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Advancing Research and Development through the National
             Cyberinfrastructure Initiatives

                07 – 09 December 2010
      The Westin Grand Cape Town Arabella Quays
                            Dear participant

                            On behalf of the Centre for High Performance Computing (CHPC), you are cordially
                            welcomed to the 2010 National Meeting.

                            The event this year takes place in Cape Town, at the Westin Grand Arabella Quays.

                            I trust you will find the array of important topics in our programme exciting and
                            beneficially. This event aims to highlight the development of the CHPC within the national
                            cyberinfrastructure intervention supported by the Department of Science and Technology.

                              The theme of the conference this year is “Advancing Research and development through
                              the National Cyberinfrastructure Initiatives”. The event is aimed at advancing research
                              networking, collaboration and competitiveness through an integrated South African National
Cyberinfrastructure Initiatives programme. The conference was preceded by the whole week of highly successful High
Performance Computing (HPC) School attended by postgraduates’ students from South Africa and Africa across various
fields of computational science. There will be a number of exciting domain specific breakaway sessions taking place
during the conference and post-conference Advanced HPC tutorials.

Furthermore, the CHPC will make use of this event to cultivate dialogues that are aimed at enhancing our service delivery
and strengthening an integrated partnership amongst local and international stakeholders.

It is hoped that through the interactive activities of this meeting, we can fully explore how the research communities can
take maximum advantage of this sizeable investment. I therefore encourage you to participate in this meeting, to share
your knowledge, voice your opinions and provide your support in pursuit of harnessing a vibrant ecosystem in the context
of DST’s cyberinfrastructure intervention

Dr Happy Sithole
Centre Manager: CHPC

Sponsors of this event:
Plenary Session

Happy Sithole (CHPC, CSIR Meraka Institute, South Africa)

How would High Performance Computing and Digital Research Data Curtation Benefit South Africa?

High Performance Computing and Data curation technologies have rapidly emerged as tools central to the advancement of
an exciting array of research and education activities. Since its establishment, the Centre for High Performance Computing
(CHPC) have had the privilege in partnering with students and researchers to promote and implement a number of cutting
edge projects to address mysteries of grand challenges in science and engineering. In addition, such types of partnership
are gradually extending to a number of industrial partnership. On one hand, the presentation will discuss the research,
human capital development highlights of the CHPC while on the other, will showcase the deployment of the cutting edge
IT technologies to date. Drawing global examples and also how South Africa and other African can take advantage of this
note worthy investment of DST and collectively assist South Africa and other countries within the African region to increase
their competitiveness

Gavin J. Pringle (University of Edinburgh, UK))

EPCC and Technology Transfer

EPCC is a unique centre for advanced computing. We research and develop novel computing solutions; write software;
manage computing systems and provide HPC training. Our combination of computing resources and expertise is unmatched
by any European university. Clients and partners include local and global industry, government and academia. In this talk,
we will present some of the mechanics to our technology transfer.

Clement Onime (ICTP, Italy)

Computational physics centres in Africa

In the last two-and-a-half years, the Abdus Salam International Centre for Theoretical Physics (ICTP), working with
UNESCO, has been involved in a project for sub-Saharan Africa funded by the Italian Government. The project is about
building environmental networks and the monitoring of the environment in Africa; conducting practical training and research
in basic and applied sciences, including education, energy, environment and health education for Africa; and developing
research infrastructure for Africa, including computational physics centres.

The component on computational physics centre(s) is about fostering the implementation of low-cost Linux-based commodity
clusters of 5-32 nodes for high performance computing (HPC) and ensuring sustainable human capacity that is self-reliant
• Implementing and maintaining Linux-based commodity clusters
• Providing application/user support in HPC environments
• Porting existing scientific applications
• Researching new HPC technologies

This work presents the unique aspects of the project, processes, the partners (international and African) and also the
results obtained in this short period of time. These include the establishment and continuing support of two centres for
HPC climate modelling and one centre for atomistic science HPC research. The presentation concludes with a look at the
engineering education process leading to the establishment of a joint Master of Science (M.Sc.) programme in three African
universities/institutions devoted to HPC. The goal is to provide continuing training at graduate level of researchers who can
then implement, support and use HPC both in academic and industry environments.

