Comparison of MPI benchmark programs on shared memory and distributed memory machines (point-to-point communication)

There are several benchmark programs available to measure the performance of MPI on parallel computers. The most common use of MPI benchmarks software are SKaMPI, Pallas MPI Benchmark, MPBench, Mpptest and MPIBench. It is interesting to analyze the differences between different benchmark. Presently, there have been few comparisons done between the different benchmarks. Thus, in this paper we discuss a comparison of the techniques used and the functionality of each benchmark, and also a comparison of the results on a distributed memory machine and shared memory machine for point-to-point communication. All of the MPI benchmarks listed above will be compared in this analysis. It is expected that the results from different benchmarks should be similar, however this analysis found substantial differences in the results for certain MPI communications, particularly for shared memory machines

Random Number Generators for Parallel Computers

Random number generators are used in many applications, from slot machines to simulations of nuclear reactors. For many computational science applications, such as Monte Carlo simulation, it is crucial that the generators have good randomness properties. This is particularly true for large-scale simulations done on high-performance parallel computers. Good random number generators are hard to find, and many widely-used techniques have been shown to be inadequate. Finding high-quality, efficient algorithms for random number generation on parallel computers is even more difficult. Here we present a review of the most commonly-used random number generators for parallel computers, and evaluate each generator based on theoretical knowledge and empirical tests. In conclusion, we provide recommendations for using random number generators on parallel computers

Strings with Extrinsic Curvature: An Analysis of the Crossover Regime

We present the results of a set of Monte Carlo simulations of Dynamically Triangulated Random Surfaces embedded in three dimensions with an extrinsic curvature dependent action. We analyze several observables in the crossover regime and discuss whether or not our observations are indicative of the presence of a phase transition.Comment: (Contribution to Lattice 92 Proceedings.) Latex file (5 pages), requires espcrc2.sty. 2 figures not included. Syracuse preprint SU-HEP-4241-52

Global Genome Biodiversity Network:saving a blueprint of the Tree of Life - a botanical perspective

Background Genomic research depends upon access to DNA or tissue collected and preserved according to high-quality standards. At present, the collections in most natural history museums do not sufficiently address these standards, making them often hard or impossible to use for whole-genome sequencing or transcriptomics. In response to these challenges, natural history museums, herbaria, botanical gardens and other stakeholders have started to build high-quality biodiversity biobanks. Unfortunately, information about these collections remains fragmented, scattered and largely inaccessible. Without a central registry or even an overview of relevant institutions, it is difficult and time-consuming to locate the needed samples. Scope The Global Genome Biodiversity Network (GGBN) was created to fill this vacuum by establishing a one-stop access point for locating samples meeting quality standards for genome-scale applications, while complying with national and international legislations and conventions. Increased accessibility to genomic samples will further genomic research and development, conserve genetic resources, help train the next generation of genome researchers and raise the visibility of biodiversity collections. Additionally, the availability of a data-sharing platform will facilitate identification of gaps in the collections, thereby empowering targeted sampling efforts, increasing the breadth and depth of preservation of genetic diversity. The GGBN is rapidly growing and currently has 41 members. The GGBN covers all branches of the Tree of Life, except humans, but here the focus is on a pilot project with emphasis on ‘harvesting’ the Tree of Life for vascular plant taxa to enable genome-level studies. Conclusion While current efforts are centred on getting the existing samples of all GGBN members online, a pilot project, GGI-Gardens, has been launched as proof of concept. Over the next 6 years GGI-Gardens aims to add to the GGBN high-quality genetic material from at least one species from each of the approx. 460 vascular plant families and one species from half of the approx. 15 000 vascular plant genera

The Global Genome Biodiversity Network (GGBN) Data Portal

The Author(s) 2013. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact [email protected] The attached file is the published pdf

Pseudospectral Calculation of Helium Wave Functions, Expectation Values, and Oscillator Strength

The pseudospectral method is a powerful tool for finding highly precise solutions of Schr\"{o}dinger's equation for few-electron problems. We extend the method's scope to wave functions with non-zero angular momentum and test it on several challenging problems. One group of tests involves the determination of the nonrelativistic electric dipole oscillator strength for the helium $1^1$S $\to 2^1$P transition. The result achieved, $0.27616499(27)$, is comparable to the best in the literature. Another group of test applications is comprised of well-studied leading order finite nuclear mass and relativistic corrections for the helium ground state. A straightforward computation reaches near state-of-the-art accuracy without requiring the implementation of any special-purpose numerics. All the relevant quantities tested in this paper -- energy eigenvalues, S-state expectation values and bound-bound dipole transitions for S and P states -- converge exponentially with increasing resolution and do so at roughly the same rate. Each individual calculation samples and weights the configuration space wave function uniquely but all behave in a qualitatively similar manner. Quantum mechanical matrix elements are directly and reliably calculable with pseudospectral methods. The technical discussion includes a prescription for choosing coordinates and subdomains to achieve exponential convergence when two-particle Coulomb singularities are present. The prescription does not account for the wave function's non-analytic behavior near the three-particle coalescence which should eventually hinder the rate of the convergence. Nonetheless the effect is small in the sense that ignoring the higher-order coalescence does not appear to affect adversely the accuracy of any of the quantities reported nor the rate at which errors diminish.Comment: 24 pages, 12 figures, 6 tables. To be submitted to Physical Review A. LANL identifier 'LA-UR-11-10986

The Phase Diagram of Fluid Random Surfaces with Extrinsic Curvature

We present the results of a large-scale simulation of a Dynamically Triangulated Random Surface with extrinsic curvature embedded in three-dimensional flat space. We measure a variety of local observables and use a finite size scaling analysis to characterize as much as possible the regime of crossover from crumpled to smooth surfaces.Comment: 29 pages. There are also 19 figures available from the authors but not included here - sorr