SCIENTIFIC Computing solutions for

COMPUTING
scientists and engineers

WORLD October/November 2018

Issue #162

High performance computing Laboratory informatics Modelling and simulation

Scaling up capacity Big data in biomedicine Intelligent optimisation

DEEP
LEARNING,
DEEP
IMPACT?
Artificial intelligence
and HPC development

www.scientific-computing.com
 Introducing the Future of
Simulation-Driven Design

The Altair Inspire™ platform is an intuitive and powerful software

technology that enables simulation-driven design throughout the
entire product development process from concept to creation.

Be Inspired at altair.com/InspirePlatform
 LEADER

Contents October/November 2018 l Issue 162 Robert

Roe
Editor
High performance computing
Deep learning 4
Rob Farber looks at the impact that AI is having on HPC
hardware and application development AI boosts HPC
This issue leads with coverage
Machine learning with FPGAs 8 exploring the impact that AI and deep
Bill Jenkins looks at the role of FPGA technology learning technology is having on
in machine learning HPC development. This has been a
OpenMP 5.0 release 12 continuing theme throughout the year,
Matthijs van Waveren shares highlights of the latest as AI technology has been rising rapidly,
iteration of the parallel computing API OpenMP both in performance and the number of
applications using the technology. This
Scaling up computing capacity 14 is driving new users to start using HPC
Wim Slagter highlights the importance HPC – they would not have done so just a few
for engineering simulation years ago.
In this issue we have a broad overview
of news and updates covering the HPC
Laboratory informatics industry, starting on page 4 with Rob
Farber’s piece on the impact of AI in
computing and HPC. The theme of AI
Big data in biomedicine 18
research continues on page 8 with Intel’s
Clare Sansom looks at the changing ways that scientists
Bill Jenkins, who discusses the use of
can use data
FPGAs in machine learning research.
AI advances healthcare research 21 On page 12 we have an update
Sophia Ktori explores the role of AI and deep learning on the OpenMP specification, which
in healthcare will be announced formally at SC18.
Finally, we have an article looking at the
Data ecosystems in the cloud 24
creation of a free benchmark tool that
Faisal Mushtaq explains the role of cloud informatics in overcoming
demonstrates performance increase on
the challenges associated with modern pharmaceutical R&D
a user’s model if they were to move to a
HPC infrastructure.
The laboratory informatics coverage
Modelling and simulation starts on page 18, with an article from
Clare Sansom on the use of big data
Decentralised systems buck data-sharing trend 26 in biomedicine. On page 21 Sophia
Adrian Giordani reports on the use of blockchain Ktori explores the use of AI technology
in the automotive industry in healthcare in the first of a two-part
series.
Intelligent optimisation 30 We also have an article from Thermo’s
Gemma Church looks at the role of optimsation Faisal Mushtaq, which looks at the role
software in modern engineering practices of cloud-based informatics software and
Suppliers directory 34 its use in modern pharmaceutical R&D.
Modelling and simulation coverage
begins with a feature from Adrian
Giordani, on page 26, which highlights
Editorial and administrative team Subscriptions: Free registration is available to qualifying individuals. the use of blockchain in the automotive
Editor: Robert Roe Register online at www.scientific-computing.com Subscriptions £180 a
year for six issues to readers outside registration requirements. Single industry, with a particular focus on
robert.roe@europascience.com issue £20. Orders to ESL, SCW Circulation, 4 Signet Court, Swann Road,
Managing editor: Tim Gillett Cambridge, CB5 8LA, UK. Tel: +44 (0)1223 221 030. Fax: +44 (0)1223 213 autonomous vehicles. On page 30,
385. ©2018 Europa Science Ltd.
editor.scw@europascience.com Gemma Church looks at the use of
Specialist reporters: Sophia Ktori, Clare Sansom, Whilst every care has been taken in the compilation of this magazine,
Design: David Houghton, Zoë Andrews errors or omissions are not the responsibility of the publishers or of optimisation in modern engineering
the editorial staff. Opinions expressed are not necessarily those of
Advertising team
the publishers or editorial staff. All rights reserved. Unless specifically
stated, goods or services mentioned are not formally endorsed by
simulation.
Advertising manager: Mike Nelson Europa Science Ltd, which does not guarantee or endorse or accept any
liability for any goods and/or services featured in this publication.
mike.nelson@europascience.com +44 (0) 1223 221039
Production manager: David Houghton US copies: Scientific Computing World (ISSN 1356-7853/USPS No
@scwmagazine
david.houghton@europascience.com +44 (0) 1223 221034 018-753) is published bi-monthly for £180 per year by Europa Science
Ltd, and distributed in the USA by DSW, 75 Aberdeen Rd, Emigsville PA
17318-0437. Periodicals postage paid at Emigsville PA. Postmaster:
Corporate team Send address corrections to Scientific Computing World PO Box 437,

SCIENTIFIC
Emigsville, PA 17318-0437.
Managing director: Warren Clark

COMPUTING
Cover: Immersion Imagery/Shutterstock.com
Scientific Computing World is published by Europa Science Ltd,

WORLD
4 Signet Court, Cambridge, CB5 8LA l ISSN 1744-8026 
Tel: +44 (0) 1223 211170 l Fax: +44 (0) 1223 213385  Subscribe for free at
Web: www.researchinformation.info www.scientific-computing.com/subscribe

www.scientific-computing.com | @scwmagazine October/November 2018 Scientific Computing World 3

