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The newsletter of EPCC, the supercomputing centre at the University of Edinburgh
news Issue 84 AUTUMN 2018
The Bayes Centre: EPCC’s new
home at the heart of the Data
Driven Innovation Programme
and supercomputing in the UK
From our Director 3
Contents
EPCC’s new home
We’ve moved!
Welcome to the Autumn 2018 power at the ACF and a fourth
edition of EPCC News. Over the computer room. 4 Prosperity Partnership
Next-generation engineering
summer EPCC has moved offices simulation
We have also successfully won a
for the first time in its 28-year
number of new projects which you
history.
can read about in this issue. The 5 Catalyst UK programme
Major Arm-based HPC system
While the process has not been largest of these is the 5-year £15m
without its challenges, we’ve now
settled into our beautiful new home
Prosperity Partnership which EPCC
leads with Rolls-Royce. This project
6 Industry roundup
Our industry partnerships
on the second floor of the £45m will develop the world’s first high-
Bayes Centre in central Edinburgh. fidelity simulation of a next- 7 Data-driven innovation
What it means for business
We’re already benefiting from this generation gas turbine engine in
central location in terms of operation.
interaction with the School of
We are also looking forward to the
8 Fortissimo review
Bringing HPC to business
Informatics and visitors to the
delivery of our first large-scale
University.
Arm-based HPC system from the 9 VESTEC project
HPC for urgent decision making
The Bayes Centre is one of the six Catalyst UK project led by HPE.
new buildings funded through the This 4,096-core system based on
Edinburgh & SE Scotland City Cavium’s ThunderX2 Arm processor 10 ISO certification
Ensuring data security
Region deal which was signed by is a new departure for us. More
the Prime Minister and First Minister
in August. As well as being a key
diversity in processor technology is
very important for the long-term
11 Data research
Supporting national policy making
organisation within the Bayes future of the HPC industry world-
Centre, EPCC is also in charge of wide - particularly as we approach 12 Humanities data
Cray Urika-GX’s data services
creating the World Class Data the Exascale.
Infrastructure which supports the
Data Driven Innovation Programme.
I hope you enjoy this issue! 14 Our MSc programmes
New beginnings
Over the next 10 years we will invest
£115 million in this infrastructure
including an increase to 32MW of
Mark Parsons, EPCC Director
m.parsons@epcc.ed.ac.uk
15 Online learning at EPCC
Study with us anywhere
16 SpiNNaker
Neuromorphic HPC at EPCC
EPCC at Supercomputing 2018
17 EPCC’s Computing Facility
Energy-efficient computing
EPCC booth: 2800
EPCC will be participating in a wide (2033). At the EPCC booth in the 18 EPiGRAM-HS project
Doing more with less
range of activities at this year’s exhibition hall you can find out
Supercomputing conference in
Dallas, including the "Open Source
about our latest work including our
involvement in the Data Driven
19 ARCHER eCSE
Funding research software
Supercomputing" workshop, the Innovation Programme. Partner
"Sustaining Research Software" booths include the European 20 Cell biology image analysis
Improving usability
panel, and BoF sessions on Exascale Project booth (237), where
“Software Engineering and Reuse in you can learn about DEEP-EST and
Computational Science and SAGE2, and booth 1847 where the 21 Women in HPC
We are now a local Chapter
Engineering", "Multi-Level Memory GEANT networking project is HPC-Europa3
and Storage for HPC and Data represented. User group meeting review
Analytics", and education, outreach
Adrian Jackson, EPCC
and training discussions.
a.jackson@epcc.ed.ac.uk 22 Research software
engineers
There will be presentations about Building a new community
different projects EPCC is involved Full details of all our activities
in, including VESTEC (see p9) and at SC’18 can be found on our
INTERTWinE at the PRACE booth website: http://bit.ly/2CPaihv 23 Outreach
EPCC at New Scientist Live
www.epcc.ed.ac.uk info@epcc.ed.ac.uk +44 (0)131 650 5030 Twitter: @EPCCed
EPCC is a supercomputing centre based at The University of Edinburgh, which is a charitable body registered in Scotland with registration
number SC005336.
2
Images of the Bayes Centre by Mark K Jackson and Mark Reynolds.
The Bayes Centre: EPCC’s new home
In August EPCC moved to the Bayes Centre, the University of
Edinburgh’s new community of academic, research and
commercial expertise located on its Central campus.
EPCC has left its original home on innovation. Education offerings for
the Kings Buildings Campus to join companies are also being
the newly established Bayes Centre developed here.
community, which will eventually
The Bayes will enable the University
house some 600 experts in data
to build on its globally recognised
science and artificial intelligence
strengths in data management,
“EPCC’s move to the
from research and industry.
artificial intelligence, theoretical Bayes Centre is a really
The move brings us into much computer science, computational important moment in its
closer contact with other data- linguistics, systems architectures
based organisations such as The and bioinformatics.
history. We’re at the
Data Lab, the Centre for Design
As part of the University’s strategy
heart of the Data Driven
Informatics, and the Alan Turing
to build multi-disciplinary Innovation Programme
Institute. Our new open-plan study
area also allows our MSc and PhD
partnerships with industry, the and supercomputing in
Bayes Centre will accommodate the UK, and this new
students to better integrate with
industrial tenants such as satellite-
EPCC’s staff (see p10).
technology provider Orbital Micro home brings us closer to
The Bayes Centre is one of the Systems (OMS), (see page 6 for our many new opportunities
University’s five innovation hubs, collaboration with this company), for collaboration in the
which are each designed to fuel and we look forward to the further
growth in industry partnerships. opportunities for knowledge region.”
World-leading technology, data exchange the Bayes will bring.
science and enterprise teams will
Mark Parsons,
Finally, we are very much enjoying EPCC Director
work together with corporate
exploring the exciting lunch
partners at the Centre to help shape
opportunities in our new
the future using data-driven
neighbourhood!
The newsletter of EPCC, the supercomputing centre at the University of Edinburgh 3
New Prosperity
Partnership to
develop world first
in high-fidelity
engineering
simulations
Rolls-Royce power gearbox.
