edikt Technical Workshop
Date: Wednesday September 16th 2009 Start: 14:00 Finish: 17:00 Venue: Rm 5215, James Clerk Maxwell Building, Kings Buildings
Purpose of workshop
The purpose of the meeting is for edikt2 participants to share information about the technical aspects of the various activities being funded through edikt2. The meeting is also open to other interested parties around the University and beyond.
The edikt (eScience Data, Information and Knowledge Transformation) project has been running since May 2002 and is using computational science to extract knowledge from vast datasets and simulation models. edikt is funded by the Scottish Funding Council.
For more information on edikt, see the project web site at http://www.edikt.org.uk.
1400 Welcome - Mr Terry Sloan (EPCC) 1405 Dr Paul Armitage (SFC Brain Imaging Research Centre) 'An update on the medical imaging aspects of edikt2' 1435 Dr Jano van Hemert (National eScience Centre) ' Rapid: giving computational science a friendly face' 1505 COFFEE 1530 Dr Nigel Binns (Division of Pathway Medicine) 'Pathway Modelling – A Boolean Approach to Predicting Gene Expression and Network Topology' 1600 Mr Terry Sloan (EPCC) 'An open source standards based portal based for accessing a European high performance computing infrastructure' 1630 Dr Alan Gray (EPCC) 'Developing research collaborations' 1645 Discussion 1700 Close
Attendance at the workshop is free with no prior registration required. For catering purposes, however, it would be very helpful if you could contact Terry Sloan (email@example.com, 0131 650 5155) beforehand with your name.
An update on the medical imaging aspects of edikt2 Dr Paul Armitage
Paul's slides eDIKT_Sept2009-PArmitage.pdf (PDF)
Rapid: giving computational science a friendly face Dr Jano van Hemert
Rapid is a unique approach to quickly designing and delivering web portal interfaces for applications that require large amounts of computing resources or that need to run on specific servers. We will demonstrate the success of Rapid in a number of projects across a wide range of disciplines: brain imaging, chemistry, microscopy, engineering and seismology.
The Rapid approach consists of defining the resources, application use and user interface in one configuration file. This file is then validated and translated directly into a live portlet that can be inserted into a portal container. The whole process can be performed without any conventional programming. Rapid provides all the necessary components for handling compute-jobs. It knows how to handle remote files stores, monitor jobs, validate input, talk to Sun Grid Engine, Condor, PBS or just use a plain SSH connection.
For Jano's slides see http://research.nesc.ac.uk/node/460
An open source standards based portal for accessing a European high performance computing infrastructure Terry Sloan
DEISA - Distributed European Infrastructure for Supercomputing Applications (http://www.deisa.eu/) - is a consortium of the 11 leading European national supercomputing centres. This consortium operates a persistent, production quality, distributed supercomputing environment – the DEISA Supercomputing Grid.
The DEISA consortium have developed, deployed and operated a Life Sciences Portal (LSP) that was based on a proprietary portal framework, EnginFrame, (http://www.enginframe.com/) . This LSP requires EnginFrame’s own proprietary infrastructure for submitting jobs to the batch schedulers on DEISA HPC platforms and for managing data movement between DEISA sites. DEISA therefore has had to install and maintain yet another infrastructure to handle operating system (OS) and batch scheduler heterogeneity of the DEISA HPC platforms. DEISA already has a UNICORE-based infrastructure (http://www.unicore.eu/) for handling such heterogeneity.
EPCC, through its involvement in eDIKT2, has collaborated with various members of the DEISA consortium to investigate two specific aspects of the LSP. Firstly can the LSP be adapted to work with a standards-based open source portal framework. Secondly, can an open-source standards based LSP work with DEISA’s existing open source UNICORE-based infrastructure for handling batch scheduler and OS heterogeneity. If it can, this potentially allows more efficient operation of the DEISA infrastructure since it will remove the need to maintain the Engin-Frame based infrastructure for accessing the HPC platforms.
This presentation will describe the architecture of an open source, standards-based portal for accessing DEISA's UNICORE infrastructure. This talk will describe some of the issues encountered in developing this and during its subsequent testing and also the potential barriers to its adoption in a production environment.
Terry's slides edikt2-Sept16-09-TSloan.pdf (PDF)