196,054 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
State-of-the-Art in Parallel Computing with R
R is a mature open-source programming language for statistical computing and graphics. Many areas of statistical research are experiencing rapid growth in the size of data sets. Methodological advances drive increased use of simulations. A common approach is to use parallel computing. This paper presents an overview of techniques for parallel computing with R on computer clusters, on multi-core systems, and in grid computing. It reviews sixteen different packages, comparing them on their state of development, the parallel technology used, as well as on usability, acceptance, and performance. Two packages (snow, Rmpi) stand out as particularly useful for general use on computer clusters. Packages for grid computing are still in development, with only one package currently available to the end user. For multi-core systems four different packages exist, but a number of issues pose challenges to early adopters. The paper concludes with ideas for further developments in high performance computing with R. Example code is available in the appendix
Integrating heterogeneous distributed COTS discrete-event simulation packages: An emerging standards-based approach
This paper reports on the progress made toward the emergence of standards to support the integration of heterogeneous discrete-event simulations (DESs) created in specialist support tools called commercial-off-the-shelf (COTS) discrete-event simulation packages (CSPs). The general standard for heterogeneous integration in this area has been developed from research in distributed simulation and is the IEEE 1516 standard The High Level Architecture (HLA). However, the specific needs of heterogeneous CSP integration require that the HLA is augmented by additional complementary standards. These are the suite of CSP interoperability (CSPI) standards being developed under the Simulation Interoperability Standards Organization (SISO-http://www.sisostds.org) by the CSPI Product Development Group (CSPI-PDG). The suite consists of several interoperability reference models (IRMs) that outline different integration needs of CSPI, interoperability frameworks (IFs) that define the HLA-based solution to each IRM, appropriate data exchange representations to specify the data exchanged in an IF, and benchmarks termed CSP emulators (CSPEs). This paper contributes to the development of the Type I IF that is intended to represent the HLA-based solution to the problem outlined by the Type I IRM (asynchronous entity passing) by developing the entity transfer specification (ETS) data exchange representation. The use of the ETS in an illustrative case study implemented using a prototype CSPE is shown. This case study also allows us to highlight the importance of event granularity and lookahead in the performance and development of the Type I IF, and to discuss possible methods to automate the capture of appropriate values of lookahead
HLA-CSPIF panel on commercial off-the-shelf distributed simulation
Commercial-off-the-shelf (COTS) simulation packages are widely used in many areas of industry. Several research groups are attempting to integrate distributed simulation principles and techniques with these packages to potentially give us COTS distributed simulation. The High Level Architecture-COTS Simulation Package Interoperation Forum (HLA-CSPIF) is a group of researchers and practitioners that are studying methodological and technological issues in this area. This panel paper presents the views of four members of this forum on the technical problems that must be overcome for this emerging field to be realized
AstroGrid-D: Grid Technology for Astronomical Science
We present status and results of AstroGrid-D, a joint effort of
astrophysicists and computer scientists to employ grid technology for
scientific applications. AstroGrid-D provides access to a network of
distributed machines with a set of commands as well as software interfaces. It
allows simple use of computer and storage facilities and to schedule or monitor
compute tasks and data management. It is based on the Globus Toolkit middleware
(GT4). Chapter 1 describes the context which led to the demand for advanced
software solutions in Astrophysics, and we state the goals of the project. We
then present characteristic astrophysical applications that have been
implemented on AstroGrid-D in chapter 2. We describe simulations of different
complexity, compute-intensive calculations running on multiple sites, and
advanced applications for specific scientific purposes, such as a connection to
robotic telescopes. We can show from these examples how grid execution improves
e.g. the scientific workflow. Chapter 3 explains the software tools and
services that we adapted or newly developed. Section 3.1 is focused on the
administrative aspects of the infrastructure, to manage users and monitor
activity. Section 3.2 characterises the central components of our architecture:
The AstroGrid-D information service to collect and store metadata, a file
management system, the data management system, and a job manager for automatic
submission of compute tasks. We summarise the successfully established
infrastructure in chapter 4, concluding with our future plans to establish
AstroGrid-D as a platform of modern e-Astronomy.Comment: 14 pages, 12 figures Subjects: data analysis, image processing,
robotic telescopes, simulations, grid. Accepted for publication in New
Astronom
Nmag micromagnetic simulation tool - software engineering lessons learned
We review design and development decisions and their impact for the open
source code Nmag from a software engineering in computational science point of
view. We summarise lessons learned and recommendations for future computational
science projects. Key lessons include that encapsulating the simulation
functionality in a library of a general purpose language, here Python, provides
great flexibility in using the software. The choice of Python for the top-level
user interface was very well received by users from the science and engineering
community. The from-source installation in which required external libraries
and dependencies are compiled from a tarball was remarkably robust. In places,
the code is a lot more ambitious than necessary, which introduces unnecessary
complexity and reduces main- tainability. Tests distributed with the package
are useful, although more unit tests and continuous integration would have been
desirable. The detailed documentation, together with a tutorial for the usage
of the system, was perceived as one of its main strengths by the community.Comment: 7 pages, 5 figures, Software Engineering for Science, ICSE201
RELEASE: A High-level Paradigm for Reliable Large-scale Server Software
Erlang is a functional language with a much-emulated model for building reliable distributed systems. This paper outlines the RELEASE project, and describes the progress in the first six months. The project aim is to scale the Erlang’s radical concurrency-oriented programming paradigm to build reliable general-purpose software, such as server-based systems, on massively parallel machines. Currently Erlang has inherently scalable computation and reliability models, but in practice scalability is constrained by aspects of the language and virtual machine. We are working at three levels to address these challenges: evolving the Erlang virtual machine so that it can work effectively on large scale multicore systems; evolving the language to Scalable Distributed (SD) Erlang; developing a scalable Erlang infrastructure to integrate multiple, heterogeneous clusters. We are also developing state of the art tools that allow programmers to understand the behaviour of massively parallel SD Erlang programs. We will demonstrate the effectiveness of the RELEASE approach using demonstrators and two large case studies on a Blue Gene
Advances in the Design and Implementation of a Multi-Tier Architecture in the GIPSY Environment
We present advances in the software engineering design and implementation of
the multi-tier run-time system for the General Intensional Programming System
(GIPSY) by further unifying the distributed technologies used to implement the
Demand Migration Framework (DMF) in order to streamline distributed execution
of hybrid intensional-imperative programs using Java.Comment: 11 pages, 3 figure
- …