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At least 19 records

A prospect for computing in porous materials research: Very large fluid flow simulations

Properties of porous materials, abundant both in nature and industry, have broad influences on societies via, e.g. oil recovery, erosion, and propagation of pollutants. The internal structure of many porous materials involves multiple scales which hinders research on the relation between structure and transport properties: typically laboratory experiments cannot distinguish contributions from individual scales while computer simulations cannot capture multiple scales due to limited capabilities. Thus the question arises how large domain sizes can in fact be simulated with modern computers. This question is here addressed using a realistic test case; it is demonstrated that current computing capabilities allow the direct pore-scale simulation of fluid flow in porous materials using system sizes far beyond what has been previously reported. The achieved system sizes allow the closing of some particular scale gaps in, e.g. soil and petroleum rock research. Specifically, a full steady-state fluid flow simulation in a porous material, represented with an unprecedented resolution for the given sample size, is reported: the simulation is executed on a CPU-based supercomputer and the 3D geometry involves 16,3843 lattice cells (around 590 billion of them are pore sites). Using half of this sample in a benchmark simulation on a GPU-based system, a sustained computational performance of 1.77 PFLOPS is observed. These advances expose new opportunities in porous materials research. The implementation techniques here utilized are standard except for the tailored high-performance data layouts as well as the indirect addressing scheme with a low memory overhead and the truly asynchronous data communication scheme in the case of CPU and GPU code versions, respectively.

Computer Science↗

Virtual Flow Simulator

Virtual Flow Simulator (VFS) is a state-of-the-art computational fluid mechanics (CFD) package that is capable of simulating multi-physics/multi-phase flows with the most advanced turbulence models (RANS, LES) over complex terrains. The flow solver is based on the Curvilinear Immersed Boundary (CURVIB) method to handle geometrically complex and moving domains. Different modules of the VFS package can provide different simulation capabilities for specific applications ranging from the fluid-structure interaction (FSI) of solid and deformable bodies, the two-phase free surface flow solver based on the level set method for ocean waves, sediment transport models in rivers and the large-scale models of wind farms based on actuator lines and surfaces. All numerical features of VFS package have been validated with known analytical and experimental data as reported in the related journal articles. VFS package is suitable for a broad range of engineering applications within different industries. VFS has been used in different projects with applications in wind and hydrokinetic energy, offshore and near-shore ocean studies, cardiovascular and biological flows, and natural streams and river morphodynamics. Over the last decade, the development of VFS has been supported and assisted with the help of various United States companies and federal agencies that are listed in the sponsor lists. In this version, VFS-Wind contains all the necessary modeling tools for wind energy applications, including land-based and offshore wind farms. VFS is highly scalable to run on either desktop computers or high performance clusters (up to 16,000 CPUs). This released version comes with a detailed user’s manual and a set of case studies designed to facilitate the learning of the various aspects of the code in a comprehensive manner. The included documentation and support material has been elaborated in a collaboration effort with Sandia National Labs under the contract DE-EE0005482. The VFS-Wind source code is distributed under the GNU General Public License (GPL 2.0), offering to the community the flexibility to use and expand the capabilities of the package. We note that future publications including academic journals that result from the use of VFS must be cited appropriately under the GPL v.2 license agreement.

Yang, Xiaolei↗

Virtual Flow Simulator

Virtual Flow Simulator (VFS) is a state-of-the-art computational fluid mechanics (CFD) package that is capable of simulating multi-physics/multi-phase flows with the most advanced turbulence models (RANS, LES) over complex terrains. The flow solver is based on the Curvilinear Immersed Boundary (CURVIB) method to handle geometrically complex and moving domains. Different modules of the VFS package can provide different simulation capabilities for specific applications ranging from the fluid-structure interaction (FSI) of solid and deformable bodies, the two-phase free surface flow solver based on the level set method for ocean waves, sediment transport models in rivers and the large-scale models of wind farms based on actuator lines and surfaces. All numerical features of VFS package have been validated with known analytical and experimental data as reported in the related journal articles. VFS package is suitable for a broad range of engineering applications within different industries. VFS has been used in different projects with applications in wind and hydrokinetic energy, offshore and near-shore ocean studies, cardiovascular and biological flows, and natural streams and river morphodynamics. Over the last decade, the development of VFS has been supported and assisted with the help of various United States companies and federal agencies that are listed in the sponsor lists. In this version, VFS-Wind contains all the necessary modeling tools for wind energy applications, including land-based and offshore wind farms. VFS is highly scalable to run on either desktop computers or high performance clusters (up to 16,000 CPUs). This released version comes with a detailed user’s manual and a set of case studies designed to facilitate the learning of the various aspects of the code in a comprehensive manner. The included documentation and support material has been elaborated in a collaboration effort with Sandia National Labs under the contract DE-EE0005482. The VFS-Wind source code is distributed under the GNU General Public License (GPL 2.0), offering to the community the flexibility to use and expand the capabilities of the package. We note that future publications including academic journals that result from the use of VFS must be cited appropriately under the GPL v.2 license agreement.

