Mapping unstructured grid problems to the connection machine

We present a highly parallel graph mapping technique that enables one to solve unstructured grid problems on massively parallel computers. Many implicit and explicit methods for solving discretizated partial differential equations require each point in the discretization to exchange data with its neighboring points every time step or iteration. The time spent communicating can limit the high performance promised by massively parallel computing. To eliminate this bottleneck, we map the graph of the irregular problem to the graph representing the interconnection topology of the computer such that the sum of the distances that the messages travel is minimized. We show that, in comparison to a naive assignment of processors, our heuristic mapping algorithm significantly reduces the communication time on the Connection Machine, CM-2

Efficient ICCG on a shared memory multiprocessor

Different approaches are discussed for exploiting parallelism in the ICCG (Incomplete Cholesky Conjugate Gradient) method for solving large sparse symmetric positive definite systems of equations on a shared memory parallel computer. Techniques for efficiently solving triangular systems and computing sparse matrix-vector products are explored. Three methods for scheduling the tasks in solving triangular systems are implemented on the Sequent Balance 21000. Sample problems that are representative of a large class of problems solved using iterative methods are used. We show that a static analysis to determine data dependences in the triangular solve can greatly improve its parallel efficiency. We also show that ignoring symmetry and storing the whole matrix can reduce solution time substantially

Robustness of fossil fish teeth for seawater neodymium isotope reconstructions under variable redox conditions in an ancient shallow marine setting

Fossil fish teeth from pelagic open ocean settings are considered a robust archive for preserving the neodymium (Nd) isotopic composition of ancient seawater. However, using fossil fish teeth as an archive to reconstruct seawater Nd isotopic compositions in different sedimentary redox environments and in terrigenous‐dominated, shallow marine settings is less proven. To address these uncertainties, fish tooth and sediment samples from a middle Eocene section deposited proximal to the East Antarctic margin at Integrated Ocean Drilling Program Site U1356 were analyzed for major and trace element geochemistry, and Nd isotopes. Major and trace element analyses of the sediments reveal changing redox conditions throughout deposition in a shallow marine environment. However, variations in the Nd isotopic composition and rare earth element (REE) patterns of the associated fish teeth do not correspond to redox changes in the sediments. REE patterns in fish teeth at Site U1356 carry a typical mid‐REE‐enriched signature. However, a consistently positive Ce anomaly marks a deviation from a pure authigenic origin of REEs to the fish tooth. Neodymium isotopic compositions of cleaned and uncleaned fish teeth fall between modern seawater and local sediments and hence could be authigenic in nature, but could also be influenced by sedimentary fluxes. We conclude that the fossil fish tooth Nd isotope proxy is not sensitive to moderate changes in pore water oxygenation. However, combined studies on sediments, pore waters, fish teeth, and seawater are needed to fully understand processes driving the reconstructed signature from shallow marine sections in proximity to continental sources

A High Stability Optical Shadow Sensor with Applications for Precision Accelerometers

Gravimeters are devices which measure changes in the value of the gravitational acceleration, \textit{g}. This information is used to infer changes in density under the ground allowing the detection of subsurface voids; mineral, oil and gas reserves; and even the detection of the precursors of volcanic eruptions. A micro-electro mechanical system (MEMS) gravimeter has been fabricated completely in silicon allowing the possibility of cost e-effective, lightweight and small gravimeters. To obtain a measurement of gravity, a highly stable displacement measurement of the MEMS is required. This requires the development of a portable electronics system that has a displacement sensitivity of $\leq 2.5$ nm over a period of a day or more. The portable electronics system presented here has a displacement sensitivity $\leq 10$ nm$/\sqrt{\textrm{Hz}}$ ($\leq 0.6$ nm at $1000$ s). The battery power system used a modulated LED for measurements and required temperature control of the system to $\pm$ 2 mK, monitoring of the tilt to $\pm$ 2 $\mu$radians, the storage of measured data and the transmission of the data to an external server.Comment: 8 Pages, 12 figures, 5 equations, currently submitted and under review at IEEE Sensors SIE

Effect of matching uncertainty on population parameter estimation in mark-recapture analysis of photo-identification data

