Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “parallel algorithms”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,729 records · Page 96
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Performance Results on CPU/GPU Exascale Architectures for OMEGA: The Ocean Model for E3SM Global Applications

The US Department of Energy (DOE) conducts climate simulations on some of the world’s largest supercomputers. These exascale machines use heterogeneous architectures with both CPUs and GPUs, and scientific codes must adapt to make full use of this computing power. Los Alamos National Lab is developing Omega: The Ocean Model for E3SM Global Applications, which is specifically designed for modern exascale computers. It uses external libraries that have been optimized for a variety of architectures to run on different supercomputers. Omega is an unstructured-mesh ocean model based on TRiSK numerical methods. It will be the new ocean component of the DOE’s Energy Exascale Earth System Model (E3SM). The algorithms in Omega follow those of the current ocean component, MPAS-Ocean, but it will be written in C++ rather than Fortran to take advantage of the Kokkos performance portability library. Omega spatial operators are written as Kokkos kernels to run efficiently on both CPUs and GPUs. Work on Omega began in 2023 with a new C++ framework for unstructured mesh partitioning, halo exchanges, parallel IO, and Kokkos interfaces. The current version, Omega-0, is being developed to solve the shallow water equations and at present includes all of the tendency terms but not time stepping. Here we share the results of Omega-0 verification and performance testing. Verification includes unit tests implemented with CTest as well as convergence tests in Polaris, an in-house python package with a large suite of test problems. Performance tests compare simulations conducted on CPUs versus GPUs and across different architectures: tests are run on Frontier, which has AMD “Optimized 3rd Gen EPYC” CPUs and AMD MI250X GPUs, as well as Perlmutter, which is composed of AMD EPYC 7763 CPUs and NVIDIA A100 GPUs.

58 GEOSCIENCES↗
DOE OSTI2016

Energy scaling advantages of resistive memory crossbar based computation and its application to sparse coding

In this study, the exponential increase in data over the last decade presents a significant challenge to analytics efforts that seek to process and interpret such data for various applications. Neural-inspired computing approaches are being developed in order to leverage the computational properties of the analog, low-power data processing observed in biological systems. Analog resistive memory crossbars can perform a parallel read or a vector-matrix multiplication as well as a parallel write or a rank-1 update with high computational efficiency. For an N × N crossbar, these two kernels can be O(N) more energy efficient than a conventional digital memory-based architecture. If the read operation is noise limited, the energy to read a column can be independent of the crossbar size (O(1)). These two kernels form the basis of many neuromorphic algorithms such as image, text, and speech recognition. For instance, these kernels can be applied to a neural sparse coding algorithm to give an O(N) reduction in energy for the entire algorithm when run with finite precision. Sparse coding is a rich problem with a host of applications including computer vision, object tracking, and more generally unsupervised learning.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

Status on the Development of a Modeling and Simulation Framework for the Economic Assessment of Nuclear Hybrid Energy Systems

An effort to design and build a modeling and simulation framework to assess the economic viability of Nuclear Hybrid Energy Systems (NHES) was undertaken in fiscal year 2015 (FY15). The purpose of this report is to document the various tasks associated with the development of such a framework and to provide a status on its progress. Several tasks have been accomplished. First, starting from a simulation strategy, a rigorous mathematical formulation has been achieved in which the economic optimization of a Nuclear Hybrid Energy System is presented as a constrained robust (under uncertainty) optimization problem. Some possible algorithms for the solution of the optimization problem are presented. A variation of the Simultaneous Perturbation Stochastic Approximation algorithm has been implemented in RAVEN and preliminary tests have been performed. The development of the software infrastructure to support the simulation of the whole NHES has also moved forward. The coupling between RAVEN and an implementation of the Modelica language (OpenModelica) has been implemented, migrated under several operating systems and tested using an adapted model of a desalination plant. In particular, this exercise was focused on testing the coupling of the different code systems; testing parallel, computationally expensive simulations on the INL cluster; and providing a proof of concept for the possibility of using surrogate models to represent the different NHES subsystems. Another important step was the porting of the RAVEN code under the Windows™ operating system. This accomplishment makes RAVEN compatible with the development environment that is being used for dynamic simulation of NHES components. A very simplified model of a NHES on the electric market has been built in RAVEN to confirm expectations on the analysis capability of RAVEN to provide insight into system economics and to test the capability of RAVEN to identify limit surfaces even for stochastic constraints. This capability will be needed in the future to enforce the stochastic constraints on the electric demand coverage from the NHES. The development team gained experience with many of the tools that are currently envisioned for use in the economic analysis of NHES and completed several important steps. Given the complexity of the project, preference has been given to a structural approach in which several independent efforts have been used to build the cornerstone of the simulation framework. While this is good approach in establishing such a complex framework, it may delay reaching more complete results on the performance of analyzed system configurations. The integration of the previously reported exergy analysis approach was initially proposed as part of this milestone. However, in reality, the exergy-based apportioning of cost will take place only in a second stage of the implementation since it will be used to properly allocate cost among the different NHES subsystems. Therefore, exergy does not appear at the level of the main drivers in the analysis framework; the latter development of the base framework is the focus of this report.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2024