Calderer, Antoni↗

Multilevel Graph Partitioning for Three-Dimensional Discrete Fracture Network Flow Simulations

We present a topology-based method for mesh-partitioning in three-dimensional discrete fracture network (DFN) simulations that takes advantage of the intrinsic multi-level nature of a DFN. DFN models are used to simulate flow and transport through low-permeability fractured media in the subsurface by explicitly representing fractures as discrete entities. The governing equations for flow and transport are numerically integrated on computational meshes generated on the interconnected fracture networks. Modern high-fidelity DFN simulations require high-performance computing on multiple processors where performance and scalability depends partially on obtaining a high-quality partition of the mesh to balance work-loads and minimize communication across all processors. The discrete structure of a DFN naturally lends itself to various graph representations, which can be thought of as coarse-scale representations of the computational mesh. Using this concept, we develop two applications of the multilevel graph partitioning algorithm to partition the mesh of a DFN. In the first, we project a partition of the graph based on the DFN topology onto the mesh of the DFN and in the second, this DFN-based projection is used as the initial condition for further partitioning refinement of the mesh. We compare the performance of these methods with standard multi-level graph partitioning using graph-based metrics (cut, imbalance, partitioning time), computational-based metrics (FLOPS, iterations, solver time), and total run time. The DFN-based and the mesh-based partitioning methods are comparable in terms of the graph-based metrics, but the time required to obtain the partition is several orders of magnitude faster using the DFN-based partitions. The computation-based metrics show comparable performance between both methods so, in combination, the DFN-based partitions are several orders of magnitude faster than the mesh-based partition. Furthermore, the method which uses the DFN-partition solution as the initial condition of the mesh partition provided cut and imbalance values that were close to the mesh-based partition but in a fraction of the time. In turn, this hybrid method outperformed both of the other methods in terms of the total run time.

58 GEOSCIENCES↗

A scalable Euler–Lagrange approach for multiphase flow simulation on spectral elements

Multiphase flow can be difficult to simulate with high accuracy due to the wide range of scales associated with various multiphase phenomena. These scales may range from the size of individual particles to the entire domain of interest. Traditionally, large scale systems can only be simulated using averaging approaches that filter out the locations of individual particles. In this work, the Euler–Lagrange method is used to simulate large-scale dense particle systems in which each individual particle is tracked. In order to accomplish this, the highly scalable spectral element code nek5000 has been extended to handle the multiple levels of multiphase coupling in these systems. These levels include what has been called one-, two-, and four-way coupling. Here, each level has been separated to detail the computational impact of each stage. A binned ghost particle algorithm has also been developed to efficiently handle the challenges of two- and four-way coupling in a parallel processing context. The algorithms and their implementations are then shown to scale to 65,536 Message Passing Interface (MPI) ranks in both the strong and weak limits. After this, validation is performed through simulation of a small-scale fluidized bed. Lastly, a large-scale fluidized bed is simulated with 65,536 MPI ranks and is able to capture the unique physics of the onset of fluidization.

Computer Science↗

LOTO Training Flow Simulator Design

The LOTO Training Flow Simulator Design poster discusses the intended purpose of the simulator along with the steps taken in the design process. It highlights the two main systems designed in the primary flow loop and the bubbler system, along with a brief description of the flow calculations made to ensure the functionality of the system.

