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At least 433 records · Page 24

Report on the ASCR Workshop on Modeling and Simulation of Exascale Systems and Applications

In the last few years, numerous studies commissioned by the Department of Energy (DOE), the Defense Advanced Research Projects Agency (DARPA), and others have examined the challenges that will have to be overcome for computational science to achieve exascale, a two order-of-magnitude increase in capability beyond what is possible today. Exponential growth in the number of devices (Moore’s Law) is expected to continue unabated, but the end of Dennard scaling, and hence the growth in performance of individual processors, has led to exponential growth in concurrency. Power consumption has also grown to the point where the cost of the electrical power for systems threatens to exceed the cost of acquiring them. Ever-shrinking devices, and the growth in their number, are expected to increase the rate of soft, or transient, errors such that applications will no longer be able to assume correct behavior of the underlying machine. Adapting to such systems will require new mathematical algorithms that minimize synchronization and data movement, and a new generation of scientific software. Rather than addressing these issues in isolation, a new process of “Co-Design” is being pursued in which application and computer scientists work toward the common goal of an exascale ecosystem of systems and applications. Modeling and simulation (ModSim) is a critical part of this process. It enables scientists and engineers to analyze future algorithms, applications, and computing systems, long before they are realized, and make the necessary design decisions such that exascale science is broadly achieved. Later, when exascale applications and systems are realized, ModSim technology will enable us to understand their behavior, debugging and optimizing them. Given the increasing importance of modeling and simulation, a workshop was organized by DOE/ASCR to assess the current state of the art and to identify research challenges that must be overcome in this field. Fifty experts, representing academia, industry, and government, participated in the workshop, and others contributed both beforehand and afterwards. This report summarizes their findings.

97 MATHEMATICS AND COMPUTING↗

Report on the ASCR Workshop on Modeling and Simulation of Exascale Systems and Applications

In the last few years, numerous studies commissioned by the Department of Energy (DOE), the Defense Advanced Research Projects Agency (DARPA), and others have examined the challenges that will have to be overcome for computational science to achieve exascale, a two order-of-magnitude increase in capability beyond what is possible today. Exponential growth in the number of devices (Moore's Law) is expected to continue unabated, but the end of Dennard scaling, and hence the growth in performance of individual processors, has led to exponential growth in concurrency. Power consumption has also grown to the point where the cost of the electrical power for systems threatens to exceed the cost of acquiring them. Ever-shrinking devices, and the growth in their number, are expected to increase the rate of soft, or transient, errors such that applications will no longer be able to assume correct behavior of the underlying machine. Adapting to such systems will require new mathematical algorithms that minimize synchronization and data movement, and a new generation of scientific software. Rather than addressing these issues in isolation, a new process of "Co-Design" is being pursued in which application and computer scientists work toward the common goal of an exascale ecosystem of systems and applications. Modeling and simulation (ModSim) is a critical part of this process. It enables scientists and engineers to analyze future algorithms, applications, and computing systems, long before they are realized, and make the necessary design decisions such that exascale science is broadly achieved. Later, when exascale applications and systems are realized, ModSim technology will enable us to understand their behavior, debugging and optimizing them. Given the increasing importance of modeling and simulation, a workshop was organized by DOE/ASCR to assess the current state of the art and to identify research challenges that must be overcome in this field. Fifty experts, representing academia, industry, and government, participated in the workshop, and others contributed both beforehand and afterwards. This report summarizes their findings.

