Ludek Matyska

Distributed and collaborative visualization of large data sets using high-speed networks

We describe an architecture for distributed collaborative visualization that integrates video conferencing, distributed data management and grid technologies as well as tangible interaction devices for visualization. High-speed, low-latency optical networks support high-quality collaborative interaction and remote visualization of large data.

The DataGrid Workload Management System: Challenges and Results

The workload management task of the DataGrid project was mandated to define and implement a suitable architecture for distributed scheduling and resource management in a Grid environment. The result was the design and implementation of a Grid Workload Management System, a super-scheduler with the distinguishing property of being able to take data access requirements into account when scheduling jobs to the available Grid resources. Many novel issues in various fields were faced such as resource management, resource reservation and co-allocation, Grid accounting. In this paper, the architecture and the functionality provided by the DataGrid Workload Management System are presented.

An Algorithm of State-Space Precomputation Allowing Non-linear Haptic Deformation Modelling Using Finite Element Method

After presenting the mathematical background of modelling elastic deformations together with finite element formulation, we propose a new algorithm allowing haptic interaction with soft tissues having both non-linear geometric and physical properties. The algorithm consists of two phases -first the configuration space is precomputed in a high-performance possibly distributed environment, then the precomputed data are used during the haptic interaction. In the paper, we focus mainly on sequential description of the first phase of the algorithm. We present some preliminary experimental results concerning the accuracy of the proposed method as well and the sketch of further extensions

On-line precomputation algorithm for real-time haptic interaction with non-linear deformable bodies

Soft tissue modelling is important in the realm of haptic interactions. The main challenge in this research area is to combine two basic conditions which are essential—the stability of the haptic interaction running on high refresh rate on one hand and realistic behavior of the tissue assuming computationally expensive mathematical models on the other.

MAPOS: a computer program for organic synthesis design based on synthon model of organic chemistry.

The program MAPOS is a logically oriented computer program for computer-aided organic synthesis design suitable both for forward and retrosynthetic synthesis planning. It is based on the synthon model of organic chemistry, introduced by the authors. The fundamentals of the model as well as the basic algorithms are described. Examples of the use of the program are given.

Improving Security in Grids Using the Smart Card Technology

Weak private key management can significantly decrease security of current grids. In this paper we present how smart cards can be used to solve private key management issues to improve security of the grid environment

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.

VirtCloud: Virtualising Network for Grid Environments First Experiences

Networking infrastructure is a vital part of virtual computer clusters. This paper describes VirtCloud, a system for interconnecting virtual clusters in a state-wide network based on advanced features available in academic networks. The system supports dynamic creation of virtual clusters without the need of run-time administrative privileges on the backbone core network, encapsulation of the clusters, controlled access to external sources for cluster hosts, full user access to the clusters, and optional publishing of the clusters. The paper describes architecture of the system, and prototype implementation in MetaCenter (Czech national Grid infrastructure) using Czech national research network CESNET2. Feasibility of the concept is evaluated through a series of measurements demonstrating that the network performance of the system is satisfactory.

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.

Distributed Data Storage with Strong Offline Access Support

In this paper, we propose a distributed data storage framework that supports unrestricted offline access. The system does not explicitly distinguish between connected and disconnected states. Its design is based on a lock-free distributed framework that avoids update conflicts through file versioning. The feasibility of this framework is confirmed by a proof-of- concept implementation. We also demonstrate that the proposed lock-free replica synchronization algorithm scales well. A future work will include also direct support for non-versioned files.