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news
The University of Edinburgh
www.epcc.ed.ac.uk
Issue 51, summer 2004
CONTENTS
2 Training at EPCC
3 PhD studentships at EPCC
Guest lectures at EPCC
4 MSc: One, two, three
6 User support in a virtual
infrastructure
7 XMLDiff: A tool for
comparing XML documents
8 eLT: e-learner tracking
9 HPCx times 2
10 Improved performance
scaling on HPCx
WOMPAT ‘04
11 PGPGrid: Grid-enabled
animations
12 MSc in High Performance
Computing
Education and training:
preparing today for
tomorrow

FOCUS: TRAINING
Editorial
Judy Hardy
This edition of EPCC News has the theme ‘education
and training’. In recent years we have expanded our
commitment to training the next generation of HPC
professionals through the MSc in High Performance
Computing. The MSc is now a well-established fixture at
EPCC, and we look forward to its continuing expansion
over the coming years. Building on from its success, we
are also very pleased to be able to offer our first PhD
studentships from September 2004. This issue includes
articles on both the MSc and PhD.
From September this year, our MSc courses will run
separately from our long-standing range of short training
courses. However, a number of intensive courses will
continue to be offered as part of the HPCx National
Service, together with a selection of courses aimed more
specifically at HPCx users. The latest of these is described
in this issue.
e-Learning is now an integral part of learning for both
students and researchers. We include articles on two
projects in this area: distributed collaborative learning via
an innovative use of Access Grid technology to facilitate
shared ‘surgeries’ between remote sites as part of the
HPC Europa programme; and a project to investigate and
understand how students use online resources.
Finally, there are also some articles which give updates
on various other EPCC projects. Of particular note is the
recent upgrade to the HPCx National Service. This is now
the most powerful academic supercomputer in Europe with
a performance of 6 Tflops.
I hope this edition of EPCC News gives you an overview
of the range of training and education activities here at
EPCC and that you find the articles both educational and
enjoyable.
Training at
EPCC Judy Hardy
EPCC is excellently equipped to provide both MSc
students and course attendees with state-of-the-art training
facilities. We have a dedicated training room which is
equipped with 26 Sun Ray flat screen terminals together
with a Sun Blade 2000 server. The Sun Rays use smart
card technology, so that once you are logged in you can
pull the smart card out at any time and the session will
reappear when the card is inserted into any of the Sun
Rays. Our courses typically comprise a mixture of lectures
and practical sessions, and one common use for the smart
cards is to transfer a student session to the trainer’s Sun
Ray and hence to the data projector – so interesting results
from a practical session can be shared with the whole class!
The standard HPC resource available for all courses is the
University HPC service ‘lomond’, a Sun Fire E15K server
installed in 2003 (see EPCC News 48). This is a single SMP
cluster with 52 UltraSPARC III processors configured
into a 4-processor front end for compilation, debugging
and testing and a 48-processor back end for batch runs.
We also offer a number of course for users of the HPCx
National Service. The newest of these courses, ‘Improved
Performance Scaling on HPCx’, is described on p10.
The EPCC Access Grid (AG) node is located next to the
Training Room. The AG node and Training Room are
separated with a removable partition, which gives us the
possibility of offering lectures, seminars or even complete
courses to remote users via Access Grid. For example,
the HPC-Europa consortium will use the AG node to run
‘surgeries’ in which visitors from different sites can meet
to discuss common issues; see ‘User support in a Virtual
Infrastructure’ on p6.
Over the last three years, most of our courses have been
shared by both MSc students and other course attendees.
As described in ‘MSc: One, Two, Three’ on p4, from
September 2004 our MSc courses will be run in a more
traditional university style of weekly lectures and practicals
and so will not generally be available for other HPC users.
However, we will continue to offer a range of intensive
short courses for HPC users as part of the HPCx service.
