ICHEC News

ISSUE 9 : SEPTEMBER 2010 : WWW.ICHEC.IE

ICHEC’s vision for GPGPUs and Irish research Since 2009 ICHEC has worked hard, and with great success, towards the goal of building Ireland’s reputation as one of the leading developers of GPGPU technologies. Our mission is to enable Irish researchers to be competitive internationally in the use of emerging CPU/GPU architectures, and in the process make Ireland even more attractive for leading edge technology investors. We have built our strategy around a team of highly skilled individuals with a strong focus on development and collaboration in this area, investing in hardware and collaborating internationally with some of the main developers in the field. We intend to roll out a National GPGPU Service in the coming months (pending funding), to enable the full implementation of the strategy described in our feature article in this issue.

We are proud of the recognition our work in GPGPUs has already achieved within the international HPC community. In June this year, ICHEC was awarded the title of CUDA Research Centre (CRC) by the world leader in graphics technology, NVIDIA, “based on the vision, quality and impact of [our] research leveraging CUDA technology”. We have also established an exclusive partnership with Silicon Graphics International (SGI) to provide consultancy services for GPGPU-based applications and, in addition, we recently signed an agreement with the Hartree Centre (of the UK’s STFC), to work together on

ICHEC’s NVIDIA CUDA team. Front row: Dr J-C Desplat (left) and Mr Gilles Civario.

Back row (from left): Dr Eoin Brazil, Dr Ruairi Nestor, and Mr Ivan Girotto. developing and porting applications to these new compute architectures.

For more on this story, go to our special feature on page 4.

Stokes system upgrade In August of this year, we undertook an upgrade of the Stokes SGI Altix ICE system, which has been in operation since December 2008. The upgrade went extremely smoothly and took two weeks, with minimal disruption to our users. During the upgrade, compute blades were changed and the operating

system was updated to SUSE Linux Enterprise Server 11 Service Pack 1; additionally, almost all packages were rebuilt. Stokes is now one of the most efficient machines of its type in the world and would now rank 204th in the top 500. For full details please see page 6.

DECI success for Irish applicants ICHEC would like to congratulate three Irish-based researchers on their recent success in the DEISA Extreme Computing Initiative (DECI) call. Dr Simone Meloni of UCD, Dr Turlough Downes of DCU and Dr Michael Peardon of TCD were all successful.

This year ICHEC was pleased to assist a number of applicants with their proposals for what was a very competitive international call where resources where heavily over-subscribed. The successful researchers have

ICHEC at ISC 2010

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secured compute time on some of Europe’s largest HPC systems, along with development assistance from personnel working on the DEISA project.

The work got off to an early start with an informal workshop for the DECI users, which was recently hosted at ICHEC’s Dublin office. The production compute time will come on stream in September and ICHEC particularly looks forward to working as a co-investigator along with Dr Meloni and Dr Downes.

Technology Transfer Consulting Service

PRACE update

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New and notable

Users’ Council: representing your views

ICHEC consultancy services Welcome to issue 9 of ICHEC News, the newsletter dedicated to bringing researchers and institutions up to date with the latest high-performance computing (HPC) news from Ireland. There is much to report on in this issue, including the recent upgrade of the Stokes machine and the successful introduction of a technology transfer programme to our operations. We will report on ICHEC’s first exhibition at the International Supercomputing Conference in Hamburg in June; the EPA Climate Change Conference, which took place during the summer; and, the very successful Quantum Espresso workshop hosted by ICHEC and the Tyndall National Institute. Our special feature highlights ICHEC’s significant GPGPU developments, including our partnership with SGI and our exclusive accreditation as an NVIDIA CUDA Research Centre. We hope you will find ICHEC News to be a valuable source of HPC news and information.

Since 2007 ICHEC has had an independent Users’ Council in place, giving its members responsibility for providing formal feedback on the National HPC Service to the ICHEC Executive Committee. The Council meets on a quarterly basis to discuss operational matters, user support, scheduling policies, software provision, etc. Membership of the Council runs for a period of three years and is composed of PIs, or their nominees, drawn at random from existing Class A/B or C projects. The Users’ Council represents the views of the entire user community of ICHEC resources, giving users the means to voice their suggestions for improvements to the National HPC Service.

