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DOE OSTI2012

Supporting the Global Arrays PGAS Model Using MPI One-Sided Communication

The industry-standard Message Passing Interface (MPI) provides one-sided communication functionality and is available on virtually every parallel computing system. However, it is believed that MPI’s one-sided model is not rich enough to support higher-level global address space parallel programming models. We present the first successful application of MPI one-sided communication as a runtime system for a PGAS model, Global Arrays (GA). This work has an immediate impact on users of GA applications, such as NWChem, who often must wait several months to a year or more before GA becomes available on a new architecture. We explore challenges present in the application of MPI-2 to PGAS models and motivate new features in the upcoming MPI-3 standard. The performance of our system is evaluated on several popular high-performance computing architectures through communication benchmarking and application benchmarking using the NWChem computational chemistry suite.

ARMCI↗

DOE OSTI2015

Constructing Surrogate Models of Complex Systems with Enhanced Sparsity: Quantifying the influence of conformational uncertainty in biomolecular solvation

Biomolecules exhibit conformational fluctuations near equilibrium states, inducing uncertainty in various biological properties in a dynamic way. We have developed a general method to quantify the uncertainty of target properties induced by conformational fluctuations. Using a generalized polynomial chaos (gPC) expansion, we construct a surrogate model of the target property with respect to varying conformational states. We also propose a method to increase the sparsity of the gPC expansion by defining a set of conformational “active space” random variables. With the increased sparsity, we employ the compressive sensing method to accurately construct the surrogate model. We demonstrate the performance of the surrogate model by evaluating fluctuation-induced uncertainty in solvent-accessible surface area for the bovine trypsin inhibitor protein system and show that the new approach offers more accurate statistical information than standard Monte Carlo approaches. Further more, the constructed surrogate model also enables us to directly evaluate the target property under various conformational states, yielding a more accurate response surface than standard sparse grid collocation methods. In particular, the new method provides higher accuracy in high-dimensional systems, such as biomolecules, where sparse grid performance is limited by the accuracy of the computed quantity of interest. Our new framework is generalizable and can be used to investigate the uncertainty of a wide variety of target properties in biomolecular systems.

coarse graining↗

DOE OSTI2013

Automated Patient Identification and Localization Error Detection Using 2-Dimensional to 3-Dimensional Registration of Kilovoltage X-Ray Setup Images

Purpose: To determine whether kilovoltage x-ray projection radiation therapy setup images could be used to perform patient identification and detect gross errors in patient setup using a computer algorithm. Methods and Materials: Three patient cohorts treated using a commercially available image guided radiation therapy (IGRT) system that uses 2-dimensional to 3-dimensional (2D-3D) image registration were retrospectively analyzed: a group of 100 cranial radiation therapy patients, a group of 100 prostate cancer patients, and a group of 83 patients treated for spinal lesions. The setup images were acquired using fixed in-room kilovoltage imaging systems. In the prostate and cranial patient groups, localizations using image registration were performed between computed tomography (CT) simulation images from radiation therapy planning and setup x-ray images corresponding both to the same patient and to different patients. For the spinal patients, localizations were performed to the correct vertebral body, and to an adjacent vertebral body, using planning CTs and setup x-ray images from the same patient. An image similarity measure used by the IGRT system image registration algorithm was extracted from the IGRT system log files and evaluated as a discriminant for error detection. Results: A threshold value of the similarity measure could be chosen to separate correct and incorrect patient matches and correct and incorrect vertebral body localizations with excellent accuracy for these patient cohorts. A 10-fold cross-validation using linear discriminant analysis yielded misclassification probabilities of 0.000, 0.0045, and 0.014 for the cranial, prostate, and spinal cases, respectively. Conclusions: An automated measure of the image similarity between x-ray setup images and corresponding planning CT images could be used to perform automated patient identification and detection of localization errors in radiation therapy treatments.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2019

AHEAD: A Tool for Projecting Next-Generation Hardware Enhancements on GPU-Accelerated Systems

Starting with the Titan supercomputer (at the Oak Ridge Leadership Computing Facility, OLCF) in 2012, top supercomputers have Increasingly leveraged the performance of GPUs to support large-scale computational science. The current No. 1 machine, the 200 petaflop Summit system at OLCF, is a GPU-based machine. Accelerator-based architectures, however, add additional complexity due to node heterogeneity. To inform procurement decisions, supercomputing centers need the tools to quickly model the impact of changes of the node architectures on application performance. We present AHEAD, a profiling and modeling tool to quantify the impact of intra-node communication mechanism (e.g., PCI or NVLink) on application performance. Our experiments show average weighted relative errors of ~19% and ~23% for five CORAL-2 (a collaboration between multiple US Department of Energy, DOE, labs to procure Exascale systems) and 12 Rodinia benchmarks respectively, without running the applications on the target future node.

