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
TOD-Tree: Task-Overlapped Direct send Tree Image Compositing for Hybrid MPI Parallelism|
A. V. P. Grosset, M. Prasad, C. Christensen, A. Knoll, C. Hansen. In Eurographics Symposium on Parallel Graphics and Visualization (2015), Edited by C. Dachsbacher, P. Navrátil, 2015.
Modern supercomputers have very powerful multi-core CPUs. The programming model on these supercomputer is switching from pure MPI to MPI for inter-node communication, and shared memory and threads for intra-node communication. Consequently the bottleneck in most systems is no longer computation but communication between nodes. In this paper, we present a new compositing algorithm for hybrid MPI parallelism that focuses on communication avoidance and overlapping communication with computation at the expense of evenly balancing the workload. The algorithm has three stages: a direct send stage where nodes are arranged in groups and exchange regions of an image, 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, show strong scaling results and explain how we generally achieve better performance than these two algorithms.
An inter-model comparison of three computation fluid dynamics techniques for step-up and step-down street canyon flows|
R. Stoll, E. Pardyjak, J.J. Kim, T. Harman, A.N. Hayati. In ASME FEDSM/ICNMM symposium on urban fluid mechanics, August, 2014.
Computational Determination of the Modified Vortex Shedding Frequency for a Rigid, Truncated, Wall-Mounted Cylinder in Cross Flow|
A. Faucett, T. Harman, T. Ameel. In Volume 10: Micro- and Nano-Systems Engineering and Packaging, Montreal, ASME International Mechanical Engineering Congress and Exposition (IMECE), International Conference on Computational Science, November, 2014.
Data-Parallel Halo Finding with Variable Linking Lengths|
W. Widanagamaachchi, P.-T. Bremer, C. Sewell, L.-T. Lo; J. Ahrens, V. Pascucci. In Proceedings of the 2014 IEEE 4th Symposium on Large Data Analysis and Visualization (LDAV), pp. 27--34. November, 2014.
State-of-the-art cosmological simulations regularly contain billions of particles, providing scientists the opportunity to study the evolution of the Universe in great detail. However, the rate at which these simulations generate data severely taxes existing analysis techniques. Therefore, developing new scalable alternatives is essential for continued scientific progress. Here, we present a dataparallel, friends-of-friends halo finding algorithm that provides unprecedented flexibility in the analysis by extracting multiple linking lengths. Even for a single linking length, it is as fast as the existing techniques, and is portable to multi-threaded many-core systems as well as co-processing resources. Our system is implemented using PISTON and is coupled to an interactive analysis environment used to study halos at different linking lengths and track their evolution over time.
In-situ feature extraction of large scale combustion simulations using segmented merge trees|
A.G. Landge, V. Pascucci, A. Gyulassy, J.C. Bennett, H. Kolla, J. Chen, P.-T. Bremer. In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC 2014), New Orleans, Louisana, IEEE Press, Piscataway, NJ, USA pp. 1020--1031. 2014.
The ever increasing amount of data generated by scientific simulations coupled with system I/O constraints are fueling a need for in-situ analysis techniques. Of particular interest are approaches that produce reduced data representations while maintaining the ability to redefine, extract, and study features in a post-process to obtain scientific insights.
Efficient I/O and storage of adaptive-resolution data|
S. Kumar, J. Edwards, P.-T. Bremer, A. Knoll, C. Christensen, V. Vishwanath, P. Carns, J.A. Schmidt, V. Pascucci. In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, IEEE Press, pp. 413--423. 2014.
We present an efficient, flexible, adaptive-resolution I/O framework that is suitable for both uniform and Adaptive Mesh Refinement (AMR) simulations. In an AMR setting, current solutions typically represent each resolution level as an independent grid which often results in inefficient storage and performance. Our technique coalesces domain data into a unified, multiresolution representation with fast, spatially aggregated I/O. Furthermore, our framework easily extends to importance-driven storage of uniform grids, for example, by storing regions of interest at full resolution and nonessential regions at lower resolution for visualization or analysis. Our framework, which is an extension of the PIDX framework, achieves state of the art disk usage and I/O performance regardless of resolution of the data, regions of interest, and the number of processes that generated the data. We demonstrate the scalability and efficiency of our framework using the Uintah and S3D large-scale combustion codes on the Mira and Edison supercomputers.
Visual Exploration of High-Dimensional Data: Subspace Analysis through Dynamic Projections|
SCI Technical Report, Shusen Liu, Bei Wang, J.J. Thiagarajan, P.-T. Bremer, V. Pascucci. No. UUSCI-2014-003, SCI Institute, University of Utah, 2014.
