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DOE OSTI2011

Experimental evaluation of the impact of packet capturing tools for web services.

Network measurement is a discipline that provides the techniques to collect data that are fundamental to many branches of computer science. While many capturing tools and comparisons have made available in the literature and elsewhere, the impact of these packet capturing tools on existing processes have not been thoroughly studied. While not a concern for collection methods in which dedicated servers are used, many usage scenarios of packet capturing now requires the packet capturing tool to run concurrently with operational processes. In this work we perform experimental evaluations of the performance impact that packet capturing process have on web-based services; in particular, we observe the impact on web servers. We find that packet capturing processes indeed impact the performance of web servers, but on a multi-core system the impact varies depending on whether the packet capturing and web hosting processes are co-located or not. In addition, the architecture and behavior of the web server and process scheduling is coupled with the behavior of the packet capturing process, which in turn also affect the web server's performance.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2024

GPU-enabled extreme-scale turbulence simulations: Fourier pseudo-spectral algorithms at the exascale using OpenMP offloading

Fourier pseudo-spectral methods for nonlinear partial differential equations are of wide interest in many areas of advanced computational science, including direct numerical simulation of three-dimensional (3-D) turbulence governed by the Navier-Stokes equations in fluid dynamics. This paper presents a new capability for simulating turbulence at a new record resolution up to 35 trillion grid points, on the world's first exascale computer, Frontier, comprising AMD MI250x GPUs with HPE's Slingshot interconnect and operated by the US Department of Energy's Oak Ridge Leadership Computing Facility (OLCF). Key programming strategies designed to take maximum advantage of the machine architecture involve performing almost all computations on the GPU which has the same memory capacity as the CPU, performing all-to-all communication among sets of parallel processes directly on the GPU, and targeting GPUs efficiently using OpenMP offloading for intensive number-crunching including 1-D Fast Fourier Transforms (FFT) performed using AMD ROCm library calls. With 99% of computing power on Frontier being on the GPU, leaving the CPU idle leads to a net performance gain via avoiding the overhead of data movement between host and device except when needed for some I/O purposes. Memory footprint including the size of communication buffers for MPI_ALLTOALL is managed carefully to maximize the largest problem size possible for a given node count. Detailed performance data including separate contributions from different categories of operations to the elapsed wall time per step are reported for five grid resolutions, from 2048 3 on a single node to 32768 3 on 4096 or 8192 nodes out of 9408 on the system. Both 1D and 2D domain decompositions which divide a 3D periodic domain into slabs and pencils respectively are implemented. The present code suite (labeled by the acronym GESTS, GPUs for Extreme Scale Turbulence Simulations) achieves a figure of merit (in grid points per second) exceeding goals set in the Center for Accelerated Application Readiness (CAAR) program for Frontier. The performance attained is highly favorable in both weak scaling and strong scaling, with notable departures only for 2048 3 where communication is entirely intra-node, and for 32768 3 , where a challenge due to small message sizes does arise. Communication performance is addressed further using a lightweight test code that performs all-to-all communication in a manner matching the full turbulence simulation code. Performance at large problem sizes is affected by both small message size due to high node counts as well as dragonfly network topology features on the machine, but is consistent with official expectations of sustained performance on Frontier. Overall, although not perfect, the scalability achieved at the extreme problem size of 32768 3 (and up to 8192 nodes — which corresponds to hardware rated at just under 1 exaflop/sec of theoretical peak computational performance) is arguably better than the scalability observed using prior state-of-the-art algorithms on Frontier's predecessor machine (Summit) at OLCF. New science results for the study of intermittency in turbulence enabled by this code and its extensions are to be reported separately in the near future.