Image: Rolls-Royce plc
A consortium led by Rolls-Royce and EPCC was recently awarded a
Prosperity Partnership worth £14.7m to develop the next generation of
engineering simulation and modelling techniques, with the aim of
developing the world’s first high-fidelity simulation of a complete gas-
turbine engine during operation.
The five-year “Strategic Partnership not a single well-defined milestone Michèle Weiland, EPCC
in Computational Science for to be reached by 2030 however. m.weiland@epcc.ed.ac.uk
Advanced Simulation and Modelling The necessary simulation capability
of Virtual Systems” (ASiMoV for is essential, but so is the evidential
short) is embarking on an extremely basis for trusting the simulation.
challenging programme of research
Requirements for speed, fidelity and
to enable this level of simulation. It
accuracy are well beyond current
will require breakthroughs at all
simulation and high performance
levels (mathematics, algorithms,
computing capability. Where
software, and security) and uniquely
simulations can be carried out at all,
combines fundamental engineering
they do not meet fidelity
and computational science research
requirements and take weeks or
to address a challenge that is well
even months to complete. True
beyond the capabilities of today’s
virtual certification simulations will
state of the art.
therefore require new high-
The ultimate long-term goal of the resolution physical models and full The partners gathered for the
Partnership’s kick-off meeting.
research is to enable the “virtual system simulations that drive us
certification” of aero engines, be from today’s model sizes (with
they gas-turbine, hybrid or fully 10-100 million cells) towards
electric, by 2030. The journey to models with trillions of cells. A result
virtual certification requires a will be the need for techniques that
thorough evidential database to can exploit future computing
convince the certification authorities platforms and the unprecedented
that the analysis can be trusted. For amounts of data they consume and
example, engine manufacturers produce, robustly, securely and In addition to Edinburgh,
working with the FAA have affordably. the Prosperity Partnership
successfully replaced the large includes four Universities
This is a transformational change
bird-strike certification test with (Bristol, Cambridge, Oxford and
requiring a transformational
analysis - it took around ten years Warwick) as well as two SMEs,
collaboration, and EPCC is
to obtain FAA approval for virtual CFMS and Zenotech.
delighted to be leading the
certification. Virtual certification is
Partnership.
4
Catalyst UK programme
brings Arm-based
HPC system to EPCC!
Areas of particular interest to the initial phase of the
Catalyst programme include weather and ocean
modelling.
© iStock.com/shayes17
Earlier this year, HPE announced the Catalyst UK programme: a
collaboration with Arm, SUSE and three UK universities to deploy one of
the largest Arm-based high performance computing (HPC) installations in
the world. EPCC was chosen as the site for one of these systems; the
other two are the Universities of Bristol and Leicester.
The HPE Apollo 70-based systems exercise will unearth issues (eg with Michèle Weiland, EPCC
will each consist of 64 compute compilers, libraries, or the network) m.weiland@epcc.ed.ac.uk
nodes with two 32-core Cavium and we will work closely with the
ThunderX2 processors (ie 4096 vendors to resolve these. A handful
cores in total), 128GB of memory of applications will be selected for
composed of 16 DDR4 DIMMs, and in-depth optimisation - areas of
Mellanox InfiniBand interconnects. particular interest are engineering,
They will be made available to both computational chemistry, and
industry and academia, with the aim weather and ocean modelling, and
to build applications that drive these will be given priority. However
economic growth and productivity it’s not an exclusive club: industry,
as outlined in the UK government’s high-performance data analytics
Industrial Strategy. and machine learning applications
are also welcome.
As part of the programme, EPCC
will port the most heavily used Catalyst training
ARCHER and Cirrus packages to
From 3–4 December, we will run a
the Catalyst system and make them
PRACE Advanced Training Centre
available as modules, so that it’s
course (free to attend for all) that
easy for users to explore the new
will teach participants about the
platform.
Catalyst system architecture and
Hewlett Packard Enterprise
Our initial focus will be on making software stack, how to compile
www.hpe.com
as many applications available as codes for Arm, as well as
possible. As documentation is a key performance hints and tips. SUSE
component of driving adoption, we www.suse.com
The installation of our Catalyst
will create detailed build process
system at EPCC’s Advanced UK Industrial Strategy
documentation as part of our
Computing Facility is imminent, and www.gov.uk/government/
porting activities and contribute to
we are eagerly looking forward to topical-events/the-uks-
the Arm HPC community on GitLab.
exploring the potential of this industrial-strategy
It is expected that the initial porting Arm-based HPC system!
The newsletter of EPCC, the supercomputing centre at the University of Edinburgh 5
Industry projects round up
EPCC is working with satellite technology provider
Orbital Micro Systems in the International Centre
for Earth Data which will improve forecasts for
sectors including shipping.
2018 continues to be a busy year for EPCC in terms of industrial © iStock.com/wissanu01
collaborations. Following our move to the new Bayes Centre, we look
forward to further exciting industrial collaborations.
Paywizard The ICED will enable near real-time Thomas Blyth, EPCC,
monitoring and improved forecasts t.blyth@epcc.ed.ac.uk
We recently completed a successful
for sectors such as insurance,
project with Paywizard, the pay-TV
agriculture, aviation, and shipping.
subscription, billing, and customer
EPCC is providing data analytics
relationship management specialist,
expertise in conjunction with the
to drive the development of new
AI-driven capabilities within its
latest in high performance HPC access
computing (HPC) research to
subscriber intelligence platform.
manage such large data sets. HPC
programmes
Our data science specialists
is crucial when dealing with the
enhanced existing machine learning EPCC’s ‘Accelerator’ and on-
petabyte levels of data required for
capabilities within the Paywizard demand access programmes for
this type of satellite-based
platform and developed further industrial users of our world-class
modelling.
predictive modelling capabilities. HPC infrastructure continue to
This multi-disciplinary project thrive. We have ongoing
A resultant AI product, Paywizard
involving EPCC and the University’s collaborations with major players
Singula, went on to win a ‘Best of
Schools of Geosciences and such as Shearwater (advanced
Show’ TV technology award at IBC,
Informatics is a great example of ocean modelling) and Screen
the industry’s largest European
the projects that will be at the LASSE (simulation support for
event.
forefront of the Bayes Centre advanced semiconductor device
Orbital Micro Systems agenda. manufacture). A collaboration with
EPCC is working closely with Sustainably ENGYS has created a cost
satellite technology provider Orbital effective, pay-per-use, simulation-
We have also just kicked off a as-a-service business model
Micro Systems (OMS) as part of the
project with the fast-growing fintech offering access to advanced CFD
newly formed International Centre
start-up, Sustainably. EPCC is modelling based on an
for Earth Data (ICED) where a
providing software and data implementation of ENGYS’ HELYX
satellite-based system is being
architecture expertise to support product.
developed that will vastly improve
the company’s rapid growth plans
monitoring and forecasting of
as it looks to scale its offering
extreme weather and natural
across the open banking network.
disasters anywhere in the world.