Watch this space Technology transfer ICHEC has been active in support of SMEs with HPC Cloud Deployments over the past few months and will present a talk on this subject to the HEAnet National Networking Conference 2010, which will be held from November 10-12 at the Lyrath Estate Hotel in Kilkenny. The talk presents a number of case studies that focus on the process,

Professor Jim Slevin Director

Contents Editorial

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Users’ Council: representing your views

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Watch this space…

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New and notable ICHEC at ISC 2010 EPA Climate Change Conference

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Special feature GPGPU in ICHEC: a strategy – a vision

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ICHEC at ISC 2010

ICHEC’s first exhibition proved very popular with ISC 2010 attendees.

This year, a team from ICHEC hosted an exhibition space at the 25th International Supercomputing Conference in Hamburg (ISC 2010), which was held from May 30 to June 3. This was the first time that ICHEC has exhibited at a conference.

ISC 2010 recorded its highest numbers of attendees to date, and the conference included 81 worldleading invited speakers, 241 contributors and 151 exhibitors from

experiences, and lessons learnt.

Many companies are unsure of how to undertake their cloud migration and several have had poor initial experiences due to the variety of charging models and platforms that exist within the cloud sphere. The approach ICHEC offers is to provide a feasibility study to a client and work through a profiling and benchmarking exercise to determine the needs and requirements of their particular software with regard to the available cloud options. In

News Quantum ESPRESSO workshop Stokes upgrade Education and training Summer scholars 2010 New courses Recent events

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49 countries, covering every aspect of supercomputing networking and storage. The ICHEC booth included promotional video and posters, and showcased our work and the work of Irish research groups to the international HPC community.

The booth space permitted ICHEC staff to exploit the strong technical focus of the conference, highlighting our expertise and attracting new collaboration. The team organised full-day meetings at

future issues of ICHEC News we will highlight elements of these case studies, ranging from capacity planning to licensing and service level agreements.

ICHEC: a year in review 201 0

Don’t miss the next issue of ICHEC News, where we will take a look back over the highligh ts of the past 12 months for ICH EC and what’s in store for the coming year.

Technology transfer

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PRACE update

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New and notable

ICHEC staff and visitors holding discussions.

An NVIDIA showcase at the ICHEC exhibition stand.

our exhibition space, most addressing our new NVIDIA partnership (see feature article for more information on this prestigious accreditation). This gave us the opportunity to explore a number of possible exciting collaborations and increase the visibility of Irish research in the European HPC community. The success of this year’s ICHEC exhibition at ISC 2010 has assured our presence there again in 2011 and will encourage us

The ICHEC stand at ISC 2010.

to exhibit at further HPC conferences worldwide in the coming year. The ICHEC exhibition space was manned by Dr J-C Desplat, Associate Director, Mr Ivan Girotto, Computational Scientist, Mr Gilles Civarrio, Computational Scientist, and Mr Eoin McHugh, System Administrator, and proved very popular with attendees. Full credit goes to Mr Ivan Girotto for putting together ICHEC's first exhibition with such success.

EPA Climate Change Conference ICHEC had a stand at the EPA Climate Change Conference in the Aviva Stadium on June 30.

Dr Shiyu Wang presented a poster on the analysis of the heavy rainfall of the last few years, showing that while there has been an increase in rainfall in Ireland since 1978, and both global and regional models predict an increase in winter rainfall under climate change, there is no evidence that the extreme rainfall of the last three years marks a change in the Irish climate. However, extreme rainfall events are expected to become more frequent, which is the focus of a lot of climate change research in Ireland.

The Conference showed that the emphasis of climate change work in Ireland has moved from showing that climate change is happening and top-level planning, to adaptation and mitigation at a local level – the changes needed for flood prevention, coastal erosion and town planning. Dr Frank McGovern from the Department of Environment, Heritage and Local Government and Prof. Ray Bates, Climate Advisor to the Office of the Chief Scientist, gave good summaries of the state of climate change politics and science.

