The Irish Centre for High-End Computing
ICHEC News -- Issue 3 :: November 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

December 10-13
3rd IEEE International Conference on e-Science and Grid Computing
Bangalore, India

December 13-14
ICHEC Annual Seminar
Royal Irish Academy, Dublin

January 27-29
HiPEAC 2008: International Conference on High Performance Embedded Architectures & Compilers
Goteborg, Sweden

January 30
Mardi Gras Conference 2008
Baton Rouge, Louisiana

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:: Previous issues

ICHEC News Issue 2

ICHEC News Issue 1


Niall WilsonWelcome to Issue 3 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 are delighted to bring you news of the HEA's funding for the National e-Infrastructure (e-INIS) initiative, along with an update on the new ICHEC Users Council. We also take a look at the latest developments in weather prediction made possible through Met Éireann's partnership with ICHEC.

In addition, look out for information on upcoming ICHEC events around the country, including the ICHEC roadshow and our much-anticipated Annual Seminar, one of the most important events in the HPC calendar.

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.

Niall Wilson, Editor


Bright outlook from Met Éireann partnership: ICHEC's collaboration with Met Éireann is proving to be a fruitful partnership, with Ireland's National Meteorological Service making strides in the areas of climate modelling and next-generation weather forecasting. The collaboration, announced in April, has seen ICHEC provide computational facilities and support to Met Éireann to enable it to run its operational high-resolution forecast models on Walton, ICHEC's distributed memory cluster.

In addition to using ICHEC systems to run its current 48-hour weather forecasting model, Met Éireann is preparing for its predictions to become even more accurate with the introduction of the next-generation HARMONIE model. Alastair McKinstry, ICHEC Software Architect, has been testing HARMONIE since April 2007, liaising with the international weather forecasting community in the development of the model. The new system will enter into operational service in 2008/2009, following an extensive evaluation phase. HARMONIE will run on a much finer grid compared with the current model and will provide a more realistic description of local weather. It will also enable Met Éireann to improve its forecasting capabilities in areas such as the prediction of road ice and the spread of weather-sensitive diseases such as the foot-and-mouth virus.

From left to right: Dennis Jennings (chairman ICHEC Oversight Board), Dr. J.-C. Desplat (ICHEC Director), Dr. Declan Murphy (Met …ireann Director), and Prof. IognŠid ” Muircheartaigh (NUI Galway President)Great advances are also being made in the area of climate modelling, thanks to the joint efforts of Met Éireann, ICHEC and University College Dublin. EC-EARTH, a project that is part of a Europe-wide initiative to improve climate modelling, will be used to simulate Ireland's future climate, looking ahead several decades. ICHEC Support Scientist Honore Tapamo is helping to roll out the project, which builds on the work done in the area of weather forecasting but incorporates new advanced components to provide a more realistic description of the climate system than current models allow. "Because of the complexity of the model it is extremely expensive in computer time to run long climate simulations," says Ray McGrath, Head of the Research and Applications Division, Met Éireann. "ICHEC, with its large computing resources and experienced staff and researchers, is well placed to engage in this type of work."

From left to right the picture shows: Dennis Jennings (chairman ICHEC Oversight Board), Dr J.-C. Desplat (ICHEC Director), Dr Declan Murphy (Met Éireann Director),and Prof Iognáid Ó Muircheartaigh (NUI Galway President).

Funding approved for National e-Infrastructure: The Higher Education Authority recently announced funding for the National e-Infrastructure (e-INIS) initiative as part of its Programme for Research in Third Level Institutions (PRTLI4). This three-year, EUR12.5 million project, led by Prof Luke Drury from the Dublin Institute for Advanced Studies, will seek to design, deploy and operate e-INIS, an initiative aimed at providing a world-class computational, networking and support infrastructure for Ireland's research community. For more details on e-INIS, see Issue 2 of ICHEC News, and look out for further news in the next issue.

Annual Seminar announced: ICHEC is delighted to announce that its Annual Seminar will be held in association with the Royal Irish Academy in Dublin on 13 and 14 December. The two-day event will address three key topics in the HPC field: capability computing, e-infrastructure in Ireland, and environmental research and climate change. ICHEC invites anyone with an interest in these areas to attend the event, which will feature expert presentations and interactive panel discussions. Look out for more information on the seminar, along with details of how to secure your place, on the ICHEC website.

