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High Level Support for Multigrid with KSPSetDM() and SNESSetDM()

Using the Explicit Runge-Kutta timestepper with variable timesteps

Memory bandwidth obtained on Intel hardware (dual socket except KNL)
over the number of processes used. One can get close to peak memory
bandwidth with only a few processes.

Schematic of a two-socket NUMA system. Processes should be spread
across both CPUs to obtain full bandwidth.

Natural Ordering and PETSc Ordering for a 2D Distributed Array (Four
Processes)

The cost of continuity: A study of the performance of isogeometric finite elements using direct solvers

The Cost of Continuity: Performance of Iterative Solvers on Isogeometric Finite Elements

The parallel {C++} statistical library {QUESO}: Quantification of Uncertainty for Estimation, Simulation and Optimization

Algorithm 799: revolve: an implementation of checkpointing for the reverse or adjoint mode of computational differentiation

Implicit-explicit formulations of a three-dimensional nonhydrostatic unified model of the atmosphere {(NUMA)}

Implicit-Explicit {R}unge-{K}utta Schemes and Applications to Hyperbolic Systems with Relaxation

Additive {R}unge-{K}utta schemes for convection-diffusion-reaction equations

Implicit-Explicit {R}unge-{K}utta schemes for hyperbolic systems and kinetic equations in the diffusion limit

Implicit-explicit {R}unge-{K}utta methods for time-dependent partial differential equations

Computer methods for ordinary differential equations and differential-algebraic equations

Segregated {Runge}--{Kutta} methods for the incompressible {Navier}--{Stokes} equations

Benchmarking stiff ode solvers for atmospheric chemistry problems {II}: {R}osenbrock solvers

In the numerical simulation of atmospheric transport-chemistry processes, a major task is the integration of the stiff systems of ordinary differential equations describing the chemical transformations. It is therefore of interest to systematically search for stiff solvers which can be identified as close to optimal for atmospheric applications. In this paper we continue our investigation from Sandu et al. (1996, CWI Report NM-R9603 and Report in Comput. Math., No. 85) and compare eight solvers on a set of seven box-models used in present day models. The focus is on Rosenbrock solvers. These turn out to be very well suited for our application when they are provided with highly efficient sparse matrix techniques to economize on the linear algebra. Two of the Rosenbrock solvers tested are from the literature, viz. and 4, and two are new and specially developed for air quality applications, viz. 3 and 3.

New {R}osenbrock {W}-methods of order 3 for partial differential algebraic equations of index 1

Highly Efficient Strong Stability-Preserving {R}unge--{K}utta Methods with Low-Storage Implementations

method of lines, strong stability-preserving, monotonicity, low-storage, RungeKutta methods

A generalized-alpha method for integrating the filtered {N}avier--{S}tokes equations with a stabilized finite element method

Error propagation of general linear methods for ordinary differential equations

We discuss error propagation for general linear methods for ordinary differential equations up to terms of order p+2, where p is the order of the method. These results are then applied to the estimation of local discretization errors for methods of order p and for the adjacent order p+1. The results of numerical experiments confirm the reliability of these estimates. This research has applications in the design of robust stepsize and order changing strategies for algorithms based on general linear methods.

Liszt: a domain specific language for building portable mesh-based PDE solvers

Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis

Designing the Language Liszt for Building Portable Mesh-based PDE Solvers

Scientific Discovery through Advanced Computing Program (SciDAC)

An Introduction to the Partitioned Global Address Space (PGAS) Programming Model

X10: an object-oriented approach to non-uniform cluster computing

International Journal of High Performance Computing Applications

{CHARM++: A Portable Concurrent Object Oriented System Based on C++}

Proceedings of the 3rd international joint conference on Artificial intelligence

Proceedings of the third conference on Hypercube concurrent computers and applications: Architecture, software, computer systems, and general issues-Volume 1

An object-oriented class library for scalable parallel heuristic search

The Amber system: Parallel programming on a network of multiprocessors

Parallex an advanced parallel execution model for scaling-impaired applications

Parallel Processing Workshops, 2009. ICPPW'09. International Conference on

Parallel \& Distributed Processing, 2009. IPDPS 2009. IEEE International Symposium on

Abstract robust coarse spaces for systems of {PDEs} via generalized eigenproblems in the overlaps

Scalable domain decomposition preconditioners for heterogeneous elliptic problems

Proceedings of SC13: International Conference for High Performance Computing, Networking, Storage and Analysis

An Introduction to Variational Inequalities and Their Applications

Domain decomposition and multigrid algorithms for elliptic problems on unstructured meshes

HOTPAR: Proceedings of the 2nd USENIX Workshop on Hot Topics in Parallelism

Sparse matrix solvers on the {GPU}: conjugate gradients and multigrid

IEEE/ACM International Conference on Computer-Aided Design, 2008. ICCAD 2008

Multigrid on {GPU}: Tackling power grid analysis on parallel SIMT platforms

Proceedings of the ACM SIGGRAPH/EUROGRAPHICS conference on Graphics hardware

A multigrid solver for boundary value problems using programmable graphics hardware

Concurrent number cruncher: {A}n efficient sparse linear solver on the {GPU}

Real-time nonlinear finite element computations on {GPU}-application to neurosurgical simulation

Symmetric {G}alerkin boundary element method in plasticity and gradient plasticity

Running unstructured grid based CFD solvers on modern graphics hardware

Proceedings of the 2008 ACM/IEEE Conference on Supercomputing (SC08)

Segmented Operations for Sparse Matrix Computation on Vector Multiprocessors

Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis

Implementing sparse matrix-vector multiplication on throughput-oriented processors

Parallel Computational Fluid Dynamics: Recent Advances and Future Directions

Streaming multigrid for gradient-domain operations on large images

Proceedings of the VI Brazilian Symposium on Computer Games and Digital Entertainment

{GPU} Acceleration of Equations Assembly in Finite Elements Method-Preliminary Results

On modelling of anisotropic viscoelasticity for soft tissue simulation: Numerical solution and {GPU} execution

Scientific computation for simulations on programmable graphics hardware

Proc. of IASTED Visualization, Imaging and Image Processing Conference (VIIP-01)

A {G}alerkin symmetric boundary-element method in elasticity: formulation and implementation

Using {GPU}s to improve multigrid solver performance on a cluster

COMPEL: The International Journal for Computation and Mathematics in Electrical and Electronic Engineering

Method of conformal transformation for the finite-element solution of axisymmetric exterior-field problems

FEAST-realization of hardware-oriented numerics for HPC simulations with finite elements

A space-time discontinuous {G}alerkin method for linearized elastodynamics with element-wise momentum balance

Interactive simulation and rendering of heterogeneous deformable bodies

Particle systems for efficient and accurate high-order finite element visualization

Data Visualization 2001: proceedings of the Joint Eurographics-IEEE TCVG Symposium on Visualization in Ascona, Switzerland, May 28-30, 2001

Parallel finite element algorithms applied to computational rheology

Proceedings of the 10th international conference on Medical image computing and computer-assisted intervention-Volume Part I

Real-time nonlinear finite element analysis for surgical simulation using graphics processing units

A finite element model study on wear resistance of pseudoelastic {TiNi} alloy

IEEE Computer Society Conference on Computer Vision and Pattern Recognition

Active part-decomposition, shape, and motion estimation of articulated objects: A physics-based approach

A {GPU}-friendly method for haptic and graphic rendering of deformable objects

{LU-GPU}: Efficient algorithms for solving dense linear systems on graphics hardware

Proceedings of the 13th ACM SIGPLAN Symposium on Principles and practice of parallel programming

Optimization principles and application performance evaluation of a multithreaded {GPU} using CUDA

Proceedings of 2nd Workshop on General Purpose Processing on Graphics Processing Units

Porting a high-order finite-element earthquake modeling application to NVIDIA graphics cards using CUDA

[El Cerrito, Calif., etc., Seismological Society of America, etc.]

The spectral element method: {A}n efficient tool to simulate the seismic response of 2D and 3D geological structures

An improved scheme of an interactive finite element model for 3D soft-tissue cutting and deformation

High-speed nonlinear finite element analysis for surgical simulation using graphics processing units.

A hybrid condensed finite element model with {GPU} acceleration for interactive 3D soft tissue cutting

Algorithm 832: {UMFPACK} V4.3---An Unsymmetric-Pattern Multifrontal Method

{STREAM}: Sustainable memory bandwidth in high performance computers

Convergence of the multigrid full approximation scheme for a class of elliptic mildly nonlinear boundary value problems

Convergence of the multigrid full approximation scheme including the {V}--cycle

Multigrid Techniques: 1984 Guide with Applications for Fluid Dynamics

Coarse-Grid Correction for Nonelliptic and Singular Perturbation Problems

A Phase Error Analysis of Multigrid Methods for Hyperbolic Equations

Implicit-Explicit Methods for Time-Dependent Partial Differential Equations

Krylov Subspace Acceleration for Nonlinear Multigrid Schemes with Application to Recirculating Flow

Implicitly Balanced Solution of the Two-Phase Flow Equations Coupled to Nonlinear Heat Conduction

A Fully Implicit Hybrid Solution Method for a Two-Phase Thermal-Hydraulic Model

The {SALOME} Open Source {CAE} Platform Application to Reactor Physics Simulation

Application of a generalized interface module to the coupling of {PARCS} with both {RELAP5} and {TRAC-M}

Proceedings of 1999 annual meeting of the American Nuclear Society

A methodology for the coupling of {RAMONA-3B} neutron kinetics and {TRAC-BF1} thermal-hydraulics

{EVENT}: A Multidimensional Finite Element-Spherical Harmonics Radiation Transport Code

Proceedings of the OECD International Seminar on 3D Deterministic Radiation Transport Codes

Verification and Validation of the 3D Finite Element Transport Theory Code {EVENT} for Shielding Applications

{AX-1}, A COMPUTING PROGRAM FOR COUPLED NEUTRONICS-HYDRODYNAMICS CALCULATIONS ON THE {IBM-704}

Coupled {CFD/CSM} vibration design methodology for generation {IV} long-life fuel and component design

4th International Conference on Supercomputing in Nuclear Applications

{Report on the {DOE} Joint {NE/SC} Workshop Simulation and Modeling for Advanced Nuclear Energy Systems}

January 9--12, 2007, Bethesda, MD, see \url{http://subsurface2007.labworks.org/}

{Report of the Fusion Energy Sciences Advisory Committee Burning Plasma Strategy Panel}

{Report of the High End Computing Revitalization Task Force (HECRTF)}

Office of Science, U.S. Department of Energy, see \url{http://www.sc.doe.gov/Scientific_User_Facilities/History/20-Year-Outlook-screen.pdf}

{POET} ({P}arallel {O}bject-Oriented {E}nvironment and {T}oolkit) and Frameworks for Scientific Distributed Computing

\url{http://www.extreme.indiana.edu/pseware}, Indiana University

High-performance language interoperability for scientific computing through {B}abel

{Sandia National Laboratory}, {C}omputations on {R}eactive {F}low, private communication

The pressure-corrected ICE finite element method for compressible flows on unstructured meshes

{CUMULVS}: Providing Fault-Tolerance, Visualization, and Steering of Parallel Applications

Theory of Inexact Krylov Subspace Methods and Applications to Scientific Computing

{PDELab}: An Object-Oriented Framework for Building Problem Solving Environments for {PDE} Based Applications

\url{http://www.llnl.gov/CASC/PVODE}, Lawrence Livermore National Laboratory

{DOE Computational Science Graduate Fellowship (CSGF) Users of PETSc}

{U}niversity of {C}hicago {C}enter on {A}strophysical {T}hermonuclear {F}lashes {W}eb Page

{S}upercomputer {S}olution of {M}assive {C}rystallographic and {M}icrotomographic {S}tructural {P}roblems {W}eb Page ({DOE} Grand Challenge Project)

Language Interoperability Mechanisms for High-Performance Scientific Applications

Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable Scientific and Engineering Computing

Divorcing Language Dependencies from a Scientific Software Library

Component Integration for Unstructured Mesh Algorithms and Software

Templates for the Solution of Linear Systems: Building Blocks for Iterative Methods

A Common Data Management Infrastructure for Parallel Adaptive Algorithms for {PDE} Solutions

{DAGH}: A Data-Management Infrastructure for Parallel Adaptive Mesh Refinement Techniques

Communication Optimizations for Irregular Scientific Computations on Distributed Memory Architectures

An Integrated Runtime and Compile-time Approach for Parallelizing Structured and Block Structured Applications

A high-performance, portable implementation of the {MPI} Message Passing Interface standard

A restricted additive {S}chwarz preconditioner for general sparse linear systems

Restricted additive {S}chwarz preconditioners with harmonic overlap for symmetric positive definite linear systems

Overlapping domain decomposition algorithms for general sparse matrices

Army High Performance Computing Research Center, University of Minnesota

Iterative solution of implicit approximations of multidimensional partial differential equations

Monitors, Messages, and Clusters: {T}he p4 Parallel Programming System

To appear (Also Argonne National Laboratory Mathematics and Computer Science Division preprint P362-0493)

Compiler and Runtime Support for Unstructured and Block Structured Problems

Efficient Support for Irregular Applications on Distributed Memory Machines

A Graphical Tool for Observing the Behavior of Parallel Logic Programs

Towards a Unified Theory of Domain Decomposition Algorithms for Elliptic Problems

Additive {S}chwarz. Surveys recent (1989) results; some comments on 3-d and how many approaches may be cast in the form of additive {S}chwarz-subspace form. 58 references, good introduction to the theory. No computations

The Efficient Parallel Iterative Solution of Large Sparse Linear Systems

Center for Supercomputing Research and Development, University of Illinois at Urbana-Chanpaign

{BlockSolve95} Users Manual: Scalable Library Software for the Parallel Solution of Sparse Linear Systems

A Scalable Parallel Algorithm For Incomplete Factor Preconditioning

Euclid User Manual (A Scalable {ILU} Preconditioning Library for the Parallel Solution of Sparse Linear Systems)

Users Manual for {KSP}: Data-Structure-Neutral Codes Implementing {K}rylov Space Methods

A Test Implementation of the {MPI} Draft Message-Passing Standard

Bi-{CGSTAB}: A fast and smoothly converging varient of {Bi-CG} for the solution of nonsymmetric linear systems

{E}ngineering and {S}cientific {S}ubroutine {L}ibrary Version 2: Guide and Reference

{IBM} {AIX} Parallel Environment Parallel Programming Subroutine Reference Release 2.0

Users Manual for tohtml: Producing true hypertext documents from {LaTeX}

Users Manual for doctext: Producing documentation from {C} source code

Users Manual for bfort: Producing {F}ortran interfaces to {C} source code

Proceedings of the 1994 Scalable High Performanc Computing Conference

Solution of Large, Sparse Systems of Linear Equations in Massively Parallel Applications

CWEB is available at ftp://pip.shsu.edu/tex-archive/web/c\_cpp/cweb

{B}lock{S}olve v1.1: Scalable Library Software for the Parallel Solution of Sparse Linear Systems

Proceedings of the Toward Teraflop Computing and New Grand Challenge Applications Conference

The Conjugate Gradient Method and Trust Regions in Large Scale Optimization

Unpublished information, {P}hysics {D}epartment, {P}urdue {U}niversity

Unpublished information, {M}athematics and {C}omputer {S}cience {D}ivision, {A}rgonne {N}ational {L}aboratory

Object Oriented Design of Multilevel {N}ewton and Continuation Methods

{OPT}++: An Object-Oriented Class Library for Nonlinear Optimization

Numerical Methods for Unconstrained Optimization and Nonlinear Equations

Mathematics and Computer Science Division, Argonne National Laboratory

Using MPI: Portable Parallel Programming with the Message Passing Interface

{GMRES}: A Generalized Minimal Residual Algorithm for Solving Nonsymmetric Linear Systems

{CGS}, A Fast {L}anczos-type Solver for Nonsymmetric Linear Systems

{B}i{CGSTAB}: A fast and smoothly converging variant of {B}i{CG} for the solution of nonsymmetric linear systems

A Transpose-Free Quasi-Minimal Residual Algorithm for Non-{H}ermitian Linear Systems

An Experimental Study on Extinction and Stablity of Tubular Flames

Combustion Theory, The Fundamental Theory of Chemically Reacting Flow Systems

The Mathematical Theory of Diffusion and Reaction in Permeable Catalysts

Finite element approximations to bifurcation problems of turning point type

Continuation-conjugate Gradient Methods fo the Least Squares Solution of Nonlinear Boundary Problems

Discretized {N}ewton-Relaxation Solution of High Resolution Flux-Difference Split Schemes

Proceedings of the AIAA Tenth Computational Fluid Dynamics Conference

P++, a {C}++ Virtual Shared Grids Based Programming Environment for Architecture-Independent Development of Structured Grid Applications

A++/{P}++ Array Classes for Architecture Independent Finite Difference Computations

Proceedings of the Second Annual Object-Oriented Numerics Conference

Mathematical Models and Software Tools in Industrial Mathematics

A Comprehensive Set of Tools for Solving Partial Differential Equations; {Diffpack}

Proceedings of the 15th IMACS World Congress on Scientific Computation, Modelling and Applied Mathematics

Diffpack: A Software Environment for Rapid Prototyping of {PDE} Solvers

Numerical Solution of Partial Differential Equations; Models, Algorithms and Software. Part I

Object-Oriented Design of Preconditioned Iterative Methods in {Diffpack}

Numerical Solution of {PDE}s on Parallel Computers Utilizing Sequential Simulators

Design and Implementation of an Object Oriented C++ Library for Nonlinear Optimization

Proceedings of the 11th International Conference on Domain Decomposition Methods

An implicit upwind algorithm for computing turbulent flows on unstructured grids

Proceedings of the AIAA Tenth Annual Computational Fluid Dynamics Conference

Computer Aided Parallelization Tools ({CAPTools}) - Conceptual Overview and Performance on the Parallelization of Structured Mesh Codes

