The Irish Centre for High-End Computing
ICHEC News -- Issue 5 :: February 2009

HPC news & information from the Irish Centre for High-End Computing
WELCOME TO ICHEC NEWS

NEW & NOTABLE

• Blue Gene ushers in capability computing era More
• Annual seminar unites researchers at HPC frontiers More
• Blue Gene workshop debut More
• Met Éireann predicts better weather forecasts More
• Stokes features at US conference More
• ICHEC helps crack crypto code More

SPECIAL FEATURE

• Stokes data cluster: new capabilities for Irish research More

TRAINING NEWS


HAVE YOUR SAY

We want to know about your experience of ICHEC's services, and what your needs are for the future. This spring we'll be contacting our community of users - past and present - to ask for their participation in a survey on ICHEC resources. Your feedback will help us improve our current service and plan the years ahead. Look out for more details coming soon on the ICHEC website and to your inbox. We look forward to hearing your views.


:: Useful HPC Resources

Web-based HPC resources of note

UKHEC
www.ukhec.ac.uk/

TOP 500 Supercomputer Sites
www.top500.org/

IBM Deep Computing
ibm.com/.../deepcomputing/

Bull High Performance Computing (HPC) solutions
www.bull.com/hpc/

Linux High Performance Computing
www.linuxhpc.org


:: ICHEC FAQ

What is ICHEC?

The Irish Centre for High-End Computing (ICHEC) delivers essential High-Performance Computing (HPC) resources to Ireland's scientific community, with financial support from the Higher Education Authority (HEA) and Science Foundation Ireland (SFI). ICHEC operates National HPC services on its SGI 8200EX cluster 'Stokes' and the IBM Blue Gene national infrastructure, allowing researchers across a range of disciplines to run computationally intensive calculations and simulations, enabling investigations of a size and scale previously not possible in Ireland. ICHEC and its expert 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 www.hpcwire.com for a complete list

March 22-27
High Performance Computing Symposium (HPC 2009)
California, USA
http://hosting.cs.vt.edu/hpc2009

March 25-26
Many-Core and Reconfigurable Supercomputing Conference (MRSC'09)
Berlin, Germany
www.mrsc2009.org

May 18-20
ACM International Conference on Computing Frontiers
Ischia, Italy
www.computingfrontiers.org/2009

May 25-29
IPDPS-09 23rd IEEE Intl Parallel and Distributed Processing Symposium
Rome, Italy
http://ipdps.org


:: Join ICHEC News

If you would like to be added to receive future issues of ICHEC News please e-mail us with your details.


:: Previous issues

ICHEC News Issue 4

ICHEC News Issue 3

ICHEC News Issue 2

ICHEC News Issue 1

:: WELCOME TO ICHEC NEWS

Prof. Jim SlevinWelcome to Issue 5 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 bring you news of the official launch of the IBM Blue Gene at ICHEC's Annual Seminar, an event that also welcomed the arrival of our newest compute cluster, Stokes. Our Special Feature provides an in-depth look at Stokes' capabilities and its potential impact on the Irish research community. We also outline new developments in weather forecasting and climate modeling resulting from Met Éireann's ongoing partnership with ICHEC. In addition, look out for information on training courses, including a brand new summer scholarship programme, as well as our regular research spotlights.

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.

Prof Jim Slevin, Director


:: NEW & NOTABLE

Blue Gene ushers in capability computing era: One of Ireland's most powerful supercomputers, the IBM Blue Gene, was formally launched at ICHEC's Annual Seminar, heralding the arrival of unprecedented computational functionality for Irish researchers.

Pictured at the official launch of the Blue Gene are (from left to right) Larry Hirst, Chairman of IBM Europe, Middle East and Africa; Tánaiste and Minister for Enterprise, Trade and Employment Mary Coughlan, TD; Prof Luke Drury of the Dublin Institute for Advanced Studies.
Pictured at the official launch of the Blue Gene are (from left to right) Larry Hirst, Chairman of IBM Europe, Middle East and Africa; Tánaiste and Minister for Enterprise, Trade and Employment Mary Coughlan, TD; Prof Luke Drury of the Dublin Institute for Advanced Studies.
A crucial part of the National Capability Service, the Blue Gene delivers 11.4 teraflops and is expected to make a major impact on the scientific community, enabling researchers in areas such as climate change, material science, astrophysics and biology to progress their work through advanced computer simulations at the topmost level.