In the afternoon there were parallel sessions covering mitigation, resource use, adaptation and modelling, and financing climate solutions. Ray McGrath from Met Éireann described work done on regional climate modelling and the need for global models in the Irish context, and the work that Met Éireann has been doing with ICHEC and UCD, among others, on the EC-Earth climate

Dr Shiyu Wang, ICHEC and Dr Emily Gleeson, Met Éireann. model. Work on adaptation included presentations from UCC and the Coastal Marine Resource Centre (CMRC) on coastal erosion; other talks included Prof.

O’Mahoney from TCD on sustainable transport and Prof. Mueller from UCD on the role of peatlands in Irish climate change.

The EPA Climate Change Conference offered many opportunities for networking: ICHEC successfully displayed its involvement in climate research in Ireland to many groups, such as Enterprise Ireland who were not aware of our work ‘behind the scenes’. Several collaborations have started because of this, and we hope to report more about these at a later date.

Much credit must go to Dr Eoin Brazil and Dr Adam Ralph for helping to make the display such a success.

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Feature

GPGPU in ICHEC: a strategy – a vision In June 2010, ICHEC was awarded the title CUDA Research Centre.

GILLES CIVARIO has the details.

Dr J-C Desplat, ICHEC Associate Director, congratulating Mr Gilles Civario on the award of CRC status for ICHEC. On June 30, 2010, ICHEC was officially awarded the title of CUDA Research Centre (CRC) by Dr David Luebke, NVIDIA Director of Research, “based on the vision, quality and impact of [its] research leveraging CUDA technology”. He continued by stating that: “We [NVIDIA] are pleased to be a partner in the outstanding research taking place at ICHEC … and look forward to future research activities this coming year”.

This CRC recognition is a great honour, and we are especially proud because only a handful of centres have received this distinction. The award will be a stepping stone for the team at ICHEC towards our final objectives: enabling Irish researchers to be competitive internationally in the HPC domain and making Ireland even more attractive for leading edge technology investors.

GPGPU – fad or disruptive technology?

Some of the problems with ‘conventional’ high-performance computing (HPC) are the space and energy consumption, as well as their associated logistical problems (cooling and heat) and operating costs. This is true even with the advent of multi-core processors. GPGPU, or General Purpose computing on Graphics Processing Units, may offer some solutions. Unlike many technological developments that rapidly proved technological dead ends, GPGPU computing is not a fad, but a genuine technology breakthrough that is already demonstrating great promise for real-life applications.

So what are GPGPUs? GPGPUs are a refinement of standard high-end graphics cards with a focus towards a wider range of applications rather than just gaming. These high-end graphics cards include hundreds of processing cores working in parallel to perform faster computations (for instance, NVIDIA’s Tesla C2050 card includes a staggering 448 cores per GPGPU chip).

ICHEC and SGI partnership to provide GPGPU consultancy We are pleased to announce that ICHEC has established an exclusive partnership with Silicon Graphics International (SGI) to provide complete consultancy services for GPGPU-based applications to both academia and industry, including many highprofile organisations in both sectors. Our consultancy partnership with SGI will enable institutions and businesses to accelerate the development, implementation and roll-out of GPGPU systems and offers a broad range of services, including proof-of-concept development, benchmarking, porting and training. SGI is a global leader in large-scale clustered computing, high-performance storage, HPC and data centre enablement and services.

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Concrete examples of real-life problems in science and engineering, where the use of GPU computing has provided crucially improved time to solution and increased return on investment are now abundant, from application areas as diverse as: the oil industry, with its widespread use of seismology and in particular a technique known as ‘Reverse-time migration’ (RTM); the financial sector, where hard-to-price asset-backed securities can be modelled using twofactor stochastic models based on Monte Carlo simulations within a much narrower time-window; or, medical diagnostics for real-time, high-throughput screening in new non-invasive and high-contrast 3D ultrasound CT.

