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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Distributed Multi-GPU Community Detection on Exascale Computing Platforms

Community detection is a fundamental operation in graph mining, and by uncovering hidden structures and patterns within complex systems it helps solve fundamental problems pertaining to social networks, such as information diffusion, epidemics, and recommender systems. Scaling graph algorithms for massive networks becomes challenging on modern distributed-memory multi-GPU (Graphics Processing Unit) systems due to limitations such as irregular memory access patterns, load imbalances, higher communication-computation ratios, and cross-platform support. We present a novel algorithm HiPDPL-GPU (distributed parallel Louvain) to address these challenges. We conduct experiments involving different partitioning techniques to achieve optimized performance of HiPDPL-GPU on the two largest supercomputers: Frontier and Summit. Remarkably, HiPDPL-GPU processes a graph with 4.2 billion edges in less than 3 minutes using 1024 GPUs. Qualitatively performance of HiPDPL-GPU is similar or better compared to other state-of-the-art CPU- and GPU-based implementations. While prior GPU implementations have predominantly employed CUDA, our first-of-its-kind implementation for community detection is cross-platform, accommodating both AMD and NVIDIA GPUs.

graph algorithms, high performance comptuing↗
DOE OSTI2021

Phasor Based Control with the Distributed, Extensible Grid Control Platform

This paper describes how to implement Phasor Based Control (PBC) using the Distributed, Extensible Grid Control (DEGC) Platform. PBC is a novel method for controlling distributed energy resources (DER) that coordinates a centralized optimization with distributed feedback controllers to enforce voltage phasor targets. DEGC is an open source software and communication platform designed for general DER control. We deployed PBC at Lawrence Berkeley Lab's FLEXLAB test site, conducting multiple hardware-in-the-loop test runs. Here, we describe how DEGC was used to implement PBC on hardware, and results demonstrating successful deployment.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2020

A Flexible and Secure Evaluation Platform for Overvoltage Protection in Power Electronics Systems

This paper summarizes the fault mechanisms specifically for the overvoltage protection schemes in power electronic converters and the resulted power electronics enabled systems. A flexible and secure evaluation platform for overvoltage protection, has also been presented based on this conceptual mechanism. The proposed platform aims at testing the protection performance of distinctive overvoltage protection schemes. It would be applied to verify the effectiveness, identify potential strengths and weaknesses, and obtain the most critical protection response time to provide sufficient engineering insights for the designer. The operation principle and detailed design guideline have been presented first. The comprehensive component stress has been analyzed. An intensive set of LTSpice simulations have been conducted to show the validity of the proposed assessment approach.

Zheng, Sheng↗
DOE OSTI2022

Seamless Wireless Communication Platform for Internet of Things Applications

The rapid growth of the Internet of Things (IoT) devices resulted in the proliferation of wireless technologies to cater to their increasing data rate requirements and support multiple applications. However, such ever-increasing wireless technologies present numerous challenges such as incompatible wireless standards, increased energy consumption, and insecure communication. The traditional gateways proposed in the literature suffers from limitations such as computational complexity, resource requirements, increased cost, and device size. We vision an era of seamless wireless communication to alleviate the aforementioned challenges in IoT applications. through three inter-dependent functionalities namely detection and identification of wireless technologies, energy-efficient transmit power control, and secure end-to-end communication. To prove the concept, a new gateway is proposed to achieve these three functionalities with only physical layer measurements so that the different communication protocols in the higher layers can be avoided. Novel schemes are conceptualized for resource-limited seamless IoT applications. Moreover, the conceptual seamless IoT platform is validated through software-based computer simulation and software-defined radio-based testbed implementation. Finally, the preliminary analysis demonstrates that the proposed platform has great potential in advancing seamless IoT applications.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Building near-real-time processing pipelines with the spark-MPI platform