For details of upcoming courses please see:
EPCC: www.epcc.ed.ac.uk/computing/training
HPCx: www.hpcx.ac.uk/support/training
2

FOCUS: TRAINING
PhD studentships at EPCC Mark Bull
EPCC is planning to build on its successful MSc in High
Performance Computing and expand its postgraduate
programme by taking on PhD students. We expect to take
students starting in the 2004/2005 academic year. Here
are two of the potential projects being considered:
Self-optimising applications
For many high-performance applications, considerable
programmer effort is required to tune the application when
it is ported to a new platform. With the likely rise in the
potential number of platforms readily available to users via
computational grids or similar resource sharing capabilities,
this task will become increasingly onerous.
The essential concept for this project is to determine to
what extent this process could be automated. Applications
can be equipped with switches (either run-time or compile
time) and tunable parameters which affect performance.
The process of tuning the code is therefore largely one
of finding the optimal settings. If the programmer can
identify the key factors affecting performance and equip
the application in a suitable way, then an automatic system
can search for the best values.
However, the search spaces can often be large and their
behaviour highly non-linear. Smart search techniques will
be needed for effective automatic tuning. Some promising
approaches from the field of adaptive compilation exploit
machine learning techniques, and this project will
investigate their use at the application level.
High performance computing and lattice gases
Lattice gases provide a very flexible computational
approach to the study of the physics of complex solid/
fluid mixtures and are becoming increasingly important in
materials research. They also have the advantage that they
are highly amenable to parallel computation.
This project will investigate the introduction of accurate
solid-fluid boundary conditions into a lattice Boltzmann
model which has been developed at EPCC. This issue is
important in the effective and efficient representation of
solid particles suspended in fluid, which is an active area
of current research.
Further information
www.epcc.ed.ac.uk/computing/training/PhD
Guest lectures at EPCC Daragh Byrne
As part of the MSc in High
Performance Computing run
at EPCC, a number of people
are invited to give a guest
lecture. These are open to all
staff and students. The lecture
topics are diverse, with
topics including cosmological
modelling, genetic analysis
and web services. This year’s
lecture series included:
• Alistair Law, Director of Vision Consulting Scotland,
who described the management of a 400-person team
developing the infrastructure for an internet bank, stressing
the need for people-orientated project management.
• Paul Burton from the University of Reading described
the work of the Met. Office in embracing HPC, focusing
in particular on recent work using the HPCx machine.
• Andrew Herbert, director of Microsoft Research UK,
reviewed the history of distributed computing from basic
remote procedure calls to web services, using concepts
from economics to predict future evolutions in the field.
• Chris Thomas of IBM discussed how all forms of
computing are applied to topics as diverse as gene
sequencing and recording the results of drug trials.
• Cronan McNamara of Trinity Centre for High
Performance Computing at Trinity College, Dublin, talked
about the MonteCarlo project, which developed high
performance software for modelling the intake of certain
chemicals by humans via food.
All in all a fascinating year, and we look forward to the
next.
If you would like to contribute, please email brief details of a
proposed talk to: d.byrne@epcc.ed.ac.uk
3

FOCUS: TRAINING
MSc: One, two, three David
Henty
We are now in the third year of the MSc in HPC, and
our successful students are just embarking on their MSc
dissertations having completed the taught part of the
programme. This year, the taught part comprised the
following ten courses:
• Fundamental Concepts of High Performance Computing
• Practical Software Development
• Shared Memory Programming
• Message Passing Programming
• Parallel Decomposition
• Core Topics in HPC and e-Science
• Object Oriented Programming for HPC
• Exploiting the Computational Grid
• Applied Numerical Algorithms
• Hardware, Compilers and Performance Programming
Almost all of these were also available externally via our
training programme. As well as attending the courses,
MSc students had to complete substantial pieces of
coursework (one for each course) amounting to 50% of
the marks, with the remaining 50% coming from written
examinations.
MSc dissertations
The dissertation is an extremely important (and hopefully
enjoyable!) part of the MSc, and one where we hope
that students especially benefit from EPCC’s working
environment with its diverse mix of research and software
development projects in HPC and e-Science. To give
a flavour of the kind of work going on, here are brief
summaries of three of the projects currently underway.
OpenMP Runtime Library
Performance
Supervisor: Mark Bull
Student: Paul Walsh
This project will
examine the performance of some key operations which
typically form a key part of an implementation of the
OpenMP runtime library.