Understanding high-dimensional data is rapidly becoming a central challenge in many areas of science and engineering. Most current techniques either rely on manifold learning based techniques which typically create a single embedding of the data or on subspace selection to find subsets of the original attributes that highlight the structure. However, the former creates a single, difficult-to-interpret view and assumes the data to be drawn from a single manifold, while the latter is limited to axis-aligned projections with restrictive viewing angles. Instead, we introduce ideas based on subspace clustering that can faithfully represent more complex data than the axis-aligned projections, yet do not assume the data to lie on a single manifold. In particular, subspace clustering assumes that the data can be represented by a union of low-dimensional subspaces, which can subsequently be used for analysis and visualization. In this paper, we introduce new techniques to reliably estimate both the intrinsic dimension and the linear basis of a mixture of subspaces extracted through subspace clustering. We show that the resulting bases represent the high-dimensional structures more reliably than traditional approaches. Subsequently, we use the bases to define different “viewpoints”, i.e., different projections onto pairs of basis vectors, from which to visualize the data. While more intuitive than non-linear projections, interpreting linear subspaces in terms of the original dimensions can still be challenging. To address this problem, we present new, animated transitions between different views to help the user navigate and explore the high-dimensional space. More specifically, we introduce the view transition graph which contains nodes for each subspace viewpoint and edges for potential transition between views. The transition graph enables users to explore both the structure within a subspace and the relations between different subspaces, for better understanding of the data. Using a number of case studies on well-know reference datasets, we demonstrate that the interactive exploration through such dynamic projections provides additional insights not readily available from existing tools.
Keywords: High-dimensional data, Subspace, Dynamic projection
Systematic Debugging of Concurrent Systems Using Coalesced Stack Trace Graphs|
D.C.B. de Oliveira, A. Humphrey, Q. Meng, Z. Rakamaric, M. Berzins, G. Gopalakrishnan. In Proceedings of the 27th International Workshop on Languages and Compilers for Parallel Computing (LCPC), September, 2014.
A central need during software development of large-scale parallel systems is tools that help help to identify the root causes of bugs quickly. Given the massive scale of these systems, tools that highlight changes--say introduced across software versions or their operating conditions (e.g., inputs, schedules)--can prove to be highly effective in practice. Conventional debuggers, while good at presenting details at the problem-site (e.g., crash), often omit contextual information to identify the root causes of the bug. We present a new approach to collect and coalesce stack traces, leading to an efficient summary display of salient system control flow differences in a graphical form called Coalesced Stack Trace Graphs (CSTG). CSTGs have helped us understand and debug situations within a computational framework called Uintah that has been deployed at large scale, and undergoes frequent version updates. In this paper, we detail CSTGs through case studies in the context of Uintah where unexpected behaviors caused by different vesions of software or occurring across different time-steps of a system (e.g., due to non-determinism) are debugged. We show that CSTG also gives conventional debuggers a far more productive and guided role to play.
Distortion-Guided Structure-Driven Interactive Exploration of High-Dimensional Data|
S. Liu, Bei Wang, P.-T. Bremer, V. Pascucci. In Computer Graphics Forum, Vol. 33, No. 3, Wiley-Blackwell, pp. 101--110. June, 2014.
Dimension reduction techniques are essential for feature selection and feature extraction of complex high-dimensional data. These techniques, which construct low-dimensional representations of data, are typically geometrically motivated, computationally efficient and approximately preserve certain structural properties of the data. However, they are often used as black box solutions in data exploration and their results can be difficult to interpret. To assess the quality of these results, quality measures, such as co-ranking [ LV09 ], have been proposed to quantify structural distortions that occur between high-dimensional and low-dimensional data representations. Such measures could be evaluated and visualized point-wise to further highlight erroneous regions [ MLGH13 ]. In this work, we provide an interactive visualization framework for exploring high-dimensional data via its two-dimensional embeddings obtained from dimension reduction, using a rich set of user interactions. We ask the following question: what new insights do we obtain regarding the structure of the data, with interactive manipulations of its embeddings in the visual space? We augment the two-dimensional embeddings with structural abstrac- tions obtained from hierarchical clusterings, to help users navigate and manipulate subsets of the data. We use point-wise distortion measures to highlight interesting regions in the domain, and further to guide our selection of the appropriate level of clusterings that are aligned with the regions of interest. Under the static setting, point-wise distortions indicate the level of structural uncertainty within the embeddings. Under the dynamic setting, on-the-fly updates of point-wise distortions due to data movement and data deletion reflect structural relations among different parts of the data, which may lead to new and valuable insights.