of experimental and computationally-predicted protein structure information continues to increase, structural biology has become a “big data” science requiring more efficient analysis tools. Results This application note presents a Python-based software package, ZMPY3D, to accelerate computation of 3D Zernike moments by vectorizing the mathematical formulae and using graphical processing units (GPUs). The package offers popular GPU-supported libraries such as CuPy and TensorFlow together with NumPy implementations, aiming to improve computational efficiency, adaptability, and flexibility in future algorithm development. The ZMPY3D package can be installed via PyPI, and the source code is available from GitHub. Volumetric-based protein 3D structural similarity scores and transform matrix of superposition functionalities have both been implemented, creating a powerful computational tool that will allow the research community to amalgamate 3D Zernike moments with existing AI/ML tools, to advance research and education in protein structure bioinformatics. Availability and implementation ZMPY3D, implemented in Python, is available on GitHub (https://github.com/tawssie/ZMPY3D) and PyPI, released under the GPL License.

Lai, Jhih-Siang (ORCID:0000000156775890)↗
DOE OSTI2022

A roadmap for the functional annotation of protein families: a community perspective

Over the last 25 years, biology has entered the genomic era and is becoming a science of ‘big data’. Most interpretations of genomic analyses rely on accurate functional annotations of the proteins encoded by more than 500 000 genomes sequenced to date. By different estimates, only half the predicted sequenced proteins carry an accurate functional annotation, and this percentage varies drastically between different organismal lineages. Such a large gap in knowledge hampers all aspects of biological enterprise and, thereby, is standing in the way of genomic biology reaching its full potential. A brainstorming meeting to address this issue funded by the National Science Foundation was held during 3–4 February 2022. Bringing together data scientists, biocurators, computational biologists and experimentalists within the same venue allowed for a comprehensive assessment of the current state of functional annotations of protein families. Further, major issues that were obstructing the field were identified and discussed, which ultimately allowed for the proposal of solutions on how to move forward.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Machine Learning-Enabled Image Classification for Automated Electron Microscopy

Abstract Traditionally, materials discovery has been driven more by evidence and intuition than by systematic design. However, the advent of “big data” and an exponential increase in computational power have reshaped the landscape. Today, we use simulations, artificial intelligence (AI), and machine learning (ML) to predict materials characteristics, which dramatically accelerates the discovery of novel materials. For instance, combinatorial megalibraries, where millions of distinct nanoparticles are created on a single chip, have spurred the need for automated characterization tools. This paper presents an ML model specifically developed to perform real-time binary classification of grayscale high-angle annular dark-field images of nanoparticles sourced from these megalibraries. Given the high costs associated with downstream processing errors, a primary requirement for our model was to minimize false positives while maintaining efficacy on unseen images. We elaborate on the computational challenges and our solutions, including managing memory constraints, optimizing training time, and utilizing Neural Architecture Search tools. The final model outperformed our expectations, achieving over 95% precision and a weighted F-score of more than 90% on our test data set. This paper discusses the development, challenges, and successful outcomes of this significant advancement in the application of AI and ML to materials discovery.

Materials Science↗
DOE OSTI2024

Automating galaxy morphology classification using k -nearest neighbours and non-parametric statistics

ABSTRACT Morphology is a fundamental property of any galaxy population. It is a major indicator of the physical processes that drive galaxy evolution and in turn the evolution of the entire Universe. Historically, galaxy images were visually classified by trained experts. However, in the era of big data, more efficient techniques are required. In this work, we present a k-nearest neighbours based approach that utilizes non-parametric morphological quantities to classify galaxy morphology in Sloan Digital Sky Survey images. Most previous studies used only a handful of morphological parameters to identify galaxy types. In contrast, we explore 1023 morphological spaces (defined by up to 10 non-parametric statistics) to find the best combination of morphological parameters. Additionally, while most previous studies broadly classified galaxies into early types and late types or ellipticals, spirals, and irregular galaxies, we classify galaxies into 11 morphological types with an average accuracy of ${\sim} 80\!-\!90 \, {{\rm per\, cent}}$ per T-type. Our method is simple, easy to implement, and is robust to varying sizes and compositions of the training and test samples. Preliminary results on the performance of our technique on deeper images from the Hyper Suprime-Cam Subaru Strategic Survey reveal that an extension of our method to modern surveys with better imaging capabilities might be possible.

