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Brian Van Straalen

Brian Van Straalen (Full-time)
Phone: +1 510 486 4976
Fax: +1 510 486 6900

Brian Van Straalen received his BASc Mechanical Engineering in 1993 and MMath in Applied Mathematics in 1995 from University of Waterloo.  He has been working in the area of scientific computing since he was an undergraduate. He worked with Advanced Scientific Computing Ltd. developing CFD codes written largely in Fortran 77 running on VAX and UNIX workstations.  He then worked as part of the thermal modeling group with Bell Northern Research.  His Master's thesis work was in the area of a posteriori error estimation for Navier-Stokes equations, which is an area that is still relevant to Department of Energy scientific computing.   He worked for Beam Technologies developing the PDESolve package: a combined symbolic manipulation package and finite element solver, running in parallel on some of the earliest NSF and DOE MPP parallel computers.  He came to LBNL in 1998 to work with Phil Colella and start up the Chombo Project, now in its 13th year of development. He is currently working on his PhD in the Computer Science department at UC Berkeley.

Journal Articles

Anshu Dubey, Ann Almgren, John Bell, Martin Berzins, Steve Brandt, Greg Bryan, Phillip Colella, Daniel Graves, Michael Lijewski, Frank Löffler, Brian O’Shea, Erik Schnetter, Brian Van Straalen, Klaus Weide, "A Survey of High Level Frameworks in Block-Structured Adaptive Mesh Refinement Packages", Journal of Parallel and Distributed Computing, 2014, doi: http://dx.doi.org/10.1016/j.jpdc.2014.07.001

Anshu Dubey, Brian Van Straalen, "Experiences from Software Engineering of Large Scale AMR Multiphysics Code Frameworks", Journal of Open Research Software 2(1):e7 Special Collection: Working towards Sustainable Software for Science: Practice and Experiences, July 9, 2014, doi: http://dx.doi.org/10.5334/jors.am

Anshu Dubey, Steve R. Brandt, Rich Brower, Merle Giles, Paul Hovland, Donald Q. Lamb, Frank Löffler, Boyana Norris, Brian W. O'Shea, Claudio Rebbi, Marc Snir, Rajiv Thakur, Petros Tzeferacos, "Software Abstractions and Methodologies for HPC Simulation Codes on Future Architectures", Journal of Open Research Software, 2014, 2(1):e14, doi: http://dx.doi.org/10.5334/jors.aw

A. Dubey, K. Antypas, A.C. Calder, C. Daley, Fryxell, J.B. Gallagher, D.Q. Lamb, D. Lee, K. Olson, L.B., P. Rich, P.M. Ricker, K.M. Riley, Rosner, A. Siegel, N.T. Taylor, F.X. Timmes, N. Vladimirova, K. Weide, J. ZuHone, "Evolution of FLASH, a Multiphysics Scientific Simulation Code for High Performance Computing", International Journal of High Performance Computing Applications, 2013,

A. Dubey, K. Weide, D. Lee, J. Bachan, C. Daley, S. Olofin, N. Taylor, P.M. Rich, L.B. Reid, "Ongoing Verification of a Multiphysics Community Code: FLASH", Software: Practice and Experience, 2013,

A. Dubey, A.C. Calder, C. Daley, R.T. Fisher, C. Graziani, G.C. Jordan, D.Q. Lamb, L.B. Reid, D.M. Townsley, K. Weide, "Pragmatic optimizations for better scientific utilization of large supercomputers", International Journal of High Performance Computing Applications, 2013, 27:360-373, doi: 0.1177/1094342012464404

A. Dubey, C. Daley, J. ZuHone, P. M. Ricker, K. Weide, C. Graziani, "Imposing a Lagrangian particle framework on an Eulerian hydrodynamics infrastructure in FLASH", ApJ Supplement, 2012, 201:27, doi: 10.1088/0067-0049/201/2/27

Chalence Safranek-Shrader, Meghann Agarwal, Christoph Federrath, Anshu Dubey, Miloš Milosavljević, Volker Bromm, "Star formation in the first galaxies – I. Collapse delayed by Lyman–Werner radiation", Monthly Notices of the Royal Astronomical Society, 2012, 426:1159--1177, doi: 10.1111/j.1365-2966.2012.21852.x

Christopher Daley, Marcos Vanella, Anshu Dubey, Klaus Weide, Elias Balaras, "Optimization of multigrid based elliptic solver for large scale simulations in the FLASH code", Concurrency and Computation: Practice and Experience, 2012, 24:2346--2361, doi: 10.1002/cpe.2821

R. Latham, C. Daley, W. Liao, K. Gao, R. Ross, A. Dubey, A. Choudhary, "A Case Study for Scientific I/O: Improving the FLASH Astrophysics Code", Computational Science and Discovery, 2012, 5:015001,