3D fast Fourier transform↗

DOE OSTI2021

AMReX: Block-structured adaptive mesh refinement for multiphysics applications

Block-structured adaptive mesh refinement (AMR) provides the basis for the temporal and spatial discretization strategy for a number of Exascale Computing Project applications in the areas of accelerator design, additive manufacturing, astrophysics, combustion, cosmology, multiphase flow, and wind plant modeling. AMReX is a software framework that provides a unified infrastructure with the functionality needed for these and other AMR applications to be able to effectively and efficiently utilize machines from laptops to exascale architectures. AMR reduces the computational cost and memory footprint compared to a uniform mesh while preserving accurate descriptions of different physical processes in complex multiphysics algorithms. AMReX supports algorithms that solve systems of partial differential equations in simple or complex geometries and those that use particles and/or particle–mesh operations to represent component physical processes. In this article, we will discuss the core elements of the AMReX framework such as data containers and iterators as well as several specialized operations to meet the needs of the application projects. In addition, we will highlight the strategy that the AMReX team is pursuing to achieve highly performant code across a range of accelerator-based architectures for a variety of different applications.

Zhang, Weiqun↗

DOE OSTI2023

DL-TODA: A Deep Learning Tool for Omics Data Analysis

Metagenomics is a technique for genome-wide profiling of microbiomes; this technique generates billions of DNA sequences called reads. Given the multiplication of metagenomic projects, computational tools are necessary to enable the efficient and accurate classification of metagenomic reads without needing to construct a reference database. The program DL-TODA presented here aims to classify metagenomic reads using a deep learning model trained on over 3000 bacterial species. A convolutional neural network architecture originally designed for computer vision was applied for the modeling of species-specific features. Using synthetic testing data simulated with 2454 genomes from 639 species, DL-TODA was shown to classify nearly 75% of the reads with high confidence. The classification accuracy of DL-TODA was over 0.98 at taxonomic ranks above the genus level, making it comparable with Kraken2 and Centrifuge, two state-of-the-art taxonomic classification tools. DL-TODA also achieved an accuracy of 0.97 at the species level, which is higher than 0.93 by Kraken2 and 0.85 by Centrifuge on the same test set. Application of DL-TODA to the human oral and cropland soil metagenomes further demonstrated its use in analyzing microbiomes from diverse environments. Compared to Centrifuge and Kraken2, DL-TODA predicted distinct relative abundance rankings and is less biased toward a single taxon.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2011

Velo: Riding the Knowledge Management Wave for Simulation and Modeling

Modern scientific enterprises are inherently knowledge-intensive. In general, scientific studies in domains such as geosciences, climate, and biology require the acquisition and manipulation of large amounts of experimental and field data in order to create inputs for large-scale computational simulations. The results of these simulations must then be analyzed, leading to refinements of inputs and models and further simulations. Further, these results must be managed and archived to provide justifications for publications and regulatory decisions that are based on these models. In this paper we describe our Velo framework that is designed as a reusable, domain independent knowledge management infrastructure for modeling and simulation. Velo leverages, integrates, and extends open source collaborative and content management technologies to create a scalable and flexible core platform that can be tailored to specific scientific domains. In this paper we describe the architecture of Velo for managing and associating the various types of data that are used and created in modeling and simulation projects, as well as the framework for integrating domain-specific tools. To demonstrate a realization of Velo, we describe the Geologic Sequestration Software Suite (GS3) that has been developed to support geologic sequestration modeling. This provides a concrete example of the inherent extensibility and utility of our approach.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2016

Select Advances in Computational Accelerator Physics

Computational accelerator physics has changed and broadened over the last decade or so. Part of the change is due to the advent of multiple ways of parallel computing. Another part comes from algorithmic developments. The multiple ways of parallel computing include distributed memory parallelism and on-chip parallelism, with the latter coming from architectures (CPU and GPU) having multiple processing elements (cores or streaming multiprocessors) and wide vector (SIMD) instruction units. The basics of these new architectures and their application to computational accelerator physics are briefly reviewed. Algorithmic advances in the select areas of spin tracking, cavity calculations, plasma acceleration, and electron cooling are also reviewed. In some cases the algorithms provide increased fidelity improving the overall accuracy, while in other cases, such as controlled dispersion, the algorithms provide increased fidelity by better modeling the essential physical interaction. Finally, the use of computational frameworks, which provide the basic computational infrastructure, while allowing the capability developer to concentrate on the math and physics, is reviewed in the context of the Vorpal application, which has found use across accelerator physics and many other fields.