Tánaiste and Minister for Enterprise, Trade and Employment Mary Coughlan, TD, officially unveiled the Blue Gene at the ICHEC event in the Royal Irish Academy in October, saying that access to the supercomputer was a "hugely important development" for researchers based in Ireland. "It demonstrates the value of investment in research infrastructure that will make Ireland more competitive internationally and continue to attract high-tech industries to this country," she said.

The Blue Gene, procured by the Dublin Institute for Advanced Studies and operated and maintained by ICHEC, has already been up and running for several months at the HEAnet's national hosting facility. In fact, the rollout of the Blue Gene represents a unique partnership for Ireland's third-level sector, with support from all seven Irish universities, the Royal College of Surgeons, DIT, and the Tyndall National Institute.

At the official launch of the IBM supercomputer, Larry Hirst, Chairman of IBM Europe, Middle East and Africa, said the investment will open up new opportunities for Ireland's development and economic prosperity. "It is good news for the academic community who can now access advanced computing technology that will spur new innovations, good news for the government who are investing in the advanced skills of its people and, above all, great news for the citizens of Ireland and the world who will benefit from the new scientific breakthroughs it generates," he said.

For more on the Blue Gene, see our 'Special Feature' in Issue 4.


Annual seminar unites researchers at HPC frontiers: The ICHEC Annual Seminar 2008 was one of the best-attended to date, and provided an opportunity for Irish and international HPC researchers in fields as diverse as the emerging developments in nanomedicine and quantum cryptography to share insights into their work. The highlight of the third annual event was undoubtedly the official launch of the IBM Blue Gene, the supercomputer that is helping Ireland's scientists to compete on the international research stage.

Dr Kimmo Koski of Finland's CSC, IT Center for Science, speaking at the ICHEC Annual Seminar
Dr Kimmo Koski of Finland's CSC, IT Center for Science, speaking at the ICHEC Annual Seminar
The theme of the two-day event in October, hosted by Dublin's Royal Irish Academy, was 'Frontiers in Computational Science'. Apart from its formal launch, the Blue Gene featured strongly, with Prof Luke Drury from the DIAS, e-INIS Principal Investigator, giving an overview of capability computing and Blue Gene, while Prof Jiri Vala of NUI Maynooth spoke about the 'quantum revolution' made possible by Blue Gene, outlining his research in the area of topological quantum materials. Dr Damien Thompson from the Tyndall National Institute described the benefits of the Blue Gene system in his field of microscale molecular simulation.

ICHEC's newest compute cluster, Stokes (see Special Feature for details), was also showcased as part of an overview of the National HPC Service given by ICHEC Associate Director Dr J-C Desplat. In addition, speakers from Finland and the UK highlighted the work being carried out by ICHEC's strategic partners overseas:

  • Dr Kimmo Koski of Finland's CSC, IT Center for Science, spoke about the European HPC ecosystem and future infrastructures;
  • University College London's Prof Peter Coveney outlined the benefits of more powerful machines in yielding higher resolution results for scientific codes;
  • Dr Kevin Stratford of the EPCC at the University of Edinburgh described the evolution of the codes used in his research into complex fluids simulations.

Learn more about the Annual Seminar presentations on www.ichec.ie, where most presentations are now available to download.


Blue Gene workshop debut: ICHEC is pleased to announce that its first ever Blue Gene workshop for researchers drew a positive response from its many participants. The event, conducted over a two-day period in October by ICHEC Support Scientist Gilles Civario, introduced the IBM Blue Gene infrastructure to the research community and demonstrated how to make the most of this powerful resource.

Held at the IBM Innovation Centre in Dublin, the event was attended by about 20 researchers from fields such as quantum mechanics, applied mathematics and life sciences, representing seven universities and research institutes from around the country. Presentations of some code performance results helped to give attendees an idea of what to expect from their own computations. Most of the presentations are available to download from www.ichec.ie.