The 4D Camera: An 87 kHz Direct Electron Detector for Scanning/Transmission Electron Microscopy

We describe the development, operation, and application of the 4D Camera—a 576 by 576 pixel active pixel sensor for scanning/transmission electron microscopy which operates at 87,000 Hz. The detector generates data at ~480 Gbit/s which is captured by dedicated receiver computers with a parallelized software infrastructure that has been implemented to process the resulting 10–700 Gigabyte-sized raw datasets. The back illuminated detector provides the ability to detect single electron events at accelerating voltages from 30 to 300 kV. Through electron counting, the resulting sparse data sets are reduced in size by 10--300× compared to the raw data, and open-source sparsity-based processing algorithms offer rapid data analysis. The high frame rate allows for large and complex scanning diffraction experiments to be accomplished with typical scanning transmission electron microscopy scanning parameters.

47 OTHER INSTRUMENTATION↗
DOE OSTI2017

Distributed-Memory Fast Maximal Independent Set

The Maximal Independent Set (MIS) graph problem arises in many applications such as computer vision, information theory, molecular biology, and process scheduling. The growing scale of MIS problems suggests the use of distributed-memory hardware as a cost-effective approach to providing necessary compute and memory resources. Luby proposed four randomized algorithms to solve the MIS problem. All those algorithms are designed focusing on shared-memory machines and are analyzed using the PRAM model. These algorithms do not have direct efficient distributed-memory implementations. In this paper, we extend two of Luby’s seminal MIS algorithms, “Luby(A)” and “Luby(B),” to distributed-memory execution, and we evaluate their performance. We compare our results with the “Filtered MIS” implementation in the Combinatorial BLAS library for two types of synthetic graph inputs.

distributed memory parallel↗
DOE OSTI2014

A new Green's function Monte Carlo algorithm for the solution of the two-dimensional nonlinear Poisson–Boltzmann equation: Application to the modeling of the communication breakdown problem in space vehicles during re-entry

The objective of this paper is the exposition of a recently-developed, novel Green's function Monte Carlo (GFMC) algorithm for the solution of nonlinear partial differential equations and its application to the modeling of the plasma sheath region around a cylindrical conducting object, carrying a potential and moving at low speeds through an otherwise neutral medium. The plasma sheath is modeled in equilibrium through the GFMC solution of the nonlinear Poisson–Boltzmann (NPB) equation. The traditional Monte Carlo based approaches for the solution of nonlinear equations are iterative in nature, involving branching stochastic processes which are used to calculate linear functionals of the solution of nonlinear integral equations. Over the last several years, one of the authors of this paper, K. Chatterjee has been developing a philosophically-different approach, where the linearization of the equation of interest is not required and hence there is no need for iteration and the simulation of branching processes. Instead, an approximate expression for the Green's function is obtained using perturbation theory, which is used to formulate the random walk equations within the problem sub-domains where the random walker makes its walks. However, as a trade-off, the dimensions of these sub-domains have to be restricted by the limitations imposed by perturbation theory. The greatest advantage of this approach is the ease and simplicity of parallelization stemming from the lack of the need for iteration, as a result of which the parallelization procedure is identical to the parallelization procedure for the GFMC solution of a linear problem. The application area of interest is in the modeling of the communication breakdown problem during a space vehicle's re-entry into the atmosphere. However, additional application areas are being explored in the modeling of electromagnetic propagation through the atmosphere/ionosphere in UHF/GPS applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Monte Carlo MP2-F12 for Noncovalent Interactions: The C 60 Dimer