97 MATHEMATICS AND COMPUTING↗

Human Factors and Technical Considerations for a Computerized Operator Support System Prototype

A prototype computerized operator support system (COSS) has been developed in order to demonstrate the concept and provide a test bed for further research. The prototype is based on four underlying elements consisting of a digital alarm system, computer-based procedures, PI&D system representations, and a recommender module for mitigation actions. At this point, the prototype simulates an interface to a sensor validation module and a fault diagnosis module. These two modules will be fully integrated in the next version of the prototype. The initial version of the prototype is now operational at the Idaho National Laboratory using the U.S. Department of Energy’s Light Water Reactor Sustainability (LWRS) Human Systems Simulation Laboratory (HSSL). The HSSL is a full-scope, full-scale glass top simulator capable of simulating existing and future nuclear power plant main control rooms. The COSS is interfaced to the Generic Pressurized Water Reactor (gPWR) simulator with industry-typical control board layouts. The glass top panels display realistic images of the control boards that can be operated by touch gestures. A section of the simulated control board was dedicated to the COSS human-system interface (HSI), which resulted in a seamless integration of the COSS into the normal control room environment. A COSS demonstration scenario has been developed for the prototype involving the Chemical & Volume Control System (CVCS) of the PWR simulator. It involves a primary coolant leak outside of containment that would require tripping the reactor if not mitigated in a very short timeframe. The COSS prototype presents a series of operator screens that provide the needed information and soft controls to successfully mitigate the event.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Identifying quenched jets in heavy ion collisions with machine learning

Measurements of jet substructure in ultra-relativistic heavy ion collisions suggest that the jet showering process is modified by the interaction with the quark-gluon plasma. Modifications of the hard substructure of jets can be explored with modern data-driven techniques. In this study, a machine learning approach to the identification of quenched jets is designed. Jet showering processes are simulated with a jet quenching model JEWEL and a non-quenching model PYTHIA 8. Sequential substructure variables are extracted from the jet clustering history following an angular-ordered sequence and are used in the training of a neural network built on top of a long short-term memory network. We show that this approach successfully identifies the quenching effect in the presence of the large uncorrelated background of soft particles created in heavy-ion collisions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Excitation spectra of quantum matter without quasiparticles. II. Random t - J models

Here, we present numerical solutions of the spectral functions of large dimension t -J models with random nearest neighbor exchange and global SU(M) spin rotation symmetry. The solutions are obtained from the saddle-point equations of the large dimension limit, followed by the large M limit. The same saddle point equations also apply to the model with all-to-all and random hopping and exchange. Such a t -J model realizes a deconfined critical state proposed as a model for the optimally doped cuprates. The large M theory involves Green’s functions for fractionalized spinons and holons carrying emergent U(1) gauge charges, obeying relations similar to those of the Sachdev-Ye-Kitaev (SYK) models. The low frequency spectral functions are compared with an analytic analysis of the operator scaling dimensions with good agreement. We also compute the low frequency and temperature behavior of experimentally observable gauge-invariant observables: the electron Green’s function, the local spin susceptibility and the optical conductivity, along with the temperature dependence of the d.c. resistivity. The time reparameterization soft mode (equivalent to the boundary graviton in holographically dual models of two-dimensional quantum gravity) makes important contributions to all observables and provides a linear-in-temperature contribution to the d.c. resistivity.

36 MATERIALS SCIENCE↗

Distributional Deep Reinforcement Learning-Based Emergency Frequency Control

Emergency frequency control is one of the most critical approaches to maintain power system stability after major disturbances. With the increasing number of grid-connected renewable energy sources, existing model-based methods of frequency control are facing up with challenges of computational speed and scalability for large-scale systems. In this paper, the emergency frequency control problem is formulated as a Markov Decision Process (MDP) and solved through a novel Distributional Deep Reinforcement Learning (DDRL) method, namely the distributional soft actor critic (DSAC) method. Compared with other RL methods that only estimate the mean value, the proposed DSAC model estimates the distribution of value function over returns. This advancement can lead to more insights and knowledge for the agent, with the benefit of a much faster and more stable learning process, and the improved frequency control performance. Here, the simulation results on IEEE 39-bus and IEEE 118-bus systems demonstrate the effectiveness and robustness of proposed models, as well as the advantage compared to other state-of-the-art DRL algorithms.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Neutron Radiography and Computed Tomography of Biological Systems at the Oak Ridge National Laboratory's High Flux Isotope Reactor

