Hybrid static/dynamic scheduling for already optimized dense matrix factorization

We present the use of a hybrid static/dynamic scheduling strategy of the task dependency graph for direct methods used in dense numerical linear algebra. This strategy provides a balance of data locality, load balance, and low dequeue overhead. We show that the usage of this scheduling in communication avoiding dense factorization leads to significant performance gains. On a 48 core AMD Opteron NUMA machine, our experiments show that we can achieve up to 64% improvement over a version of CALU that uses fully dynamic scheduling, and up to 30% improvement over the version of CALU that uses fully static scheduling. On a 16-core Intel Xeon machine, our hybrid static/dynamic scheduling approach is up to 8% faster than the version of CALU that uses a fully static scheduling or fully dynamic scheduling. Our algorithm leads to speedups over the corresponding routines for computing LU factorization in well known libraries. On the 48 core AMD NUMA machine, our best implementation is up to 110% faster than MKL, while on the 16 core Intel Xeon machine, it is up to 82% faster than MKL. Our approach also shows significant speedups compared with PLASMA on both of these systems

Domain-decomposed preconditionings for transport operators

The performance was tested of five different interface preconditionings for domain decomposed convection diffusion problems, including a novel one known as the spectral probe, while varying mesh parameters, Reynolds number, ratio of subdomain diffusion coefficients, and domain aspect ratio. The preconditioners are representative of the range of practically computable possibilities that have appeared in the domain decomposition literature for the treatment of nonoverlapping subdomains. It is shown that through a large number of numerical examples that no single preconditioner can be considered uniformly superior or uniformly inferior to the rest, but that knowledge of particulars, including the shape and strength of the convection, is important in selecting among them in a given problem

Adjacency Matrices of Configuration Graphs

In 1960, Hoffman and Singleton \cite{HS60} solved a celebrated equation for square matrices of order $n$, which can be written as $$(\kappa - 1) I_n + J_n - A A^{\rm T} = A$$ where $I_n$, $J_n$, and $A$ are the identity matrix, the all one matrix, and a $(0,1)$--matrix with all row and column sums equal to $\kappa$, respectively. If $A$ is an incidence matrix of some configuration $\cal C$ of type $n_\kappa$, then the left-hand side $\Theta(A):= (\kappa - 1)I_n + J_n - A A^{\rm T}$ is an adjacency matrix of the non--collinearity graph $\Gamma$ of $\cal C$. In certain situations, $\Theta(A)$ is also an incidence matrix of some $n_\kappa$ configuration, namely the neighbourhood geometry of $\Gamma$ introduced by Lef\`evre-Percsy, Percsy, and Leemans \cite{LPPL}. The matrix operator $\Theta$ can be reiterated and we pose the problem of solving the generalised Hoffman--Singleton equation $\Theta^m(A)=A$. In particular, we classify all $(0,1)$--matrices $M$ with all row and column sums equal to $\kappa$, for $\kappa = 3,4$, which are solutions of this equation. As a by--product, we obtain characterisations for incidence matrices of the configuration $10_3F$ in Kantor's list \cite{Kantor} and the $17_4$ configuration #1971 in Betten and Betten's list \cite{BB99}

An agent-based approach to immune modelling

This study focuses on trying to understand why the range of experience with respect to HIV infection is so diverse, especially as regards to the latency period. The challenge is to determine what assumptions can be made about the nature of the experience of antigenic invasion and diversity that can be modelled, tested and argued plausibly. To investigate this, an agent-based approach is used to extract high-level behaviour which cannot be described analytically from the set of interaction rules at the cellular level. A prototype model encompasses local variation in baseline properties contributing to the individual disease experience and is included in a network which mimics the chain of lymphatic nodes. Dealing with massively multi-agent systems requires major computational efforts. However, parallelisation methods are a natural consequence and advantage of the multi-agent approach. These are implemented using the MPI library

Breakup of the aligned H2_2 molecule by xuv laser pulses: A time-dependent treatment in prolate spheroidal coordinates

We have carried out calculations of the triple-differential cross section for one-photon double ionization of molecular hydrogen for a central photon energy of $75$~eV, using a fully {\it ab initio}, nonperturbative approach to solve the time-dependent \Schro equation in prolate spheroidal coordinates. The spatial coordinates $\xi$ and $\eta$ are discretized in a finite-element discrete-variable representation. The wave packet of the laser-driven two-electron system is propagated in time through an effective short iterative Lanczos method to simulate the double ionization of the hydrogen molecule. For both symmetric and asymmetric energy sharing, the present results agree to a satisfactory level with most earlier predictions for the absolute magnitude and the shape of the angular distributions. A notable exception, however, concerns the predictions of the recent time-independent calculations based on the exterior complex scaling method in prolate spheroidal coordinates [Phys.~Rev.~A~{\bf 82}, 023423 (2010)]. Extensive tests of the numerical implementation were performed, including the effect of truncating the Neumann expansion for the dielectronic interaction on the description of the initial bound state and the predicted cross sections. We observe that the dominant escape mode of the two photoelectrons dramatically depends upon the energy sharing. In the parallel geometry, when the ejected electrons are collected along the direction of the laser polarization axis, back-to-back escape is the dominant channel for strongly asymmetric energy sharing, while it is completely forbidden if the two electrons share the excess energy equally.Comment: 17 pages, 9 figure