Abdelhafez, Hazem A.↗

DOE OSTI2019

Stochastic self-tuning hybrid algorithm for reaction-diffusion systems

Many biochemical phenomena involve reactants with vastly different concentrations, some of which are amenable to continuum-level descriptions, while the others are not. We present a hybrid self-tuning algorithm to model such systems. The method combines microscopic (Brownian) dynamics for diffusion with mesoscopic (Gillespie-type) methods for reactions and remains efficient in a wide range of regimes and scenarios with large variations of concentrations. Furthermore, its accuracy, robustness, and versatility are balanced by redefining propensities and optimizing the mesh size and time step. We use a bimolecular reaction to demonstrate the potential of our method in a broad spectrum of scenarios: from almost completely reaction-dominated systems to cases where reactions rarely occur or take place very slowly. The simulation results show that the number of particles present in the system does not degrade the performance of our method. This makes it an accurate and computationally efficient tool to model complex multireaction systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2014

WE-G-BRD-03: Development of a Real-Time Optical Tracking Goggle System (OTGS) for Intracranial Stereotactic Radiotherapy

Purpose: Optical tracking systems (OTS) are an acceptable alternative to frame-based stereotactic radiotherapy (SRT). However, current surface-based OTS lack the ability to target exclusively rigid/bony anatomical features. We propose a novel marker-based optical tracking goggle system (OTGS) that provides real-time guidance based on the nose/facial bony anatomy. This ongoing study involves the development and characterization of the OTGS for clinical implementation in intracranial stereotactic radiotherapy. Methods: The OTGS consists of eye goggles, a custom thermoplastic nosepiece, and 6 infrared markers pre-attached to the goggles. A phantom and four healthy volunteers were used to evaluate the calibration/registration accuracy, intrafraction accuracy, interfraction reproducibility, and end-to-end accuracy of the OTGS. The performance of the OTGS was compared with that of the frameless SonArray system and cone-beam computed tomography (CBCT) for volunteer and phantom cases, respectively. The performance of the OTGS with commercial immobilization devices and under treatment conditions (i.e., couch rotation and translation range) was also evaluated. Results: The difference in the calibration/registration accuracy of 24 translations or rotation combinations between CBCT and in-house OTS software was within 0.5 mm/0.4°. The mean intrafraction and interfraction accuracy among the volunteers was 0.004+/−0.4mm with −0.09+/−0.5° (n=6,170) and −0.26+/−0.8mm with 0.15+/0.8° (n=11), respectively. The difference in end-to-end accuracy between the OTGS and CBCT was within 1.3 mm/1.1°. The predetermined marker pattern (1) minimized marker occlusions, (2) allowed for continuous tracking for couch angles +/− 90°, (3) and eliminated individual marker misplacement. The device was feasible with open and half masks for immobilization. Conclusion: Bony anatomical localization eliminated potential errors due to facial hair changes and/or soft tissue deformation. The OTGS offers a workflow-friendly, patient-friendly solution for intracranial SRT, while being comparable to other real-time options. The minimum rotation uncertainty of the OTGS can be combined with CBCT to ensure maximum accuracy for high-precision SRT.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2012

