Jan Kmuníček

Experimental evaluation of job provenance in ATLAS environment

Grid middleware stacks, including gLite, matured into the state of being able to process up to millions of jobs per day. Logging and Bookkeeping, the gLite job-tracking service, keeps pace with this rate; however, it is not designed to provide a long-term archive of information on executed jobs. ATLAS — representative of a large user community — addresses this issue with its own job catalogue (ProdDB). Development of such a customized service, not easily reusable, took considerable effort which is not affordable by smaller communities. On the contrary, Job Provenance (JP), a generic gLite service designed for long-term archiving of information on executed jobs focusing on scalability, extensibility, uniform data view, and configurability, allows more specialized catalogues to be easily built. We present the first results of an experimental JP deployment for the ATLAS production infrastructure where a JP installation was fed with a part of ATLAS jobs, and also stress tested with real production data. The main outcome of this work is a demonstration that JP can complement large-scale application-specific job catalogue services, while serving a similar purpose where there are none available.

Multiple Ligand Trajectory Docking Study - Semiautomatic Analysis of Molecular Dynamics Simulations using EGEE gLite Services

Interactions between large biomolecules and smaller bio-active ligands are usually studied through a process called docking. Its aim is to find an energetically favorable orientation of a ligand within an active site of a biomolecule. Chemical reactions take place in active site and the role of the ligand is either to speed up, slow down or change the reaction (e.g., an enzyme catalyzed hydrolysis), which is why it can have huge pharmaceutical or other commercial impact. We present a tool that supports effective management and control of a typical workflow of docking parametric study. Selected subsets of ligands and protein trajectory snapshots can be displayed in three different views and further analyzed. Finally, the application supports spawning and steering underlying computations running on the grid.

The EUAsiaGrid Roadmap Paths to a Sustainable, Persistent e-Infrastructure in the Asia-Pacific Region

The EUAsiaGrid project has developed a Roadmap towards the establishment of a persistent and sustainable e-Infrastructure for research in the Asia- Pacific region. This paper describes its aims and context, the decisions make in its creation and outlines the proposal for an Asia-Pacific Grid Initiative that will allow partners from different countries in the region to coordinate their national initiatives and align themselves with the emerging infrastructure in the region as well as developments elsewhere in the world.

Applicability of Free Energy Calculations Using High–Throughput Grid Approach

Free energy calculations tightly bind together experimental observations and computer-aided design through corresponding simulations at atomic level. Nowadays, free energy calculations represent a cornerstone for obtaining deeper insight into any biomolecular system, its molecular structure and especially dynamic behaviour. Despite this fact, several challenges have to be considered before routine utilization of this type of calculations. At first one has to deal properly with so-called sampling problem. Secondly, the appropriate way how to treat their extreme time demands has to be applied for obtaining converged and reliable data comparable with the experimental ones. Here we present the experience obtained through design, implementation and subsequent application of Multiple Walkers Approach (MWA) connected with Adaptive Biasing Force (ABF) and corresponding advantages and added values of MWA ABF run within distributed, heterogeneous grid environment under the EUAsia virtual organization (VO).

Catch-All Virtual Organizations - Solution for Heterogeneous and Disperse Grid Users Communities

The virtual organizations form a key concept for seamless utilization of all advanced features of available worldwide grid environments, the EGEE Grid in particular. However, apart from large, well organized user communities there is a substantial, non-trivial activation barrier in adopting grid concept and creating a new VO for small research groups. To minimize this barrier, a so-called “catch-all” virtual organization approach has been implemented. Here we present two successful use cases of catch-all virtual organizations (Virtual Organization for Central Europe and for EUAsia), demonstrating the strengths of this approach, discussing their setups, encountered challenges and suggesting corresponding solutions.