Trends in Algorithms for Nonuniform Applications on Hierarchical Distributed Architectures

Proceedings of the Workshop on Computational Aerosciences for the 21st Century

Toward a Common Component Architecture for High-Performance Scientific Computing

{POOMA}: A High-Performance Distributed Simulation Environment for Scientific Applications

See {\tt http://\-www.cs.purdue.edu/\-research/\-cse/\-pellpack/}

{UG} -- A Flexible Software Toolbox for Solving Partial Differential Equations

See {\tt http://\-www.icsi.berkeley.edu/\-\~{ }bilmes/\-phipac/}

Flexible Communication Mechanisms for Dynamic Structured Applications

See {\tt http://\-www-cse.ucsd.edu/\-groups/\-hpcl/\-scg/\-kelp/}

The Use of Object-Oriented Design Patterns in the {SAMRAI} Structured {AMR} Framework

Proceedings of the SIAM Workshop on Object-Oriented Methods for Inter-Operable Scientific and Engineering Computing

Overture: An Object-Oriented Framework for Solving Partial Differential Equations on Overlapping Grids

A Comprehensive Set of Tools for Solving Partial Differential Equations: {D}iffpack

Implementing Linear Algebra Algorithms for Dense Matrices on a Vector Pipeline Machine

The authors examine common implementations of linear algebra algorithms, such as matrix-vector multiplication, matrix-matrix multiplication and the solution of linear equations. The different versions are examined for efficiency on a computer architecture which uses vector processing and has pipelined instruction execution. By using the advanced architectural features of such machines, one can usually achieve maximum performance, and tremendous improvements in terms of execution speed can be seen over conventional computers.

computer programming --- Algorithms; dense matrices; linear algebra algorithms; mathematical programming; vector pipeline machine

Using {MOL} to Solve a high order nonlinear {PDE} with a moving boundary in the simulation of a sintering process

The sintering of two particles by surface and grain boundary diffusion - a three-dimensional numerical study

A Domain-Specific Languages for Regular Sets of Strings and Trees

Architecturing software using a methodology for language development

Proceedings of the 10th International Symposium on Programming Languages, Implementations, Logics and Programs

{SUNDIALS}: Suite of Nonlinear and Differential/Algebraic Equation Solvers

Center for Applied Scientific Computing, Lawrence Livermore National Laboratory

{SUNDIALS:} Suite of Nonlinear and Differential/Algebraic Equation Solvers

Proceedings of the 5th International Conference on Multibody Systems, Nonlinear Dynamics and Control, Long Beach, CA

User Documentation for {KINSOL}, A Nonlinear Solver for Sequential and Parallel Computers

First-order system least squares {(FOSLS)} for convection-diffusion problems: numerical results

Performance Optimizations and Bounds for Sparse Matrix-Vector Multiply

An optimal control approach to a posteriori error estimation in finite element methods

The post-processing approach in the finite element method, {I}: Calculations of displacements, stresses, and other higher derivatives of the displacements

The post-processing approach in the finite element method, {II}: The calculation of stress intensity factors

The post-processing approach in the finite element method, {III}: A posteriori error estimation and adaptive mesh refinement

Optimal accumulation of {J}acobian matrices by elimination methods on the dual computational graph

Preprint ANL/MCS-P944-0402, Argonne National Laboratory, April 2002

Asymptotic Analysis of Two Reduction Methods for Systems of Chemical Reactions

A Parallel Algorithm for Multilevel Graph Partitioning and Sparse Matrix Ordering

{ParMETIS}: Parallel graph partitioning and sparse matrix ordering library

{NWChem}, A Computational Chemistry Package for Parallel Computers, Version 4.1

{TC}hem: {A} Software Toolkit for the Analysis of Complex Kinetic Models

Advanced Computing for 21st Century Accelerator Science and Technology Web page

A semi-{L}agrangian {C}rank-{N}icholson algorithm for the numerical solution of advection-diffusion problems

18th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP)

{Triangle: A Two-Dimensional Quality Mesh Generator and Delaunay Triangulator}

{TetGen: A Quality Tetrahedral Mesh Generator and Three-Dimensional Delaunay Triangulator}

{WIT}: {I}ntegrated system for high-throughput genome sequence analysis and metabolic reconstruction

Estimation of sparse {J}acobian matrices and graph coloring problems

A reconstruction of the metabolism of Methanococcus jannaschii from sequence data

A posteriori error estimates for the mixed hybrid finite element method

On the convergence of high resolution methods with multiple time scales for hyperbolic conservation laws

High resolution schemes for conservation laws with locally varying time steps

Solution of parabolic equations by backward Euler-mixed finite element methods on a dynamically changing mesh

{\em A posteriori} Error Estimation for Discontiuous {G}alerkin Approximations of Hyperbolic Systems

Iterative Methods by Space Decomposition and Subspace Correction

Multi-Level Adaptive Techniques(MLAT) for singular-perturbation problems

Algorithmic bombardment for the iterative solution of linear systems: A polyIterative approach

Towards polyalgorithmic linear system solvers for nonlinear elliptic problems,

Tight-binding molecular-dynamics simulation of impurities in ultrananocrystalline diamond grain boundaries,

The Subspace Projected Approximate Matrix {(SPAM)} Modification of the {D}avidson Method

Eigenvalue Computation from the Optimization Perspective: On {Jacobi-Davidson, IIGD, RQI and Newton} Updates

Interpolating moving least squares methods for fitting potential energy surfaces: Detailed analysis of one-dimensional applications

A distributed {L}agrange multiplier/fictitious domain model for viscoelastic particulate flows

Interrogations of Direct Numerical Simulations of Sloid-Liquid Flows

Triangle: {E}ngineering a {2D} Quality Mesh Generator and {D}elaunay Triangulator

Implicit Integration of the Time-Dependent {Ginzburg-Landau} Equations of Superconductivity

Quantum Mechanical Model of Localized Electrons on the Surface of Polymer Nanospheres

Efficient Management of Parallelism in Object Oriented Numerical Software Libraries

A fully asynchronous multifrontal solver using distributed dynamic scheduling

{SuperLU\_DIST}: a scalable distributed-memory sparse direct solver for unsymmetric linear systems

A scalable parallel algorithm for incomplete factor preconditioning

{BoomerAMG}: A parallel algebraic multigrid solver and preconditioner

Jacobian-free {Newton-Krylov} Methods: A Survey of Approaches and Applications

New Physics-based Preconditioning of Implicit Methods for Non-Equilibrium Radiation Diffusion

Physics-based Preconditioning and the {Newton-Krylov} Method for Non-Equilibrium Radiation Diffusion

{Framework Application for Core-Edge Transport Simulations (FACETS)}

Modeling Multiscale-Multiphase-Multicomponent Subsurface Reactive Flows Using Advanced Computing

{Modeling Multiscale-Multiphase-Multicomponent Subsurface Reactive Flows Using Advanced Computing}

{Program Announcement LAB 07-09, SciDAC: Accelerator Science and Simulation}

Maps of {RF} cavities generated from electromagnetic simulations

to appear in Proceedings of the 2007 Particle Accelerator Conference (PAC07), Albuquerque, NM, 2007

{International Thermonuclear Experimental Reactor (ITER) homepage}

Revealing the Hidden Nature of Space and Time: Charting the Course for Elementary Particle Physics

{Committee on Elementary Particle Physics in the 21st Century, National Research Council}

Community Petascale Project for Accelerator Science and Simulation (ComPASS)

Energy Frontier Research Center, see \url{https://inlportal.inl.gov/portal/server.pt/community/center_for_materials_science_of_nuclear_fuel}

Large-Scale Differential Variational Inequalities for Heterogeneous Materials

Two-Dimensional Electric Fields and Drifts near the Magnetic Separatrix in Divertor Tokamak

also see user manual at http://www.mfescience.org, then UEDGE link

Low-to-High Confinement Transition Simulations in Divertor Geometry

Simulation of Plasma Transport in a Toroidal Annulus with TEMPEST

A Component Architecture for High-Performance Scientific Computing

Advances in Geophysical and Environmental Mechanics and Mathematics

TChem-a software toolkit for the analysis of complex kinetic models

{The Model Coupling Toolkit}: A New {Fortran90} Toolkit for Building Multi-Physics Parallel Coupled Models

Computational performance of ultra-high-resolution capability in the Community Earth System Model

The {DOE} Parallel Climate Model {(PCM)}: The Computational Highway and Backroads

Proc. International Conference on Computational Science (ICCS) 2001

Computational Design and Performance of the {Gast} Ocean Atmosphere Model

New generation of multi-scale {NWP} system {(GRAPES)}: General scientific design

Proc. Second MIT Conference on Computational Fluid and Solid Mechanics

Multi-domain multi-model formulation for compressible flows: Conservative interface coupling and parallel implicit solvers for {3D} unstructured meshes

A distributed computing portal for coupling multi-physics and multiple domains in porous media

An explicit multi-model compressible flow formulation based on the full potential equation and the {Euler} equations on {3D} unstructured meshes

Coupling Multi-Component Models with {MPH} on Distributed Memory Computer Architectures

Proceedings of the AIAA Joint Propulsion Conference, AIAA2002-4345

A Physics-Based Software Framework for Sun-Earth Connection Modeling

Multiscale Coupling of Sun-Earth Processes, Proceedings of the Conference on the Sun-Earth Connection

California Institute of Technology, see \url{http://csdrm.caltech.edu}

University of Illinois at Urbana-Champaign, see \url{http://www.csar.uiuc.edu}

Stanford University, see \url{http://www.stanford.edu/group/cits}

An Eulerian-Lagrangian Approach for Large Deformation Fluid Structure Interaction Problems, Part 1: Algorithm Development

University of Utah, Center for the Simulation of Accidental Fires and Explosions

Toward a Multi-Model Hierarchy to Support Multiscale Simulations

also available as SCOREC Report 2007-2, Rensselaer Polytechnic Institute

VECPAR'2002, 5th International Conference, Lecture Notes in Computer Science

Robust Linear and Nonlinear Strategies for Solution of the Transonic {Euler} Equations

Global Convergence of Inexact {Newton} Methods for Transonic Flow

Toward an Integrated Multimodeling Interface: A Human-Computer Interface Approach to Interrelating Model Structures

{RUBE}: A Customized {2D} and {3D} Modeling Framework for Simulation

Development of an Information Visualization Tool Using Virtual Reality

Ptolemy: A Framework for Simulating and Prototyping Heterogeneous Systems

Multidisciplinary Problem Solving using Agents in a Cluster Environment

Emory Universtity, Department of Mathematics and Computer Science

Extensibe Component-Based Architecture for {FLASH}, a Massively Parallel Multiphysics Simulation Code

Managing Application Complexity in the SAMRAI Object-Oriented Framework

{Design Patterns is a modern classic in the literature of object-oriented development, offering timeless and elegant solutions to common problems in software design. It describes patterns for managing object creation, composing objects into larger structures, and coordinating control flow between objects. The book provides numerous examples where using composition rather than inheritance can improve the reusability and flexibility of code. Note, though, that it's not a tutorial but a catalog that you can use to find an object-oriented design pattern that's appropriate for the needs of your particular application--a selection for virtuoso programmers who appreciate (or require) consistent, well-engineered object-oriented designs.} {Now on CD, this internationally acclaimed bestseller is more valuable than ever! Use the contents of the CD to create your own design documents and reusable components. The CD contains: 23 patterns you can cut and paste into your own design documents; sample code demonstrating pattern implementation; complete Design Patterns content in standard HTML format, with numerous hyperlinked cross-references; accessed through a standard web browser; Java-based dynamic search mechanism, enhancing online seach capabilities; graphical user environment, allowing ease of navigation. First published in 1995, this landmark work on object-oriented software design presents a catalog of simple and succinct solutions to common design problems. Created by four experienced designers, the 23 patterns contained herein have become an essential resource for anyone developing reusable object-oriented software. In response to reader demand, the complete text and pattern catalog are now available on CD-ROM. This electronic version of Design Patterns enables programmers to install the book directly onto a computer or network for use as an online reference for creating reusable object-oriented software. The authors first describe what patterns are and how they can help you in the design process. They then systematically name, explain, evaluate, and catalog recurring designs in object-oriented systems. All patterns are compiled from real-world examples and include code that demonstrates how they may be implemented in object-oriented programming languages such as C++ and Smalltalk. Readers who already own the book will want the CD to take advantage of its dynamic search mechanism and ready-to-install patterns.}

1995 algorithms architecture book books computer computing design design-pattern design-patterns design_patterns designpatterns development diplom entwurfsmuster four gang gof java mathgamespatterns no-tag object object-orientation object-oriented of oo-patterns oop oriented pattern patterns programming se software software-development software-engineering software_design softwareengineering standard

Supercomputing '95: Proceedings of the 1995 ACM/IEEE Conference on Supercomputing (CDROM)

{ Fibre bundles, now an integral part of differential geometry, are also of great importance in modern physics--such as in gauge theory. This book, a succinct introduction to the subject by renown mathematician Norman Steenrod, was the first to present the subject systematically. It begins with a general introduction to bundles, including such topics as differentiable manifolds and covering spaces. The author then provides brief surveys of advanced topics, such as homotopy theory and cohomology theory, before using them to study further properties of fibre bundles. The result is a classic and timeless work of great utility that will appeal to serious mathematicians and theoretical physicists alike. }

{MOAB}-{SD}: Integrated Structured and Unstructured Mesh Representation

8th International conference on numerical grid generation in computational field simulations

A Flexible Distributed Mesh Data Structure to Support Parallel Adaptive Analysis

Proceedings of the 8th US National Congress on Computational Mechanics

A comparison of techniques for geometry access related to mesh generation

Some aspects of adaptive grid technology related to boundary and interior layers

A sparse matrix arithmetic based on {$\mathcal H$}-matrices. Part {I}: Introduction to {$\mathcal H$}-matrices

A {G}reen's function preconditioner for the steady-state {N}avier-{S}tokes equations

Existence of {$\mathcal H$}-matrix approximants to the inverse {FE}-matrix of elliptic operators with {$L^\infty$}-coefficients

Direct {S}chur complement method by domain decomposition based on {$\mathcal H$}-matrix approximation

special issue on "Program Generation, Optimization, and Adaptation"

Evaluation of three unstructured multigrid methods on 3D finite element problems in solid mechanics

Finite element exterior calculus, homological techniques, and applications

Algorithm 839: {FIAT}, a new paradigm for computing finite element basis functions

Advanced {C}omputing {R}esearch {C}entre{,} {University of Bristol}

Proceedings of the Second International Workshop on Domain-specific Program Development (DSPD'08)

{Die Berechnung optischer und elektrostatischer Gitterpotentiale}

A New Version of the Fast Multipole Method for the Laplace Equation in Three Dimensions

Order {N} algorithm for computation of electrostatic interactions in biomolecular systems

Derivation of {P}oisson and {N}ernst-{P}lanck equations in a bath and channel from a molecular model

The adaptive multilevel finite element solution of the {P}oisson-{B}oltzmann equation on massively parallel computers

A Comparison of {P}article-{P}article, {P}article-{M}esh and {E}wald Methods for Calculating Electrostatic Interactions in Periodic Molecular Systems

Domain decomposition preconditioners for multiscale flows in high-contrast media

Scalable adaptive mantle convection simulation on petascale supercomputers

The p4est library: A parallel scalable forest of adaptive octrees

Algorithm 795: PHCpack: a general-purpose solver for polynomial systems by homotopy continuation

Dynamical density functional theory for molecular and colloidal fluids: A microscopic approach to fluid mechanics

colloids; continuum mechanics; density functional theory; free energy; glass transition; statistical distributions; stochastic processes

Mixed finite element methods for viscoelastic flow analysis: a review

Proceedings of the Royal Society of London. Series A, Mathematical and Physical Sciences

Proceedings of IEEE International Conference on Cluster Computing, San Diego

{Applied Mathematics at the U.S. Department of Energy: Past, Present, and a View to the Future}

{Scientific Grand Challenges: Crosscutting Technologies for Computing at the Exascale}

Report on the Workshop on Extreme-Scale Solvers: Transitions to Future Architectures

Office of Advanced Scientific Computing Research, U.S. Department of Energy

{Workshop on Science Based Nuclear Energy Systems Enabled by Advanced Modeling and Simulation at the Extreme Scale}

{Workshop on Challenges for Understanding the Quantum Universe and the Role of Computing at the Extreme Scale}

{Modeling and Simulation at the Exascale for Energy and the Environment}

{Panel on Recent Significant Advancements in Computational Science}

Community Petascale Project for Accelerator Science and Simulation: Advancing Computational Science for Future Accelerators and Accelerator Technologies

Multiscale, Multiphysics Beam Dynamics Framework Design and Applications

Two-tiered Component Design and Performance Analysis of {Synergia2} Accelerator Simulations

Proceedings of the 2009 Workshop on Component-Based High Performance Computing {(CBHPC 2009)}

{MOOSE}: A Parallel Computational Framework for Coupled Systems of Nonlinear Equations

Parallel Multiphysics Algorithms and Software for Computational Nuclear Engineering

Three Dimensional Coupled Simulation of Thermomechanics, Heat, and Oxygen Diffusion in {UO$_2$} Nuclear Fuel Rods

A Multiphysics and Multiscale Software Environment for Modeling Astrophysical Systems

Department of Electrical and Computer Engineering, Duke University

Efficient parallel implementations of multipole-based {$N$}-body algorithms

We report on an efficient adaptive N-body method which we have recently designed and implemented. The algorithm computes the forces on an arbitrary distribution of bodies in a time which scales as N log N with the particle number. The accuracy of the force calculations is analytically bounded, and can be adjusted via a user defined parameter between a few percent relative accuracy, down to machine arithmetic accuracy. Instead of using pointers to indicate the topology of the tree, we identify...

