Alistair P. Rendell

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X10 is an emerging Partitioned Global Address Space (PGAS) language intended to increase significantly the productivity of developing scalable HPC applications. The language has now matured to a point where it is meaningful to consider writing large scale scientific application codes in X10. This paper reports our experiences writing three codes from the(More)
We employ the entire experimentally determined protein structure for the KcsA potassium channel from Streptomyces lividans in molecular dynamics calculations to observe hydrated channel protein structure, ion solvation, selectivity, multiple ion configurations, and diffusion. Free energy perturbation calculations display a significant ion discrimination of(More)
Modern shared memory multiprocessor systems commonly have non-uniform memory access (NUMA) with asymmetric memory bandwidth and latency characteristics. Operating systems now provide application programmer interfaces allowing the user to perform specific thread and memory placement. To date, however, there have been relatively few detailed assessments of(More)
Water is ubiquitous on our planet and plays an essential role in several key chemical and biological processes. Accurate models for water are crucial in understanding, controlling and predicting the physical and chemical properties of complex aqueous systems. Over the last few years we have been developing a molecular-level based approach for a macroscopic(More)
With energy efficiency and power consumption being the primary impediment in the path to exascale systems, low-power high performance embedded systems are of increasing interest. The Parallella System-on-module (SoM) created by Adapteva combines the Epiphany-IV 64-core coprocessor with a host ARM processor housed in a Zynq System-on-chip. The Epiphany(More)
Quality data recorded in varied realistic environments is vital for effective human face related research. Currently available datasets for human facial expression analysis have been generated in highly controlled lab environments. We present a new dynamic 2D facial expressions database based on movies capturing diverse scenarios. A new XML schema based(More)
The CUDA model for GPUs presents the programmer with a plethora of different programming options. These includes different memory types, different memory access methods, and different data types. Identifying which options to use and when is a non-trivial exercise. This paper explores the effect of these different options on the performance of a routine that(More)
The field of reinforcement learning has developed techniques for choosing beneficial actions within a dynamic environment. Such techniques learn from experience and do not require teaching. This paper explores how reinforcement learning techniques might be used to determine efficient storage formats for sparse matrices. Three different storage formats are(More)
The simulation of nonlinear ultrasound propagation through tissue realistic media has a wide range of practical applications. However, this is a computationally difficult problem due to the large size of the computational domain compared to the acoustic wavelength. Here, the k-space pseudospectral method is used to reduce the number of grid points required(More)
Model-based treatment planning and exposimetry for high-intensity focused ultrasound requires the numerical simulation of nonlinear ultrasound propagation through heterogeneous and absorbing media. This is a computationally demanding problem due to the large distances travelled by the ultrasound waves relative to the wavelength of the highest frequency(More)