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All sourcesNASA NTRSDOE OSTI
NASA NTRS1995

Scalability of Parallel Spatial Direct Numerical Simulations on Intel Hypercube and IBM SP1 and SP2

The implementation and performance of a parallel spatial direct numerical simulation (PSDNS) approach on the Intel iPSC/860 hypercube and IBM SP1 and SP2 parallel computers is documented. Spatially evolving disturbances associated with the laminar-to-turbulent transition in boundary-layer flows are computed with the PSDNS code. The feasibility of using the PSDNS to perform transition studies on these computers is examined. The results indicate that PSDNS approach can effectively be parallelized on a distributed-memory parallel machine by remapping the distributed data structure during the course of the calculation. Scalability information is provided to estimate computational costs to match the actual costs relative to changes in the number of grid points. By increasing the number of processors, slower than linear speedups are achieved with optimized (machine-dependent library) routines. This slower than linear speedup results because the computational cost is dominated by FFT routine, which yields less than ideal speedups. By using appropriate compile options and optimized library routines on the SP1, the serial code achieves 52-56 M ops on a single node of the SP1 (45 percent of theoretical peak performance). The actual performance of the PSDNS code on the SP1 is evaluated with a "real world" simulation that consists of 1.7 million grid points. One time step of this simulation is calculated on eight nodes of the SP1 in the same time as required by a Cray Y/MP supercomputer. For the same simulation, 32-nodes of the SP1 and SP2 are required to reach the performance of a Cray C-90. A 32 node SP1 (SP2) configuration is 2.9 (4.6) times faster than a Cray Y/MP for this simulation, while the hypercube is roughly 2 times slower than the Y/MP for this application. KEY WORDS: Spatial direct numerical simulations; incompressible viscous flows; spectral methods; finite differences; parallel computing.

Joslin, Ronald D.↗
DOE OSTI2020

First-principles calculation of the configurational energy density of states for a solid-state ion conductor with a variant of the Wang and Landau algorithm

In this work, a variant of the Wang and Landau algorithm for calculation of the configurational energy density of states is proposed. The algorithm was developed for the purpose of using first-principles simulations, such as density functional theory, to calculate the partition function of disordered sublattices in crystal materials. The expensive calculations of first-principles methods make a parallel algorithm necessary for a practical computation of the configurational energy density of states within a supercell approximation of a solid-state material. The algorithm developed in this work is tested with the two-dimensional (2d) Ising model to bench mark the algorithm and to help provide insight for implementation to a materials science application. Tests with the 2d Ising model revealed that the algorithm has good performance compared to the original Wang and Landau algorithm and the 1/$\textit{t}$ algorithm, in particular the short iteration performance. Further, a proof of convergence is presented within an adiabatic assumption, and the analysis is able to correctly predict the time dependence of the modification factor to the density of states. The algorithm was then applied to the lithium and lanthanum sublattice of the solid-state lithium ion conductor Li 0.5 La 0.5 TiO 3 . This was done to help understand the disordered nature of the lithium and lanthanum. The results find, overall, that the algorithm performs very well for the 2d Ising model and that the results for Li 0.5 La 0.5 TiO 3 are consistent with experiment while providing additional insight into the lithium and lanthanum ordering in the material. The primary result is that the lithium and lanthanum become more mixed between layers along the c axis for increasing temperature. In part, the simulation of the disordered Li 0.5 La 0.5 TiO 3 system serves as a benchmark for what size systems are currently and in the near future practical to calculate with density functional theory methods.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Filters from taxis air conditioning system: A tool to characterize driver's occupational exposure to bioburden?