ICHEC and GPU – love at first sight Regular readers of ICHEC News will remember the commissioning of the Stoney cluster back in Q2 2009. This 512 Intel Nehalem cores–InfiniBand DDR cluster came fitted with two NVIDIA Tesla S1070 cabinets – these resources had been included on the recommendation of the cluster owner, Dr Andy Shearer (NUIG). Though the machine itself was due to be operated by ICHEC for the national service, these Tesla cabinets were not fully available to the national service. ICHEC exploited this opportunity to undertake a comprehensive assessment of the potential of this new technology and its relevance to Irish computational science. The initial GPGPU team at ICHEC comprised Gilles Civario (lead) and computational scientist Dr Christos Kartsaklis. After only two months of initial investigation of the architecture and code development, Christos had made significant progress in developing low-level tools and libraries, and in June 2009 submitted a paper to NVIDIA for the GPU Technology Conference, which was accepted for a talk and publication. The assessment itself proved so conclusive that the decision was made to acquire our own GPGPU capability, by purchasing an additional four NVIDIA Tesla S1070 cabinets. Those cabinets, the state-of-the-art for GPGPU computing at the time, added two GPGPUs each to eight Stoney compute nodes. This gave us an eight node–16 GPU cluster for testing and development of new codes.

The conference was an eye opener: while there, we met an amazing community consisting of some of the very best GPGPU developers in the world and highly enthusiastic scientists and industry leaders. All of this reinforced our assessment that GPGPU was a technology destined to become a significant component of HPC, and one that we should and must engage with. As a consequence, we strengthened our GPU team in Q4, employing Ivan Girotto and Nicola McDonnell, and three projects were undertaken in parallel: n porting STFC’s DL_POLY MD code to CUDA; n evaluating the CUDA version of NCAR’s WRF; and, n porting the PWScf module of Quantum ESPRESSO to GPGPU with HMPP. All of these projects were undertaken by ICHEC staff as part of international collaborations with the main developers of the codes, and with researchers both nationally and internationally.

Feature

New generation Tesla C2050.

ICHEC and the UK’s Hartree Centre merge forces for accelerated development in GPGPU applications The UK’s premier research software centre, the Hartree Centre (part of the UK’s Science and Technology Facilities Council [STFC]), develops multidisciplinary, multi-scale simulation and modelling for the UK computational research community. As a result of a successful joint effort to port the important molecular dynamics software code DL_POLY to GPU-enabled compute systems, ICHEC and the Hartree Centre have now signed an agreement to work together on developing further applications for hybrid compute architectures. The GPU-enabled code DL_POLY4 is due for general release in September. Gilles Civario presented this work at the 2010 GTC Conference in September in San Jose, California.

Bringing us up to date More new staff have now joined our GPU team and new projects have been undertaken. Obviously our strategy for GPGPU computing is an integral part of, and is closely aligned with, our overarching strategy of bringing Irish researchers to a position where they are among the earlier adopters of this disruptive technology. This is core to ICHEC’s mission as providers of the National HPC Service, and we remain fully committed to this mission.

In the case of GPGPU computing, this will be of special interest for two groups of researchers in particular: 1. Research groups that have limited computing needs – too limited to justify the payload of moving from their desktops to a centralised computing facility, but with needs that would greatly benefit from speed-up of local compute resources.

2. Research groups that are concerned with large-scale and Grand Challenge problems, and require access to compute resources with capability beyond that offered by national ‘general purpose’ clusters.

