The Irish Centre for High-End Computing
ICHEC News -- Issue 2 :: April 2007

HPC news & information from the Irish Centre for High-End Computing




:: Useful HPC Resources

Web-based HPC resources of note


TOP 500 Supercomputer Sites

IBM Deep Computing

Bull High Performance Computing (HPC) solutions

Linux High Performance Computing


What is ICHEC?

The Irish Centre for High-End Computing (ICHEC) delivers essential high-performance computing resources to Ireland's scientific community, with financial support from Science Foundation Ireland and the PRTLI project CosmoGrid. ICHEC Walton and Hamilton clusters allow researchers across a range of disciplines to run massively parallel calculations and simulations, enabling investigations of a size and scale previously not possible in Ireland. The Centre and its small support staff devote as much of their time and resources as possible to developing a nationwide community of researchers skilled in HPC methods, for the long-term improvement of Ireland's competitive position in world-class science.

:: HPC Events

See for a complete list

May 1, 2007
UCD CASL Computational Science Seminar
The Seminar Room, UCD CASL, Clonskeagh, Dublin 4
Brian Reville, UCD School of Mathematical Sciences discusses cosmic ray current driven instabilities and particle transport properties in turbulent self excited magnetic fields.

May 21 - 22, 2007
Annual DEISA Symposium
Munich, Germany
Distributed European Infrastructure for Supercomputing Applications

May 27-30, 2007
ICCS 2007: International Conference on Computational Science
Beijing, China

May 30-31, 2007
GridWorld 2007
Tokyo, Japan

June 7-8, 2007
IAHPC meeting
NUI Galway
Researchers interested in giving a 30 minute presentation on the computational aspects of their current research are urged to contact the iahpc. See more info at

June 15-19, 2007
ICNS07: Third International Conference on Networking and Services
Athens, Greece

June 26-29, 2007
International Supercomputing Conference (ISC07)
Dresden, Germany

July 8-20, 2007
International Summer School on Grid Computing 2007
Mariefred, Sweden

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JC Desplat, Acting Director, ICHECWelcome to Issue 2 of ICHEC News, the periodical dedicated to bringing researchers and institutions up to date with the latest high-performance computing news from Ireland. In this issue we look at the emerging area of e-infrastructure and its value to the Irish research community, as well as exciting new developments in ICHEC's course offerings and in the ICHEC team. As always, we would encourage you to contact us if you have any views on ICHEC's services or on how you believe this national resource should continue to develop.

JC Desplat, Acting Director, ICHEC


National Research e-Infrastructure proposed for Ireland: The HEA is considering a proposal under PRTLI cycle 4 for the Irish National e-Infrastructure (e-INIS), an initiative aimed at providing a world-class computational, networking and support infrastructure for Ireland's research community. The proposal, submitted by DIAS and including ICHEC, Grid-Ireland and HEAnet as major partners, seeks to provide researchers across disciplines with the best information technology facilities, including leading-edge HPC and data storage services. The proposal is aimed at consolidating the proven success of ICHEC and Grid-Ireland and expanding upon them to create a robust national research infrastructure.

Vision for e-INIS/e-PSIBuilding on HEAnet and grid technology from Grid-Ireland, e-INIS would be available at nodes nationwide and interlinked with similar European e-infrastructures. It would also be staffed by dedicated scientists responsible for the ongoing training and support of researchers.

Professor Luke Drury, coordinator of the proposal, said the infrastructure is vital to the future of Irish research. "Datasets and HPC facilities must be brought together to allow Irish researchers to do their work in a new way," he said, including via innovations such as virtual observatories. "The two historic pillars of science are the construction of theoretical models, and observation and experimentation. There's a third pillar now, of computer-assisted simulations and analysis of large data sets. In addition to research in vivo and in vitro, valuable work is being done in silico."

Dr Conor Masterson of DIAS said e-INIS would provide a national centre with the large-scale data management and HPC facilities essential to international scale research. "Ireland is just going to be peripheral in large projects if it doesn't have something like e-INIS to make a real contribution," he said.