A number of algorithms for implementing tree-based
lock free barriers have been published in the research
literature. However, there have been few recent
studies on their comparative performance on the latest
shared-memory architectures. Part of this project will
implement a number of barrier algorithms and test their
performance on Sun 15K and IBM p690+ platforms.
The dissertations for all the projects will be available on
the MSc webpage from October this year.
The future of the MSc
The MSc is now a well established part of EPCC’s
activities, and we are pleased to announce that we have
recently secured long-term funding from the University of
Edinburgh’s School of Physics to continue the programme
after our initial EPSRC grant expires. As part of a general
reorganisation of course structure at Edinburgh, which
includes a move to a two-semester rather than three-term
academic year, we will also be significantly changing the
way that courses are offered. From September 2004, our
MSc courses will be offered in a more traditional ‘longthin’
style rather than the current delivery method of
intensive, three-day blocks. Each course will occupy a
single morning or afternoon slot every week, and will last
for a whole semester. There will also be two new courses:
‘Scientific Visualisation’ and ‘Advanced Topics in HPC and
e-Science’.
This reorganisation, coupled with an expected increase in
student numbers, means that we will no longer be able
to accommodate external attendees on these courses.
However, many of the core HPC courses will still be
offered as part of the National HPCx Supercomputer
Service.
MSc home page: www.epcc.ed.ac.uk/msc
EPCC training programme:
www.epcc.ed.ac.uk/computing/training/courses
HPCx courses: www.hpcx.ac.uk/support/training
Since both these architectures are mildly NUMA, one
interesting question is whether it is worth trying to
map the tree structure of the barrier to the underlying
architecture. Many barrier algorithms require threads to
spin on a global flag which is then toggled by one thread
when all other threads are known to have arrived at the
barrier. However, other mechanisms are possible, and
may perform better on these machines.
A second important operation in the OpenMP runtime is
array reduction. There are a number of possible ways to
implement this, and their relative performance depends
on the size of the array and the number of threads. In
this project we will investigate these different methods
and try to determine which method is most appropriate
in a range of different circumstances.
4

FOCUS: TRAINING
Domain Decomposition for Colloid Clusters
Supervisor: Kevin Stratford
Student: Pedro Gomez
It is possible to represent small solid particles, known as
colloids, in a numerical model of fluid flow (the ‘lattice
Boltzmann’ method). The particles move around freely
in the fluid and can bounce off each other according to
Newton’s Laws. Particles that approach each other more
closely than a certain critical distance are said to form
clusters. Clusters of many particles can arise, forming
complex aggregates in three dimensions. Numerically,
the clusters must be treated as a single object at certain
stages of the calculation.
Parallelisation with domain decomposition then presents
a problem: each sub-domain contains a number of
particles locally, but a large cluster of many particles
might span two or more sub-domains. Information about
all the particles must then be available across the subdomains.
Developing a Client Toolkit for Data Services
Supervisors: Ally Hume and Amy Krause
Student: Craig Munro
Web services provide a language-neutral and
machine-independent means of machine-to-machine
communication using XML-based technologies. Over
the last few years they have been increasingly used in
the commercial world to support business-to-business
relationships. Within roughly the same time frame,
Grid Computing has adopted web services as a basis
for linking and sharing large scale computing and data
resources. Web service protocols have been extended
slightly to address scientific based problems. Of late an
attempt is being made to reconcile these two slightly
disparate views.
The OGSA-DAI project aims to develop middleware
that will allow data resources – currently mainly
database systems – to be accessed and integrated into a
Grid environment. This allows both science and business
applications to publish and access data using the same
language-neutral and machine-independent methods as
are used in web and Grid services.
The aim of this project is to design and create a ‘toy’
model which represents particles in a three-dimensional
box subject to a regular decomposition. Then:
• particles close together must be identified as belonging
to the same cluster
• information about all the particles in large clusters that
span sub-domains must be distributed to the appropriate
processes
• this procedure must be repeated as the particles move
around. The data structures and communication patterns
required to do this effectively and efficiently must be
identified.