Atomistically detailed simulations of concentrated protein solutions: the effects of salt, {pH}, point mutations, and protein concentration in simulations of 1000-molecule systems

{Simplifying Parallelization of Scientific Codes by a Function-Centric Approach in Python}

Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science - Programming Languages

invited minisymposium session at the SIAM Annual Meeting, July 9-10, 2009, Denver, CO, speakers were: C. Woodward (LLNL), E. Myra (Univ. of Michigan), J. White (Stanford Univ.), A. Barker (Univ. of Colorado, Boulder), L. Wilcox (Univ. of Texas at Austin), R. Mills (ORNL), B. F. Smith (ANL), J. Shadid (SNL), D. Knoll (INL), G. Hansen (INL), J. Cary (Tech-X Corp.), T. Wildey (Univ. of Texas at Austin).

FSP Planning Workshop, General Atomics, Feb 8-11, 2011, see \url{https://ice.txcorp.com/trac/2011_FspDefinitionWorkshop}

Progress in Large-Scale Differential Variational Inequalities for Heterogeneous Materials

minisymposium presentation at the 2011 SIAM Conference on Computational Science and Engineering, March 3, 2011

Preconditioning for the steady-state {Navier-Stokes} equations for low viscosity

A preconditioning for the steady-state {Navier-Stokes} equations

Large-Scale Computation of Pseudospectra Using {ARPACK} and \texttt{eigs}

Software available at \url{http://www.comlab.ox.ac.uk/pseudospectra/eigtool}

Finite difference and spectral methods for ordinary and partial differential equations

Cornell University-Department of Computer Science and Center for Applied Mathematics

Spectra and pseudospectra: the behavior of nonnormal matrices and operators

Isogeometric analysis of the isothermal {N}avier-{S}tokes-{K}orteweg equations

Isogeometric analysis of the {C}ahn-{H}illiard phase-field model

{SciDAC Frameworks, Algorithms, and Scalable Technologies for Mathematics (FASTMath) Institute}

{Scalable Implicit-Explicit (IMEX) Algorithms and Software for Time-Dependent Multimodel PDEs}

Newton's Method for Large Bound-constrained Optimization Problems

Bridging the gap between geometric and algebraic multigrid methods

For non-M-matrices, this paper proposes an unstructured multigrid method that only attempts to interpolate in the directions of geometrical smoothness. These directions are determined by analyzing samples of algebraically smooth error, e. Neighboring grid points i and j are called smoothly coupled if e i and e j are consistently nearby in value. In addition, these dierences may be used to dene interpolation weights. These new ideas may be incorporated into the algebraic multigrid method. Test results show that the new method can have much lower grid and operator complexities compared to AMG, leading to lower solve timings. 1

{This paper contains the main ideas for an AMGe (algebraic multigrid for finite elements) method based on element agglomeration. In the method, coarse grid elements are formed by agglomerating fine grid elements. Compatible interpolation operators are constructed which yield coarse grid basis functions with a minimal energy property. Heuristics based on interpolation quality measures are used to guide the agglomeration procedure. The performance of the resulting method is demonstrated in two-level numerical experiments.}

65f10,ams,especially since the popularization,gate gradient,general purpose iterative methods,gmres,krylov subspace methods,mos,non-hermitian systems,of precondition-,preconditioned conju-,subject classi cations,variable preconditioners

Highly Efficient Strong Stability Preserving {Runge-Kutta} Methods with Low-Storage Implementations

{Boundary conditions in approximate commutator preconditioners for the Navier-Stokes equations}

{A taxonomy and comparison of parallel block multi-level preconditioners for the incompressible Navier-Stokes equations}

{Efficient preconditioning of the linearized Navier-Stokes equations for incompressible flow}

{Preconditioning for the steady-state Navier-Stokes equations with low viscosity}

{A calculation procedure for heat, mass and momentum transfer in three-dimensional parabolic flows}

Finite Element Methods for the Incompressible {N}avier-{S}tokes Equations

{Block-implicit multigrid solution of Navier-Stokes equations in primitive variables}

Variational iterative methods for nonsymmetric systems of linear equations

Parallel scalable adjoint-based adaptive solution of variable-viscosity {Stokes} flow problems

The dynamics of plate tectonics and mantle flow: From local to global scales

Modelling compressible mantle convection with large viscosity contrasts in a three-dimensional spherical shell using the yin-yang grid

The accuracy of finite element solutions of {S}tokes' flow with strongly varying viscosity

Numerical investigation of {2D} convection with extremely large viscosity variations

Focal depths of intra-continental and intraplate earthquakes and their implications for the thermal and mechanical properties of the lithosphere

Strength of the continental lithosphere: time to abandon the jelly sandwich?

The long-term strength of continental lithosphere: jelly sandwich or creme brulee?

The Improved {BiCGStab} Method for Large and Sparse Unsymmetric Linear Systems on Parallel Distributed Memory Architectures

Proceedings of the Fifth International Conference on Algorithms and Architectures for Parallel Processing

Communication-optimal parallel and sequential {QR} and {LU} factorizations

{pARMS}: A package for the parallel iterative solution of general large sparse linear systems user's guide

M\'emoire sur la th\'eorie des \'equations aux d\'eriv\'ees partielles et la m\'ethode des approximations successives

Numerical Solution of Partial Differential Equations on Parallel Computers

Parallel {PDE}-Based Simulations Using the {Common Component Architecture}

Stabilization and scalable block preconditioning for the {Navier–Stokes} equations

We consider multiphysics applications from algorithmic and architectural perspectives, where ``algorithmic'' includes both mathematical analysis and computational complexity and ``architectural'' includes both software and hardware environments. Many diverse multiphysics applications can be reduced, en route to their computational simulation, to a common algebraic coupling paradigm. Mathematical analysis of multiphysics coupling in this form is not always practical for realistic applications, but model problems representative of applications discussed herein can provide insight. A variety of software frameworks for multiphysics applications have been constructed and refined within disciplinary communities and executed on leading-edge computer systems. We examine several of these, expose some commonalities among them, and attempt to extrapolate best practices to future systems. From our study, we summarize challenges and forecast opportunities.

ExaScale Computing Study: {T}echnology Challenges in achieving exascale systems

Office of Science, U.S. Department of Energy, see \url{http://extremecomputing.labworks.org/workshops.stm}

U.S. Department of Energy, {\footnotesize \url{http://energy.gov/articles/secretary-chu-announces-2011-ernest-orlando-lawrence-award-winners}}

Navier-Stokes, Boussinesq, Finite element approximation, Time stepping, Adaptivity, Preconditioning, Algebraic multigrid

Algebraic multigrid by smoothed aggregation for second and fourth order elliptic problems

Convergence of algebraic multigrid based on smoothed aggregation

Algebraic multigrid methods based on compatible relaxation and energy minimization

Anasazi software for the numerical solution of large-scale eigenvalue problems

An Algebraic Substructuring Method for Large-Scale Eigenvalue Calculation

A General Interpolation Strategy for Algebraic Multigrid Using Energy Minimization

algebraic multigrid, interpolation, non-Hermitian, nonsymmetric, smoothed aggregation

ACM/IEEE Proceedings of SC2004: High Performance Networking and Computing

Ultrascalable implicit finite element analyses in solid mechanics with over a half a billion degrees of freedom

Algebraic multigrid methods for constrained linear systems with applications to contact problems in solid mechanics

Toward textbook multigrid efficiency for fully implicit resistive magnetohydrodynamics

Multi-level {M}onte {C}arlo finite volume methods for nonlinear systems of conservation laws in multi-dimensions

Conservation laws, Euler, MHD, Uncertainty quantification, Multi-level Monte Carlo, Parallelization

ETH Zentrum, Seminar für Angewandte Mathematik, Rämistrasse 101, 8092 Zurich, Switzerland

Multi-Level {M}onte {C}arlo Finite Element method for elliptic {PDE}s with stochastic coefficients

Spectral and High Order Methods for Partial Differential Equations

{Plasma Surface Interactions: Bridging from the Surface to the Micron Frontier through Leadership Class Computing}

{Integrated Multiscale Modeling for Plasma Analysis and Control of Tokamak Stability (IMMPACTS)}

{Design of Damage-Tolerance Material Interfaces for Extreme Stress-Temperature-Corrosion Environments: Algorithms and Methods for Multi-Petaflops Simulations}

Elemental: A New Framework for Distributed Memory Dense Matrix Computations

Proceedings of the Fifth ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP)

{LAPACK}: A portable linear algebra library for high-performance computers

On the Performance Enhancement of Paging Systems Through Program Analysis and Transformations

{deal.II} -- a General Purpose Object Oriented Finite Element Library

Generic and Indexed Programming: International Spring School, SSGIP 2010, Oxford, UK, March 22-26, 2010, Revised Lectures

clawpack,finite volumes,godunov type methods,high order methods,hyperbolic PDEs,sharpclaw,software

:Users/ketch/Documents/Mendeley Desktop/Nilsen et al/2010 - Simplifying the parallelization of scientific codes by a function-centric approach in Python.pdf:pdf

{Simplifying the parallelization of scientific codes by a function-centric approach in Python}

{PyCUDA} and {PyOpenCL}: A scripting-based approach to {GPU} run-time code generation

Synchronization-reducing and Communication-reducing Algorithms and Programming Models for Large-scale Simulations

Workshop sponsored by the Institute for Computational and Experimental Research in Mathematics (ICERM), Jan. 9-13, 2012, Providence, RI, \url{http://icerm.brown.edu/tw12-1-exascale}

Implementation of a multigrid solver on {GPU} for {Stokes} equations with strongly variable viscosity based on {Matlab} and {CUDA}

{GPU} Implementation of {Stokes} Equation with Strongly Variable Coefficients

Automated solutions of differential equations by the finite element method

{FIAT}: Numerical Construction of Finite Element Basis Functions

Analysis of Charged Particle/Photon Correlations in Hadronic Multiparticle Production

Search for disoriented chiral condensate at the {Fermilab} {Tevatron}

Bounding the Electrostatic Free Energies Associated with Linear Continuum Models of Molecular Solvation

Selected for the March 15, 2009 issue of Virtual Journal of Biological Physics Research

Accurate Atom-by-Atom Predictions of Solvation Electrostatics Using a Hydration-Shell {Poisson}-{Boltzmann} Model

Solvation Thermodynamics of Neutral and Charged Solutes Using the Solvation-Layer Interface Condition (SLIC) Continuum Dielectric Model

{Reproducible Research: addressing the need for data and code sharing in computational science}

Conference Review: High Performance Computing and Hybrid Programming Concepts for Hyperbolic PDE Codes

Biomolecular electrostatics using a fast multipole {BEM} on up to 512 {GPU}s and a billion unknowns

Mathematical Analysis of the {BIBEE} Approximation for Molecular Solvation: Exact Results for Spherical Inclusions

Unstructured Geometric Multigrid in Two and Three Dimensions on Complex and Graded Meshes

Computational science and re-discovery: open-source implementations of ellipsoidal harmonics for problems in potential theory

Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding

Analytical Nonlocal Electrostatics Using Eigenfunction Expansions of Boundary-Integral Operators

Modeling Charge-Sign Asymmetric Solvation Free Energies With Nonlinear Boundary Conditions

A Nonlinear Boundary Condition for Continuum Models of Biomolecular Electrostatics

Generalising the mean spherical approximation as a multiscale, nonlinear boundary condition at the solute-solvent interface

Predicting Solvation Free Energies and Thermodynamics in Polar Solvents and Mixtures Using a Solvation-Layer Interface Condition

Extending the Solvation-Layer Interface Condition {(SLIC)} Continum Electrostatic Model to Linearized {Poisson}-{Boltzmann} Solvent

{Prospects for scalable 3D FFTs on heterogeneous exascale systems}

Hiding global communication latency in the {GMRES} algorithm on massively parallel machines

Hiding Global Synchronization Latency in the Preconditioned Conjugate Gradient Algorithm

Pipelined Mixed Precision Algorithms on {FPGA}s for Fast and Accurate PDE Solvers from Low Precision Components

Proceedings of the 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines

Electromagnetic Scattering with the Boundary Integral Method on {MIMD} Systems

{Implementation and Performance Analysis of Non-Blocking Collective Operations for MPI}

Proceedings of the 2007 International Conference on High Performance Computing, Networking, Storage and Analysis, SC07

{Scalable Communication Protocols for Dynamic Sparse Data Exchange}

Proceedings of the 2010 ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP'10)

Pipelined iterative solvers with kernel fusion for graphics processing units

Parallel Iterative {S-step} Methods for Unsymmetric Linear Systems

Reducing the effect of global communication in {GMRES(m)} and {CG} on parallel distributed memory computers

Parallelizable restarted iterative methods for nonsymmetric linear systems. part I: Theory

A hybrid {Chebyshev} {Krylov}-subspace algorithm for solving nonsymmetric systems of linear equations

{Chebyshev} semi-iterative methods, successive overrelaxation iterative methods, and second-order {Richardson} iterative methods, parts {I} and {II}

An efficient hierarchical preconditioner for quadratic discretizations of finite element problems

Multigrid Algorithms for Inverse Problems with Linear Parabolic {PDE} Constraints

Model problems for the multigrid optimization of systems governed by differential equations

A multigrid scheme for elliptic constrained optimal control problems

Multigrid methods for parabolic distributed optimal control problems

Receding horizon optimal control for infinite dimensional systems

Solving discretized optimization problems by partially reduced {SQP} methods

Aerodynamic shape optimization using simultaneous pseudo-timestepping

On multilevel iterative methods for integral equations of the second kind and related problems

On the regularizing properties of a full multigrid method for ill-posed problems

A multi-grid method with a priori and a posteriori level choice for the regularization of nonlinear ill-posed problems

Regularizing {N}ewton-{K}aczmarz Methods for Nonlinear Ill-Posed Problems

Optimal order multilevel preconditioners for regularized ill-posed problems

Multiplicative and additive parallel multigrid algorithms for the acceleration of compressible flow computations on unstructured meshes

Parallel Processing for Scientific Computing, MA Heroux, P. Raghavan, and HD Simon, eds

Multi-Level Approaches to Discrete-State and Stochastic Problems

Multigrid methods II: proceedings of the 2nd European Conference on Multigrid Methods, held at Cologne, October 1-4, 1985

Finding Structure with Randomness: Probabilistic Algorithms for Constructing Approximate Matrix Decompositions

Minimizing inner product data dependencies in conjugate gradient iteration

Proceedings of the IEEE International Conference on Parallel Processing

Quantitative performance modeling of scientific computations and creating locality in numerical algorithms

Block {K}rylov space methods for linear systems with multiple right-hand sides: an introduction

Modern Mathematical Models, Methods and Algorithms for Real World Systems

Krylov subspace techniques for reduced-order modeling of large-scale dynamical systems

Stable reduced models for nonlinear descriptor systems through piecewise-linear approximation and projection

IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems

Localized Bases for Finite-Dimensional Homogenization Approximations with Nonseparated Scales and High Contrast

Flux norm approach to finite dimensional homogenization approximations with non-separated scales and high contrast

Optimal Local Approximation Spaces for Generalized Finite Element Methods with Application to Multiscale Problems

Quantitative phase-field modeling of dendritic growth in two and three dimensions

Non-linear model reduction for uncertainty quantification in large-scale inverse problems

On the abstract theory of additive and multiplicative {Schwarz} algorithms

A constraint mapping approach to the structural optimization of an expensive model using surrogates

Airfoil design optimization using reduced order models based on proper orthogonal decomposition

Response surface methodology: process and product optimization using designed experiments

The {GNAT} method for nonlinear model reduction: effective implementation and application to computational fluid dynamics and turbulent flows

A multilevel algorithm for inverse problems with elliptic {PDE} constraints

Block-triangular preconditioners for {PDE}-constrained optimization

Preconditioning Iterative Methods for the Optimal Control of the {S}tokes Equations

Flexible {BiCG} and flexible {Bi-CGSTAB} for nonsymmetric linear systems

Parallel Performance of Preconditioned {Krylov} Solvers for the {Richards} Equation

Theory of Inexact {Krylov} Subspace Methods and Applications to Scientific Computing

{FQMR}: A Flexible {Quasi-Minimal Residual} Method with Inexact Preconditioning

Inexact Preconditioned {Conjugate Gradient} Method with Inner-Outer Iteration

{IDR}(s): A Family of Simple and Fast Algorithms for Solving Large Nonsymmetric Systems of Linear Equations

A Black Box Generalized {Conjugate Gradient} Solver with Inner Iterations and Variable-Step Preconditioning

Exploiting {BiCGstab($\ell$)} strategies to induce dimension reduction

Flexible and Multi-Shift Induced Dimension Reduction Algorithms for solving Large Sparse Linear Systems

A Closed-form Equation for Predicting the Hydraulic Conductivity of Unsaturated Soils

Provably Good Partitioning and Load Balancing Algorithms for Parallel Adaptive N-Body Simulation

N-body simulation, adaptive computing, hierarchical methods, load balancing, parallel processing, partitioning, scientific computing, the fast multipole method, tree-codes

Understanding the causes of performance variability in HPC workloads

Workload Characterization Symposium, 2005. Proceedings of the IEEE International

Globalization techniques for {N}ewton-{K}rylov methods and applications to the fully coupled solution of the {N}avier-{S}tokes equations

Experiments with quasi-{N}ewton methods in solving stiff {ODE} systems

{BiCGSTAB(l)} for Linear Equations involving Unsymmetric Matrices with Complex Spectrum

Multigrid Techniques: 1984 Guide with Applications to Fluid Dynamics, Revised Edition

Analysis of iterative methods for saddle point problems: a unified approach

Using multiple levels of parallelism to enhance the performance of domain decomposition solvers

A Mesh-Independence Principle for Operator Equations and Their Discretizations

Validity of the Single Processor Approach to Achieving Large Scale Computing Capabilities

Proceedings of the April 18-20, 1967, Spring Joint Computer Conference

Multi-language and multi-environment generation of nonlinear finite element codes

Characterizing Application Sensitivity to OS Interference Using Kernel-level Noise Injection

Sur les op\'erations dans les ensembles abstraits et leur application aux \'equations int\'egrales

