Alumni Project

External Impact of TOPS Scalable Solver Software

PIs: S. Benson1, X. Cai6, E. Chow3, J. Demmel5, F. Dobrian4, J. Dongarra7, V. Eijkhout7, R. Falgout3, M. Knepley1, S. Li2,5, J. More1, T. Munson1, A. Pothen4, R. Serban3, B. Smith1, P. Vassilevski3, C. Woodward3, H. Zhang1

1 Argonne National Lab, 2 Lawrence Berkeley National Lab, 3 Lawrence Livermore National Lab, 4 Old Dominion U., 5 U. California-Berkeley, 6 U. Colorado-Boulder, 7 U. Tennessee


Software developed and supported by the Terascale Optimal PDE Simulations (TOPS) project is in use in projects similar to those in the SciDAC portfolio around the globe.

SciDAC applications groups are actively assisting TOPS in the development of scalable solver software by using it, porting it, “breaking” it, comparing it to other solvers, asking for additional functionality, suggesting changes, and in some cases, actually contributing new routines to it. However, SciDAC-supported users are not the only users contributing to TOPS software development in this manner. Some of the software packages developed, made interoperable, and maintained through TOPS have active user communities numbering in the hundreds, including Hypre, PETSc, SUNDIALS, SuperLU, and TAO. The user communities of these and other TOPS packages span many areas included in the DOE Office of Science portfolio. In the interest of encouraging the sharing of information about TOPS software across user groups, some representative publications produced with the aid of TOPS software within the past two years are listed here.


H. P. Pfeiffer, G. B. Cook & S. A. Teukolsky, 2002, Comparing initial-data sets for binary black holes , Phys. Rev. D66, 024047.

H. P. Pfeiffer, L. E. Kidder, M. A. Scheel & S. A. Teukolsky, Saul A., 2003, A multidomain spectral method for solving elliptic equations , Comp. Phys. Comm. 152 :253-273.


M. F. Adams, H. H. Bayraktar, T. M. Keaveny & P. Papadopoulos, 2003, Applications of Algebraic Multigrid to Large-Scale Finite Element Analysis of Whole Bone Micro-Mechanics on the IBM SP , Proc. SC2003.

S. K. Warfield, F. Talos, A. Tei, A. Bharatha, A. Nabavi, M. Ferrant, P. M. Black, F. A. Jolesz & R. Kikinis, 2002, Real-time registration of volumetric brain MRI by biomechanical simulation of deformation during image guided neurosurgery , Comput. Vis. Science, 5 :3-11.


A. H. Aarrestad, 2003, Time Dependent Solution of the Schrodinger Equation for Parallel Computers , University of Bergen (dissertation).

Cognitive Sciences

R. Malouf, 2002, A comparison of algorithms for maximum entropy parameter estimation, Proc. Sixth Conf. Nat. Lang. Learning , 49-55.


R. Rawat, J. P. Spinti, W. Yee & P. J. Smith, 2002, Parallelization and Integration of a Large Scale Hydrocarbon Pool Fire in the Uintah PSE, Proc. Ninth Int. Conf. Numer. Combust.

Electrical Engineering

D. Lahaye, S. Vandewalle & K. Hameyer, 2004, An Algebraic Multilevel Preconditioner for Field-Circuit Coupled Problems , J. Comput. Appl. Math. (to appear).


V. Akcelik, J. Bielak, G. Biros, I. Epanomeritakis, A. Fernandez, O. Ghattas, E.-J. Kim, D. O'Hallaron & T. Tu, 2003, High Resolution Forward and Inverse Earthquake Modeling on Terascale Computers , Proc. SC2003 [a 2003 Gordon Bell Prize winner] .

S. Danilov, G. Kivman & J. Schroeter, 2004, A finite-element ocean model: principles and evaluation , Ocean Modelling 6 :125-150.


L. A. Barba, 2004, Computing high-Reynolds number vortical flows: a highly accurate method with a fully meshless formulation , Proc. Parallel CFD'04 (submitted).

C. E. Kees & C. T. Miller, 2002, Higher Order Time Integration Methods for Two-Phase Flow, Adv. Water Resources, 25 :159-177.

B. G. M. Van Wachem & J. C. Schouten, 2002, Experimental Validation of 3-D Lagrangian VOF Model: Bubble Shape and Rise Velocity , AIChE J. 48 :2744-2753.

Materials Science

H. Vande Sande, H. De Gersem, F. Henrotte & K. Hameyer, 2003, Solving Nonlinear Magnetic Problems Using Newton Trust Region Methods , IEEE Trans. Magnetics 39 :1709-1712.


M. F. Adams, 2004, Algebraic multigrid methods for constrained linear systems with applications to contact problems in solid mechanics , Numer. Linear Alg. Appls. (to appear).


A. K. M. Fahimuddin & H. Fassbender, 2004, Model Reduction for Large Scale Applications in Microsystem Technology , Proc. SIAM Conf. Par. Proc. (submitted).

W. Scholz, J. Fidler, T. Schrefl, D. Suess, R. Dittrich, H. Forster & V. Tsiantos, 2003, Scalable Parallel Micromagnetic Solvers for Magnetic Nanostructures , Comp. Mater. Sci. 28 :366-383.

Numerical Analysis

M. E. Argentati, 2003, Principal Angles Between Subspaces as Related to Rayleigh Quotient and Rayleigh Ritz Inequalities with Applications to Eigenvalue Accuracy and an Eigenvalue Solver , Univ. of Colorado (dissertation).

V. Hernandez, J. E. Roman, V. Vidal, 2002, SLEPc: Scalable Library for Eigenvalue Problem Computations , Proc. VECPAR02.

L. Ying, G. Biros, D. Zorin & H. Langston, 2003, A New Parallel Kernel-independent Fast Multipole Method , Proc. SC2003 [awarded “Best Student Paper”] .


O. Saut, 2004, Bidimensional Study of the Maxwell-Bloch Model in a Nonlinear Crystal , SIAM J. Sci. Comput. (submitted).

Porous media

G. E. Hammond, 2003, Innovative Methods for Solving Multicomponent Biogeochemical Groundwater Transport on Supercomputers , Univ. Illinois (dissertation).

G. E. Hammond, A. J. Valocchi & P. C. Lichtner, 2002, Numerical Modeling of NAPL Source Zone Treatment , AGU Fall 2002 Meeting [awarded “Best Student Paper”] .

S. Lanteri & C. Raffourt, 2004, Strategies for reducing computing time of nuclear waste management simulations using the PORFLOW software , Comput. Geosci. (to appear).

Shape Optimization

Z. Dostal, D. Horak, J. Szweda & V. Vondrak, Scalabilities of FETI for variational inequalities and contact shape optimization , Proc. 13 th Intl. Conf. Domain Decomp. Meths., 361-369.

TOPS solver software has been incorporated into numerous other packages, some commercial and some freely available. We list here some widely distributed packages maintained outside of the SciDAC program that employ or interface to TOPS software “under the hood”:

Dspice, EMSolve, FEMLAB ® , FIDAP ® , Global Arrays, HP Mathematical Library ® , libMesh, Magpar, Mathematica ® , NIKE, Prometheus, SCIRun, SLEPc, Snark, Trilinos.

TOPS software is taught in many courses in the U.S. and abroad, and forms a core of the DOE ACTS toolkit tutorial. TOPS software is also regularly featured in short courses at professional meetings.

The TOPS project webpage may be found at .

For further information on this subject contact:
Prof. David E. Keyes, Project Lead
Columbia University
Phone: 212-854-1120

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