Improving Performance of Iterative Methods by Lossy Checkponting

Iterative methods are commonly used approaches to solve large, sparse linear systems, which are fundamental operations for many modern scientific simulations. When the large-scale iterative methods are running with a large number of ranks in parallel, they have to checkpoint the dynamic variables periodically in case of unavoidable fail-stop errors, requiring fast I/O systems and large storage space. To this end, significantly reducing the checkpointing overhead is critical to improving the overall performance of iterative methods. Our contribution is fourfold. (1) We propose a novel lossy checkpointing scheme that can significantly improve the checkpointing performance of iterative methods by leveraging lossy compressors. (2) We formulate a lossy checkpointing performance model and derive theoretically an upper bound for the extra number of iterations caused by the distortion of data in lossy checkpoints, in order to guarantee the performance improvement under the lossy checkpointing scheme. (3) We analyze the impact of lossy checkpointing (i.e., extra number of iterations caused by lossy checkpointing files) for multiple types of iterative methods. (4)We evaluate the lossy checkpointing scheme with optimal checkpointing intervals on a high-performance computing environment with 2,048 cores, using a well-known scientific computation package PETSc and a state-of-the-art checkpoint/restart toolkit. Experiments show that our optimized lossy checkpointing scheme can significantly reduce the fault tolerance overhead for iterative methods by 23%~70% compared with traditional checkpointing and 20%~58% compared with lossless-compressed checkpointing, in the presence of system failures.Comment: 14 pages, 10 figures, HPDC'1

An algebraic interpretation of the Wheeler-DeWitt equation

We make a direct connection between the construction of three dimensional topological state sums from tensor categories and three dimensional quantum gravity by noting that the discrete version of the Wheeler-DeWitt equation is exactly the pentagon for the associator of the tensor category, the Biedenharn-Elliott identity. A crucial role is played by an asymptotic formula relating 6j-symbols to rotation matrices given by Edmonds.Comment: 10 pages, amstex, uses epsf.tex. New version has improved presentatio

A genome-wide investigation of the worldwide invader Sargassum muticum shows high success albeit (almost) no genetic diversity

Twenty years of genetic studies of marine invaders have shown that successful invaders are often characterized by native and introduced populations displaying similar levels of genetic diversity. This pattern is presumably due to high propagule pressure and repeated introductions. The opposite pattern is reported in this study of the brown seaweed, Sargassum muticum, an emblematic species for circumglobal invasions. Albeit demonstrating polymorphism in the native range, microsatellites failed to detect any genetic variation over 1,269 individuals sampled from 46 locations over the Pacific-Atlantic introduction range. Single-nucleotide polymorphisms (SNPs) obtained from ddRAD sequencing revealed some genetic variation, but confirmed severe founder events in both the Pacific and Atlantic introduction ranges. Our study thus exemplifies the need for extreme caution in interpreting neutral genetic diversity as a proxy for invasive potential. Our results confirm a previously hypothesized transoceanic secondary introduction from NE Pacific to Europe. However, the SNP panel unexpectedly revealed two additional distinct genetic origins of introductions. Also, conversely to scenarios based on historical records, southern rather than northern NE Pacific populations could have seeded most of the European populations. Finally, the most recently introduced populations showed the lowest selfing rates, suggesting higher levels of recombination might be beneficial at the early stage of the introduction process (i.e., facilitating evolutionary novelties), whereas uniparental reproduction might be favored later in sustainably established populations (i.e., sustaining local adaptation).Agence Nationale de la Recherche - ANR-10-BTBR-04; European Regional Development Fund; Fundacao para a Ciencia e a Tecnologia - SFRH/BPD/107878/2015, UID/Multi/04326/2016, UID/Multi/04326/2019; Brittany Region;info:eu-repo/semantics/publishedVersio