NEAMS Update: Quarterly Report for October - December 2011

The Advanced Modeling and Simulation Office within the DOE Office of Nuclear Energy (NE) has been charged with revolutionizing the design tools used to build nuclear power plants during the next 10 years. To accomplish this, the DOE has brought together the national laboratories, U.S. universities, and the nuclear energy industry to establish the Nuclear Energy Advanced Modeling and Simulation (NEAMS) Program. The mission of NEAMS is to modernize computer modeling of nuclear energy systems and improve the fidelity and validity of modeling results using contemporary software environments and high-performance computers. NEAMS will create a set of engineering-level codes aimed at designing and analyzing the performance and safety of nuclear power plants and reactor fuels. The truly predictive nature of these codes will be achieved by modeling the governing phenomena at the spatial and temporal scales that dominate the behavior. These codes will be executed within a simulation environment that orchestrates code integration with respect to spatial meshing, computational resources, and execution to give the user a common 'look and feel' for setting up problems and displaying results. NEAMS is building upon a suite of existing simulation tools, including those developed by the federal Scientific Discovery through Advanced Computing and Advanced Simulation and Computing programs. NEAMS also draws upon existing simulation tools for materials and nuclear systems, although many of these are limited in terms of scale, applicability, and portability (their ability to be integrated into contemporary software and hardware architectures). NEAMS investments have directly and indirectly supported additional NE research and development programs, including those devoted to waste repositories, safeguarded separations systems, and long-term storage of used nuclear fuel. NEAMS is organized into two broad efforts, each comprising four elements. The quarterly highlights October-December 2011 are: (1) Version 1.0 of AMP, the fuel assembly performance code, was tested on the JAGUAR supercomputer and released on November 1, 2011, a detailed discussion of this new simulation tool is given; (2) A coolant sub-channel model and a preliminary UO{sub 2} smeared-cracking model were implemented in BISON, the single-pin fuel code, more information on how these models were developed and benchmarked is given; (3) The Object Kinetic Monte Carlo model was implemented to account for nucleation events in meso-scale simulations and a discussion of the significance of this advance is given; (4) The SHARP neutronics module, PROTEUS, was expanded to be applicable to all types of reactors, and a discussion of the importance of PROTEUS is given; (5) A plan has been finalized for integrating the high-fidelity, three-dimensional reactor code SHARP with both the systems-level code RELAP7 and the fuel assembly code AMP. This is a new initiative; (6) Work began to evaluate the applicability of AMP to the problem of dry storage of used fuel and to define a relevant problem to test the applicability; (7) A code to obtain phonon spectra from the force-constant matrix for a crystalline lattice has been completed. This important bridge between subcontinuum and continuum phenomena is discussed; (8) Benchmarking was begun on the meso-scale, finite-element fuels code MARMOT to validate its new variable splitting algorithm; (9) A very computationally demanding simulation of diffusion-driven nucleation of new microstructural features has been completed. An explanation of the difficulty of this simulation is given; (10) Experiments were conducted with deformed steel to validate a crystal plasticity finite-element code for bodycentered cubic iron; (11) The Capability Transfer Roadmap was completed and published as an internal laboratory technical report; (12) The AMP fuel assembly code input generator was integrated into the NEAMS Integrated Computational Environment (NiCE). More details on the planned NEAMS computing environment is given; and (13) The NEAMS program website (neams.energy.gov) is nearly ready to launch.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2014

Cross-Layer Self-Adaptive/Self-Aware System Software for Exascale Systems

The extreme level of parallelism coupled with the limited available power budget expected in the exascale era brings unprecedented challenges that demand optimization of performance, power and resiliency in unison. Scalability on such systems is of paramount importance, while power and reliability issues may change the execution environment in which a parallel application runs. To solve these challenges exascale systems will require an introspective system software that combines system and application observations across all system stack layers with online feedback and adaptation mechanisms. In this paper we propose the design of a novel self-aware, self-adaptive system software in which a kernel-level Monitor, which continuously inspects the evolution of the target system through observation of Sensors, is combined with a user-level Controller, which reacts to changes in the execution environment, explores opportunities to increase performance, save power and adapts applications to new execution scenarios. We show that the monitoring system accurately monitors the evolution of parallel applications with a runtime overhead below 1-2%. As a test case, we design and implement a user-runtime system that aims at optimizing application’s performance and system power consumption on complex hierarchical architectures. Our results show that our adaptive system reaches 98% of performance efficiency of manually-tuned applications.

High Performance computing, Self-aware/self-adapti↗

DOE OSTI2016

SU-F-J-47: Inherent Uncertainty in the Positional Shifts Determined by a Volumetric Cone Beam Imaging System

Purpose: To quantify inherent uncertainty associated with a volumetric imaging system in its determination of positional shifts. Methods: The study was performed on an Elekta Axesse™ linac’s XVI cone beam computed tomography (CBCT) system. A CT image data set of a Penta- Guide phantom was used as reference image by placing isocenter at the center of the phantom.The phantom was placed arbitrarily on the couch close to isocenter and CBCT images were obtained. The CBCT dataset was matched with the reference image using XVI software and the shifts were determined in 6-dimensions. Without moving the phantom, this process was repeated 20 times consecutively within 30 minutes on a single day. Mean shifts and their standard deviations in all 6-dimensions were determined for all the 20 instances of imaging. For any given day, the first set of shifts obtained was kept as reference and the deviations of the subsequent 19 sets from the reference set were scored. Mean differences and their standard deviations were determined. In this way, data were obtained for 30 consecutive working days. Results: Tabulating the mean deviations and their standard deviations observed on each day for the 30 measurement days, systematic and random errors in the determination of shifts by XVI software were calculated. The systematic errors were found to be 0.03, 0.04 and 0.03 mm while random errors were 0.05, 0.06 and 0.06 mm in lateral, craniocaudal and anterio-posterior directions respectively. For rotational shifts, the systematic errors were 0.02°, 0.03° and 0.03° and random errors were 0.06°, 0.05° and 0.05° in pitch, roll and yaw directions respectively. Conclusion: The inherent uncertainties in every image guidance system should be assessed and baseline values established at the time of its commissioning. These shall be periodically tested as part of the QA protocol.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Quantum computing for nuclear physics

