Dušan Vudragović

Development of Grid e-Infrastructure in South-Eastern Europe

Over the period of six years and three phases, the SEE-GRID programme has established a strong regional human network in the area of distributed scientific computing and has set up a powerful regional Grid infrastructure. It attracted a number of user communities and applications from diverse fields from countries throughout the South-Eastern Europe. From the infrastructure point view, the first project phase has established a pilot Grid infrastructure with more than 20 resource centers in 11 countries. During the subsequent two phases of the project, the infrastructure has grown to currently 55 resource centers with more than 6,600 CPUs and 750 TBs of disk storage, distributed in 16 participating countries. Inclusion of new resource centers to the existing infrastructure, as well as a support to new user communities, has demanded setup of regionally distributed core services, development of new monitoring and operational tools, and close collaboration of all partner institution in managing such a complex infrastructure. In this paper we give an overview of the development and current status of SEE-GRID regional infrastructure and describe its transition to the NGI-based Grid model in EGI, with the strong SEE regional collaboration.

OpenMP Fortran and C programs for solving the time-dependent Gross-Pitaevskii equation in an anisotropic trap

We present new version of previously published Fortran and C programs for solving the Gross–Pitaevskii equation for a Bose–Einstein condensate with contact interaction in one, two and three spatial dimensions in imaginary and real time, yielding both stationary and non-stationary solutions. To reduce the execution time on multicore processors, new versions of parallelized programs are developed using Open Multi-Processing (OpenMP) interface. The input in the previous versions of programs was the mathematical quantity nonlinearity for dimensionless form of Gross–Pitaevskii equation, whereas in the present programs the inputs are quantities of experimental interest, such as, number of atoms, scattering length, oscillator length for the trap, etc. New output files for some integrated one- and two-dimensional densities of experimental interest are given. We also present speedup test results for the new programs.

OpenMP GNU and Intel Fortran programs for solving the time-dependent Gross-Pitaevskii equation

We present Open Multi-Processing (OpenMP) version of Fortran 90 programs for solving the Gross–Pitaevskii (GP) equation for a Bose–Einstein condensate in one, two, and three spatial dimensions, optimized for use with GNU and Intel compilers. We use the split-step Crank–Nicolson algorithm for imaginary- and real-time propagation, which enables efficient calculation of stationary and non-stationary solutions, respectively. The present OpenMP programs are designed for computers with multi-core processors and optimized for compiling with both commercially-licensed Intel Fortran and popular free open-source GNU Fortran compiler. The programs are easy to use and are elaborated with helpful comments for the users. All input parameters are listed at the beginning of each program. Different output files provide physical quantities such as energy, chemical potential, root-mean-square sizes, densities, etc. We also present speedup test results for new versions of the programs.

Discovering, Indexing and Interlinking Information Resources

The social media revolution is having a dramatic effect on the world of scientific publication. Scientists now publish their research interests, theories and outcomes across numerous channels, including personal blogs and other thematic web spaces where ideas, activities and partial results are discussed. Accordingly, information systems that facilitate access to scientific literature must learn to cope with this valuable and varied data, evolving to make this research easily discoverable and available to end users. In this paper we describe the incremental process of discovering web resources in the domain of agricultural science and technology. Making use of Linked Open Data methodologies, we interlink a wide array of custom-crawled resources with the AGRIS bibliographic database in order to enrich the user experience of the AGRIS website. We also discuss the SemaGrow Stack, a query federation and data integration infrastructure used to estimate the semantic distance between crawled web resources and AGRIS.The social media revolution is having a dramatic effect on the world of scientific publication. Scientists now publish their research interests, theories and outcomes across numerous channels, including personal blogs and other thematic web spaces where ideas, activities and partial results are discussed. Accordingly, information systems that facilitate access to scientific literature must learn to cope with this valuable and varied data, evolving to make this research easily discoverable and available to end users. In this paper we describe the incremental process of discovering web resources in the domain of agricultural science and technology. Making use of Linked Open Data methodologies, we interlink a wide array of custom-crawled resources with the AGRIS bibliographic database in order to enrich the user experience of the AGRIS website. We also discuss the SemaGrow Stack, a query federation and data integration infrastructure used to estimate the semantic distance between crawled web resources and AGRIS.