A scalable stochastic algorithm is presented that can evaluate explicitly correlated (F12) second-order many-body perturbation (MP2) energies of weak, noncovalent, intermolecular interactions. It first transforms the formulas of the MP2 and F12 energy differences into a short sum of high-dimensional integrals of Green’s functions in real space and imaginary time. Furthermore, these integrals are then evaluated by the Monte Carlo method augmented by parallel execution, redundant-walker convergence acceleration, direct-sampling autocorrelation elimination, and control-variate error reduction. By sharing electron-pair walkers across the supermolecule and its subsystems spanned by the joint basis set, the statistical uncertainty is reduced by one to 2 orders of magnitude in the MP2 binding energy corrected for the basis-set incompleteness and superposition errors. The method predicts the MP2-F12/aug-cc-pVDZ binding energy of 19.1 ± 4.0 kcal mol –1 for the C 60 dimer at the center distance of 9.748 Å.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

24.77 Pflops on a Gravitational Tree-Code to Simulate the Milky Way Galaxy with 18600 GPUs, In: SC '14: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis

We have simulated, for the first time, the long term evolution of the Milky Way Galaxy using 51 billion particles on the Swiss Piz Daint supercomputer with our N-body gravitational tree-code Bonsai. Herein, we describe the scientific motivation and numerical algorithms. The Milky Way model was simulated for 6 billion years, during which the bar structure and spiral arms were fully formed. This improves upon previous simulations by using 1000 times more particles, and provides a wealth of new data that can be directly compared with observations. We also report the scalability on both the Swiss Piz Daint and the US ORNL Titan. On Piz Daint the parallel efficiency of Bonsai was above 95%. The highest performance was achieved with a 242 billion particle Milky Way model using 18600 GPUs on Titan, thereby reaching a sustained GPU and application performance of 33.49 Pflops and 24.77 Pflops respectively.

Computer Science↗
DOE OSTI2023

VTK-m: Visualization for the Exascale Era and Beyond

A recent trend in modern high-performance computing is the increasing use of hybrid architectures, where the vast majority of performance comes from accelerators. Modern accelerators are based on Graphics Processing Units (GPU) that contain many low power cores that in their aggregate provides an extremely high computation rate. Current and future CPU processors are requiring more explicit parallelism as each successive version of the hardware packs in more cores, and technologies like hyperthreading and vector operations require even more parallel processing to leverage each core’s full potential. As an example, the Frontier supercomputer installed at Oak Ridge National Laboratories recently hit a record breaking 1.1 exaflops1 on the LINPACK HPC benchmark [Shoemaker 2022]. The system contains 37632 AMD MI250x GPUs which requires more than half a billion threads to keep the system fully utilized [Khizeran 2022].VTK-m is a toolkit of scientific visualization algorithms for these emerging processor architectures. VTK-m supports the fine-grained concurrency for data analysis and visualization algorithms required to drive extreme scale computing by providing abstract models for data and execution that can be applied to a variety of algorithms across many different processor architectures.

Bolstad, Mark↗
DOE OSTI2015

Formulas for robust, parallel computation of arbitrary-order, arbitrary-variate, statistical moments with arbitrary weights and compounding

Formulas for incremental or parallel computation of second order central moments have long been known, and recent extensions of these formulas to univariate and multivariate moments of arbitrary order have been developed. Such formulas are of key importance in scenarios where incremental results are required and in parallel and distributed systems where communication costs are high. We survey these recent results, and recall the first generalizations which we had obtained in [P$\acute0$8]. We then improve these arbitrary-order, numerically stable one-pass formulas to arbitrary-variate formulas which we further extend to arbitrary weights and compound variants. We also develop a generalized correction factor for standard two-pass algorithms that enables the maintenance of accuracy over nearly the full representable range of the input, avoiding the need for extended-precision arithmetic.