Future quantum computers are anticipated to be able to perform simulations of quantum many-body systems and quantum field theories that lie beyond the capabilities of classical computation. This will lead to new insights and predictions for systems ranging from dense non-equilibrium matter, to low-energy nuclear structure and reactions, to high-energy collisions. I present an overview of digital quantum simulations in nuclear physics, with select examples relevant for studies of quark matter.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2019

High-Fidelity Calibration and Characterization of Hyperspectral Computed Tomography System

This document archives the results developed by the Lab Directed Research and Development (LDRD) project sponsored by Sandia National Laboratories (SNL). In this work, a numerical study was performed to show the feasibility of approximating the non-linear operator of SNL's unique high-energy hyperspectral computed tomography system as a sequence of linear operators. The four main results gained from this work include the development of a simulation test-bed using a particle-transport Monte Carlo approach; the demonstration to assemble a linear operator of almost-arbitrary resolution for a given narrow energy window, developing a compression approach to dramatically reduce the size of the linear operator via a spline approach, and the demonstration of using the linear operator to perform processing of x-ray data; in this case, the development of an iterative reconstruction method. This numerical study has indicated that if these results can be replicated on the SNL system, the improved performance could be revolutionary as the method to approximate the nonlinear operator for a hyperspectral CT system is not feasible to perform on a traditional CT system.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2019

SimCCS: An open-source tool for optimizing CO 2 capture, transport, and storage infrastructure

Commercial-scale carbon capture and storage (CCS) technology will involve deploying infrastructure on a massive and costly scale. This effort will require careful and comprehensive planning to ensure that capture locations, storage sites, and the dedicated CO 2 distribution pipelines are selected in a robust and cost-effective manner. Presented in 2009, SimCCS is an optimization model for integrated system design that enables researchers, stakeholders, and policy makers to design CCS infrastructure networks. SimCCS 2.0 is a complete, ground-up redesign that is now a portable software package, useable and shareable by the CCS research, industrial, policy, and public communities. SimCCS 2.0 integrates multiple new capabilities including a refined optimization model, novel candidate network generation techniques, and optional integration with high-performance computing platforms. Accessing user-provided CO 2 source, sink, and transportation data, SimCCS 2.0 creates candidate transportation routes and formalizes an optimization problem that determines the most cost-effective CCS system design. This optimization problem is further solved either through a high-performance computing interface, or through third-party software on a local desktop computing platform. Finally, SimCCS 2.0 employs an open-access geographic information system framework to enable analysis and visualization capabilities. SimCCS 2.0 is written in Java and is publicly available via GitHub to encourage collaboration, modification, and community development.

42 ENGINEERING↗

DOE OSTI2025

Verification of the PERSENT Software

Ongoing commercial design activities require a thorough verification of the Argonne Reactor Computation codes be performed. DIF3D is central to this system and substantial work has been done to verify its accuracy on several identified commercial needs. This manuscript details the verification work done on PERSENT which relies upon the DIF3D code for its forward and adjoint flux solution. Previous work identified the PERSENT features required to be verified to support commercial design activities, features of which are generally applicable to hexagonal-Z fast reactor designs. The scope of this verification effort includes verifying PERSENT’s ability to correctly calculate four key quantities: perturbation worth distributions, kinetics parameters, sensitivity coefficients, and cross section uncertainty quantification. This manuscript provides the verification tasks and their results with respect to these quantities needed for commercial design activities. For the perturbation worth distributions, hand calculations are deployed to verify the PERSENT calculated results. Similarly, hand calculation of the PERSENT computed kinetics parameters is also used to verify the PERSENT results. In both of these, the input to PERSENT is manipulated to ensure the hand calculation exactly matches the equations PERSENT is calculating. The sensitivity coefficients involve calculating the derivatives of a parameter (such as reactivity worth), with respect to the cross section data. Direct finite difference calculations with DIF3D are used to verify the PERSENT calculated results. For the uncertainty quantification, manufactured input to PERSENT is used to allow an exact hand calculation to reproduce the PERSENT calculated results. The work detailed in this report verified that significant issues were identified for earlier versions of PERSENT for sensitivity coefficients which were corrected in this work and thus version 12.1.0 of PERSENT must be used to reproduce all of the verified work in this report.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2014