42 - ENGINEERING↗

Outcomes from the DOE Workshop on Turbulent Flow Simulation at the Exascale

This paper summarizes the outcomes from the Turbulent Flow Simulation at the Exascale: Opportunities and Challenges Workshop, which was held 4-5 August 2015, and was sponsored by the U.S. Department of Energy Office of Advanced Scientific Computing Research. The workshop objective was to define and describe the challenges and opportunities that computing at the exascale will bring to turbulent-flow simulations in applied science and technology. The need for accurate simulation of turbulent flows is evident across the U.S. Department of Energy applied-science and engineering portfolios, including combustion, plasma physics, nuclear-reactor physics, wind energy, and atmospheric science. The workshop brought together experts in turbulent-flow simulation, computational mathematics, and high-performance computing. Building upon previous ASCR workshops on exascale computing, participants defined a research agenda and path forward that will enable scientists and engineers to continually leverage, engage, and direct advances in computational systems on the path to exascale computing.

97 MATHEMATICS AND COMPUTING↗

Turbulent Flow Simulation at the Exascale: Opportunities and Challenges Workshop: August 4-5, 2015, Washington, D.C.

This report details the impact exascale will bring to turbulent-flow simulations in applied science and technology. The need for accurate simulation of turbulent flows is evident across the DOE applied-science and engineering portfolios, including combustion, plasma physics, nuclear-reactor physics, wind energy, and atmospheric science. The workshop brought together experts in turbulent-flow simulation, computational mathematics, and high-performance computing. Building upon previous ASCR workshops on exascale computing, participants defined a research agenda and path forward that will enable scientists and engineers to continually leverage, engage, and direct advances in computational systems on the path to exascale computing.

97 MATHEMATICS AND COMPUTING↗

Deep learning for in situ data compression of large turbulent flow simulations

As the size of turbulent flow simulations continues to grow, in situ data compression is becoming increasingly important for visualization, analysis, and restart checkpointing. For these applications, single-pass compression techniques with low computational and communication overhead are crucial. In this paper we present a deep-learning approach to in situ compression using an autoencoder architecture that is customized for three-dimensional turbulent flows and is well suited for contemporary heterogeneous computing resources. The autoencoder is compared against a recently introduced randomized single-pass singular value decomposition (SVD) for three different canonical turbulent flows: decaying homogeneous isotropic turbulence, a Taylor-Green vortex, and turbulent channel flow. Our proposed fully convolutional autoencoder architecture compresses turbulent flow snapshots by a factor of 64 with a single pass, allows for arbitrarily sized input fields, is cheaper to compute than the randomized single-pass SVD for typical simulation sizes, performs well on unseen flow configurations, and has been made publicly available. The results reported here show that the autoencoder dramatically outperforms a randomized single-pass SVD with similar compression ratio and yields comparable performance to a higher-rank decomposition with an order of magnitude less compression in regard to preserving a number of important statistical quantities such as turbulent kinetic energy, enstrophy, and Reynolds stresses.

97 MATHEMATICS AND COMPUTING↗

Parallel Fokker–Planck-DSMC algorithm for rarefied gas flow simulation in complex domains at all Knudsen numbers

A major challenge for the conventional Direct Simulation Monte Carlo (DSMC) technique lies in the fact that its computational cost becomes prohibitive in the near continuum regime, where the Knudsen number (Kn)—characterizing the degree of rarefaction—becomes small. In contrast, the Fokker–Planck (FP) based particle Monte Carlo scheme allows for computationally efficient simulations of rarefied gas flows in the low and intermediate Kn regime. The Fokker–Planck collision operator—instead of performing binary collisions employed by the DSMC method—integrates continuous stochastic processes for the phase space evolution in time. This allows for time step and grid cell sizes larger than the respective collisional scales required by DSMC. Dynamically switching between the FP and the DSMC collision operators in each computational cell is the basis of the combined FP-DSMC method, which has been proven successful in simulating flows covering the whole Kn range. Until recently, this algorithm had only been applied to two-dimensional test cases. In this contribution, we present the first general purpose implementation of the combined FP-DSMC method. Utilizing both shared- and distributed-memory parallelization, this implementation provides the capability for simulations involving many particles and complex geometries by exploiting state of the art computer cluster technologies.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Gene flow simulations demonstrate resistance of long-lived species to genetic erosion from habitat fragmentation

