Recent Advances in Graph Partitioning

We survey recent trends in practical algorithms for balanced graph partitioning together with applications and future research directions

A domain decomposing parallel sparse linear system solver

The solution of large sparse linear systems is often the most time-consuming part of many science and engineering applications. Computational fluid dynamics, circuit simulation, power network analysis, and material science are just a few examples of the application areas in which large sparse linear systems need to be solved effectively. In this paper we introduce a new parallel hybrid sparse linear system solver for distributed memory architectures that contains both direct and iterative components. We show that by using our solver one can alleviate the drawbacks of direct and iterative solvers, achieving better scalability than with direct solvers and more robustness than with classical preconditioned iterative solvers. Comparisons to well-known direct and iterative solvers on a parallel architecture are provided.Comment: To appear in Journal of Computational and Applied Mathematic

A scalable parallel finite element framework for growing geometries. Application to metal additive manufacturing

This work introduces an innovative parallel, fully-distributed finite element framework for growing geometries and its application to metal additive manufacturing. It is well-known that virtual part design and qualification in additive manufacturing requires highly-accurate multiscale and multiphysics analyses. Only high performance computing tools are able to handle such complexity in time frames compatible with time-to-market. However, efficiency, without loss of accuracy, has rarely held the centre stage in the numerical community. Here, in contrast, the framework is designed to adequately exploit the resources of high-end distributed-memory machines. It is grounded on three building blocks: (1) Hierarchical adaptive mesh refinement with octree-based meshes; (2) a parallel strategy to model the growth of the geometry; (3) state-of-the-art parallel iterative linear solvers. Computational experiments consider the heat transfer analysis at the part scale of the printing process by powder-bed technologies. After verification against a 3D benchmark, a strong-scaling analysis assesses performance and identifies major sources of parallel overhead. A third numerical example examines the efficiency and robustness of (2) in a curved 3D shape. Unprecedented parallelism and scalability were achieved in this work. Hence, this framework contributes to take on higher complexity and/or accuracy, not only of part-scale simulations of metal or polymer additive manufacturing, but also in welding, sedimentation, atherosclerosis, or any other physical problem where the physical domain of interest grows in time

Automating Fault Tolerance in High-Performance Computational Biological Jobs Using Multi-Agent Approaches

Background: Large-scale biological jobs on high-performance computing systems require manual intervention if one or more computing cores on which they execute fail. This places not only a cost on the maintenance of the job, but also a cost on the time taken for reinstating the job and the risk of losing data and execution accomplished by the job before it failed. Approaches which can proactively detect computing core failures and take action to relocate the computing core's job onto reliable cores can make a significant step towards automating fault tolerance. Method: This paper describes an experimental investigation into the use of multi-agent approaches for fault tolerance. Two approaches are studied, the first at the job level and the second at the core level. The approaches are investigated for single core failure scenarios that can occur in the execution of parallel reduction algorithms on computer clusters. A third approach is proposed that incorporates multi-agent technology both at the job and core level. Experiments are pursued in the context of genome searching, a popular computational biology application. Result: The key conclusion is that the approaches proposed are feasible for automating fault tolerance in high-performance computing systems with minimal human intervention. In a typical experiment in which the fault tolerance is studied, centralised and decentralised checkpointing approaches on an average add 90% to the actual time for executing the job. On the other hand, in the same experiment the multi-agent approaches add only 10% to the overall execution time.Comment: Computers in Biology and Medicin

Algebraic Methods in the Congested Clique

In this work, we use algebraic methods for studying distance computation and subgraph detection tasks in the congested clique model. Specifically, we adapt parallel matrix multiplication implementations to the congested clique, obtaining an $O(n^{1-2/\omega})$ round matrix multiplication algorithm, where $\omega < 2.3728639$ is the exponent of matrix multiplication. In conjunction with known techniques from centralised algorithmics, this gives significant improvements over previous best upper bounds in the congested clique model. The highlight results include: -- triangle and 4-cycle counting in $O(n^{0.158})$ rounds, improving upon the $O(n^{1/3})$ triangle detection algorithm of Dolev et al. [DISC 2012], -- a $(1 + o(1))$-approximation of all-pairs shortest paths in $O(n^{0.158})$ rounds, improving upon the $\tilde{O} (n^{1/2})$-round $(2 + o(1))$-approximation algorithm of Nanongkai [STOC 2014], and -- computing the girth in $O(n^{0.158})$ rounds, which is the first non-trivial solution in this model. In addition, we present a novel constant-round combinatorial algorithm for detecting 4-cycles.Comment: This is work is a merger of arxiv:1412.2109 and arxiv:1412.266