The CHPC is an initiative funded by the Department of Science and Technology of South Africa managed by CSIR Meraka Institute
Thomas Franz (Cardiovascular Research Unit, Chris Barnard Division of Cardiothoracic Surgery, University of Cape
Town, Observatory, South Africa; Centre for Research in Computational and Applied Mechanics, University of Cape Town,
Rondebosch, South Africa; Centre for High Performance Computing, CSIR, Rosebank, South Africa)

Computational mechanics in treatment and prevention of cardiovascular diseases

Cardiovascular diseases (CVD) will become the leading cause of death by 2020 superseding infectious diseases such
as HIV, TB, and malaria. The risk of CVD has been reported to increase with the improvement of economic wealth and
social environment, in particular in Africa. The same study revealed a higher risk for acute myocardial infarction, the
leading causes of congestive heart failure, in the black African group in sub-Saharan Africa due to an increased level of
hypertension. Similarly, the American Heart Association expects in the near future a dramatic increase in CVD incidences in
Africa, in particular in the younger population, in conjunction with the emergence of a new epidemic of obesity, diabetes and
uncontrolled hypertension. Rheumatic fever, eradicated in developed countries due to the improvement of socio-economic
conditions, has now become a health problem of almost exclusively the developing world. Caused by a streptococcal
infection in particular in the young population, this rheumatic fever leads to rheumatic heart disease, if not treated effectively.
Therapies for cardiovascular diseases reach from purely artificial prostheses, such as mechanical heart valves and
synthetic vascular grafts, to tissue engineering and regenerative medicine including stem cell approaches. The research
into cardiovascular diseases, along with the improvement of prevention and treatment strategies, require increasingly multi-
disciplinary approaches. Biomechanics and biomedical engineering, comprising computational and applied mechanics,
mechanical and materials engineering, have been a crucial element of such approaches along with other disciplines such
as regenerative medicine, cell biology, biochemistry, chemistry and polymer sciences. While biomechanical engineering has
been playing a role in some areas of cardiovascular research, such as vascular grafts, prosthetic heart valves, and cardiac
assist devices, its importance is only in an emerging state in other fields amongst of which are myocardial infarction and
restenosis. The synergy of a wide range of disciplines such as medicine, polymer sciences, cell biology, and computational
and applied mechanics will provide scarce skills development at various levels and offers potential to create outstanding
benefits for the health sciences. This talk will address challenges of biomechanics and the increasing role of computational
mechanics in treatment and prevention of cardiovascular diseases.

Steven Damelin (GSU, USA and Wits, South Africa)

Point cloud recognition problems, medical imaging and computational harmonic analysis in high performance computing

The talk focuses on central themes related to the flagship, Computational research initiative in imaging and remote sensing,
for the period, 2010-2013. The purpose of this talk is to discuss three research themes in the proposed research: point
cloud recognition problems, medical imaging and computational harmonic analysis in high performance computing. It deals
with current and future research, and introduces the many students and collaborators around the world, who are part of the

Catherine Cress (University of Western Cape, South Africa)

Galaxy Evolution and Cosmology: HPC, MeerKAT/SKA and SALT

We recently completed a state-of-the-art simulation of structure evolution in the universe using facilities at the CHPC.
The simulation involves modelling dark matter, gas and star formation in a representative volume of the universe. I will
describe how we are using these simulations to probe questions in galaxy evolution and cosmology and describe the role
these simulations play in designing experiments we plan to carry out using the Southern African Large Telescope and the
MeerKAT/SKA radio telescope.

