ICHEC Newsletter Issue 6: July 2009

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ISSUE 6 : JULY 2009 : WWW.ICHEC.IE

HUB launched as a collaborative working space ICHEC’s National HighPerformance Computing (HPC) HUB at TCD’s Technology and Enterprise Centre was formally launched at a function in the Royal Irish Academy on February 26, 2009. The HUB is designed as a meeting place for researchers and ICHEC’s team of expert computational scientists to foster collaboration and shorten the path to scientific discovery. ICHEC Director, Professor Jim Slevin,

stated: “Having only moved into the HUB at the start of the year, it is very encouraging to report both the number of visitors and the enthusiasm that is evident in their feedback to us. We work very hard here to maintain a strong customer focus in the operation of the HUB and in all our services to researchers”.

A full decription of the HUB and the ethos behind it can be found on pages 4 and 5..

At the launch were (from left): Luke Drury of the Dublin Institute for Advanced Studies (DIAS); Michael Kelly, Chairman of the Higher Education Authority (HEA); Jim Slevin, Director of ICHEC; and, JC Desplat, Associate Director of ICHEC.

ICHEC and extreme computing Associate Director of ICHEC, JC Desplat, reports that as part of the Distributed European Infrastructure for Supercomputing Applications (DEISA – www.deisa.eu) consortium, ICHEC offers a conduit for Irish researchers to the DEISA Extreme Computing Initiative (DECI). The main purpose of this initiative is to enable a number of “grand challenge” applications in all areas of science and technology. These leading, ground-breaking applications must deal with complex, demanding and innovative simulations that would not be possible without the DEISA infrastructure, and which benefit from the exceptional resources provided by the Consortium.

“Effectively,” says JC, “DECI allows Irish scientists access to the most powerful supercomputers in Europe so that these scientists can compete at the highest level of international research.”

The latest development in European supercomputing is the Project for Advanced Computing in Europe (PRACE – www.prace-project.eu). PRACE seeks to establish a small number of world-class supercomputers to enable and support world-class science. The preparatory phase is coming to an end

DECI allows for complex, demanding and innovative simulations that would not be possible without the DEISA infrastructure. in the coming months, and we expect access for production to open by early 2010.

ICHEC is the Irish conduit to both DEISA and PRACE and JC Desplat (j­ c.desplat@ichec.ie) is the person to contact for any researcher who thinks that this level of supercomputing might be advantageous to their work.

Emerging collaboration on GPGPU technology

The HUB goes active

Upcoming ICHEC events

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Appointments

New look, more information Welcome to issue six of ICHEC News, the periodical dedicated to bringing researchers and institutions up to date with the latest High-Performance Computing news from Ireland.

ICHEC News now has a fresh new look and more space, allowing us to give you even more in-depth HPC news. In this issue we bring you information on the ICHEC National Survey and how important your participation will be for us; our special feature focuses on the new HPC HUB in Dublin and on the official launch of the HUB and Stokes service; our e-INIS update highlights the Digital Humanities Observatory; and, we will also update you on ICHEC training and research news, and on developments in ICHEC general infrastructure.

We trust you will enjoy the new look ICHEC News and will find it a valuable source for HPC news and information.

New members of ICHEC staff (from left): Christos Kartsaklis; Alin M. Elena; Ivan Girotto; David De La Harpe Golden; Kashif Iqbal; and, Rosemarie Lalor.

Christos Kartsaklis joined ICHEC in May 2009 as a computational scientist. He has an MSc in HighPerformance Computing from the University of Edinburgh and is expecting his PhD in computer science from the University of Manchester by the end of the summer. Christos worked for one of the leading supercomputer centres in Europe, EPCC, as an applications consultant. His previous experience includes distributed computing, HPC library lifecycle and HPC remote paging networks.

Alin M. Elena joined ICHEC in February 2009 as a computational scientist. He studied for his PhD at Queen's University, Belfast in the Atomistic Simulation Centre with Prof Tony Paxton and Dr Tchavdar Todorov. In Belfast he studied timedependent tight binding with applications to fluorescent molecules. Alin has an undergraduate degree specialising in atomic and molecular physics from the Faculty of Physics at the

Professor Jim Slevin Director

University of Bucharest, having graduated with the class of 2004.

