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At least 1,423 records · Page 79
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Accelerating the Global Arrays ComEx Runtime using Multiple Progress Ranks

Partitioned Global Address Space (PGAS) models are part of system software that are being designed to support communication runtime for exascale applications. Suitability of using MPI as a scalable PGAS communication subsystem has been shown as a viable option due to its standardization and higher performance. We used MPI two-sided semantics with a combination of automatic and user defined splitting of MPI communicators to achieve asynchronous progress. Our implementation can make use of multiple asynchronous progress ranks (PR) per node that can be mapped to the computing architecture of a node in a distributed cluster. We are able to show significant speed up of over 2.0X and scaling of communication bound computational chemistry application over 1024 nodes of state- of-the-art HPC clusters. Our results show that while running a communication bound application workload on a certain number of cluster nodes, a use of optimum number of ranks dedicated for communication may be used to achieve asynchronous communication progress and obtain highest performance.

PGAS, global-arrays, NWCHEM, NWChemEx, HPC, GPGPU↗
DOE OSTI2017

Design and Implementation of Papyrus: Parallel Aggregate Persistent Storage

A surprising development in recently announced HPC platforms is the addition of, sometimes massive amounts of, persistent (nonvolatile) memory (NVM) in order to increase memory capacity and compensate for plateauing I/O capabilities. However, there are no portable and scalable programming interfaces using aggregate NVM effectively. This paper introduces Papyrus: a new software system built to exploit emerging capability of NVM in HPC architectures. Papyrus (or Parallel Aggregate Persistent -YRU- Storage) is a novel programming system that provides features for scalable, aggregate, persistent memory in an extreme-scale system for typical HPC usage scenarios. Papyrus mainly consists of Papyrus Virtual File System (VFS) and Papyrus Template Container Library (TCL). Papyrus VFS provides a uniform aggregate NVM storage image across diverse NVM architectures. It enables Papyrus TCL to provide a portable and scalable high-level container programming interface whose data elements are distributed across multiple NVM nodes without requiring the user to handle complex communication, synchronization, replication, and consistency model. We evaluate Papyrus on two HPC systems, including UTK Beacon and NERSC Cori, using real NVM storage devices.

Kim, Jungwon↗
DOE OSTI2017

The Trinity Center of Excellence Co-Design Best Practices

Co-design between application developers and the vendors providing high-performance computing systems is essential to efficiently using current-generation HPC systems and shaping next-generation architectures. Application developers are faced with the challenge of effectively orchestrating many hardware threads and exploiting vector instructions, which can require code modifications. Will refactoring applications for current-generation systems apply to future-generation systems? Is there help available for this enormous task? Over the past 10 years, a partnership has evolved to address these issues. Centers of Excellence are mutually beneficial collaborations between application developers and vendors; vendors receive a better understanding of the needs of their users, and users receive a better understanding of the characteristics of the hardware, system software, and tools available to address their challenges. Lastly, this article describes the partnership between two vendors, Cray and Intel, and the application teams working together in the Trinity Center of Excellence.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Scalable Comparative Visualization of Ensembles of Call Graphs

Optimizing the performance of large-scale parallel codes is critical for efficient utilization of computing resources. Code developers often explore various execution parameters, such as hardware configurations, system software choices, and application parameters, and are interested in detecting and understanding bottlenecks in different executions. They often collect hierarchical performance profiles represented as call graphs, which combine performance metrics with their execution contexts. The crucial task of exploring multiple call graphs together is tedious and challenging because of the many structural differences in the execution contexts and significant variability in the collected performance metrics (e.g., execution runtime). In this paper, we present Ensemble CallFlow to support the exploration of ensembles of call graphs using new types of visualizations, analysis, graph operations, and features. We introduce ensemble-Sankey , a new visual design that combines the strengths of resource-flow (Sankey) and box-plot visualization techniques. Whereas the resource-flow visualization can easily and intuitively describe the graphical nature of the call graph, the box plots overlaid on the nodes of Sankey convey the performance variability within the ensemble. Our interactive visual interface provides linked views to help explore ensembles of call graphs, e.g., by facilitating the analysis of structural differences, and identifying similar or distinct call graphs. Finally, we demonstrate the effectiveness and usefulness of our design through case studies on large-scale parallel codes.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Uncertainty Visualization of Critical Points of 2D Scalar Fields for Parametric and Nonparametric Probabilistic Models