The CHPC is an initiative funded by the Department of Science and Technology of South Africa managed by CSIR Meraka Institute
Michael Bearpark (Imperial College, London)

Challenges for computational chemistry

2011 has been designated the International Year of Chemistry. Twenty years ago, computational chemistry was largely a
specialised research area, separate from mainstream chemical research. Just over ten years ago, John Pople was jointly
awarded the Nobel Prize for “development of computational methods in quantum chemistry”, and partly as a result of this
pioneering work, computational methods are now widely used by non-specialists studying chemical structure and reactivity.
One consequence of this success, however, is that computational chemistry itself might be thought of as a ‘solved problem’.
The challenges to be presented, suggest that this is far from true. The focus will be applications of computational chemistry
in other research areas (such as biomolecular spectroscopy, ultrafast molecular physics, astrophysics and chemistry of
the interstellar medium); new methods that are far from being standardised ‘levels of theory’ yet; related developments in
computer hardware; and finally a challenge for chemical education.

Veerle Van den Eynden (UK Data Archive, UK)

Sharing research data – policy, infrastructure, people

Digital data sharing is high on the agenda of research funders and policy makers. Effective sharing of research data
requires a combination of policy support, data sharing infrastructures and researcher skills. The UK Data Archive engages
with all three pillars by liaising with research funders and publishers on data policy developments and their implementation;
through data infrastructures to curate research data and make them accessible for the academic community; and by actively
supporting researchers in managing and sharing data. The archive’s expertise is in social, economic and humanities data
and it plays a leading role in UK and international data sharing initiatives, data technologies and tool development.

Wim Hugo (SAEON, South Africa)

Meta-Data: A New Data Mining Resource

Worldwide standardisation, and interoperability initiatives such as GBIF, Open Access and GEOSS (to name but three of
many) have led to the emergence of interlinked and overlapping meta-data repositories containing potentially hundreds of
millions of entries collectively. This forms the backbone of an emerging global scientific data infrastructure that is both driven
by changes in the way we work, and opens up new possibilities in research methods and approaches.
Several initiatives are concentrated on building a generalised, shared, easily available, and indefinitely preserved scientific
data infrastructure to aid future scientific work. The vision is that of the ‘fourth paradigm’, where massively data-intensive
research opens new areas of enquiry and insight.

This article deals with the parallel aspects of the meta-data that will be used to support the global scientific data infrastructure.
There are obvious practical issues (size of meta-data sets and speed of transfer/ processing being the most important), but
we are more concerned with some of the conceptual questions:
• Can we use meta-data to assess, identify and reduce duplication of meta-data and overlaps of mandate?

•   What possibilities exist for mining the relationships that exist implicitly in very large meta-data collections?

•   Is it possible to define an explicit ‘scientific data infrastructure’ as a complex, multi-relational network database that can
    become self-maintaining in true Web 2.0 and ‘social networking’ fashion?

The article provides a blueprint for a new approach to massive meta-data collections, its encoding, and how this can be
processed using established analysis techniques to answer the questions posed.

The CHPC is an initiative funded by the Department of Science and Technology of South Africa managed by CSIR Meraka Institute
Ralph Rudd (IBM, South Africa)

What does it mean to be smarter?
Intelligence is being infused into the systems and processes that make the world work—into things no one would recognise
as computers: Cars, appliances, roadways, power grids, clothes, even natural systems such as agriculture and waterways.

It is no longer a question as to whether the technology to build a smarter planet is real. Now, we need to know what to do
next. How do you infuse intelligence into a system for which no one enterprise or agency is responsible? How do you bring
all the necessary constituents together? How do you make the case for budget? Where should you start?

We’ve learnt a lot over the past year about what it takes to build a smarter planet. Importantly, we’ve learnt that our
companies, our cities and our world are complex systems—indeed, systems of systems—that require new things of us as
leaders, as workers and as citizens. A smarter planet will require a profound shift in management and governance toward
far more collaborative approaches.

Simon See (ORACLE, South Africa)

Computing for science and engineering - where we are going?

Computing has become an important tool for research in science and engineering.                           The author looks at where new
applications are heading and what type of technology will be needed.

Alex Cyr (Microsoft Technical Computing – Middle East and Africa)

The Microsoft technical computing initiative

As modern science increasingly relies on integrated information technologies to collect, process, and analyze complex data,
the computer science research community and Microsoft technologies can assist scientists make breakthrough discoveries.

