Numerical simulation of real-world phenomena provides fertile ground for building interdisciplinary relationships. The SCI Institute has a long tradition of building these relationships in a win-win fashion – a win for the theoretical and algorithmic development of numerical modeling and simulation techniques and a win for the discipline-specific science of interest. High-order and adaptive methods, uncertainty quantification, complexity analysis, and parallelization are just some of the topics being investigated by SCI faculty. These areas of computing are being applied to a wide variety of engineering applications ranging from fluid mechanics and solid mechanics to bioelectricity.
CIBC. Note: BioImage: A SCIRun Power App for processing and visualizing medical image volumes. Scientific Computing and Imaging Institute (SCI), Download from: http://www.scirun.org, 2014. |
Scalable large-scale fluid–structure interaction solvers in the Uintah framework via hybrid task-based parallelism algorithms Q. Meng, M. Berzins. In Concurrency and Computation: Practice and Experience, 2013. DOI: 10.1002/cpe Uintah is a software framework that provides an environment for solving fluid–structure interaction problems on structured adaptive grids for large-scale science and engineering problems involving the solution of partial differential equations. Uintah uses a combination of fluid flow solvers and particle-based methods for solids, together with adaptive meshing and a novel asynchronous task-based approach with fully automated load balancing. When applying Uintah to fluid–structure interaction problems, the combination of adaptive mesh- ing and the movement of structures through space present a formidable challenge in terms of achieving scalability on large-scale parallel computers. The Uintah approach to the growth of the number of core counts per socket together with the prospect of less memory per core is to adopt a model that uses MPI to communicate between nodes and a shared memory model on-node so as to achieve scalability on large-scale systems. For this approach to be successful, it is necessary to design data structures that large numbers of cores can simultaneously access without contention. This scalability challenge is addressed here for Uintah, by the development of new hybrid runtime and scheduling algorithms combined with novel lock-free data structures, making it possible for Uintah to achieve excellent scalability for a challenging fluid–structure problem with mesh refinement on as many as 260K cores. |
Data and Range-Bounded Polynomials in ENO Methods M. Berzins. In Journal of Computational Science, Vol. 4, No. 1-2, pp. 62--70. 2013. DOI: 10.1016/j.jocs.2012.04.006 Essentially Non-Oscillatory (ENO) methods and Weighted Essentially Non-Oscillatory (WENO) methods are of fundamental importance in the numerical solution of hyperbolic equations. A key property of such equations is that the solution must remain positive or lie between bounds. A modification of the polynomials used in ENO methods to ensure that the modified polynomials are either bounded by adjacent values (data-bounded) or lie within a specified range (range-bounded) is considered. It is shown that this approach helps both in the range boundedness in the preservation of extrema in the ENO polynomial solution. |
Extreme-Scale Visual Analytics P.C. Wong, H. Shen, V. Pascucci. In IEEE Computer Graphics and Applications, Vol. 32, No. 4, pp. 23--25. 2012. DOI: 10.1109/MCG.2012.73 Extreme-scale visual analytics (VA) is about applying VA to extreme-scale data. The articles in this special issue examine advances related to extreme-scale VA problems, their analytical and computational challenges, and their real-world applications. |
Efficient data restructuring and aggregation for I/O acceleration in PIDX S. Kumar, V. Vishwanath, P. Carns, J.A. Levine, R. Latham, G. Scorzelli, H. Kolla, R. Grout, R. Ross, M.E. Papka, J. Chen, V. Pascucci. In Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis, IEEE Computer Society Press, pp. 50:1--50:11. 2012. ISBN: 978-1-4673-0804-5 Hierarchical, multiresolution data representations enable interactive analysis and visualization of large-scale simulations. One promising application of these techniques is to store high performance computing simulation output in a hierarchical Z (HZ) ordering that translates data from a Cartesian coordinate scheme to a one-dimensional array ordered by locality at different resolution levels. However, when the dimensions of the simulation data are not an even power of 2, parallel HZ ordering produces sparse memory and network access patterns that inhibit I/O performance. This work presents a new technique for parallel HZ ordering of simulation datasets that restructures simulation data into large (power of 2) blocks to facilitate efficient I/O aggregation. We perform both weak and strong scaling experiments using the S3D combustion application on both Cray-XE6 (65,536 cores) and IBM Blue Gene/P (131,072 cores) platforms. We demonstrate that data can be written in hierarchical, multiresolution format with performance competitive to that of native data-ordering methods. |