Highlights: • Filters from air conditioning system are a suitable method to characterize bioburden in vehicles. • Fungi and bacteria occur widely in taxis and personal vehicles. • The genera Aspergillus, Cladosporium and Penicillium were often detected. • Filters should be more frequently replaced to avoid bioburden proliferation and reaerosolization. • Culture based and molecular methods used in parallel enabled an improved risk characterization. Bioburden proliferation in filters from air conditioning systems of taxis represents a possible source of occupational exposure. The aim of this study was to determine the occurrence of fungi and bacteria in filters from the air conditioning system of taxis used for patient transportation and to assess the exposure of drivers to bioburden. Filters from the air conditioning systems of 19 taxis and 28 personal vehicles (used as controls) operating in three Portuguese cities including the capital Lisbon, were collected during the winter season. The occurrence and significance of bioburden detected in the different vehicles are reported and discussed in terms of colony-forming units (CFU) per 1 m{sup 2} of filter area and by the identification of the most frequently detected fungal isolates based on morphology. Azole-resistant mycobiota, fungal biomass, and molecular detection of Aspergillus species/strains were also determined. Bacterial growth was more prevalent in taxis (63.2%) than in personal vehicles (26.3%), whereas fungal growth was more prevalent in personal vehicles (53.6%) than in taxis (21.1–31.6%). Seven different azole-resistant species were identified in this study in 42.1% taxi filters. Levels of fungal biomass were above the detection limit in 63% taxi filters and in 75% personal vehicle filters. No toxigenic species were detected by molecular analysis in the assessed filters. The results obtained show that bioburden proliferation occurs widely in filters from the air conditioning systems of taxis, including the proliferation of azole-resistant fungal species, suggesting that filters should be replaced more frequently. The use of culture based-methods and molecular tools combined enabled an improved risk characterization in this setting.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1990

SIAM Conference on Parallel Processing for Scientific Computing, 4th, Chicago, IL, Dec. 11-13, 1989, Proceedings

Attention is given to such topics as an evaluation of block algorithm variants in LAPACK and presents a large-grain parallel sparse system solver, a multiprocessor method for the solution of the generalized Eigenvalue problem on an interval, and a parallel QR algorithm for iterative subspace methods on the CM2. A discussion of numerical methods includes the topics of asynchronous numerical solutions of PDEs on parallel computers, parallel homotopy curve tracking on a hypercube, and solving Navier-Stokes equations on the Cedar Multi-Cluster system. A section on differential equations includes a discussion of a six-color procedure for the parallel solution of elliptic systems using the finite quadtree structure, data parallel algorithms for the finite element method, and domain decomposition methods in aerodynamics. Topics dealing with massively parallel computing include hypercube vs. 2-dimensional meshes and massively parallel computation of conservation laws. Performance and tools are also discussed.

Dongarra, Jack↗
NASA NTRS1985

Solution of partial differential equations on vector and parallel computers

The present status of numerical methods for partial differential equations on vector and parallel computers was reviewed. The relevant aspects of these computers are discussed and a brief review of their development is included, with particular attention paid to those characteristics that influence algorithm selection. Both direct and iterative methods are given for elliptic equations as well as explicit and implicit methods for initial boundary value problems. The intent is to point out attractive methods as well as areas where this class of computer architecture cannot be fully utilized because of either hardware restrictions or the lack of adequate algorithms. Application areas utilizing these computers are briefly discussed.

Ortega, J. M.↗
NASA NTRS1985

Solution of partial differential equations on vector and parallel computers

The present status of numerical methods for partial differential equations on vector and parallel computers was reviewed. The relevant aspects of these computers are discussed and a brief review of their development is included, with particular attention paid to those characteristics that influence algorithm selection. Both direct and iterative methods are given for elliptic equations as well as explicit and implicit methods for initial boundary value problems. The intent is to point out attractive methods as well as areas where this class of computer architecture cannot be fully utilized because of either hardware restrictions or the lack of adequate algorithms. Application areas utilizing these computers are briefly discussed.

Ortega, J. M.↗
NASA NTRS1998

Globalized Newton-Krylov-Schwarz Algorithms and Software for Parallel Implicit CFD

Implicit solution methods are important in applications modeled by PDEs with disparate temporal and spatial scales. Because such applications require high resolution with reasonable turnaround, "routine" parallelization is essential. The pseudo-transient matrix-free Newton-Krylov-Schwarz (Psi-NKS) algorithmic framework is presented as an answer. We show that, for the classical problem of three-dimensional transonic Euler flow about an M6 wing, Psi-NKS can simultaneously deliver: globalized, asymptotically rapid convergence through adaptive pseudo- transient continuation and Newton's method-, reasonable parallelizability for an implicit method through deferred synchronization and favorable communication-to-computation scaling in the Krylov linear solver; and high per- processor performance through attention to distributed memory and cache locality, especially through the Schwarz preconditioner. Two discouraging features of Psi-NKS methods are their sensitivity to the coding of the underlying PDE discretization and the large number of parameters that must be selected to govern convergence. We therefore distill several recommendations from our experience and from our reading of the literature on various algorithmic components of Psi-NKS, and we describe a freely available, MPI-based portable parallel software implementation of the solver employed here.