A. Dubey, K. Antypas, C. Daley, "Parallel algorithms for moving Lagrangian data on block structured Eulerian meshes", Parallel Computing, 2011, 37:101 - 113, doi: DOI: 10.1016/j.parco.2011.01.001

D. Lee, G. Xia, C. Daley, A. Dubey, S. Gopal, C. Graziani, D.Q. Lamb, K. Weide, "Progress in Development of HEDP Capabilities in FLASH s Unsplit Staggered Mesh MHD Solver", HEDLA 2010: Astrophysics and Space Science Special Issue, 2010,

A. Dubey, K. Antypas, M.K. Ganapathy, L.B., K. Riley, D. Sheeler, A. Siegel, K. Weide, "Extensible Component Based Architecture for FLASH, A Massively Parallel, Multiphysics Simulation Code", Parallel Computing, 2009, 35:512-522, doi: DOI: 10.1016/j.parco.2009.08.001

Bronis R de Supinski, Sadaf Alam, David H Bailey, Laura, Chris Daley, Anshu Dubey, Todd Gamblin, Dan, Paul D Hovland, Heike Jagode, Karen Karavanic, Marin, John Mellor-Crummey, Shirley Moore, Boyana, Leonid Oliker, Catherine Olschanowsky, Philip C, Martin Schulz, Sameer Shende, Allan Snavely, Wyatt, Mustafa Tikir, Jeff Vetter, Pat Worley, Nicholas Wright, "Modeling the Office of Science ten year facilities plan: The PERI Architecture Tiger Team", Journal of Physics: Conference Series, 2009, 180:012039, doi: 10.1088/1742-6596/180/1/012039

R. Fisher, S. Abarzhi, K. Antypas, S.M. Asida, Calder, F. Cattaneo, P. Constantin, A. Dubey, Foster, J.B. Gallagher, M.K. Ganapathy, C.C. Glendenin, L., D.Q. Lamb, S. Needham, M. Papka, T. Plewa, L.B. Reid, P. Rich, K. Riley, D. Sheeler, "Terascale Turbulence Computation on BG/L Using the FLASH3 Code", IBM Journal of Research and Development, 2008, 52:127--137,

A. Dubey, L.B. Reid, R. Fisher, "Introduction to FLASH 3.0, with application to supersonic turbulence", Physica Scripta, 2008, T132,

E.-J. Rijkhorst, T. Plewa, A. Dubey, G. Mellema, "Hybrid characteristics: 3D radiative transfer for parallel adaptive mesh refinement hydrodynamics", Astronomy and Astrophysics, 2006, 452:907-920, doi: 10.1051/0004-6361:20053401

M. Comparato, V. Antonuccio, U. Becciani, A. Dubey, T. Plewa, D. Sheeler, "FLY-FLASH: A Software Interface for Adaptive Mesh Refinement - Treecode Simulations .", Memorie della Societa Astronomica Italiana Supplement, 2006, 9:448-+,

A. Dubey, D. Tessera, "Redistribution Strategies in portable parallel FFTs", Concurrency, Practice and Experience, 2001, 13:209-220,

Y.-N. Young, H. Tufo, A. Dubey, R. Rosner, "On the miscible Rayleigh-Taylor instability: two and three dimensions", Journal of Fluid Mechanics, 1999, 447:377-408,

A. Dubey, M. Zubair, C.E. Grosch, "A General Purpose Subroutine for Fast Fourier Transform on a Distributed Memory Parallel Machine", Parallel Computing, 1994, 20:1697-1710,

A. Dubey, M. Zubair, C.E. Grosch, "Real Fourier Transforms on a Massively Parallel Machine", Computer Systems, Science and Engineering, 1992, 7:243-248,

A. Dubey, M. Zubair, C.E. Grosch, "Computing the Fourier Transform of Real Data on a Hypercube", Journal of Scientific Computing, 1990, 5:293-309,

Conference Papers

P. Mohapatra, A. Dubey, C. Daley, M. Vanella, E. Balaras, "Parallel Algorithms for Using Lagrangian Markers in Immersed Method with Adaptive Mesh Refinement in FLASH", SBAC-PAD, 2013, 2013,

A. Dubey, P. Mohapatra, K. Weide, "Fault Tolerance Using Lower Fidelity Data in Adaptive Mesh Applications", FTXS 13, New York, NY, USA., 2013,

A. Dubey, K. Antypas, A. Calder, B. Fryxell, Lamb, P. Ricker, L. Reid, K. Riley, R. Rosner, A. Siegel, F. Timmes, N. Vladimirova, Klaus Weide, "The Software Development Process of FLASH, a Multiphysics Simulation Code", SE-CSE San Francisco, USA, 2013,

