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Linux High Performance Computing
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:: ICHEC FAQ

:: NEW & NOTABLE

EC-EARTH partners propose new roadmap: Climate experts involved in the EC-EARTH programme agreed to establish a new roadmap at the most recent meeting of the project's partners in Dublin. Under the EC-EARTH programme, climate experts from across Europe are working together with the intention of building a unified, complex model of the global climate. This all-encompassing model aims to enable more realistic simulations of the world's climate, improve the understanding of climate change, and give a more accurate picture of the global climate of the future.

The third meeting of the EC-EARTH project, which took place in University College Dublin, was opened by Ireland's Minister for the Environment, John Gormley. Representatives from the project's Irish partners -- ICHEC, Met Éireann and UCD -- were on hand to provide an update of their work, alongside participants from many of the European partner countries, including Switzerland, Sweden, Italy, the Netherlands, Denmark and Norway. Met Éireann's Ray McGrath presented plans for using the EC-EARTH system for tasks such as downscaling climate changes to regional level, while ICHEC's Honore Tapamo highlighted the results of implementing the system on ICHEC's machines.

Among the many action items agreed at the meeting, the Steering Group agreed to set up a roadmap with milestones and deliverables and to report regularly on progress. Meanwhile, the various Working Groups agreed to collaborate on technical issues and the exchange of data and to provide recommendations on strategic and scientific issues regarding the implementation of new components of the EC-EARTH system.

The minutes of the meeting can be downloaded here. The next EC-EARTH meeting is due to take place in June in Reading, UK. More information on the EC-EARTH project is available here.

Wednesday is Blue Gene open day: Researchers with Class B projects are being invited to try out the new IBM Blue Gene supercomputing infrastructure, which has been successfully up and running under the National Capability Service since February. Currently, the service is only being made available to Class A projects, but under a new open day every Wednesday, existing Class B projects can gain access to the Blue Gene to assess the portability and scalability of their research before committing to prepare a full Class A application. Interested researchers can contact ICHEC via the Helpdesk to discuss their needs. (See elsewhere in this issue for more on the Blue Gene.)

New team members add momentum for e-INIS: ICHEC has recruited two software developers to support new initiatives under the National e-Infrastructure (e-INIS) programme. The PRTLI-4 funded e-INIS project, led by Prof Luke Drury from the Dublin Institute for Advanced Studies, aims to provide a world-class computational, networking and support infrastructure for Ireland's research community. ICHEC has hired Dr Bruno Voisin and Dr Gabriel Maatescu to support two collaborative projects under e-INIS: one in the area of humanities, working with the Royal Irish Academy on the Digital Humanities Observatory; the other in the area of life sciences, working with NUI Maynooth on the National Bioinformatics Information Resource. Elsewhere, plans for major upgrades to the national HPC facilities are well advanced, and an invitation to tender for the new capacity cluster was issued in April. (For more information on e-INIS, see Issue 2 of ICHEC News.)

Better weather forecasts on the horizon: Met Éireann is expanding its weather forecasting activities, and has committed to making greater use of ICHEC's resources for the purpose. Ireland's National Meteorological Service has renewed its collaboration agreement with ICHEC for another year, following the successful launch of the partnership in 2007.

A new data assimilation system (4D-VAR) will be tested with a view to operational implementation towards the end of the year. "This will make more effective use of weather observations, providing a more accurate description of the initial state of the atmosphere for the forecast process," says Ray McGrath, Head of the Research and Applications Division, Met Éireann.

ICHEC is also continuing to work closely with Met Éireann on the HARMONIE and EC-EARTH projects. Alastair McKinstry, ICHEC Software Architect, is helping to make progress on the development of the next-generation HARMONIE weather forecasting model. The system, which will help provide more realistic descriptions of local weather and improve forecasting capabilities, is expected to come into operation in 2009.

Meanwhile, ICHEC Support Scientist Honoré Tapamo is working with Met Éireann on EC-EARTH, part of a Europe-wide initiative to improve climate modelling. The work involves porting the coupled atmosphere-ocean global climate model to run efficiently on ICHEC's systems. The scalability of the code is also being explored with a view to porting it onto the new Blue Gene system.

New appointments: ICHEC is pleased to announce the appointment of Professor Jim Slevin as its new Director. Prof Slevin has had an outstanding career as an academic, working at CERN and the Jet Propulsion Laboratory (Pasadena), as well as at the University of Stirling (Scotland) and NUI, Maynooth. Most recently Prof Slevin was an Officer of the Royal Irish Academy and has been its President since 2005. For more information on Prof Slevin's appointment, see www.ichec.ie.