Ivan Girotto joined ICHEC in May 2009 as a computational scientist.

He is a graduate in computer science from the Ferrara University in Italy. From there he joined the supercomputing group of CINECA, the Italian National HPC centre, and worked in user support and program development across industry and academia. During this time he was also a member of DEISA and was involved in user support for the DEISA Extreme Computing Initiative (DECI).

David De La Harpe Golden joined ICHEC in April 2009 as a systems programmer. From 2004 to 2007 he worked as a systems administrator and programmer for the Cosmogrid project, running clusters in University College Dublin (UCD) and the Dublin Institute for Advanced Studies (DIAS). Prior to that, he worked as an information technology consultant for ESB International (ESBI). He received an MEng in mechanical

engineering from UMIST (now part of the University of Manchester) in 2000, specialising in CFD. Kashif Iqbal joined ICHEC in November 2008 as a software developer, where he works on the eINIS initiative. Kashif received his bachelor degree in information technology from the National University of Sciences and Technology, Pakistan. Before joining ICHEC, he worked as a researcher and part-time PhD candidate at the Digital Enterprise Research Institute (DERI), NUI Galway.

Rosemarie Lalor joined ICHEC in February 2009 as a part-time administrative assistant. She has an MSc in Biological Anthropology and a BA in Audio Visual Media.

Previously she worked in New York city in the American Museum of Natural History and in financial services.

Further details, including biographies of all ICHEC staff, can be found at http://www.ichec.ie/ about_us/contact.

Contents Editorial Appointments

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News National Survey

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Collaboration on GPGPU Climate modelling European Group of SGI ICE users

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Feature HUB goes active

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Education and training Summer scholarships 2009 Events calendar

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e-INIS update Digital resources for the humanities

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Research update 7 A computational analysis of the microscale forces that drive cellderived tissue formation: a tissue engineering solution General infrastructure update 8 New InfiniBand cluster User tips

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News

Emerging collaboration on GPGPU technology

ICHEC is exploring collaboration with British and French scientists.

Bull is another high-performance computer vendor that supplies equipment used by ICHEC. Following the delivery by Bull of a new cluster to NUI Galway, to be operated by ICHEC as part of the national computing service (see article page

8), ICHEC and Bull decided to explore areas where collaboration could be mutually beneficial. After a very promising two-day meeting at the HPC HUB, during which Bull engineers and ICHEC computational scientists exchanged expertise in

areas of common interest such as climate modelling and GPGPU programming, both parties agreed to maintain active contacts in certain key areas.

The most promising is in the area of GPGPU programming, where ICHEC is also in discussion with other HPC centres of expertise in the UK and France to extend the collaboration.

Just as is the case with the emerging collaboration with CINES and the creation of the European SGI ICE Users Group, we expect this new initiative to benefit the Irish research community by enabling ICHEC to provide leading-edge services to the local community, and ensuring that they are suitably equipped to compete internationally on large-scale HPC infrastructures, such as those to be provided next year as part of the PRACE project.

Optimising tools for climate modelling The environmental science section of ICHEC has started a national initiative to optimise standard tools used by climate groups using ICHEC’s facilities. These groups are based at UCD, NUI Galway and NUI Maynooth. To begin with, ICHEC is working on optimising the Climate Data Operators (CDO) tool. It is hoped that this may lead to a reduction of up to 75% on time required to carry out calculations.

Meanwhile, work has been carried out to optimise the OASIS intercoupler used by multiple climate groups (the OASIS application permits the coupling of

models dealing with various aspects of the simulation, e.g., atmospheric model, ocean model). It has been optimised specifically for two groups, the EC-EARTH consortium and a group in NUI Galway led by Dr Michael Hartnett. The code changes which have been implemented will certainly be of benefit to other projects.

