Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Let's read! We will often find out this sentence everywhere. When still being a kid, mom used to order us to always read, so did the teacher. Some books are fully read in a week and we need the obligation to support reading. What about now? Do you still love reading? Is reading only for you who have obligation? Absolutely not! We here offer you a new book enPDFd the perception of the visual world to read.

The Perception of the Visual World. By James J. Gibson. U.S.A.: Houghton Mifflin Company, 1950 (George Allen & Unwin, Ltd., London). Price 35s.

A Viking Lander 1 image was modeled as mixtures of reflectance spectra of palagonite dust, gray andesitelike rock, and a coarse rocklike soil. The rocks are covered to varying degrees by dust but otherwise appear unweathered. Rocklike soil occurs as lag deposits in deflation zones around stones and on top of a drift and as a layer in a trench dug by the lander. This soil probably is derived from the rocks by wind abrasion and/or spallation. Dust is the major component of the soil and covers most of the surface. The dust is unrelated spectrally to the rock but is equivalent to the global-scale dust observed telescopically. A new method was developed to model a multispectral image as mixtures of end-member spectra and to compare image spectra directly with laboratory reference spectra. The method for the first time uses shade and secondary illumination effects as spectral end-members; thus the effects of topography and illumination on all scales can be isolated or removed. The image was calibrated absolutely from the laboratory spectra, in close agreement with direct calibrations. The method has broad applications to interpreting multispectral images, including satellite images.

Spectral mixture modeling - A new analysis of rock and soil types at the Viking Lander 1 site. [on Mars]

Workflows and e-Science: An overview of workflow system features and capabilities

Multiagent Systems is the title of a collection of papers dedicated to surveying specific themes of Multiagent Systems (MAS) and Distributed Artificial Intelligence (DAI). All of them authored by leading researchers of this dynamic multidisciplinary field.

/pdf/multiagent-systems-a-modern-approach-to-distributed-5fon0donq1.pdf

Multiagent systems: a modern approach to distributed artificial intelligence

The main objective of Science Gateways is to give users remote access to supercomputers and large-scale computing environments in an interactive, web-based and graphical manner We present a tool, called Vine Toolkit, that has been successfully used as a core web platform for various Science Gateways Vine Toolkit is a modular, extensible and easy-to-use tool as well as a high-level Application Programming Interface (API) for various applications, visualization components and building blocks In a nutshell, it allows interoperability between many different HPC and grid technologies within the service layer As a result, Vine Toolkit provides an ability to build a portal upon different HPC technologies working together to deliver a complete solution to the users In this article, we briefly describe our most complex and feature-rich project --- the Nanotechnology Gateway, as well as a set of tools relevant to advanced scientific portals, development of which was driven by various requirements defined by scientists and gathered in scope of the PL-Grid project

Online web-based science gateway for nanotechnology research

In this paper we present our motivations and ideas for workflow management based on our experiences gained in two projects: GridLab and PROGRESS. In these projects we have been dealing with real use cases and end users' requirements for workflow management. Therefore, we were able to define and implement functional workflow extensions to the Grid(Lab) Resource Management System (GRMS). GRMS is a resource management system with a workflow engine that executes and manages jobs on remote Grid resources. One can submit to GRMS workflow experiments based on an XML workflow schema, defining flexible mechanisms for dynamic workflow control, including various types of precedence constraints, different locations of the final data products and executables, etc. All of these features allow end users to speed up remote workflow calculations and improve data management mechanisms. Copyright © 2005 John Wiley & Sons, Ltd.

Workflow applications in GridLab and PROGRESS projects

https://onlinelibrary.wiley.com/doi/pdf/10.1111/itor.12368

Scheduling aspects in keyword extraction problem

We present the Multiscale Coupling Library and Environment: MUSCLE 2. This multiscale component-based execution environment has a simple to use Java, C++, C, Python and Fortran API, compatible with MPI, OpenMP and threading codes. We demonstrate its local and distributed computing capabilities and compare its performance to MUSCLE 1, file copy, MPI, MPWide, and GridFTP. The local throughput of MPI is about two times higher, so very tightly coupled code should use MPI as a single submodel of MUSCLE 2; the distributed performance of GridFTP is lower, especially for small messages. We test the performance of a canal system model with MUSCLE 2, where it introduces an overhead as small as 5% compared to MPI.

Distributed Multiscale Computing with MUSCLE 2, the Multiscale Coupling Library and Environment

Science Gateway is a set of tools for scientists to facilitate access to their computational resources in a comprehensive, efficient and easy manner. The most common instance of Science Gateway comes in the form of a web portal. It provides space for communities, collaboration, data sharing and visualization along with the possibility of defining, running and managing computational tasks. The main objective of such a portal is to allow users to access the computational resources, to process and analyze their data and to obtain results in a uniform and user friendly way. In this publication we briefly describe solutions for Nanomechanics, Quantum Chemistry and Molecular Physics fields with the use of Vine Toolkit and QosCosGrid tools and different domain-specific applications.

Krzysztof Kurowski

Papers

Online web-based science gateway for nanotechnology research

Workflow applications in GridLab and PROGRESS projects

Scheduling aspects in keyword extraction problem

Distributed Multiscale Computing with MUSCLE 2, the Multiscale Coupling Library and Environment

Easy Development and Integration of Science Gateways with Vine Toolkit