Blocked All-Pairs Shortest Paths Algorithm on Intel Xeon Phi KNL Processor: A Case Study

Manycores are consolidating in HPC community as a way of improving performance while keeping power efficiency. Knights Landing is the recently released second generation of Intel Xeon Phi architecture. While optimizing applications on CPUs, GPUs and first Xeon Phi's has been largely studied in the last years, the new features in Knights Landing processors require the revision of programming and optimization techniques for these devices. In this work, we selected the Floyd-Warshall algorithm as a representative case study of graph and memory-bound applications. Starting from the default serial version, we show how data, thread and compiler level optimizations help the parallel implementation to reach 338 GFLOPS.Comment: Computer Science - CACIC 2017. Springer Communications in Computer and Information Science, vol 79

Beyond homozygosity mapping: family-control analysis based on Hamming distance for prioritizing variants in exome sequencing

A major challenge in current exome sequencing in autosomal recessive (AR) families is the lack of an effective method to prioritize single-nucleotide variants (SNVs). AR families are generally too small for linkage analysis, and length of homozygous regions is unreliable for identification of causative variants. Various common filtering steps usually result in a list of candidate variants that cannot be narrowed down further or ranked. To prioritize shortlisted SNVs we consider each homozygous candidate variant together with a set of SNVs flanking it. We compare the resulting array of genotypes between an affected family member and a number of control individuals and argue that, in a family, differences between family member and controls should be larger for a pathogenic variant and SNVs flanking it than for a random variant. We assess differences between arrays in two individuals by the Hamming distance and develop a suitable test statistic, which is expected to be large for a causative variant and flanking SNVs. We prioritize candidate variants based on this statistic and applied our approach to six patients with known pathogenic variants and found these to be in the top 2 to 10 percentiles of ranks

Impurity Effects on Quantum Depinning of Commensurate Charge Density Waves

We investigate quantum depinning of the one-dimensional (1D) commensurate charge-density wave (CDW) in the presence of one impurity theoretically. Quantum tunneling rate below but close to the threshold field is calculated at absolute zero temperature by use of the phase Hamiltonian within the WKB approximation. We show that the impurity can induce localized fluctuation and enhance the quantum depinning. The electric field dependence of the tunneling rate in the presence of the impurity is different from that in its absence.Comment: 14 pages with 13 figures. Submitted to J. Phys. Soc. Jp

Numerical computations of facetted pattern formation in snow crystal growth

Facetted growth of snow crystals leads to a rich diversity of forms, and exhibits a remarkable sixfold symmetry. Snow crystal structures result from diffusion limited crystal growth in the presence of anisotropic surface energy and anisotropic attachment kinetics. It is by now well understood that the morphological stability of ice crystals strongly depends on supersaturation, crystal size and temperature. Until very recently it was very difficult to perform numerical simulations of this highly anisotropic crystal growth. In particular, obtaining facet growth in combination with dendritic branching is a challenging task. We present numerical simulations of snow crystal growth in two and three space dimensions using a new computational method recently introduced by the authors. We present both qualitative and quantitative computations. In particular, a linear relationship between tip velocity and supersaturation is observed. The computations also suggest that surface energy effects, although small, have a larger effect on crystal growth than previously expected. We compute solid plates, solid prisms, hollow columns, needles, dendrites, capped columns and scrolls on plates. Although all these forms appear in nature, most of these forms are computed here for the first time in numerical simulations for a continuum model.Comment: 12 pages, 28 figure

Earth Matter Effects at Very Long Baselines and the Neutrino Mass Hierarchy

We study matter effects which arise in the muon neutrino oscillation and survival probabilities relevant to atmospheric neutrino and very long baseline beam experiments. The inter-relations between the three probabilities P_{\mu e}, P_{\mu \tau} and P_{\mu \mu} are examined. It is shown that large and observable sensitivity to the neutrino mass hierarchy can be present in P_{\mu \mu} and P_{\mu \tau}. We emphasize that at baselines of > 7000 Km, matter effects in P_{\mu \tau} can be large under certain conditions. The muon survival rates in experiments with very long baselines thus depend on matter effects in both P_{\mu \tau} and P_{\mu e}. We indicate where these effects are sensitive to \theta_{13}, and identify ranges of E and L where the event rates increase with decreasing \theta_{13}, providing a handle to probe small \theta_{13}. The effect of parameter degeneracies in the three probabilities at these baselines and energies is studied in detail. Realistic event rate calculations are performed for a charge discriminating 100 kT iron calorimeter which demonstrate the possibility of realising the goal of determining the neutrino mass hierarchy using atmospheric neutrinos. It is shown that a careful selection of energy and baseline ranges is necessary in order to obtain a statistically significant signal, and that the effects are largest in bins where matter effects in both P_{\mu e} and P_{\mu \tau} combine constructively. Under these conditions, upto a 4\sigma signal for matter effects is possible (for \Delta_{31}>0) within a timescale appreciably shorter than the one anticipated for neutrino factories.Comment: 40 pages, 27 figures, version to match the published versio

Application of Hamamatsu MPPC to T2K Neutrino Detectors

A special type of Hamamatsu MPPC, with a sensitive area of 1.3x1.3mm^2 containing 667 pixels with 50x50um^2 each, has been developed for the near neutrino detector in the T2K long baseline neutrino experiment. About 60 000 MPPCs will be used in total to read out the plastic scintillator detectors with wavelength shifting fibers. We report on the basic performance of MPPCs produced for T2K.Comment: Contribution to the proceedings of NDIP 2008, Aix-les-Bains, France, June 15-20, 200