DJ Alexander
The programme will capture and
analyse data from OMS’ planned In a similar vein, EPCC is Contact our business team
constellation of 40 satellites – each supporting the Edinburgh-based to find out more.
about the size of a large shoebox. property management company DJ
These missions will include the first Alexander, which will launch an George Graham:
launch of the recently announced innovative online platform in 2019. g.graham@epcc.ed.ac.uk
UK spaceflight programme, using We are providing software Thomas Blyth:
the planned spaceport on engineering expertise to its growing t.blyth@epcc.ed.ac.uk
Scotland’s north coast. development team.
6
Data-driven innovation
for business
© iStock.com/enot-polosku
There is a lot of hype around big data and big computing for
business, but it is undeniable that the influence of data-driven
innovation will be profound.
The expertise and support available projects for industry, academia or Thomas Blyth and Mark Sawyer,
in Scotland has created a massive both, and – by bringing together EPCC
opportunity for our engineering and regional, national and international t.blyth@epcc.ed.ac.uk
manufacturing sectors and, with the datasets – facilitating new products, m.sawyer@epcc.ed.ac.uk
launch of the £500m Data-Driven services, and research.
Innovation (DDI) strand of the
The WCDI’s high-resiliency data and To understand the potential impact
Edinburgh and South-East Scotland
computing facilities will support of data-driven innovation, consider
City Region Deal, this is an exciting
work with complex, high volume, the case of a manufacturing
time for exploring how technology
real-time datasets from across the production line, running 24 hours a
can benefit business.
City Region and beyond. We are day: an unexpected breakdown will
Industry can gain huge benefits by already seeing demand from a wide be extremely costly.
combining data science expertise, range of sectors including fintech
HPC hardware, and readily- and other financial services, space A modern production line generates
available software and data and satellite, data analytics, and a huge amount of data from fault-
analytics tools. HPC enables data tech start-ups. The establishment of detecting sensors. If machine
scientists to manage, process and this data hub and the production of learning could predict faults before
work with extremely large and new applications will in turn lead to they occur, the number of times the
complex datasets, which in turn new companies. line breaks down would be
allows businesses to develop new dramatically reduced, leading to
EPCC collaborates with companies massive savings. This kind of
products and revenue streams.
of all sizes to tackle real-life application, where computers make
The Bayes Centre in Edinburgh is problems or enhance business predictions based on meaningful
home to a community of world- processes, and the direct results patterns in data sets, will increase
leading data science and artificial can include gaining a competitive in importance as the amount of data
intelligence teams, including EPCC, advantage, reducing costs, or grows.
and it is set to play a key role in improving operational or research
delivering the DDI programme. and development processes. Here
Central to the programme is a new at EPCC we see the WCDI as a
facility for the secure hosting and unique opportunity for companies Contact our business team
analysis of huge and varied to adopt data-driven innovation. It to find out more.
datasets. This £70m investment in will offer state-of-the-art data and
the World-Class Data Infrastructure compute infrastructure, supported George Graham:
(WCDI) will be fundamental in by data analytics and modelling g.graham@epcc.ed.ac.uk
positioning the City Region as data skills from across the University of Thomas Blyth:
capital of Europe, acting as an Edinburgh and the wider region. t.blyth@epcc.ed.ac.uk
enabler for many data science
The newsletter of EPCC, the supercomputing centre at the University of Edinburgh 7
Fortissimo:
a boost for Swedish SME Koenigsegg develops and produces
high-performance, limited-edition motor vehicles.
Its use of HPC-based simulation for the production
European business
of a new car configuration led to a 30% saving in
design costs, a reduction of 50% in wind tunnel
and physical testing, a 60% saving in prototyping
costs, and a 30% shortening of time to market.
December 2018 marks the end of the Fortissimo project. EPCC has been
collaborating in the programme since 2013, and during this time 92
business experiments have been carried out with over 100 small European
companies, many of which had no previous experience of using HPC.
The overall purpose of Fortissimo whether this is related directly to Mark Sawyer
was to demonstrate that the HPC or associated with the specific m.sawyer@epcc.ed.ac.uk
benefits which the cloud has business in question. The
brought to enterprise computing Fortissimo approach was to bring
can be replicated in engineering together the necessary expertise in
fields such as modelling and small partnerships that could then
simulation, and also in high- focus on a specific business
performance data-analytics. Cloud problem. There was a stringent
computing reduces an enterprise’s selection process for these The Fortissimo
cost and complexity by removing experiments, with a series of
the need for it to buy and operate competitive calls for proposals. We
experiments came from
its own computing equipment. learned that there is great demand a diverse range of
Instead it can access services to trial HPC in this way, with the industry sectors. You
provided by third parties, allowing it calls being oversubscribed almost
to focus on its core expertise. ten-fold.
can read about each
Fortissimo has shown that similar Fortissimo Marketplace
experiment on the
benefits can be obtained by offering Fortissimo website:
The Fortissimo project led directly
high performance computing (HPC)
to the creation of the Fortissimo www.fortissimo-project.
in this way. Most small companies
cannot afford the high entry cost of
Marketplace, which offers services eu/success-stories.
developed in the experiments and
acquiring and operating an HPC
by HPC centres and other
system, even though it is a proven
providers. This Marketplace will
technology. By providing access to
enable companies to access
HPC systems as a service,
advanced modelling, simulation and
Fortissimo has allowed companies
data-analytics services using a
to trial engineering techniques that
pay-per-use model, with the
were previously out of reach.
ultimate aim of improving the
Fortissimo Marketplace
Access to resources is, however, competitiveness of the European
only part of the solution. Another economy. www.fortissimo-project.eu/
vital component is expertise,
8
VESTEC: saving the
world one byte at a time
© iStock.com/JPhilipson
With jobs submitted to a batch system, supercomputing has traditionally
been centred around an offline, non-interactive approach to running codes
such as simulations. However, it is our belief that there is great potential in
fusing HPC with real-time data for use as part of urgent decision-making
processes in response to natural disasters and crises.