Gropp, W. D.↗
DOE OSTI2021

PAGANI: a parallel adaptive GPU algorithm for numerical integration

We present a new adaptive parallel algorithm for the challenging problem of multi-dimensional numerical integration on massively parallel architectures. Adaptive algorithms have demonstrated the best performance, but efficient many-core utilization is difficult to achieve because the adaptive work-load can vary greatly across the integration space and is impossible to predict a priori. Existing parallel algorithms utilize sequential computations on independent processors, which results in bottlenecks due to the need for data redistribution and processor synchronization. Our algorithm employs a high-throughput approach in which all existing sub-regions are processed and sub-divided in parallel. Repeated sub-region classification and filtering improves upon a brute-force approach and allows the algorithm to make efficient use of computation and memory resources. A CUDA implementation shows orders of magnitude speedup over the fastest open-source CPU method and extends the achievable accuracy for difficult integrands. Our algorithm typically outperforms other existing deterministic parallel methods.

Sakiotis, Ioannis↗
NASA NTRS1998

Parallelization of ARC3D with Computer-Aided Tools

A series of efforts have been devoted to investigating methods of porting and parallelizing applications quickly and efficiently for new architectures, such as the SCSI Origin 2000 and Cray T3E. This report presents the parallelization of a CFD application, ARC3D, using the computer-aided tools, Cesspools. Steps of parallelizing this code and requirements of achieving better performance are discussed. The generated parallel version has achieved reasonably well performance, for example, having a speedup of 30 for 36 Cray T3E processors. However, this performance could not be obtained without modification of the original serial code. It is suggested that in many cases improving serial code and performing necessary code transformations are important parts for the automated parallelization process although user intervention in many of these parts are still necessary. Nevertheless, development and improvement of useful software tools, such as Cesspools, can help trim down many tedious parallelization details and improve the processing efficiency.

Jin, Haoqiang↗
DOE OSTI2018

Performance analysis and implementation details of the Energy Conserving Semi-Implicit Method code (ECsim)

We present in this work the implementation of the Energy Conserving Semi-Implicit Method in a parallel code called ECsim. This new code is a three-dimensional, fully electromagnetic particle in cell (PIC) code. It is written in C/C++ and uses MPI to allow massive parallelization. ECsim is unconditionally stable in time, eliminates the finite grid instability, and has the same cycle scheme as the explicit code with a computational cost comparable to other semi-implicit PIC codes. All these features make it a very valuable tool to address situations which have not been possible to analyze until now with other PIC codes. In this work, we show the details of the algorithm implementation and we study its performance in different systems. ECsim is compared with another semi-implicit PIC code with different time and spectral resolution, showing its ability to address situations where other codes fail.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Energy-Screened Many-Body Expansion for Protein–Ligand Interactions: Examining Convergence for Metalloenzymes Through Seven–Body Interactions

Fragment-based quantum chemistry is a powerful strategy for calculating protein−ligand interaction energies using quantum chemistry methods. Rigorous convergence often requires hundreds of atoms in the protein binding-site model, especially if that model is constructed using distance-based criteria to select amino acid residues, while three- and four-body calculations exhibit instability related to combinatorial proliferation in the number of subsystem calculations. Here, we report an energy-based screening protocol for the many-body expansion applied to protein−ligand interactions, implemented in the open-source FRAGME∩T code. Using a combination of aggressive screening based on semiempirical quantum chemistry, with an improved graph-theoretical algorithm to eliminate unimportant subsystems, we are able to perform n-body calculations up to n = 7 using density functional theory in triple-ζ basis sets. Distance cutoffs further reduce the cost without compromising accuracy. Rapid and stable convergence of the many-body expansion is obtained by n = 4, for a pair of metalloenzymes in which a divalent ion coordinates directly to the ligand. As compared to previous results that relied solely on distance cutoffs, oscillations in the n-body corrections are reduced or eliminated, although residual errors remain in one case. This work demonstrates that benchmark-quality protein−ligand interaction energies can be systematically converged using a method with excellent parallel efficiency and scalability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Direct simulation Monte Carlo on petaflop supercomputers and beyond