Algorithms and Data Structures for Massively Parallel Generic Adaptive Finite Element Codes

Adaptive mesh refinement, object-orientation, parallel algorithms, software design

Inexact {N}ewton Methods with Restricted Additive {S}chwarz Based Nonlinear Elimination for Problems with High Local Nonlinearity

Users manual for bfort: Producing {F}ortran interfaces to {C} source code

Users Manual for doctext: Producing Documentation from Source Code

{SWIG}: An easy to use tool for integrating scripting languages with {C} and {C++}

Extreme-Scale Scientific Application Software Productivity: Harnessing the Full Capability of Extreme-Scale Computing

whitepaper submitted to DOE, available via \url{http://www.orau.gov/swproductivity2014/reference.htm}

{Interoperable Design of Extreme-Scale Application Software (IDEAS)}

First Steps Toward a Multiphysics Exemplars and Benchmarks Suite

{Multifaceted Mathematics for Complex Energy Systems (M2ACS) {W}eb page}

Exposing and Expanding Compiler Technologies to Improve Software Productivity in Developing Mathematical Libraries and Simulation Codes

whitepaper submitted to DOE Workshop on Software Productivity for Extreme-Scale Science, available via \url{http://www.orau.gov/swproductivity2014/papers.htm}

An empirical interpolation method: application to efficient reduced-basis discretization of partial differential equations

Hybrid supercapacitor-battery materials for fast electrochemical charge storage

Review of Electrochemical Capacitors Based on Carbon Nanotubes and Graphene

A review of steric interactions of ions: Why some theories succeed and others fail to acount for ion size

Density functional theory of the electrical double layer: the RFD functional

Selective adsorption of ions with different diameter and valence at highly-charged interfaces

Energetics of divalent selectivity in a calcium channel: the ryanodine receptor case study

Modeling of rock friction: 1. Experimental results and constitutive equations

Selective transport through a model calcium channel studied by Local Equilibrium Monte Carlo simulations coupled to the Nernst--Planck equation

Multiscale solvers and systematic upscaling in computational physics

Free-energy model for the inhomogeneous hard-sphere fluid mixture and density-functional theory of freezing

Adsorption of Chain Molecules in Slit-Shaped Pores: Development of a SAFT-FMT-DFT Approach

The approximate arithmetical solution by finite differences of physical problems including differential equations, with an application to the stresses in a masonry dam

Theory of Solutions of Molecules Containing Widely Separated Charges with Special Application to Zwitterions

Gmsh: A 3-D finite element mesh generator with built-in pre-and post-processing facilities

Argonne National Laboratory and the Emergence of Computer and Computational Science, 1946--1992

The Finite Element Method: Linear Static and Dynamic Finite Element Analysis

Roofline: an insightful visual performance model for multicore architectures

{Optimization principles for collective neighborhood communications}

International Conference for High Performance Computing, Networking, Storage and Analysis, SC

Top Ten Reasons to Not Share Your Code (and why you should anyway)

Fjos: Practical, predictable, and efficient system support for fork/join parallelism

Real-Time and Embedded Technology and Applications Symposium (RTAS), 2014 IEEE 20th

Proceedings of the 22nd IEEE International Symposium on Parallel and Distributed Processing (IPDPS)

{On nonlinear preconditioners in {N}ewton-{K}rylov methods for unsteady flows}

Some metric aspects of the open mapping and closed graph theorems

Institute of Mathematics, Academy of Sciences of the Czech Republic

Nondiscrete mathematical induction and iterative existence proofs

Pt\'ak's nondiscrete induction and its application to matrix iterations

Sur une esp\'ece de g\'eom\'etrie analytique des syst\'emes de fonctions sommables

Concrete representation of abstract {(M)}-spaces. (A characterization of the space of continuous functions.)

Discontinuous Galerkin methods for plasma physics in the scrape-off layer of tokamaks

Proceedings of the 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis

Parallel \& Distributed Processing Symposium (IPDPS), 2012 IEEE 26th International

Scalable and efficient algorithms for the propagation of uncertainty from data through inference to prediction for large-scale problems, with application to flow of the {Antarctic} ice sheet

Solution of nonlinear {S}tokes equations discretized by high-order finite elements on nonconforming and anisotropic meshes, with application to ice sheet dynamics

An extreme-scale implicit solver for complex {PDEs}: highly heterogeneous flow in earth's mantle

Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis

Triangular factorization and inversion by fast matrix multiplication

On optimality of Krylov's information when solving linear operator equations

{SIAM/ACM} {P}rize in {C}omputational {S}cience and {E}ngineering

Firedrake: automating the finite element method by composing abstractions

Topological optimization of the evaluation of finite element matrices

Cross-Loop Optimization of Arithmetic Intensity for Finite Element Local Assembly

Finite element integration, SIMD vectorization, compilers, local assembly, optimizations

Finite element assembly strategies on multi- and many-core architectures

Towards generating optimised finite element solvers for GPUs from high-level specifications

Unified embedded parallel finite element computations via software-based Fr{\'e}chet differentiation

Low-Complexity Finite Element Algorithms for the de Rham Complex on Simplices

Fast simplicial finite element algorithms using Bernstein polynomials

Framework for massively parallel adaptive finite element computational fluid dynamics on tetrahedral meshes

Automating the solution of PDEs on the sphere and other manifolds in FEniCS 1.2

Automated solution of differential equations by the finite element method: The FEniCS book

Symplectic-mixed finite element approximation of linear acoustic wave equations

Finite element approximation and preconditioners for a coupled thermo-acoustic model

Preconditioning and the conjugate gradient method in the context of solving PDEs

Reducing the effect of global communication in GMRES(m) and \{CG\} on parallel distributed memory computers

Volume reconstruction of point cloud data sets derived from computational geodynamic simulations

StgDomain--scalable parallel domain software components for particle-in-cell finite element methods

Gauge Invariant Integration and Perturbation of Petrov Type D Spacetimes

Numerically Stable Exact Solutions for Variable-Viscosity Stokes Equations

Convergence and complexity of Newton iteration for operator equations

Steepest descent preconditioning for nonlinear {GMRES} optimization

A nonlinearly preconditioned conjugate gradient algorithm for {rank-R} canonical tensor approximation

Nonlinearly preconditioned optimization on {Grassman} manifolds for computing approximate {Tucker} tensor decompositions

Nonlinear computational structural mechanics: {N}ew approaches and non-incremental methods of calculation

An accelerated fixed-point iteration for solution of variably saturated flow

Proc. XVIII International Conference on Water Resources, Barcelona

An accelerated {P}icard method for nonlinear systems related to variably saturated flow

Communication Reduced Parallel Multigrid: Analysis and Experiments

Fast methods for the numerical solution of boundary value problems

Textbook multigrid efficiency for the incompressible Navier--Stokes equations: high Reynolds number wakes and boundary layers

A {DLM} immersed boundary method based wave-structure interaction solver for high density ratio multiphase flows

Simulating water-entry/exit problems using {Eulerian}-{Lagrangian} and fully-{Eulerian} fictitious domain methods within the open-source {IBAMR} library

A minimally-resolved immersed boundary model for reaction-diffusion problems

Fully resolved immersed electrohydrodynamics for particle motion, electrolocation, and self-propulsion

Hydrodynamics of suspensions of passive and active rigid particles: a rigid multiblob approach

A fully resolved active musculo-mechanical model for esophageal transport

Convergent evolution of mechanically optimal locomotion in aquatic invertebrates and vertebrates

Energy efficiency and allometry of movement of swimming and flying animals

A unified mathematical framework and an adaptive numerical method for fluid--structure interaction with rigid, deforming, and elastic bodies

Consequences of viscous anisotropy in a deforming, two-phase aggregate. Part 1. Governing equations and linearized analysis

Fredholm, Hilbert, Schmidt: Three Fundamental Papers on Integral Equations

nterior Estimates for Elliptic Systems of Partial Differential Equations

Shape Representation and Classification Using the Poisson Equation

Analysis of errors in {Still's} equation for macromolecular electrostatic solvation energies

Analytical electrostatics for biomolecules: {Beyond} the generalized {Born} approximation

Design of ion-implanted {MOSFET's} with very small physical dimensions

{BLIS}: A Framework for Rapidly Instantiating {BLAS} Functionality

Numerical calculation of time-dependent viscous incompressible flow of fluid with free surface

Fostering Interactions Between the Geosciences and Mathematics, Statistics, and Computer Science

Density functional theory for liquid structure and thermodynamics

Molecular solvent model of cylindrical electric double layers: a systematic study by {Monte Carlo} simulations and density functional theory

{ASKIT:} An efficient, parallel library for high-dimensional kernel summations

Improved fast gauss transform and efficient kernel density estimation

Proceedings of the Ninth IEEE International Conference on Computer Vision

SIAM Conf. on Data Mining. Workshop on High Performance Analytics-Algorithms, Implementations, and Applications

Reconciling surface plate motions with rapid three-dimensional mantle flow around a slab edge

The role of rheology and slab shape on rapid mantle flow: Three-dimensional numerical models of the Alaska slab edge

Magmagenesis within the {H}unter {R}idge {R}ift {Z}one resolved from olivine-hosted melt inclusions and geochemical modelling with insights from geodynamic models

Styles of rifting and fault spacing in numerical models of crustal extension

Tectonic drivers of the {Wrangell}-block forearc sliver: Insights from 3D geodynamic models

Inferring the thermochemical structure of the upper mantle from seismic data

Constraints on thermochemical convection of the mantle from plume heat flux, plume excess temperature, and upper mantle temperature

Rheology of the upper mantle and the mantle wedge: A view from the experimentalists

The subduction zone flow field from seismic anisotropy: A global view

Mantle flow in subduction systems: The mantle wedge flow field and implications for wedge processes

Arc-parallel flow in the mantle wedge beneath Costa Rica and Nicaragua

Seismic anisotropy and mantle deformation: what have we learned from shear wave splitting?

Dynamic data-driven inversion for terascale simulations: Real-time identification of airborne contaminants

Multigrid solution of a distributed optimal control problem constrained by the {Stokes} equations

Compressive fluorescence microscopy for biological and hyperspectral imaging

A {Bayesian} hierarchical model to predict benthic oxygen demand from organic matter loading in estuaries and coastal zones

Goal-oriented inference: Approach, linear theory, and application to advection diffusion

{FaIMS}: A fast algorithm for the inverse medium problem with multiple frequencies and multiple sources for the scalar {Helmholtz} equation

On the solution of three-dimensional inverse obstacle acoustic scattering problems by a regularized {Newton} method

Aerodynamic shape optimization of supersonic aircraft configurations via an adjoint formulation on distributed memory parallel computers

Weighted {BFBT} Preconditioner for {Stokes} Flow Problems with Highly Heterogeneous Viscosity

A globalization strategy for the multigrid solution of elliptic optimal control problems

Solution of the Euler equations for two dimensional transonic flow by a multigrid method

Mantle convection and plate tectonics: Toward an integrated physical and chemical theory

Initiation of subduction zones along transform and accreting plate boundaries, triple-junction evolution, and forearc spreading centres—implications for ophiolitic geology and obduction

Seismicity and structure in central {Mexico}: Evidence for a possible slab tear in the {South Cocos} plate

Multiple plates subducting beneath Colombia, as illuminated by seismicity and velocity from the joint inversion of seismic and gravity data

2013 SC-International Conference for High Performance Computing, Networking, Storage and Analysis (SC)

Why it is difficult to solve Helmholtz problems with classical iterative methods

The finite element method for {MHD} flow at high {Hartmann} numbers

Control of Slab Width on Subduction-Induced Upper Mantle Flow and Associated Upwellings: Insights from Analog Models

Automated Solution of Differential Equations by the Finite Element Method: The FEniCS Book

Efficient assembly of {H(div)} and {H(curl)} conforming finite elements

Philosophical Transactions of the Royal Society B: Biological Sciences

Manycore parallel computing for a hybridizable discontinuous {Galerkin} nested multigrid method

A hybridizable discontinuous Galerkin method for two-phase flow in heterogeneous porous media

A high order hybridizable discontinuous Galerkin method for incompressible miscible displacement in heterogeneous media

Families of Interior Penalty Hybridizable discontinuous Galerkin methods for second order elliptic problems

A {GPU}-Accelerated Hybridizable Discontinuous {Galerkin} Method for Linear Elasticity

An Implicit Discontinuous Galerkin Method For Modeling Acute Edema and Resuscitation In The Small Intestine

Anisotropic Diffusion and Traveling Waves of Toxic Proteins in Neurodegenerative Diseases

Accurate Discretization Of Poroelasticity Without {Darcy} Stability -- {Stokes-Biot} Stability Revisited

An elementary treatise on Fourier's series: and spherical, cylindrical, and ellipsoidal harmonics, with applications to problems in mathematical physics

Water Supply and Water Resources Division, National Risk Management Research Laboratory, Cincinnati, OH 45268

Quadrature by expansion: A new method for the evaluation of layer potentials

WorkStream--A Design Pattern for Multicore-Enabled Finite Element Computations

On the representation of continuous functions of several variables as superpositions of continuous functions of one variable and addition

Improvement in the smoothness of functions in the {Kolmogorov Superposition Theorem}

Proceedings of the International Joint Conference on Neural Networks

Representation properties of networks: {Kolmogorov's} theorem is irrelevant

Analysis of {Kolmogorov's} superpostion theorem and its implementation in applications with low and high dimensional data

Kolmogorov superposition theorem and its application to wavelet image decompositions

Electronic Imaging-Wavelet Applications in Industrial Processing VI, Proceedings of the SPIE

A measure-theoretic interpretation of sample based numerical integration with applications to inverse and prediction problems under uncertainty

On orienting edges of unstructured two-and three-dimensional meshes

An Algorithm for Computing {Lipschitz} Inner Functions in {Kolmogorov's Superposition Theorem}

Numerical performance of smoothers in coupled multigrid methods for the parallel solution of the incompressible Navier-Stokes equations

Block-implicit multigrid calculation of two-dimensional recirculating flows

{MATPOWER}: Steady-state operations, planning and analysis tools for power systems research and education

Development and Verification of Thermoelectric Power Plant Model for Assessing Energy and Water Nexus

Exploring network structure, dynamics, and function using {NetworkX}

Proceedings of the 7th Python in Science Conference (SciPy2008), Ga\"{e}l Varoquaux, Travis Vaught, and Jarrod Millman (Eds), (Pasadena, CA USA)

{SC '16}: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis

{10M-Core} Scalable Fully-Implicit Solver for Nonhydrostatic Atmospheric Dynamics

{SC '15}: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis

An Extreme-Scale Implicit Solver for Complex {PDEs}: Highly Heterogeneous Flow in Earth's Mantle

Improving and accelerating scientific discovery through better software

{DOE Office of Science} 40th anniversary collection of 40 major papers that have changed the face of science

{Society for Industrial and Applied Mathematics, Fellows Program}

{xSDK} Community Installation Policies: {GNU Autoconf} and {CMake} Options

What Are Interoperable Software Libraries: Introducing the {xSDK}

IDEAS {\em WhatIs} document, version 0.2, April 25, 2016, available via \url{https://ideas-productivity.org/resources/howtos/}

available via \url{https://arxiv.org/abs/1610.02608}, to appear in {\em SIAM Review}

{Report on the 2017 ASCR Applied Mathematics Principal Investigators Meeting}

{Report on the DOE Workshop on Integrated Simulations for Magnetic Fusion Energy Sciences}

Introduction to {SISC} Special section associated with {CSE15} on {'CSE Software'} and {'Big Data in CSE'}

{xSDK} Foundations: Toward an Extreme-scale Scientific Software Development Kit

SciDAC project, \url{https://collab.cels.anl.gov/display/FissionGasSciDAC2}

2018 IEEE International Parallel and Distributed Processing Symposium (IPDPS)

{WDMApp: High-Fidelity Whole Device Modeling of Magnetically Confined Fusion Plasmas}

{Subsurface: Exascale Subsurface Simulator of Coupled Flow, Transport, Reactions, and Mechanics}

High-Resolution Simulation of Pore-Scale Reactive Transport Processes Associated with Carbon Sequestration

Optimization Stories, Documenta Mathematica. Extra Volume: Optimization Stories

Some Numerical Experiments with Variable-Storage {Quasi-Newton} Algorithms

Inverse problem theory and methods for model parameter estimation

Large displacement body-fitted {FSI} simulations using a mesh-connectivity-change moving mesh strategy

Metric-based anisotropic mesh adaptation for three-dimensional time-dependent problems involving moving geometries

Time-accurate anisotropic mesh adaptation for three-dimensional time-dependent problems with body-fitted moving geometries

First Benchmark of the Unstructured Grid Adaptation Working Group

Unstructured Grid Adaptation and Solver Technology for Turbulent Flows

An anisotropic mesh adaptation approach for regional tidal energy hydrodynamics modelling

Pipelined Iterative Solvers with Kernel Fusion for Graphics Processing Units

BiCGStab method, CUDA, GMRES method, GPU, Iterative solvers, OpenCL, conjugate gradient method

Diffusive molecular dynamics simulations of lithiation of silicon nanopillars

Evaluation of {PETS}c on a Heterogeneous Architecture, the {OLCF} {S}ummit System: Part 1: Vector Node Performance

PDE constrained optimization, error estimation and control with spectral elements using PETSc and TAO

Evaluation of overlapping restricted additive Schwarz preconditioning for parallel solution of very large power flow problems

{PETSc:} An Advanced Math and Computing Framework for Rapidly Developing Parallel Smart Grid Applications

A graphical extension for the Windows version of the Parallel Finite Element Micromagnetics Package (MagParExt)

Micromagnetic Simulation of Magnetic Particles with Surface Anisotropy

Micromagnetic simulation of the magnetic dispersion angle and effective damping factor for the single-phase soft magnetic films

Micromagnetic simulation and experimental study on microwave permeability of nano-magnetic films

Micromagnetic study of magnetization reversal in patterned DyFeCo thin films

Magnetic Configurations and Phase Diagrams of sub-100 nm NiFe Nanorings

A Systematic Approach to Multiphysics Extensions of Finite-Element-Based Micromagnetic Simulations: Nmag.