Engineering↗

DOE OSTI2014

Computational Nanophotonics: modeling optical interactions and transport in tailored nanosystem architectures

This report describes research by George Schatz and Mark Ratner that was done over the period 10/03-5/09 at Northwestern University. This research project was part of a larger research project with the same title led by Stephen Gray at Argonne. A significant amount of our work involved collaborations with Gray, and there were many joint publications as summarized later. In addition, a lot of this work involved collaborations with experimental groups at Northwestern, Argonne, and elsewhere. The research was primarily concerned with developing theory and computational methods that can be used to describe the interaction of light with noble metal nanoparticles (especially silver) that are capable of plasmon excitation. Classical electrodynamics provides a powerful approach for performing these studies, so much of this research project involved the development of methods for solving Maxwell’s equations, including both linear and nonlinear effects, and examining a wide range of nanostructures, including particles, particle arrays, metal films, films with holes, and combinations of metal nanostructures with polymers and other dielectrics. In addition, our work broke new ground in the development of quantum mechanical methods to describe plasmonic effects based on the use of time dependent density functional theory, and we developed new theory concerned with the coupling of plasmons to electrical transport in molecular wire structures. Applications of our technology were aimed at the development of plasmonic devices as components of optoelectronic circuits, plasmons for spectroscopy applications, and plasmons for energy-related applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2019

Quantifying Reaction and Rate Heterogeneity in Battery Electrodes in 3D through Operando X-ray Diffraction Computed Tomography

In composite battery electrode architectures, local limitations in ionic and electronic transport can result in nonuniform energy storage reactions. Understanding such reaction heterogeneity is important to optimizing battery performance, including rate capability and mitigating degradation and failure. Here, we use spatially resolved X-ray diffraction computed tomography to map the reaction in a composite electrode based on the LiFePO 4 active material as it undergoes charge and discharge. Accelerated reactions at the electrode faces in contact with either the separator or the current collector demonstrate that both ionic and electronic transport limit the reaction progress. The data quantify how nonuniformity of the electrode reaction leads to variability in the charge/discharge rate, both as a function of time and position within the electrode architecture. Importantly, this local variation in the reaction rate means that the maximum rate that individual cathode particles experience can be substantially higher than the average, control charge/discharge rate, by a factor of at least 2-5 times. As a result, this rate heterogeneity may accelerate rate-dependent degradation pathways in regions of the composite electrode experiencing faster-than-average reaction and has important implications for understanding and optimizing rate-dependent battery performance. Benchmarking multiscale continuum model parameters against the observed reaction heterogeneity permits extension of these models to other electrode geometries.

25 ENERGY STORAGE↗

DOE OSTI2023

Integrating 5G Technology for Improved Process Monitoring and Network Slicing in ICS

Industrial Control Systems (ICS) are crucial for monitoring physical processes that support essential cyber-enabled services like power generation. The use of proprietary communication and lack of effective intrusion detection mechanisms pose constraints for efficient operation. Therefore, there is a need to modernize these systems with decentralized technologies like Edge Computing and 5G. However, integrating 5G and Edge Computing into large-scale ICS networks presents implementation and performance challenges. To address these challenges, this paper proposes an integrated ICS architecture that combines 5G and Edge Computing technologies with traditional ICS protocols. The objective is to minimize implementation and operational difficulties while improving the monitoring of physical processes and enabling robust intrusion detection. The proposed architecture outlines the necessary components, services, and communication protocols required for the integration of 5G and Edge Computing.

