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    ABSTRACT: The statistical language R and its Bioconductor package are favoured by many biostatisticians for processing microarray data. The amount of data produced by some analyses has reached the limits of many common bioinformatics computing infrastructures. High Performance Computing systems offer a solution to this issue. The Simple Parallel R Interface (SPRINT) is a package that provides biostatisticians with easy access to High Performance Computing systems and allows the addition of parallelized functions to R. Previous work has established that the SPRINT implementation of an R permutation testing function has close to optimal scaling on up to 512 processors on a supercomputer. Access to supercomputers, however, is not always possible, and so the work presented here compares the performance of the SPRINT implementation on a supercomputer with benchmarks on a range of platforms including cloud resources and a common desktop machine with multiprocessing capabilities. Copyright © 2011 John Wiley & Sons, Ltd.
    Concurrency and Computation Practice and Experience 12/2011; 23(17):2258-2268. DOI:10.1002/cpe.1787
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    ABSTRACT: The effective exploitation of current high performance computing (HPC) platforms in molecular simulation relies on the ability of the present generation of parallel molecular dynamics code to make effective utilisation of these platforms and their components, including CPUs and memory. In this paper, we investigate the efficiency and scaling of a series of popular molecular dynamics codes on the UK's national HPC resources, an IBM p690+ cluster and an SGI Altix 3700. Focusing primarily on the AMBER, DL_POLY and NAMD simulation codes, we demonstrate the major performance and scalability advantages that arise through a distributed, rather than a replicated data approach.
    Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences 09/2005; 363(1833):1987-98. DOI:10.1098/rsta.2005.1624
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    ABSTRACT: We discuss the design and implementation of a parallel adaptive P 3 M code, for massively parallel architectures. The code, although primarily designed for conducting gravitational simulations in a cosmological context, also includes a Smoothed Particle Hydrodynamics solver. The code is written in a combination of C, FORTRAN 77 and FORTRAN 90. The MPI-2 remote memory access standard is used for one-sided message passing thereby enabling more time to be spent in raw computation. The design decision has lead to a number of interesting problems and circumstances, which we discuss in detail. Raw performance figures are presented in terms of numbers of particles per second to compare to alternative codes. Nous discutons de la conception et de l'implémentation d'un code P 3 Mparalì ele et adaptif pour les architectures massivementparalì eles. Le code, quoique conçu principalement pour les simulations gravitationnelles dans le contexte de la cosmologie, comprend aussi un code hydrodynamique basé sur des particules. Le code es ecrit en C, FORTRAN 77 et FORTRAN 90. Le standard MPI-2 est utilisé pour le passage unidirectionnel des messages, ce qui permet de laisser plus de temps aux calculs proprement dits. La plan adopté a men a certains probì emes et circonstances, que nous discutons en détail. Les performances sont présentées en fonction du nombre de particules par seconde, dans le but de compare a d'autres codes existants.
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    ABSTRACT: To obtain data on seasonal variations of sperm parameters in an andrology laboratory. Semen parameter values and hormone values of 2454 patients attending our infertility clinic between 1990 and 1997 were analysed. Seasonal trends were calculated using the method of Edwards [Ann. Hum. Genet. 25 (1961) 83]. The total group of mean sperm count did not show a significant variation, but a significant circannual trend occurred of patients born in the groups 1950-1954, 1955-1959 and 1965-1969. A significant variation of acrosin activity occurred with a maximum in March. The other parameters did no show significant variations. The knowledge on circannual variation of semen parameters and hormone values may be of value in diagnostic and therapeutic decisions in reproductive medicine.
    European Journal of Obstetrics & Gynecology and Reproductive Biology 04/2002; 101(2):175-8. DOI:10.1016/S0301-2115(01)00562-0
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    ABSTRACT: Increasing interest is being shown in the use of Java for large scale or Grande applications. This new use of Java places speci.c demands on the Java execution environments that can be tested using the Java Grande benchmark suite [5], [6], [7]. The large processing requirements of Grande applications makes parallelisation of interest. A suite of parallel benchmarks has been developed from the serial Java Grande benchmark suite, using three parallel programming models: Java native threads, MPJ (a message passing interface) and JOMP (a set of OpenMP-like directives). The contents of the suite are described, and results presented for a number of platforms.