Advances in detectors and computational technologies provide new opportunities for applied research and the fundamental sciences. Concurrently, dramatic increases in the three V's (Volume, Velocity, and Variety) of experimental data and the scale of computational tasks produced the demand for new real-time processing systems at experimental facilities. Recently, this demand was addressed by the Spark-MPI approach connecting the Spark data-intensive platform with the MPI high-performance framework. In contrast with existing data management and analytics systems, Spark introduced a new middleware based on resilient distributed datasets (RDDs), which decoupled various data sources from high-level processing algorithms. The RDD middleware significantly advanced the scope of data-intensive applications, spreading from SQL queries to machine learning to graph processing. Spark-MPI further extended the Spark ecosystem with the MPI applications using the Process Management Interface. The paper explores this integrated platform within the context of online ptychographic and tomographic reconstruction pipelines.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Leveraging Compiler-Based Translation to Evaluate a Diversity of Exascale Platforms

Accelerator-based heterogeneous computing is the de facto standard in current and upcoming exascale machines. These heterogeneous resources empower computational scientists to select a machine or platform well-suited to their domain or applications. However, this diversity of machines also poses challenges related to programming model selection: inconsistent availability of programming models across different exascale systems, lack of performance portability for those programming models that do span several systems, and inconsistent performance between different models on a single platform. We explore these challenges on exascale-similar hardware, including AMD MI100 and NVIDIA A100 GPUs. By extending the sourceto-source compiler OpenARC, we demonstrate the power of automated translation of applications written in a single frontend programming model (OpenACC) into a variety of backend models (OpenMP, OpenCL, CUDA, HIP) that span the upcoming exascale environments. This translation enables us to compare performance within and across devices and to analyze programming model behavior with profiling tools.

Lambert, Jacob↗
DOE OSTI2016

Cyber-Physical Test Platform for Microgrids: Combining Hardware, Hardware-in-the-Loop, and Network-Simulator-in-the-Loop

This paper presents a cyber-physical testbed, developed to investigate the complex interactions between emerging microgrid technologies such as grid-interactive power sources, control systems, and a wide variety of communication platforms and bandwidths. The cyber-physical testbed consists of three major components for testing and validation: real time models of a distribution feeder model with microgrid assets that are integrated into the National Renewable Energy Laboratory's (NREL) power hardware-in-the-loop (PHIL) platform; real-time capable network-simulator-in-the-loop (NSIL) models; and physical hardware including inverters and a simple system controller. Several load profiles and microgrid configurations were tested to examine the effect on system performance with increasing channel delays and router processing delays in the network simulator. Testing demonstrated that the controller's ability to maintain a target grid import power band was severely diminished with increasing network delays and laid the foundation for future testing of more complex cyber-physical systems.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2019

An Asynchronous Real-time Co-simulation Platform for Modeling Interaction between Microgrids and Power Distribution Systems

This paper presents the modeling framework of an asynchronous, real-time co-simulation platform for modeling the interactions between microgrids and power distribution systems. Components of each microgrid are simulated on the OPAL-RT eMEGASIM platform so that electromagnetic transients of the inverter units are modeled at a time step of 100 microseconds. The 3-phase unbalanced distribution feeder that microgrids are connected to is simulated by using the OPAL-RT ePHASORSIM so that load transients, capacitor switching, and tap-changing events can be modeled. A MATLAB-based microgrid controller will interface controllable microgrid components through the Modbus communication. This co-simulation framework allows different microgrid controller logic to be developed and tested on a hardware-in-the-loop testbed considering both the inverter-level transient and the dynamic response of loads and utility equipment. Because the controller communicates with controllable devices via actual communication links, the impact of communication errors, delays, or denial-of-service can also be properly quantified.