The gold-standard definition of the Direct Simulation Monte Carlo (DSMC) method is given in the 1994 book by Bird [Molecular Gas Dynamics and the Direct Simulation of Gas Flows (Clarendon Press, Oxford, UK, 1994)], which refined his pioneering earlier papers in which he first formulated the method. In the intervening 25 years, DSMC has become the method of choice for modeling rarefied gas dynamics in a variety of scenarios. The chief concern to applying DSMC to more dense or even continuum flows is its computational expense compared to continuum computational fluid dynamics methods. The dramatic (nearly billion-fold) increase in speed of the largest supercomputers over the last 30 years has thus been a key enabling factor in using DSMC to model a richer variety of flows, due to the method’s inherent parallelism. We have developed the open-source SPARTA DSMC code with the goal of running DSMC efficiently on the largest machines, both current and future. It is largely an implementation of Bird’s 1994 formulation. In this work, we describe algorithms used in SPARTA to enable DSMC to operate in parallel at the scale of many billions of particles or grid cells, or with billions of surface elements. We highlight a few examples of the kinds of fundamental physics questions and engineering applications that DSMC can address at these scales.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Introducing GAMER: A fast and accurate method for ray-tracing galaxies using procedural noise

We developed a novel approach for fast and accurate ray-tracing of galaxies using procedural noise fields. Our method allows for efficient and realistic rendering of synthetic galaxy morphologies, where individual components such as the bulge, disk, stars, and dust can be synthesized in different wavelengths. These components follow empirically motivated overall intensity profiles but contain an additional procedural noise component that gives rise to complex natural patterns that mimic interstellar dust and star-forming regions. These patterns produce more realistic-looking galaxy images than using analytical expressions alone. The method is fully parallelized and creates accurate high- and low- resolution images that can be used, for example, in codes simulating strong and weak gravitational lensing. In addition to having a user-friendly graphical user interface, the C++ software package GAMER is easy to implement into an existing code.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Relativistic R -matrix calculations for the electron-impact excitation of neutral molybdenum

A recent PISCES-B Mod experiment [Nishijima et al., J. Phys. B 43, 225701 (2010)] has revealed up to a factor of 5 discrepancy between measurement and the two existing theoretical models [Badnell et al., J. Phys. B 29, 3683 (1996); Bartschat et al., J. Phys. B 35, 2899 (2002)], providing important diagnostics for M O I . In the following paper we address this issue by employing a relativistic atomic structure and R -matrix scattering calculations to improve upon the available models for future applications and benchmark results against a recent Compact Toroidal Hybrid experiment [Hartwell et al., Fusion Sci. Technol. 72, 76 (2017)]. We determine the atomic structure of M O I using GRASP 0 , which implements the multiconfigurational Dirac-Fock method. Fine structure energies and radiative transition rates are presented and compared to existing experimental and theoretical values. The electron-impact excitation of M O I is investigated using the relativistic R -matrix method and the parallel versions of the Dirac atomic R -matrix codes. Electron-impact excitation cross sections are presented and compared to the few available theoretical cross sections. Throughout, our emphasis is on improving the results for the z 5 P$^{o}_{1, 2, 3}$ → a 5 S 2 , z 7 P$^{o}_{2, 3, 4}$ → a 7 S 3 and y 7 P$^{o}_{2, 3, 4}$ → a 7 S 3 electric dipole transitions of particular relevance for diagnostic work.

Smyth, R. T.↗
DOE OSTI2015

SU-E-T-185: Clinically-Relevant Investigation of Flattening Filter Free Skin Dose

Purpose: Flattening-filter-free (FFF) beams are increasingly used for small-field treatments due to inherent advantages like higher MU efficiency and reduced treatment time and scatter dose. Removal of the flattening-filter increases the electron contamination and low-energy x-rays. As such, surface-dose characteristics are different from traditional flattened (FF) beams. The goal of this work is to investigate surface dose of 6/10 MV FFF and FF beams under conditions representative of emerging complex techniques like small-field stereotactic treatments which use small fields formed with multi-leaf-collimators (MLCs) at closer SSDs. Methods: A parallel-plate PTW Markus-chamber (N23343) placed in custom air- and water-equivalent phantoms was used to measure surface-dose at 2/3/4/6/8/10/20/30 cm{sup 2} field sizes, at 80/90/100 cm source-to-surface distances, and at fields defined by jaws and MLCs. The effect of dose rate (600 and 1400/2400 MU/min) was also investigated at 100 cm SSD. Measurements were performed on TrueBeam linac (Varian Medical Systems, Palo Alto, CA) for 6X/6XFFF/10X/10XFFF beam energies. Results: No dose-rate dependence was seen for FFF skin-dose. Air-phantom measurements were, on average, 5±3% larger than for water-phantom measurements. With SSD increase from 80 to 100 cm, skin-dose decreased by an average of 3.9±2.5%. FFF beams were found to be more sensitive to SSD changes in comparison to FF beams. The difference in skin dose between MLC- and jaw-fields was less variable with field size for FFF compared to FF beams. 10 MV beams showed greater difference in FFF-to-FF ratio, 50% (jaws) and 22% (MLC), between the largest and smallest field sizes compared to 6 MV beams, 30% (jaws) and 9% (MLC). Conclusion: Under clinically-relevant conditions, surface dose for FFF beams was higher at small field size (<10 cm), lower at largest field size (30 cm), more sensitive to SSD changes, and had less variation with field size compared to dose for FF beams.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