Further information on e-INIS, including a white paper outlining the details of the project, is at

Ireland joins SIRENE - Sharing Infrastructure and REsources iN Europe: In line with the growing recognition of the importance of e-infrastructures, Ireland has just joined in the signing of the Memorandum of Understanding (MoU) to form SIRENE, a collaboration project that focuses on sharing high-end computing and storage systems among the smaller countries of Europe. Ireland, which joins SIRENE through ICHEC, will also work with the 10 other member countries to pool expertise, data, software and standards, allowing all participants to reap the benefits of this high-level collaboration.

Grid infrastructures and high-end computing are increasingly having an impact on research and science, and the smaller European countries are now recognising the importance of collaboration in this area, particularly as a means of making an impression on pan-European policies. Working together, the countries involved in SIRENE can keep up, and indeed remain at the forefront, of developments in grids and IT infrastructures, both in terms of technology and policies. In order to support its core activities, the group will submit a number of applications for funding to the European Commission's Framework 7 Programme.

The countries involved in SIRENE, who will work together on the initial setup and deployment of interoperable grid infrastructures, are dedicated to setting an "outstanding example of cooperative efforts and tangible results" in the area of grids and high-end computing. For more information, see

Participants from 11 smaller European countries come together at the signing of the SIRENE Mou
Participants from 11 smaller European countries come together at the signing of the SIRENE MoU

ICHEC announces new acting director: The Board of ICHEC has appointed Dr Jean-Christophe Desplat as Acting Director of ICHEC until 1st June 2007. Prior to his appointment, Dr Desplat, who has 16 years experience in HPC, occupied the position of Technical Manager, and was instrumental in establishing ICHEC and setting up Ireland's first National HPC Service. As well as 10 years spent at the Edinburgh Parallel Computing Centre (EPCC) in the UK, Dr Desplat has been involved in a number of high profile European projects. He has also collaborated with Prof. Michael E. Cates' research group at the University of Edinburgh with whom he co-authored a number of high profile publications. "I am particularly proud of the vote of confidence which the ICHEC Board has expressed through my appointment," said Dr Desplat. "This appointment occurs at a very interesting time when ICHEC is consolidating its involvement in the community through its Consortium support and training activities, and playing a major part in laying the foundations of Ireland's emerging e-Infrastructure."

ICHEC considers new Users Council: A proposal has been drafted for the creation of a new ICHEC Users Council, a group which would be responsible for providing formal feedback to the ICHEC Executive Committee on key operational matters, including support activities and scheduling policies. Plans for the council are still at a draft stage, but it's envisioned that the body would operate in parallel to the existing ICHEC user group meetings (UGM), and would consist of fifteen members drawn from existing projects. The overriding responsibility of the council, which would meet on a quarterly basis and consult openly with the UGM twice a year, will be to defend and represent the views of the ICHEC user community. The objective is to ensure that ICHEC continues to evolve into a national HPC facility and support service that truly reflects the needs of its users. For more information contact

New courses expand HPC training in Ireland: Students of HPC will have the opportunity to learn a range of new programming techniques following the announcement of two new courses from ICHEC. Dr Timothy Stitt, ICHEC's newly appointed training coordinator, is overseeing the development of the new courses, the first of which is being offered during May as part of a week-long session in NUI Maynooth. OpenMP, which will be addressed on the final two days of the course, is considered to be one of the easier to use techniques, allowing researchers to incrementally develop their code for use on Hamilton, the ICHEC shared memory machine. With OpenMP, programmers can parallelise their code a piece at a time, and continue to use the code as it is being developed. The training week at NUI Maynooth will be repeated at UCD and NUI Galway. The second new course, expected to be offered in the second half of 2007, will train students in the use of numerical libraries, which offer reusable, optimised code for commonly needed mathematical operations. For more details on any ICHEC courses or to reserve your place, see or contact Training Coordinator Timothy Stitt at For those of you who have already taken an ICHEC course but have not yet provided feedback, we are most keen to get your views. Feedback forms are available on the ICHEC training pages.