They
all
lived
happily
ever
GlobusWorld 2004 - www.ogsadai.org.uk
after
Use OGSA-DAI to provide the middleware
tools to grid-enable existing databases
access
transformation
discovery
collaboration
integration
This MSc project will design and implement a new
Client Toolkit API in Perl or C, drawing on the
existing Java implementation. This will allow legacy
HPC and scientific applications to utilise OGSA-DAI
services.
The project will require good software engineering
principles and good design as the transfer of data
using the Client Toolkit must be efficient in order to
be usable. In particular, care must be taken to avoid
copying of data wherever possible.
1
5

FOCUS: TRAINING
User support in a virtual
infrastructure J-C Desplat and Catherine Inglis
The HPC-Europa consortium (presented in EPCC News
50) aims to integrate the provision of HPC services
to the European research community in an innovative
and coherent manner. HPC-Europa consists of several
interrelated projects, at the core of which lies the
transnational access visitor programme 1 . This will allow
some 800 researchers based in the EU and Associated
States to visit one of the many universities and
research institutes associated with the six HPC centres
participating in the visitor programme. The combination
of the stimulating intellectual environment provided by
the host research department, the technical expertise of
the staff at the HPC centres and access to some of the
most powerful HPC systems in the world allows visitors
to explore new avenues and make significant advances in
their research.
Over the next four years, our consortium will explore
a novel approach using Access Grid (AG) technology
to bring together the complementary expertise of staff
across the six centres in order to provide a higher
standard of user support to visiting researchers. This
approach also meets one of the European Commission’s
key objectives: to achieve a long-term structuring effect
on both users of our facilities and the operators of our
large-scale infrastructures.
One strength of the previous visitor programme was the
successful fostering of a spirit of collaboration between
local research communities and European visitors. Now
HPC-Europa aims to extend this co-operative spirit
across the consortium as a whole. This is key to the
success of the project as it will lead to the emergence
of virtual communities of researchers and facilitate crossdisciplinary
fertilisation.
Surgery sessions via Access Grid
The concept of distributed user support over the Grid
is currently a hot topic of conversation. Although
we do not plan to ‘distribute’ user support over the
consortium per se (each centre remains responsible for
its own systems), we can certainly exploit economies
of scale and synergies across the consortium. One easy
way to do this is by setting up joint ‘surgery sessions’
(group tutorials) across two or more HPC centres via
AG. For these surgery sessions, an expert at one of
the centres will be asked to prepare a short tutorial on
an appropriate topic eg MPI, OpenMP or some other
specific aspect of HPC. Visitors will be informed a few
days in advance and will be able to send questions to the
expert or suggest topics for discussion. This will help
the expert draw up an agenda for the meeting based
on the questions and topics most frequently raised. The
meeting itself will take place via AG across all interested
HPC-Europa centres. Exploiting AG technology in this
way will provide the following benefits:
• local expertise can be shared with all visitors at
participating centres: eg if specific expertise only exists
at certain centres then HPC-Europa visitors – and even
staff – at any centre will have the opportunity to benefit
from this knowledge
• economy of scale: participating centres will take it in
turns to provide experts for common topics such as, say,
MPI or OpenMP
• educational benefits: surgeries will allow our visitors to
meet other researchers tackling similar problems to their
own. By removing technical problems from the context
of the specific application area, a multidisciplinary
audience can come to realise that they have more in
common than they might have assumed. We hope that
the visitors will continue to interact after the workshop
has taken place
• structuring effect on the infrastructures: events of this
type will allow the HPC-Europa centres to combine
their skills to long-lasting and practical effect (one of
the key objectives of the European Commission’s 6th
Framework Programme)
• promote best practice by example: by raising
researchers’ awareness of the potential benefits to their
working practices of new technology such as AG, we
aim to facilitate collaborations across geographicallydispersed
research groups.
Continued opposite
6

FOCUS: TRAINING
XMLDiff: a tool for
comparing XML documents
George Beckett, Matthew Egbert, Linsday Pottage and Craig McNeile
XMLDiff is a small but powerful application that enables
scientists to compare and validate numerical data rapidly
and effectively.
