Publications

J. Chai, H. Su, M. Wen, X. Cai, N. Wu, and C. Zhang. Resource-efficient utilization of CPU/GPU-based heterogeneous supercomputers for Bayesian phylogenetic inference, Accepted for publication in The Journal of Supercomputing, 2013.

W. Wei, S. Clark, H. Su, M. Wen, and X. Cai. Balancing efficiency and accuracy for sediment transport simulations, Submitted to journal, 2013.

O. Al-Khayat and H. P. Langtangen. Computational aspects of multiscale simulation with the lumped particle framework, Communications in Computational Physics 12(4):1257-1274, 2012.

T. Gillberg, Ø. Hjelle, and A. M. Bruaset. Accuracy and Efficiency of Stencils for the Eikonal Equation in Earth Modelling, Computational Geosciences 16(4):933-952, 2012.

T. Gillberg, Ø. Hjelle, and A. M. Bruaset. A Parallel 3D Front Propagation Algorithm for Simulation of Geological Folding on GPUs, In: EAGE 74th Conference & Exhibition, Copenhagen, ed. by Eage, EAGE, EarthDoc. Extended Abstracts, 2012.

M. Wen, H. Su, W. Wei, N. Wu, X. Cai, and C. Zhang. Using 1000+ GPUs and 10000+ CPUs for Sedimentary Basin Simulations, In: Proceedings of IEEE Cluster 2012, ed. by , pp. 27-35, IEEE, 2012.

W. Zhang and X. Cai. Efficient implementations of the Adams-Bashforth-Moulton method for solving fractional differential equations, In: Proceedings of FDA'12, 2012.

T. Gillberg. A Parallel 3D Front Propagation Algorithm for Simulation of Geological Folding on GPUs, EAGE 74th Conference & Exhibition, 2012.

S. Hippchen, B. Ghorbal, C. Moder, and S. R. Clark. Geology, Tectonics, and Intraplate Deformation in South America: Revisited Block Boundaries, 2012.

L. Vynnytska, D. Stegman, and S. R. Clark. The Afar Region: Numerical Modeling Using Geological Data, EGU general assembly, 2012.

X. Cai and M. Wen. Simulating basin evolution on GPU-enhanced hybrid supercomputers, META Magazine, Issue 02/2012, pages 22-25, 2012.

T. Gillberg. A Semi-Ordered Fast Iterative Method (SOFI) for Monotone Front Propagation in Simulations of Geological Folding, In: MODSIM2011, 19th International Congress on Modelling and Simulation, ed. by Chan, F. and Marinova, D. and Anderssen, B., pp. 631-647, Modelling and Simulation Society of Australia and New Zealand, Modelling and Simulation Society of Australia and New Zealand Inc. (MSSANZ) (ISBN: 978-0-9872143-1-7), 2011.

W. Wei, O. Al-Khayat, and X. Cai. An OpenMP-enabled parallel simulator for particle transport in fluid flows, In: Proceedings of the International Conference on Computational Science, ICCS 2011, ed. by M. Sato and S. Matsuoka, vol. 4, pp. 1475-1484, Elsevier Science. Procedia Computer Science, 2011.

X. Cai. A function-centric generic framework for parallelization, Talk at CLS Workshop at UiO on April 13, 2011.

X. Cai. Study of the computational efficiency for different usages of Pythoning, Talk at CLS Workshop at UiO on April 13, 2011.

X. Cai. Parallel simulation of particle transport using OpenMP, Guest lecture at UCSD on January 31, 2011.

L. Vynnytska and S. R. Clark. Simulation of 2D Mantle Convection using FEniCS Framework, SAMPLE workshop in Potsdam, Germany (June, 7 - 10, 2011), 2011.

A. Tveito, H. P. Langtangen, B. F. Nielsen, and X. Cai. Elements of Scientific Computing, Springer, 2010.

O. Al-Khayat. Mesoscale modeling of particle flow, PhD thesis, University of Oslo, 2010.

O. Al-Khayat, A. M. Bruaset, and H. P. Langtangen. A lumped particle modeling framework for simulating particle transport in fluids , Communications in Computational Physics 8(1):115-142, 2010.

P. Li, W. Wei, X. Cai, C. Soeller, M. Cannell, and A. V. Holden. Computational modeling of the initiation and development of spontaneous intracellular Ca2+ waves in ventricular myocytes, Philosophical Transactions of the Royal Society A 368(1925):3953-3965, 2010.

J. K. Nilsen, X. Cai, B. Høyland, and H. P. Langtangen. Simplifying the parallelization of scientific codes by a function-centric approach in Python, Computational Science & Discovery 3(0):015003, 2010.

S. R. Clark, W. Wei, and X. Cai. Numerical analysis of a dual-sediment transport model applied to Lake Okeechobee, Florida, In: Proceedings of the 2010 Ninth International Symposium on Parallel and Distributed Computing, ed. by Can Ozturan, pp. 189--194, IEEE Computer Society Press. ISPDC '10, 2010.

A. Schroll. Automatic Calibration of Depositional Models, In: Automated Scientific Computing, ed. by Logg, Anders and Mardal, Kent-Andre and Wells, Garth N.. Springer Berlin Heidelberg, chap. , pp. , 2010.

J. T.-C. Yeh, X. Cai, H. P. Langtangen, J. Zhu, and Chuen-F. Ni. Parallel computing engines for subsurface imaging technologies, In: Advanced Computational Infrastructures for Parallel and Distributed Adaptive Applications, ed. by M. Parashar, X. Li. John Wiley & Sons, Inc., Hoboken, New Jersey, chap. 3, pp. 29-43. Wiley Series of Parallel and Distributed Computing, 2010.