It is not just HPC that has benefited disruption cause by geomagnetic Nick Brown, EPCC
from phenomenal developments in storms), and mosquito-borne n.brown@epcc.ed.ac.uk
hardware: our ability to physically diseases. Not only do these areas
collect data, for example via entail risk to life, they also have a
high-velocity sensors, has also significant economic impact
undergone a revolution in recent (estimated at billions of dollars a
years. year). We hope that by combining
traditional simulations with high-
Until now, the role that HPC can
velocity sensor data, it will be
play in complementing this and
possible to make correlations
turning data streaming into valuable
between simulations and
collateral has been overlooked. But
observations such that much more
this is not a simple job and entails
precise and reliable predictions can Image shows Wildfire Analyst, one of the
much more than hooking up some
be generated. These would feed VESTEC partners and three project use-cases.
data sources to HPC machines. It models the spread of forest fires, and is used
into disaster recovery or even to assist in disaster planning and mitigation.
Instead, to fuse HPC with real-time
prevention. The VESTEC project will develop infrastructure
data, a large number of challenges which enables this application to be fed with real
need to be tackled, from the low At EPCC we are leading the work- time sensor data and run ensemble fashion on
supercomputers. The end result will be a step
level software stack up to package on interactive change in capability for disaster recovery teams,
interactive visualisation tools. supercomputing. This is especially where they can much more accurately advise fire
fighting teams on the ground to contain the fire
interesting for us as it combines our
The VESTEC project will tackle and ultimately save lives.
expertise in traditional HPC with
these challenges to make HPC
that of data, to challenge some of
more interactive and capable of
the assumptions that the current
processing raw data arriving in real
generation of HPC machines are
time, so creating a tool for use in
built upon. I think it is going to be Meet us at SC’18
urgent decision-making. It is our
fascinating to see how, over the
hypothesis that combining HPC Our BoF at SC18, “HPC meets
next three years of the project, the
computational models with real- Real-Time Data: Interactive
technology and techniques that we
time data will significantly aid in Supercomputing for Urgent
will develop as part of VESTEC
urgent decision-making, ultimately Decision Making” will run
contribute to solving the challenges
saving lives and reducing economic between 12:15 and 13:15 on
we have identified and their
loss. Thursday 15th November. If
resulting wider societal impact.
VESTEC is focusing on three use VESTEC is funded by the EU’s Horizon2020
you are going to SC, it would
cases: forest fires, the impact of programme. It started in September 2018 and will be great to see you there!
run for three years. The project has eleven partners,
space weather (specifically the each with a different area of expertise.
The newsletter of EPCC, the supercomputing centre at the University of Edinburgh 9
Your data is
secure with
EPCC!
The UK Research Data Facility, hosted by EPCC.
Image: Craig Manzi.
EPCC has recently been certified for the ISO 27001 Information Security
standard for all the HPC and Data Services that we run, including ARCHER,
Cirrus, the RDF, Farr National Safe Haven and Tesseract.
Here at EPCC we aim to be a leader datasets hosted and managed by Anne Whiting, EPCC
in the secure hosting and EPCC. Key to the success of EPCC a.whiting@epcc.ed.ac.uk
management of huge and varied in providing data services is trust
datasets to support data from its customers that it provides
research. For example we host and best practice in information security
manage Safe Havens on behalf of and data handling. ISO 27001
the Farr Institute and Scottish certification introduces a framework
Genome Partnership, with a Safe to deliver best practice and to
Haven for the Alan Turing Institute demonstrate this achievement to
under development. our customer and user base.
A Safe Haven is a secure ISO 27001 is a specification for an
environment in which data is linked information security management BUSINESS ASSURANCE
MANAGEMENT SYSTEM CERTIFICATION
and accessed. It provides a high system (ISMS). An ISMS is a
powered computing service, secure framework of policies and
About ISO 27001
A value to communicate
Guidelines with year
September 2016
analytic environment, secure file procedures that includes all legal, ISO 27001 requires management
SAFER, SMARTER, GREENER
transfer protocol for receipt of data, physical and technical controls to:
and provision of a range of analytic involved in an organisation’s
Systematically examine the
software. Safe havens allow data information risk management
organisation’s information security
from electronic records to be used processes.
risks, taking account of the threats,
to support research when it is not
EPCC has designed an ISMS to vulnerabilities, and impacts;
practicable to obtain individual
provide services and systems to
patient or subject consent, and Design and implement a coherent
meet the terms of the relevant
protect patient or subject identity and comprehensive suite of
contracts and agreements with
and privacy. Data from different information security controls and/or
respect to confidentiality, integrity,
sources can be linked to answer other forms of risk treatment (such
accessibility and availability. It has
specific research questions, subject as risk avoidance or risk transfer) to
also been designed to meet the
to the required information address those risks that are
information security risk appetite of
governance. deemed unacceptable; and
its stakeholders. With ISO 27001
The University of Edinburgh is set to and ISO 9001 Quality Management Adopt an overarching management
play a key role in the Edinburgh and certifications, we are confident that process to ensure that the
South East Scotland City Region we have the processes and information security controls
Deal, delivering the deal’s Data- information security framework continue to meet the organisation’s
Driven Innovation programme. which deliver best practice services information security needs on an
Underpinning new data innovation to our customers and provide a ongoing basis.
hubs across the University will be mechanism to continually improve
an exciting new facility for the our services to meet customer and
secure and trustworthy hosting and user requirements.
analysis of huge and varied
10Scottish Administrative
Data Research Partnership
© iStock.com/Rawpixel
EPCC has received funding via the Economic and Social
Research Council (ESRC) to continue its work with the
Scottish Administrative Data Research Partnership (S-ADRP).