Xie, Fuhong↗
DOE OSTI2021

CPS Testbed Architectures for WAMPAC using Industrial Substation and Control Center Platforms and Attack-Defense Evaluation

Advanced persistent threats and cyberattacks can impact wide-area monitoring, protection, and control (WAMPAC) system operation. Many cyber-physical system (CPS) testbeds have been developed for attack-defense experimentation and attack-resiliency tools evaluation for WAMPAC, but they are limited to a simulation-and-emulation based environment. This paper presents a quasi-realistic CPS attack-defense testbed-based framework for WAMPAC applications using the industrial substation and control center platforms such as eTerra integrated with the hardware-in-the-loop CPS smart grid testbed available at Iowa State University. The proposed framework includes various combinations of industry-grade substation and control center platforms, communication topologies, real-time digital simulators, and a novel cyber-physical distributed intrusion-and-anomaly detection system (D-IADS) for WAMPAC applications. The D-IADS includes a master at the control center and geographically distributed sensor devices at each substation. Each D-IADS sensor deployed at a substation or control center network monitors ingress and egress traffic, detect intrusions, and dispatch alerts to the D-IADS master. The D-IADS master centrally monitors and analyze the alerts and controls D-IADS sensors. We considered an EMP60 synthetic CPS grid as a case study to demonstrate the framework and proposed D-IADS for WAMPAC applications against cyberattack vectors such as Man-in-the-Middle DNP3 attack, denial-of-service, and data-integrity attacks.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2011

Towards Composing Data Aware Systems Biology Workflows on Cloud Platforms: A MeDICi-based Approach

Cloud computing is being increasingly adopted for deploying systems biology scientific workflows. Scientists developing these workflows use a wide variety of fragmented and competing data sets and computational tools of all scales to support their research. To this end, the synergy of client side workflow tools with cloud platforms is a promising approach to share and reuse data and workflows. In such systems, the location of data and computation is essential consideration in terms of quality of service for composing a scientific workflow across remote cloud platforms. In this paper, we describe a cloud-based workflow for genome annotation processing that is underpinned by MeDICi - a middleware designed for data intensive scientific applications. The workflow implementation incorporates an execution layer for exploiting data locality that routes the workflow requests to the processing steps that are colocated with the data. We demonstrate our approach by composing two workflowswith the MeDICi pipelines.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

An Islanding Detection Test Platform for Multi-Inverter Islands Using Power HIL

When an unintentional island is formed on the electric power system, distributed energy resources (DERs) are typically required to detect and de-energize the island. This requirement may become more challenging as the number of DERs in an island rises. Thus, it is of interest to experimentally verify whether DERs can successfully detect and de-energize islands containing many DERs connected at different points. This paper presents a power hardware-in-the-loop (PHIL) platform for testing the duration of islands containing multiple inverters connected at multiple points in a network. The PHIL platform uses real-time simulation to represent islanded distribution circuits, with DER inverters connected in hardware. This allows efficient testing of a large number of island configurations simply by changing the distribution circuit model in the real-time simulator. A method for calculating the quality factor of an arbitrary distribution circuit in real time, designed for anti-islanding tests, is also presented. Experimental results are included demonstrating the use of the PHIL method to test a variety of three-inverter islands.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2024

IRIS: A Performance-Portable Framework for Cross-Platform Heterogeneous Computing

From edge to exascale, computer architectures are becoming more heterogeneous and complex. The systems typically have fat nodes, with multicore CPUs and multiple hardware accelerators such as GPUs, FPGAs, and DSPs. This complexity is causing a crisis in programming systems and performance portability. Several programming systems are working to address these challenges, but the increasing architectural diversity is forcing software stacks and applications to be specialized for each architecture. As we show, all of these approaches critically depend on their software framework for discovery, execution, scheduling, and data orchestration. To address this challenge, we believe that a more agile and proactive software framework is essential to increase performance portability and improve user productivity. To this end, we have designed and implemented IRIS: a performance-portable framework for cross-platform heterogeneous computing. IRIS can discover available resources, manage multiple diverse programming platforms (e.g., CUDA, Hexagon, HIP, Level Zero, OpenCL, OpenMP) simultaneously in the same execution, respect data dependencies, orchestrate data movement proactively, and provide for user-configurable scheduling. To simplify data movement, IRIS introduces a shared virtual device memory with relaxed consistency among different heterogeneous devices. IRIS also adds an automatic kernel workload partitioning technique using the polyhedral model so that it can resize kernels for a wide range of devices. Our evaluation on three architectures, ranging from Qualcomm Snapdragon to a Summit supercomputer node, shows that IRIS improves portability across a wide range of diverse heterogeneous architectures with negligible overhead.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Development of polarization-sensitive optical coherence tomography imaging platform and metrics to quantify electrostimulation-induced peripheral nerve injury in vivo in a small animal model