Habitat fragmentation restricts the movement of individuals across a landscape. In terrestrial and aquatic systems, barriers to movement can modify population and community dynamics at local or regional scales. This research contrasted life history traits related to lifespan with habitat fragmentation to determine impacts on species population genetic structure in the Neuse River Basin, USA. For this, we simulated gene flow among evenly-spaced populations in a river network and tracked individual and population genetics for 200 years. The modeled scenarios represent a full cross between five life history strategies and four riverscapes representing varying degrees of fragmentation. The five life history strategies include species (based on freshwater mussels) with average lifespans ranging from 10 to 50 years and age at maturity from 2 to 6 years. The movement landscapes included a (1) panmictic, (2) stepping-stone landscape allowing movement to only neighboring populations during each dispersal event, (3) partially-fragmented landscape divided by dams currently in the network, and (4) fully-fragmented landscape. Results suggest species with shorter lifespans have higher population genetic structure in fragmented landscapes than species with longer lifespans. Additionally, species with shorter lifespans in highly fragmented landscapes may be harboring genetic degradation or decline as allele fixation and loss. Although anthropogenic fragmentation of many river systems is only 100–200 years old, the simulation indicates that species can respond genetically in that period of time. Moreover, the time frame of the simulation suggests that genetic impacts of habitat fragmentation in some species present in the Neuse River Basin may not yet be manifesting and restoration activities could be successful.

13 HYDRO ENERGY↗

Iterative Workflow for Quantification and Minimization of Reduced Chemistry-Induced Uncertainties in Reacting Flow Simulation

Reduced chemistry models mitigate computational cost but introduce two sources of uncertainties in reacting flow simulation, including chemical information loss due to model reduction, and approximation errors due to non-optimal projection. We present an iterative workflow for quantification and minimization of reduced chemistry-induced uncertainties in reacting flow simulations.

chemistry↗

Parallel exponential time differencing methods for geophysical flow simulations

Two ocean models are considered for geophysical flow simulations: the multilayer shallow water equations and the multilayer primitive equations. For the former, we investigate the parallel performance of exponential time differencing (ETD) methods, including exponential Rosenbrock–Euler, ETD2wave, and B-ETD2wave. For the latter, we take advantage of the splitting of barotropic and baroclinic modes and propose a new two-level method in which an ETD method is applied to solve the fast barotropic mode. Furthermore, these methods could improve the computational efficiency of numerical simulations because ETD methods allow for much larger time step sizes than traditional explicit time-stepping techniques that are commonly used in existing computational ocean models. Several standard benchmark tests for ocean modeling are performed and comparison of the numerical results demonstrates a great potential of applying the parallel ETD methods for simulating real-world geophysical flows.

54 ENVIRONMENTAL SCIENCES↗

On the utility of GPU accelerated high-order methods for unsteady flow simulations: A comparison with industry-standard tools

First- and second-order accurate numerical methods, implemented for CPUs, underpin the majority of industrial CFD solvers. Whilst this technology has proven very successful at solving steady-state problems via a Reynolds Averaged Navier–Stokes approach, its utility for undertaking scale-resolving simulations of unsteady flows is less clear. High-order methods for unstructured grids and GPU accelerators have been proposed as an enabling technology for unsteady scale-resolving simulations of flow over complex geometries. In this study we systematically compare accuracy and cost of the high-order Flux Reconstruction solver PyFR running on GPUs and the industry-standard solver STAR-CCM+ running on CPUs when applied to a range of unsteady flow problems. Specifically, we perform comparisons of accuracy and cost for isentropic vortex advection (EV), decay of the Taylor–Green vortex (TGV), turbulent flow over a circular cylinder, and turbulent flow over an SD7003 aerofoil. We consider two configurations of STAR-CCM+: a second-order configuration, and a third-order configuration, where the latter was recommended by CD-adapco for more effective computation of unsteady flow problems. Results from both PyFR and STAR-CCM+ demonstrate that third-order schemes can be more accurate than second-order schemes for a given cost e.g. going from second- to third-order, the PyFR simulations of the EV and TGV achieve 75× and 3× error reduction respectively for the same or reduced cost, and STAR-CCM+ simulations of the cylinder recovered wake statistics significantly more accurately for only twice the cost. Moreover, advancing to higher-order schemes on GPUs with PyFR was found to offer even further accuracy vs. cost benefits relative to industry-standard tools.