97 MATHEMATICS AND COMPUTING↗
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 OSTI2025

Computing material volume fractions on a superimposed mesh as applied to Monte Carlo particle transport simulations

Here, we present a newly implemented ray tracing algorithm in OpenMC for efficiently computing material volume fractions on superimposed meshes in complex geometries. By firing rays along each coordinate direction through the geometry, the approach accumulates track-length data in each mesh element, thereby determining the fractional composition of each material. Scaling studies on three different models—a random tetrahedra configuration, the Frascati Neutron Generator ITER dose rate benchmark, and a stellarator design—show excellent parallel performance, with nearly linear speedup on modern multi-threaded and distributed-memory systems. An analysis of the residual error relative to high-resolution reference solutions demonstrated that under optimal conditions it decreases as 1/R, where R is the number of rays fired, making it straightforward to achieve user-prescribed accuracy. This new functionality enables practical, mesh-based approaches for detailed nuclear analyses in production Monte Carlo workflows without resorting to expensive, fully conformal or unstructured meshing.

Monte Carlo↗
DOE OSTI2015

Exploring Memory Hierarchy to Improve Scientific Data Read Performance, In: 2015 IEEE International Conference on Cluster Computing

Improving read performance is one of the major challenges with speeding up scientific data analytic applications. Utilizing the memory hierarchy is one major line of researches to address the read performance bottleneck. Related methods usually combine solide-state-drives(SSDs) with dynamic random-access memory(DRAM) and/or parallel file system(PFS) to mitigate the speed and space gap between DRAM and PFS. However, these methods are unable to handle key performance issues plaguing SSDs, namely read contention that may cause up to 50% performance reduction. In this paper, we propose a framework that exploits the memory hierarchy resource to address the read contention issues involved with SSDs. The framework employs a general purpose online read algorithm that able to detect and utilize memory hierarchy resource to relieve the problem. To maintain a near optimal operating environment for SSDs, the framework is able to orchastrate data chunks across different memory layers to facilitate the read algorithm. Compared to existing tools, our framework achieves up to 50% read performance improvement when tested on datasets from real-world scientific simulations.

Computer Science↗
DOE OSTI2015

Pushing back the limit of ab-initio quantum transport simulations on hybrid supercomputers, In: SC '15 Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis

The capabilities of CP2K, a density-functional theory package and OMEN, a nano-device simulator, are combined to study transport phenomena from first-principles in unprecedentedly large nanostructures. Based on the Hamiltonian and overlap matrices generated by CP2K for a given system, OMEN solves the Schrödinger equation with open boundary conditions (OBCs) for all possible electron momenta and energies. To accelerate this core operation a robust algorithm called SplitSolve has been developed. It allows to simultaneously treat the OBCs on CPUs and the Schrödinger equation on GPUs, taking advantage of hybrid nodes. Our key achievements on the Cray-XK7 Titan are (i) a reduction in time-to-solution by more than one order of magnitude as compared to standard methods, enabling the simulation of structures with more than 50000 atoms, (ii) a parallel efficiency of 97% when scaling from 756 up to 18564 nodes, and (iii) a sustained performance of 15 DP-PFlop/s.

Computer Science↗
DOE OSTI2015

SU-E-J-208: Feasibility Study On Using Small Plastic Phantoms for Auditing Radiation Output of MR-Linac Systems

Purpose: To study feasibility of using small plastic phantoms designed for conventional linac output auditing to measure the output of MR-Linac systems. Methods: For simulations, the CT scan of an IROC(formerly RPC) acrylic block phantom designed for 8 MV beams was imported in a research version of the treatment planning system (Monaco). Dose delivered to three TLDs in the block was calculated with a Monte Carlo algorithm and a beam model based on an MR-linac prototype with and without a magnetic field (B=1.5T). In a large mathematical water phantom, the same beam was used to calculate dose in full scatter conditions. The block factor (F) was calculated as the ratio of the average dose to the block TLDs to the dose at the reference point in the mathematical phantom. For experimental measurement, four IROC blocks were irradiated with the MR-linac prototype, and data were analyzed by IROC. Results: The F factor without a B field was 1.053. When a B field was applied, it changed the dose distribution in the block, especially on the edges. With a B field parallel to the long axes of the TLD, F was 1.038. However, with a perpendicular B field, F factor increased slightly to 1.075. In the IROC report, the output determined with two blocks parallel to the B field was 2.3% higher than the output by the two blocks perpendicular to the B field. The average of all four blocks was within 2% of machine output measured with an ion chamber. Conclusion: It may be feasible to expand the utility of the acrylic block phantoms for radiation output auditing from conventional linacs to MR-linacs. However, the scatter correction factor can change due to the B field and its orientation to the block. More symmetric phantom designs may be less prone to mistakes. We acknowledge research support from Elekta.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Discontinuous finite element space-angle treatment of the first order linear Boltzmann transport equation with magnetic fields: Application to MRI-guided radiotherapy