Thanks also to the SeaDoc Society, Molly and John Bailey, the Richardson family, Sarah Haney (Canadian Whale Institute), National Geographic, and Beto Bedolfe at the Marisla Foundation for financial support over the years, and to The Willow Grove Foundation for supporting the Knight Inlet expedition that made 2010 so productive. Erin thanks Air Canada’s Aeroplan Beyond Miles program for travel support. Erin was a beneficiary of a writing retreat for women in science supported by Lyda Hill Philanthropies and the National Geographic Explorers Program.Quantifying and dealing with uncertainty are key aspects of ecological studies. Population parameter estimation from mark-recapture analyses of photo-identification data hinges on correctly matching individuals from photographs and assumes that identifications are detected with certainty, marks are not lost over time, and that individuals are recognised when they are resighted. Matching photographs is an inherently subjective process. Traditionally, two photographs are not considered a “match” unless the photo reviewer is 100% certain. This decision may carry implications with respect to sample size and the bias and precision of the resultant parameter estimates. Here, we present results from a photo-identification experiment on Pacific white-sided dolphins to assign one of three levels of certainty that a pair of photographs represented a match. We then illustrate how estimates of abundance and survival varied as a function of the matching certainty threshold used. As expected, requiring 100% certainty of a match resulted in fewer matches, which in turn led to higher estimates of abundance and lower estimates of survival than if a lower threshold were used to determine a match. The tradition to score two photographs as a match only when the photo reviewer is 100% certain stems from a desire to be conservative, but potential over-estimation of abundance means that there may be applications (e.g., assessing sustainability of bycatch) in which it is not precautionary. We recommend exploring the consequences of matching uncertainty and incorporating that uncertainty into the resulting estimates of abundance and survival.Publisher PDFPeer reviewe

On the acceleration of wavefront applications using distributed many-core architectures

In this paper we investigate the use of distributed graphics processing unit (GPU)-based architectures to accelerate pipelined wavefront applications—a ubiquitous class of parallel algorithms used for the solution of a number of scientific and engineering applications. Specifically, we employ a recently developed port of the LU solver (from the NAS Parallel Benchmark suite) to investigate the performance of these algorithms on high-performance computing solutions from NVIDIA (Tesla C1060 and C2050) as well as on traditional clusters (AMD/InfiniBand and IBM BlueGene/P). Benchmark results are presented for problem classes A to C and a recently developed performance model is used to provide projections for problem classes D and E, the latter of which represents a billion-cell problem. Our results demonstrate that while the theoretical performance of GPU solutions will far exceed those of many traditional technologies, the sustained application performance is currently comparable for scientific wavefront applications. Finally, a breakdown of the GPU solution is conducted, exposing PCIe overheads and decomposition constraints. A new k-blocking strategy is proposed to improve the future performance of this class of algorithm on GPU-based architectures

An investigation of the performance portability of OpenCL

This paper reports on the development of an MPI/OpenCL implementation of LU, an application-level benchmark from the NAS Parallel Benchmark Suite. An account of the design decisions addressed during the development of this code is presented, demonstrating the importance of memory arrangement and work-item/work-group distribution strategies when applications are deployed on different device types. The resulting platform-agnostic, single source application is benchmarked on a number of different architectures, and is shown to be 1.3–1.5× slower than native FORTRAN 77 or CUDA implementations on a single node and 1.3–3.1× slower on multiple nodes. We also explore the potential performance gains of OpenCL’s device fissioning capability, demonstrating up to a 3× speed-up over our original OpenCL implementation

Eigenvalue Spacing Distribution for the Ensemble of Real Symmetric Toeplitz Matrices

Consider the ensemble of Real Symmetric Toeplitz Matrices, each entry iidrv from a fixed probability distribution p of mean 0, variance 1, and finite higher moments. The limiting spectral measure (the density of normalized eigenvalues) converges weakly to a new universal distribution with unbounded support, independent of p. This distribution's moments are almost those of the Gaussian's; the deficit may be interpreted in terms of Diophantine obstructions. With a little more work, we obtain almost sure convergence. An investigation of spacings between adjacent normalized eigenvalues looks Poissonian, and not GOE.Comment: 24 pages, 3 figure