This paper presents a novel end-to-end framework for closed-form computation and visualization of critical point uncertainty in 2D uncertain scalar fields. Critical points are fundamental topological descriptors used in the visualization and analysis of scalar fields. The uncertainty inherent in data (e.g., observational and experimental data, approximations in simulations, and compression), however, creates uncertainty regarding critical point positions. Uncertainty in critical point positions, therefore, cannot be ignored, given their impact on downstream data analysis tasks. Here, in this work, we study uncertainty in critical points as a function of uncertainty in data modeled with probability distributions. Although Monte Carlo (MC) sampling techniques have been used in prior studies to quantify critical point uncertainty, they are often expensive and are infrequently used in production-quality visualization software. We, therefore, propose a new end-to-end framework to address these challenges that comprises a threefold contribution. First, we derive the critical point uncertainty in closed form, which is more accurate and efficient than the conventional MC sampling methods. Specifically, we provide the closed-form and semianalytical (a mix of closed-form and MC methods) solutions for parametric (e.g., uniform, Epanechnikov) and nonparametric models (e.g., histograms) with finite support. Second, we accelerate critical point probability computations using a parallel implementation with the VTK-m library, which is platform portable. Finally, we demonstrate the integration of our implementation with the ParaView software system to demonstrate near-real-time results for real datasets.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2013

The art and power of data imaging

Data imaging and visual data assessment are veritable gold mines in the scientist's quest to understand and accurately interpret numerical data. Graphical displays of various aspects of a dataset offer the analyst insight to the data that no mathematical computation or statistic can provide. It is difficult, at best, for even a skilled and observant statistician to understand the underlying structure of a dataset. Often, there is either too little data to get a good 'picture' of the structure that might be present or there is so much data that one cannot readily assimilate it. Of course, the latter problem (too much data) is, in reality, no problem at all given the abilities of modern computers and software systems to manage large amounts of data. Advances in computer technology and the advent of the global positioning satellite system have enabled scientists from many fields of endeavor to collect and view data in its spatial context. Visual images constructed from spatially referenced data reveal the inherent richness and structure in the data and lead to more informed conclusions. So powerful is data collected with spatial context that a relatively new branch of mathematical statistics, geo-spatial statistics, has emerged. Geo-spatial statistics seek to exploit this context rich data form to better understand the spatial and co-relationships that might exist, but would be otherwise hidden in tabular data or obscured with classic statistical approaches. This paper (and accompanying presentation) will show the power that visual data assessment possesses to understand radiological scanning data and to make confident and accurate decisions based on the data images. It will challenge the traditional mathematical concept of detection limits for scanning. It will demonstrate that more data, even if the individual datum comprising the dataset is of 'poorer quality' (i.e., has a larger uncertainty and, thus, a larger calculated minimum detection value), is significantly more powerful than a smaller dataset comprised of higher quality measurements. This presentation will cause the open-minded health physicist to rethink how they prescribe, collect, evaluate, and make decisions based upon radiological scan data. (authors)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2014

SU-E-T-362: Automatic Catheter Reconstruction of Flap Applicators in HDR Surface Brachytherapy

Purpose: Catheter reconstruction is crucial for the accurate delivery of radiation dose in HDR brachytherapy. The process becomes complicated and time-consuming for large superficial clinical targets with a complex topology. A novel method for the automatic catheter reconstruction of flap applicators is proposed in this study. Methods: We have developed a program package capable of image manipulation, using C++class libraries of The-Visualization-Toolkit(VTK) software system. The workflow for automatic catheter reconstruction is: a)an anchor point is placed in 3D or in the axial view of the first slice at the tip of the first, last and middle points for the curved surface; b)similar points are placed on the last slice of the image set; c)the surface detection algorithm automatically registers the points to the images and applies the surface reconstruction filter; d)then a structured grid surface is generated through the center of the treatment catheters placed at a distance of 5mm from the patient's skin. As a result, a mesh-style plane is generated with the reconstructed catheters placed 10mm apart. To demonstrate automatic catheter reconstruction, we used CT images of patients diagnosed with cutaneous T-cell-lymphoma and imaged with Freiburg-Flap-Applicators (Nucletron™-Elekta, Netherlands). The coordinates for each catheter were generated and compared to the control points selected during the manual reconstruction for 16catheters and 368control point Results: The variation of the catheter tip positions between the automatically and manually reconstructed catheters was 0.17mm(SD=0.23mm). The position difference between the manually selected catheter control points and the corresponding points obtained automatically was 0.17mm in the x-direction (SD=0.23mm), 0.13mm in the y-direction (SD=0.22mm), and 0.14mm in the z-direction (SD=0.24mm). Conclusion: This study shows the feasibility of the automatic catheter reconstruction of flap applicators with a high level of positioning accuracy. Implementation of this technique has potential to decrease the planning time and may improve overall quality in superficial brachytherapy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