The aim of the partnership is to ensure that legal and ethical Mark Sawyer, EPCC
enable research that leads to policy practices (such as the removal of m.sawyer@epcc.ed.ac.uk
decisions that will in turn will help data that enables identification of
Scotland progress towards the an individual) are followed.
vision outlined in the National
The technical infrastructure that will
Performance Framework. This
support this is a Safe Haven
framework helps to shape high level
operated by EPCC, which protects
research priorities for Scottish
patient identity and privacy while
Government, including tackling
allowing data from electronic
poverty, providing quality jobs and
records to be used to support
fair work for all, and ensuring that
research when it is not practicable
we live in inclusive, empowered,
to obtain individual patient consent.
resilient and safe communities.
S-ADRP consists of a number of The partners are currently
Strategic Impact Programmes investigating ways to link the data
(SIPs) each dealing with a research derived from various databases so
priority. that it can be used by researchers
working in the SIPs. This linked data
Underpinning all this is data.
must provide the information
EPCC’s role in the partnership will
needed by the researchers to derive
be to help provide research-ready
useful findings, but must also
data from the numerous sources
preserve the privacy of individuals
that will be needed to support
according to the governance
policy-making decisions. These
policies.
sources include health and
educational records, police and In addition to this is the task of
judicial databases, census data and making the data ready for research.
emergency services data. Of This includes ‘cleaning’ the data (for
course, there are governance issues example identifying and dealing
related to the use of this data, as it with records containing data that is Scottish Administrative
comes from many sources and clearly out of range) and, since the Data Research Partnership
contains sensitive information. The databases will be large, optimising https://adrn.ac.uk/about/
framework that will allow them to support the types of query network/scotland/
researchers to use this data must that the researchers will generate.
The newsletter of EPCC, the supercomputing centre at the University of Edinburgh 11Analysing
humanities
data using Plot of proportion of books mentioning
‘cholera’ against publication date.
Cray Urika-GX
In our role as members of the Research Engineering Group of the Alan
Turing Institute, we have been working with Melissa Terras, University of
Edinburgh’s College of Arts, Humanities and Social Sciences (CAHSS), and
Raquel Alegre, Research IT Services, University College London (UCL), to
explore text analysis of humanities data.
Our collaboration aimed to run text access the DataStore via the mount
analysis codes developed by UCL points. Also, by moving the data to
upon data used by CAAHSS to Lustre, we minimised the need for
exercise the data access, transfer data movement and network
and analysis services of the Turing transfer during analysis.
Institute’s deployment of a Cray
To exercise Urika’s data analytics
Urika-GX system.
capabilities, we ran two text The Cray Urika GX
We used two data sets of interest to analysis codes, one for each
CAHSS and hosted within the collection, which were initially system is a high-
University of Edinburgh’s DataStore: developed by UCL with the British performance analytics
British Library newspapers data Library. cluster with a pre-
(around 1tb of digitised newspapers
from the 18th–20th centuries), and
UCL’s code for analysing the integrated stack of
newspapers data is written in
British Library books data (around
Python and runs queries via the
popular analytics
224gb of compressed digitised
Apache Spark framework. A range packages, including
books from the 16th–19th
centuries). Both are collections of
of queries are supported eg count Apache Spark, Apache
the number of articles per year,
XML documents, but have been
count the frequencies of a given list
Hadoop, Jupyter
organised differently and conform to
of words, find expressions matching notebooks and
different XML schemas, so affecting
how the data can be queried.
a pattern. complemented by
To access both data sets from
UCL’s code for analysing the books frameworks to develop
within Urika, we mounted the
data is also written in Python and data analytics
runs queries via mpi4py, a wrapper
DataStore directories into our home
for the message-passing interface applications in Python,
directories on Urika using SSHFS.
We then copied the data into Urika’s
(MPI) for parallel programming. Scala, R and Java.
However, work had been started on
own Lustre file system. We did this
migrating some of these queries to
because, unlike Urika’s login nodes,
use Spark. A range of queries are
Urika’s compute nodes have no
supported eg count the total
network access and so cannot
number of pages across all books,
12count the frequencies of a given list how these occurrences change over Rosa Filgueira and Mike Jackson,
of words, etc. This code is time. Taken together, one can EPCC
complemented with a set of Jupyter examine the extent to which r. filgueira@epcc.ed.ac.uk
notebooks to visualise query results references to specific diseases m.jackson@epcc.ed.ac.uk
and to perform further analyses. change in literature over time.
To run the codes within Urika we We compared the results of running
needed to modify them both to run the modified code on Urika to the
without any dependence on UCL’s original results and they were
local environment, and instead generally consistent but with some
access data located within Lustre. anomalies which we identified as
As a result, the modified arising from data missing from the Our updated codes and
newspapers code now allows the books data set held within documentation on how to run
location of XML documents to be DataStore, which has been reported them are publicly available on
specified using either URLs or back to Melissa. GitHub.
absolute file paths. The modified
Urika is designed with the use of • Newspaper code:
books code now runs its MPI-based
Spark in mind and Spark is well- http://bit.ly/2EQrYvS
queries via Urika’s Apache Mesos
suited for this form of text analysis.
resource manager. • Books code (Spark version):
Migrating the mpi4py books queries
For the books data, Melissa to Spark would be a good area for http://bit.ly/2qeCwL7
suggested that we try to reproduce future work, combining this with the • Books code (MPI version):
the results from her Jisc Research newspapers code which already http://bit.ly/2ES63EJ
Data Spring 2015 project at UCL. uses Spark and can handle several
This project developed queries to XML Schemas. This would then • Jupyter notebook for books:
search for the names of thirteen yield a single code, with a common http://bit.ly/2JmcIoZ
diseases (eg “cholera”, underlying data model, that could
“tuberculosis” etc) and return the run queries across both the Research Engineering Group of
total number of occurrences of each newspapers and books data. the Alan Turing Institute
name, and to then to normalise the This work was funded by Scottish Enterprise as www.turing.ac.uk/research/
results by the number of books, part of the Alan Turing Institute-Scottish Enterprise research-engineering
pages and words per year to see Data Engineering Programme.