The project was motivated by the needs of the UKQCD
Collaboration. One of their key activities is to develop
a repository of numerical experiments, which consume
significant amounts of computational power and generate
large volumes of numerical data (in the form of XML
documents). These experiments are constantly being
extended to take advantage of a growing understanding of
the underlying physics and to exploit innovations in HPC
technology.
When an experiment is modified, it is fundamental that
UKQCD can confirm the continued correctness of the
supporting numerical code. This is done by validating the
numerical data generated against reference results sets.
Until now, this comparison has been done in one of two
ways:
• Visual inspection of the output datasets, which is a
simple though time-consuming and error-prone approach.
• Script-based comparison, which provides some level of
automation but cannot easily be generalised to multiple
experiments.
Neither of these approaches is particularly satisfactory.
Thus EPCC, in collaboration with UKQCD, has developed
an application (XMLDiff) that can quickly and reliably
complete the comparison of experimental data without the
need for manual intervention.
To use XMLDiff, a scientist creates a description of the
semantics of a dataset, capturing this information in a
simple and compact form called a metric. With this
metric, XMLDiff can validate any dataset that conforms
to the metric specification, highlighting discrepancies or
failures. The information produced by XMLDiff facilitates
rapid diagnosis of problems in the numerical code.
XMLDiff is supported by PPARC.
For more information or to download the software, see:
http://forge.nesc.ac.uk/projects/xmldiff/
Workshops and seminars via Access Grid
In addition to existing workshops and seminars run locally
(eg EPCC MSc guest lectures or NeSC events), we intend
to hold half-day seminars quarterly across our consortium
using AG technology. We will invite a researcher of
international reputation to chair these events, to ensure
high attendance and active participation from HPC-Europa
visitors and local research communities. With a minimum
of two HPC-Europa sites taking part in each of these
events, these seminars have the potential to achieve many
of the benefits of ordinary seminars for a fraction of the
cost. In doing this, we can demonstrate to researchers
– including both our local research community and visitors
– how new Grid-based technology offers them an effective
means to collaborate remotely with other research groups.
To encourage better integration into their host department,
HPC-Europa visitors are actively encouraged to give
a presentation of their work. However, should there
be enough interest within the distributed HPC-Europa
community, we would propose that the host department
relocate their talk to HPC-Europa’s AG facilities to enable
visitors at all centres to participate. These AG-based
workshops and seminars have the potential to make a
considerable impact on Europe’s research communities, yet
the costs involved and effort required are modest.
The HPC-Europa project represents a unique opportunity
to establish our partnership as the world-leading
consortium in HPC and pioneer the spirit of what
constitutes a global infrastructure (where the value of
the ‘infrastructure’ is based on its users rather than just
hardware).
Further information
www.hpc-europa.org
See also the related article on distance learning at:
www.enacts.org
References
1. CEPBA (Barcelona), CINECA (Bologna), EPCC (Edinburgh), HLRS
(Stuttgart), IDRIS (Paris), SARA (Amsterdam).
7

FOCUS: TRAINING
eLT:
e-learner tracking
Judy Hardy
e-Learning is becoming an increasingly important vehicle
to enhance a student’s learning experience. It is important
– but often hard – to evaluate the effectiveness of the
e- learning strategy underpinning the design and delivery of
an online component of a course. Detailed understanding
of the way that students interact with online course
resources can help inform this process, and can be used
as a basis for future development and refinement of the
course. The e-learner tracking (eLT) project aims to
analyse the way that students use e-learning resources and
to relate the findings to the guiding principles used in the
course design.
At present there are almost 5,000 University of Edinburgh
courses with a presence in the University-wide virtual
learning environment WebCT – although many of these
may not be active – with a total of over 10,000 individual
files. This project will examine the activities of students on
a large mainstream Physics course ‘Foundations of Physics’.
This course has a long-established WebCT presence, and
contains almost 50% of the total content stored within
WebCT at the University of Edinburgh.
