Special Section on Two Themes: CSE Software and Big Data in CSE|
H. De Sterck, C. Johnson,, L. C. McInnes. In SIAM J. Sci. Comput, Vol. 38, No. 5, SIAM, pp. S1--S2. 2016.
The 2015 SIAM Conference on Computational Science and Engineering (CSE) was held March 14-18, 2015, in Salt Lake City, Utah. The SIAM Journal on Scientific Computing (SISC) created this special section in association with the CSE15 conference. The special section focuses on two topics that are of significant current interest to CSE researchers: CSE software and big data in CSE.
Research and Education in Computational Science and Engineering|
Subtitled Report from a workshop sponsored by the Society for Industrial and Applied Mathematics (SIAM) and the European Exascale Software Initiative (EESI-2), U. Rüde, K. Willcox, L. C. McInnes, H. De Sterck, G. Biros, H. Bungartz, J. Corones, E. Cramer, J. Crowley, O. Ghattas, M. Gunzburger, M. Hanke, R. Harrison, M. Heroux, J. Hesthaven, P. Jimack, C. Johnson, K. E. Jordan, D. E. Keyes, R. Krause, V. Kumar, S. Mayer, J. Meza, K. M. Mørken, J. T. Oden, L. Petzold, P. Raghavan, S. M. Shontz, A. Trefethen, P. Turner, V. Voevodin, B. Wohlmuth, C. S. Woodward. Aug, 2016.
Over the past two decades the field of computational science and engineering (CSE) has penetrated both basic and applied research in academia, industry, and laboratories to advance discovery, optimize systems, support decision-makers, and educate the scientific and engineering workforce. Informed by centuries of theory and experiment, CSE performs computational experiments to answer questions that neither theory nor experiment alone is equipped to answer. CSE provides scientists and engineers of all persuasions with algorithmic inventions and software systems that transcend disciplines and scales. Carried on a wave of digital technology, CSE brings the power of parallelism to bear on troves of data. Mathematics-based advanced computing has become a prevalent means of discovery and innovation in essentially all areas of science, engineering, technology, and society; and the CSE community is at the core of this transformation. However, a combination of disruptive developments---including the architectural complexity of extreme-scale computing, the data revolution that engulfs the planet, and the specialization required to follow the applications to new frontiers---is redefining the scope and reach of the CSE endeavor. This report describes the rapid expansion of CSE and the challenges to sustaining its bold advances. The report also presents strategies and directions for CSE research and education for the next decade.
Optimizing Multi-Image Sort-Last Parallel Rendering|
M. Larsen, K. Moreland, C.R. Johnson,, H. Childs. In Symposium on Large Data Analysis and Visualization, IEEE, 2016.
Sort-last parallel rendering can be improved by considering the rendering of multiple images at a time. Most parallel rendering algorithms consider the generation of only a single image. This makes sense when performing interactive rendering where the parameters of each rendering are not known until the previous rendering completes. However, in situ visualization often generates multiple images that do not need to be created sequentially. In this paper we present a simple and effective approach to improving parallel image generation throughput by amortizing the load and overhead among multiple image renders. Additionally, we validate our approach by conducting a performance study exploring the achievable speed-ups in a variety of image-based in situ use cases and rendering workloads. On average, our approach shows a 1.5 to 3.7 fold improvement in performance, and in some cases, shows a 10 fold improvement.
Visualization for Understanding Uncertainty in Activation Volumes for Deep Brain Stimulation|
B. Hollister, G. Duffley, C. Butson,, C.R. Johnson. In Eurographics Conference on Visualization, Edited by K.L. Ma G. Santucci, and J. van Wijk, 2016.
We have created the Neurostimulation Uncertainty Viewer (nuView or nView) tool for exploring data arising from deep brain stimulation (DBS). Simulated volume of tissue activated (VTA), using clinical electrode placements, are recorded along withpatient outcomes in the Unified Parkinson's disease rating scale (UPDRS). The data is volumetric and sparse, with multi-value patient results for each activated voxel in the simulation. nView provides a collection of visual methods to explore the activated tissue to enhance understanding of electrode usage for improved therapy with DBS.
TOD-Tree: Task-Overlapped Direct send Tree Image Compositing for Hybrid MPI Parallelism and GPUs|
A. V. P. Grosset, M. Prasad, C. Christensen, A. Knoll, C. Hansen. In IEEE Transactions on Visualization and Computer Graphics, IEEE, pp. 1--1. 2016.
