EUROGRID—European computational grid testbed

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Abstract

In this paper, we describe developed grid tools for biomolecular applications. We have used UNICORE infrastructure as framework for European computational grid. The EUROGRID provides users with seamless and secure access to the resources, with site autonomy conserved. The strength of presented approach is ability to easy development of application specific interfaces to the grid applications.

Introduction

Large problems need resources on a variety of systems at different locations. Users are faced with different site polices and practices such as different security, different user identification, and so on. Distributed computational resources cannot be effectively utilized using typical Unix tools based on remote login. In such situation easy and uniform access to the remote computer systems becomes crucial for users.

Recent advances in computer technology, especially grid tools make them good candidate for development of user interfaces to computing programs and resources [7]. Computational grids enable sharing a wide variety of geographically distributed resources and allow selection and aggregation of distributed resources across multiple organizations for solving large-scale computational and data intensive problems in science. The special challenge is to join resources from different organizations and countries, where various local policies and security models must be considered. Especially, in the case of European HPC Centers this problem becomes crucial and difficult to solve.

The high performance computing is required for number of disciplines and scientific areas. Molecular biology and quantum chemistry traditionally provides large number of important, nontrivial and computationally intensive problems. Weather forecasting is another example of important computation intensive application. The third group of applications which requires access to the distributed resources are various mechanical engineering programs used for the design and tests of complicated systems such as cars, aircrafts, etc. Complexity of the studied systems leads to the computational intensive tasks which must be solved. Because majority codes are based on the finite element methods, they can be run efficiently in the geographically distributed grid.

To attract users grid interfaces, possibly web based, must be easy to install, simple to use especially in a distributed environment. Providing powerful user interface, web technology cannot achieve high numerical efficiency required for most simulation problems. This leads us to solutions consisting on web interface for the user and traditional, usually batch type, numerical simulation engine.

Easy access to high-performance resources is being developed significantly in last few years. However most of the development goes to the design and production of general tools which can be used in different situations and provide simple access to remote resources. The existing solutions like Globus, [4] Legion, [12] LSF, [10] address many important issues. Unfortunately, in order to provide required functionality user application must be modified, sometimes significantly. This is not possible for commercial or legacy codes which cannot be easily adopted by the user. Most grid solutions have limited user interface not addressing application specific issues. Often security model applied is not sufficient for the HPC centers which makes most important resources available to the user. However, attempts to improve security usually ends up with the uncomfortable solutions not acceptable by the user. As a result, grid technology cannot be widely used.

For the more comfortable access to the resources the user can find WebMo [13] which is web based submission systems for quantum chemistry codes such as Gaussian, Gamess and Mopac but this system is limited to the local batch systems and has no grid capabilities. The web submission to the geographically distributed systems is possible within BioCore [1] which is web interface to the molecular dynamics code NAMD [6]. Currently, this system is limited to the particular MD code and single visualization package (VMD). Similar functionality for Gamess provides NPACI Portal [11].

The user's point of view is the most important principle in the development of the UNICORE [9] software. UNICORE provides uniform interface to the computer resources which allows user to prepare, submit and control application specific jobs and file transfers. Jobs to be run on the same system can be grouped in job groups. The user specifies a target system for job group as well as resource requirements for CPU time, number of CPUs, amount of memory and disk space for job. Job can have complex structure with various job subgroups which can be run on different systems and at different sites. Subgroups, jobs, and file transfers can be ordered through user defined dependency. The user input is mapped to the target system specific commands and options by the UNICORE infrastructure.

Section snippets

The UNICORE architecture

The UNICORE architecture is based, as other grid middleware, on three-tier model. It consists of user, server, and target system tier. The user tier consists of the graphical user interface—the UNICORE client—written as a Java application. It offers the functions to prepare and control jobs and to set up and maintain the user's security environment.

From the user's input the UNICORE client generates an Abstract Job Object (AJO) which is sent to the other components of the UNICORE infrastructure.

The user interface

The graphical user interface offers functions to maintain security, to prepare UNICORE jobs and to submit and monitor them (Fig. 2). The UNICORE job can be build from multiple parts which can be executed asynchronously or dependently on different systems at different UNICORE sites. Basic elements are:

  • •

    script task, to submit job scripts;

  • •

    transfer task to specify data transfer between different jobs groups;

  • •

    job groups, to build subjobs for other systems.


All elements can be added and edited

User applications in UNICORE

UNICORE software provides general framework for running user applications. On the other hand, there exists wide range of applications which are commonly used in the quantum chemistry, molecular biology or used for weather prediction or mechanical engineering. For the advanced user it is possible to develop scripts for running application within UNICORE, but this takes time and requires some experience. In the simplest approach one can prepare script job specifying program which should be run.

UNICORE plugins for biomolecular applications

UNICORE script job still requires knowledge of the input files for the biomolecular applications. In most cases it is performed with standard text editor and requires significant experience from the user. Any mistake in the file format results with an error and extends time in which results will be obtained.

We have used UNICORE as framework for development dedicated user interface to the biomolecular and quantum chemistry applications. This includes plugins for Carr Parrinello Molecular

The EUROGRID testbed

A key objective of the EUROGRID project is to demonstrate the feasibility of Grid Computing using the existing European Network [3]. In addition to the BioGrid, described in detail in this paper, a MeteoGrid, a CAE-Grid and a general purpose HPC-Grid has been created to prove the concepts in different disciplines of science and engineering. The testbed is fully operational and is used by the selected number of users involved in the tests and development of components of the software. After the

Conclusions

We have used UNICORE as the main grid middleware for the development of the EUROGRID—European computational grid. Compared with other grid tools and applications this solution is easy to install, both at the server and client side and provides user with simple and intuitive interface. UNICORE client provides general mechanisms for user authentication and job preparation, submission and control. It is also used as framework for development application specific interfaces. In particular plugins

Acknowledgments

This work is supported by European Commission under IST Grant 20247. The software was used using EUROGRID facilities at ICM Warsaw University (Poland), Forschungcentrum Juelich (Germany), University of Manchester—CSAR (UK), IDRIS (France) and University of Bergen, Parallab (Norway).

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