EC-EARTH is an international consortium which was established to develop a new climate model, bringing together state-of-the-art component models for the atmosphere, ocean and land; its goal is to deliver a full so-called Earth

System Model that will be a major tool in providing input for consideration in the next IPCC Assessment Report. ICHEC, UCD and Met Éireann are the Irish partners in EC-Earth. For further information, see http://ecearth.knmi.nl

Climate change database A large (200 TB) public database for data from the EC-EARTH project for the next Inter-Governmental Panel on Climate Change (IPCC) report is being created within the e-INIS project. Storage has been purchased for the data and the web portal is being created currently.

Ireland and France join forces to establish European Group of SGI ICE users ICHEC and its French counterpart CINES (Centre Informatique National de l’Enseignement Supérieur) have much in common. Besides owning similar computer clusters to operate a national service, both centres also have similar missions to provide computing resources and expertise to their national research community.

The realisation that both centres

could greatly benefit from sharing their expertise on the SGI ICE platform, whether it is in terms of systems administration, operational configuration, or applications tuning and optimisation, led to a first exploratory meeting, as part of which ICHEC’s Niall Wilson and Gilles Civario visited CINES in Montpellier.

This was followed by a visit of a

CINES delegation led by their Director, Francis Daumas, the following month. ICHEC and CINES have since extended this collaboration by officially starting a Europe-wide initiative to establish a European group for the users of SGI ICE. We will report on this initiative in more detail in the next issue of ICHEC News.

National Survey results to assist in planning services Existing users of ICHEC services, along with very many other members of the academic community, are being asked to respond to an online survey on the area of HPC. Michael Browne of ICHEC says that the survey is an in-depth exercise carried out only once every three years. The 2006 Survey proved a major success, and the largest of its kind ever conducted in Ireland: 233 researchers were contacted, and 104 responded, representing a total of 584 researchers. This year almost 900 researchers are being contacted. This substantial increase will mean the survey can reach a wider community and emerging users, as new disciplines begin to adopt HPC. Potential respondents are invited to take part by email with a link to the online survey. A great deal of thought has been put into the questions and the areas where comment is invited. In addition, there are follow-up interviews. Michael says: “It’s really all about the users and their needs and problems. We have a customer-focused strategy and resources and our users tell us what they want and what they think they will want in future. That gives us a chance to see if our strategy and resources are aligned with our users' needs and anticipated future needs”. It is also hoped that the process will encourage research groups to think carefully about HPC and how they can exploit this increasingly popular way of doing science. The timeframe for this year’s survey is over the summer.

Invitations to take part were issued by email in recent weeks and respondents were given about a month to reply, although it only takes about 15 minutes to complete the survey.

Follow-up interviews are likely to take place during July, with ICHEC reaching conclusions by the end of the summer.

Results from the survey will be used to develop the Centre’s long-term planning. If you have any questions or if you wish to have your views included the contact email address is survey2009@ichec.ie.

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Feature

The HUB goes active

Since early 2009, ICHEC has been operating from a fully-resourced facility in Dublin 2.

Following a major fit-out, including superb tele-conferencing and video­ conferencing facilities, the national HUB for High-Performance Computing in Ireland is active at the Trinity Technology and Enterprise Campus on Grand Canal Quay in Dublin 2. This fully-resourced, self-contained

space with meeting rooms and an immersive visualisation facility is on the top floor of the Tower building.

Right environment The key thought behind the planning of the HUB’s office space is that it should be a meeting place for researchers and

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ICHEC’s team of computational scientists. It provides an ideal location for researchers to spend time with ICHEC’s scientists, learning best practice in software development and numerical modelling from some of the country’s leading experts. The HUB is designed to act as a catalyst for the creation and dissemination of ideas and expertise; to facilitate problemsolving; to foster collaboration between staff and visiting researchers; and to shorten the time-

to-solution for software development and optimisation.

Flexibility is another important aspect of the operation of the HUB. Visits can vary in length from as short as half an hour to as long as a number of days, and all visits offer the opportunity to speak to as many or as few experts as the researcher needs.

Feedback already coming in Already, ICHEC has been garnering strong feedback from users.

Jonathan Mackey, of the Department of Astronomy and Astrophysics at the Dublin Institute for Advanced Studies said after a visit: "The MacPro visualisation machine is very powerful, capable of significantly speeding up the visual analysis of my astrophysics simulations. I look forward to doing more visualisation of large 3D datasets in the HUB over the next few months”.