ICHEC also wishes to welcome Dr Simon Wong to the position of Support Scientist and Training Coordinator, a role he takes over from Dr Timothy Stitt. Dr Wong holds an undergraduate degree in human genetics from Trinity College Dublin, where he also completed his PhD on yeast genome evolution in Prof Ken Wolfe's lab at the Genetics Department in 2004. He has recently returned to Dublin after a postdoctoral position in Prof Mark Ragan's lab at the University of Queensland in Brisbane, Australia.

ICHEC roadshow comes to DCU: The ICHEC roadshow is continuing to travel around the country, in a nationwide tour of higher-level institutions. These sessions offer an opportunity for ICHEC to meet with researchers across the country and to bring them up-to-date with the latest developments in HPC. ICHEC staff are also able to outline the storage and computational resources that are available to help meet researchers' needs, along with support and consultancy services. The roadshow has already visited NUI Maynooth and UCD and is scheduled to reach DIT, DIAS and RCSI by the end of June.

Annual seminar highlights key HPC themes: ICHEC's well-attended second annual seminar, hosted by Dublin's Royal Irish Academy, addressed three key topics in the HPC field: capability computing, e-infrastructure and environmental science. The opening session addressed capability computing, centring on the formal announcement of the addition of the new IBM Blue Gene to ICHEC's service. IBM's Dr Nicholas Allsopp gave a detailed outline of the Blue Gene architecture, while Dr Jiri Vala of NUI Maynooth and Prof Stefano Sanvito of Trinity College Dublin presented their plans to exploit the new leap in performance in the areas of topological quantum materials and computational nanoscience, respectively.

A session on e-infrastructure saw IBM's vice president for Deep Computing, Dave Turek, give a talk on the emergence and impact of new computational designs, while ICHEC's Niall Wilson reported on e-infrastructure initiatives taking place in Ireland, alongside news of ongoing work in Poland, the UK, and at EU level. The third theme of the event, environmental science, featured presentations from UCD's Prof Peter Lynch and Met Éireann's Ray McGrath on climate modelling, while ICHEC's Alastair McKinstry gave an update on meteorological code development at ICHEC. A number of the presentations are available from the ICHEC website.

:: SPECIAL FEATURE

Key collaboration: National Capability Service

The recent launch of the National Capability Service has given ICHEC the opportunity to support research at the highest level, as the service's new IBM Blue Gene supercomputing infrastructure makes its debut in Ireland. Hopes are high that the power of this new system will enable researchers across the country to achieve significant scientific breakthroughs over the next few years.

The scale and ambition of the project is evident from its impact on the scientific community: the launch of the National Capability Service marks the first time the entire third-level research sector has come together to collaborate on a project crucial to the strategic development of computing in Ireland.

ICHEC support scientists are playing a key role in maintaining the Blue Gene, which was procured by the Dublin Institute for Advanced Studies (DIAS) and has been installed at the national hosting facility of HEAnet, Ireland's national education and research network. This unique partnership is also being supported by all seven Irish universities, the Royal College of Surgeons in Ireland, DIT and the Tyndall National Institute. "This is a genuinely collaborative project and this is the first time such collaboration has happened on this scale," says Prof Luke Drury from the School of Cosmic Physics at the DIAS.

The arrival of Blue Gene /L and Blue Gene /P in Ireland will enable advanced computer simulations at the topmost level, and only Class A research projects will initially have access to the new systems (although there will be a regular open day for Class B projects; see the 'New and Notable' section for details). One such Class A project is the investigation of topological quantum materials by Dr Jiri Vala at the Department of Mathematical Physics at NUI Maynooth. Dr Vala, whose team was the first to use the Blue Gene, says the new system offers a "unique capability that allows us to perform computational physics research at the highest possible level". So far, he says, "the power of the machine has exceeded our expectations. We were able to do our calculations in a considerably shorter time-frame, with the ability to investigate considerably larger systems."

Other research areas where the Blue Gene will be of huge benefit include climate change, material science, astrophysics and biology. Priority access to the systems is being given to projects that aim to produce internationally competitive science, with the ICHEC support scientists having responsibility for evaluating the technical requirements of each research project, as part of a peer review process to assess suitability. ICHEC is carefully monitoring system usage, and scheduling of projects will be reviewed on a regular basis. Dr Vala says he is very satisfied with ICHEC's administration of the Blue Gene and the level of expertise shown by the support scientists.

Dr J-C Desplat, Associate Director of ICHEC, says that additional staff are being hired under the e-INIS project to maintain the level of critical support needed to run the Blue Gene. "High-end computing systems are notoriously difficult to use as they typically require highly tuned codes, capable of scaling to thousands of processors," he notes. "Most applications will require extensive tuning to reach the desired level of performance. And this is not an easy task. The contribution of the ICHEC support scientists will be key to making effective use of these resources."