Microsoft is committed to collaborating with the global scientific community to find solutions for some of the toughest
challenges facing humanity, in diverse disciplines such as life sciences, environmental science, and engineering. This is
based on understanding the critical connection between science and computing, and the importance of developing software
solutions that can support and enhance scientific research processes.

This short presentation outlines some of Microsoft’s external research projects, amongst others:
Project Trident - a workbench for scientific workflows
The Microsoft computational biology tools
The World-wide Telescope
Dryad and DryadLink
The Microsoft academic conference management service

Rick Afonso (Cisco systems engineer, South Africa)

Future trends in data centre architecture / design

Data centre professionals are being challenged to address major market, globalisation, and technology trends that will
drastically change the way data centre infrastructures are deployed and operated over the next decade. Therefore, a new
data centre architecture is emerging in response to these challenges, which will based on a shared, virtualised infrastructure
model: Services abstracted from the underlying physical assets, which can be dynamically adapted to changing application
and service level requirements.

The CHPC is an initiative funded by the Department of Science and Technology of South Africa managed by CSIR Meraka Institute
This architecture enables the emerging enterprise and service provider ‘cloud’ models. This transformation is more heavily
reliant on the network than ever before. Indeed, in many ways the network now becomes the underlying foundation upon
which the virtualised data centre infrastructure runs. The network has uniquely desirable characteristics for this expanded
role. This will be expanded during the Cisco plenary session.

The CHPC is an initiative funded by the Department of Science and Technology of South Africa managed by CSIR Meraka Institute
                                                      CHPC National Meeting 2010

                   Advancing Research and Development though the National Cyber-Infrastructure Initiative

         Tuesday 07 December 2010
         TIME                                   SPEAKER                                                   TOPIC
         08:00             Registration: Arrival Tea / Coffee
                            Theme: Genesis and Evolution of National Cyber-Infrastructure in SA
                           Happy Sithole
                           Centre for High Performance Computing, SA                Welcome Speech
                           Department of Science and Technology
                                                                                    Speech by Department of Science and
         09:00             Official
                           Department of Science and Technology, SA
                                                                                    How would high performance computing
                           Happy Sithole
         09:30                                                                      and digital research data curatorship
                           Centre for High Performance Computing, SA
                                                                                    benefit South Africa?
         10:20              Q&A
         10:30             Morning Tea / Coffee Interlude
                                                Theme: The International HPC Trends
                           Danny Powell
                                                                                    The National Center for Supercomputing
         11:00             National Center for Supercomputing
                           Applications, USA
                           Gavin J Pringle
         11:30                                                                      EPCC and Technology Transfer
                           EPCC, The University of Edinburgh, UK
                           Clement Onime
         12:00             The Abdus Salam International Centre for                 Computational Physics Centres in Africa
                           Theoretical Physics, Italy
         12:30             Q&A
         12:40             Networking Lunch
                                        Theme: Past and Present CHPC Flagship Projects
                           Thomas Franz                                             Computational Mechanics in Treatment and
         13:30             University of Cape Town, SA                              Prevention of Cardiovascular Diseases
                                                                                    Point Cloud Recognition Problems, Medical
                           Steven Damelin
         14:00                                                                      Imaging and Computational Harmonic
                           GSU, USA and Wits, SA
                                                                                    Analysis in High Performance Computing
                           Catherine Cress                                          Galaxy Evolution and Cosmology: HPC,
                           University of Western Cape, SA                           MeerKAT/SKA and SALT
         15:00             Q&A
         15:10             Afternoon Tea / Coffee Interlude
                                                Theme: Research using HPC and Data
                           Michael Bearpark
         15:30                                                                      Challenges for Computational Chemistry
                           Imperial College, London
                           Veerle Van Den Eynden                                    Sharing research data – Policy,
                           UK Data Archive, UK                                      Infrastructure, People
                           Wim Hugo
         16:30             The South African Environmental                          Meta-Data: A new Data Mining Resource
                           Observation Network, SA
         17:00             Q&A

