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Ensemble Grouping Strategies for Embedded Stochastic Collocation Methods Applied to Anisotropic Diffusion Problems

SIAM/ASA Journal on Uncertainty Quantification

D'Elia, Marta D.; Phipps, Eric T.; Edwards, Harold C.; Hu, Jonathan J.; Rajamanickam, Sivasankaran R.

Previous work has demonstrated that propagating groups of samples, called ensembles, together through forward simulations can dramatically reduce the aggregate cost of sampling-based uncertainty propagation methods [E. Phipps, M. D'Elia, H. C. Edwards, M. Hoemmen, J. Hu, and S. Rajamanickam, SIAM J. Sci. Comput., 39 (2017), pp. C162--C193]. However, critical to the success of this approach when applied to challenging problems of scientific interest is the grouping of samples into ensembles to minimize the total computational work. For example, the total number of linear solver iterations for ensemble systems may be strongly influenced by which samples form the ensemble when applying iterative linear solvers to parameterized and stochastic linear systems. In this paper we explore sample grouping strategies for local adaptive stochastic collocation methods applied to PDEs with uncertain input data, in particular canonical anisotropic diffusion problems where the diffusion coefficient is modeled by truncated Karhunen--Loève expansions. Finally, we demonstrate that a measure of the total anisotropy of the diffusion coefficient is a good surrogate for the number of linear solver iterations for each sample and therefore provides a simple and effective metric for grouping samples.

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TYPE Journal Article YEAR 2018
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Ensemble grouping strategies for embedded stochastic collocation methods applied to anisotropic diffusion problems

SIAM-ASA Journal on Uncertainty Quantification

D'Elia, Marta D.; Edwards, Harold C.; Hu, J.; Phipps, Eric T.; Rajamanickam, Sivasankaran R.

Previous work has demonstrated that propagating groups of samples, called ensembles, together through forward simulations can dramatically reduce the aggregate cost of sampling-based uncertainty propagation methods [E. Phipps, M. D'Elia, H. C. Edwards, M. Hoemmen, J. Hu, and S. Rajamanickam, SIAM J. Sci. Comput., 39 (2017), pp. C162-C193]. However, critical to the success of this approach when applied to challenging problems of scientific interest is the grouping of samples into ensembles to minimize the total computational work. For example, the total number of linear solver iterations for ensemble systems may be strongly influenced by which samples form the ensemble when applying iterative linear solvers to parameterized and stochastic linear systems. In this work we explore sample grouping strategies for local adaptive stochastic collocation methods applied to PDEs with uncertain input data, in particular canonical anisotropic diffusion problems where the diffusion coefficient is modeled by truncated Karhunen-Loève expansions. We demonstrate that a measure of the total anisotropy of the diffusion coefficient is a good surrogate for the number of linear solver iterations for each sample and therefore provides a simple and effective metric for grouping samples.

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TYPE Conference Poster YEAR 2018
ScopusOSTI

Trends in Data Locality Abstractions for HPC Systems

IEEE Transactions on Parallel and Distributed Systems

Unat, Didem; Dubey, Anshu; Hoefler, Torsten; Shalf, John B.; Abraham, Mark; Bianco, Mauro; Chamberlain, Bradford L.; Cledat, Romain; Edwards, Harold C.; Finkel, Hal; Fuerlinger, Karl; Hannig, Frank; Jeannot, Emmanuel; Kamil, Amir; Keasler, Jeff; Kelly, Paul H.J.; Leung, Vitus J.; Ltaief, Hatem; Maruyama, Naoya; Newburn, Chris J.; Pericas, Miquel

The cost of data movement has always been an important concern in high performance computing (HPC) systems. It has now become the dominant factor in terms of both energy consumption and performance. Support for expression of data locality has been explored in the past, but those efforts have had only modest success in being adopted in HPC applications for various reasons. them However, with the increasing complexity of the memory hierarchy and higher parallelism in emerging HPC systems, locality management has acquired a new urgency. Developers can no longer limit themselves to low-level solutions and ignore the potential for productivity and performance portability obtained by using locality abstractions. Fortunately, the trend emerging in recent literature on the topic alleviates many of the concerns that got in the way of their adoption by application developers. Data locality abstractions are available in the forms of libraries, data structures, languages and runtime systems; a common theme is increasing productivity without sacrificing performance. This paper examines these trends and identifies commonalities that can combine various locality concepts to develop a comprehensive approach to expressing and managing data locality on future large-scale high-performance computing systems.

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TYPE Journal Article YEAR 2017
ScopusOSTIDOI

Kokkos' Task DAG Capabilities

Edwards, Harold C.; Ibanez-Granados, Daniel A.

This report documents the ASC/ATDM Kokkos deliverable "Production Portable Dy- namic Task DAG Capability." This capability enables applications to create and execute a dynamic task DAG ; a collection of heterogeneous computational tasks with a directed acyclic graph (DAG) of "execute after" dependencies where tasks and their dependencies are dynamically created and destroyed as tasks execute. The Kokkos task scheduler executes the dynamic task DAG on the target execution resource; e.g. a multicore CPU, a manycore CPU such as Intel's Knights Landing (KNL), or an NVIDIA GPU. Several major technical challenges had to be addressed during development of Kokkos' Task DAG capability: (1) portability to a GPU with it's simplified hardware and micro- runtime, (2) thread-scalable memory allocation and deallocation from a bounded pool of memory, (3) thread-scalable scheduler for dynamic task DAG, (4) usability by applications.