Picture shows a Blue Gene /P node card; slotting vertically into it are compute cards with copper heat sinks. Each compute card contains a quad-core processor and each node card supports up to 128 cores.

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:: TRAINING NEWS

Newly appointed Training Coordinator Dr Simon Wong is currently finalising plans for a one-week training course, to be held in Dublin in the near future. The structure of the course will be similar to previous ICHEC courses, with the following format:

• Day 1: Introduction to High Performance Computing (HPC)
• Day 2 & 3: Introduction to Message Passing Interface (MPI)
• Day 4 & 5: Introduction to OpenMP

For more details and for regular updates on training news, please visit the ICHEC website, www.ichec.ie/training. If you have already taken a course with ICHEC, please take the time to fill out a feedback form on the site. Your comments are greatly valued as we seek to develop as robust a training programme as possible.

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:: RESEARCH UPDATE

Better living through chemistry: harnessing molecular recognition in natural and synthetic systems

Dr Damien Thompson, Tyndall National Institute, Cork

Understanding how molecules 'recognise' and decide to network with each other in physical and chemical terms, and designing new molecules with tailored recognition properties, is the focus of Dr Damien Thompson's research at the Tyndall National Institute in Cork.

One major potential societal benefit of this research is in the emerging nanomedicine field; it involves using nanomaterials to 'coat' drugs so as to improve their transport, targeting and degradation in the body. "In the longer term, as our understanding increases, nanomedicine could potentially replace traditional treatment-based medicine and provide a form of healthcare based on prediction and prevention," explains Dr Thompson.

But understanding the science of molecular recognition is an enormously complex task, and this is where ICHEC comes in. Dr Thompson's team is using the power of ICHEC's systems for combined simulation and experimental efforts in order to understand and fine-tune molecular recognition.

"The national HPC facility, with its state-of-the-art hardware and software and dedicated support staff, is essential to maintain Ireland's growth in the ICT and biotechnology sectors," notes Dr Thompson. "Experimentally validated computer simulations can and do speed up the design of new materials, most strikingly perhaps in the drug design field, where the accurate prediction of inhibitor potency and toxicity can save years of trial-and-error in the lab."

He also welcomes the arrival of the new IBM Blue Gene, describing it as "an invaluable tool" for his team's research efforts. "In a new multidisciplinary project, we hope to describe, for the first time, the atom-scale features of the molecular tunnel junctions used in nanoelectronic devices, and this work will only be feasible, at least using national resources, via massively-parallel simulations on Blue Gene."

Picture shows dynamics and energetics of amino acid binding to aminoacyl tRNA synthetase enzymes.

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Drug discovery: a structure-based approach towards a therapeutic route for cancer treatment

Dr Gemma Kinsella, Trinity College Dublin

Researcher Dr Gemma Kinsella in Dr David Lloyd's Molecular Design Group at Trinity College Dublin is focusing her efforts on the early stages of drug development for treating cancers such as prostate cancer. Dr Kinsella uses a computer-based drug design approach, using computational chemistry to discover drugs and related biologically active molecules.

In particular, Dr Kinsella's research focuses on structure-based drug design. A ligand is a molecule that can trigger certain signals by binding to a target protein. Knowledge of how the ligand interacts with the protein and what structural changes it induces is essential in the drug discovery process, as researchers armed with this knowledge are able to design drugs that cause these specific interactions.

A ligand that can bind to a receptor (a protein found within a cell nucleus), alter its function and trigger/prevent a physiological response is called an agonist/antagonist for that receptor. Dr Kinsella's research is focused on the androgen receptor, which is associated with the hormone testosterone.

Her work aims to develop small molecule modulators of the androgen receptor, as a therapeutic route for prostate cancer treatment. The latest data from the National Cancer Registry of Ireland reveals that 2,406 new cases of prostate cancer were diagnosed in 2005, and it's estimated there will be a 275 percent increase in sufferers by 2020.

In order to locate ligands that elicit the desired responses from the target proteins, Dr Kinsella runs multiple simulations on the supercomputers at ICHEC, using the available throughput to process these simulations efficiently.

"It is clusters like those at ICHEC and Trinity College that make my research feasible," according to Dr Kinsella, who says that the number of simulations that are conducted would take months of 'ordinary' computer time. In using the facilities at ICHEC, this time-frame can be reduced to days.

Using computational power, researchers can more quickly reduce the number of potential hits for a drug target that are investigated further through laboratory trials. This method of drug discovery can in effect help to speed up the drug design process.

Picture shows 3D structure of the androgen receptor (PDB: 2AXA).

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