Met Éireann predicts better weather forecasts: Met Éireann has ambitious plans for 2009 to enhance its involvement in operational weather forecasting and research in climate change - and its ongoing partnership with ICHEC will be key in working toward these goals. ICHEC and Met Éireann have been collaborating since 2007, and they have now formally committed to work together until the end of 2011.

An intense Atlantic storm that caused widespread disruption on 17 January 2009. The storm was forecast by Met Éireann's operational model running on Stokes.
An intense Atlantic storm that caused widespread disruption on 17 January 2009. The storm was forecast by Met Éireann's operational model running on Stokes.
Technical tests of the 4D-VAR data assimilation system have been completed, and comprehensive meteorological tests are now being prepared. "This new system will better utilise high temporal resolution observations, leading to improved forecasts," says Ray McGrath, Head of Met Éireann's Research and Applications Division. Met Éireann hopes to have testing finished by the end of the first quarter of 2009.

Work is also advancing on the ambitious EC-EARTH project, a Europe-wide programme that aims to build a unified, complex model of the global climate. The programme's Irish partners are Met Éireann, UCD and ICHEC. The coupled atmosphere-ocean global climate model has now been ported onto ICHEC's systems and been extensively evaluated on both the Stokes and Blue Gene platforms.

Progress continues to be made on HARMONIE, the next-generation weather forecasting model that Met Éireann says will provide more realistic descriptions of local weather. "HARMONIE has been tested on Walton and is currently being developed further to make full use of the increased computing power now available to us through the Stokes platform," says McGrath.


Stokes features at US conference: ICHEC got a chance to showcase developments in Irish supercomputing at the prestigious SC08 conference, held in Austin, Texas in November. SC08 - also known as the International Conference for High Performance Computing, Networking, Storage and Analysis - is a key event in the HPC calendar, bringing together scientists, engineers, researchers, programmers and system administrators to demonstrate and discuss the newest ideas, discoveries and technologies from around the world.

This year, ICHEC Associate Director Dr J-C Desplat was in attendance, along with ICHEC Support Scientists Dr Michael Browne and Gilles Civario and System Administrator Marc Doumayrou. Addressing the conference with a presentation that outlined the latest developments in Ireland's national supercomputing facility, Dr Desplat introduced ICHEC's newest compute cluster, the powerful Stokes SGI ICE, giving an overview of its technical capabilities and outlining its impact on the Irish research community (see Special Feature for more on Stokes). Dr Desplat noted that while Ireland is a small country, its scientists are involved in world-class research in areas such as bioinformatics, nanotechnology and climate change, and machines like Stokes will play a key role in enabling them to compete on the international stage.

Look out for more details on the conference in a future issue.


ICHEC helps crack crypto code: Two DCU researchers have successfully cracked the 30-year-old McEliece cryptography system, with some help from ICHEC resources. Neil Costigan and Prof Michael Scott announced on 18 October at the Post-Quantum Cryptography conference in Cincinnati that they had succeeded in cracking the crypto system published 30 years ago by coding theorist Robert J McEliece.

Costigan and Scott ran software at ICHEC for 8,000 CPU hours before they achieved their first breakthrough on 2 October. Cryptographers in four other countries were also working to break the code, as part of an international coordinated effort. With McEliece's system being touted as a leading candidate for future public-key cryptography, the successful attack shows that the originally proposed key sizes for McEliece's system are too small and need to be increased.


:: SPECIAL FEATURE

Stokes data cluster: new capabilities for Irish research

The introduction of the Stokes infrastructure to ICHEC's computing resources is enabling Irish scientists to engage in large-scale, cutting-edge research with a speed and performance unattainable with previous compute clusters.

"In terms of performance, Stokes far exceeds what we had expected," says Dr J-C Desplat, ICHEC's Associate Director. Stokes - named after the 20th century Irish mathematician and physicist Sir George Gabriel Stokes - is an SGI Altix ICE 8200EX with 320 nodes. Each node has two Intel Xeon E5462 quad-core processors and 16GB of RAM, resulting in a whopping 2,560 cores and 5,120GB of RAM. With ConnectX Infiniband (DDR) operating as the communications infrastructure between each node, and 84 terabytes of storage space, the supercomputer is capable of competing with the world's best.