The newsletter of EPCC, the supercomputing centre at the University of Edinburgh 13Left: Students of the Class of 2019 during
Induction Week. Image: Mario Antonioletti.
Above: Part of the MSc students’ new
communal work area in the Bayes Centre.
New beginnings
Image: Mark Reynolds.
An update on our MSc programmes in High Performance
Computing (HPC) and HPC with Data Science.
Every new academic year is filled programmes and their new city, and Ben Morse, EPCC
with new beginnings, and 2018/19 also staff, who were acclimatising b.morse@epcc.ed.ac.uk
is certainly not short of them with: to teaching in the new location of
the University’s Central Area. EPCC
• 36 students commencing their
has always welcomed students into
Farewell to the
studies on the MSc programmes
• EPCC’s first year in its new home
the heart of the centre’s community class of 2018
and the design of our space in the The class of 2018 graduated in
in the Bayes Centre in the
Bayes Centre emphasises this, with November, with 20 students
University’s Central Area
our MSc and PhD students having completing the programme. We
• Increased cooperation with the study space in the building and
School of Informatics wish them well in their next
sharing facilities with staff. endeavours, which range from
• Four new courses in the MSc PhDs within the University to
Curriculum changes
programmes and four new careers with multinational
Personal Tutors As well as enjoying new facilities, companies. One of the class of
• A scholarship and industrial the Class of 2019 will be our first 2018 has already become a
dissertation project with the cohort to take the programmes’ Teaching Assistant on the
Registers of Scotland to celebrate newly streamlined Degree programme, while two members of
its 400th anniversary Programme Table and four new TeamEPCC at this year’s ISC
optional courses (see EPCC News Student Cluster Competition have
Welcoming the Class of 2019 83 for details). returned to talk to the current class
The first cohort of EPCC students Staffing Update about their exploits and encourage
to call the Bayes Centre ‘home’ is those who might follow in their
our Class of 2019: 36 students of The increased size of the MSc
footsteps at ISC 2019.
16 nationalities with backgrounds programmes necessitated a larger
as diverse as biology, electrical student support team and we are
engineering, economics, computer delighted to welcome Arno Proeme, Read about our MSc
science, and physics. Darren White, Weronika Filinger (an programmes, including our
MSc in HPC alumna), and Jane industry-based projects, on the
Induction Week proved to be a new Kennedy (a second-generation
experience for students, as they EPCC website:
member of EPCC staff) as Personal www.epcc.ed.ac.uk/msc
familiarised themselves with the Tutors.
14Online learning
at EPCC
Our online learning options allow you to study
with us wherever you are in the world.
Supercomputing MOOC service. The final week consolidates David Henty and Jane Kennedy,
learning by going through several EPCC
In Summer 2017, EPCC in HPC case studies. In particular, the d.henty@epcc.ed.ac.uk
collaboration with SURFsara in the topic of Quantum Computing j.kennedy@epcc.ed.ac.uk
The Netherlands launched the first captured the imagination of this
Supercomputing MOOC on the cohort!
FutureLearn platform.
Massively open online courses
Technical online courses
(MOOCs) are free courses delivered EPCC is also starting to deliver
over a relatively short period. This, more technical courses online.
plus the mode of delivery through Complementing the long-running
videos, articles, and discussion series of ARCHER Virtual Tutorials
forums, means they can be run (usually held at 3pm on the second
even with a very large audience, Wednesday of each month), we
(hence ‘massive’). The number of now run parallel programming
participants for the latest run of our courses using the Blackboard
Image: FutureLearn
Supercomputing MOOC was Collaborate webinar system to
smaller than for previous iterations, deliver live audio and video, and
however we still had over 900 enable interaction with remote Our free 5-week Supercomputing
people register in 95 countries. attendees via chat sessions. MOOC is designed for
There is no programming required In 2018 we ran both the MPI and anyone interested in leading-
or involved in the course. Instead OpenMP courses online, with edge computing technology.
concepts such as message passing attendees given access to EPCC’s Registrations are open for
and shared memory are explained Tier2 HPC system, Cirrus, for the next run (start date to be
using simple analogies that are practical sessions. Sessions are confirmed). See:
easier for non-technical learners to typically run over four consecutive www.futurelearn.com/courses/
visualise and understand. For Wednesday afternoons with around supercomputing
example, Amdahl’s Law is explained two hours of lecture content per Our MPI and OpenMP courses
by looking at the speed-up when week. The format is designed to will run again in 2019. See the
travelling via Concorde versus a give attendees time to attempt the ARCHER training pages for
jumbo jet over varying distances but hands-on practical exercises in the information, also for details of
with fixed times for check-in, travel gap between each session, and we upcoming face-to-face training
to and from the airport, and so on. spend time reviewing the previous evens and virtual tutorials:
exercises at the start of each week. www.archer.ac.uk/training/
In addition to parallel programming,
The ability to easily share the
our Supercomputing MOOC also Read about all our online
presenter’s screen means that we
covers HPC hardware, from the offerings at:
can do live coding sessions to
basics of computer hardware to www.epcc.ed.ac.uk/online-
explain key points from the
examining a blade from HECToR, learning
exercises or to answer questions.
the UK’s previous supercomputing
The newsletter of EPCC, the supercomputing centre at the University of Edinburgh 15SpiNNaker
arrives at
EPCC
The SpiNNaker neuromorphic high-performance computing Alan Stokes and the SpiNNaker machine at
platform, which aims to run 1% of the human brain in real time, EPCC in the Bayes Centre. Alan will be at
the Bayes for three weeks each month.
arrived at EPCC this year. SpiNNaker is a novel hardware
platform due to its massive parallelism, multi-cast
communication fabric and low power design.
