Dynamic load balancing for the distributed mining of molecular structures

In molecular biology, it is often desirable to find common properties in large numbers of drug candidates. One family of methods stems from the data mining community, where algorithms to find frequent graphs have received increasing attention over the past years. However, the computational complexity of the underlying problem and the large amount of data to be explored essentially render sequential algorithms useless. In this paper, we present a distributed approach to the frequent subgraph mining problem to discover interesting patterns in molecular compounds. This problem is characterized by a highly irregular search tree, whereby no reliable workload prediction is available. We describe the three main aspects of the proposed distributed algorithm, namely, a dynamic partitioning of the search space, a distribution process based on a peer-to-peer communication framework, and a novel receiverinitiated load balancing algorithm. The effectiveness of the distributed method has been evaluated on the well-known National Cancer Institute’s HIV-screening data set, where we were able to show close-to linear speedup in a network of workstations. The proposed approach also allows for dynamic resource aggregation in a non dedicated computational environment. These features make it suitable for large-scale, multi-domain, heterogeneous environments, such as computational grids.

Decentralized load balancing for highly irregular search problems

In this paper, we present a distributed computing framework for problems characterized by a highly irregular search tree, whereby no reliable workload prediction is available. The framework is based on a peer-to-peer computing environment and dynamic load balancing. The system allows for dynamic resource aggregation, does not depend on any specific meta-computing middleware and is suitable for large-scale, multi-domain, heterogeneous environments, such as computational Grids. Dynamic load balancing policies based on global statistics are known to provide optimal load balancing performance, while randomized techniques provide high scalability. The proposed method combines both advantages and adopts distributed job-pools and a randomized polling technique. The framework has been successfully adopted in a parallel search algorithm for subgraph mining and evaluated on a molecular compounds dataset. The parallel application has shown good calability and close-to linear speedup in a distributed network of workstations.

A wavenumber independent boundary element method for an acoustic scattering problem

In this paper we consider the impedance boundary value problem for the Helmholtz equation in a half-plane with piecewise constant boundary data, a problem which models, for example, outdoor sound propagation over inhomogeneous. at terrain. To achieve good approximation at high frequencies with a relatively low number of degrees of freedom, we propose a novel Galerkin boundary element method, using a graded mesh with smaller elements adjacent to discontinuities in impedance and a special set of basis functions so that, on each element, the approximation space contains polynomials ( of degree.) multiplied by traces of plane waves on the boundary. We prove stability and convergence and show that the error in computing the total acoustic field is O( N-(v+1) log(1/2) N), where the number of degrees of freedom is proportional to N logN. This error estimate is independent of the wavenumber, and thus the number of degrees of freedom required to achieve a prescribed level of accuracy does not increase as the wavenumber tends to infinity.

A high-wavenumber boundary-element method for an acoustic scattering problem

In this paper we show stability and convergence for a novel Galerkin boundary element method approach to the impedance boundary value problem for the Helmholtz equation in a half-plane with piecewise constant boundary data. This problem models, for example, outdoor sound propagation over inhomogeneous flat terrain. To achieve a good approximation with a relatively low number of degrees of freedom we employ a graded mesh with smaller elements adjacent to discontinuities in impedance, and a special set of basis functions for the Galerkin method so that, on each element, the approximation space consists of polynomials (of degree $\nu$) multiplied by traces of plane waves on the boundary. In the case where the impedance is constant outside an interval $[a,b]$, which only requires the discretization of $[a,b]$, we show theoretically and experimentally that the $L_2$ error in computing the acoustic field on $[a,b]$ is ${\cal O}(\log^{\nu+3/2}|k(b-a)| M^{-(\nu+1)})$, where $M$ is the number of degrees of freedom and $k$ is the wavenumber. This indicates that the proposed method is especially commendable for large intervals or a high wavenumber. In a final section we sketch how the same methodology extends to more general scattering problems.

How to save a bad element with weak boundary conditions

The P-1-P-1 finite element pair is known to allow the existence of spurious pressure (surface elevation) modes for the shallow water equations and to be unstable for mixed formulations. We show that this behavior is strongly influenced by the strong or the weak enforcement of the impermeability boundary conditions. A numerical analysis of the Stommel model is performed for both P-1-P-1 and P-1(NC)-P-1 mixed formulations. Steady and transient test cases are considered. We observe that the P-1-P-1 element exhibits stable discrete solutions with weak boundary conditions or with fully unstructured meshes. (c) 2005 Elsevier Ltd. All rights reserved.

Finite element approximation of a sixth order nonlinear degenerate parabolic equation

We consider a finite element approximation of the sixth order nonlinear degenerate parabolic equation ut = ?.( b(u)? 2u), where generically b(u) := |u|? for any given ? ? (0,?). In addition to showing well-posedness of our approximation, we prove convergence in space dimensions d ? 3. Furthermore an iterative scheme for solving the resulting nonlinear discrete system is analysed. Finally some numerical experiments in one and two space dimensions are presented.

An adaptive finite element water column model using the Mellor-Yamada level 2.5 turbulence closure scheme

A one-dimensional water column model using the Mellor and Yamada level 2.5 parameterization of vertical turbulent fluxes is presented. The model equations are discretized with a mixed finite element scheme. Details of the finite element discrete equations are given and adaptive mesh refinement strategies are presented. The refinement criterion is an "a posteriori" error estimator based on stratification, shear and distance to surface. The model performances are assessed by studying the stress driven penetration of a turbulent layer into a stratified fluid. This example illustrates the ability of the presented model to follow some internal structures of the flow and paves the way for truly generalized vertical coordinates. (c) 2005 Elsevier Ltd. All rights reserved.