1,604 research outputs found
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
gcodeml: A Grid-enabled Tool for Detecting Positive Selection in Biological Evolution
One of the important questions in biological evolution is to know if certain
changes along protein coding genes have contributed to the adaptation of
species. This problem is known to be biologically complex and computationally
very expensive. It, therefore, requires efficient Grid or cluster solutions to
overcome the computational challenge. We have developed a Grid-enabled tool
(gcodeml) that relies on the PAML (codeml) package to help analyse large
phylogenetic datasets on both Grids and computational clusters. Although we
report on results for gcodeml, our approach is applicable and customisable to
related problems in biology or other scientific domains.Comment: 10 pages, 4 figures. To appear in the HealthGrid 2012 con
Scientific workflow orchestration interoperating HTC and HPC resources
8 páginas, 7 figuras.-- El Pdf del artículo es la versión pre-print.In this work we describe our developments towards the provision of a unified
access method to different types of computing infrastructures at the interop-
eration level. For that, we have developed a middleware suite which bridges
not interoperable middleware stacks used for building distributed computing
infrastructues, UNICORE and gLite. Our solution allows to transparently
access and operate on HPC and HTC resources from a single interface. Using
Kepler as workflow manager, we provide users with the needed integration of
codes to create scientific workflows accessing both types of infrastructures.Peer reviewe
The Gridbus Toolkit for Service Oriented Grid and Utility Computing: An Overview and Status Report
Grids aim at exploiting synergies that result from cooperation of autonomous
distributed entities. The synergies that result from grid cooperation include
the sharing, exchange, selection, and aggregation of geographically distributed
resources such as computers, data bases, software, and scientific instruments
for solving large-scale problems in science, engineering, and commerce. For
this cooperation to be sustainable, participants need to have economic
incentive. Therefore, "incentive" mechanisms should be considered as one of key
design parameters of Grid architectures. In this article, we present an
overview and status of an open source Grid toolkit, called Gridbus, whose
architecture is fundamentally driven by the requirements of Grid economy.
Gridbus technologies provide services for both computational and data grids
that power the emerging eScience and eBusiness applications.Comment: 11 pages, 3 figures, 3 table
The next-generation ARC middleware
The Advanced Resource Connector (ARC) is a light-weight, non-intrusive, simple yet powerful Grid middleware capable of connecting highly heterogeneous computing and storage resources. ARC aims at providing general purpose, flexible, collaborative computing environments suitable for a range of uses, both in science and business. The server side offers the fundamental job execution management, information and data capabilities required for a Grid. Users are provided with an easy to install and use client which provides a basic toolbox for job- and data management. The KnowARC project developed the next-generation ARC middleware, implemented as Web Services with the aim of standard-compliant interoperability
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