34,588 research outputs found
Towards a lightweight generic computational grid framework for biological research
Background: An increasing number of scientific research projects require access to large-scale computational resources. This is particularly true in the biological field, whether to facilitate the analysis of large high-throughput data sets, or to perform large numbers of complex simulations â a characteristic of the emerging field of systems biology. Results: In this paper we present a lightweight generic framework for combining disparate computational resources at multiple sites (ranging from local computers and clusters to established national Grid services). A detailed guide describing how to set up the framework is available from the following URL: http://igrid-ext.cryst.bbk.ac.uk/portal_guide/. Conclusion: This approach is particularly (but not exclusively) appropriate for large-scale biology projects with multiple collaborators working at different national or international sites. The framework is relatively easy to set up, hides the complexity of Grid middleware from the user, and provides access to resources through a single, uniform interface. It has been developed as part of the European ImmunoGrid project
Steering in computational science: mesoscale modelling and simulation
This paper outlines the benefits of computational steering for high
performance computing applications. Lattice-Boltzmann mesoscale fluid
simulations of binary and ternary amphiphilic fluids in two and three
dimensions are used to illustrate the substantial improvements which
computational steering offers in terms of resource efficiency and time to
discover new physics. We discuss details of our current steering
implementations and describe their future outlook with the advent of
computational grids.Comment: 40 pages, 11 figures. Accepted for publication in Contemporary
Physic
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Leveraging legacy codes to distributed problem solving environments: A web service approach
This paper describes techniques used to leverage high performance legacy codes as CORBA components to a distributed problem solving environment. It first briefly introduces the software architecture adopted by the environment. Then it presents a CORBA oriented wrapper generator (COWG) which can be used to automatically wrap high performance legacy codes as CORBA components. Two legacy codes have been wrapped with COWG. One is an MPI-based molecular dynamic simulation (MDS) code, the other is a finite element based computational fluid dynamics (CFD) code for simulating incompressible Navier-Stokes flows. Performance comparisons between runs of the MDS CORBA component and the original MDS legacy code on a cluster of workstations and on a parallel computer are also presented. Wrapped as CORBA components, these legacy codes can be reused in a distributed computing environment. The first case shows that high performance can be maintained with the wrapped MDS component. The second case shows that a Web user can submit a task to the wrapped CFD component through a Web page without knowing the exact implementation of the component. In this way, a userâs desktop computing environment can be extended to a high performance computing environment using a cluster of workstations or a parallel computer
WavePacket: A Matlab package for numerical quantum dynamics. I: Closed quantum systems and discrete variable representations
WavePacket is an open-source program package for the numerical simulation of
quantum-mechanical dynamics. It can be used to solve time-independent or
time-dependent linear Schr\"odinger and Liouville-von Neumann-equations in one
or more dimensions. Also coupled equations can be treated, which allows to
simulate molecular quantum dynamics beyond the Born-Oppenheimer approximation.
Optionally accounting for the interaction with external electric fields within
the semiclassical dipole approximation, WavePacket can be used to simulate
experiments involving tailored light pulses in photo-induced physics or
chemistry.The graphical capabilities allow visualization of quantum dynamics
'on the fly', including Wigner phase space representations. Being easy to use
and highly versatile, WavePacket is well suited for the teaching of quantum
mechanics as well as for research projects in atomic, molecular and optical
physics or in physical or theoretical chemistry.The present Part I deals with
the description of closed quantum systems in terms of Schr\"odinger equations.
The emphasis is on discrete variable representations for spatial discretization
as well as various techniques for temporal discretization.The upcoming Part II
will focus on open quantum systems and dimension reduction; it also describes
the codes for optimal control of quantum dynamics.The present work introduces
the MATLAB version of WavePacket 5.2.1 which is hosted at the Sourceforge
platform, where extensive Wiki-documentation as well as worked-out
demonstration examples can be found
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