Writer Flux Closure and Transition Degradation Mechanism in Perpendicular Recording.

Effect of write current waveform on magnetization and head field dynamics of perpendicular recording heads

Effect of thermal fluctuation field on the noise performance of a perpendicular recording system

Micromagnetic simulations of the dependence of domain wall width with grain size in systems with cubic and uniaxial anisotropy.

A Micromagnetic Study of the Effect of Spatial Variations in Damping in Perpendicular Recording Heads

Computational Engineering and Design Group, School of Engineering Sciences, University of Southampton, United Kingdom

A Case Study Using Automatic Performance Tuning for Large-Scale Scientific Programs

High Performance Distributed Computing, 2006 15th IEEE International Symposium

Nonlinear Magnetization Dynamics in Thin-Films and Nanoparticles

Micromagnetic Simulations of Domainstructures in Softmagnetic Thin Films

Micromagnetic Simulation of Head Field and Write Bubble Dynamics in Perpendicular Recording

Micromagnetic Modeling of Head Field Rise Time for High Data-Rate Recording

Multiprocessing of the Time Domain Analysis of Thin-Wire Antennas and Scatterers

12th Euromicro Conference on Parallel, Distributed and Network-Based Processing (PDP'04)

Proceedings of PIERS (Progress In Electromagnetic Research Symposium)

Numerical Micromagnetic Simulation of Fe-Pt Nanoparticles with Multiple Easy Axes

High Density Magnetic Random Access Memory Using a Pair of Asymmetrical Cell

Micromagnetic simulation of magnetization reversal in small particles with surface anisotropy

Micromagnetic simulation of the pinning and depinning process in permanent magnets

Transition from single-domain to vortex state in soft magnetic cylindrical nanodots

Scalable Parallel Micromagnetic Solvers for Magnetic Nanostructures

Implementation of a high performance parallel finite element micromagnetics package

Performance of MOL for Surface Motion Driven by a Laplacian of Curvature

Numerical Treatment of Multiphase Flows in Porous Media, Lecture Notes in Physics, vol. 552

Combined Atomistic and Mesoscale simulation of grain growth in nanocrystalline thin films

Mesoscopic simulation of two dimensional grain growth with anisotropic grain-boundary properties

Bidimensional Study of the Maxwell-Bloch Model in a Nonlinear Crystal

Simulating Patient Specific Multiple Time-Point {MRIs} from a Biophysical Model of Brain Deformation in {Alzheimer's} Disease

Computational Biomechanics for Medicine: Imaging, Modeling and Computing

Parallel implementation of the accelerated BEM approach for EMSI of the human brain

Finite-element simulation of cooling of realistic 3-D human head and neck

{A parallel reduced-space sequential-quadratic programming algorithm for frequency-domain small animal optical tomography}

{Using domain decomposition techniques for the calculation of low-frequency electric current densities in high-resolution 3D human anatomy models}

Computation of currents induced by ELF electric fields in anisotropic human tissues using the Finite Integration Technique

Computation of electrostatic fields in anisotropic human tissues using the Finite Integration Technique (FIT)

Computational arterial flow modeling using a parallel {Navier-Stokes} solver

Poster at Second International Conference on Systems Biology (ICSB) 2001

University of Tubingen, ZBIT - Zentrum fur Bioinformatik Tubingen

Two-level Newton and hybrid Schwarz preconditioners for fluid-structure interaction

Scalable parallel methods for monolithic coupling in fluid-structure interaction with application to blood flow modeling

NKS for fully coupled fluid-structure interaction with application

Evaluation of an in silico cardiac safety assay: using ion channel screening data to predict QT interval changes in the rabbit ventricular wedge

A scalable multi-level preconditioner for matrix-free $\mu$-finite element analysis of human bone structures

Applications of Algebraic Multigrid to Large-Scale Finite Element Analysis of Whole Bone Micro-Mechanics on the IBM SP

ACM/IEEE Proceedings of SC2003: High Performance Networking and Computing

Parallel Multiscale {Gauss-Newton-Krylov} Methods For Inverse Wave Propagation

Winner of SC2002 Best Paper. A parallel algorithm for inverse problems governed by time-dependent PDEs, and scalability results for an inverse wave propagation problem of determining the material field of an acoustic medium. Using the algorithm, they solved a synthetic inverse wave propagation problem though a pelvic bone geometry involving 2.1 million inversion parameters in 3 hours on 256 processors.

A Parallel Dynamic-Mesh Lagrangian Method for Simulation of Flows with Dynamic Interfaces

Blood flow modeling at the microscale including effects on individual blood cells, for designing heart assist pumps, etc.

Computational Electrocardiology: mathematical and numerical modeling

Determining recovery times from transmembrane action potentials and unipolar electrograms in normal heart tissue

{Framework for Modular, Flexible and Efficient Solving the Cardiac Bidomain Equations Using PETSc}

Monodomain Simulations of Excitation and Recovery in Cardiac Blocks with Intramural Heterogeneity

On the order of accuracy of the immersed boundary method: Higher order convergence rates for sufficiently smooth problems

An adaptive, formally second order accurate version of the immersed boundary method

Simulating the blood-muscle-valve mechanics of the heart by an adaptive and parallel version of the immersed boundary method

Parallel Algorithms and Software for Time-Dependent System of Nonlinear Partial Differential Equations with an Application in Computational Biology

Parallel multigrid preconditioner for the cardiac bidomain model

Computational Tools for Modeling Electrical Activity in Cardiac Tissue

Proceedings of the 15th International Conference on Domain Decomposition Methods

Springer, Lecture Notes in Computational Science and Engineering (LNCSE).

A parallel solver for reaction-diffusion systems in computational electrocardiology

Simulating patterns of excitation, repolarization and action potential durationwith cardiac Bidomain and Monodomain models

Effects of transmural electrical heterogeneities and electrotonic interactions on the dispersion of cardiac repolarization and action potential duration: a simulation study

MODELING ANISOTROPIC AND HETEROGENEOUS CARDIAC MODELS: PARALLEL SIMULATIONS

MEDICON and HEALTH TELEMATICS 2004, Health in the Information Society, X Mediterranean Conference on Medical and Biological Engineering

A fully implicit parallel algorithm for simulating the non-linear electrical activity of the heart

{Monitoring and Migration of a PETSc-based Parallel Application for Medical Imaging in a Grid computing PSE}

Towards a parallel component for imaging in PETSc programming environment: a case study in 3-D echocardiography

Distributed software environment, Image denoising, Non linear PDE, Parallel component

Integration of emerging computer technologies for an efficient image sequences analysis

Image sequence, pipe and filters, parallel computing, multicore processors

Fast Implicit Simulation of Oscillatory Flow in Human Abdominal Bifurcation using a Schur Complement Preconditioner

Aortic aneurysm, flow simulation, streamline diffusion FEM, indefinite matrix, parallel Krylov solver

A deformable digital brain atlas system according to Talairach and Tournoux

In April, the Lonestar supercomputer at the Texas Advanced Computing Center in Austin performed laser surgery on a dog in Houston without the intervention of a surgeon. The treatment was developed collaboratively by computational experts from the Institute for Computational Engineering and Sciences (ICES) at UT-Austin, leading technologists from the M.D. Anderson Cancer Center in Houston, and cyberinfrastructure specialists and systems from TACC. Using precise lasers, state-of-the-art thermal imaging technology, and advanced computational methods, dynamic, data-driven treatments are being pursued as a minimally invasive alternative to the standard treatment of cancer.

Nanoshell-Mediated Laser Surgery Simulation for Prostate Cancer Treatment

Computational Infrastructure for the Real-Time Patient-Specific Treatment of Cancer

Evaluation of the Adjoint Equation Based Algorithm for Elasticity Imaging

A Dynamic Data Driven Grid System for Intra-Operative Image Guided Neurosurgery

A parallel implementation of non-rigid registration using a volumetric biomechanical model

Second International Workshop on Biomedical Image Registration {WBIR'03}

Medical Image Computing and Computer-Assisted Intervention - MICCAI 2001

Capturing intraoperative deformations: research experience at Brigham and Women's hospital

Real-Time Registration of Volumetic Brain {MRI} by Biomechanical Simulation of Deformation during Image Guided Neurosurgery

Registration of {3D} Intraoperative {MR} Images of the Brain using a Finite Element Biomechanical Model

Real-Time Biomechanical Simulation of Volumetric Brain Deformation for Image Guided Neurosurgery

Parallelized Bayesian inversion for three-dimensional dental X-ray imaging

Work/Precision Tradeoffs in Continuum Models of Biomolecular Electrostatics

Proceedings of ASME 2015 International Mechanical Engineering Congress \& Exposition

Multiscale models and approximation algorithms for protein electrostatics

{Landau} Collision Integral Solver with Adaptive Mesh Refinement on Emerging Architectures

Comparison of particle trajectories and collision operators for collisional transport in nonaxisymmetric plasmas

Radially global delta-f computation of neoclassical phenomena in a tokamak pedestal

First Results from Core-Edge Parallel Composition in the {FACETS} Project

Concurrent, Parallel, Multiphysics Coupling in the {FACETS} Project

Coupled Whole Device Simulations of Plasma Transport in Tokamaks with the {FACETS} Code

Concurrent, Parallel, Coupled Core-Edge Simulations of Pedestal Formation Using the {FACETS} Framework

Proceedings of the 23rd annual IAEA Fusion Energy Conference (FEC 2010), Daejon, Republic of Korea

{FACETS}: A Framework for Parallel Coupling of Fusion Components

Proceedings of Euromicro PDP 2010 (The 18th Euromicro International Conference on Parallel, Distributed and Network-Based Computing), Pisa, Italy

The hypersecant Jacobian approximation for quasi-Newton solves of sparse nonlinear systems

Performance enhancements to ELMFIRE gyrokinetic code leading to new ranges of application

Intermediate nonlinear evolution of the Parker instability: Formation of convection-induced discontinuities and absence of finite-time singularities

Solution of Reduced Resistive Magnetohydrodynamics using Implicit Adaptive Mesh Refinement

Proceedings of the 16th International Conference on Domain Decomposition methods

Solution of Equilibrium Radiation Diffusion Problems using Adaptive Mesh Refinement

A finite element Poisson solver for gyrokinetic particle simulations in a global field aligned mesh

Global gyrokinetic Particle-in-cell Simulations with Trapped Electrons

Electromagnetic gyrokinetic simulation with a fluid-kinetic hybrid electron model

Numerical studies of a steady state axisymmetric co-axial helicity injection plasma

Inclusion of electromagnetic effects into gyrokinetic particle simulations

American Physical Society 45th Annual Meeting Division of Plasma Physics, Albuquerque, New Mexico, October 2003

Presented at 10th Society for Industrial and Applied Mathematics (SIAM) Conference on Parallel Processing for Scientific Computing, Portsmouth, Virginia, March 12-14, 2001.

Parallel Implementation of a {PETSc-Based} Framework for the General Curvilinear Coastal Ocean Model

Implicit solution of the material transport in Stokes flow simulation: Toward thermal convection simulation surrounded by free surface

Simulating faults and plate boundaries with a transversely isotropic plasticity model

On the solvability of incompressible Stokes with viscoplastic rheologies in geodynamics

Modular and flexible spectral-element waveform modelling in two and three dimensions

Fully Parallel Mesh {I/O} using {PETSc} {DMPlex} with an Application to Waveform Modeling

Hybrid simulations of coupled Farley-Buneman/gradient drift instabilities in the equatorial E region ionosphere

Three-dimensional multifluid modeling of atmospheric electrodynamics in Mars' dynamo region

Representation of topography by partial steps using the immersed boundary method in a vector vorticity equation model (VVM)

A scalable, matrix-free multigrid preconditioner for finite element discretizations of heterogeneous {S}tokes flow

Support for Non-conformal Meshes in {PETSc}'s {DMPlex} Interface

Flexible, Scalable Mesh and Data Management using {PETSc DMPlex}

Proceedings of the Exascale Applications and Software Conference

{PCPATCH}: software for the topological construction of multigrid relaxation methods

High level implementation of geometric multigrid solvers for finite element problems: Applications in atmospheric modelling

Automated generation and symbolic manipulation of tensor product finite elements

A structure-exploiting numbering algorithm for finite elements on extruded meshes, and its performance evaluation in {Firedrake}

Performance-Portable Finite Element Assembly Using {PyOP2} and {FEniCS}

Proceedings of 28th International Supercomputing Conference, ISC 2013

Application of hierarchical matrices to linear inverse problems in geostatistics

Oil and Gas Science and Technology-Revue de l'IFP-Institut Francais du Petrole

Influences of surface processes on fold growth during {3-D} detachment folding

Fold interaction and wavelength selection in 3D models of multilayer detachment folding

Constraining effective rheology through parallel joint geodynamic inversion

Quantifying the impact of mechanical layering and underthrusting on the dynamics of the modern {India-Asia} collisional system with {3-D} numerical models

Analytical and numerical investigation of 3D multilayer detachment

On the asymptotic derivation of Winkler-type energies from {3D} elasticity

Proceedings of the 38th Workshop on Geothermal Reservoir Engineering Stanford University, Stanford, CA

A Variational Approach To The Modeling And Numerical Simulation Of Hydraulic Fracturing Under In-Situ Stresses

Crack patterns obtained by unidirectional drying of a colloidal suspension in a capillary tube: experiments and numerical simulations using a two-dimensional variational approach

A variational approach to the fracture of brittle thin films under out of plane loading

Proceedings of the 2012 SPE Annual Technical Conference and Exhibition

A Variational Approach to the Numerical Simulation of Hydraulic Fracturing

Numerical simulation of water resources problems: Models, methods, and trends

A finite element sea ice model of the Canadian Arctic Archipelago

Ocean modelling; Unstructured meshes; Sea ice; Arctic Ocean; Canadian Arctic Archipelago; Freshwater flux

Towards preconditioned nonlinear conjugate gradients for generic geophysical inversions

Kinematic interpretation of the 3D shapes of metamorphic core complexes

Comparing thin-sheet models with {3-D} multilayer models for continental collision

Multiple-domain, simultaneous joint inversion of geophysical data with application to subsalt imaging

Optimal, scalable forward models for computing gravity anomalies

Numerical Simulation of Reservoir Stimulation - A Variational Approach

Proceedings of the 34th Annual Meeting of the Geothermal Resources Council

Full 3D tomography for the crustal structure of the Los Angeles region

Versuchsanstalt für Wasserbau, Hydrologie und Glaziologie (VAW), ETH Zürich, Zürich, Switzerland

Efficient Nonlinear Solvers for Nodal High-Order Finite Elements in {3D}

Achieving textbook multigrid efficiency for hydrostatic ice flow

Low-rank quasi-{N}ewton updates for robust {J}acobian lagging in {N}ewton-type methods

International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering

Block Preconditioners and Advanced Software for Multiphysics Problems in Solid Earth Geodynamics

presentation at the 2010 SIAM Conference on Parallel Processing for Scientific Computing

Large scale simulation of wave propagation in soils interacting with structures using {FEM} and {SBFEM}

Achieving textbook multigrid efficiency for hydrostatic ice sheet flow

The Role of Volatiles in Reactive Melt Transport in the Asthenosphere

Melting and channelized magmatic flow in chemically heterogeneous, upwelling mantle

Consequences of mantle heterogeneity for melt extraction at mid-ocean ridges

Porosity-driven convection and asymmetry beneath mid-ocean ridges

Melting above the anhydrous solidus controls the location of volcanic arcs

Plate-Driven Mantle Dynamics and Global Patterns of Mid-Ocean Ridge Bathymetry

Stress balances of ice streams in a vertically integrated, higher-order formulation

{Consequences of viscous anisotropy in a deforming, two-phase aggregate: 1. Governing equations and linearised analysis}

{Consequences of viscous anisotropy in a deforming, two-phase aggregate: 2. Numerical solutions of the full equations}

{TerraFERMA: The Transparent Finite Element Rapid Model Assembler for multi-physics problems in the solid Earth sciences}

0560 COMPUTATIONAL GEOPHYSICS Numerical solutions, 1902 INFORMATICS Community modeling frameworks, 1906 INFORMATICS Computational models, algorithms

{Shallow shelf approximation as a ``sliding law'' in a thermomechanically coupled ice sheet model}

{Exact solutions to the thermomechanically coupled shallow ice approximation: effective tools for verification}

{Fast computation of a viscoelastic deformable Earth model for ice-sheet simulations}

Exact solutions and numerical verification for isothermal ice sheets

{Programming on Numerical Simulation of Tsunami with PETSc and FEPG}

Proceedings of the 2013 IEEE 21st Annual International Symposium on Field-Programmable Custom Computing Machines

Field Programmable Logic and Applications (FPL), 2014 24th International Conference on

A highly-efficient and green data flow engine for solving euler atmospheric equations

A Domain Decomposition Approach to Implementing Fault Slip in Finite-Element Models of Quasi-static and Dynamic Crustal Deformation

fault slip, finite-element modeling, crustal deformation, earthquake physics

{PyLith}: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal Deformation

Acceleration of low order finite element computation with {GPUs} (Invited)

Development of software for studying earthquakes across multiple spatial and temporal scales by coupling quasi-static and dynamic simulations

Modeling of Multiple Earthquake Cycles in Southern California Using the {SCEC} Community Fault Model

Two New Approaches in Solving the Nonlinear Shallow Water Equations for Tsunamis

Magma dynamics with the enthalpy method: {B}enchmark solutions and magmatic focusing at mid-ocean ridges

On preconditioning for a parallel solution of the Richards equation

Preconditioned iterative methods for {Stokes} flow problems arising in computational geodynamics

{R}ecent Advances in Computational Geodynamics: Theory, Numerics and Applications