For these groups, GPGPU can offer great opportunities: n The first group might experience some significant speed-ups of their codes locally, allowing them to greatly extend the scope of their research (how would you improve your method of computing if computations were running 10+ times faster? If a one-hour result was available in only five minutes? In one minute? Would you really undertake computations in the same way?) There are exciting possibilities here for the researcher. For instance, ICHEC has demonstrated as part of a ‘proof of concept’ exercise that a simple CRC32 algorithm could be sped up by over 30 times! n The second group would benefit from access to those very exciting and

Stoney’s Tesla S1070 subsystem.

powerful GPU-enabled supercomputers, either through PRACE or through other international collaboration frameworks. For the time being, with two of these machines ranked among the 10 fastest in the world (#2 and #8), GPGPU computing has made a big step in this area. Even if such architectures are not present on a large scale in PRACE at present, there is no doubt that some will appear in the coming months. The ability to exploit this technology effectively will greatly facilitate access to this class of infrastructure through internationally competitive peer-review processes, and the resulting production of high-impact science. Our objective is to do just that: ‘research enablement’ through technical readiness in partnership with ICHEC computational scientists.

Future plans and concluding remarks Beyond PRACE access, ICHEC intends to roll out a small National GPGPU Service in the coming months (pending funding), to enable the full implementation of the strategy described in this article.

Porting applications to this new architecture is not for the faint hearted, and requires very high levels of technical skills. But the returns on the investment are very significant. In times of economic difficulty, greater emphasis will be placed on leveraging investments in expensive hardware, and Ireland (through ICHEC) should be proud to be among the leading countries able to exploit leading-edge technologies such as GPGPU. It is further evidence for foreign companies, if such evidence were needed, that Ireland is home to a very highly skilled workforce.

Opportunities for Ireland GPGPU expertise is still limited, but demand for it is increasing and will continue to increase as this new disruptive technology gains traction. By developing a high profile in this field, and by undertaking education and training activities around the country, ICHEC can help to build Ireland’s reputation as a smart economy and make a contribution to the national effort to attract inward investment in the IT area. All in all, this initial modest investment in hardware that we made one year ago has created significant momentum that we expect to continue to build in the years to come.

Mr Gilles Civario ICHEC Computational Scientist and Head of the Capability Computing and Novel Architecture Group.

ISSUE 9 : SEPTEMBER 2010 : PAGE 5

News

Quantum ESPRESSO workshop As mentioned in our last issue, ICHEC, together with the Tyndall National Institute, hosted a workshop on the theory and practical use of Quantum ESPRESSO during the summer, with topics from a range of contemporary Quantum ESPRESSO applications covered on the programme. The workshop was attended by postgraduates and researchers from Ireland and abroad who are familiar with the field and proved very successful, as the testimonials below indicate; worldclass experts in the field presented lectures and ICHEC staff assisted with tutorials: “It was great to see so many people glued to their terminals for once, and avidly learning all the fundamentals of quantum simulations. The school was a great success, and I greatly

enjoyed my hospitality at Tyndall.”

Professor Nicola Marzari, Statutory Chair and Director of the Materials Modelling Laboratory at Oxford University, speaker at the Quantum ESPRESSO Workshop.

“The ICHEC-sponsored tutorial on Quantum ESPRESSO brought researchers and students in the Electronics Theory Group at Tyndall face to face with both code developers and high-performance computing experts. This high level of interaction and the hands-on nature of the tutorial is invaluable for developing the expertise we need to perform large-scale simulations. In particular, as we are able to push the limits of electronic structure packages such as Quantum ESPRESSO to larger systems, we are better able to intersect the technology roadmaps of

Attendees at the recent Quantum ESPRESSO workshop in Cork. our industrial partners. This greatly enhances the relevance of research programmes. The tutorial was, from our perspective, a great success.”

Dr Jim Greer, Head of Group – Computational Modelling and Head of Graduate Studies at the Tyndall National Institute.

“I found the workshop to be very

beneficial in terms of its scope and breadth and depth of coverage, as well as providing great hands-on support. As a video conference participant, I felt that the provision of training material and Q&A was not too problematic at all.”