SU-E-T-562: Scanned Percent Depth Dose Curve Discrepancy for Photon Beams with Physical Wedge in Place (Varian IX) Using Different Sensitive Volume Ion Chambers

Purpose: To investigate and report the discrepancy of scanned percent depth dose (PDD) for photon beams with physical wedge in place when using ion chambers with different sensitive volumes. Methods/Materials: PDD curves of open fields and physical wedged fields (15, 30, 45, and 60 degree wedge) were scanned for photon beams (6MV and 10MV, Varian iX) with field size of 5x5 and 10x10 cm using three common scanning chambers with different sensitive volumes - PTW30013 (0.6cm3), PTW23323 (0.1cm3) and Exradin A16 (0.007cm3). The scanning system software used was OmniPro version 6.2, and the scanning water tank was the Scanditronix Wellhoffer RFA 300.The PDD curves from the three chambers were compared. Results: Scanned PDD curves of the same energy beams for open fields were almost identical between three chambers, but the wedged fields showed non-trivial differences. The largest differences were observed between chamber PTW30013 and Exradin A16. The differences increased as physical wedge angle increased. The differences also increased with depth, and were more pronounced for 6MV beam. Similar patterns were shown for both 5x5 and 10x10 cm field sizes. For open fields, all PDD values agreed with each other within 1% at 10cm depth and within 1.62% at 20 cm depth. For wedged fields, the difference of PDD values between PTW30013 and A16 reached 4.09% at 10cm depth, and 5.97% at 20 cm depth for 6MV with 60 degree physical wedge. Conclusion: We observed a significant difference in scanned PDD curves of photon beams with physical wedge in place obtained when using different sensitive volume ion chambers. The PDD curves scanned with the smallest sensitive volume ion chamber showed significant difference from larger chamber results, beyond 10cm depth. We believe this to be caused by varying response to beam hardening by the wedges.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2014

TU-PIS-Exhibit Hall-01: CT Dose Optimization Technologies II

Partners in Solutions is an exciting new program in which AAPM partners with our vendors to present practical “hands-on” information about the equipment and software systems that we use in our clinics. The imaging topic this year is CT scanner dose optimization capabilities. Note that the sessions are being held in a special purpose room built on the Exhibit Hall Floor, to encourage further interaction with the vendors. Siemens‘ Commitment to the Right Dose in Computed Tomography Presentation Time: 11:15 - 11:45 AM Providing sustainable clinical results at highest patient safety: This is the challenge in medical imaging. Especially for Computed Tomography this means applying not simply the lowest, but the right dose for sound diagnostic imaging. Consequently, Siemens is committed to deliver the right dose in CT. In order to reduce radiation to the right dose, the first step is to provide the right dose technology. Through decades of research and development in CT imaging, Siemens CT has constantly introduced new ideas leading to a comprehensive portfolio of unique CARE technologies to deliver the right dose. For example automated kV adjustment based on patient size and the clinical question with CARE kV and three generations of iterative reconstruction. Based on the right dose technology, the next step is to actually scan at the right dose. For this, it is key to know the right dose targets for every examination. Siemens continuously involves CT experts to push developments further and outline how users can best adapt their procedures to the right dose. For users to know whether they met the right dose targets, it is therefore important to understand and monitor the actual absolute dose values. All scanners are delivered with defined default protocols which automatically use the available right dose technologies. Finally, to deliver the right dose not just in singular cases, but ideally to patients everywhere, organizations need then to manage dose across their institutions. Here Siemens offers the right dose management tools for administrations to analyze and document dose, to train their clinical staff and to continuously optimize the application of the right dose in clinical routine. Siemens CT is not only adhering to the ALARA principle, but is inspired by it. With CARE Right Siemens show their commitment to the right dose in CT. Toshiba Aquilion CT Dose Management Tools Presentation Time: 11:45 - 12:15 PM A practical review of Toshiba’s CT dose management technologies from the physicist’s perspective. This presentation will include an overview of Toshiba’s CT dose reduction technologies and dose safeguards. Content will include answers to frequently asked questions relating to dose management, dose tracking, CTDI measurement, ACR accreditation, ACR QC, and protocol review on Toshiba CT systems. Specific topics will include the following: Toshiba’s mechanism of tube current modulation; Exposure record format and interpretation of the values; Dose reporting and dose safeguard tools; Use of AIDR 3D iterative reconstruction; The configuration of task specific image quality target and its integration with AIDR 3D; Tips for scanning the ACR phantom with wide beam geometry; Measuring CTDI for wide beam geometry; Discussion of daily QC procedures and specifications; Tips for annual QC evaluation; Protocol management tools.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Quantifying the performance of in vivo portal dosimetry in detecting four types of treatment parameter variations

