Big data scalability of bayesPhylogenies on Harvard’s ozone 12k cores

Computational Phylogenetics is classed as a grand challenge data driven problem in the fourth paradigm of scientific discovery due to the exponential growth in genomic data, the computational challenge and the potential for vast impact on data driven biosciences. Petascale and Exascale computing offer the prospect of scaling Phylogenetics to big data levels. However the computational complexity of even approximate Bayesian methods for phylogenetic inference requires scalable analysis for big data applications. There is limited study on the scalability characteristics of existing computational models for petascale class massively parallel computers. In this paper we present strong and weak scaling performance analysis of BayesPhylogenies on Harvard’s Ozone 12k cores. We perform evaluations on multiple data sizes to infer the scaling complexity and find that strong scaling techniques along with novel methods for communication reduction are necessary if computational models are to overcome limitations on emerging complex parallel architectures with multiple levels of concurrency. The results of this study can guide the design and implementation of scalable MCMC based computational models for Bayesian inference on emerging petascale and exascale systems

Modelling the Performance of a Shallow Water Code

Peer reviewe

Performance Modelling for Climate Models

Peer reviewe

On the influence of gamma prime upon machining of advanced nickel based superalloy

Whilst gamma prime (γ’) phase is the strengthening phase in Ni-based superalloys its influence on machining has been seldom investigated. This paper reports for the first time on the effect of γ’ upon machining of Ni-based superalloys when cutting with parameters yielding different cutting temperature intervals which lead to strengthening/softening effects on the workpiece (sub)surface. In-depth XRD, SEM/FIB, EBSD analysis and unique micro-pillar testing in the workpiece superficial layers indicated that with the increase of γ’ fraction the grain plastic deformation significantly decreased, while specific cutting energy can switch from low to high values influenced by the real cutting temperature

Compositional technique for synthesising multi-phase regular arrays

We describe a high-level design method to synthesize multi-phase regular arrays. The method is based on deriving component designs using classical regular (or systolic) array synthesis techniques and composing these separately evolved component designs into a unified global design. Similarity transformations are applied to component designs in the composition stage in order to align data flow between the phases of the computations. Three transformations are considered: rotation, reflection and translation. The technique is aimed at the design of hardware components for high-throughput embedded systems applications and we demonstrate this by deriving a multi-phase regular array for the 2D DCT algorithm which is widely used in many video communications applications

Hierarchical composite regular parallel architecture

The design space of emerging heterogenous multi-core architectures with re-configurability element makes it feasible to design mixed fine-grained and coarse-grained parallel architectures. This paper presents a hierarchical composite array design which extends the curret design space of regular array design by combining a sequence of transformations. This technique is applied to derive a new design of a pipelined parallel regular array with different dataflow between phases of computation

Fine-grained multi-phase array designs

Hybrid multiprocessor architectures which combine re-configurable computing and multiprocessors on a chip are being proposed to transcend the performance of standard multi-core parallel systems. Both fine-grained and coarse-grained parallel algorithm implementations are feasible in such hybrid frameworks. A compositional strategy for designing fine-grained multi-phase regular processor arrays to target hybrid architectures is presented in this paper. The method is based on deriving component designs using classical regular array techniques and composing the components into a unified global design. Effective designs with phase-changes and data routing at run-time are characteristics of these designs. In order to describe the data transfer between phases, the concept of communication domain is introduced so that the producer–consumer relationship arising from multi-phase computation can be treated in a unified way as a data routing phase. This technique is applied to derive new designs of multi-phase regular arrays with different dataflow between phases of computation