Dr Niall English, UCD School of Chemical & Bioprocess Engineering.

decisions tailored to the new processor architecture. Users who build their own codes rather than use ICHEC-installed packages are encouraged to contact us if they require assistance updating their make files, etc., to exploit this opportunity. While the physical networking infrastructure has remained the same, the upgrade has facilitated the enablement of dual rail support in the Stokes infiniband network. If your application(s) is network bandwidth bound it may benefit from the enablement of dual rail. If you are interested in testing this, please contact us. One common measure of the performance of HPC systems is the Linpack benchmark. It is based on linear algebra operations. In the current top 500 list (www.top500.org), Stokes would now rank 204th, though it will be somewhat lower when it appears in the updated list due in November. The ratio of a system’s theoretical peak performance relative to that achieved is a measure of how efficient a system is. We are very pleased to report that Stokes has achieved a score of over 89%, which makes it one of the most efficient machines of its type anywhere.

The upgrade means that now is an opportune time to revise the limits ICHEC applies to project resources with the aim of offering as much time as possible to users while balancing this against the problem of excessive contention. We are currently consulting with both the Science Council and Users Council on this issue and hope to roll out revised limits in the near future.

Stokes upgrade The Stokes SGI Altix ICE system has served its users well since it was commissioned in December 2008, and has set a high bar for the newly upgraded system in terms of efficiency and reliability. The upgrade sought to maximise performance and value. In doing so, all infrastructure was retained, such as chassis, networking, storage and login and service nodes.

Only the compute blades were changed. Each new blade or node, as users see them, has two six-core 2.67GHz Intel Westmere processors and 24GB of RAM. The physical swapping of blades was carried out by SGI engineers with the assistance of members of the ICHEC systems team and UCD Research IT. This step took one working day, after which SGI staff proceeded to install the base operating system and management software.

Once complete, ICHEC’s team of system administrators, led by Niall Wilson, took over the system and began customising and tuning it further, and integrating it with ICHEC’s other systems. One week after taking the system offline to begin the upgrade, the ICHEC computational scientists could begin to rebuild and

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update the extensive portfolio of preinstalled packages. Once key packages were in place and testing had shown the system to be reliable, a small number of users were invited to start using the system. Their real world jobs and realistic workload patterns gave us the confidence to return the system to operational use on August 24. ICHEC would like to express its thanks particularly to the staff of UCD Research IT, who operate the hosting centre that is home to Stokes, for their co-operation and assistance during the upgrade.

New operating system The Westmere processors are a newer architecture than those they replace so we have taken the opportunity to update the operating system to SUSE Linux Enterprise Server (SLES) 11 Service Pack 1 and to rebuild almost all packages. Recompiling the packages has led to numerous examples of significant performance increases over and above what one would expect from simply running an old binary on the new processors. This is because recompiling with the appropriate flags allows the compiler to make new

Grateful for patience While we are very happy that the system was offline for such a short period given the scale of the work involved, we are grateful for the patience and co-operation of the user community during the upgrade. It is our firm belief that Stokes will now continue to serve as the workhorse of Irish computational science for some time to come. Finally, it is worth noting that while the name has remained the same, a lot has changed on the Stokes system. If you notice that your application is not performing as expected do let us know and we will be happy to investigate.

Education and training

Summer Scholars 2010 Two students – Renato Miceli and Yang Yang – were awarded the annual ICHEC Summer Scholarships, which provide funding for undergraudates to participate in 10-week projects. Below are brief introductions to Renato and Yang, who were both involved in projects that are related to GPGPU, a field where ICHEC has made considerable progress and achievements.

Renato Miceli

Yang Yang

Renato is an undergraduate student in computer science at the Federal University of Campina Grande (UFCG). He has a strong background in distributed computing middleware where he worked in the development team for the OurGrid project (www.ourgrid.org) as well as the Beehive File System project. He also carried out research for the Hybrid Clouds project, which aims to combine cloud computing and computational peer-to-peer grids.

More recently, he was a system administrator of a compute cluster at the computational physics laboratory at UFCG, where he provided support to researchers and parallelised sequential code. Apart from these extensive involvements in project work, Renato was also a teaching assistant for various courses and he was President of the Informatics Students’ Academic Center (CAESI), the representative body of all computer science students at UFCG. Renato’s summer project was entitled ‘Implementation of the multiple polynomial sieve factoring algorithm on the GPU architecture’. This project was supervised by Gilles Civario from ICHEC and also involved collaboration with Dr Mike Scott from Dublin City University.