D. Lee, A. Dubey, K. Olson, K. Weide, K. Antypas, "Exploiting the Extensibility of the FLASH code Architecture for Unsplit Time Integration", Numerical Modeling of Space Plasma Flows: ASTRONUM, ASP Series, N.V. Pogorelov, E. Audit, and G.P. Zank, editors, 2010, 429 (4):247-252,

A. Dubey, R. Fisher, C. Graziani, IV Jordan, D. Q. Lamb, L. B. Reid, P. Rich, D. Sheeler, D. Townsley, K. Weide, "Challenges of Extreme Computing using the FLASH code", Astronomical Society of the Pacific Conference Series, 2008, 385:145-+,

D. M. Townsley, R. A. Bair, A. Dubey, R. T. Fisher, N. C. Hearn, D. Q. Lamb, K. M. Riley, "Large-scale simulations of buoyancy-driven turbulent nuclear burning", Journal of Physics Conference Series, 2008, 125:012009-+, doi: 10.1088/1742-6596/125/1/012009

A. C. Calder, N. T. Taylor, K. Antypas, D. Sheeler, A. Dubey, "A Case Study of Verifying and Validating an Astrophysical Simulation Code", Astronomical Society of the Pacific Conference Series, 2006, 119-+,

K.B. Antypas, A.C. Calder, A. Dubey, J.B. Joshi Gallagher, D.Q. Lamb, T. Linde, E.L. Lusk, Messer, A. Mignone, H. Pan, M. Papka, F. Peng, T., K.M. Riley, P.M. Ricker, D. Sheeler, Siegel, N. Taylor, J.W. Truran, N. Vladimirova, G. Weirs, D. Yu, J. Zhang, "FLASH: Applications and Future", Parallel Computational Fluid Dynamics -- Theory and Applications, 2006, 325+,

K. Antypas, A.C. Calder, A. Dubey, R. Fisher, Ganapathy, J.B. Gallagher, L.B. Reid, K. Riley, K. Sheeler, N. Taylor, "Scientific Applications on the Massively Parallel BG/L Machine.", PDPTA, 2006, 292--298,

D. Tessera, A. Dubey, "Communication Policies Performance: A Case Study", 9th Euromicro Workshop on Parallel and Distributed Processing, 2001,

A. Dubey, F. Cattaneo, A. Malagoli, "PFFT: A Portable and Efficient Framework for Parallel FFT s", Proceedings of High Performance Computing, 2000,

A. Dubey, T. Clune, "Optimization Techniques for Pseudospectral codes on MPPs", Proceedings of Frontiers 99, 1999,

A. Malagoli, A. Dubey, F. Cattaneo, "Parallel Implementation of a Pseudospectral MHD Code", Proceedings of the 1997 Simulation Multconference (HPC), 1997,

A. Malagoli, A. Dubey, F. Cattaneo, D. Levine, "A Portable and Efficient code for Astrophysical Fluid Dynamics", Proceedings of Parallel CFD 95, 1995,

M. Zubair, A. Dubey, "A Hybrid Algorithm for Inverting Matrices on a Massively Parallel Machine (AMT DAP-510)", Advances in Parallel Computing, 1993,

A. Dubey, M. Zubair, C.E. Grosch, U.S. Shirahatti, "Implementation of Boundary Element Method for Solving Acoustic Problems on a Massively Parallel Machine", Second International Congress on Recent Developments in Air- and Structure-Borne Sound and Vibration, 1992, 2,


C. Daley, J. Bachan, S. Couch, A. Dubey, M. Fatenejad, B. Gallagher, D. Lee, K. Weide, "Adding shared memory parallelism to FLASH for many-core architectures", TACC-Intel Highly Parallel Computing Symposium, 2012,

A. Dubey, D. Q. Lamb, K. Weide, D. Lee, G. Xia, C. Graziani, C. Daley, S. Gopal, "Adding Capabilities to FLASH to Create Open Toolset for High-Energy Density Physics Simulations", Bulletin of the American Physical Society, 2010,

A. Dubey, E. Balaras, S. Couch, C. Daley, Gopal, C. Graziani, D. Lamb, D. Lee, M. Vanella, K. Weide, G. Xia, "FLASH Capabilities, Architecture, and Future Directions", Bulletin of the American Physical Society, 2010,

S.M. Couch, A. Dubey, "Implementation of Laser Energy Deposition in FLASH", Bulletin of the American Physical Society, 2010,

D.Q. Lamb, S. Couch, A. Dubey, S. Gopal, C. Graziani, D. Lee, and K. Weide, G. Xia, "Making FLASH an Open Code for the Academic High-Energy Density Physics Community", Bulletin of the American Physical Society, 2010,