The work builds on a small-scale trial that has already been
completed. The results of that work were very encouraging
and provided partial answers to generic questions such as:
• How do students actually utilise e-learning materials
• Does this change as the course progresses
• Do students perceptions of what they believe is valuable
and useful map onto those of the course authors and
teachers
• Do what students perceive to be more challenging
aspects of the course material receive more or less
attention in an e-learning environment
• Is there any mapping between students’ use of online
material and their ability (eg as evidenced by their course
marks)
The eLT project is developing a set of stand-alone tools
that track, analyse and display students’ use of online
material. These will be tailored to work within WebCT.
Our aim is to present views of the data that can be
understood in terms of the overall course design. To do
this, views are constructed that correspond to the logical
structure of the course eg into chapters, sections etc.
rather than the way that it has been decomposed into html
files.
The tracking mechanisms already available within WebCT,
or even datamining the web server logs, only provide a
restricted view of what is required and will not log all
of the features used within ‘Foundations of Physics’ such
as pop-up windows and in-line panels activated through
JavaScript and DHTML.
The tracking tools could in principle be applied to
other courses packaged within WebCT. We expect the
lessons learned and experience gained in the analysis and
interpretation of this type of data for large student cohorts
using a complex e-learning package to be applicable to a
wide range of e-learning courses across the University.
This project is a collaboration between EPCC and the
School of Physics. It is funded under the University
e- learning Project Fund.
For more information and to investigate the prototype tools see:
www.epcc.ed.ac.uk/projects/elt/
Or contact the project team at: elt@epcc.ed.ac.uk
8

FOCUS: TRAINING
HPCx
times 2
Alan Simpson and John Fisher
160000
120000
80000
Available
Used
Usage during upgrade
40000
0
1-Apr 1-May 1-Jun
HPCx, the UK’s national capability computing service, has
doubled its performance to more than 6 Tflops by moving
to the second phase of its development. This makes it
once again the most powerful academic computing system
in Europe. The new platform has now been accepted as
fully operational by EPSRC.
The word upgrade is not really an adequate description
of this move. In effect, the second phase platform is an
entirely new system. The 40 IBM Regatta frames have
been replaced with 50 Regatta H+ frames, giving us
1600 1.7 MHz Power 4+ processors. The communication
interconnect between the frames has been replaced by the
new High Performance Switch technology and disk space
has doubled.
This was a long and extremely complex operation,
probably the major technical challenge of the whole HPCx
project. A plan was agreed between EPSRC and HPCx
which minimised downtime and disruption to users over
the period of the change. For example, in April, when
the first part of the change was made, the processor time
available to users was reduced by less than 10%. In May,
although for a time the number of frames in use had to
be reduced to 20, we nonetheless delivered to users more
processing time units than in any previous month.
We can follow the stages in the changeover on the diagram
above. The first frames were installed in the computer
room while the old service was still running, and by 31
March there were 20 of them, containing 640 processors.
On that date we started an early-use service, during which
a number of users tried out the system and provided useful
feedback, especially about the new documentation. On 26
April, the old service was closed. During the next three
days, there was a break while the service was transferred
to the new platform – all the projects and user accounts
and the entire file store, nearly 2.5 million files – and
the system was configured for general use. Corresponding
changes were made to the HPCx database and its software.
The new service opened to all users on 29 April with 20
frames. During May extra frames were added using normal
maintenance sessions. There was another break in service
on May 26 and 27 for testing and benchmarking, and the
complete platform opened with 50 frames on 28 May.
As can be seen from the diagram, the breaks in service
were quite short. It is also interesting to note how closely
utilisation follows the changes in the available resource.
(The dip at the end of May resulted from a problem in
the external network.)
All this was achieved without any significant problems
by close co-operation between Mike Brown, the HPCx
systems group and the IBM technical team. We also need
to thank the users of HPCx for their co-operation and
forbearance.
Benchmark trials on the new platform indicate that the
performance of real jobs has more than doubled, with
a particular improvement for those jobs which did not
scale very well on the first phase interconnect. We can
now routinely run jobs using 1280 processors. It is clear
that this event represents a really significant increase in
the capability resource available to UK researchers, and
an opportunity to attack problems which up to now have
been out of reach.
The second upgrade to HPCx will double its performance
yet again. This will be complete by the end of 2006, and
planning is already well under way.
The University of Edinburgh, through EPCC, is the lead
contractor for the HPCx service, working with CLRC Daresbury
Laboratory and IBM.