Yang is an undergraduate student in computer science and applied mathematics at the Hong Kong University of Science and Technology (HKUST).

Along with a distinguished list of academic credentials, Yang has received numerous honours and awards that feature several scholarships and achievements in competitions such as the China Provincial Olympiad of Physics, ACM/ICPC Collegiate Programming Contest (Hong Kong) and the International Genetically Engineered Machine Competition (iGEM, MIT Boston). Yang was a research assistant in a parallel data mining project using graphics processors, and he was a software design engineer intern in the HPC Team of Microsoft Shanghai, where he gained practical experience in CUDA. In 2009, he took part in an academic exchange programme at the University of Washington. Following his summer project at ICHEC, Yang will be pursuing a PhD in the field of computer graphics at the University of Maryland.

Yang’s summer project was entitled ‘Development of a General Matrix Multiply (GEMM) library for hybrid CPU-GPU architectures’, and was supervised by ICHEC computational scientist Ivan Girotto.

New courses ICHEC has developed three new courses that are available to researchers nationwide. As with all our courses, these can be arranged based on demand, i.e., once there is an expression of interest from individuals or groups, and a suitable venue and date can be arranged. For anyone who is interested, please send an email to training@ichec.ie to arrange a course or obtain further information.

Introduction to modern Fortran Fortran is widely used by the scientific community, in certain fields being the de facto standard.

This three-day course is designed for those who are getting started with Fortran and for those who wish to refresh their knowledge of the subject. It presents the main programming concepts and how these are implemented in the

Fortran 95/2003 standards. The emphasis is on the coding and concepts behind the programming language rather than the algorithmics.

Advanced MPI This two-day course looks at some of the more advanced features of MPI that are beyond the scope of our ‘Introduction to MPI’ course, which addresses the fundamentals of writing simple MPI programs using a small subset of MPI routines. It covers several concepts that are frequently employed in complex, high-performance parallel code, with particular emphasis on MPI-2 features (e.g., intercommunicator and one-sided communication, parallel I/O, dynamic process management) as well as an introduction to hybrid programming with MPI and OpenMP.

Software engineering and carpentry for scientists This course will introduce the fundamentals of scientific software engineering through tools and techniques that enhance the design, development, execution and testing phases of the software life cycle. Particular emphasis will be placed on correct program design and its efficient,

organised and robust implementation in both C and Fortran. By ‘carpentry’, we mean that the course concentrates on the 20% of software engineering techniques that represent 80% of the real world use of software engineering; the tools of the trade of programming. This is the software equivalent of good laboratory techniques.

EDUCATION AND TRAINING CALENDAR – RECENT EVENTS May 17-20:

Introductory HPC courses at the University of Limerick.

June 9-11:

Introduction to modern Fortran at the Tyndall National Institute.

June 14-18:

Workshop: ‘Theory and Practical Use of Quantum ESPRESSO’ (in collaboration with the Tyndall National Institute).

July 21-23:

Introduction to modern Fortran at the Dublin Institute of Advanced Studies.

August 10-12: Introduction to modern Fortran at the Dublin Institute of Advanced Studies.

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Technology transfer

Introducing ICHEC’s technology transfer services worked together to facilitate the commercial licensing of and access to a range of forecasting solutions. An example of ICHEC’s green technology work is with Gael Force Wind Energy (http://www.gaelforcekerry.com/), where weather prediction, statistical methods and computational modelling are being combined to generate forecasts for wind power production. This work allows wind farm operators to utilise their historic information and high resolution forecasting to determine what energy their turbines will produce over the coming days. The forecast uncertainties of numerical weather models are addressed through the use of the ensemble technique. Ensembles use different forecast models to explore the same area and time. They can provide better guidance on what the most likely scenario, the average scenario, or the most damaging scenario will be than using a single forecast model. This information can help to improve revenue predictions and assist in the scheduling of turbine maintenance.