A stabilization algorithm for geodynamic numerical simulations with a free surface

Discretization errors and free surface stabilization in the finite difference and marker-in-cell method for applied geodynamics: A numerical study

Development of a {Stokes} flow solver robust to large viscosity jumps using a {Schur} complement approach with mixed precision arithmetic

Numerical modelling of magma dynamics coupled to tectonic deformation of lithosphere and crust

Evolution and diversity of subduction zones controlled by slab width

A comparison of numerical surface topography calculations in geodynamic modelling: an evaluation of the sticky air method

Influence of trench width on subduction hinge retreat rates in 3-D models of slab rollback

{pTatin3D}: {H}igh-performance methods for long-term lithospheric dynamics

Proceedings of {SC14}: The {International Conference for High Performance Computing, Networking, Storage and Analysis}

A scalable, matrix-free multigrid preconditioner for finite element discretizations of heterogeneous {Stokes} flow

A free surface capturing discretization for the staggered grid finite difference scheme

Analysis of block-preconditioners for models of coupled magma/mantle dynamics

Simulation of directional solidification, thermochemical convection, and chimney formation in a {H}ele-{S}haw cell

Full waveform inversion for seismic velocity and anelastic losses in heterogeneous structures

The dynamics of melt and shear localization in partially molten aggregates

Large-Scale Scientific Computing: 4th International Conference, LSSC 2003, Sozopol, Bulgaria, June 4-8, 2003

{PFLOTRAN}: Massively Parallel {3-D} Simulator for {CO2} Sequestration in Geologic Media

Fourth Annual Conference on Carbon Capture and Sequestration DOE/NETL

Decoupling and Block Preconditioning for Sedimentary Basin Simulations

Versatile multilevel Schwarz preconditioners for multiphase flow

Submarine groundwater discharge as a possible formation mechanism for permafrost-associated gas hydrate on the circum-Arctic continental shelf

Mantle convection modeling with viscoelastic/brittle lithosphere: Numerical and computational methodology

Lecture Notes in Computer Science, volume 2659, part of the ICCS Conference Proceedings

Proceedings of the Ninth SIAM Conference on Parallel Processing for Scientific Computing

The deep roots of volcanoes: models of magma dynamics with applications to subduction zones

Argonne National Laboratory Mathematics and Computer Science Division Argonne IL USA

Ridge migration, asthenospheric flow and the origin of magmatic segmentation in the global mid-ocean ridge system

Numerical simulation of geodynamic processes with the {Portable Extensible Toolkit for Scientific Computation}

{Development of a package for modeling stress in the lithosphere}

Lithosphere tearing at STEP faults: response to edges of subduction zones

Towards Rapid Geoscience Model Development - The {Snark} Project

Proceedings of 3rd ACES (APEC Cooperation for Earthquake Simulation) Workshop

High Resolution Forward and Inverse Earthquake Modeling on Terascale Computers

A winner of the Gordon Bell Prize for special achievement at SC2003

Simultaneous Joint Inversion of Refraction Tomography and Magnetic Data

A computational framework for simulation of biogeochemical tracers in the ocean

Evaluation of an eddy-permitting finite-element ocean model in the North Atlantic

Data Assimilation with the Ensemble Kalman Filter and the SEIK Filter applied to a Finite Element Model of the North Atlantic

Realizing teracomputing: proceedings of the tenth ECMWF Workshop on the Use of High Performance Computing in Meteorology: Reading, UK, 4-8 November, 2002

GrossrAumige Zirkulationsstrukturen in einem nichtlinearen adaptiven AtmosphArenmodell

Unsteady analytical solutions of the spherical shallow water equations

GrossAumige Zirkulationsstrukturen in einem nichtlinearen adaptiven AtmosphArenmodell

FoSSI : The Family of Simplified Solver Interfaces for the rapid development of parallel numerical atmosphere and ocean models

A Newton-CG method for large-scale three-dimensional elastic full-waveform seismic inversion

We present a nonlinear optimization method for large-scale 3D elastic full-waveform seismic inversion. The method combines outer Gauss-Newton nonlinear iterations with inner conjugate gradient linear iterations, globalized by an Armijo backtracking line search, solved on a sequence of finer grids and higher frequencies to remain in the vicinity of the global optimum, inexactly terminated to prevent oversolving, preconditioned by L-BFGS/Frankel, regularized by a total variation operator to capture sharp interfaces, finely discretized by finite elements in the Lam\'{e} parameter space to provide flexibility and avoid bias, implemented in matrix-free fashion with adjoint-based computation of reduced gradient and reduced Hessian-vector products, checkpointed to avoid full spacetime waveform storage, and partitioned spatially across processors to parallelize the solutions of the forward and adjoint wave equations and the evaluation of gradient-like information. Several numerical examples demonstrate the grid independence of linear and nonlinear iterations, the effectiveness of the preconditioner, the ability to solve inverse problems with up to 17 million inversion parameters on up to 2048 processors, the effectiveness of multiscale continuation in keeping iterates in the basin of attraction of the global minimum, and the ability to fit the observational data while reconstructing the model with reasonable resolution and capturing sharp interfaces.

Modeling subsurface reactive flows using leadership-class computing

{Simulating subsurface flow and transport on ultrascale computers using PFLOTRAN}

A parallel, fully coupled, fully implicit solution to reactive transport in porous media using the preconditioned {J}acobian-{F}ree {N}ewton-{K}rylov Method

Reactive transport, Jacobian-Free Newton-Krylov, Physics-based block preconditioner

Recent Advances in Parallel Virtual Machine and Message Passing Interface: 10th European PVM/MPI User's Group Meeting

Proceedings of the International Conference on Parallel Computing in Electrical Engineering

High-Performance Simulation of Surface-Subsurface Coupled Flow and Reactive Transport at Watershed Scale

{An efficient parallel method for large-scale groundwater flow equation based on PETSc}

Information, Computing and Telecommunication, 2009. YC-ICT'09. IEEE Youth Conference on

The South Florida Regional Simulation Model and Hydrologic Simulation Engine

Simulates overland, groundwater and canal flows for south Florida. Uses PETSc for its linear solves

Dynamic data driven inversion for terascale simulations: real-time indentification of airborne contaminants

Comparison of Two Local Refinement Methods for Large Scale Air Pollution Simulations

Large-Scale Scientific Computing: 4th International Conference, LSSC 2003

Object-Oriented Framework for Large Scale Air Pollution Modeling

Large-Scale Scientific Computing : Third International Conference, LSSC 2001, Sozopol, Bulgaria

Mineralogical heterogeneity in fractured, porous media and its representation in reactive transport models

The impact of climate change on vadose zone pore waters and its implication for long-term monitoring

Reactive transport modeling: An essential tool and a new research approach for the Earth sciences

A General-Purpose Hierarchical Mesh Partitioning Method with Node Balancing Strategies for Large-Scale Numerical Simulations

2018 IEEE/ACM 9th Workshop on Latest Advances in Scalable Algorithms for Large-Scale Systems (scalA)

Hierarchical parallelisation for the solution of stochastic finite element equations

Poster at American Geophysical Union Fall 2002 Meeting, San Francisco, CA.

Innovative Methods for Solving Multicomponent Biogeochemical Groundwater Transport on Supercomputers

Parallel Least-Squares Finite Element Method for Large Eddy Simulation of Large Scale Environmental Flows and Transport Processes

EPA funded work to simulate turbulent dispersion of toxic chemicals around buildings and in Green Bay. Used PETSc for its linear solvers

Modeling Multicomponent Reactive Transport on Parallel Computers Using {J}acobian-Free {N}ewton {K}rylov with Operator-Split Preconditioners

Proceedings of the XIV International Conference on Computational Methods in Water Resources, Delft, The Netherlands.

Software for modeling multicomponent, multidimensional reactive transport

A coupled model for transport of multiple chemical-species and kinetic precipitation dissolution reactions with application to reactive flow in single-phase hydrothermal systems

OS3D/GIMRT, Software for Multicomponent-Multidimensional reactive transport: User's manual and programmer's guide

Application of {J}acobian-free {N}ewton-{K}rylov with physics-based preconditioning to biogeochemical transport

A Markov random field model of contamination source identification in porous media flow

Advanced Simulation Technique for Modeling Multiphase Fluid Flow in Porous Media

Parallel Implementation of Finite Element Groundwater Flow Model

A parallel RMA2 model for simulating large-scale free surface flows

An Efficient Scalable Finite Element Model for Simulating Large Scale Hydrodynamic Flows

Proceedings of the American Society of Civil Engineers 16th Engineering Mechanics Conference

Modeling Thermal-Hydrological-Chemical ({THC}) Coupled Processes with Applications to Underground Nuclear Tests at the Nevada Test Site; A Grand Challenge Supercomputing Problem

MPU Workshop: Conceptual Model Development for Subsurface Reactive Transport Modeling of Inorganic Contaminants, Radionuclides and Nutrients

Parallel Compositional Reservior Simulation on Clusters of {PC}s

Preconditioned Newton Methods for Simulation of Reservoirs with Surface Facilities

Experience with Parallel Computing for Reservoir and Geomechanics Simulation on a Win32 Cluster

A Fully Implicit Parallel {EOS} Compositional Simulator for Large Scale Reservoir Simulation

Proceedings of the 1999 Society of Petroleum Engineers 15th Reservoir Simulation Symposium

An augmented {Lagrangian} preconditioner for the {3D} stationary incompressible {Navier-Stokes} equations at high {Reynolds} number

Block-preconditioners for the incompressible {Navier}--{Stokes} equations discretized by a finite volume method

Newton--Krylov methods in applications of two-phase flow problems with phase appearance/disappearance

Nonlinear magnetohydrodynamics in axisymmetric heterogeneous domains using a Fourier/finite element technique and an interior penalty method

The numerical simulation of the wing kinematics effects on near wake topology and aerodynamic performance in hovering Drosophila flight

A parallel monolithic algorithm for the numerical simulation of large-scale fluid structure interaction problems

A parallel adaptive nonlinear elimination preconditioned inexact {Newton} method for transonic full potential equation

Nonlinear Preconditioning Techniques for Full-Space Lagrange--Newton Solution of PDE-Constrained Optimization Problems

Direct numerical simulation of saturated deformable porous media using parallel hybrid Lattice-Boltzmann and finite element method

Modeling the deformation of saturate porous media using direct numerical simulation

Simulations of Zigzag Maneuvers for a Container Ship with Direct Moving Rudder and Propeller

Fluid-Structure Interaction for an Elastic Structure Interacting with Free Surface in a Rolling Tank

Bubble size distribution prediction for large-scale ship flows: {Model} evaluation and numerical issues

Turn and Zigzag Maneuvers of a Surface Combatant Using a {URANS} Approach with Dynamic Overset Grids

Eulerian polydispersed modeling of bubbly flows around ships with application to {Athena} {R}/V,

Overset simulations of a {Submarine} in {Towed}, {Self}-{Propelled} and {Maneuvering} {Conditions}

{CFD} Simulation and Validation of Added Resistance of {KVLCC}2 with Fixed and Free Surge Conditions in Short and Long Head Waves

CFD Simulations of a Submarine Propeller and Application to Self-Propulsion of a Submarine

CFD Analysis of Broaching for a Model Surface Combatant with Explicit Simulation of Moving Rudders and Rotating Propellers

URANS Simulations of Static and Dynamic Maneuvering for Surface Combatant-Part 1: Verification and Validation for Forces, Moment, and Hydrodynamic Derivatives

URANS Simulations of Static and Dynamic Maneuvering for Surface Combatant-Part 2: Analysis and Validation of Local Flow Characteristics

A geometry-based level set method for curvilinear overset grids with application to ship hydrodynamics

Computations of self-propulsion free to sink and trim and of motions in head waves of the {KRISO} {Container} {Ship} ({KCS}) model

Scalability and Validation Study for Large Scale Surface Combatant Computations Using {CFDShip}-Iowa

Full scale self-propulsion computations using discretized propeller for the {KRISO} container ship {KCS}

Multi-fidelity Optimization of a High-speed Foil-assisted Semi-planing Catamaran for Low Wake

CFD Validation Studies for a High-speed Foil-assisted Semi-planing Catamaran

CFD System-Based and {EFD} Study of Ship Dynamic Instability Events: Surf Riding, Periodic Motion and Broaching

Development and Validation of Harmonic Wave Group Single-Run Procedure for {RAO} with Comparison to Regular Wave and Transient Wave Group Procedures Using {URANS}

Large-Scale {DES} Computations of the Forward Speed Diffraction and Pitch and Heave Problems for a Surface Combatant

Self-Propulsion Computations Using Speed Controller and Discretized Propeller with Dynamic Overset Grids

Evaluation of Linear and Non-Linear Convection Schemes on Multidimensional Non-Orthogonal Grids with Applications to {KVLCC}2 Tanker

{Modeling hypersonic entry with the fully-implicit Navier--Stokes (FIN-S) stabilized finite element flow solver}

Computational simulations of {3D} large-scale time-dependent viscoelastic flows in high performance computing environment

Parallel computations, Viscoelastic flows, DEVSS-G, \{PETSc\}, Finite element method, High performance computing

PDE framework; Octree-like Cartesian grids; Computational fluid dynamics; Thermohydraulics; Two-phase flow

{On {CFL} Evolution Strategies for Implicit Upwind Methods in Linearized {E}uler Equations}

Parallel unstructured three-dimensional turbulent flow analyses using efficiently preconditioned newton-krylov solver

University of Basilicata Dip.to di Ingegneria e Fisica dell’Ambiente Potenza Italy

Performance Analysis of Parallel Algebraic Preconditioners for Solving the RANS Equations Using Fluctuation Splitting Schemes

Dip.to di Ingegneria e Fisica dell’Ambiente, University of Basilicata, Potenza, Italy

EulFS: A Parallel {CFD} Code for the Simulation of {Euler and Navier-Stokes} Problems on Unstructured Grids

Applied Parallel Computing. State of the Art in Scientific Computing

A methodology for the development of discrete adjoint solvers using automatic differentiation tools

Variational Space-time (Dis)continuous Galerkin Method for Linear Free Surface Waves

Towards Numerical Simulation of Flapping Foils on Fixed Cartesian Grids

A MULTILEVEL FINITE VOLUME METHOD WITH MULTISCALE-BASED GRID ADAPTATION FOR STEADY COMPRESSIBLE FLOWS

European Conference on Computational Fluid Dynamics: ECCOMAS CFD 2006

Parallel three-dimensional simulation of the injection molding process

a parallel coupled algorithm for collocated grids and its application to Large Eddy Simulation of a turbulent wake

A Compact Momentum Interpolation Method for unsteady flows and relaxation

Preconditioning based on a partially implicit implementation of Momentum Interpolation for coupled solvers

Effect of Various Approximations of the Discrete Adjoint on Gradient-Based Optimization

Proceedings of the 44th AIAA Aerospace Sciences Meeting and Exhibit, Reno NV. AIAA-2006-0690

Efficiency Improvements of {RANS}-Based Analysis and Optimization using Implicit and Adjoint Methods on Unstructured Grids

Workshop Proceedings Current Development in Shallow Water Models on the Sphere March, 10-14, 2003, Munich University of Technology, German

The Embedded Boundary Integral Method (EBI) for the Incompressible {Navier-Stokes} equations

IABEM 2002, International Association for Boundary Element Methods, UT Austin

Benchmarking of a {3D}, unstructured, finite volume code for incompressible {Navier-Stokes} equation on a cluster of distributed-memory computers

Proceedings of the 19th International Symposium on High Performance Computing Systems and Applications

Multidimensional Residual Distribution Schemes for the Pseudo-Compressible {Euler} and {Navier-Stokes} equations on Unstructured Meshes

International Conference On Preconditioning Techniques For Large Sparse Matrix Problems In Industrial Applications

Fast Elliptic Solver for Incompressible {Navier Stokes} Flow and Heat Transfer Problems on the Grid

An unsteady single-phase level set method for viscous free surface flows

A Multidimensional Two-Phase Flow Model for the Total Dissolved Gas Downstream of Spillways

Unsteady RANS Method for Ship Motions with Application to Roll for a Surface Combatant

Unsteady RANS Simulation of the Ship Forward Speed Diffraction Problem

Toward Large-Scale Computations of Ship Motions with Dynamic Overset Curvilinear Grids

Proceedings of the 27th Symposium on Naval Hydrodynamics, Seoul, Korea

Application of Algebraic Multigrid Methods to the Solution of Stratified Flows About Submerged Bodies

Detached-Eddy Simulation of High Reynolds Number Beveled-Trailing-Edge Flows and Wakes

Computational Study of the Wake and Contaminant Transport of a Walking Human

Computation of Maneuvering Coefficients for Non-Body-of-Revolution Submarines Using Unsteady {RANS} {CFD}

Prediction of Forces and Moments on a Sonobuoy Configuration Using Overset Grids and DES

Localized turbulence simulation for naval hydrodynamics: issues in using overset refinement grids and detached-eddy simulation

Experimental and Computational Study of Cavitation Inception on Co-Flow Nozzles

A Physics-Based Simulation Methodology for Predicting Trailing-Edge Singing

Detached-Eddy Simulation of High Reynolds Number Trailing-Edge Flows and Wakes

Symposium on LES Advancements and Applications, ASME FED Summer Meeting

Simulation of Steady Circulation Control for the General Aviation Circulation Control Wing

Simulation of Steady and Pulsed Circulation Controlfor Marine-Vehicle Control Surfaces

Proceedings of the 2nd Conference on Advances and Applications of GiD

On the use of the PETSc library for unstructured {CFD} applications

Computing high-Reynolds number vortical flows: a highly accurate method with a fully meshless formulation

International Conference on Parallel CFD, Grand Canary, May 2004

Experimental Validation of 3-D Lagrangian VOF Model: Bubble Shape and Rise Velocity

Laboratory of Chemical Reactor Engineering, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands

Precondizionatori paralleli per la fluidodinamica computazionale

Dipartimento Interuniversitario di Matematica Universiti degli Studi-Politecnico di Bari Italy