SPEEDUP Code for Calculation of Transition Amplitudes via the Effective Action Approach

We present Path Integral Monte Carlo C code for calculation of quantum mechanical transition amplitudes for 1D models. The SPEEDUP C code is based on the use of higher-order short-time effectiveactions and implemented to the maximal order p=18 in the time of propagation (Monte Carlo time step), which substantially improves the convergence of discretized amplitudes to their exact continuum values. Symbolic derivation of higher-order effective actions is implemented in SPEEDUP Mathematica codes, using the recursive Schrodinger equation approach. In addition to the general 1D quantum theory, developed Mathematica codes are capable of calculating effective actions for specific models, for general 2D and 3D potentials, as well as for a general many-body theory in arbitrary number of spatial dimensions.

SEE-GRID eInfrastructure for Regional eScience

In the past 6 years, a number of targeted initiatives, funded by the European Commission via its information society and RTD programmes and Greek infrastructure development actions, have articulated a successful regional development actions in South East Europe that can be used as a role model for other international developments. The SEEREN (South-East European Research and Education Networking initiative) project, through its two phases, established the SEE segment of the pan-European G ´EANT network and successfully connected the research and scientific communities in the region. Currently, the SEE-LIGHT project is working towards establishing a dark-fiber backbone that will interconnect most national Research and Education networks in the region. On the distributed computing and storage provisioning i.e. Grid plane, the SEE-GRID (South-East European GRID e-Infrastructure Development) project, similarly through its two phases, has established a strong human network in the area of scientific computing and has set up a powerful regional Grid infrastructure, and attracted a number of applications from different fields from countries throughout the South-East Europe. The current SEEGRID-SCI project, ending in April 2010, empowers the regional user communities from fields of meteorology, seismology and environmental protection in common use and sharing of the regional e-Infrastructure. Current technical initiatives in formulation are focusing on a set of coordinated actions in the area of HPC and application fields making use of HPC initiatives. Finally, the current SEERA-EI project brings together policy makers – programme managers from 10 countries in the region. The project aims to establish a communication platform between programme managers, pave the way towards common e-Infrastructure strategy and vision, and implement concrete actions for common funding of electronic infrastructures on the regional level. The regional vision on establishing an e-Infrastructure compatible with European developments, and empowering the scientists in the region in equal participation in the use of pan- European infrastructures, is materializing through the above initiatives. This model has a number of concrete operational and organizational guidelines which can be adapted to help e-Infrastructure developments in other world regions. In this paper we review the most important developments and contributions by the SEEGRID- SCI project.

Science Gateway for the Serbian Condensed Matter Physics Community

The Academic and Educational Grid Initiative of Serbia hosts and maintains the scientific gateway of the Serbian condensed matter physics community. The gateway is built around a code set addressing problems from the physics of ultracold quantum gases, solving the nonlinear Schroedinger equation, the Gross–Pitaevskii equation in real and imaginary time, and a path integral algorithm for estimation of quantum-mechanical transition amplitudes, which are relevant for various applications. Here we present the realization of the gateway and technologies used for its implementation.

Implementation and Benchmarking of New FFT Libraries in Quantum ESPRESSO

Quantum ESPRESSO (QE) software package allows electronic-structure calculations and materials modeling at the nanoscale, based on density-functional theory, plane waves, and pseudopotentials. It extensively uses Fast Fourier Transform (FFT) during all computations. In addition to the built-in FFT libraries, QE enables integration of newly developed FFT algorithms. Since Fastest Fourier Transform of the East (FFTE) library has shown performance comparable with the widely used and vendor-supplied libraries, the same behavior is foreseen in QE. In this paper we present FFTE-enabled and thread-enabled FFTW3 extensions of QE, together with benchmarking and performance results.