Neuromodulation devices are rapidly evolving for the treatment of neurological diseases and conditions. Injury from implantation or long-term use without obvious functional losses is often only detectable through terminal histology. New technologies are needed that assess the peripheral nervous system (PNS) under normal and diseased or injured conditions. We aim to demonstrate an imaging and stimulation platform that can elucidate the biological mechanisms and impacts of neurostimulation in the PNS and apply it to the sciatic nerve to extract imaging metrics indicating electrical overstimulation. A sciatic nerve injury model in a 15-rat cohort was observed using a newly developed imaging and stimulation platform that can detect electrical overstimulation effects with polarization-sensitive optical coherence tomography. The sciatic nerve was electrically stimulated using a custom-developed nerve holder with embedded electrodes for 1 h, followed by a 1-h recovery period, delivered at above-threshold Shannon model k-values in experimental groups: sham control (SC, n = 5, 0.0 mA / 0 Hz), stimulation level 1 (SL1, n = 5, 3.4 mA / 50 Hz, and k = 2.57), and stimulation level 2 (SL2, n = 5, 6.8 mA / 100 Hz, and k = 3.17). The stimulation and imaging system successfully captured study data across the cohort. When compared to a SC after a 1-week recovery, the fascicle closest to the stimulation lead showed an average change of +4 % / – 309 % (SL1/SL2) in phase retardation and –79 % / – 148 % in optical attenuation relative to SC. Analysis of immunohistochemistry (IHC) shows a +1 % / – 36 % difference in myelin pixel counts and –13 % / + 29 % difference in axon pixel counts, and an overall increase in cell nuclei pixel count of +20 % / + 35 % . These metrics were consistent with IHC and hematoxylin/eosin tissue section analysis. The poststimulation changes observed in our study are manifestations of nerve injury and repair, specifically degeneration and angiogenesis. Optical imaging metrics quantify these processes and may help evaluate the safety and efficacy of neuromodulation devices.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2011

A wireless sensor tag platform for container security and integrity

Cargo containers onboard ships are widely used in the global supply chain. The need for container security is evidenced by the Container Security Initiative launched by the U.S. Bureau of Customs and Border Protection (CBP). One method of monitoring cargo containers is using low power wireless sensor tags. The wireless sensor tags are used to set up a network that is comprised of tags internal to the container and a central device. The sensor network reports alarms and other anomalies to a central device, which then relays the message to an outside network upon arrival at the destination port. This allows the port authorities to have knowledge of potential security or integrity issues before physically examining the container. Challenges of using wireless sensor tag networks for container security include battery life, size, environmental conditions, information security, and cost among others. PNNL developed an active wireless sensor tag platform capable of reporting data wirelessly to a central node as well as logging data to nonvolatile memory. The tags, operate at 2.4 GHz over an IEEE 802.15.4 protocol, and were designed to be distributed throughout the inside of a shipping container in the upper support frame. The tags are mounted in a housing that allows for simple and efficient installation or removal prior to, during, or after shipment. The distributed tags monitor the entire container volume. The sensor tag platform utilizes low power electronics and provides an extensible sensor interface for incorporating a wide range of sensors including chemical, biological, and environmental sensors.