Multilevel Parallel High Order Schemes for Invisid Flow Computations on 3D Unstructured Meshes

Parallel Building Blocks for Finite Element Simulations: Application to Solid-Liquid Mixture Flows

Globalized {N}ewton-{K}rylov-{S}chwarz Algorithms and Software for Parallel Implicit {CFD}

Achieving High Sustained Performance in an Unstructured Mesh {CFD} Application

ACM/IEEE Proc. of SC 99: High Performance Networking and Computing

Finite Difference lattice Boltzmann model for Liquid Vapour Systems

Proceedings of the Romanian Academy, Series A: Mathematics, Physics, Technical Sciences, Information Sciences

Two component lattice Boltzmann model with flux limiter techniques

Finite-difference lattice Boltzmann model with flux limiters for liquid-vapor systems

Latency, Bandwidth, and Concurrent Issue Limitations in High-Performance {CFD}

Proceedings of the First MIT Conference on Computational Fluid and Solid Mechanics

Understanding the Parallel Scalability of An Implicit Unstructured Mesh {CFD} Code

Proceedings of the 7th International Conference on High Performance Computing (HiPC '2000)

Performance Modeling and Tuning of an Unstructured Mesh {CFD} Application

On the Interaction of Architecture and Algorithm in the Domain-Based Parallelization of an Unstructured Grid Incompressible Flow Code

Proceedings of the 10th International Conference on Domain Decomposition Methods

{N}ewton-{K}rylov-{S}chwarz Methods for Aerodynamic Problems: Compressible and Incompressible Flows on Unstructured Grids

Parallel Simulation of Compressible Flow Using Automatic Differentiation and {PETSc}

special issue of Parallel Computing on ``Parallel Computing in Aerospace''

Fast Multipole Method for particle interactions: an open source parallel library component

A parallel nonlinear additive {Schwarz} preconditioned inexact {Newton} algorithm for incompressible {Navier-Stokes} equations

Emergence and evolution of tripole vortices from net-circulation initial conditions

Multi-material incompressible flow simulation using the moment-of-fluid method

On the convergence of shifted {L}aplace preconditioner combined with multilevel deflation

Helmholtz equation, shifted Laplace preconditioner, multigrid deflation, Fourier analysis

A parallel computing approach for solving the Helmholtz equation in 3D domains: Application to the study of acoustic behaviour of silencers

Eurppean Congress on Computational Methods in Applied Sciences and Engineering (ECCOMAS)

Comparison of Quasi Minimal Residual and Bi-Conjugate Gradient Iterative Methods to Solve Complex Symmetric Systems Arising from Time-Harmonic Simulations

Proceedings of the Fourth International Conference on Mathematical and Numerical Aspects of Wave Propagation, Golden, Colorado, June 1--5

Overlapping {S}chwarz Methods for {M}axwell's Equations in Conductive Media

Parallel Solution of {H}elmholtz Problems using Additive {S}chwarz Methods

Additive {S}chwarz Methods with Nonreflecting Boundary Conditions for the Parallel Computation of {H}elmholtz Problems

Proceedings of the 10th Intl. Conf. on Domain Decomposition Methods

Overlapping {S}chwarz Algorithms for Solving {H}elmholtz's Equation

Parallel Computing Using {S}chwarz Domain Decomposition Method for Aeroacoustic Problems

Parallel Computation of Harmonic Waves using Domain Decomposition, Part {I}: General Formulation

Parallel Computation of Harmonic Waves using Domain Decomposition, Part {II}: Numerical Implementation and Applications

Overlapping {S}chwarz methods for solving {H}elmholtz's Equation

Pet{C}law: A Scalable Parallel Nonlinear Wave Propagation Solver for {P}ython

{PyClaw}: Accessible, Extensible, Scalable Tools for Wave Propagation Problems

The impact of enabling multiple subdomains per MPI process in the TFETI domain decomposition method

A parallel two-level domain decomposition based one-shot method for shape optimization problems

Parallel Fully Coupled {Lagrange-Newton-Krylov-Schwarz} Algorithms and Software for Optimization Problems Constrained by Partial Differential Equations

Parallel multilevel restricted {Schwarz} preconditioners with pollution removing for {PDE}-constrained optimization

Parallel full space {SQP Lagrange-Newton-Krylov-Schwarz} algorithms for {PDE}-constrained Optimization Problems

Domain decomposition methods for {PDE}-constrained optimization problems

Three-dimensional anisotropic mesh adaptation for phase change problems

A {Lagrange-Newton-Krylov-Schur} Method for {PDE} Constrained Optimization

A case study in the performance and scalability of optimization algorithms

Parallel preconditioners for {KKT} systems arising in optimal control of viscous incompressible flows

Proceedings of Parallel CFD '99, Williamsburg, Virginia, USA, May 23-26, 1999

Using Automatic Differentiation for Second-order Matrix-free Methods in PDE-constrained Optimization

Automatic Differentiation of Algorithms: From Simulation to Optimization

Parallel Lagrange-Newton-Krylov-Schur Methods for PDE-Constrained Optimization. Part I: The Krylov-Schur Solver

Laboratory for Mechanics, Algorithms, and Computing, Carnegie Mellon University

Parallel {Lagrange-Newton-Krylov-Schur} Methods for {PDE}-Constrained Optimization. Part II: The {Lagrange-Newton} Solver, and its Application to Optimal Control of Steady Viscous Flows

{PetRBF} -- A parallel {O(N)} algorithm for radial basis function interpolation

{PetFMM} -- A dynamically load-balancing parallel fast multipole library

A sub-grid scale finite element agglomeration multigrid method with application to the Boltzmann transport equation

IDEA -- An API for Parallel Computing with Large Spatial Datasets

Proceedings of the 2011 International Conference on Parallel Processing

cluster, parallelization, spatial dataset, dependency, data partitioning

Cu(ii)-porphyrin molecular dynamics as seen in a novel EPR/Stochastic Liouville equation study

Implicit numerical schemes for the stochastic Liouville equation in Langevin form

A Differential Variational Inequality Approach for the Simulation of Heterogeneous Materials

A time-discrete model for dynamic fracture based on crack regularization

Spectrum of the non-abelian phase in Kitaev's honeycomb lattice model

Discriminative language modeling with conditional random fields and the perceptron algorithm

Proceedings of the 42nd Annual Meeting on Association for Computational Linguistics

{Parallel performance of the PETSc Krylov methods applied to linear systems of 3D nanodevice simulators}

Proceedings of The National Conference On Undergraduate Research (NCUR)

Parallel Newton-Krylov-Schwarz algorithms for the three-dimensional Poisson-Boltzmann equation in numerical simulation of colloidal particle interactions

Parallel pseudo-transient Newton-Krylov-Schwarz continuation algorithms for bifurcation analysis of incompressible sudden expansion flows

A parallel additive Schwarz preconditioned Jacobi-Davidson algorithm for polynomial eigenvalue problems in quantum dot simulation

{A Parallel Scalable PETSc-Based Jacobi-Davidson Polynomial Eigensolver with Application in Quantum Dot Simulation}

{Sequential and parallel resolution of the two-group transient neutron diffusion equation using second-degree iterative methods}

High Performance Computing for Computational Science-VECPAR 2006

Enabling High Fidelity Neutron Transport Simulations on Petascale Architectures

ACM/IEEE Proceedings of SC2009: High Performance Networking and Computing

An Efficient Algorithm for Classical Density Functional Theory in Three Dimensions: Ionic Solutions

{Energetics of Calcium Selectivity: A Three-Dimensional Classical Density Functional Theory Approach}

PARALLEL FINITE ELEMENT METHOD FOR COUPLED CHLORIDE MOISTURE DIFFUSION IN CONCRETE

Centro Internacional de Methodos Numericos en Ingenieria, Argentina

High Performance Simulations of Electrokinetic Flow and Transport in Microfluidic Chips

Institut für Angewandte Mechanik, Technische Universität Carolo-Wilhelmina zu Braunschweig, Spielmannstraße 11, 38106 Braunschweig, Germany

Parallel Computation of 3-D Soil-Structure Interaction in Time Domain with a Coupled FEM/SBFEM Approach

Parallel Finite Element Computations for Soil-Foundation-Structure Interaction Problems Report

Fast 3D frequency-dependent Radiative Transfer for Magneto-Hydrodynamics

Multidimensional multiphysics simulation of nuclear fuel behavior

COBRA-TF parallelization and application to PWR reactor core subchannel DNB analysis

Joint International Conference on Mathematics and Computation, Supercomputing in Nuclear Applications and the Monte Carlo Method

Solving Nonlinear Solid Mechanics Problems with the {J}acobian-{F}ree {N}ewton {K}rylov Method

Proceedings of the International Conference on the Physics of Reactors, Nuclear Power: A Sustainable Resource

Joint International Topical Meeting on Mathematics and Computation and Supercomputing in Nuclear Applications

Object-oriented programming for fast-and-easy development of parallel applications in forming processes simulation

Proceedings of the Second MIT Conference on Computational Fluid and Solid Mechanics

Parallel computation for solving efficiently viscoelastic fluid flow problems

Parallel computation applied to 3D FE simulation of polymer injection molding

Sparse Triangular Solves for {ILU} Revisited: Data Layout Crucial to Better Performance

The detachment of a viscous drop in a viscous solution in the presence of a soluble surfactant

Phase Field Simulations of Liquid-Liquid Demixing During Immersion Precipitation of Polymeric Membranes in 2D and 3D

Proceedings of the NINTH INTERNATIONAL CONFERENCE ON NUMERICAL COMBUSTION

A numerical method for inverse design based on the inverse Euler equations

A Numerical Method for the Design of Internal Flow Configurations Based on the Inverse Euler Equations

A fast, higher-order solver for scattering by penetrable bodies in three dimensions

PARALLEL SOLUTION OF HIGH ORDER FINITE DIFFERENCE SCHEMES FOR PRICING MULTI-DIMENSIONAL AMERICAN OPTIONS

A DIAL-AN-OPERATOR APPROACH TO SIMULATION OF IMPURITY DIFFUSION IN SEMICONDUCTORS

{KULL}: {LLNL}'s {ASCI} Inertial Confinement Fusion Simulation Code

Physor 2000 American Nuclear Society Topical Meeting on Advances in Reactor Physics and Mathematics and Computation into the Next Millennium

An Implicit Fluctuation Splitting Scheme for Turbomachinery Flows

High Performance Algorithms for Scalable Spin-Qubit Circuits with Quantum Dots

Proceedings of the 5th International Conference on Linux Clusters

Spin configurations in circular and rectangular vertical quantum dots in a magnetic field: Three-dimensional self-consistent simulation

Comparison Between Non-Equilibrium Green's Function and Monte Carlo Simulations for Transport in a Silicon Quantum Wire Structure

One-level Newton-Krylov-Schwarz algorithm for unsteady nonlinear radiation diffusion problem

Floating Solids: Combining Phase Field and Fluid-Structure Interactions

Accuracy analysis of the thrust force in 2D-3D finite element models

International Journal for Computation and Mathematics in Electrical and Electronic Engineering (COMPEL)

Finite element modelling of ion convection by electrostatic forces

Algebraic Multigrid Techniques for Strongly Indefinite Linear Systems from Direct Frequency Response Analysis in Solid Mechanics

Computational Modeling of Ion Beam-Neutralizer Interactions in Two and Three Dimensions

Parallelizing Pre-rendering Computations on a Net Juggler PC Cluster

Hybrid and concurrent algorithms for nonlinear magnetic field problems

Development and Performance Analysis of a Parallel Finite Element Application Implemented in an Object-Oriented Programming Framework

Least-Squares Finite Element Methods for Electromagnetic Applications

A Moving Overset Grid Method for Interface Dynamics Applied to Non-Newtonian Hele Shaw Flow

Stability of explicit-implicit hybrid time-stepping schemes for Maxwells equations

Comparison of two implementations of AMG-preconditioned CG considering an electrostatic problem

Analysis of Parallel Numerical Libraries to Solve the 3D Electron Continuity Equation

Simulation of Sandia Flame D Using Velocity-Scalar Filtered Density Function

Scalable Newton-Krylov Solver for Very Large Power Flow Problems

Development of an implicitly coupled electromechanical and electromagnetic transients simulator for power systems

Using {PETSc} to develop scalable applications for next-generation power grid

Proceedings of the 1st International Workshop on High Performance Computing, Networking and Analytics for the Power Grid

Development of a parallel three-phase transient stability simulator for power systems

An implicitly-coupled solution approach for combined electromechanical and electromagnetic transients simulation

Scalable Newton-Krylov solver for very large Power Flow problems

A distributed implementation of multi-area power system state estimation on a cluster of computers

Modulized Coupled Simulation of Localized Pit Initiation in Stainless Steel

Algorithms and Computing Architectures for Solving Differential-Algebraic Equation Systems Typically Encountered in Models of Corrosion Pit Initiation

A multiscale modeling approach to crack initiation in metallic polycrystals

44th AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics, and Materials Conference

Modeling of 3D Metallic Polycrystals and Simulation of Crack Initiation

International Conference ON Computational Engineering and Sciences

Use of Polycrystal Plasticity Theory in Assessing Material Performance

Simulation of materials processing: Theory, methods, and applications - Proceedings of the Sixth International Conference, NUMIFORM'98

Modelling and Finite Element Simulation of Non-Linear and Anisotropic Quasi-Static Electromagnetic Systems

Reducing the Computation Time of Non-Linear Problems by an Adaptive Linear System Tolerance

Extended Lifetime in Computational Evolution of Isolated Black Holes

Initial data for {E}instein's equations with superposed gravitational waves

Solves nonlinear coupled 3-D elliptic equations that arise in general relativity. For a related online version, see arXiv:gr-qc/0202096

Finding apparent horizons and other 2-surfaces of constant expansion

Solving Nonlinear Magnetic Problems Using Newton Trust Region Methods

Parallelization and Integration of a Large Scale Hydrocarbon Pool Fire in the Uintah PSE

In Proceedings of Ninth Internation Conference on Numerical Combustion - ICNC 2002

An Inherently-Parallel Method for Solving Discretized Diffusion Equations

Funded under the ASCI Level III: Computational Transport Issues for Large-Scale Parallel Simulations

A scalable modular convex solver for regularized risk minimization

Proceedings of the 13th ACM SIGKDD international conference on Knowledge discovery and data mining

A comparison of algorithms for maximum entropy Parameter estimation

In Proceedings of the Sixth Conference on Natural Language Learning (CoNLL-2002)

Computing the Lambda Modes of a Nuclear Reactor with {SLEPc} and {PETSc}

Solving finite difference schemes arising in trivariate option pricing

Comparison of three algorithms for nonlinear metal cutting problems

{M}ulti-{M}odel {M}ulti-{D}omain {C}omputational {M}ethods in {A}erodynamics and {A}coustics {W}eb Page

International Symposium on Parallel and Distributed Processing with Applications

{N}ew {G}eneration {F}ramework for {P}etroleum, {R}eservoir {S}imulation

Solutions of TEAM Problem \#13 Using Integral Equations in a Sequential and Parallel Computing Environment

Florida International University, Department of Electrical Engineering and Computing Science

Solutions of TEAM Problems 13 and 20 Using a Volume Integral Formulation

Computational Electromagnetics and Parallel Dense Matrix Computations

Proceedings of the SIAM Parallel Processing for Scientific Computing Conference

Evaluation of Multigrid as a Solver for Stress Analysis Problems in Semiconductor Process Simulation

Multigrid Methods VI: Proceedings of the Sixth European Multigrid Conference Held Gent, Belgium, September 27--30, 1999.

Solving large sparse linear systems in a grid environment: the GREMLINS code versus the PETSc library

Asynchronous iterations; Grid computing; Iterative method; Multisplitting method; Sparse linear solver

This is no longer supported. A set of preconditioners built on PETSc

We have developed a numerical model of ice sheets called PISM (a Parallel Ice Sheet Model). The thickness, temperature, velocity and age of the ice are all simulated, as is the deformation of the earth underneath the ice. New techniques for fast ice dynamics, earth deformation, and verification have are included.

DENDRO: a parallel geometric multigrid library for trilinear finite elements on octree meshes

SIFFEA:Scalable Integrated Framework for Finite Element Analysis

DistSolve: An Open Source Web Service for Solving Sparse Systems of Equations

CFDShip-Iowa is a multiblock free surface flow solver that uses overset structured grids, designed for ship applications

MultiFlow is a curvlinear, multiblock, multiprocessor flowsolver for multiphase flows.

The Idea and Concept of {Metos3D}: {A} Marine Ecosystem Toolkit for Optimization and Simulation in {3-D}

{Metos3D}: {A} Marine Ecosystem Toolkit for Optimization and Simulation in 3-D

{libMesh}:a C++ framework for the numerical simulation of partial differential equations on serial and parallel platforms

Multiphysics {O}bject-{O}riented {S}imulation {E}nvironment ({MOOSE})

MOOSE: {A} parallel computational framework for coupled systems of nonlinear equations

An object-oriented finite element framework for multiphysics phase field simulations

Computational approaches to studying non-linear dynamics of the crust and mantle

Chaste: a test-driven approach to software development for biological modelling

A continually updated technical report. \url{http://fenicsproject.org}

Snark: A suite of software for geoscientific applications and a philosophy of scientific software development

Innovative Modern Object-Oriented Solving Environment - {iMOOSE}

FoSSI: Family of Simplified Solver Interfaces, offers scalable access to MPI-parallel solvers from CSR-matrix format frequently used in sequential/vector codes

A finite element code for fluid dynamics, solid mechanics, thermal and multiphysics

PETSc-FEM: A General Purpose, Parallel, Multi-Physics FEM Program

Centro Internacional de Metodos Computacionales en Ingenieria (CIMEC)

Fluent's commercial finite element fluid code uses PETSc for parallel linear solves.

deal.II is a C++ library targeting adaptive finite elements and error estimation. It allows PETSc linear algebra and solvers to be used underneath.