Mukundan, Kavya↗
DOE OSTI2020

Novel Fault Location Method for Power Systems Based on Attention Mechanism and Double Structure GRU Neural Network

Fault location is one of the most essential techniques to maintain the stable operation of power systems. A fast and accurate fault location allows operators to restore power grids faster and avoid economic losses. Conventional methods rely on expert knowledge to extract the necessary features (e.g. DWT, DFT). For large systems, more coupling effects of transmission lines require more complex feature engineering, and incomplete features can easily introduce large errors. To overcome this, a deep learning approach without manual feature extraction is introduced to the fault location model under big data application. Towards this end, in the proposed method, the attention mechanism, the Bi-GRU and a dual structure network are applied to analyze the current data from different perspectives. Complete information for the fault features is extracted for the fault location. Based on a time series model and benefit from the ability to internally acquire the information architecture of faulty line, the established model is adaptive to the power grids with very complex topologies. Simulation results indicate that the proposed double-structure model reduces the maximum error and is less affected by noise. In comparison with different structures and different models, the proposed method shows better performance in IEEE 39-bus system.

42 ENGINEERING↗
DOE OSTI2024

CMOS-Based Single-Cycle in-Memory XOR/XNOR

Big data applications are on the rise, and so is the number of data centers. The ever-increasing massive data pool needs to be periodically backed up in a secure environment. Moreover, a massive amount of securely backed-up data is required for training binary convolutional neural networks for image classification. XOR and XNOR operations are essential for large-scale data copy verification, encryption, and classification algorithms. The disproportionate speed of existing compute and memory units makes the von Neumann architecture inefficient to perform these Boolean operations. Compute-in-memory (CiM) has proved to be an optimum approach for such bulk computations. The existing CiM-based XOR/XNOR techniques either require multiple cycles for computing or add to the complexity of the fabrication process. Here, we propose a CMOS-based hardware topology for single-cycle in-memory XOR/XNOR operations. Our design provides at least 2× improvement in the latency compared with other existing CMOS-compatible solutions. We verify the proposed system through circuit/system-level simulations and evaluate its robustness using a 5000-point Monte Carlo variation analysis. This all-CMOS design paves the way for practical implementation of CiM XOR/XNOR at scaled technology nodes.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

A Flexible-blocking Based Approach for Performance Tuning of Matrix Multiplication Routines for Large Matrices with Edge Cases

Efficient and scalable matrix operations are being highly demanding in the recent era of Machine Learning, Deep Learning, and Big Data Analytics. The two commonly used matrix-matrix operations in the Basic Linear Algebra Subprograms (BLAS) specification are General Matrix-Matrix multiplication (GEMM) and Symmetric Rank-k update (SYRK). The SYRK routine is a specialization of the GEMM routine, where half of the multiplications are skipped as the resultant matrix is known to be symmetric. Fortunately, several linear algebra libraries implement these BLAS routines quite efficiently. The libraries usually partition the input matrices into blocks and place them in processor caches, thus improving performance by leveraging the caches. However, the contemporary libraries are highly optimized for squarish matrices, but the performance degrades significantly for the matrices with edge case (strictly thin or strictly fat shapes) in the multicore machine. The primary reason is that the current state-of-the-art libraries make fixed block shapes based on a processor architecture, and do not consider the shape of the input matrices. In this paper, we propose a new blocking approach, we name it Flexible-blocking, to mitigate the scalability issues. In contrast to the contemporary libraries, our approach formulates the blocks of the input matrices based on the shapes of the matrices as well as the number of threads used in the implementation. Our proposed technique shows noticeable performance improvement on multicore shared-memory machines for the edge case matrices.

Hossain, Md Mosharaf↗
DOE OSTI2022

Latent Learning with pyroMind.2020

This paper is for the Proceedings of the IEEE Big Data 2021 Conference (IEEE BigData 2021) published by IEEE Computer Society.

Romanov, Vyacheslav↗
DOE OSTI2014

PLAStiCC: Predictive Look-Ahead Scheduling for Continuous dataflows on Clouds

Scalable stream processing and continuous dataflow systems are gaining traction with the rise of big data due to the need for processing high velocity data in near real time. Unlike batch processing systems such as MapReduce and workflows, static scheduling strategies fall short for continuous dataflows due to the variations in the input data rates and the need for sustained throughput. The elastic resource provisioning of cloud infrastructure is valuable to meet the changing resource needs of such continuous applications. However, multi-tenant cloud resources introduce yet another dimension of performance variability that impacts the application’s throughput. In this paper we propose PLAStiCC, an adaptive scheduling algorithm that balances resource cost and application throughput using a prediction-based look-ahead approach. It not only addresses variations in the input data rates but also the underlying cloud infrastructure. In addition, we also propose several simpler static scheduling heuristics that operate in the absence of accurate performance prediction model. These static and adaptive heuristics are evaluated through extensive simulations using performance traces obtained from public and private IaaS clouds. Our results show an improvement of up to 20% in the overall profit as compared to the reactive adaptation algorithm.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

