Fredrik Hedman

KTH Royal Institute of Technology | KTH · PDC Center for High Performance Computing

Ewald summation method, based on Non-Uniform FFTs (ENUF) to compute the electrostatic interactions and forces, is implemented in two different particle simulation schemes to model molecular and soft matter, in classical all-atom Molecular Dynamics and in Dissipative Particle Dynamics for coarse-grained particles. The method combines the traditional...

We sketch an O(N log N) approach, recently proposed by us, that is based on the traditional Ewald summation technique. It can can be used to calculate the electrostatic energies and forces in molecular computer simulations and appears to conserve both energy and momen-tum. The method is straightforward to implement in existing simulation programs....

This paper evaluates the performance of the emerging OGF standard OGSA - Basic Execution Service (BES) on three fundamentally different Grid middleware platforms: UNICORE 5/6, Globus Toolkit 4 and gLite. The particular focus within this paper is on the OGSA-BES implementation of UNICORE 6. A comparison is made with baseline measurements, for UNICOR...

In the last couple of years, many e-Science infrastructures have begun to offer production services to e-Scientists with an increasing number of applications that require access to different kinds of computational resources. Within Europe two rather different multi-national e-Science infrastructures evolved over time namely Distributed European Inf...

In a distributed grid environment with ambitious service demands the job submission and management interfaces provide functionality of major importance. Emerging e-science and grid infrastructures such as EGEE and DEISA rely on highly available services that are capable of managing scientific jobs. It is the adoption of emerging open standard inter...

We propose a black-box approach to performance analysis of grid middleware and present the architecture of a non-invasive platform-independent evaluation tool that quantifies the effects of the overhead imposed by grid middleware on both the throughput of the system and on the turnaround times of grid applications. This approach is a step towards p...

Authentication interoperability between the UNICORE grid middleware system and other Grid middleware systems is addressed. An approach to extending the UNICORE authentication model to support a proxy certificate (RFC3280) profile is presented. This optional feature can then be enabled based on site policy. Furthermore, the addition capacitates furt...

In a distributed Grid environment with ambitious service demands the job submission and management interfaces provide functionality of major importance. Emerging e-Science and Grid infrastructures such as EGEE and DEISA rely on highly available services that are capable of managing scientific jobs. It is the adoption of emerging open standard inter...

A method to perform embarrassingly parallel ab initio molecular dynamics simulations of liquids on Born-Oppenheimer surfaces is described. It uses atomic energy gradient forces at an arbitrary level of quantum chemical methodology. The computational scheme is implemented with an MD program interfaced to a quantum chemistry package. Parallelization...

We present a novel O(N log N) approach, that combines the traditional Ewald summation technique with the nonuniform Fast Fourier transform to calculate the electrostatic energies and forces in molecular computer simulations. The method can easily be implemented in existing simulation programs. We report here some results from our implementation, wh...

We examine the performance of the molecular dynamics code Parallacs and the time-domain (TD) codes in the General ElectroMagnetic Solvers (GEMS) code suite for a 32 CPUs IBM 1.1 GHz pwr4 node. Parallacs is an easily portable molecular dynamics (MD) benchmark code, which contains most features found in current general-purpose production MD codes. Ti...

A very straightforward parallel scheme to perform Born–Oppenheimer quantum molecular dynamics simulations of liquids is presented. It is analogous to Linear Scaling methods, used in electronic structure calculations. The instantaneous liquid configurations of molecules moving in the simulation cell with periodic boundaries and minimum image convent...

A parallel implementation to perform quantum molecular dynamics simulations of liquids on Born-Oppenheimer surfaces is evaluated. The MD method allows the use of atomic energy gradient forces at an arbitrary level of quantum chemical methodology and electronic state. The computational scheme is very simple to implement, although still expensive to...

An approach to large-scale data-parallel molecular dynamics for simulations of systems which include Coulombic interactions is investigated. Short-range interactions are calculated with a method based on the use coarse-grained cells. In this method the simulation cell is decomposed into equally sized subcells, with the shortest side being larger th...

An efficient approach to large scale data parallel short-range molecular dynamics for liquids is presented. The method is based on the coarse-grained cell method in which the simulation cell is decomposed into equally sized subcells, with the shortest side being larger than the cut-off radius. To avoid a large fraction of the nonproductive calculat...

An efficient data parallel computational scheme is presented for large-scale molecular dynamics (MD) simulations of liquids with short-range interactions. The method is based on decomposition of the simulation cell into equally sized subcells, with the shortest side length equal to the cutoff radius. Inter- and intracell interactions are calculated...