Steven Manos

Microstructured polymer optical fibre

The first microstructured polymer optical fibre is described. Both experimental and theoretical evidence is presented to establish that the fibre is effectively single moded at optical wavelengths. Polymer-based microstructured optical fibres offer key advantages over both conventional polymer optical fibres and glass microstructured fibres. The low-cost manufacturability and the chemical flexibility of the polymers provide great potential for applications in data communication networks and for the development of a range of new polymer-based fibre-optic components.

Recent progress in microstructured polymer optical fibre fabrication and characterisation

Recent progress in microstructured polymer optical fibre fabrication and characterisation will be presented. A wide range of different optical functionalities can now be obtained by modifications of the microstructure, as is demonstrated by the fibres presented here. Microstructured fibres that are single-mode, highly birefringent or show twin-core coupling are described, in addition to graded-index microstructured fibres and hollow core fibres, the latter case being where light is guided in an air core. Microstructured polymer optical fibres are an exciting new development, offering opportunities to develop fibres for a wide range of applications in telecommunications and optical sensing.

Electron tomography and computer visualisation of a three-dimensional ‘photonic’ crystal in a butterfly wing-scale

A combination of transmission electron tomography and computer modelling has been used to determine the three-dimensional structure of the photonic crystals found in the wing-scales of the Kaiser-I-Hind butterfly (Teinopalpus imperialis). These scales presented challenges for electron microscopy because the periodicity of the structure was comparable to the thickness of a section and because of the complex connectivity of the object. The structure obtained has been confirmed by taking slices of the three-dimensional computer model constructed from the tomography and comparing these with transmission electron microscope (TEM) images of microtomed sections of the actual scale. The crystal was found to have chiral tetrahedral repeating units packed in a triclinic lattice.

Patient-specific simulation as a basis for clinical decision-making.

Patient-specific medical simulation holds the promise of determining tailored medical treatment based on the characteristics of an individual patient (for example, using a genotypic assay of a sequence of DNA). Decision-support systems based on patient-specific simulation can potentially revolutionize the way that clinicians plan courses of treatment for various conditions, ranging from viral infections to arterial abnormalities. Basing medical decisions on the results of simulations that use models derived from data specific to the patient in question means that the effectiveness of a range of potential treatments can be assessed before they are actually administered, preventing the patient from experiencing unnecessary or ineffective treatments. We illustrate the potential for patient-specific simulation by first discussing the scale of the evolving international grid infrastructure that is now available to underpin such applications. We then consider two case studies, one concerned with the treatment of patients with HIV/AIDS and the other addressing neuropathologies associated with the intracranial vasculature. Such patient-specific medical simulations require access to both appropriate patient data and the computational resources on which to perform potentially very large simulations. Computational infrastructure providers need to furnish access to a wide range of different types of resource, typically made available through heterogeneous computational grids, and to institute policies that facilitate the performance of patient-specific simulations on those resources. To support these kinds of simulations, where life and death decisions are being made, computational resource providers must give urgent priority to such jobs, for example by allowing them to pre-empt the queue on a machine and run straight away. We describe systems that enable such priority computing.

Distributed mpi cross-site run performance using mpig

Large scale supercomputing applications typically run on clusters using vendor message passing libraries, limiting the application to the availability of memory and CPU resources on that single machine. The ability to run inter-cluster parallel code is attractive since it allows the consolidation of multiple large scale resources for computational simulations not possible on a single machine, and it also allows the conglomeration of small subsets of CPU cores for rapid turnaround, for example, in the case of high-availability computing. MPIg is a grid-enabled implementation of the Message Passing Interface (MPI), extending the MPICH implementation of MPI to use Globus Toolkit services such as resource allocation and authentication. To achieve co-availability of resources, HARC, the Highly-Available Resource Co-allocator, is used. Here we examine two applications using MPIg: LAMMPS (Large-scale Atomic/ Molecular Massively Parallel Simulator), is used with a replica exchange molecular dynamics approach to enhance binding affinity calculations in HIV drug research, and HemeLB, which is a lattice-Boltzmann solver designed to address fluid flow in geometries such as the human cerebral vascular system. The cross-site scalability of both these applications is tested and compared to single-machine performance. In HemeLB, communication costs are hidden by effectively overlapping non-blocking communication with computation, essentially scaling linearly across multiple sites, and LAMMPS scales almost as well when run between two significantly geographically separated sites as it does at a single site.