Meanwhile, John Fitzpatrick of the Department of Electronic Engineering at NUI Maynooth reported: “Our project seeks to develop wave-energy conversion devices that can adapt to the wide variety of sea conditions to maximise the amount of energy converted. Due to the fact that we are simulating real world sea conditions, our computing needs are large and ICHEC has filled that need admirably. A recent visit to the HUB proved to me that the support available from the staff of ICHEC is at least as important as the computing firepower available. The

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Feature

HUB itself is housed in a lovely stone tower and is filled with white-boards, light and energy.

The lasting impression is of a team which wants to help you achieve your research aims”.

Niall English of the School of Chemical and Bioprocess Engineering, UCD, commented: “The staff are experienced, helpful and very flexible. I make full use of the close-contact working style of the HUB, and I find it very beneficial to work on code compilation projects there with

ICHEC staff, and to discuss code optimisation”.

Encouraging start Professor James Slevin, Director of ICHEC, says: “Having only moved into the HUB at the start of the year, it is very encouraging to see both the growing number of visitors and the enthusiasm that is evident in their feedback to us. We work very hard here to maintain a strong customer-focus in the operation of the HUB and in all our services to researchers.”

Also at the launch was Mary Crowe of UCD, pictured with Michael Kelly of the HEA , and Jim Slevin, Director of ICHEC.

Clockwise from top left: Fully fitted meeting rooms are available at the HUB; the open plan style also features plenty of workstations for visiting researchers to use; researchers are encouraged to visit the HUB; and, the HUB is specifically designed to encourage interaction between scientists.

Left and right: Tele- and video-conferencing facilities are also available at the HUB.

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Education and training

Summer scholarships 2009 Earlier this year, ICHEC offered summer scholarships for two talented students to take part in various projects related to High-Performance Computing (HPC) and computational science. The two were selected from a pool of 40 applicants from nine countries and some of the most prestigious universities worldwide. We congratulate the successful candidates who were chosen at the end of a very challenging selection

Events calendar *Researchers who are not currently ICHEC users are also very welcome to attend all ICHEC events.*

Upcoming events 2009 October 14-16: ACAM workshop: Towards microscale molecular simulations with HighPerformance Computing.

Past events in 2009 February 16-19: Introductory HPC courses at Armagh Observatory.

March 24-27: Introductory HPC courses at University College Dublin.

process; they are Tim Hayes from Trinity College Dublin and Colin MacSweeny from the University of Limerick. The scholarships provide funding for undergraduate students to take part in 10-week summer projects at our offices in Galway or Dublin. They include living expenses in the form of a ¤2,750 stipend, relocation travel expenses (¤300­ ¤800 depending on location) and free accommodation provided by ICHEC.

Each student will work on a project both devised and supervised by our computational scientists. The project is selected by the student from a list of eight that encompass a diverse range of topics such as debugging and profiling tools, Chapel (a language aimed at parallel programming), Message Passing Interface (MPI) on the BlueGene architecture, meteorology and bioinformatics.

May 5-8: Introductory HPC courses at Dublin Institute for Advanced Studies.

June 2-5: Introductory HPC courses at University College Cork.

■ a person to co-ordinate matters at the host institution; and, ■ booking of a suitable venue with laptops/computers for each attendee.

Courses on demand ICHEC delivers HPC courses on demand and *free of charge* to any third-level institution in the country.

You do not have to be a current user of ICHEC to arrange or attend a course in your institution. In order for ICHEC to deliver a course at your institution, all you need is the following: ■ at least eight people willing to attend the course;

If there are fewer than eight people interested, we also have the facilities to hold courses for small groups at our HPC HUB in Dublin (www.ichec.ie/ infrastructure/hpc_hub).

So if you know a few people in your research group or department who would be interested, please visit our website (www.ichec.ie/education_ training/training_courses) or contact us at training@ichec.ie for further details.

These scholarships represent the first of their kind for ICHEC and very positive outcomes are anticipated for both ICHEC and the students. The projects expand the range of activities in HPC research and student mentoring; and for the students, it is an opportunity to gain valuable experience at a national HPC centre.