Neutrons have historically been used for a broad range of biological applications employing techniques such as small-angle neutron scattering, neutron spin echo, diffraction, and inelastic scattering. Unlike neutron scattering techniques that obtain information in reciprocal space, attenuation-based neutron imaging measures a signal in real space that is resolved on the order of tens of micrometers. The principle of neutron imaging follows the Beer-Lambert law and is based on the measurement of the bulk neutron attenuation through a sample. Greater attenuation is exhibited by some light elements (most notably, hydrogen), which are major components of biological samples. Contrast agents such as deuterium, gadolinium, or lithium compounds can be used to enhance contrast in a similar fashion as it is done in medical imaging, including techniques such as optical imaging, magnetic resonance imaging, X-ray, and positron emission tomography. For biological systems, neutron radiography and computed tomography have increasingly been used to investigate the complexity of the underground plant root network, its interaction with soils, and the dynamics of water flux in situ. Moreover, efforts to understand contrast details in animal samples, such as soft tissues and bones, have been explored. This manuscript focuses on the advances in neutron bioimaging such as sample preparation, instrumentation, data acquisition strategy, and data analysis using the High Flux Isotope Reactor CG-1D neutron imaging beamline. The aforementioned capabilities will be illustrated using a selection of examples in plant physiology (herbaceous plant/root/soil system) and biomedical applications (rat femur and mouse lung).

Bilheux, Hassina↗

TH-CD-202-06: A Method for Characterizing and Validating Dynamic Lung Density Change During Quiet Respiration

Purpose: To obtain a functional relationship that calibrates the lung tissue density change under free breathing conditions through correlating Jacobian values to the Hounsfield units. Methods: Free-breathing lung computed tomography images were acquired using a fast helical CT protocol, where 25 scans were acquired per patient. Using a state-of-the-art deformable registration algorithm, a set of the deformation vector fields (DVF) was generated to provide spatial mapping from the reference image geometry to the other free-breathing scans. These DVFs were used to generate Jacobian maps, which estimate voxelwise volume change. Subsequently, the set of 25 corresponding Jacobian and voxel intensity in Hounsfield units (HU) were collected and linear regression was performed based on the mass conservation relationship to correlate the volume change to density change. Based on the resulting fitting coefficients, the tissues were classified into parenchymal (Type I), vascular (Type II), and soft tissue (Type III) types. These coefficients modeled the voxelwise density variation during quiet breathing. The accuracy of the proposed method was assessed using mean absolute difference in HU between the CT scan intensities and the model predicted values. In addition, validation experiments employing a leave-five-out method were performed to evaluate the model accuracy. Results: The computed mean model errors were 23.30±9.54 HU, 29.31±10.67 HU, and 35.56±20.56 HU, respectively, for regions I, II, and III, respectively. The cross validation experiments averaged over 100 trials had mean errors of 30.02 ± 1.67 HU over the entire lung. These mean values were comparable with the estimated CT image background noise. Conclusion: The reported validation experiment statistics confirmed the lung density modeling during free breathing. The proposed technique was general and could be applied to a wide range of problem scenarios where accurate dynamic lung density information is needed. This work was supported in part by NIH R01 CA0096679.

60 APPLIED LIFE SCIENCES↗

The Facial Reconstruction of a Mesolithic Dog, Muge, Portugal

This paper presents the facial reconstruction of a Mesolithic dog whose skeleton was recovered from the Muge shell middens (Portugal) in the 19th century. We used the anatomical deformation approach based on a collection of computer tomography images as an attempt to reconstruct the Muge dog’s head appearance. We faced a few challenges due to the level of bone displacement and the absence of some cranium anatomical parts, as well as accurate information on soft tissue thickness for modern dogs. This multidisciplinary study combined anatomical, veterinary, zooarchaeological, artistic and graphic aspects to allow for the facial reconstruction of the Muge dog. Albeit an approximation, it confers a recognition to this prehistoric finding.