Aguayo, Jared M.↗

DOE OSTI2026

Supporting multiple hardware architectures at CMS: the integration and validation of POWER9

Computing resources in the Worldwide LHC Computing Grid (WLCG) have been based entirely on the x86 architecture for more than two decades. In the near future, however, heterogeneous non-x86 resources, such as ARM, POWER and Risc-V, will become a substantial fraction of the resources that will be provided to the LHC experiments, due to their presence in existing and planned world-class HPC installations. The CMS experiment, one of the four large detectors at the LHC, has started to prepare for this situation, with the CMS software stack (CMSSW) already compiled for multiple architectures. In order to allow for a production use, the tools for workload management and job distribution need to be extended to be able to exploit heterogeneous architectures. Profiting from the opportunity to exploit the first sizable IBM Power9 allocation available on Marconi100 HPC system at CINECA, CMS developed all the needed modifications to the CMS workload management system. After a successful proof of concept, a full physics validation has been performed in order to bring the system in production. The experiences are of very high value, when it comes to commissioning of the similar (even larger) Summit HPC system at Oak Ridge, where CMS is also expecting a resource allocation. Moreover the compute power of those systems is being provided also via GPUs and this represents an extremely valuable opportunity to exploit the offloading capability already implemented in CMSSW. The status of the current integration including the exploitation of the GPUs, the results of the validation as well as the future plans will be shown and discussed.

Boccali, Tommaso [INFN, Pisa]↗

DOE OSTI2021

Randomized Algorithms for Scientific Computing (RASC)

Randomized algorithms have propelled advances in artificial intelligence (AI) and represent a foundational research area in advancing AI for Science. Future advancements in DOE Office of Science priority areas such as climate science, astrophysics, fusion, advanced materials, combustion, and quantum computing all require randomized algorithms for surmounting challenges of complexity, robustness, and scalability. Advances in data collection and numerical simulation have changed the dynamics of scientific research and motivate the need for randomized algorithms. For instance, advances in imaging technologies such as X-ray ptychography, electron microscopy, electron energy loss spectroscopy, or adaptive optics lattice light-sheet microscopy collect hyperspectral imaging and scattering data in terabytes, at breakneck speed enabled by state-of-the-art detectors. The data collection is exceptionally fast compared with its analysis. Likewise, advances in high-performance architectures have made exascale computing a reality and changed the economies of scientific computing in the process. Floating-point operations that create data are essentially free in comparison with data movement. Thus far, most approaches have focused on creating faster hardware. Ironically, this faster hardware has exacerbated the problem by making data still easier to create. Under such an onslaught, scientists often resort to heuristic deterministic sampling schemes (e.g., low-precision arithmetic, sampling every nth element) and sacrifice potentially valuable accuracy. Dramatically better results can be achieved via randomized algorithms, reducing the data size as much as or more than naive deterministic subsampling can achieve, while retaining the high accuracy of computing on the full data set. By randomized algorithms we mean those algorithms that employ some form of randomness in internal algorithmic decisions to accelerate time to solution, increase scalability, or improve reliability. Examples include matrix sketching for solving large-scale least-squares problems (see Figure 1) and stochastic gradient descent for training machine learning models. We are not recommending heuristic methods but rather randomized algorithms that have certificates of correctness and probabilistic guarantees of optimality and near-optimality. Such approaches can be useful beyond acceleration, for example, in understanding how to avoid measure zero worst-case scenarios that plague methods such as QR matrix factorization.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Scaling Graph Community Detection on the Tilera Many-core Architecture