    Supercomputing, ACM/IEEE 2001 Conference; 12/2001
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    ABSTRACT: The scale parameter is computed on the lattice in the quenched approximation and for Nf=2 flavors of light dynamical quarks. The dynamical calculation is done with non-perturbatively O(a) improved Wilson fermions. In the continuum limit we obtain MeV and MeV, respectively.
    Physics Letters B 11/2001; 519(3-4-519):229-237. DOI:10.1016/S0370-2693(01)01103-0
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    ABSTRACT: The nucleation of sodium, rubidium and potassium dodecyl sulphates are examined using temperature programmed milli-scale batch crystallisation experiments using optical turbidometry detection. As sodium dodecyl sulphate (SDS) crystallises as a hydrated system from aqueous solution, studies have also been carried out in the presence of sodium citrate, which causes the anhydrous phase to crystallise. The meta-stable zone widths (MSZW) and solution properties (the enthalpies and entropies of dissolution) as well as the nucleation reaction orders, are measured. The temperature of dissolution decreases with the decrease in cooling/heating rate whilst the temperature of crystallisation increases for all the systems, resulting in a decrease in the meta-stable zone width with decreasing temperature change rate. The enthalpies and entropies of dissolution of sodium, potassium and rubidium dodecyl sulphate increased with increasing alkali metal ionic radii. Very large values of MSZW for sodium citrate containing solutions occur. Extremely high reaction orders occur with SDS, at high concentrations when pure and at low concentrations when with sodium citrate.
    Journal of Crystal Growth 06/2001; 226(1-226):158-167. DOI:10.1016/S0022-0248(01)01368-9
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    ABSTRACT: A Lattice Boltzmann model is developed to account for the competition between surface tension and dipolar interaction in magnetic fluids. The description of the interactions was kept as simple as possible to identify and isolate the nature of the essential interactions in the examined situations. The model is used thereafter in order to simulate the deformation of a magnetic fluid drop under the action of an external magnetic field, as well as the onset of the normal field instability in magnetic fluids. The success of the model, and easily identified deviations, demonstrate that the model is a powerful and versatile tool for the study of magnetic and nonmagnetic fluid systems with interfaces.
    Physics of Condensed Matter 02/2001; 20(1):141-149. DOI:10.1007/s100510170292
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    ABSTRACT: The structure of anhydrous sodium dodecyl sulphate (SDS) was determined using a combination of high resolution, synchrotron, powder X-ray diffraction and molecular modelling techniques, including the use of a systematic search method to select suitable inter-molecular packing configurations for subsequent Rietveld refinement. Anhydrous SDS is monoclinic, space group P21/c, the unit cell dimensions are and β=93.29° and the asymmetric unit is comprised of a single SDS molecule. The packing motif consists of double layers of molecules. Molecules in adjacent layers are related by 21 axes, whilst within layers the adjacent molecules are related by c glide planes. The sulphur atom in the head group is displaced from the (100) plane by 2.1 Å and the methyl carbon is displaced by a perpendicular distance of 1.2 Å from the (200) plane. Electrostatic interactions between the headgroups dominate the packing and largely determine the alignment of the hydrocarbon chains with respect to the long axis of the unit cell. The average area per polar head group is 19.4 Å2. The present structure is compared with previously determined structures for three hydrated phases of SDS in terms of the observed intermolecular packing motifs.
    Journal of Molecular Structure 11/2000; 554(2-3-554):173-182. DOI:10.1016/S0022-2860(00)00666-9
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    ABSTRACT: The lack of a portable programming interface for parallel computers has inhibited the development of applications for such systems, and thus restricted the exploitation of this technology. In this paper we discuss various efforts to provide a portable interface to parallel computers, and present the Edinburgh CHIMP (Common High-level Interface to Message-Passing), and PUL (Parallel Utilities Library) activities in this context. The concepts behind these projects are described, with details of the range of parallel systems on which they are available. An important consequence of the portability offered by the CHIMP message passing layer is the ability for applications programmers to reuse entire programs, as well as code modules. PUL assists this by providing a set of reusable components for implementing parallel applications. Developed on top of CHIMP, the PUL utilities are themselves portable across a range of platforms. Finally, this paper summarises experience using CHIMP and PUL to implement parallel applications in collaboration with both industrial and academic groups.
    Future Generation Computer Systems 03/1995; 11(2-11):211-219. DOI:10.1016/0167-739X(94)00063-K
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