Moraes, Cicero (ORCID:0000000294790028)↗

Pseudo-random number generation for Brownian Dynamics and Dissipative Particle Dynamics simulations on GPU devices

Highlights: {yields} Molecular Dynamics codes implemented on GPUs have achieved two-order of magnitude computational accelerations. {yields} Brownian Dynamics and Dissipative Particle Dynamics simulations require a large number of random numbers per time step. {yields} We introduce a method for generating small batches of pseudorandom numbers distributed over many threads of calculations. {yields} With this method, Dissipative Particle Dynamics is implemented on a GPU device without requiring thread-to-thread communication. - Abstract: Brownian Dynamics (BD), also known as Langevin Dynamics, and Dissipative Particle Dynamics (DPD) are implicit solvent methods commonly used in models of soft matter and biomolecular systems. The interaction of the numerous solvent particles with larger particles is coarse-grained as a Langevin thermostat is applied to individual particles or to particle pairs. The Langevin thermostat requires a pseudo-random number generator (PRNG) to generate the stochastic force applied to each particle or pair of neighboring particles during each time step in the integration of Newton's equations of motion. In a Single-Instruction-Multiple-Thread (SIMT) GPU parallel computing environment, small batches of random numbers must be generated over thousands of threads and millions of kernel calls. In this communication we introduce a one-PRNG-per-kernel-call-per-thread scheme, in which a micro-stream of pseudorandom numbers is generated in each thread and kernel call. These high quality, statistically robust micro-streams require no global memory for state storage, are more computationally efficient than other PRNG schemes in memory-bound kernels, and uniquely enable the DPD simulation method without requiring communication between threads.

97 MATHEMATICS AND COMPUTING↗

SU-E-J-33: Comparison Between Soft Tissue Alignment and Bony Alignment for Pancreatic Cancer Radiotherapy

Purpose An IGRT modality for pancreatic cancer treatment with dose escalation at our institution is in-room daily CT imaging. The purpose of this study is to assess the difference between soft tissue alignment and bony alignment for pancreatic tumor localization. Methods Eighteen patients with pancreatic tumors who underwent IMRT treatment with an inspiration breath-hold technique between July 2012 and February 2015 are included in this study. Prior to each treatment, a CT scan was acquired. The CT image guidance started with auto-alignment to either the bony anatomy (vertebral bodies) or fiducials (for the six patients with the stent in/near the tumor) and then, when necessary, manual adjustments were made based on soft tissue alignment using clinical software (CT-Assisted Targeting system). The difference between soft tissue alignment and bony/fiducial alignment was evaluated. Results Of all 380 treatments, manual adjustment was made in 225 treatments, ranging from 11% (3 treatments out of 28) to 96% (27 treatments out of 28) per patient. The mean of the difference between soft tissue alignment and bony/fiducial alignment per patient ranged from −3.6 to 0.3 mm, −1.5 to 2.8 mm, and −3.3 to 3.4 mm in the AP, SI, and RL directions, respectively. The maximum difference over all treatments was −9.5, −14.6, and −14.6 mm in the AP, SI, and RL directions, respectively. Conclusion About 60% of the time, manual adjustment based on soft tissue alignment was required. The extent of manual adjustment was usually small but varied significantly from patient to patient. The ultimate goal of the IGRT modality using daily CT imaging is not to fully cover the target but to spare organs-at-risk as much as possible to avoid them moving into higher dose gradients than accepted in the treatment plan. To this end, manual adjustment based on soft tissue alignment is critically important.