TH-EF-BRB-08: Robotic Motion Compensation for Radiation Therapy: A 6DOF Phantom Study

Purpose: The high accuracy of frame-based stereotactic radiosurgery (SRS), which uses a rigid frame fixed to the patient’s skull, is offset by potential drawbacks of poor patient compliance and clinical workflow restrictions. Recent research into frameless SRS has so far resulted in reduced accuracy. In this study, we investigate the use of a novel 6 degree-of-freedom (6DOF) robotic head motion cancellation system that continuously detects and compensates for patient head motions during a SRS delivery. This approach has the potential to reduce invasiveness while still achieving accuracies better or equal to traditional frame-based SRS. Methods: A 6DOF parallel kinematics robotics stage was constructed, and controlled using an inverse kinematics-based motion compensation algorithm. A 6DOF stereoscopic infrared (IR) marker tracking system was used to monitor real-time motions at sub-millimeter and sub-degree levels. A novel 6DOF calibration technique was first applied to properly orient the camera coordinate frame to match that of the LINAC and robotic control frames. Simulated head motions were measured by the system, and the robotic stage responded to these 6DOF motions automatically, returning the reflective marker coordinate frame to its original position. Results: After the motions were introduced to the system in the phantom-based study, the robotic stage automatically and rapidly returned the phantom to LINAC isocenter. When errors exceeded the compensation lower threshold of 0.25 mm or 0.25 degrees, the system registered the 6DOF error and generated a cancellation trajectory. The system responded in less than 0.5 seconds and returned all axes to less than 0.1 mm and 0.1 degree after the 6DOF compensation was performed. Conclusion: The 6DOF real-time motion cancellation system was found to be effective at compensating for translational and rotational motions to current SRS requirements. This system can improve frameless SRS by automatically returning patients to isocenter with high 6DOF accuracy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Dielectric Parameters of Elastically Strained Heteroepitaxial SrTiO{sub 3} Films

Three-layer epitaxial SrRuO{sub 3}/SrTiO{sub 3}/SrRuO{sub 3} heterostructures with the 900-nm-thick intermediate layer of strontium titanate have been grown on single-crystal (001)La{sub 0.29}Sr{sub 0.71}Al{sub 0.65}Ta{sub 0.35}O{sub 3} substrates by the laser evaporation method. Plane-parallel film capacitors have been formed on the basis of the grown heterostructures using photolithography and ion etching. Temperature dependences of the dissipation factor have been measured for these capacitors at different bias voltages applied to strontium ruthenate electrodes. Temperature dependences of the permittivity of the intermediate SrTiO{sub 3} layer in the formed capacitor structures are visualized with compensation of the internal electric field and without it. The reasons for the sharp increase in the dielectric loss in the formed film capacitors at temperatures below 50 K are analyzed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

The Target-Matrix Optimization Paradigm for High-Order Meshes

Here, we describe a framework for controlling and improving the quality of high-order finite element meshes based on extensions of the Target-Matrix Optimization Paradigm (TMOP) of [P. Knupp, Eng. Comput., 28 (2012), pp. 419--429]. This approach allows high-order applications to have a very precise control over local mesh quality, while still improving the mesh globally. We address the adaption of various TMOP components to the settings of general isoparametric element mappings, including the mesh quality metric in 2D and 3D, the selection of sample points and the solution of the resulting mesh optimization problem. We also investigate additional practical concerns, such as tangential relaxation and restricting the deviation from the original mesh. The benefits of the new high-order TMOP algorithms are illustrated on a number of test problems and examples from a high-order arbitrary Lagrangian--Eulerian (ALE) application [BLAST: High-order curvilinear finite elements for shock hydrodynamics, http://www.llnl.gov/CASC/blast]. Our implementation is freely available in an open-source library form [MFEM: Modular parallel finite element methods library, http://mfem.org].

97 MATHEMATICS AND COMPUTING↗