ICHEC is working with SMEs, multinational enterprises (MNEs), semi-state companies and state bodies to provide solutions. We are currently providing consultancy and training in data mining, GPGPU development, renewable technologies, HPC/cloud application migration and visualisation. We look forward to discussing more case studies in these areas as a regular feature in ICHEC News.

Small and medium enterprises (SMEs) often find it difficult to find and apply the most appropriate science and technology to grow their business. This is why Science Foundation Ireland has supported ICHEC in developing and providing a consultancy service to help Irish companies grow their business through the application of high-end computing, cloud computing, technical services and the application of scientific research to address their business problems. ICHEC’s technology transfer activities are bringing the benefits from leading edge science to industry, society and the environment.

ICHEC gives companies efficient and cost-effective access to a complete portfolio of consulting services tailored to the needs of industry. The breadth and depth of expertise of ICHEC’s staff, as well as our extensive facilities, are available to support each project. ICHEC’s software engineering and problem-solving skill sets are solving increasingly complex and challenging problems. ICHEC offers a flexible range of options covering the use of computational facilities, consultancy services, application development, and porting/optimisation services. These options include once-off and periodic use of facilities, fixed price development and long-term support. Solutions are developed on a case-by-case basis using appropriate technologies with a vendor agnostic viewpoint. Projects are delivered using a fixed-price basis utilising a comprehensive project management process based on the PRINCE2® methodology.

Case study: predicting the wind for power generation ICHEC's climate division has a longstanding relationship with Met Éireann and technology transfer is one area where this expertise is being leveraged to provide solutions to the green technology sector. Met Éireann and ICHEC have

Dr Eoin Brazil ICHEC Senior Software Developer and Technology Transfer Consultant.

PRACE update

PRACE kicks off in Munich August 30 and 31 were a significant milestone for the Partnership for Advanced Computing in Europe (PRACE) project, as PRACE held a meeting for the first implementation phase of the project at the LeibnizRechenzentrum (LRZ), the computing centre for the Bavarian Academy of Sciences. The meeting brought together representatives from across Europe, and ICHEC was represented

by Mr Gilles Civario, Dr Simon Wong and Dr Michael Browne. Aside from assisting Irish researchers to access and use PRACE resources, ICHEC’s primary focus in PRACE lies in the technical area, where we will be contributing in the fields of novel architectures and associated

European co-operation is key

programming languages. We will also be involved in the area of engineering and re-engineering applications to enable them to better exploit petaflop-scale hardware. This will build on the work ICHEC has been successfully doing in recent months on the mainstream DL_POLY and Quantum ESPRESSO packages. ICHEC will also be involved in the training PRACE work package. There is a keen awareness that the looming changes in hardware architectures and relentless increase in core counts necessitates a proactive stance on delivering training if the systems are to be used effectively. ICHEC is ably represented in this role by Dr Simon Wong.

While this meeting was significant, it does not define the entire future course of PRACE, which continues to evolve and is, under European Commission direction, looking at other areas of the high-performance computing ecosystem. Ireland’s position as a smaller European nation makes this a priority for ICHEC and is an example of how co-operation at European level has the potential to deliver benefits to all and not just the handful of countries large enough to host petaflop-scale systems. While Irish researchers have availed of access to PRACE prototype projects for many millions of compute hours on numerous architectures, to date larger

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R O I N N

OIDEACHAIS AGUS EOLAÍOCHTA

PAGE 8 : ISSUE 9 : SEPTEMBER 2010

DEPARTMENT OF

EDUCATION AND SCIENCE

scale production time applications have only been possible for the mammoth JUGENE Blue Gene/P system. This is set to change towards the end of the year with the addition of a second PRACE system, hosted by the French Atomic Energy and Alternative Energies Commission (CEA). The machine will be manufactured by Bull (makers of the Stoney system), and will be a more conventional cluster architecture and better suited to a wider spectrum of codes than JUGENE. ICHEC users interested in using this new system should contact ICHEC for further details. A further PRACE access call is expected to roughly coincide with the commissioning of the machine.