36 MATERIALS SCIENCE↗
DOE OSTI2014

SU-E-T-508: End to End Testing of a Prototype Eclipse Module for Planning Modulated Arc Therapy On the Siemens Platform

Purpose: The latest clinical implementation of the Siemens Artiste linac allows for delivery of modulated arcs (mARC) using full-field flattening filter free (FFF) photon beams. The maximum doserate of 2000 MU/min is well suited for high dose treatments such as SBRT. We tested and report on the performance of a prototype Eclipse TPS module supporting mARC capability on the Artiste platform. Method: our spine SBRT patients originally treated with 12/13 field static-gantry IMRT (SGIMRT) were chosen for this study. These plans were designed to satisfy RTOG0631 guidelines with a prescription of 16Gy in a single fraction. The cases were re-planned as mARC plans in the prototype Eclipse module using the 7MV FFF beam and required to satisfy RTOG0631 requirements. All plans were transferred from Eclipse, delivered on a Siemens Artiste linac and dose-validated using the Delta4 system. Results: All treatment plans were straightforwardly developed, in timely fashion, without challenge or inefficiency using the prototype module. Due to the limited number of segments in a single arc, mARC plans required 2-3 full arcs to yield plan quality comparable to SGIMRT plans containing over 250 total segments. The average (3%/3mm) gamma pass-rate for all arcs was 98.5±1.1%, thus demonstrating both excellent dose prediction by the AAA dose algorithm and excellent delivery fidelity. Mean delivery times for the mARC plans(10.5±1.7min) were 50-70% lower than the SGIMRT plans(26±2min), with both delivered at 2000 MU/min. Conclusion: A prototype Eclipse module capable of planning for Burst Mode modulated arc delivery on the Artiste platform has been tested and found to perform efficiently and accurately for treatment plan development and delivered-dose prediction. Further investigation of more treatment sites is being carried out and data will be presented.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

IBEX: An open infrastructure software platform to facilitate collaborative work in radiomics

Purpose: Radiomics, which is the high-throughput extraction and analysis of quantitative image features, has been shown to have considerable potential to quantify the tumor phenotype. However, at present, a lack of software infrastructure has impeded the development of radiomics and its applications. Therefore, the authors developed the imaging biomarker explorer (IBEX), an open infrastructure software platform that flexibly supports common radiomics workflow tasks such as multimodality image data import and review, development of feature extraction algorithms, model validation, and consistent data sharing among multiple institutions. Methods: The IBEX software package was developed using the MATLAB and C/C++ programming languages. The software architecture deploys the modern model-view-controller, unit testing, and function handle programming concepts to isolate each quantitative imaging analysis task, to validate if their relevant data and algorithms are fit for use, and to plug in new modules. On one hand, IBEX is self-contained and ready to use: it has implemented common data importers, common image filters, and common feature extraction algorithms. On the other hand, IBEX provides an integrated development environment on top of MATLAB and C/C++, so users are not limited to its built-in functions. In the IBEX developer studio, users can plug in, debug, and test new algorithms, extending IBEX’s functionality. IBEX also supports quality assurance for data and feature algorithms: image data, regions of interest, and feature algorithm-related data can be reviewed, validated, and/or modified. More importantly, two key elements in collaborative workflows, the consistency of data sharing and the reproducibility of calculation result, are embedded in the IBEX workflow: image data, feature algorithms, and model validation including newly developed ones from different users can be easily and consistently shared so that results can be more easily reproduced between institutions. Results: Researchers with a variety of technical skill levels, including radiation oncologists, physicists, and computer scientists, have found the IBEX software to be intuitive, powerful, and easy to use. IBEX can be run at any computer with the windows operating system and 1GB RAM. The authors fully validated the implementation of all importers, preprocessing algorithms, and feature extraction algorithms. Windows version 1.0 beta of stand-alone IBEX and IBEX’s source code can be downloaded. Conclusions: The authors successfully implemented IBEX, an open infrastructure software platform that streamlines common radiomics workflow tasks. Its transparency, flexibility, and portability can greatly accelerate the pace of radiomics research and pave the way toward successful clinical translation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