First principles materials design of transparent conducting oxides
Dr Michael Nolan, Tyndall National Institute, Cork
One of the most challenging areas of materials design is the creation of new semiconducting materials as the basis for future electronics. One class of semiconductors called transparent conducting oxides (TCOs) has the unique ability to let light pass through; this means that TCOs could facilitate the creation of transparent electronics, from automobile window demisters to transparent solar panels.

Delocalised p-type acceptor states in copper oxideSuch inventions are years away, however, because scientists are still seeking a crucial building block: a so-called p-type TCO. They believe that some derivative of copper oxide is what they're looking for, and Dr Michael Nolan at the Tyndall National Institute is using the ICHEC facilities to help in the search.

"Historically, materials design involves a tremendous amount of trial and error, synthesising materials that don't turn out to have the right properties," Dr Nolan said. "We're trying to bypass all that."

First principles modelling is being used to compute the optical and electrical properties of candidate TCOs in order to provide a screening process for potential TCO materials. The most promising candidates are passed to the experimentalists, who synthesise the material, test its properties and give feedback to the modelling work.

"The ICHEC facilities are essential to this work," Dr Nolan said. "We're screening so many potential materials and we need to do it quickly and efficiently. Without HPC, materials design would take just as long as trial-and-error in the lab. With HPC, our time and throughput is significantly improved."

Simulating the influence of multifluid physics in molecular clouds: towards a better understanding of the movement of magnetic fields
Dr Stephen O'Sullivan, UCD School of Mathematical Sciences and Dr Turlough Downes, Dublin City University
One of the main assumptions of ideal magnetohydrodynamics (MHD), which describes the interaction of electrically conducting fluids such as plasma with magnetic fields, is that the plasma behaves like a single fluid with a firmly embedded magnetic field. However, in many environments, such as those found in dense molecular clouds, the physics is richer than what single-fluid models can describe, and in order to better understand these environments a multifluid MHD model is necessary.

Structure in two turbulent molecular cloud simulations under the influence of different multifluid effectsSo far though, numerical research has made few forays beyond the single fluid MHD model, due mainly to the unsuitability of conventional numerical methods to 'simulate' these types of large scale environments.

In pioneering research, Dr O'Sullivan and Dr Turlough Downes have developed a numerical technology that has seen them successfully publish results from simulations describing the influence of multifluid physics in turbulent molecular clouds. The scope of the research is currently being extended to work on larger scale and more varied problems.

"ICHEC resources have been essential in carrying out our development of this innovative new technology," said Dr O'Sullivan. "In the longer term, if we are to capitalise on our world-leader status in this green-field area of astrophysics, it is crucial that we continue to have state-of-the-art hardware, as well as software, technologies available to our research groups."


The Irish Centre for High End Computing is pleased to announce the appointment of the following staff:

Timothy Stitt, HPC Support Scientist, ICHECTimothy Stitt, an HPC Support Scientist for ICHEC, has been appointed as the Centre's Training Coordinator. He received his Ph.D. in Computational Physics from Queen's University in Belfast in 2006. While pursuing his Ph.D, Timothy worked as a computer science lecturer in the Department of Mathematics and Computer Science at the University of the West Indies, Kingston, Jamaica. Prior to this Timothy spent a year undertaking research with Prof. Mike Atkinson at the Department of Computer Science, University of St. Andrews, Scotland after obtaining a BSc in Computer Science from Queen's University in Belfast.

Honore Tapamo, Research Support Scientist, ICHEC Honoré Tapamo has been appointed as a Research Support Scientist at ICHEC, having obtained his Ph.D in 2005. While living in Germany, Honore worked as a research and training assistant with the applied computer science group in the Department of Mathematics at the University of Wuppertal. Prior to that experience Honore attained a Masters in Computer Science from the University of Yaounde I, Cameroon in 2001.