2 research outputs found
From Quantity to Quality: Massive Molecular Dynamics Simulation of Nanostructures under Plastic Deformation in Desktop and Service Grid Distributed Computing Infrastructure
The distributed computing infrastructure (DCI) on the basis of BOINC and
EDGeS-bridge technologies for high-performance distributed computing is used
for porting the sequential molecular dynamics (MD) application to its parallel
version for DCI with Desktop Grids (DGs) and Service Grids (SGs). The actual
metrics of the working DG-SG DCI were measured, and the normal distribution of
host performances, and signs of log-normal distributions of other
characteristics (CPUs, RAM, and HDD per host) were found. The practical
feasibility and high efficiency of the MD simulations on the basis of DG-SG DCI
were demonstrated during the experiment with the massive MD simulations for the
large quantity of aluminum nanocrystals (-). Statistical
analysis (Kolmogorov-Smirnov test, moment analysis, and bootstrapping analysis)
of the defect density distribution over the ensemble of nanocrystals had shown
that change of plastic deformation mode is followed by the qualitative change
of defect density distribution type over ensemble of nanocrystals. Some
limitations (fluctuating performance, unpredictable availability of resources,
etc.) of the typical DG-SG DCI were outlined, and some advantages (high
efficiency, high speedup, and low cost) were demonstrated. Deploying on DG DCI
allows to get new scientific from the simulated
of numerous configurations by harnessing sufficient computational power to
undertake MD simulations in a wider range of physical parameters
(configurations) in a much shorter timeframe.Comment: 13 pages, 11 pages (http://journals.agh.edu.pl/csci/article/view/106
IMP Science Gateway: from the Portal to the Hub of Virtual Experimental Labs in Materials Science
"Science gateway" (SG) ideology means a user-friendly intuitive interface
between scientists (or scientific communities) and different software
components + various distributed computing infrastructures (DCIs) (like grids,
clouds, clusters), where researchers can focus on their scientific goals and
less on peculiarities of software/DCI. "IMP Science Gateway Portal"
(http://scigate.imp.kiev.ua) for complex workflow management and integration of
distributed computing resources (like clusters, service grids, desktop grids,
clouds) is presented. It is created on the basis of WS-PGRADE and gUSE
technologies, where WS-PGRADE is designed for science workflow operation and
gUSE - for smooth integration of available resources for parallel and
distributed computing in various heterogeneous distributed computing
infrastructures (DCI). The typical scientific workflows with possible scenarios
of its preparation and usage are presented. Several typical use cases for these
science applications (scientific workflows) are considered for molecular
dynamics (MD) simulations of complex behavior of various nanostructures
(nanoindentation of graphene layers, defect system relaxation in metal
nanocrystals, thermal stability of boron nitride nanotubes, etc.). The user
experience is analyzed in the context of its practical applications for MD
simulations in materials science, physics and nanotechnologies with available
heterogeneous DCIs. In conclusion, the "science gateway" approach - workflow
manager (like WS-PGRADE) + DCI resources manager (like gUSE)- gives opportunity
to use the SG portal (like "IMP Science Gateway Portal") in a very promising
way, namely, as a hub of various virtual experimental labs (different software
components + various requirements to resources) in the context of its practical
MD applications in materials science, physics, chemistry, biology, and
nanotechnologies.Comment: 6 pages, 5 figures, 3 tables; 6th International Workshop on Science
Gateways, IWSG-2014 (Dublin, Ireland, 3-5 June, 2014). arXiv admin note:
substantial text overlap with arXiv:1404.545