SU-E-T-499: Initial Developments of An OpenCL-Based Cross-Platform Monte Carlo Dose Engine for Carbon Ion Therapy

Purpose Dose calculation is of critical importance for carbon ion therapy. Monte Carlo (MC) simulation is considered to be the most accurate method for calculation of absorbed dose and of all the more fundamental physical quantities related to biological effects. The long computation time, however, limits its routine clinical applications. We have recently started developing a fast MC package, gCMC for carbon therapy on a parallel processing platform, e.g. GPU, aiming at achieving sufficient efficiency to enable MC in clinically important tasks. This abstract reports our progress. Methods gCMC was developed in OpenCL environment. Our initial developments focused on water material. gCMC supported carbon ion transport in the energy range of 1–450 MeV/u. A Class II condensed history algorithm was implemented for charged particle transport simulations with stopping power computed via Bethe-Bloch equation. Energy straggling and multiple scattering were modeled. Total cross section of nuclear interaction was extracted from Geant4. At present, nuclear interaction events were sampled but transports of secondary particles were not included. Results We tested cases with a homogeneous water phantom and a pencil carbon ion beam with energy of 200–400 MeV/u. When only electro-magnetic channel was included, dose/fluence difference between gCMC and Geant4 results averaged within 10% isodose line was <0.5% of the maximum dose/fluence. After enabling nuclear interactions without transporting secondary particles, dose and fluence agreed with the corresponding results computed by Geant4 with <1% difference. Due to the support for multiple platforms of OpenCL, gCMC was executable on NVidia and AMD GPUs, and Intel CPUs. It took ∼50 sec to transport 107 200MeV/u source carbon ions on an NVidia Titan GPU card. Conclusion Preliminary studies have demonstrated the accuracy and efficiency of gCMC. With further developments in near future, gCMC will potentially achieve clinically acceptable fast and accurate MC simulations for carbon ion therapy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

TU-AB-303-08: GPU-Based Software Platform for Efficient Image-Guided Adaptive Radiation Therapy

Purpose: In this study, we develop an integrated software platform for adaptive radiation therapy (ART) that combines fast and accurate image registration, segmentation, and dose computation/accumulation methods. Methods: The proposed system consists of three key components; 1) deformable image registration (DIR), 2) automatic segmentation, and 3) dose computation/accumulation. The computationally intensive modules including DIR and dose computation have been implemented on a graphics processing unit (GPU). All required patient-specific data including the planning CT (pCT) with contours, daily cone-beam CTs, and treatment plan are automatically queried and retrieved from their own databases. To improve the accuracy of DIR between pCT and CBCTs, we use the double force demons DIR algorithm in combination with iterative CBCT intensity correction by local intensity histogram matching. Segmentation of daily CBCT is then obtained by propagating contours from the pCT. Daily dose delivered to the patient is computed on the registered pCT by a GPU-accelerated superposition/convolution algorithm. Finally, computed daily doses are accumulated to show the total delivered dose to date. Results: Since the accuracy of DIR critically affects the quality of the other processes, we first evaluated our DIR method on eight head-and-neck cancer cases and compared its performance. Normalized mutual-information (NMI) and normalized cross-correlation (NCC) computed as similarity measures, and our method produced overall NMI of 0.663 and NCC of 0.987, outperforming conventional methods by 3.8% and 1.9%, respectively. Experimental results show that our registration method is more consistent and roust than existing algorithms, and also computationally efficient. Computation time at each fraction took around one minute (30–50 seconds for registration and 15–25 seconds for dose computation). Conclusion: We developed an integrated GPU-accelerated software platform that enables accurate and efficient DIR, auto-segmentation, and dose computation, thus supporting an efficient ART workflow. This work was supported by NIH/NCI under grant R42CA137886.

60 APPLIED LIFE SCIENCES↗