Modern supercomputers have thousands of nodes, each with CPUs and/or GPUs capable of several teraflops. However, the network connecting these nodes is relatively slow, on the order of gigabits per second. For time-critical workloads such as interactive visualization, the bottleneck is no longer computation but communication. In this paper, we present an image compositing algorithm that works on both CPU-only and GPU-accelerated supercomputers and focuses on communication avoidance and overlapping communication with computation at the expense of evenly balancing the workload. The algorithm has three stages: a parallel direct send stage, followed by a tree compositing stage and a gather stage. We compare our algorithm with radix-k and binary-swap from the IceT library in a hybrid OpenMP/MPI setting on the Stampede and Edison supercomputers, show strong scaling results and explain how we generally achieve better performance than these two algorithms. We developed a GPU-based image compositing algorithm where we use CUDA kernels for computation and GPU Direct RDMA for inter-node GPU communication. We tested the algorithm on the Piz Daint GPU-accelerated supercomputer and show that we achieve performance on par with CPUs. Lastly, we introduce a workflow in which both rendering and compositing are done on the GPU.
Dynamically Scheduled Region-Based Image Compositing|
A.V. P. Grosset, A. Knoll, C.D. Hansen. In Eurographics Symposium on Parallel Graphics and Visualization, June, 2016.
Algorithms for sort-last parallel volume rendering on large distributed memory machines usually divide a dataset equally across all nodes for rendering. Depending on the features that a user wants to see in a dataset, all the nodes will rarely finish rendering at the same time. Existing compositing algorithms do not often take this into consideration, which can lead to significant delays when nodes that are compositing wait for other nodes that are still rendering. In this paper, we present an image compositing algorithm that uses spatial and temporal awareness to dynamically schedule the exchange of regions in an image and progressively composite images as they become available. Running on the Edison supercomputer at NERSC, we show that a scheduler-based algorithm with awareness of the spatial contribution from each rendering node can outperform traditional image compositing algorithms.
Physical Mechanisms of DDT in an Array of PBX 9501 Cylinders Initiation Mechanisms of DDT|
J. Beckvermit, T. Harman, C. Wight, M. Berzins. SCI Institute, April, 2016.
The Deflagration to Detonation Transition (DDT) in large arrays (100s) of explosive devices is investigated using large-scale computer simulations running the Uintah Computational Framework. Our particular interest is understanding the fundamental physical mechanisms by which convective deflagration of cylindrical PBX 9501 devices can transition to a fully-developed detonation in transportation accidents. The simulations reveal two dominant mechanisms, inertial confinement and Impact to Detonation Transition. In this study we examined the role of physical spacing of the cylinders and how it influenced the initiation of DDT.
Radiative Heat Transfer Calculation on 16384 GPUs Using a Reverse Monte Carlo Ray Tracing Approach with Adaptive Mesh Refinement|
A. Humphrey, D. Sunderland, T. Harman, M. Berzins. In 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), pp. 1222-1231. May, 2016.
Modeling thermal radiation is computationally challenging in parallel due to its all-to-all physical and resulting computational connectivity, and is also the dominant mode of heat transfer in practical applications such as next-generation clean coal boilers, being modeled by the Uintah framework. However, a direct all-to-all treatment of radiation is prohibitively expensive on large computers systems whether homogeneous or heterogeneous. DOE Titan and the planned DOE Summit and Sierra machines are examples of current and emerging GPUbased heterogeneous systems where the increased processing capability of GPUs over CPUs exacerbates this problem. These systems require that computational frameworks like Uintah leverage an arbitrary number of on-node GPUs, while simultaneously utilizing thousands of GPUs within a single simulation. We show that radiative heat transfer problems can be made to scale within Uintah on heterogeneous systems through a combination of reverse Monte Carlo ray tracing (RMCRT) techniques combined with AMR, to reduce the amount of global communication. In particular, significant Uintah infrastructure changes, including a novel lock and contention-free, thread-scalable data structure for managing MPI communication requests and improved memory allocation strategies were necessary to achieve excellent strong scaling results to 16384 GPUs on Titan.
Extending the Uintah Framework through the Petascale Modeling of Detonation in Arrays of High Explosive Devices|
M. Berzins, J. Beckvermit, T. Harman, A. Bezdjian, A. Humphrey, Q. Meng, J. Schmidt,, C. Wight. In SIAM Journal on Scientific Computing (Accepted), 2016.