More information: www.hpcx.ac.uk
9

FOCUS: TRAINING
Workshop: OpenMP Applications and Tools (WOMPAT ‘04)
Mark Bull
WOMPAT is one of three
annual workshops organised by
cOMPunity, the community
of OpenMP researchers and
developers. Since its release
in 1997, OpenMP has gained
popularity and strong industry support as a de facto
standard for programming shared memory parallel
computers. WOMPAT is the US workshop, held this year
at the University of Houston, Texas. The other workshops
are EWOMP (Europe) and WOMPEI (Asia/Pacific).
I was invited to attend WOMPAT this year to give a
presentation on the work of the language committee of
the OpenMP ARB, of which I am currently the chair. The
committee is producing a new version of the OpenMP
language specification, merging the Fortran and C/C++
specifications, and resolving inconsistencies between them.
A number of other committee members were there, some
of whom I had never seen in person, despite speaking to
them every week during phone conferences!
The first two days of the workshop consisted of submitted
papers and invited talks. Some of the highlights were:
• An announcement of a trial product from Intel,
supporting OpenMP on Linux clusters via a virtual shared
memory system.
• A session on autoscoping, which tries to combine the
power of autoparallelising compilers with the portability of
OpenMP.
• An invited talk by John Gustafson on the problem of
heat in future architectures.
• Benchmark results from large shared memory systems
such as the Sun Fire 25K and SGI Altix.
The last two days of the workshop consisted of practical
lab sessions, where compilers and analysis tools from both
academia and industry were presented and made available
for workshop attendees to try out.
Participating vendors included Fujitsu, HP, IBM, Intel,
ParaWise and Sun. Other compilers and tools were
Dragon/Open64, Omni and TAU.
For further details see:
WOMPAT 04: www.tlc2.uh.edu/wompat2004
OpenMP: www.openmp.org
cOMPunity: www.compunity.org
Improved performance scaling on HPCx
Lorna Smith
EPCC has offered a wide range of training courses to
HPC users in the UK and Europe over many years.
The latest in this series of courses is the ‘Improved
Performance Scaling on HPCx’ course. Aimed primarily
at users of the HPCx National Service, the course is
also applicable to users with an interest in constellation
systems.
Constellation systems, or clustered symmetric
multiprocessing (SMP) systems, have gradually become
more prominent in the HPC market, with many of the
top supercomputing systems now being based on this
type of architecture. For example, in addition to HPCx,
of the top three systems in the world, two are based on
clustered SMP architectures (The Earth Simulator and
ASCI Q, see www.top500.org).
As these systems have become more prominent, it has
become essential for applications to scale effectively
on this type of architecture. On HPCx, we have
found that for some applications to achieve effective
scaling, it has been necessary to consider the underlying
clustered nature of the HPCx architecture. For example,
many codes have benefited from a cluster-aware
implementation of MPI collective routines.
The aim of this course is to introduce the tools and
techniques required to achieve optimal performance and
scaling on HPCx, and more generally on constellation
systems. We cover techniques for optimising interand
intra-node communication, such as overlapping
communication, cluster-aware message passing, mixed
mode programming and processor mapping. Tools for
profiling communication patterns are also covered, as
are a range of additional topics, such as effective IO and
memory usage.
If you are interested in attending this course, please see the
HPCx website:
www.hpcx.ac.uk/support/training/HPCxScale.html
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FOCUS: TRAINING
PGPGrid:
Grid-enabled
animations
Kostas Kavoussanakis
PGPGrid aims to use the computational power of the Grid
to enable the production of realistic, computer-generated
animations (CGAs). This project is a collaboration between
EPCC, Peppers Ghost Productions Limited (PGP) and 3D-
Matic Laboratory at The University of Glasgow. (See issue
49 of EPCC News for the initial announcement.) PGPGrid
addresses three areas of CGAs:
• the capture of human-actor sequences of images on 3D-
Matic’s capture rig and conformance of their features to
those of PGP’s animation characters
• the Grid-enabled extraction of 3D information from a
series of 2D images into 3D models (stereo-correlation)
• the Grid-enabled rendering of the 3D models to generate
animation sequences. On a different level, we also
investigate the formation of Virtual Organisations (VOs) in
the animation industry.