Ranked as number 45 in the Green500 list, Stokes is Ireland's most power-efficient compute cluster.
Ranked as number 45 in the Green500 list, Stokes is Ireland's most power-efficient compute cluster.
Stokes is replacing the Walton machine, which was turned off for the last time in mid-December. The new infrastructure brings improvements on several levels compared to its predecessor, says Dr Desplat, including greater throughput, lower latency, vastly improved internal networking and greater scalability. "Stokes offers much higher capabilities than Walton. It allows us to run more jobs concurrently than we could before and enables our users to tackle more complex problems than was previously possible," he says.

The biggest improvement over Walton lies in Stokes' Infiniband interconnect technology, says Niall Wilson, ICHEC's Infrastructure Manager. "The Infiniband interconnect technology brings higher bandwidth, improved networking and low latency. We have three times the number of processors available and yet the potential performance is ten times greater than the previous cluster's," says Wilson. Stokes offers computational speeds of 25.1 teraflops, compared to Walton's 3.14 teraflops.

Stokes is already making a positive impact on the Irish scientific community, says ICHEC Support Scientist Dr Michael Browne. "The big difference that we've seen right away is in the sheer volume of jobs that can be accommodated. And the user-friendly nature of the software installation on Stokes has meant that projects that were migrated over from Walton are already moving very quickly," he says. "Not only is each individual processor in Stokes of the order of three to four times faster, but our researchers can also efficiently use more processors. For most users, that is the key difference."

Stokes was up and running within 24 hours of its arrival at ICHEC facilities.
Stokes was up and running within 24 hours of its arrival at ICHEC facilities.
Stokes will help Irish life sciences researchers to compete on a global scale, particularly in the areas of high-throughput genomics and phylogenetics, says ICHEC Support Scientist Dr Simon Wong. "These days even a small lab can generate a lot of DNA and protein sequences and they need lots of processing power to analyse the data that's coming out. Additional computing power allows modeling and simulation of biological processes with greater accuracy and higher resolution," he says.

In addition, Met Éireann's day-to-day operational forecasts already run on Stokes, but there's even more advanced climate modeling work to come, says ICHEC Support Scientist Alastair McKinstry, who describes Stokes' computational power as a "quantum leap" beyond ICHEC's older clusters. "We're collaborating with Met Éireann to develop the next generation of weather forecast models using Stokes," he says. (See New and Notable section for more details.)

Stokes is also a vital component of the forthcoming IPCC AR-5 climate modeling report - an internationally peer-reviewed project involving all European meteorological services. "Stokes is one of the main supercomputers in Europe involved in this report, allowing Ireland to take a major role in the project. In practice, it wouldn't have been possible to do this on Walton," says McKinstry.

*** ICHEC is inviting all interested parties to attend the launch of the National High-Performance Computing Service (Stokes) and the National HPC Hub. The event will take place as part of a seminar to be held at the Royal Irish Academy in Dublin on 26 February. High-level speakers due to take part in the event include Dr Eng Lim Goh, Chief Technical Officer of Silicon Graphics SGI; Dr Gordon Graylish, Vice President of Intel; and Chris Weeden of Panasas. Stokes will be formally launched by Michael Kelly, Chairman, Higher Education Authority. Representatives from Irish higher education institutions, funding agencies and other National HPC Centres are also cordially invited. Please visit www.ichec.ie for more details. ***


:: TRAINING NEWS

Dr. Simon Wong

Our Training Coordinator, Dr Simon Wong, is continuing to run introductory training courses in the following areas: HPC (High Performance Computing), MPI (Message Passing Interface), and OpenMP. In 2008 we ran courses at Trinity College Dublin, University College Dublin, University of Limerick, and Dublin City University. The next round of courses takes place in February at Armagh Observatory.

For more details on these courses and for regular updates on training news, visit the ICHEC website. 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.

Summer scholarship: ICHEC will run its first Summer Scholarship Scheme this year, employing suitable undergraduates to conduct projects in the field of high performance computing and/or scientific computing. Details are posted on www.ichec.ie, or contact training@ichec.ie now for more information.


HEA SFI
e-INIS