97 MATHEMATICS AND COMPUTING↗

In situ feature analysis for large-scale multiphase flow simulations

The study of multiphase flow is essential for designing chemical reactors such as fluidized bed reactors (FBR), as a detailed understanding of hydrodynamics is critical for optimizing reactor performance and stability. An FBR allows scientists to conduct different types of chemical reactions involving multiphase materials, especially interaction between gas and solids. During such complex chemical processes, the formation of void regions in the reactor, generally termed as bubbles, is an important phenomenon. The study of these bubbles has a deep implication in predicting the reactor’s overall efficiency. But physical experiments needed to understand bubble dynamics are costly and non-trivial due to the technical difficulties involved and harsh working conditions of the reactors. Therefore, to study such chemical processes and bubble dynamics, a state-of-the-art computational simulation MFIX-Exa is being developed. Despite the proven accuracy of MFIX-Exa in modeling bubbling phenomena, the large-scale output data prohibits the use of traditional post hoc analysis capabilities in both storage and I/O time. Herein, to address these issues and allow the application scientists to explore the bubble dynamics in an efficient and timely manner, we have developed an end-to-end analytics pipeline that enables in situ detection of bubbles, followed by a flexible post hoc visual exploration methodology of bubble dynamics. The proposed method enables interactive analysis of bubbles, along with quantification of several bubble characteristics, enabling experts to understand the bubble interactions in detail. Positive feedback from the experts has indicated the efficacy of the proposed approach for exploring bubble dynamics in very-large-scale multiphase flow simulations.

97 MATHEMATICS AND COMPUTING↗

Upscaling ab-initio chemistry models to non-equilibrium flow simulations

Thermochemical nonequilibrium is generated by hypersonic cruise vehicles, high speed combustion and detonations. Nonequilibrium interactions affect reaction rates and energy transfer that are critical for many engineering applications. Ab-initio potential energy surfaces can be used in quasi-classical trajectory (QCT) calculations to calculate state-specific dissociation rates and cross sections, as well as state-to-state energy exchange rates and cross sections. These rates and cross sections are needed for simulating such nonequilibrium flows. However, there are two main challenges in extending QCT calculations to modeling all chemical processes found in typical engineering flowfields. First, ab-initio surfaces for many collision partners are not available and when available their fidelity is not quantified. Second, state-to-state cross section datasets are typically on the order of 1000 4, , and are too large to be efficiently implemented in engineering simulations. This work focuses on O 2 +O interactions because of prevalence of oxygen in many engineering application; however, all of the models developed here may be applied to other diatom-atom interactions and can be extended to other diatom-diatom combinations. It is shown in this work that at temperatures between 2,500 and 20,000K, state-specific cross sections are not highly sensitive to potentials and a Morse additive pairwise (MAP) potential is proposed for modeling collisions for which ab-initio potentials are not available. Next, this work suggests an approach to model state-to-state cross sections based on maximum entropy considerations. The calculated cross sections are fit to a new model with just 8 parameters, which can be easily scaled up to flow simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Classroom aerosol dispersion modeling: experimental assessment of a low-cost flow simulation tool

The purpose of this study was to assess the utility of a low-cost flow simulation tool for an indoor air modeling application by comparing its outputs with the results of a physical experiment, as well as those from a more advanced computational fluid dynamics (CFD) software package. In this study, five aerosol dispersion tests were performed in two different classrooms by releasing a CO 2 tracer gas from six student locations. Resultant steady-state concentrations were monitored at 13 locations around the periphery of the room. Subsequently, the experiments were modeled using both a low-cost tool (SolidWorks Flow Simulation) and a more sophisticated tool (STAR-CCM+). Models were evaluated based on their ability to predict the experimentally measured concentrations at the 13 monitoring locations by calculating four performance parameters commonly used in the evaluation of dispersion models: fractional mean bias (FB), normalized mean-square error (NMSE), fraction of predicted value within a factor of two (FAC2), and normalized absolute difference (NAD). The more sophisticated model performed better in 15 of the 20 possible cases (five tests at four parameters each), with parameters meeting acceptance criteria in 19 of 20 cases. However, the lower-cost tool was only slightly worse, with parameters meeting acceptance criteria in 18 of 20 cases, and it performed better than the other tool in 3 of 20 cases. Because it provides useful results at a fraction of the monetary and training cost and is already widely accessible to many institutions, such a tool may be worthwhile for many indoor aerosol dispersion applications, especially for students or researchers just beginning CFD modeling.

54 ENVIRONMENTAL SCIENCES↗