DeepFreeze: Towards Scalable Asynchronous Checkpointing of Deep Learning Models

In the age of big data, deep learning has emerged as a powerful tool to extract insight and exploit its value, both in industry and scientific applications. One common pattern emerging in such applications is frequent checkpointing of the state of the learning model during training, needed in a variety of scenarios: analysis of intermediate states to explain features and correlations with training data, exploration strategies involving alternative models that share a common ancestor, knowledge transfer, resilience, etc. However, with increasing size of the learning models and popularity of distributed data-parallel training approaches, simple checkpointing techniques used so far face several limitations: low serialization performance, blocking I/O, stragglers due to the fact that only a single process is involved in checkpointing. This paper proposes a checkpointing technique specifically designed to address the aforementioned limitations, introducing efficient asynchronous techniques to hide the overhead of serialization and I/O, and distribute the load over all participating processes. Experiments with two deep learning applications (CANDLE and ResNet) on a pre-Exascale HPC platform (Theta) shows significant improvement over state-of-art, both in terms of checkpointing duration and runtime overhead.

checkpointing↗
DOE OSTI2017

SharP Hash: A High-Performing Distributed Hash for Extreme-Scale Systems

A high-performing distributed hash is critical for achieving performance in many applications and system software using extreme-scale systems. It is also a central part of many Big-Data frameworks including Memcached, file systems, and job schedulers. However, there is a lack of high-performing distributed hash implementations. In this work, we propose, design, and implement, SharP Hash, a high-performing, RDMA-based distributed hash for extreme-scale systems. SharP Hash's high performance is obtained through the use of high-performing networks and one-sided semantics. We perform an evaluation of SharP Hash and demonstrate its performance characteristics with a synthetic micro-benchmark and implementation of a Key Value (KV) store, Memcached.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Parallel I/O Evaluation Techniques and Emerging HPC Workloads: A Perspective

Emerging workloads such as artificial intelligence, big data analytics and complex multi-step workflows alongside future exascale applications are anticipated future HPC workloads, which will result in a more diverse I/O system workload and even less predictable I/O behavior and access patterns. Along with the ever increasing gap between the compute and storage performance capabilities, the in-depth understanding of extreme-scale I/O behavior and the I/O performance modeling and prediction are essential tools of the large-scale I/O evaluation process for addressing the needs of extreme-scale hybrid workloads. In this survey article, we focus on the state-of-the-art of the I/O behavior and performance analysis process for HPC systems in a 5-year time window and identify future research challenges.

Neuwirth, Sarah↗
DOE OSTI2020

CoSim: A Simulator for Co-Scheduling of Batch and On-Demand Jobs in HPC Datacenters

The increasing scale and complexity of scientific applications are rapidly transforming the ecosystem of tools, methods, and workflows adopted by the high-performance computing (HPC) community. Big data analytics and deep learning are gaining traction as essential components in this ecosystem in a variety of scenarios, such as, steering of experimental instruments , acceleration of high-fidelity simulations through surrogate computations, and guided ensemble searches. In this context, the batch job model traditionally adopted by the supercomputing in-frastructures needs to be complemented with support to schedule opportunistic on-demand analytics jobs, leading to the problem of efficient preemption of batch jobs with minimum loss of progress. In this paper, we design and implement a simulator, CoSim, that enables on-the-fly analysis of the trade-offs arising between delaying the start of opportunistic on-demand jobs, which leads to longer analytics latency, and loss of progress due to preemption of batch jobs, which is necessary to make room for on-demand jobs. To this end, we propose an algorithm based on dynamic programming with predictable performance and scalability that enables supercomputing infrastructure schedulers to analyze the aforementioned trade-off and take decisions in near real-time. Compared with other state-of-art approaches using traces of the Theta pre-Exascale machine, our approach is capable of finding the optimal solution, while achieving high performance and scalability.