Purpose: To quantify the ability of electronic portal imaging device (EPID) dosimetry used during treatment (in vivo) in detecting variations that can occur in the course of patient treatment. Methods: Images of transmitted radiation from in vivo EPID measurements were converted to a 2D planar dose at isocenter and compared to the treatment planning dose using a prototype software system. Using the treatment planning system (TPS), four different types of variability were modeled: overall dose scaling, shifting the positions of the multileaf collimator (MLC) leaves, shifting of the patient position, and changes in the patient body contour. The gamma pass rate was calculated for the modified and unmodified plans and used to construct a receiver operator characteristic (ROC) curve to assess the detectability of the different parameter variations. The detectability is given by the area under the ROC curve (AUC). The TPS was also used to calculate the impact of the variations on the target dose–volume histogram. Results: Nine intensity modulation radiation therapy plans were measured for four different anatomical sites consisting of 70 separate fields. Results show that in vivo EPID dosimetry was most sensitive to variations in the machine output, AUC = 0.70 − 0.94, changes in patient body habitus, AUC = 0.67 − 0.88, and systematic shifts in the MLC bank positions, AUC = 0.59 − 0.82. These deviations are expected to have a relatively small clinical impact [planning target volume (PTV) D{sub 99} change <7%]. Larger variations have even higher detectability. Displacements in the patient’s position and random variations in MLC leaf positions were not readily detectable, AUC < 0.64. The D{sub 99} of the PTV changed by up to 57% for the patient position shifts considered here. Conclusions: In vivo EPID dosimetry is able to detect relatively small variations in overall dose, systematic shifts of the MLC’s, and changes in the patient habitus. Shifts in the patient’s position which can introduce large changes in the target dose coverage were not readily detected.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

TU-FG-201-03: Automatic Pre-Delivery Verification Using Statistical Analysis of Consistencies in Treatment Plan Parameters by the Treatment Site and Modality

Purpose: A novel computer software system, namely APDV (Automatic Pre-Delivery Verification), has been developed for verifying patient treatment plan parameters right prior to treatment deliveries in order to automatically detect and prevent catastrophic errors. Methods: APDV is designed to continuously monitor new DICOM plan files on the TMS computer at the treatment console. When new plans to be delivered are detected, APDV checks the consistencies of plan parameters and high-level plan statistics using underlying rules and statistical properties based on given treatment site, technique and modality. These rules were quantitatively derived by retrospectively analyzing all the EBRT treatment plans of the past 8 years at authors’ institution. Therapists and physicists will be notified with a warning message displayed on the TMS computer if any critical errors are detected, and check results, confirmation, together with dismissal actions will be saved into database for further review. Results: APDV was implemented as a stand-alone program using C# to ensure required real time performance. Mean values and standard deviations were quantitatively derived for various plan parameters including MLC usage, MU/cGy radio, beam SSD, beam weighting, and the beam gantry angles (only for lateral targets) per treatment site, technique and modality. 2D-based rules of combined MU/cGy ratio and averaged SSD values were also derived using joint probabilities of confidence error ellipses. The statistics of these major treatment plan parameters quantitatively evaluate the consistency of any treatment plans which facilitates automatic APDV checking procedures. Conclusion: APDV could be useful in detecting and preventing catastrophic errors immediately before treatment deliveries. Future plan including automatic patient identify and patient setup checks after patient daily images are acquired by the machine and become available on the TMS computer. This project is supported by the Agency for Healthcare Research and Quality (AHRQ) under award 1R01HS0222888. The senior author received research grants from ViewRay Inc. and Varian Medical System.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

TH-CD-201-10: Highly Efficient Synchronized High-Speed Scintillation Camera System for Measuring Proton Range, SOBP and Dose Distributions in a 2D-Plane

Purpose: Proton therapy (PT) delivery is complex and extremely dynamic. Therefore, quality assurance testing is vital, but highly time-consuming. We have developed a High-Speed Scintillation-Camera-System (HS-SCS) for simultaneously measuring multiple beam characteristics. Methods: High-speed camera was placed in a light-tight housing and dual-layer neutron shield. HS-SCS is synchronized with a synchrocyclotron to capture individual proton-beam-pulses (PBPs) at ∼504 frames/sec. The PBPs from synchrocyclotron trigger the HS-SCS to open its shutter for programmed exposure-time. Light emissions within 30×30×5cm3 plastic-scintillator (BC-408) were captured by a CCD-camera as individual images revealing dose-deposition in a 2D-plane with a resolution of 0.7mm for range and SOBP measurements and 1.67mm for profiles. The CCD response as well as signal to noise ratio (SNR) was characterized for varying exposure times, gains for different light intensities using a TV-Optoliner system. Software tools were developed to analyze ∼5000 images to extract different beam parameters. Quenching correction-factors were established by comparing scintillation Bragg-Peaks with water scanned ionization-chamber measurements. Quenching corrected Bragg-peaks were integrated to ascertain proton-beam range (PBR), width of Spared-Out-Bragg-Peak (MOD) and distal.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2022