ICHEC Users Council moves ahead: The chairs of the new ICHEC Users Council have been named as Professor Stefano Sanvito of Trinity College Dublin and Doctor Jiri Vala of the Department of Mathematical Physics, NUI, Maynooth. The object of the new Users Council, which is to have its first meeting in mid-November, is to represent the views and concerns of ICHEC users to the management of the organisation, on topics as diverse as scheduling, courses and current and future ICHEC systems. "It is important to us that the Users Council be a representative sample of users from all participating third level institutions in Ireland," Prof Sanvito said. "We're looking for a good geographic representation as well as participation from researchers working on large-scale projects, users doing smaller-scale projects and users who are beginners." Both Prof Sanvito and Dr Vala are Principal Investigators leading Class A projects on ICHEC resources. All users are invited to suggest topics for discussion by emailing the chairs at

ICHEC roadshow kicks off: The 2007 ICHEC roadshow is already under way, and NUI Maynooth and University College Dublin were the first universities to be paid a visit in a countrywide tour of higher-level institutions. The sessions, which include a 30-minute presentation followed by a Q&A session, aim to provide an opportunity for ICHEC to meet with researchers across the country and bring them up-to-date with the latest developments in HPC. ICHEC staff will also outline the storage and computational resources that are available to help meet researchers' needs, along with support and consultancy services. Over the next six months, the roadshow will visit institutions in Dublin, Cork, Galway, Limerick, Belfast and Armagh.

SIRENE workshop in Dublin: ICHEC's first technical workshop under the SIRENE initiative took place at the end of October in Dublin. SIRENE (Sharing Infrastructure and REsources iN Europe) is a collaboration project that focuses on sharing high-end computing and storage systems among the smaller countries of Europe. A two-day workshop on the subject of e-infrastructures was held at the Dublin Institute for Advanced Studies on the 29th and 30th of October. (See Issue 2 of ICHEC News for more information on SIRENE.)


Team focus: System administrators

System administratorA good system administrator is one you don't notice. At least that's according to Eoin McHugh, one of ICHEC's small team of system administrators, who play a key role in the smooth running of its HPC services. ICHEC's system administration team is led by Niall Wilson and includes Marc Doumayrou as well as McHugh. These IT professionals, who among them boast more than 32 years' experience in system administration, are continually working away in the background to ensure that the researchers and scientists who use ICHEC's facilities have trouble-free access to the computational resources they need to run their large-scale, complex projects.

High-performance computing by its nature involves a large number of interacting pieces of software and hardware, requiring constant vigilance and in-depth knowledge in order to guarantee an optimal service for end-users. "The major challenge of working for ICHEC is simultaneously providing high performance and reliability on large, tightly integrated systems," says McHugh. "Many of the issues that arise are often unique to this area and don't appear on smaller systems." The system administrators take care of all of the machines at ICHEC's facilities -- some 500 individual servers -- from initial configuration to suit clients' specific needs to maintaining the computers, monitoring performance and diagnosing system and network problems on a daily basis.

Indeed, trouble-shooting is a key area in the daily running of ICHEC's HPC facilities. The network is analysed round the clock by special monitoring tools that instantly alert the system administrators via email or SMS if there is a fault, ensuring a speedy resolution to any issues that arise. An online helpdesk is also available where end-users can log any difficulties they experience and get support from the system administrators. Most problems to date have been resolved within half an hour. "You need to have a problem-solving mentality," says McHugh. "What's more, you need to be able to focus on how to do something on a large scale. It's not like trying to fix one machine; you have to think about how to fix a thousand machines at the same time, and how to manage that task."

McHugh, who has a background in science and engineering, says he was drawn to working at ICHEC through an interest in HPC and enthusiasm for the kind of research carried out at its facilities. "The reward of the job is using and growing your skills while helping to advance leading edge scientific research in Ireland. Satisfaction comes from knowing that you've helped a major scientific project progress."


ICHEC is continuing to run introductory training courses in the areas of HPC (High Performance Computing), MPI (Message Passing Interface) and OpenMP, along with its recently launched numerical libraries course. The most recent round of courses took place at NUI Galway in September, and the next round will likely take place in early 2008. For more details on these courses visit

Have you taken a course with ICHEC? If so, please take the time to fill out a feedback form, if you haven't already done so. Your comments are invaluable as we seek to develop as robust a training programme as possible.