3D-Matic are currently developing the production
workflow that will enable them to produce cost effective,
high quality animation from captured sequences. The
problem most recently addressed was noise in the 3D
models: the solution is to smooth the trajectory of each
individual point over time, using a high-frequency filter.
With respect to stereo-correlation, 3D-Matic have
developed JPie, a Java API based on Milner’s Pi-Calculus 1 .
This satisfies the requirement of our application to spawn
processes rapidly and dynamically for solving a subset of
the problem. A first prototype of JPie is now complete.
EPCC is working on a web services-based, JPie resource
locator. This allows JPie servers to register their availability
with a central locator entity, which is queried by clients
wanting to spawn a JPie process on appropriate servers.
In order to allow Grid-enabled rendering, EPCC is
working with PGP on the specification of a suitable
environment. Our aim is to demonstrate seamless
rendering and transfer of data from the animator to
a distributed render farm and back, within a Grid
environment. EPCC has released the first version of
the Virtual Organisation Report 2 . This draws on the
experiences of animation and other IT VOs to propose
a series of recommendations adopted by the PGPGrid
VO. These will be complemented with experiences and
recommendations for animation-producing VOs later in the
project.
PGPGrid will participate in the 2004 e-Science AllHands
meeting in Nottingham with a demonstrator, a paper and a
poster covering all angles of the project. We look forward
to seeing you there.
PGPGrid is funded under the Grid Core Programme of the
DTI.
For a selection of demos and papers, please visit our project
website: www.epcc.ed.ac.uk/pgpgrid/
References
1. ‘Communicating and mobile systems: the pi calculus’, Robin
Milner, ISBN 052164320, Cambridge University Press
2. ‘PGPGrid Virtual Organisation Report’, Ali Anjomshoaa:
www.epcc.ed.ac.uk/pgpgrid/WP1/PGPGrid-VO-Report.pdf
11

FOCUS: TRAINING
MSc in High Performance Computing
EPCC, a technology transfer centre within the University
of Edinburgh, offers a one-year Masters course in High
Performance Computing (HPC). A number of EPSRC
studentships are available, which cover the full fees for
EU residents. UK residents also qualify for a maintenance
grant.
EPCC has an international reputation in the application
of novel computing solutions to real-life problems. It is
the lead contractor for the HPCx National Service, which
provides the largest academic supercomputing resource in
Europe for the UK research community. This postgraduate
qualification, awarded by the University of Edinburgh,
has a strong practical focus. It is of particular appeal
to students who have a keen interest in programming
and in HPC research and applications, but also covers
topics relevant to a wide spectrum of careers including
computational science research and commercial software
development.
MSc students will have access to an impressive range
of leading-edge parallel supercomputers and HPC
technologies, including the HPCx national supercomputer.
Graduates of this course will hold one of the few
university accredited postgraduate HPC qualifications in
Europe.
The entrance requirement is a good honours degree or
equivalent work experience. No prior HPC knowledge is
assumed, but candidates must be competent in Java, C++,
C or Fortran.
The MSc runs annually, starting each September, and can
be studied full or part-time. The taught part comprises a
series of courses, with associated tutorials, course work
and examinations. Students also submit a dissertation based
on 16-weeks independent research work.
Applications are encouraged from science, engineering,
computer science and mathematic graduates who have
prior programming experience, and from those currently
working in a relevant field.
Taught Courses
• Fundamental Concepts of HPC
• Practical Software Development
• Shared Memory Programming
• Message Passing Programming
• Parallel Decomposition
• Core Topics in HPC and e-Science
• Object Oriented Programming for HPC
• Hardware, Compilers and Performance
Programming
• Applied Numerical Algorithms
• Exploiting the Computational Grid
• Scientific Visualisation
• Advanced Topics in HPC and e-Science
For more information and application details see:
www.epcc.ed.ac.uk/msc/
Or email: msc@epcc.ed.ac.uk
This MSc is supported by:
12
www.epcc.ed.ac.uk/msc/