Finally, we are working hard to ensure that the scholarships will continue on an annual basis and we will be looking for applications in early 2010.

So keep an eye on our website (http://www.ichec.ie/education_trai ning/summer_scholarships) and do not hesitate to contact us at training@ichec.ie if you would like to be kept informed of future developments.

Dr Simon Wong Computational Scientist and Training Co-ordinator

e-INIS update Digital resources for the humanities The Digital Humanities Observatory (DHO) is a central component within the Humanities Serving Irish Society (HSIS) initiative. The DHO was established under the auspices of the Royal Irish Academy to manage and co-ordinate the increasingly complex e-resources created in the arts and humanities. Its objective is to enable researchers in Ireland to keep abreast of international developments in the creation, use, and preservation of digital resources. It fulfils these objectives by: ■ serving as a knowledge base in Ireland via consultations with project partners;

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■ setting national standards to ensure the inter-operability, preservation, and long-term accessibility of digital resources; and, ■ establishing a central repository which will provide access to a wide variety of interdisciplinary, multilingual, and multimodal digital resources created on the island of Ireland.

Of the three points, ICHEC's collaboration with the DHO under the e-INIS project is mainly focused on the third point: development of the DHO

repository for which we provide hardware (three servers in total) and design/development. Dr Bruno Voisin co-ordinates ICHEC’s contribution to the Digital Humanities Observatory.

General activities The deployment of the National eInfrastructure is making good progress, with the commissioning of the first tranche of the National Distributed Storage Infrastructure, providing in the region of 600TB, accessible in the coming months to support major national initiatives and large-scale projects. Further nodes in Cork, Dublin and Galway will follow shortly.

The second major development is in the area of networking, with the definition of a project plan for the e-INIS network infrastructure, and the introduction of the "HEAnet Lambda Service". A working group with representatives from the IT departments has recently been set up to consider policies and procedures. The e-INIS service is expected to provide multiple 10Gbit/s point to point circuits between the e-INIS partners.

For further information, see http://www.e-inis.ie/ or contact the e-INIS Co-ordinator Keith Rochford at rochfordk@cp.dias.ie.

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Research update

A computational analysis of the microscale forces that drive

cell-derived tissue formation: a tissue engineering solution.

Dr Adam Stops and Dr Noel Harrision, NUI Galway. Co-author: Professor Peter McHugh.

Tissue engineering attempts to grow tissue from individual cells in a laboratory setting. As with many building processes, a scaffold is used to provide a temporary structure to organise cell function and encourage tissue growth. An artificial foam-like biomaterial provides this host environment; yet, the scaffold does not just assist in delivering a geometrical structure to organise tissue shape, but it also interacts with the seeded cells in the form of biophysical signalling (biophysical refers to the net product of mechanical stretch and fluid flow). Given that cells are biophysically sensitive, and that the type of tissue synthesised by the cells is hugely dependent upon the level of biophysical stimuli, then the biophysical environment within these scaffolds is of paramount interest to the tissue engineer.

Typically, a bioreactor is used to create the biophysical environment for cell culture. For example, the cells are seeded within the scaffold so that the scaffold-cell construct can then be placed within the bioreactor. Subsequently, the bioreactor is then used to impose a mechanical stretch onto the construct whilst simultaneously forcing fluid to flow through. This methodology results in a complex scenario whereby mechanical deformations and fluid flows both influence cell function. At the moment, very little is known about the optimal magnitudes of scaffold stretch or fluid velocities to grow tissue. Thus, the work undertaken in this investigation used a computational analysis to determine whether a laboratory setting can impart an optimal level of biophysical stimuli onto the cells seeded within a scaffold.

Furthermore, this work attempted

to link particular levels of mechanical stimuli with specific types of tissue, i.e. bone, cartilage or fibrous tissue.