Multiscale Modeling of High Explosives for Transportation Accidents J.R. Peterson, J.C. Beckvermit, T. Harman, M. Berzins, C.A. Wight. In Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond, 2012. DOI: 10.1145/2335755.2335828 The development of a reaction model to simulate the accidental detonation of a large array of seismic boosters in a semi-truck subject to fire is considered. To test this model large scale simulations of explosions and detonations were performed by leveraging the massively parallel capabilities of the Uintah Computational Framework and the XSEDE computational resources. Computed stress profiles in bulk-scale explosive materials were validated using compaction simulations of hundred micron scale particles and found to compare favorably with experimental data. A validation study of reaction models for deflagration and detonation showed that computational grid cell sizes up to 10 mm could be used without loss of fidelity. The Uintah Computational Framework shows linear scaling up to 180K cores which combined with coarse resolution and validated models will now enable simulations of semi-truck scale transportation accidents for the first time. |
Adaptive High-Order Discontinuous Galerkin Solution of Elastohydrodynamic Lubrication Point Contact Problems H. Lu, M. Berzins, C.E. Goodyer, P.K. Jimack. In Advances in Engineering Software, Vol. 45, No. 1, pp. 313--324. 2012. DOI: 10.1016/j.advengsoft.2011.10.006 This paper describes an adaptive implementation of a high order Discontinuous Galerkin (DG) method for the solution of elastohydrodynamic lubrication (EHL) point contact problems. These problems arise when modelling the thin lubricating film between contacts which are under sufficiently high pressure that the elastic deformation of the contacting elements cannot be neglected. The governing equations are highly nonlinear and include a second order partial differential equation that is derived via the thin-film approximation. Furthermore, the problem features a free boundary, which models where cavitation occurs, and this is automatically captured as part of the solution process. The need for spatial adaptivity stems from the highly variable length scales that are present in typical solutions. Results are presented which demonstrate both the effectiveness and the limitations of the proposed adaptive algorithm. |
Dark Regions of No-Reflow on Late Gadolinium Enhancement Magnetic Resonance Imaging Result in Scar Formation After Atrial Fibrillation Ablation C.J. McGann, E.G. Kholmovski, J.J. Blauer, S. Vijayakumar, T.S. Haslam, J.E. Cates, E.V. DiBella, N.S. Burgon, B. Wilson, A.J. Alexander, M.W. Prastawa, M. Daccarett, G. Vergara, N.W. Akoum, D.L. Parker, R.S. MacLeod, N.F. Marrouche. In Journal of the American College of Cardiology, Vol. 58, No. 2, pp. 177--185. 2011. DOI: 10.1016/j.jacc.2011.04.008 PubMed ID: 21718914 Objectives: The aim of this study was to assess acute ablation injuries seen on late gadolinium enhancement (LGE) magnetic resonance imaging (MRI) immediately post-ablation (IPA) and the association with permanent scar 3 months post-ablation (3moPA). Background: Success rates for atrial fibrillation catheter ablation vary significantly, in part because of limited information about the location, extent, and permanence of ablation injury at the time of procedure. Although the amount of scar on LGE MRI months after ablation correlates with procedure outcomes, early imaging predictors of scar remain elusive. Methods: Thirty-seven patients presenting for atrial fibrillation ablation underwent high-resolution MRI with a 3-dimensional LGE sequence before ablation, IPA, and 3moPA using a 3-T scanner. The acute left atrial wall injuries on IPA scans were categorized as hyperenhancing (HE) or nonenhancing (NE) and compared with scar 3moPA. Results: Heterogeneous injuries with HE and NE regions were identified in all patients. Dark NE regions in the left atrial wall on LGE MRI demonstrate findings similar to the "no-reflow" phenomenon. Although the left atrial wall showed similar amounts of HE, NE, and normal tissue IPA (37.7 ± 13%, 34.3 ± 14%, and 28.0 ± 11%, respectively; p = NS), registration of IPA injuries with 3moPA scarring demonstrated that 59.0 ± 19% of scar resulted from NE tissue, 30.6 ± 15% from HE tissue, and 10.4 ± 5% from tissue identified as normal. Paired t-test comparisons were all statistically significant among NE, HE, and normal tissue types (p less than 0.001). Arrhythmia recurrence at 1-year follow-up correlated with the degree of wall enhancement 3moPA (p = 0.02). Conclusion: Radiofrequency ablation results in heterogeneous injury on LGE MRI with both HE and NE wall lesions. The NE lesions demonstrate no-reflow characteristics and reveal a better predictor of final scar at 3 months. Scar correlates with procedure outcomes, further highlighting the importance of early scar prediction. (J Am Coll Cardiol 2011;58:177–85) © 2011 by the American College of Cardiology Foundation |