PETSc TSAdjoint: A Discrete Adjoint ODE Solver for First-Order and Second-Order Sensitivity Analysis

Here, we present a new software system PETSc TSAdjoint for first-order and second order adjoint sensitivity analysis of time-dependent nonlinear differential equations. The derivative calculation in PETSc TSAdjoint is essentially a high-level algorithmic differentiation process. The adjoint models are derived by differentiating the timestepping algorithms and implementing them based on the parallel infrastructure in PETSc. Full differentiation of the library code, including MPI routines, is avoided, and users do not need to derive their own adjoint models for their specific applications. PETSc TSAdjoint can compute the first-order derivative, that is, the gradient of a scalar functional, and the Hessian-vector product, which carries second-order derivative information, while requiring minimal input (a few callbacks) from the users. The adjoint model employs optimal checkpointing schemes in a manner that is transparent to users. Finally, usability, efficiency, and scalability are demonstrated through examples from a variety of applications.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

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

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

42 ENGINEERING↗
DOE OSTI2023

SeeQ: A Programming Model for Portable Data-Driven Building Applications

This paper introduces SeeQ, a programming model and an abstraction framework that facilitates the development of portable data- driven building applications. Data-driven approaches can provide insights into building operations and guide decision-making to achieve operational objectives. Yet the configuration of such applications per building requires extensive effort and tacit knowledge. In SeeQ, we propose a portable programming model and build a software system that enables self-configuration and execution across diverse buildings. The configuration of each building is captured in a unified data model - in this paper, we work with the Brick ontology without loss of generality. SeeQ focuses on the distinction between the application logic and the configuration of an application against building-specific data inputs and systems. We test the proposed approach by configuring and deploying a diverse range of applications across five heterogeneous real-world buildings. The analysis shows the potential of SeeQ to significantly reduce the efforts associated with the delivery of building analytics.

analytics↗
DOE OSTI2014

Clock Agreement Among Parallel Supercomputer Nodes

This dataset presents measurements that quantify the clock synchronization time-agreement characteristics among several high performance computers including the current world's most powerful machine for open science, the U.S. Department of Energy's Titan machine sited at Oak Ridge National Laboratory. These ultra-fast machines derive much of their computational capability from extreme node counts (over 18000 nodes in the case of the Titan machine). Time-agreement is commonly utilized by parallel programming applications and tools, distributed programming application and tools, and system software. Our time-agreement measurements detail the degree of time variance between nodes and how that variance changes over time. The dataset includes empirical measurements and the accompanying spreadsheets.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2013

Multiphysics Application Coupling Toolkit

This particular consortium implementation of the software integration infrastructure will, in large part, refactor portions of the Rocstar multiphysics infrastructure. Development of this infrastructure originated at the University of Illinois DOE ASCI Center for Simulation of Advanced Rockets (CSAR) to support the center's massively parallel multiphysics simulation application, Rocstar, and has continued at IllinoisRocstar, a small company formed near the end of the University-based program. IllinoisRocstar is now licensing these new developments as free, open source, in hopes to help improve their own and others' access to infrastructure which can be readily utilized in developing coupled or composite software systems; with particular attention to more rapid production and utilization of multiphysics applications in the HPC environment. There are two major pieces to the consortium implementation, the Application Component Toolkit (ACT), and the Multiphysics Application Coupling Toolkit (MPACT). The current development focus is the ACT, which is (will be) the substrate for MPACT. The ACT itself is built up from the components described in the technical approach. In particular, the ACT has the following major components: 1.The Component Object Manager (COM): The COM package provides encapsulation of user applications, and their data. COM also provides the inter-component function call mechanism. 2.The System Integration Manager (SIM): The SIM package provides constructs and mechanisms for orchestrating composite systems of multiply integrated pieces.

Campbell, MichaelT.↗
DOE OSTI2013

Fast Global File Status

Fast Global File Status (FGFS) is a system software package that implimints a scalable mechanism to retrieve file information, such as its degree of distribution or replication and consistency.

Ahn, D.H.↗