Onboard functional and molecular imaging: A design investigation for robotic multipinhole SPECT

Purpose: Onboard imaging—currently performed primarily by x-ray transmission modalities—is essential in modern radiation therapy. As radiation therapy moves toward personalized medicine, molecular imaging, which views individual gene expression, may also be important onboard. Nuclear medicine methods, such as single photon emission computed tomography (SPECT), are premier modalities for molecular imaging. The purpose of this study is to investigate a robotic multipinhole approach to onboard SPECT. Methods: Computer-aided design (CAD) studies were performed to assess the feasibility of maneuvering a robotic SPECT system about a patient in position for radiation therapy. In order to obtain fast, high-quality SPECT images, a 49-pinhole SPECT camera was designed which provides high sensitivity to photons emitted from an imaging region of interest. This multipinhole system was investigated by computer-simulation studies. Seventeen hot spots 10 and 7 mm in diameter were placed in the breast region of a supine female phantom. Hot spot activity concentration was six times that of background. For the 49-pinhole camera and a reference, more conventional, broad field-of-view (FOV) SPECT system, projection data were computer simulated for 4-min scans and SPECT images were reconstructed. Hot-spot localization was evaluated using a nonprewhitening forced-choice numerical observer. Results: The CAD simulation studies found that robots could maneuver SPECT cameras about patients in position for radiation therapy. In the imaging studies, most hot spots were apparent in the 49-pinhole images. Average localization errors for 10-mm- and 7-mm-diameter hot spots were 0.4 and 1.7 mm, respectively, for the 49-pinhole system, and 3.1 and 5.7 mm, respectively, for the reference broad-FOV system. Conclusions: A robot could maneuver a multipinhole SPECT system about a patient in position for radiation therapy. The system could provide onboard functional and molecular imaging with 4-min scan times.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2013

Network support for system initiated checkpoints

A system, method and computer program product for supporting system initiated checkpoints in parallel computing systems. The system and method generates selective control signals to perform checkpointing of system related data in presence of messaging activity associated with a user application running at the node. The checkpointing is initiated by the system such that checkpoint data of a plurality of network nodes may be obtained even in the presence of user applications running on highly parallel computers that include ongoing user messaging activity.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Network support for system initiated checkpoints

Chen, Dong↗

DOE OSTI2020

An empirical study of I/O separation for burst buffers in HPC systems

To meet the exascale I/O requirements for the High-Performance Computing (HPC), a new I/O subsystem, Burst Buffer, based on solid state drives (SSD), has been developed. However, the diverse HPC workloads and the bursty I/O pattern cause severe data fragmentation that requires costly garbage collection (GC) and increases the number of bytes written to the SSD. To address this data fragmentation challenge, a new multi-stream feature has been developed for SSDs. In this work, we develop an I/O Separation scheme called BIOS to leverage this multi-stream feature to group the I/O streams based on the user IDs. We propose a stream-aware scheduling policy based on burst buffer pools in the workload manager, and integrate the BIOS with the workload manager to optimize the I/O separation scheme in burst buffer. We evaluate the proposed framework with a burst buffer I/O traces from Cori Supercomputer including a diverse set of applications. Experimental results show that the BIOS could improve the performance by 1.44x on average and reduce the Write Amplification Factor (WAF) by up to 1.20x. Finally, these demonstrate the potential benefits of the I/O separation scheme for solid state storage systems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Development and Commercialization of an IDAES-Based Power Plant Performance Monitoring and Optimization System

DOE and NETL have created an advanced, open-source computational platform through the Institute for the Design of Advanced Energy Systems (IDAES). The IDAES platform is a very extensive modeling environment that can be used for a broad range of power plant and process applications. MapEx Software is developing and commercializing a software application that makes it easier to set-up and run IDAES-based analyses. The MapEx-developed software application will replace the need for custom Python language coding with a user-friendly graphical user interface where the user can construct a flowsheet diagram of the IDAES model by inserting icons representing the plant equipment onto the screen. This application will make the implementation of modeling and optimization of existing fossil-fired power plants more straight-forward and less time-consuming. The effort focuses on performance monitoring and optimization of plant operations for the existing coal-fired power plant fleet but is built on a structure that allows expansion into the broad range of applications where IDAES methods may be applied.

20 FOSSIL-FUELED POWER PLANTS↗