“…the large-scale computations afforded a novel analysis of mechano­ regulatory growth of tissue…”

Two computational methods used The microstructural architecture of a tissue engineering scaffold was collated by using μ-Computer Tomography (μCT) images. From the resulting 3D meshes, two computational methods were employed to simulate the biophysical environment of a cellseeded scaffold within a bioreactor: finite element (FE) analysis was used to model the mechanical deformations, and Computational Fluid Dynamics (CFD) was implemented to reproduce the fluid flow conditions. While the FE software utilised a parallel OpenMP F90 code, viz. the FEEBE solver was written in F90 by Dr Noel Harrison and Dr Denis O’Mahoney (National University of Ireland, Galway), the CFD software employed a parallel platform supplied by ANSYS CFX (ANSYS Inc., USA). Importantly, these two simulations surpassed previous computational models by being able to represent significant geometries through large mesh sizes (the FE models consisted of 6-7 million elements while the CFD meshes used 40-45 million elements). Consequently, a typical FE simulation required 5,000­ 8,000 hours CPU time and 12GB of RAM on a high-performance parallel computer using up to 16 processors.

Predictions of mechanics and fluid flow.

Predictions for a range of settings Using the computed deformations and fluid velocities, cell functions were predicted for a range of bioreactor settings. Subsequently, given that a biophysical-sensitive selection decides the differentiated form of the cell, i.e., an osteoblast, fibroblast or chondrocyte, and the differentiated form of the cell dictates the type of tissue (generally, osteoblasts produce bone, fibroblasts produce skin and chondrocytes produce cartilage), tissue formation predictions were offered so that specific bioreactor settings could be linked with particular tissue types.

Interestingly, an optimal combination of mechanical deformations and fluid velocities, as provided by a specific bioreactor setting, was found for osteoblast and fibroblast cells.

However, chondrocyte cells did not favour one particular combination of biophysical stimuli, though there were a range of magnitudes suitable for chondrocyte growth. This could lead to a development of the current theories used to grow cartilage in a laboratory. Furthermore, the results suggested that tissue growth is highly sensitive to bioreactor settings, and perhaps, in the context of previous work, may be more sensitive than first thought.

Importantly, this biophysical environment is the driving force in cell function and so the ability to engineer the desired tissue is of great interest to the tissue engineer. It is hoped that the findings in this work will help experimental researchers to further develop the current tissue engineering procedures.

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General infrastructure update

New InfiniBand cluster

The Stoney cluster was installed at NUI Galway recently and a novel feature is that it uses water-cooled doors.

The arrival of the new e-INIS cluster, Stoney, is the latest hardware news from ICHEC and will be officially launched in NUI Galway in the autumn. Dr Andy Shearer was responsible for the procurement of this new and important facility and has arranged for it to be hosted in the School of Physics’ machine room in NUI Galway. ICHEC has agreed with Andy to administer and manage the

system and make it available to the national service.

This system is an InfiniBand cluster of 512 cores of the new Intel Nehalem processor. Each of the 64 nodes comprises eight cores and 48GB of memory. Due to the much improved memory bandwidth capabilities of the Nehalem architecture and the 48GB of memory on each node, this system will offer a more suitable platform

than Stokes for projects which have particularly high memory requirements. Another novel feature of the cluster is that it uses water cooled doors at the rear of the racks to more efficiently dissipate the heat produced by such densely packed high power equipment; these doors also reduce the running costs by 30%.

The purchase of Stoney was funded by the Higher Education

1. A principal investigator (PI) submits an online application via one of the following: www.ichec.ie/services/ national_capability_service for Capability class Blue Genebased projects, or www.ichec.ie/services/ full_national_service for everybody else.

2. If the project is accepted, an account is automatically created for the PI with a generated usename and password (if the PI is not already an ICHEC user).

3. New users to ICHEC (apart from the PI) who wish to take part in the project should individually register with ICHEC (see

Authority through the PRTLI-4 eINIS project.

Niall Wilson Infrastructure Manager

User tips Applying for access, maintaining and troubleshooting your account, and efficient use of the resources on offer at ICHEC – answers to these FAQs can be found on our website at www.ichec.ie/support/faq.

The application process for access to ICHEC resources is very straightforward. Just follow this procedure:

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www.ichec.ie/services/) and apply to join the project.

4. The PI approves users who wish to join the project.

5. Users and PI log in and run jobs.

Further information on gaining access to ICHEC resources is available at www.ichec.ie/support/ faq#faqitem1.