batch job preemption↗
DOE OSTI2017

On Analytics of File Transfer Rates over Dedicated Wide-Area Connections

File transfers between the decentralized storage sites over dedicated wide-area connections are becoming increasingly important in high-performance computing and big data scenarios. Designing such scientific workflows for large file transfers is extremely challenging as they depend on the file, I/O, host, and local- and wide-area network subsystems, and their interactions. To gain insights into file-transfer rate profiles, we develop polynomial, bagging, and boosting regression models for Lustre and XFS file transfer measurements, which are collected using XDD over a suite of 10 Gbps connections with 0-366 ms round trip times (RTTs). In addition to overall trends and analytics, these regressions also provide file-transfer rate estimates for RTTs and number of parallel flows at which measurements might not have been collected. They show that bagging and boosting techniques provide closer data fits than the polynomial regression. We develop probabilistic bounds on the generalization error of these methods, which combined with the cross-validation error establish that former two are more accurate estimators than the polynomial regression. In addition, we present a method to efficiently determine the number of parallel flows to achieve a peak file-transfer rate using fewer than full sweep measurements; in our measurements, the peak is achieved in 96% of cases with 15-25% of measurements of a full sweep.

Sen, Satyabrata↗
DOE OSTI2016

Experimental Analysis of File Transfer Rates over Wide-Area Dedicated Connections

File transfers over dedicated connections, supported by large parallel file systems, have become increasingly important in high-performance computing and big data workflows. It remains a challenge to achieve peak rates for such transfers due to the complexities of file I/O, host, and network transport subsystems, and equally importantly, their interactions. We present extensive measurements of disk-to-disk file transfers using Lustre and XFS file systems mounted on multi-core servers over a suite of 10 Gbps emulated connections with 0-366 ms round trip times. Our results indicate that large buffer sizes and many parallel flows do not always guarantee high transfer rates. Furthermore, large variations in the measured rates necessitate repeated measurements to ensure confidence in inferences based on them. We propose a new method to efficiently identify the optimal joint file I/O and network transport parameters using a small number of measurements. We show that for XFS and Lustre with direct I/O, this method identifies configurations achieving 97% of the peak transfer rate while probing only 12% of the parameter space.

Rao, Nageswara S.↗
DOE OSTI2022

Strategies for Integrating Deep Learning Surrogate Models with HPC Simulation Applications

The emerging trend of the convergence of high performance computing (HPC), machine learning/deep learning (ML/DL), and big data analytics presents a host of challenges for large-scale computing campaigns that seek best practices to interleave traditional scientific simulation-based workloads with ML/DL models. A portfolio of systematic approaches to incorporate deep learning into modeling and simulation serves a vital need when we support AI for science at a computing facility. In this paper, we evaluate several strategies for deploying deep learning surrogate models in a representative physics application on supercomputers at the Oak Ridge Leadership Computing Facility (OLCF). We discuss a set of recommended deployment architectures and implementation approaches. We analyze and evaluate these alternatives and show their performance and scalability up to 1000 GPUs on two mainstream platforms equipped with different deep learning hardware and software stacks.

Yin, Junqi↗
DOE OSTI2017

A Hierarchical Modeling for Reactive Power Optimization With Joint Transmission and Distribution Networks by Curve Fitting

Here, in order to solve the reactive power optimization with joint transmission and distribution networks, a hierarchical modeling method is proposed in this paper. It allows the reactive power optimization of transmission and distribution networks to be performed separately, leading to a master–slave structure and improves traditional centralized modeling methods by alleviating the big data problem in a control center. Specifically, the transmission-distribution-network coordination issue of the hierarchical modeling method is investigated. First, a curve-fitting approach is developed to provide a cost function of the slave model for the master model, which reflects the impacts of each slave model. Second, the transmission and distribution networks are decoupled at feeder buses, and all the distribution networks are coordinated by the master reactive power optimization model to achieve the global optimality. Finally, numerical results on two test systems verify the effectiveness of the proposed hierarchical modeling and curve-fitting methods.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2024

Enabling HPC Scientific Workflows for Serverless

The convergence of edge computing, big data analytics, and AI with traditional scientific calculations is increasingly being adopted in HPC workflows. Workflow management systems are crucial for managing and orchestrating these complex computational tasks. However, it is difficult to identify patterns within the growing population of HPC workflows. Serverless has emerged as a novel computing paradigm, offering dynamic resource allocation, quick response time, fine-grained resource management and auto-scaling. In this paper, we propose a framework to enable HPC scientific workflows on serverless. Our approach integrates a widely used traditional HPC workflow generator with an HPC serverless workflow management system to create benchmark suites of scientific workflows with diverse characteristics. These workflows can be executed on different serverless platforms. We comprehensively compare executing workflows on traditional local containers and serverless computing platforms. Our results show that serverless can reduce CPU and memory usage respectively by 78.11% and 73.92% without compromising performance.

Andrei da silva, Anderson↗