Transport properties of organic macromolecules: modelling at the boundaries between biology and nano-electronics

Professor Stefano Sanvito (Principal Investigator), Trinity College Dublin

The biological properties of DNA, including self-assembly and molecular recognition, have long excited scientists. For a number of years researchers have examined whether these properties of DNA could be exploited to employ the molecule as part of next generation nano-electronics -- devices that far transcend the power of today's microelectronics.

Simulated STM image of a benzene thiol-thiolated attached to a gold surface and scanned with a gold tip. The plot has been obtained with Smeagol by performing full ab-initio I-V calculations for 25 non-equivalent  tip-sample positions and then by interpolating between them.But creating the nanoscale wiring to connect such devices to a power source is a major developmental hurdle. Scientists have hoped that, if filaments of DNA can be coaxed into carrying an electric current, maybe they could be used as wiring which would self-assemble at the molecular scale, connecting the electronic device to its power source through wiring systems that are generated spontaneously instead of physically machined.

Professor Stefano Sanvito's research team at Trinity College Dublin is among the world's leading groups exploring this interface between biology and nano-electronics. Using their expertise in modeling the current flow in nanostructures, the team has written and maintains SMEAGOL, a state-of-the-art computer code used to simulate and calculate the transport properties of nanoscale devices.

SMEAGOL is perhaps the most computationally advanced code being developed worldwide today, and it has been optimised and parallelised to exploit the full resources of ICHEC.

"If you consider how computationally intensive these calculations are, it is obvious why a facility like ICHEC is absolutely essential to our work," Prof Sanvito explains. "A single calculation needs to run over 256 computers in parallel for typically one week, 24 hours a day. And of course, we're not running just one calculation. Our work is constantly expanding because we're trying to get to the bottom of how to optimise DNA to be as good a conductor as possible in different conditions."

While early results of the research seemed to indicate that DNA behaves more like a semiconductor than a metal, the team is now looking at how DNA can be modified to exhibit more metallic properties, without sacrificing its valuable biological functionalities such as molecular recognition and self-assembly.

"ICHEC as a shared resource in Ireland is so valuable to us because within a single research group it would not be conceivable to raise the funds needed to purchase the computational power necessary for our science. Moreover it would be expensive and non-practical to maintain the necessary computer support," Prof Sanvito concludes. "For projects like ours, ICHEC is exactly what's needed."

Picture shows simulated STM image of a benzene thiol-thiolated attached to a gold surface and scanned with a gold tip. The plot has been obtained with Smeagol by performing full ab-initio I-V calculations for 25 non-equivalent tip-sample positions and then by interpolating between them.

BurnQuest: Understanding the combustion process in order to work with automotive engine manufacturers on improving fuel efficiency

Dr Henry Curran (Director), National University of Ireland, Galway and Professor John Simmie (Director Emeritus), National University of Ireland, Galway

Researchers at the Combustion Chemistry Centre in the National University of Ireland, Galway, are working on a four-year project funded by the EU -- begun in mid-2005 -- which seeks to understand the minute chemical details of what happens when fuels such as hydrogen, natural gas, petrol/gasoline, diesel and biofuels burn. "We want to know how the fuel gets transformed to water or carbon dioxide, as well as a multitude of side products," explains Professor John Simmie.

In addition to working to improve the efficiency of fuels, the group hopes to discover and understand the numerous emissions that occur during the combustion process and gauge whether those emissions can be minimised.

Utilising specialised machines -- shock tubes and rapid compression machines -- the group studies combustion at medium to high temperatures and at elevated pressures. The research primarily involves examining the theoretical framework of various fuels and assessing the chemical reactions that occur when they burn. Literally hundreds of reactions occur during the process; however, there are so many, and they happen so quickly, that they have never been measured or fully assessed by researchers. These reactions, though formed in one-hundredth of a second, are vital in understanding the combustion process.

In order to calculate the velocity of these chemical reactions, superior computational power is required. These high-level calculations demand chemical accuracy; this is where ICHEC fits in, according to Prof Simmie. "We have access to the supercomputers of ICHEC to use a selection of quantum chemistry applications such as Gaussian-03, GaussRate and Polyrate," he says. "Without ICHEC this project would be virtually impossible."

Picture shows transition state for abstraction of gamma-hydrogen of n-butanol (a second generation biofuel) by hydroperoxyl radical; note the assist provided by the OH group.