R. Lorentzen. Allocation of Students to Study Groups — Working Paper, Simula Research Laboratory, Working Paper (Simula Technical Report Series 2010-02), 2010.

R. Lorentzen, Ø. Hjelle, H. P. Langtangen, and A. M. Bruaset. Extrapolation from a very Low Number of Computer Experiments, Simula Research Laboratory, (Simula Technical Report Series 2010-06), 2010.

O. Al-Khayat. A lumped particle modeling framework for the transport of particles, Talk at CBC workshop on Tsunami Modelling, 2010.

O. Al-Khayat. A multiscale lumped particle modeling framework for the simulation of turbidity currents, Poster at the 7th EGU General Assembly, vol 12, Vienna, 2010.

H. C. Bender, A. Thurmond, J. Skogseid, and S. R. Clark. Microplate Modeling of the Afar Depression using 4D lithospheric model (4DLM) and Splates: Implications for Development of Plate Boundaries, Talk given at Geological Society of America, 2010.

X. Cai. Parallel programming using Python, CBC Seminar on advanced use of Python programming language, 2010.

X. Cai, D. Unat, and S. Baden. Detailed Numerical Analyses of the Aliev-Panfilov Model on GPGPU, Talk at PARA2010 Conference, 2010.

H. P. Langtangen. Computational Modeling of Huge Tsunamis From Asteroid Impacts, Computational Geoscience seminar, 2010.

A. Schroll. Scientific Computing - the (he)art of modern sciences, Forskningens Dag, SDU, 2010.

W. Wei. Parallel Programming, OpenMP, CBC Lecture on Parallel Programming, OpenMP, March 17, 2010.

W. Wei and X. Cai. OpenMP: An Easy Parallel Approach for Scientific Computing on Multi-core Architecture, A short course respectively given at Simula in March and University of Oslo in May, 2010.

X. Cai. A non-invasive approach to parallelizing sequential simulators of partial differential equations, Guest lecture at UCSD on October 28, 2010.

A. M. Bruaset, C. Tarrou, T. V. Stensby, and J. Skogseid. Geological modelling, UK Patent 2465079, 2010.

O. Al-Khayat. A multiscale lumped particle modeling framework for the simulation of turbidity currents, In: 7th EGU General Assembly, vol. 12, Copernicus GmbH, 2010.

S. R. Clark. Geodynamic models assist in determining the South Loyalty Basin's slab location and its implications for regional topography, In: Geophysical Research Abstracts, vol. 11, European Geoscience Union, Copernicus GmbH, 2010.

A. Schroll. Automatic Calibration of Depositional Models, In: Book of Abstracts, Scientific Computing Seminar, Christian-Albrechts-Universität zu Kiel, 2010.

A. Schroll. On high-resolution shock simulations - breaking the course of Godunov's theorem , In: Book of Abstracts, Cut Cell Methods for Atmosphere and Ocean Modeling, Freie Universität Berlin, 2010.

W. Wei, S. R. Clark, X. Cai, and A. M. Bruaset. Three numerical methods and their parallelisation for dual-Lithology sedimentation, In: Geophysical Research Abstracts, vol. 12, European Geoscience Union, Copernicus GmbH, 2010.

B. F. Nielsen, X. Cai, J. Sundnes, and A. Tveito. Towards a computational method for imaging the extracellular potassium concentration during regional ischemia, Mathematical Biosciences 220(2):118-130, 2009.

J. Zhu, X. Cai, and J. T.-C. Yeh. Analysis of Tracer Tomography Using Temporal Moments of Tracer Breakthrough Curves, Advances in Water Resources 32(3):391-400, 2009.

S. R. Clark, A. M. Bruaset, T. O. Sømme, and T. M. Løseth. A Flexible Stochastic Approach to Constraining Uncertainty in Forward Stratigraphic Models, In: 18th World IMACS Congress and MODSIM09 International Congress on Modelling and Simulation, ed. by Anderssen, R.S. and Braddock, R.D. and Newham, L.T.H., Modelling and Simulation Society of Australia and New Zealand and International Association for Mathematics and Computers in Simulation, 2009.

P. Li, W. Wei, X. Cai, C. Soeller, M. Cannell, and A. V. Holden. Evolution of Intracellular Ca2+ Waves from about 10,000 RyR Clusters: Towards Solving a Computationally Daunting Task, In: Proceedings of Fifth International Conference on Functional Imaging and Modeling of the Heart, ed. by Ayache, Nicholas and Delingette, Hervé and Sermesant, Maxime, pp. 11-20, Springer. Lecture Notes in Computer Science, vol. 5528, 2009.

H. Osnes, S. R. Clark, and J. Sundnes. Uncertainty analysis of the mechanics of the heart, In: Proceedings of the Twenty Second Nordic Seminar on Computational Mechanics, ed. by Damkilde, L. and Andersen, L. and Kristensen, A.S. and Lund, E. , chap. 245-248, Aalborg University. Department of Civil Engineering. DCE Technical Memorandum, 2009.

A. Logg, H. P. Langtangen, and X. Cai. Past and Future Perspectives on Scientific Software, In: Simula Research Laboratory - by thinking constantly about it, ed. by Tveito, Aslak and Bruaset, Are Magnus and Lysne, Olav . Springer, Heidelberg, chap. 23, pp. 321--362, 2009.

A. Schroll. Mathematical Modeling, SDU Science Day, 2009.