The CHPC is an initiative funded by the Department of Science and Technology of South Africa managed by CSIR Meraka Institute
                           Theme: Vendors and Perspective on Future HPC and Data Technology
         17:10             Ralph Rudd
                                                                                    Smarter Planet Presentation
                           IBM, SA
         17:40             Simon See                                                Computing for Science and Engineering -
                           ORACLE                                                   Where we are going?
         18:10             Alex Cyr
                           Microsoft Technical Computing, Middle East               Microsoft Technical Computing Initiatives
                           and Africa
         18:40             Rick Afonso                                              Future trends in data centre architecture /
                           Cisco Systems                                            design
         19:10             Q&A
         19:15             Remark of the Day
         19:30             Network Cocktail Function – Old Harbour Lobby

The CHPC is an initiative funded by the Department of Science and Technology of South Africa managed by CSIR Meraka Institute
         Wednesday 08 December 2010
         TIME                                   SPEAKER                                                   TOPIC
         08:00             Each breakaway session will be coordinated by the co-chairs. Unless it is previously
                           specified by the co-chairs, the format of the breakaway sessions will be as follows:

                           •    Advanced Gaussian Workshop
                           •    Computational Physics
                           •    Social Science Data Documentation and Management
                           •    Parallel Computing & High Performance Computing-aided Science and Engineering
                           •    Operational Oceanography & High Performance Computing
                           •    ICT Specialists
                           •    Computational Initiative in Image Processing and Remote Sensing
         08:00             Registration: Arrival Tea / Coffee Interlude
         09:00             Morning Session 1
         10:30             Morning Tea / Coffee
         11:00             Morning Session 2
         12:30             Networking Lunch
         13:30             Afternoon Session 1
         15:30             Afternoon Tea / Coffee
         16:30             Afternoon Session 2
         17:00             Session Closes
         17:30             Network Cocktail Function – Old Harbour Lobby
                           Poster Presentations to take place during the Network Cocktail

         Thursday 09 December 2010
         TIME                                   SPEAKER                                                   TOPIC
         08:00             Registration: Arrival Tea / Coffee Interlude
         09:00             Morning Session 1
         10:30             Morning Tea / Coffee
         11:00             Morning Session 2
         12:30             Networking Lunch
         13:30             Afternoon Session 1
         15:30             Afternoon Tea / Coffee
         16:30             Afternoon Session 2
         17:00             Session Closes

The CHPC is an initiative funded by the Department of Science and Technology of South Africa managed by CSIR Meraka Institute
Friday 10 December 2010

The following Advanced HPC Tutorials are taking place at the Center for High Performance Office:
•        OpenFOAM & PARAVIEW
•        MATLAB