{deal.II---A general-purpose object-oriented finite element library}

Preliminary implementation of Hybrid {MPI}/pthread programming model in {PETSc}

{PETSc's} software strategy for the design space of composable extreme-scale solvers

{DOE} Exascale Research Conference, April 16-18, 2012, Portland, OR

Coping at the User-Level with Resource Limitations in the {Cray} Message Passing Toolkit {MPI} at Scale

Engineering {PFLOTRAN} for Scalable Performance on {Cray} {XT} and {IBM} {BlueGene} Architectures

GPU Solutions to Multi-scale Problems in Science and Engineering

{GPU} Implementation of Multigrid Solver for {S}tokes Equation with Strongly Variable Viscosity

Implementation of a multigrid solver on {GPU} for {S}tokes equations with strongly variable viscosity based on {M}atlab and {CUDA}

PETSc, the Portable, Extensible Toolkit for Scientific computing

Computaci\'on cient\'ifica en paralelo con interfaz MATLAB a PETSc

Explaining StGermain: An aspect oriented environment for building extensible computational mechanics modeling software

Vectorized sparse matrix multiply for compressed row storage format

The COOLFluiD Framework: Design Solutions for High Performance Object Oriented Scientific Computing Software

Proceedings of *XIV Congress on Numerical Methods and its Applications (ENIEF). Bariloche, Argentina

Block Locally Optimal Preconditioned Eigenvalue Xolvers {(BLOPEX)} in {Hypre} and {PETSc}

Time Dependent Solution of the Schrodinger Equation for Parallel Computers

Performance Modeling and Prediction for the Scalable Solution of Partial Differential Equations on Unstructured Grids

Chalmers Finite Element Center, Chalmers University of Technology

Discribes a finite element software package that uses PETSc for its solvers

IX SIAM Conference on Parallel Processing for Scientific Computing

Describes software that uses PETSc for its parallel linear solves

Parallel Components for PDEs and Optimization: Some Issues and Experiences

Making Automatic Differentiation Truly Automatic: Coupling {PETSc} with {ADIC}

Exploiting Existing Software in Libraries: Successes, Failures, and Reasons Why

Developing a Derivative-Enhanced Object-Oriented Toolkit for Scientific Computations

Instytut Matematyki, Stosowanej i Mechaniki, Uniwersytet Warszawski

Integrating Automatic Differentiation with Object-Oriented Toolkits for High-Performance Scientific Computing

{PETS}c 2.0: A Case Study of Using {MPI} to Develop Numerical Software Libraries

Scalable Libraries for Solving Systems of Nonlinear Equations and Unconstrained Minimization Problems

nonlinear equations, optimization, superconductivity, parallel computing

The Design of Data-structure-neutral Libraries for the Iterative Solution of Sparse Linear Systems

A Microkernel Design for Component-based Parallel Numerical Software Systems

A Comparison of the {PETSc} Library and {HPF} Implementations of an Archetypal {PDE} Computation

Infrastructure and Interfaces for Large-Scale Numerical Software

to appear in the Proceedings of the 1999 International Conference on Parallel and Distributed Processing Techniques and Applications, June 28 - July 1, 1999, Las Vegas, Nevada

{On Combining Computational Differentiation and Toolkits for Parallel Scientific Computing}

Euro-Par 2000 -- Parallel Processing, Proceedings of the 6th International Euro-Par Conference, Munich, Germany, August/September 2000

{PETSc and Overture}: Lessons Learned Developing an Interface between Components

Proceedings of the International Federation for Information Processing Working Conference on Software Architectures for Scientific Computing, Kluwer

An Interface for Efficient Vector Scatters and Gathers on Parallel Machines

The Transition of Numerical Software: From Nuts-and-Bolts to Abstraction

Using {ADIFOR} and {ADIC} to Provide a {J}acobian for the {SNES} Component of {PETSc}

Numerical Analysis of Nonlinear Boundary Integral Equations Arising in Molecular Biology

Efficient Evaluation of Ellipsoidal Harmonics for Potential Modeling

SIAM Parallel Processing Conference, To Thread or Not To Thread Minisymposium, \url{https://www.cse.buffalo.edu/~knepley/presentations/SIAMPP2016_1.pdf}

A performance spectrum for parallel computational frameworks that solve {PDEs}

Comparative study of finite element methods using the Time-Accuracy-Size {(TAS)} spectrum analysis

Composable solvers for the four-field double porosity/permeability model

Anisotropic mesh adaptation in {Firedrake} with {PETSc} {DMPlex}

Proceedings of the {Platform for Advanced Scientific Computing Conference}

GPU, HPC, agglomeration, coarse-level solver, multigrid, parallel computing, preconditioning

A hybrid geometric+ algebraic multigrid method with semi-iterative smoothers

Enhanced balancing Neumann-Neumann preconditioning in computational fluid and solid mechanics

Agglomeration-based physical frame d{G} discretizations: {A}n attempt to be mesh free

{Multiscale modeling using goal-oriented adaptivity and numerical homogenization. Part II: Algorithms for the Moore-Penrose pseudoinverse}

Parallel Two-Grid Semismooth Newton-Krylov-Schwarz Method for Nonlinear Complementarity Problems

Complementarity problem, Grid sequencing, Parallel computing, Schwarz preconditioners, Semismooth Newton, Two-level methods

We present a novel finite element integration method for low order elements on GPUs. We achieve more than 100GF for element integration on first order discretizations of both the Laplacian and Elasticity operators on an NVIDIA GTX285, which has a nominal single precision peak flop rate of 1 TF/s and bandwidth of 159 GB/s, corresponding to a bandwidth limited peak of 40 GF/s.

Hierarchical {Krylov} and nested {Krylov} methods for extreme-scale computing

Hierarchical {Krylov} and Nested {Krylov} Methods for Extreme-Scale Computing

Proceeedings of the 11th {International Symposium on Parallel and Distributed Computing} ({ISPDC} 2012)

Numerical implementation of overlapping balancing domain decomposition methods on unstructured meshes

A parallel geometric multigrid method for finite elements on octree meshes

Bottom-up construction and 2:1 balance refinement of linear octrees in parallel

Low-constant parallel algorithms for finite element simulations using linear octrees

{Dynamic data-driven inversion for terascale simulations: real-time identification of airborne contaminants}

Using Distributed Computers to Deterministically Approximate Higher Dimensional Convection Diffusion Equations

Some Parallel Linear and Nonlinear {Schwarz} Methods with Applications in Computational Fluid Dynamics

On improving the performance of the linear solver restarted {GMRES}

A Parallel Implementation of Dual-Primal FETI-DP Methods for Three Dimensional Linear Elasticity Using a Transformation of Basis

Robust FETI-DP Methods for Heterogeneous Three Dimensional Elasticity Problems

Performance of a parallel mixed finite element implementation for fourth order clamped anisotropic plate bending problems in distributed memory environments

In an implicit Newton-Krylov method for inviscid, compressible fluid flow, the derivation of the analytic flux Jacobian can become quite complicated depending on the complexity of the numerical flux calculation. Practically, the derivation of the exact Jacobian by hand is an unrealistic option because of the enormous man-hour investment needed. In this work, automatic differentiation is used to evaluate the exact Jacobian of upwind schemes implemented in the flow solver QUADFLOW. We compare the use of exact Jacobians and Jacobians numerically approximated by first-order forward differences. For a two-dimensional airfoil under three different flight conditions (quasi-incompressible flow, compressible subsonic flow, and transonic flow), we show that the robustness and performance of the present finite volume scheme is significantly improved by using exact Jacobians.

An explicit expression for the penalty parameter of the interior penalty method

A component decomposition preconditioning for 3D stress analysis problems

Numerical experiments with parallel orderings for {ILU} preconditioners

Fast parallel algorithms for a broad class of nonlinear variational diffusion approaches

A Domain Decomposition Based Two-Level Newton Scheme for Nonlinear Problems

Some Computational Results for Dual-Primal FETI Methods for Elliptic Problems in 3D

Improving Robustness and Parallel Scalability of {Newton's} Method Through Nonlinear Preconditioning

Balancing {Neumann-Neumann} for (In)Compressible Linear Elasticity and (Generalized) {Stokes} and Parallel Implementation

Proceedings of the 14th International Conference on Domain Decomposition Methods

Toward scalable FETI algorithm for variational inequalities with applications to composites

Scalabilities of FETI for variational inequalities and contact shape optimization

Proceedings of the 13th International Conference on Domain Decomposition Methods

A Nonlinear Additive Schwarz Preconditioned Inexact Newton Method for Shocked Duct Flows

Multiplicative-additive preconditioning combination for general sparse linear systems

2003 International Conference on Preconditioning Techniques for Large Sparse Matrix Problems in Scientific and Industrial Applications

Hessian-based model reduction for large-scale systems with initial-condition inputs

Hessian-Based Model Reduction for Large-Scale Data Assimilation Problems

Fast algorithms for {B}ayesian uncertainty quantification in large-scale linear inverse problems based on low-rank partial {H}essian approximations

Model Reduction for Large Scale Applications in Microsystem Technology

Parallel Computation of a Fully Implicit Finite Volume Method Using Different Ordering Strategies

A Comparative Study of Preconditioned Methods for Solving Fully Coupled Fluid Flow Equations

The Employment of Algebraic Multigrid as a Preconditioner to Solve Fully Implicit Mixed Convection Equations

Using Different Preconditioned Krylov Subspace Methods to Solve Coupled Fluid Flow Equations

An Algebraic Multilevel Preconditioner for Field-Circuit Coupled Problems

Faster {PDE}-based Simulations Using Robust Composite Linear Solvers

Adaptive Sparse Linear Solvers for Implicit {CFD} Using {Newton-Krylov} Algorithms

The Role of Multi-Method Linear Solvers in {PDE}-based Simulations

Proceedings of the 2003 International Conference on Computational Science and its Applications, Lecture notes in Computer Science 2677

Newton-Krylov-FAC Methods for Problems Discretized on Locally Refined Grids

Parallel multigrid smoothing: polynomial versus {G}auss--{S}eidel

A distributed memory unstructured {G}auss-{S}eidel algorithm for multigrid smoothers

Static and Dynamic Graph Partitioning. A comparative study of existing algorithms

Uses PETSc's high quality parallel algorithms to provide a framework to compare different graph partitioning algorithms

Pseudo-Transient Continuation and Differential-Algebraic Equations

Submitted to the special issue of the SIAM Journal of Scientific Computing dedicated to papers from the 2002 Copper Mountain Conference on Iterative Methods

Balancing Neumann-Neumann Preconditioners for Mixed Approximations of Heterogeneous Problems in Linear Elasticity

Scalability and FETI based algorithm for large discretized variational inequalities

36 Scalabilities of FETI for Variational Inequalities and Contact Shape Optimization

Nonlinear additive {Schwarz} preconditioners and applications in computational fluid dynamics

A nonlinear additive {Schwarz} preconditioned inexact {Newton} method for shocked duct flow

A Class of Parallel Two-Level Nonlinear {Schwarz} Preconditioned Inexact {Newton} Algorithms

A Distributed Memory Unstructured {G}auss-{S}eidel Algorithm for Multigrid Smoothers

ACM/IEEE Proceedings of SC2001: High Performance Networking and Computing

Algebraic Multigrid for Two Dimensional Time-Harmonic Magnetic Field Computations

Parallel Multigrid Solvers for 3{D} Unstructured Finite Element Problems in Large Deformation Elasticity and Plasticity

Evaluation of Three Unstructured Multigrid Methods on 3{D} Finite Element Problems in Solid Mechanics

Parallel Multigrid Solver Algorithms and Implementations for 3{D} Unstructured Finite Element Problems

Overlapping {S}chwarz Methods on Unstructured Meshes using Non-matching Coarse Grids

The parallel construction of maximal independent sets is a useful building block for many algorithms in the computational sciences, including graph coloring and multigrid coarse grid creation on unstructured meshes. We present an efficient asynchronous maximal independent set algorithm for use on parallel computers, for ``well partitioned'' graphs, that arise from finite element (FE) models. For appropriately partitioned bounded degree graphs, it is shown that the running time of our algorithm under the P-RAM computational model is of $O(1)$, which is an improvement over the previous best P-RAM complexity for this class of graphs. We present numerical experiments on an IBM SP, that confirm our P-RAM complexity model is indicative of the performance one can expect with practical partitions on graphs from FE problems.

An Optimal Preconditioner for a Class of Saddle Point Problems with a Penalty Term

Departamento de Matem\'atica—ICEx, Universidade Federal de Minas Gerais, Av. Ant\^onio Carlos 6627, Caixa Postal 702, 30161-970 Belo Horizonte, MG, Brazil

Computing the First Eigenpair of the $p$-{L}aplacian via Inverse Iteration of Sublinear Supersolutions

{User friendly permeability predicting software for technical textiles}

Hong Kong Polytechnic University, Hong Kong Institution of Textile and Apparel

Domain Decomposition: Parallel Multilevel Methods for Elliptic Partial Differential Equations

{PETSc-FEM}: A General Purpose, Parallel, Multi-physics {FEM} Program

{\texttt{libMesh}: A C++ Library for Parallel Adaptive Mesh Refinement/Coarsening Simulations}

{SISIPHUS}: Scalable Ice-Sheet Solvers and Infrastructure for Petascale, High-Resolution, Unstructured Simulations

Improving parallel scalability for edge plasma transport simulations with neutral gas species

Focus on 22nd International Conference on Numerical Simulations of Plasmas (ICNSP 2011)

High-order wave propagation algorithms for general hyperbolic systems

{Parallel {Lagrange-Newton-Krylov-Schur} methods for {PDE} constrained optimization. Part I: The {Krylov-Schur} solver}

Society for Industrial and Applied Mathematics Philadelphia, PA, USA

Parallel {Lagrange-Newton-Krylov-Schur} methods for {PDE}-constrained optimization. Part {II}: The {Lagrange Newton} solver, and its application to optimal control of steady viscous flows

Spatial patterns of basal drag inferred using control methods from a full-{S}tokes and simpler models for {P}ine {I}sland {G}lacier, {W}est {A}ntarctica

Multiple timescale calculations of sawteeth and other global macroscopic dynamics of tokamak plasmas

Computer Science - Mathematical Software, Computer Science - Computational Engineering, Finance, and Science

{Programming CUDA and OpenCL: A Case Study Using Modern C++ Libraries}

Computer Science - Mathematical Software, Computer Science - Distributed, Parallel, and Cluster Computing, Physics - Computational Physics

{ViennaCL - A High Level Linear Algebra Library for GPUs and Multi-Core CPUs}

Whitepaper for the DOE High Performance Computing Operational Review (HPCOR) on Scientific Software Architecture for Portability and Performance

On The Evolution Of User Support Topics in Computational Science and Engineering Software

Whitepaper for Computational Science \& Engineering Software Sustainability and Productivity Challenges

First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE), held at SC13

Package Management Practice Essential for Interoperability: Lessons Learned and Strategies Developed for {FASTMath}

Predicting band structure of 3{D} mechanical metamaterials with complex geometry via {XFEM}

Compaction around a rigid, circular inclusion in partially molten rock

Analysis of block preconditioners for models of coupled magma mantle dynamics

Pipe Poiseuille flow of viscously anisotropic, partially molten rock

Low-communication techniques for extreme-scale multilevel solvers

Scalable smoothing strategies for a geometric multigrid method for the immersed boundary equations

An overlapping Domain Decomposition preconditioning method for monolithic solution of shear bands

{PETSc} {DMNetwork}: A Library for Scalable Network PDE-Based Multiphysics Simulations

Vectorized Parallel Sparse Matrix-Vector Multiplication in {PETSc} Using {AVX-512}

submitted to the International Conference on Parallel Processing (ICPP) 2018

SIAM News, available via \url{https://sinews.siam.org/Details-Page/extensibility-in-petsc}

On the Evolution of User Support Topics in Computational Science and Engineering Software

Workshop on CSE Software Sustainability and Productivity (CSESSP) Challenges, Oct 15-16, 2015

Numerical Library Support for High-Performance Mixed Language Applications and Legacy Code

Proceedings of the Platform for Advanced Scientific Computing (PASC)

Parallel implementation of AC optimal power flow and time-constrained optimal power flow using high-performance computing

IEEE 9th Annual Computing and Communication Workshop and Conference (CCWC 2019)

Newton–Krylov–Schwarz Methods for Distributed Power Flow and Related Applications

Efficient management of parallelism in object oriented numerical software libraries.

A microkernel design for component-based parallel numerical software systems.

, chapter PETSc, the Portable, Extensible Toolkit for Scientific computing.

, chapter Providing Mixed Language and Legacy Support within a Library.

Users manual for doctext: producing documentation from source code.

Technical Report ANL/MCS-TM-206, Argonne National Laboratory, 1995.

Technical Report ANL/MCS-TM-208, Argonne National Laboratory, 1995.

Technical Report CU-CS 843-97, Computer Science Department, University of Colorado-Boulder, 1997.

Variational iterative methods for nonsymmetric systems of linear equations.

Hiding global synchronization latency in the preconditioned conjugate gradient algorithm.

tokes equations discretized by high-order finite elements on nonconforming and anisotropic meshes, with application to ice sheet dynamics.

: a generalized minimal residual algorithm for solving nonsymmetric linear systems.

Technical Report ANL-91/15, Argonne National Laboratory, August 1991.

utta schemes for hyperbolic systems and kinetic equations in the diffusion limit.

Error propagation of general linear methods for ordinary differential equations.

Implicit-explicit formulations of a three-dimensional nonhydrostatic unified model of the atmosphere 

utta schemes and applications to hyperbolic systems with relaxation.

-methods of order 3 for partial differential algebraic equations of index 1.

Sandu, J.G. Verwer, J.G. Blom, E.J. Spee, G.R. Carmichael, and F.A. Potra.

Benchmarking stiff ode solvers for atmospheric chemistry problems 