In an era when power constraints and data movement are proving to be significant barriers for the application of high-end computing, the Tilera many-core architecture offers a low-power platform exhibiting many important characteristics of future systems, including a large number of simple cores, a sophisticated network-on-chip, and fine-grained control over memory and caching policies. While this emerging architecture has been previously studied for structured compute-intensive kernels, benchmarking the platform for data-bound, irregular applications present significant challenges that have remained unexplored. Community detection is an advanced prototypical graph-theoretic operation with applications in numerous scientific domains including life sciences, cyber security, and power systems. In this work, we explore multiple design strategies toward developing a scalable tool for community detection on the Tilera platform. Using several memory layout and work scheduling techniques we demonstrate speedups of up to 46x on 36 cores of the Tilera TileGX36 platform over the best serial implementation, and also show results that have comparable quality and performance to mainstream x86 platforms. To the best of our knowledge this is the first work addressing graph algorithms on the Tilera platform. This study demonstrates that through careful design space exploration, low-power many-core platforms like Tilera can be effectively exploited for graph algorithms that that embody all the essential characteristics of an irregular application.

community detection↗

DOE OSTI2018

A Magnetoencephalographic/Encephalographic (MEG/EEG) Brain-Computer Interface Driver for Interactive iOS Mobile Videogame Applications Utilizing the Hadoop Ecosystem, MongoDB, and Cassandra NoSQL Databases

In Phase I, we collected data on five subjects yielding over 90% positive performance in Magnetoencephalographic (MEG) mid-and post-movement activity. In addition, a driver was developed that substituted the actions of the Brain Computer Interface (BCI) as mouse button presses for real-time use in visual simulations. The process was interfaced to a flight visualization demonstration utilizing left or right brainwave thought movement, the user experiences, the aircraft turning in the chosen direction, or on iOS Mobile Warfighter Videogame application. The BCI’s data analytics of a subject’s MEG brain waves and flight visualization performance videogame analytics were stored and analyzed using the Hadoop Ecosystem as a quick retrieval data warehouse. In Phase II portion of the project involves the Emotiv Encephalographic (EEG) Wireless Brain–Computer interfaces (BCIs) allow for people to establish a novel communication channel between the human brain and a machine, in this case, an iOS Mobile Application(s). The EEG BCI utilizes advanced and novel machine learning algorithms, as well as the Spark Directed Acyclic Graph (DAG), Cassandra NoSQL database environment, and also the competitor NoSQL MongoDB database for housing BCI analytics of subject’s response and users’ intent illustrated for both MEG/EEG brainwave signal acquisition. The wireless EEG signals that were acquired from the OpenVibe and the Emotiv EPOC headset can be connected via Bluetooth to an iPhone utilizing a thin Client architecture. The use of NoSQL databases were chosen because of its schema-less architecture and Map Reduce computational paradigm algorithm for housing a user’s brain signals from each referencing sensor. Thus, in the near future, if multiple users are playing on an online network connection and an MEG/EEG sensor fails, or if the connection is lost from the smartphone and the webserver due to low battery power or failed data transmission, it will not nullify the NoSQL document-oriented (MongoDB) or column-oriented Cassandra databases. Additionally, NoSQL databases have fast querying and indexing methodologies, which are perfect for online game analytics and technology. In Phase II, we collected data on five MEG subjects, yielding over 90% positive performance on iOS Mobile Applications with Objective-C and C++, however on EEG signals utilized on three subjects with the Emotiv wireless headsets and (n < 10) subjects from the OpenVibe EEG database the Variational Bayesian Factor Analysis Algorithm (VBFA) yielded below 60% performance and we are currently pursuing extending the VBFA algorithm to work in the time-frequency domain referred to as VBFA-TF to enhance EEG performance in the near future. The novel usage of NoSQL databases, Cassandra and MongoDB, were the primary main enhancements of the BCI Phase II MEG/EEG brain signal data acquisition, queries, and rapid analytics, with MapReduce and Spark DAG demonstrating future implications for next generation biometric MEG/EEG NoSQL databases.

McClay, Wilbert↗

DOE OSTI2016

Using redundant transactions to verify the correctness of program code execution

In the described embodiments, a processor core (e.g., a GPU core) receives a section of program code to be executed in a transaction from another entity in a computing device. The processor core sends the section of program code to one or more compute units in the processor core to be executed in a first transaction and concurrently executed in a second transaction, thereby creating a “redundant transaction pair.” When the first transaction and the second transaction are completed, the processor core compares a read-set of the first transaction to a read-set of the second transaction and compares a write-set of the first transaction to a write-set of the second transaction. When the read-sets and the write-sets match and no transactional error condition has occurred, the processor core allows results from the first transaction to be committed to an architectural state of the computing device.