The Uintah framework for solving a broad class of fluid-structure interaction problems uses a layered taskgraph approach that decouples the problem specification as a set of tasks from the adaptove runtime system that executes these tasks. Uintah has been developed by using a problem-driven approach that dates back to its inception. Using this approach it is possible to improve the performance of the problem-independent software components to enable the solution of broad classes of problems as well as the driving problem itself. This process is illustrated by a motivating problem that is the computational modeling of the hazards posed by thousands of explosive devices during a Deflagration to Detonation Transition (DDT) that occurred on Highway 6 in Utah. In order to solve this complex fluid-structure interaction problem at the required scale, algorithmic and data structure improvements were needed in a code that already appeared to work well at scale. These transformations enabled scalable runs for our target problem and provided the capability to model the transition to detonation. The performance improvements achieved are shown and the solution to the target problem provides insight as to why the detonation happened, as well as to a possible remediation strategy.
Big data from scientific simulations|
J. Edwards, S. Kumar, V. Pascucci. In Big Data and High Performance Computing, Vol. 26, IOS Press, pp. 32. 2015.
Scientic simulations often generate massive amounts of data used for debugging, restarts, and scientic analysis and discovery. Challenges that practitioners face using these types of big data are unique. Of primary importance is speed of writing data during a simulation, but this need for fast I/O is at odds with other priorities, such as data access time for visualization and analysis, ecient storage, and portability across a variety of supercomputer topologies, congurations, le systems, and storage devices. The computational power of high-performance computing systems continues to increase according to Moore's law, but the same is not true for I/O subsystems, creating a performance gap between computation and I/O. This chapter explores these issues, as well as possible optimization strategies, the use of in situ analytics, and a case study using the PIDX I/O library in a typical simulation.
Approximating the Generalized Voronoi Diagram of Closely Spaced Objects|
J. Edwards, E. Daniel, V. Pascucci, C. Bajaj. In Computer Graphics Forum, Vol. 34, No. 2, Wiley-Blackwell, pp. 299-309. May, 2015.
Generalized Voronoi Diagrams (GVDs) have far-reaching applications in robotics, visualization, graphics, and simulation. However, while the ordinary Voronoi Diagram has mature and efficient algorithms for its computation, the GVD is difficult to compute in general, and in fact, has only approximation algorithms for anything but the simplest of datasets. Our work is focused on developing algorithms to compute the GVD efficiently and with bounded error on the most difficult of datasets -- those with objects that are extremely close to each other.
Paint and Click: Unified Interactions for Image Boundaries|
B. Summa, A. A. Gooch, G. Scorzelli, V. Pascucci. In Computer Graphics Forum, Vol. 34, No. 2, Wiley-Blackwell, pp. 385--393. May, 2015.
Image boundaries are a fundamental component of many interactive digital photography techniques, enabling applications such as segmentation, panoramas, and seamless image composition. Interactions for image boundaries often rely on two complementary but separate approaches: editing via painting or clicking constraints. In this work, we provide a novel, unified approach for interactive editing of pairwise image boundaries that combines the ease of painting with the direct control of constraints. Rather than a sequential coupling, this new formulation allows full use of both interactions simultaneously, giving users unprecedented flexibility for fast boundary editing. To enable this new approach, we provide technical advancements. In particular, we detail a reformulation of image boundaries as a problem of finding cycles, expanding and correcting limitations of the previous work. Our new formulation provides boundary solutions for painted regions with performance on par with state-of-the-art specialized, paint-only techniques. In addition, we provide instantaneous exploration of the boundary solution space with user constraints. Finally, we provide examples of common graphics applications impacted by our new approach.
Reducing overhead in the Uintah framework to support short-lived tasks on GPU-heterogeneous architectures|
B. Peterson, H. K. Dasari, A. Humphrey, J.C. Sutherland, T. Saad, M. Berzins. In Proceedings of the 5th International Workshop on Domain-Specific Languages and High-Level Frameworks for High Performance Computing (WOLFHPC'15), ACM, pp. 4:1-4:8. 2015.
|Developing Uintah’s Runtime System For Forthcoming Architectures,
Subtitled Refereed paper presented at the RESPA 15 Workshop at SuperComputing 2015 Austin Texas, B. Peterson, N. Xiao, J. Holmen, S. Chaganti, A. Pakki, J. Schmidt, D. Sunderland, A. Humphrey, M. Berzins. SCI Institute, 2015.
|Spectral and High Order Methods for Partial Differential Equations,
Subtitled Selected Papers from the ICOSAHOM'14 Conference, June 23-27, 2014, Salt Lake City, UT, USA., R.M. Kirby, M. Berzins, J.S. Hesthaven (Editors). In Lecture Notes in Computational Science and Engineering, Springer, 2015.