The SpiNNaker communication from the get go. This all makes Alan Stokes, School of Computing
fabric takes a very different SpiNNaker a very interesting Science, University of Manchester
approach to normal HPC systems. environment to work with. stokesa6@cs.man.ac.uk
It is designed to be efficient in
SpiNNaker at the Bayes
sending small data packets very
quickly to many places, instead of The SpiNNaker machine directly
the standard approach of large available to users in the Bayes is a
blocks of data to be sent to a few three-board toroid, which provides
places periodically. With HPC the user with up to 2304 Arm cores
systems becoming more multi-core to work with as shown in the image
systems, a platform such as here.
SpiNNaker is in an interesting
Any user who requires more
position to explore massive parallel
resources can get access to the half
designs.
million cores currently available
As each SpiNNaker chip is benched from Manchester University. This
at 1W, the entire one-million core machine will have grown to one
machine utilises approx. 140kw of million cores by the end of the year.
power, when taking into account
Current plans for use of the
the cooling and the FPGAs that
SpiNNaker platform at the Bayes
each board uses to create the Find out more
include supporting research into
torus-shaped communication To learn about SpiNNaker or
executing MicroPython in a
fabric. This is a magnitude lower how to utilise the platform
distributed fashion, as well as
power than HPC systems for the speak to me directly, or
supporting the standard users in
same processor capability, and is a contact the SpiNNaker team
computational neuroscience. Please
step towards future HPC systems, through the user mailing list:
keep an eye out for Masters
which need to reduce the power https://groups.google.com/
projects which will use the
used to operate them in today’s forum/#!forum/spinnakerusers
SpiNNaker platform for a multitude
culture. Applications that work
of uses. http://apt.cs.manchester.ac.uk/
efficiently on the SpiNNaker
machine are likely to also work well [1] Full-scale simulation of a cortical microcircuit on projects/SpiNNaker/
SpiNNaker.
when ported back to traditional http://apt.cs.manchester.
[2] ATIS + SpiNNaker: a Fully Event-based Visual
HPC systems, as SpiNNaker forces Tracking Demonstration. ac.uk/ftp/pub/apt/papers/
the user to think about their [3] https://groups.google.com/forum/#!forum/ LAP_IEEEDandT_07.pdf
problem in a distributed fashion spinnakerusers
[4] http://www.cs.man.ac.uk/~stokesa6/
16On the
frontline of
energy-efficient
computing
One of the ACF’s roof-mounted
dry air cooling towers.
The Advanced Computing Facility (ACF) on the outskirts
of Edinburgh is the high performance computing data
centre of EPCC.
Built in the 1970s and operated by Manager Calum Muir, I also have Paul Clark, EPCC
EPCC since the turn of the overall responsibility for the HPC p.clark@epcc.ed.ac.uk
millennium, the ACF site has had Systems team who design, build,
significant investment over the commission, host and support a
years. At present, there are three number of HPC systems within the
Computer Rooms, imaginatively ACF, including the National Tier 1
called: Computer Room 1 (CR1), and Tier 2 systems, ARCHER and
Computer Room 2 (CR2), and Cirrus, to name a few.
Computer Room 3 (CR3).
We have the experience and skills
Each hosts specific HPC equipment to help continue to deliver future
and is supported by associated systems and projects, and relish
Any data centre is an
plant rooms which provide working at the bleeding edge of exercise in
dedicated power and cooling technology and innovation. thermodynamics – a
infrastructure for each room. We
have several pieces of equipment
As an example (as EPCC Director computer turns
and racks at our site which are
Mark Parsons explained in EPCC electrical energy into
News 83), the University of
“traditionally” air cooled, but the
Edinburgh and EPCC will play a heat energy as it runs,
majority of our equipment and
speciality high-performance
major role in the Edinburgh and which in turn has to be
computers are water cooled.
South East Scotland City Region managed and cooled.
Deal by delivering the deal’s Data-
Yes. Water and electricity! Driven Innovation Programme. By utilising water to
Thanks to the Scottish climate, for At the heart of this programme is
help with the cooling
much of the year the ACF benefits the World-Class Data Infrastructure process of the
from something called free cooling. (WCDI). This is the development machines, which is
The water which supports our and delivery of a new, state-of-the-
cooling infrastructure is pumped to art computer room at the ACF to
significantly more
our roof-mounted dry air cooling accommodate the underpinning effective than air alone,
towers and back again, allowing the infrastructure for the City Region the ACF is an extremely
(cold!) outside temperature to cool Deal.
our water as it passes through
efficient data centre.
This will be called, you’ve guessed
them. It is only on extremely warm
it, Computer Room 4 (CR4)!
summer days when there is no free
cooling and we need to use our Future editions of EPCC News will
large-scale mechanical chillers to provide updates to this exciting
cool the water circuits. project and the development of our
future masterplan.
Alongside the management of the
data centre with our Data Centre
The newsletter of EPCC, the supercomputing centre at the University of Edinburgh 17Making complex
machines easier
to use efficiently
© iStock.com/matejmo
Supercomputers are getting more complex. Faster components would be
impossible to cool but, by doing more with less, we can still solve bigger
problems faster than ever before.
Hardware designers are trying to give high performance but avoid Dan Holmes, EPCC
innovative designs and novel requiring the user to know about, or d.holmes@epcc.ed.ac.uk
hardware options such as the new deal with, the intimate details of
tensor unit in Volta GPUs, compute- each piece of novel hardware in
in-network capabilities, and several each machine. Other partners will
new technologies for memory – investigate how MPI and GPI can
HBM, NVM, storage class memory be used directly on GPUs and
and others. Future supercomputers FPGAs.
will combine all of these specialised
In collaboration with other partners,
hardware components to create
EPCC will also help to define
general-purpose computing
suitable abstractions for memory
resources, but how much of this
usage, and create a unified interface
complexity should be exposed to,
applicable to all memory and
and controlled by, programmers?
storage devices. The intention is
What will that new functionality look
that this will make programming
like? How can we get high
easier because code will be more
performance of applications and
portable, even between hardware
high efficiency of resource usage?
devices and components with
The vision of the EPiGRAM-HS vastly different capabilities.
project is to enable extreme scale
A further technical challenge in the
applications on heterogeneous
project is how to integrate novel
hardware. This means figuring out
compute hardware such as FPGAs.
how to use new hardware
This is partly a scheduling problem:
capabilities and how to combine
on which compute device should
different components to get the
each piece of code execute? And
best result. Together we will look at
partly it is an API design choice:
the challenge from four directions:
how should novel compute
network, memory, compute, and
capability be exposed to
applications.
programmers?