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TYPE SAND Report YEAR 2017
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Embedded ensemble propagation for improving performance, portability, and scalability of uncertainty quantification on emerging computational architectures

SIAM Journal on Scientific Computing

Phipps, Eric T.; D'Elia, Marta D.; Edwards, Harold C.; Hoemmen, M.; Hu, J.; Rajamanickam, Sivasankaran R.

Quantifying simulation uncertainties is a critical component of rigorous predictive simulation. A key component of this is forward propagation of uncertainties in simulation input data to output quantities of interest. Typical approaches involve repeated sampling of the simulation over the uncertain input data and can require numerous samples when accurately propagating uncertainties from large numbers of sources. Often simulation processes from sample to sample are similar, and much of the data generated from each sample evaluation could be reused. We explore a new method for implementing sampling methods that simultaneously propagates groups of samples together in an embedded fashion, which we call embedded ensemble propagation. We show how this approach takes advantage of properties of modern computer architectures to improve performance by enabling reuse between samples, reducing memory bandwidth requirements, improving memory access patterns, improving opportunities for fine-grained parallelization, and reducing communication costs. We describe a software technique for implementing embedded ensemble propagation based on the use of C++ templates and describe its integration with various scientific computing libraries within Trilinos. We demonstrate improved performance, portability, and scalability for the approach applied to the simulation of partial differential equations on a variety of multicore and manycore architectures, including up to 16,384 cores on a Cray XK7 (Titan).

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TYPE Journal Article YEAR 2017
ScopusOSTIDOI

Kokkos/Qthreads task-parallel approach to linear algebra based graph analytics

2016 IEEE High Performance Extreme Computing Conference, HPEC 2016

Wolf, Michael W.; Edwards, Harold C.; Olivier, Stephen L.

The Graph BLAS effort to standardize a set of graph algorithms building blocks in terms of linear algebra primitives promises to deliver high performing graph algorithms and greatly impact the analysis of big data. However, there are challenges with this approach, which our data analytics miniapp miniTri exposes. In this paper, we improve upon a previously proposed task-parallel approach to linear algebra-based miniTri formulation, addressing these challenges and describing a Kokkos/Qthreads task-parallel implementation that performs as well or slightly better than the highly optimized, baseline OpenMP data-parallel implementation.

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TYPE Conference Poster YEAR 2016
ScopusOSTIDOI

Hierarchical Task-Data Parallelism using Kokkos and Qthreads

Edwards, Harold C.; Olivier, Stephen L.; Berry, Jonathan W.; Mackey, Greg; Rajamanickam, Sivasankaran R.; Wolf, Michael W.; Kim, Kyungjoo K.; Stelle, George

This report describes a new capability for hierarchical task-data parallelism using Sandia's Kokkos and Qthreads, and evaluation of this capability with sparse matrix Cholesky factor- ization and social network triangle enumeration mini-applications. Hierarchical task-data parallelism consists of a collection of tasks with executes-after dependences where each task contains data parallel operations performed on a team of hardware threads. The collection of tasks and dependences form a directed acyclic graph of tasks - a task DAG . Major chal- lenges of this research and development effort include: portability and performance across multicore CPU; manycore Intel Xeon Phi, and NVIDIA GPU architectures; scalability with respect to hardware concurrency and size of the task DAG; and usability of the application programmer interface (API).

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TYPE SAND Report YEAR 2016
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Task Parallel Incomplete Cholesky Factorization using 2D Partitioned-Block Layout

Kim, Kyungjoo K.; Rajamanickam, Sivasankaran R.; Stelle, George; Edwards, Harold C.; Olivier, Stephen L.

We introduce a task-parallel algorithm for sparse incomplete Cholesky factorization that utilizes a 2D sparse partitioned-block layout of a matrix. Our factorization algorithm follows the idea of algorithms-by-blocks by using the block layout. The algorithm-byblocks approach induces a task graph for the factorization. These tasks are inter-related to each other through their data dependences in the factorization algorithm. To process the tasks on various manycore architectures in a portable manner, we also present a portable tasking API that incorporates different tasking backends and device-specific features using an open-source framework for manycore platforms i.e., Kokkos. A performance evaluation is presented on both Intel Sandybridge and Xeon Phi platforms for matrices from the University of Florida sparse matrix collection to illustrate merits of the proposed task-based factorization. Experimental results demonstrate that our task-parallel implementation delivers about 26.6x speedup (geometric mean) over single-threaded incomplete Choleskyby- blocks and 19.2x speedup over serial Cholesky performance which does not carry tasking overhead using 56 threads on the Intel Xeon Phi processor for sparse matrices arising from various application problems.

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TYPE Other Report YEAR 2016
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Results 1–50 of 142
Results 1–50 of 142