Gurumurthi, Sudhanva↗

DOE OSTI2015

A Survey of Techniques for Modeling and Improving Reliability of Computing Systems

Recent trends of aggressive technology scaling have greatly exacerbated the occurrences and impact of faults in computing systems. This has made `reliability' a first-order design constraint. To address the challenges of reliability, several techniques have been proposed. In this study, we provide a survey of architectural techniques for improving resilience of computing systems. We especially focus on techniques proposed for microarchitectural components, such as processor registers, functional units, cache and main memory etc. In addition, we discuss techniques proposed for non-volatile memory, GPUs and 3D-stacked processors. To underscore the similarities and differences of the techniques, we classify them based on their key characteristics. We also review the metrics proposed to quantify vulnerability of processor structures. Finally, we believe that this survey will help researchers, system-architects and processor designers in gaining insights into the techniques for improving reliability of computing systems.

3D-stacked processors↗

DOE OSTI2019

DeepDriveMD: Deep-Learning Driven Adaptive Molecular Simulations for Protein Folding

Simulations of biological macromolecules are important in understanding the physical basis of complex processes such as protein folding. However, even with increasing computational capacity and specialized architectures, the ability to simulate protein folding at atomistic scales still remains challenging. This stems from the dual aspects of high dimensionality of protein conformational landscapes, and the inability of atomistic molecular dynamics (MD) simulations to sufficiently sample these landscapes to observe folding events. Machine learning/deep learning (ML/DL) techniques, when combined with atomistic MD simulations offer the opportunity to potentially overcome these limitations by: (1) effectively reducing the dimensionality of MD simulations to automatically build latent representations that correspond to biophysically relevant reaction coordinates (RCs), and (2) driving MD simulations to automatically sample potentially novel conformational states based on these RCs. We examine how coupling DL approaches with MD simulations can lead to effective approaches to fold small proteins on supercomputers. In particular, we study the computational costs and effectiveness of scaling DL-coupled MD workflows implemented using RADICAL-Cybertools in folding two prototypical systems, namely Fs-peptide and the fast-folding variant of the villin head piece protein. We demonstrate that a DL-coupled MD workflow is able to effectively learn latent representations and drive adaptive simulations. Compared to traditional MD-based approaches, our approach achieves an effective performance gain in sampling the folded states by at least 2.3x. Together, our study provides quantitative basis to understand how coupling DL approaches to MD simulations, can lead to effective performance gains and reduced times to solution on supercomputing resources.

Lee, Hyungro↗

DOE OSTI2018

Post Moore's Law Report

Moore's law is driving an information revolution, worldwide economic growth, and is a tool for national security. This report explains how dire proclamations that "Moore's law is ending" are due to a natural redefinition of the phrase, but computing remains positioned to both drive economic growth and support national security. The computer industry used to be led by the semiconductor companies that made ever faster microprocessors with larger memories. However, control is shifting to new ways of designing computers, notably based on 3D chips and new analog and digital architectures. While artificial intelligence and quantum computing research have become mainstream pursuits, these latter two areas seem destined split off from Moore's law rather than become a part of it. We include a discussion of recent developments and opportunities in optical communications and computing.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Architecture and properties of TCR fuel form

The fuel form developed for the Transformational Challenge Reactor demonstration program leverages recent advances in manufacturing, materials, and computational sciences, delivering a new architecture for production of high-performance microencapsulated nuclear fuels. The fuel consists of conventionally manufactured uranium nitride tristructural isotropic fuel particles embedded inside a 3D-printed silicon carbide matrix. Finally, this paper describes the overall architecture and manufacturing process for this fuel form, its properties and behavior, and the ongoing development activities.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