Task-based adaptive multiresolution for time-space multi-scale reaction-diffusion systems on multi-core architectures

A new solver featuring time-space adaptation and error control has been recently introduced to tackle the numerical solution of stiff reaction-diffusion systems. Based on operator splitting, finite volume adaptive multiresolution and high order time integrators with specific stability properties for each operator, this strategy yields high computational efficiency for large multidimensional computations on standard architectures such as powerful workstations. However, the data structure of the original implementation, based on trees of pointers, provides limited opportunities for efficiency enhancements, while posing serious challenges in terms of parallel programming and load balancing. The present contribution proposes a new implementation of the whole set of numerical methods including Radau5 and ROCK4, relying on a fully different data structure together with the use of a specific library, TBB, for shared-memory, task-based parallelism with work-stealing. The performance of our implementation is assessed in a series of test-cases of increasing difficulty in two and three dimensions on multi-core and many-core architectures, demonstrating high scalability

Resolution of Linear Algebra for the Discrete Logarithm Problem Using GPU and Multi-core Architectures

In cryptanalysis, solving the discrete logarithm problem (DLP) is key to assessing the security of many public-key cryptosystems. The index-calculus methods, that attack the DLP in multiplicative subgroups of finite fields, require solving large sparse systems of linear equations modulo large primes. This article deals with how we can run this computation on GPU- and multi-core-based clusters, featuring InfiniBand networking. More specifically, we present the sparse linear algebra algorithms that are proposed in the literature, in particular the block Wiedemann algorithm. We discuss the parallelization of the central matrix--vector product operation from both algorithmic and practical points of view, and illustrate how our approach has contributed to the recent record-sized DLP computation in GF($2^{809}$).Comment: Euro-Par 2014 Parallel Processing, Aug 2014, Porto, Portugal. \<http://europar2014.dcc.fc.up.pt/\&gt

Preparing sparse solvers for exascale computing.

Sparse solvers provide essential functionality for a wide variety of scientific applications. Highly parallel sparse solvers are essential for continuing advances in high-fidelity, multi-physics and multi-scale simulations, especially as we target exascale platforms. This paper describes the challenges, strategies and progress of the US Department of Energy Exascale Computing project towards providing sparse solvers for exascale computing platforms. We address the demands of systems with thousands of high-performance node devices where exposing concurrency, hiding latency and creating alternative algorithms become essential. The efforts described here are works in progress, highlighting current success and upcoming challenges. This article is part of a discussion meeting issue 'Numerical algorithms for high-performance computational science'

Solving Sequences of Generalized Least-Squares Problems on Multi-threaded Architectures

Generalized linear mixed-effects models in the context of genome-wide association studies (GWAS) represent a formidable computational challenge: the solution of millions of correlated generalized least-squares problems, and the processing of terabytes of data. We present high performance in-core and out-of-core shared-memory algorithms for GWAS: By taking advantage of domain-specific knowledge, exploiting multi-core parallelism, and handling data efficiently, our algorithms attain unequalled performance. When compared to GenABEL, one of the most widely used libraries for GWAS, on a 12-core processor we obtain 50-fold speedups. As a consequence, our routines enable genome studies of unprecedented size