60 APPLIED LIFE SCIENCES↗

The Design and Optimization of Plasmonic Crystals for Surface Enhanced Raman Spectroscopy Using the Finite Difference Time Domain Method

We present computational studies of quasi three-dimensional nanowell (NW) and nanopost (NP) plasmonic crystals for applications in surface enhanced Raman spectroscopy (SERS). The NW and NP plasmonic crystals are metal coated arrays of cylindrical voids or posts, respectively, in a dielectric substrate characterized by a well/post diameter ( D ), relief depth ( RD ), periodicity ( P ), and metal thickness ( MT ). Each plasmonic crystal is modeled using the three-dimensional finite-difference time-domain (FDTD) method with periodic boundary conditions in the x- and y-directions applied to a computational unit cell to simulate the effect of a periodic array.

36 MATERIALS SCIENCE↗

Simulation-guided analysis of resonant soft X-ray scattering for determining the microstructure of triblock copolymers

Resonant soft X-ray scattering (RSoXS) probes structure with chemical sensitivity that is useful for determining the morphology of multiblock copolymers. However, the hyperspectral scattering data produced by this technique can be challenging to interpret. Here, in this study, we use computational scattering simulations to extract the microstructure of a model triblock copolymer from the energy-dependent scattering from RSoXS. An ABC triblock terpolymer formed from poly(4-methylcaprolactone) (P4MCL), poly(2,2,2-trifluoroethylacrylate) (PTFEA), and poly (dodecylacrylate) (PDDA), P4MCL-block-PTFEA-block-PDDA, was synthesized as the model triblock system. Through quantitative evaluation of simulated scattering data from a physics-informed set of candidate structure models against experimental RSoXS data, we find the best agreement with hexagonally packed core–shell cylinders. This result is also consistent with electron-density reconstruction from hard X-ray scattering data evaluated against electron-density maps generated with the same model set. These results demonstrate the utility of simulation-guided scattering analysis to study complex microstructures that are challenging to image by microscopy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Transient structured fluctuations in a two-dimensional system with multiple ordered phases

We report the structure of transient fluctuations in the liquid phase of a two-dimensional system that exhibits several ordered phases with different symmetries. The density-temperature phase diagram of the system studied, composed of particles with a repulsive shouldered soft-core pair interaction, has regions with stable liquid and hexatic phases, a square solid phase, two separate hexagonal solid phases, and a quasi-crystalline phase with 12-fold symmetry. We have examined the character of the structured fluctuations by computing the same-time aperture cross correlation function of particle configurations in several fluid regions near to and far from phase transition lines. The two primary goals of our study are (1) determination if the spectrum of structures of the fluctuations in the liquid is broader than or limited to the motifs exhibited by the ordered phases supported by the system and (2) determination of the density domains in the liquid that support particular transient structured fluctuations. In the system studied, along a low-temperature isotherm in the temperature-density plane that intersects all the ordered phases we find that the liquid phase exhibits structured fluctuations with hexagonal symmetry near both liquid-hexatic transition lines. Along the same isotherm and in the stable liquid between the lower density hexatic-to-liquid and the higher density liquid-to-square solid transitions, we find that transient hexagonal ordered fluctuations dominate the liquid region near the hexatic-to-liquid transition and square ordered fluctuations dominate the liquid region near the liquid-to square solid transition, but both of these structured fluctuations occur at all densities between these transition lines. At a higher temperature, at phase points in the liquid above, but close to the density maximum of an underlying transition, there are ordered fluctuations that can be correlated with the structure of the lower temperature phase. Although it is expected that very close to a liquid-ordered phase boundary a structured fluctuation in the liquid will have the same symmetry as the ordered phase, it is not obvious that structured fluctuations in thermodynamic states deep in the liquid phase will be similarly restricted. The most striking result of our calculations is that no evidence is found in the liquid phase for structured fluctuations with other symmetries than those of the ordered phases of the system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A quality assurance framework for the fully automated and objective evaluation of image quality in cone-beam computed tomography