Beyond the bandwidth-length product: Graded index microstructured polymer optical fiber

Large core multimode polymer fibers for high data rate transmission are an important growth area. The conventional approach to reducing the intermodal dispersion in such fibers is to use a graded index (GI) profile. More recently, microstructures rather than differences in chemical composition have been used to produce the GI structure. We compare the bandwidth performance of two GI microstructured fibers to a conventional GI fiber made from the same material. The microstructured fibers not only show excellent bandwidth performance but also their bandwidth has an unconventional length dependence: no additional pulse broadening beyond a characteristic length.

Real science at the petascale

We describe computational science research that uses petascale resources to achieve scientific results at unprecedented scales and resolution. The applications span a wide range of domains, from investigation of fundamental problems in turbulence through computational materials science research to biomedical applications at the forefront of HIV/AIDS research and cerebrovascular haemodynamics. This work was mainly performed on the US TeraGrid ‘petascale’ resource, Ranger, at Texas Advanced Computing Center, in the first half of 2008 when it was the largest computing system in the world available for open scientific research. We have sought to use this petascale supercomputer optimally across application domains and scales, exploiting the excellent parallel scaling performance found on up to at least 32 768 cores for certain of our codes in the so-called ‘capability computing’ category as well as high-throughput intermediate-scale jobs for ensemble simulations in the 32–512 core range. Furthermore, this activity provides evidence that conventional parallel programming with MPI should be successful at the petascale in the short to medium term. We also report on the parallel performance of some of our codes on up to 65 636 cores on the IBM Blue Gene/P system at the Argonne Leadership Computing Facility, which has recently been named the fastest supercomputer in the world for open science.

Large scale computational science on federated international grids: The role of switched optical networks

The provision of high performance compute and data resources on a grid has often been the primary concern of grid resource providers, with the network links used to connect them only a secondary matter. Certain large scale distributed scientific simulations, especially ones which involve cross-site runs or interactive visualisation and steering capabilities, often require high quality of service, high bandwidth, low latency network interconnects between resources. In this paper, we describe three applications which require access to such network infrastructure, together with the middleware and policies needed to make them possible.

Multi-objective and constrained design of fibre Bragg gratings using Evolutionary Algorithms

We apply a multi-objective evolutionary algorithm to a grating problem where only very specific features of the transmission spectrum are specified during the optimisation process. The design problem analysed here relates to the passive extraction of 10 GHz clock signals from a 10 Gbps OTDM RZ encoded data stream. Four spectral features of interest such as bandwidth and passband quality are explicitly defined. Using a real-encoded evolutionary algorithm along with an elitist multi-objective selection method, we arrive at a group of solutions which each satisfy the objectives to various degrees in the presence of manufacturing and other design constraints.

In situ ray tracing and computational steering for interactive blood flow simulation

Recent algorithm and hardware developments have significantly improved our capability to interactively visualise time-varying flow fields. However, when visualising very large dynamically varying datasets interactively there are still limitations in the scalability and efficiency of these methods. Here we present a rendering pipeline which employs an efficient in situ ray tracing technique to visualise flow fields as they are simulated. The ray casting approach is particularly well suited for the visualisation of large and sparse time-varying datasets, where it is capable of rendering fluid flow fields at high image resolutions and at interactive frame rates on a single multi-core processor using OpenMP. The parallel implementation of our in situ visualisation method relies on MPI, requires no specialised hardware support, and employs the same underlying spatial decomposition as the fluid simulator. The visualisation pipeline allows the user to operate on a commodity computer and explore the simulation output interactively. Our simulation environment incorporates numerous features that can be utilised in a wide variety of research contexts.