Improving Accuracy In Particle Methods Using Null Spaces and Filters|
C. Gritton, M. Berzins, R. M. Kirby. In Proceedings of the IV International Conference on Particle-Based Methods - Fundamentals and Applications, Barcelona, Spain, Edited by E. Onate and M. Bischoff and D.R.J. Owen and P. Wriggers and T. Zohdi, CIMNE, pp. 202-213. September, 2015.
While particle-in-cell type methods, such as MPM, have been very successful in providing solutions to many challenging problems there are some important issues that remain to be resolved with regard to their analysis. One such challenge relates to the difference in dimensionality between the particles and the grid points to which they are mapped. There exists a non-trivial null space of the linear operator that maps particles values onto nodal values. In other words, there are non-zero particle values values that when mapped to the nodes are zero there. Given positive mapping weights such null space values are oscillatory in nature. The null space may be viewed as a more general form of the ringing instability identified by Brackbill for PIC methods. It will be shown that it is possible to remove these null-space values from the solution and so to improve the accuracy of PIC methods, using a matrix SVD approach. The expense of doing this is prohibitive for real problems and so a local method is developed for doing this.
DOE Advanced Scientific Computing Advisory Committee (ASCAC) Report: Exascale Computing Initiative Review|
D. Reed, M. Berzins, R. Lucas, S. Matsuoka, R. Pennington, V. Sarkar, V. Taylor. Note: DOE Report, 2015.
DOI: DOI 10.2172/1222712
Fourier Series of Atomic Radial Distribution Functions: A Molecular Fingerprint for Machine Learning Models of Quantum Chemical Properties|
O. A. von Lilienfeld, R. Ramakrishanan, M., A. Knoll. In International Journal of Quantum Chemistry, Wiley Online Library, 2015.
We introduce a fingerprint representation of molecules based on a Fourier series of atomic radial distribution functions. This fingerprint is unique (except for chirality), continuous, and differentiable with respect to atomic coordinates and nuclear charges. It is invariant with respect to translation, rotation, and nuclear permutation, and requires no pre-conceived knowledge about chemical bonding, topology, or electronic orbitals. As such it meets many important criteria for a good molecular representation, suggesting its usefulness for machine learning models of molecular properties trained across chemical compound space. To assess the performance of this new descriptor we have trained machine learning models of molecular enthalpies of atomization for training sets with up to 10 k organic molecules, drawn at random from a published set of 134 k organic molecules with an average atomization enthalpy of over 1770 kcal/mol. We validate the descriptor on all remaining molecules of the 134 k set. For a training set of 10k molecules the fingerprint descriptor achieves a mean absolute error of 8.0 kcal/mol, respectively. This is slightly worse than the performance attained using the Coulomb matrix, another popular alternative, reaching 6.2 kcal/mol for the same training and test sets.
|Data Science: What Is It and How Is It Taught?,
H. De Sterck, C.R. Johnson. In SIAM News, SIAM, July, 2015.
|A Scalable Algorithm for Radiative Heat Transfer Using Reverse Monte Carlo Ray Tracing,
A. Humphrey, T. Harman, M. Berzins, P. Smith. In High Performance Computing, Lecture Notes in Computer Science, Vol. 9137, Edited by Kunkel, Julian M. and Ludwig, Thomas, Springer International Publishing, pp. 212-230. 2015.
Radiative heat transfer is an important mechanism in a class of challenging engineering and research problems. A direct all-to-all treatment of these problems is prohibitively expensive on large core counts due to pervasive all-to-all MPI communication. The massive heat transfer problem arising from the next generation of clean coal boilers being modeled by the Uintah framework has radiation as a dominant heat transfer mode. Reverse Monte Carlo ray tracing (RMCRT) can be used to solve for the radiative-flux divergence while accounting for the effects of participating media. The ray tracing approach used here replicates the geometry of the boiler on a multi-core node and then uses an all-to-all communication phase to distribute the results globally. The cost of this all-to-all is reduced by using an adaptive mesh approach in which a fine mesh is only used locally, and a coarse mesh is used elsewhere. A model for communication and computation complexity is used to predict performance of this new method. We show this model is consistent with observed results and demonstrate excellent strong scaling to 262K cores on the DOE Titan system on problem sizes that were previously computationally intractable.
Keywords: Uintah; Radiation modeling; Parallel; Scalability; Adaptive mesh refinement; Simulation science; Titan