Purpose: Thousands of cone-beam computed tomography (CBCT) scanners for vascular, maxillofacial, neurological, and body imaging are in clinical use today, but there is no consensus on uniform acceptance and constancy testing for image quality (IQ) and dose yet. The authors developed a quality assurance (QA) framework for fully automated and time-efficient performance evaluation of these systems. In addition, the dependence of objective Fourier-based IQ metrics on direction and position in 3D volumes was investigated for CBCT. Methods: The authors designed a dedicated QA phantom 10 cm in length consisting of five compartments, each with a diameter of 10 cm, and an optional extension ring 16 cm in diameter. A homogeneous section of water-equivalent material allows measuring CT value accuracy, image noise and uniformity, and multidimensional global and local noise power spectra (NPS). For the quantitative determination of 3D high-contrast spatial resolution, the modulation transfer function (MTF) of centrally and peripherally positioned aluminum spheres was computed from edge profiles. Additional in-plane and axial resolution patterns were used to assess resolution qualitatively. The characterization of low-contrast detectability as well as CT value linearity and artifact behavior was tested by utilizing sections with soft-tissue-equivalent and metallic inserts. For an automated QA procedure, a phantom detection algorithm was implemented. All tests used in the dedicated QA program were initially verified in simulation studies and experimentally confirmed on a clinical dental CBCT system. Results: The automated IQ evaluation of volume data sets of the dental CBCT system was achieved with the proposed phantom requiring only one scan for the determination of all desired parameters. Typically, less than 5 min were needed for phantom set-up, scanning, and data analysis. Quantitative evaluation of system performance over time by comparison to previous examinations was also verified. The maximum percentage interscan variation of repeated measurements was less than 4% and 1.7% on average for all investigated quality criteria. The NPS-based image noise differed by less than 5% from the conventional standard deviation approach and spatially selective 10% MTF values were well comparable to subjective results obtained with 3D resolution pattern. Determining only transverse spatial resolution and global noise behavior in the central field of measurement turned out to be insufficient. Conclusions: The proposed framework transfers QA routines employed in conventional CT in an advanced version to CBCT for fully automated and time-efficient evaluation of technical equipment. With the modular phantom design, a routine as well as an expert version for assessing IQ is provided. The QA program can be used for arbitrary CT units to evaluate 3D imaging characteristics automatically.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

SU-E-J-176: Results of Images Acquired with Backscattered MV Radiation Using a Pinhole Collimator

Purpose: To ascertain the feasibility of acquiring real time images of small lung tumors from scattered photons while undergoing radiation treatment.There are several methodologies currently used to track tumor location such as MV-cine acquisition and kV fluoroscopy. However, MVcine offers no information parallel to the beam axis while kV fluoroscopy offers little potential for soft tissue discernability while also increasing the patient dose. This study investigates the feasibility of observing an actual simulated tumor while exploring techniques that may improve image quality. Methods: A prototype imager consisting of a gamma camera pinhole collimator and a computed radiography (CR) plate were used in conjunction with a Varian TrueBeam linac. One study consisted of a 2.5 cm diameter solid water cylinder representing a solid tumor imbedded within a lung equivalent material slab. The cylinder with the lung slab was sandwiched between 1 cm lung equivalent slabs and these were sandwiched between 2 slabs of solid water. The top water slab was 1 cm thick. The other imaging study consisted of three different density plugs, 0.46, 1.09, and 1.82 g/cm3 placed on the accelerator couch. The gantry was orientated 70° relative to the CR plate. The slabs and plugs were irradiated with 2000 MU and 500 MU respectively using the 6FFF mode. Results: The solid water plug was visually discernible in the slab phantom. The ratio of the signal coming from the higher density plugs (placed on the treatment couch) to that between the plugs increased from 1.02 to about 3.0 after subtracting the background image acquired with no plugs present. Conclusion: Preliminary results indicate that a lung tumor could be visualized with scattered radiation during treatment. Improvements in discerning an object can be enhanced by filtering out the head leakage and background scattered radiation not emanating from the imaged object.

60 APPLIED LIFE SCIENCES↗