Poster Presentations

The below Poster Presentations are taking place at the Network Cocktail Function on Wednesday 08 December 2010
                                               Title                                                    Name               Surname
      FEARCF : A free energy method for calculating sugar ring pucker                           Chris                  Barnett
      Temporal variability of primary production in the Benguela and Agulhas                    Ray                    Barlow
      Developing a climatology of Mesoscale Convective Systems over South                       Ross                   Blamey
      Numerical modeling of the Southern Ocean mixed layer                                      Nicolette              Chang
      Large Scale Biochemical simulations using highly Parallelizable code on                   Werner                 Crous
      A Theoretical Investigation of Isotope Effects on the Vibrational Spectra                 JC                     Davies
      of [PtCl6]2
      Catalysing the Study of Chemical Catalysis                                                Kyle                   Fernandes
      Coarse-Grained Molecular Dynamics from Free Energy Adaptive                               Riedaa                 Gamieldien
      Reaction Coordinate Forces (FEARCF)
      In search of high speed hybrid Quantum/Classical simulations                              Krishna                Govender
      Evaluation of the modified advection scheme recently implemented in                       Issufo                 Halo
      ROMS, in the waters of the Mozambique Channel
      Tropical Temperate Toughs over southern Africa                                            Neil                   Hart
      Designing Inhibitors of Herpes Simplex Virus using Free Energy                            Umraan                 Hendricks
      Perturbation Computation Methods
      Can altimetry data be used to predict phytoplankton and zooplankton Jenny                                        Huggett
      biomass associated with mesoscale eddies in the Mozambique Channel?
      Zooplankton and ichthyoplankton spatial distributions associated with a                   Jenny                  Huggett
      dipole eddy system in the western Mozambique Channel
      Meso-scale structuring of the pelagic ecosystem in the Mozambique                         Yonss                  Jose
      channel: a modelling approach
      Hydrodynamics circulation at the Quirimbas’s Archipelago region                           Yonss                  Jose
      Measuring Phytoplankton Flatulence; VHOCs in the Southern African                         Brett                  Kuyper
      Marine Troposphere
      Hydrographic and satellite observations in the Delagoa Bight, southern                    Tarron                 Lamont
      Predicting Fundamental Processes in Inorganic Chemistry using Potential Richard                                  Matthews
      of Mean Forces
      Can an oceanic gateway alter the evolutionary trajectory of inshore fish                  Kate                   Munnik
      species in the Benguela region?
      The Ocean Surface Layer at high resolution: Satellite observations and                    Nicolas                Rascle
      Ocean-Waves-Atmosphere coupled dynamics
      Using Free Energy Perturbation to explain TB’s MshB Inhibition                            Ian                    Rodgers
      A Primary Validation of MERIS Case 2 Ocean Colour Products in the                         Marie                  Smith
      Natal Bight, South Africa
      Southern Ocean chlorophyll in reference to ocean fronts and mesoscale                     Sebastiaan             Swart
      From games to GAMESS (-UK): GPU Acceleration of Integral Analysis                         Karl                   Wilkinson

The CHPC is an initiative funded by the Department of Science and Technology of South Africa managed by CSIR Meraka Institute
Computational Platforms                                                                                          and
IBM e1350 Cluster – 640 CPUs at 2.5
teraflops measured performance.                                                  The CHPC is part of South Africa’s
                                                                                 national cyberinfrastructure intervention:
IBM Blue Gene-P – 11.5 teraflops                                                 Supported by the Department of Science
measured performance.                                                            and Technology (DST) and hosted by
                                                                                 the Council for Scientific and Industrial
IBM P690 SMP – 166 gigaflops peak                                                Research (CSIR). Other complementary
performance.                                                                     national cyberinfrastructure includes:
                                                                                 South African National Research Network
Sun SPARC Enterprise M9000 server with                                           (SANReN) – provision of highspeed, high-
64 SPARC64 VII quad-core processors, and                                         bandwidth connectivity, and Very Large
a cluster of four Sun Blade 6048 Modular                                         Data Sets (VLDS) – effective curation of a
Systems. The cluster houses a total of 192                                       variety of notably large data sets.
nodes based on the next-generation Intel
Xeon E5450 processor (Nehalem) – 27                                              Advancement of scientific boundaries
teraflops total peak performance.                                                by enabling world-class research
                                                                                 through promoting and facilitating the
Storage solution based on ten AMD                                                use of computational technologies and
Opteron-powered Sun Fire X4540 Open                                              techniques amongst researchers.
Storage servers, providing 480 terabytes of
data with the Lustre parallel file system for                                    Fostering of innovation through effective
extreme I/O performance and reliability.                                         partnership for training a new generation
                                                                                 of skilled researchers in areas underpinned
Range of clusters with other                                                     by high performance computing and data
computational components:                                                        curation, particularly those of strategic
GPGPU – General Purpose computing on                                             national and continental importance.
Graphics Processing Units
FPGA – Field-Programmable Gate Arrays.                                           Promoting private public partnership
                                                                                 and the utilisation of the high
                                                                                 performance computing by the
                                                                                 commercial sector.

The CHPC invites all researchers to take                                         The CHPC seeks joint research and HCD
advantage of its cyberinfrastructure.                                            initiatives with its stakeholders.

For more information
The CHPC is an initiative funded by the Department of Science and Technology of South Africa managed by CSIR Meraka Institute

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