Purpose: The advent of magnetic resonance imaging (MRI) guided radiotherapy systems demands the incorporation of the magnetic field into dose calculation algorithms of treatment planning systems. This is due to the fact that the Lorentz force of the magnetic field perturbs the path of the relativistic electrons, hence altering the dose deposited by them. Building on the previous work, the authors have developed a discontinuous finite element space-angle treatment of the linear Boltzmann transport equation to accurately account for the effects of magnetic fields on radiotherapy doses. Methods: The authors present a detailed description of their new formalism and compare its accuracy to GEANT4 Monte Carlo calculations for magnetic fields parallel and perpendicular to the radiation beam at field strengths of 0.5 and 3 T for an inhomogeneous 3D slab geometry phantom comprising water, bone, and air or lung. The accuracy of the authors’ new formalism was determined using a gamma analysis with a 2%/2 mm criterion. Results: Greater than 98.9% of all points analyzed passed the 2%/2 mm gamma criterion for the field strengths and orientations tested. The authors have benchmarked their new formalism against Monte Carlo in a challenging radiation transport problem with a high density material (bone) directly adjacent to a very low density material (dry air at STP) where the effects of the magnetic field dominate collisions. Conclusions: A discontinuous finite element space-angle approach has been proven to be an accurate method for solving the linear Boltzmann transport equation with magnetic fields for cases relevant to MRI guided radiotherapy. The authors have validated the accuracy of this novel technique against GEANT4, even in cases of strong magnetic field strengths and low density air.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2023

Coupled cluster theory on modern heterogeneous supercomputers

This study examines the computational challenges in elucidating intricate chemical systems, particularly through ab-initio methodologies. This work highlights the Divide-Expand-Consolidate (DEC) approach for coupled cluster (CC) theory—a linear-scaling, massively parallel framework—as a viable solution. Detailed scrutiny of the DEC framework reveals its extensive applicability for large chemical systems, yet it also acknowledges inherent limitations. To mitigate these constraints, the cluster perturbation theory is presented as an effective remedy. Attention is then directed towards the CPS (D-3) model, explicitly derived from a CC singles parent and a doubles auxiliary excitation space, for computing excitation energies. The reviewed new algorithms for the CPS (D-3) method efficiently capitalize on multiple nodes and graphical processing units, expediting heavy tensor contractions. As a result, CPS (D-3) emerges as a scalable, rapid, and precise solution for computing molecular properties in large molecular systems, marking it an efficient contender to conventional CC models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Low synchronization Gram–Schmidt and generalized minimal residual algorithms

The Gram–Schmidt process uses orthogonal projection to construct the A = QR factorization of a matrix. When Q has linearly independent columns, the operator P = I - Q(QTQ)-1QT defines an orthogonal projection onto Q⊥. In finite precision, Q loses orthogonality as the factorization progresses. A family of approximate projections is derived with the form P = I - QTQT, with correction matrix T. When T = (QTQ)-1, and T is triangular, it is postulated that the best achievable orthogonality is $\mathcal{O}(ε)\mathcal{K}(A)$. We present new variants of modified (MGS) and classical Gram–Schmidt algorithms that require one global reduction step. An interesting form of the projector leads to a compact WY representation for MGS. In particular, the inverse compact WY MGS algorithm is equivalent to a lower triangular solve. Our main contribution is to introduce a backward normalization lag into the compact WY representation, resulting in a $\mathcal{O}(ε)\mathcal{K}[r_0, AV_m])$ stable Generalized Minimal Residual Method (GMRES) algorithm that requires only one global reduce per iteration. Finally, further improvements in performance are achieved by accelerating GMRES on GPUs.

97 MATHEMATICS AND COMPUTING↗