The Molecular Interstellar Medium in Ultraluminous Infrared Galaxies

We present CO observations of a large sample of ultraluminous IR galaxies out to z = 0.3. Most of the galaxies are interacting, but not completed mergers. All but one have high CO(1-0) luminosities, log(Lco [K-km/s-pc^2]) = 9.92 +/- 0.12. The dispersion in Lco is only 30%, less than that in the FIR luminosity. The integrated CO intensity correlates Strongly with the 100 micron flux density, as expected for a black body model in which the mid and far IR radiation are optically thick. We use this model to derive sizes of the FIR and CO emitting regions and the enclosed dynamical masses. Both the IR and CO emission originate in regions a few hundred parsecs in radius. The median value of Lfir/Lco = 160 Lsun/(K-km/s-pc^2), within a factor of two of the black body limit for the observed FIR temperatures. The entire ISM is a scaled up version of a normal galactic disk with densities a factor of 100 higher, making even the intercloud medium a molecular region. Using three different techniques of H2 mass estimation, we conclude that the ratio of gas mass to Lco is about a factor of four lower than for Galactic molecular clouds, but that the gas mass is a large fraction of the dynamical mass. Our analysis of CO emission reduces the H2 mass from previous estimates of 2-5e10 Msun to 0.4-1.5e10 Msun, which is in the range found for molecular gas rich spiral galaxies. A collision involving a molecular gas rich spiral could lead to an ultraluminous galaxy powered by central starbursts triggered by the compression of infalling preexisting GMC's.Comment: 34 pages LaTeX with aasms.sty, 14 Postscript figures, submitted to ApJ Higher quality versions of Figs 2a-f and 7a-c available by anonymous FTP from ftp://sbast1.ess.sunysb.edu/solomon/

Cosmological Deformation of Lorentzian Spin Foam Models

We study the quantum deformation of the Barrett-Crane Lorentzian spin foam model which is conjectured to be the discretization of Lorentzian Plebanski model with positive cosmological constant and includes therefore as a particular sector quantum gravity in de-Sitter space. This spin foam model is constructed using harmonic analysis on the quantum Lorentz group. The evaluation of simple spin networks are shown to be non commutative integrals over the quantum hyperboloid defined as a pile of fuzzy spheres. We show that the introduction of the cosmological constant removes all the infrared divergences: for any fixed triangulation, the integration over the area variables is finite for a large class of normalization of the amplitude of the edges and of the faces.Comment: 37 pages, 7 figures include

A mutation in amino acid permease AAP6 reduces the amino acid content of the Arabidopsis sieve elements but leaves aphid herbivores unaffected

The aim of this study was to investigate the role of the amino acid permease gene AAP6 in regulating phloem amino acid composition and then to determine the effects of this altered diet on aphid performance. A genotype of Arabidopsis thaliana (L.) was produced in which the function of the amino acid permease gene AAP6 (At5g49630) was abolished. Plants homozygous for the insertionally inactivated AAP6 gene had a significantly larger mean rosette width than the wild type and a greater number of cauline leaves. Seeds from the aap6 mutant were also significantly larger than those from the wild-type plants. Sieve element (SE) sap was collected by aphid stylectomy and the amino acids derivatized, separated, and quantified using Capillary Electrophoresis with Laser Induced Fluorescence (CE-LIF). In spite of the large variation across samples, the total amino acid concentration of SE sap of the aap6 mutant plants was significantly lower than that of the wild-type plants. The concentrations of lysine, phenylalanine, leucine, and aspartic acid were all significantly lower in concentration in the aap6 mutant plants compared with wild-type plants. This is the first direct demonstration of a physiological role for an amino acid transporter in regulating SE composition in vivo. The amino acid availability in sieve element sap is thought to be the major limiting factor for aphid growth and reproduction. Despite the changes in their diet, the aphid Myzus persicae (Sulzer) displayed only small changes in feeding behaviour on mutant plants when measured using the Electronic Penetration Graph (EPG) technique. Salivation by the aphid into the SE (E1 phase) was increased on mutant plants but there was no significant effect on other feeding EPG behaviours, or in the rate of honeydew production. Consistent with the small effect on aphid feeding behaviour, there was only a small effect of reduced sieve element amino acid concentration on aphid reproduction. The data are discussed in relation to the regulation of phloem composition and the role of phloem amino acids in regulating aphid performance

Bell's Jump Process in Discrete Time

The jump process introduced by J. S. Bell in 1986, for defining a quantum field theory without observers, presupposes that space is discrete whereas time is continuous. In this letter, our interest is to find an analogous process in discrete time. We argue that a genuine analog does not exist, but provide examples of processes in discrete time that could be used as a replacement.Comment: 7 pages LaTeX, no figure

Provably Secure Experimental Quantum Bit-String Generation

Coin tossing is a cryptographic task in which two parties who do not trust each other aim to generate a common random bit. Using classical communication this is impossible, but non trivial coin tossing is possible using quantum communication. Here we consider the case when the parties do not want to toss a single coin, but many. This is called bit string generation. We report the experimental generation of strings of coins which are provably more random than achievable using classical communication. The experiment is based on the ``plug and play'' scheme developed for quantum cryptography, and therefore well suited for long distance quantum communication.Comment: 4 pages, 3 figures. Submitted to Phys. Rev. Lett. A complete security analysis for the experiment is given in quant-ph/040812