EPCC will focus on exploiting The EPiGRAM-HS project is part
All of the work at the programming
heterogeneity for high performance of the EU’s Horizon 2020. The
model level and on prototype
communication, building on proven project partners are: KTH, ETH,
implementations will be validated
programming models. We will use EPCC, Fraunhofer, Cray, and
using real applications. The partners
the newly standardised interface for ECMWF.
have expertise in traditional HPC
persistent collective operations in
applications like Nek5000, iPIC3D, To stay up to date with the
MPI to implement efficient high-
and IFS, and also in data science project, please subscribe to our
level communication patterns. Here
applications like lung cancer quarterly newsletter by visiting
the aim is to hide as much of the
detection using TensorFlow. The our website:
hardware complexity as possible
project will also push for changes to
and instead give the user access to https://epigram-hs.eu
international standards to support
a high-level abstraction. The goal is
heterogeneous systems.
18eCSE programme:
funding software
development for
UK computational
science Hull University’s VOX-FE is a bespoke bone
modelling software tool for in silico experiments
such as testing bone growth under stressed
conditions. The eCSE programme enabled
EPCC to work with Richard Fagan at Hull to
The embedded Computational Science and Engineering (eCSE) greatly improve VOX-FE’s modelling capabilities
programme has allocated funding to the UK computational science on machines such as ARCHER.
community over a period of six years. Integral to ARCHER, the National
HPC Service, there has been a series of regular eCSE Calls to fund
software development activities.
The last of the Calls has now closed science skills base and provide Lorna Smith, EPCC
and all funding has been allocated. expert assistance and high quality l.smith@epcc.ed.ac.uk
Although a number of projects are RSE work embedded within
still on-going, this seems a good research communities across the
time to review the benefits of the UK. As the map (right) shows,
programme and to see whether its technical staff have been spread all
aims have been met. across the UK.
The programme aimed to: Enhancing the quality, quantity and
range of science produced on the
• Enhance the quality, quantity and
ARCHER service is obviously core
range of science produced on the
to the programme. Scientific output
ARCHER service through
and impact will continue to be
improved software.
delivered throughout the lifetime of
• Develop the computational the ARCHER service and beyond,
science skills base, and provide hence the full scientific benefit of
expert assistance embedded the programme will not be known
within research communities, and realised for some time.
across the UK. However one metric we can
measure is the financial saving
• Provide an enhanced and
achieved from a number of projects.
sustainable set of HPC software
Many projects involved
for UK science.
performance optimisation, resulting The location of the technical members of staff on all
To achieve this we set out to in a reduction in CPU utilisation and eCSe projects, with darker colours representing a
greater number of people.
provide a high quality, fair and a related financial saving. This
objective eCSE selection process, saving is re-invested to allow
delivering maximum value to the scientists to achieve more science
community. Selection was made by from the same resource allocation.
a series of independent panel
Carrying out these measurements is
members, we had regular Calls, and
tricky, but helps demonstrate the
the programme was not-for-profit,
with all funds being spent on
value of investment in software Embedded CSE webpages
development and research software
projects. In total, 46 institutions For further information and
engineering. Overall the eCSE
were involved across 100 eCSE project reports, see:
programme cost around £6m and to
projects.
date we have seen a reported www.archer.ac.uk/community/
A key outcome of the eCSE benefit of around £21m, a more eCSE/
programme relates to people. We than three times return on
aim to develop the computational investment.
The newsletter of EPCC, the supercomputing centre at the University of Edinburgh 19Exploratory
image analysis
in cell biology © iStock.com/the-lightwriter
PickCells is an image analysis platform developed by the Centre for
Regenerative Medicine (CRM) at The University of Edinburgh. It combines
generic image analysis algorithms, visualisation modules and data mining
functionality within a stand-alone Java application.
PickCells provides a graphical developed using the Hugo static Mike Jackson, EPCC
environment within which biologists website generator to render content, m.jackson@epcc.ed.ac.uk
can study multidimensional and GitLab’s continuous integration
biological images and explore 3D functionality, GitLab CI, is used to
spatial relationships between trigger rebuilds of the website in
objects within complex biological response to any changes in
systems such as stem cell niches, documentation held within any of
organoids, and embryos. the source code repositories.
Since January 2018, EPCC has During our collaboration, Sally
been working with CRM on the secured a Wellcome Trust
development of the platform and its “enrichment” award to support
supporting resources. further collaboration on PickCells.
This next phase of work, which
My EPCC colleagues Elena
began in September, seeks to
Breitmoser, Arno Proeme and
improve the usability of PickCells for
myself worked with CRM’s Sally
biologists who wish to extract
Lowell and Guillaume Blin to take
information from their imaging data.
PickCells into a state suitable for
more widespread promotion with Our objectives are to:
the intention of encouraging deeper
•d
evelop an in-application
community engagement by users
interactive assistant to help users
and developers. We focused on
get started with analyses using
creating a website for users,
PickCells filter information
developers and contributors and
providing consultancy on •p
roduce video tutorials The PickCells website is still in
developing and supporting open development, but please feel
•u
ndertake a usability evaluation of
source software. free to visit it at:
PickCells
PickCells is highly-modular, and the https://pickcellslab.frama.io/
•u
pdate PickCells and its
documentation for each component docs/
supporting resources based upon
is held within the associated source
the outcomes of this usability Our work was funded by the
code repository for that component.
evaluation. Wellcome Trust Institutional
These source code repositories are
hosted by Framagit, a deployment We look forward to reporting on our Strategic Support Fund and The
of GitLab for free open source experiences in a future post. Software Sustainability Institute.
software. A website framework was
20You can also read