 HIGH PERFORMANCE COMPUTING
The impact of AI
ROB FARBER CONSIDERS
THE EFFECT THAT AI IS
HAVING ON HPC HARDWARE
AND APPLICATION
DEVELOPMENT
Just as technology changes in
the personal computer market
brought about a revolution in the
design and implementation of the systems
and algorithms used in high performance
computing (HPC), so are recent
technology changes in machine learning
bringing about an AI revolution in the HPC
community. Expressed as a single word,
one can describe the extent of the impact
of AI on HPC as ‘everywhere’.
Deep learning, in particular, has been
revolutionising visual recognition tasks
that previously could only be performed
by humans. It is truly remarkable that
these deep types of artificial neural
networks (DNNs) are able to match and
even outperform human abilities on a
wide variety of visual tasks. The scientific
applications are being investigated by
scientists and HPC centres worldwide,
using some of the largest supercomputers
in the world.
Reflecting this trend, the Argonne
Leadership Computing Facility (ALCF)
continues its effort to create an
environment that supports traditional
simulation-based research, as well as
emerging data science and machine
learning approaches in preparation
for Aurora, the first US exascale
supercomputer.
4 Scientific Computing World October/November 2018
Overall, machine learning is changing
how scientists perform research and
interact with data, with remarkable
research efforts bringing AI technology
to exascale computation, high-energy
physics (HEP) , materials design, climate
simulation, and more.
Don’t be misled that the impact is
limited to high-profile research projects
or big computer centres. The use of AI
in HPC permeates everything HPC, from
research and software, to hardware design
technology, including the use of data flow
hardware such as FPGAs, ASICs, together
with the impact on more ‘traditional’
hardware like CPUs and GPUs (graphics
processing units). Along with Feynman’s
quantum conjecture, researchers believe
that machine learning maps well to
quantum hardware.
Looking to the future, hardware
implementations of neuromorphic
computing promise to redefine edge
computing, using sensors and Internet of
Things (IoT) due to orders of magnitude
that will increase efficiency.
Just as DNNs brought artificial neural
networks (ANNs) into the mainstream, so
may neuromorphic computing multiply
that impact through ubiquity and the
removal of humans from the data-
“This work demonstrates
the viability of machine
learning models
in physics-based
simulations”
Federico Carminati,
project coordinator, CERN
intensive preparation of clean and relevant
training sets, as neuromorphic computing
systems can identify their own training
sets. Overall, big data, extreme computing,
and machine learning are causing us to
rethink the role of a supercomputer.
At the moment, HPC modelling and
simulation is experiencing a revolutionary
change in mindset as ANNs are now
being incorporated directly into strict
physics-based codes. More specifically,
new algorithmic efforts at high-profile
institutions like CERN use GANs
(generative adversarial networks), which
have been shown to bring orders-of-
magnitude increased performance to
physics-based modeling and simulation,
while preserving accuracy and without
introducing non-physical effects. More
indirectly, reduced precision support for
AI is redefining the numerical and matrix
methods that are core to HPC .
Everywhere you look, AI is being
incorporated by researchers into new
hardware, techniques and technologies.
Same bandwagon – computation driven
adoption
For a period of roughly 10 years
starting in the mid-1980s, the field of
machine learning exploded with the
advent of nonlinear neural networks,
backpropagation, the work of John
Holland in genetic algorithms, work in
Hidden Markov Models, and precursor
work for neuromorphic computing
performed by Carver Mead.
The field stagnated for a number of
years due to a lack of computational
power, coupled with promises made by
many who entered the field but did not
fully understand the limitations of the
technology. As a result of many broken g
@scwmagazine | www.scientific-computing.com
 HIGH PERFORMANCE COMPUTING

ShadeDesign/Shutterstock.com

www.scientific-computing.com | @scwmagazine October/November 2018 Scientific Computing World 5

 HIGH PERFORMANCE COMPUTING
g promises, investment and funding slowed
to a trickle.
The field reemerged in the early 2000s
with the advent of DNNs and their ability
to perform commercially viable image
recognition. Further, these DNNs could
be trained in reasonable amounts of
time, due to the significant increase in
computational power that modern CPUs
and GPUs could provide.
Currently, people refer collectively
to all these technologies as AI, but it is
important to heed the warnings from the
past and not over-promise. In fact, the use
of ‘AI’ is in itself misleading, as is the use
of the word ‘learning’ for ANNs, although
both are commonly used. For example,
it has been known since the 1980s that
ANNs do not ‘learn’ or ‘think’, but rather fit
multidimensional surfaces which are used
for inferencing.
New analytic techniques
Two highly impactful projects at CERN and
the ALCF demonstrate the power of AI as
a new analytic technique.
An award-winning effort at CERN
has demonstrated the adoption and
the ability of AI-based models to act as
orders-of-magnitude-faster replacements
for computationally expensive tasks in
simulation. More specifically, the team
demonstrated that energy showers
detected by calorimeters can be
interpreted as a 3D image. Adapting
existing deep learning techniques, they
then decided to train a GAN to act as a
replacement for the expensive Monte
Carlo methods used in HEP simulations.
During validation, they observed a
‘remarkable’ agreement between the
images from the GAN generator and the
Monte Carlo images, along with orders-
of-magnitude-faster runtime. The CERN
team points out that the impact for High-
Energy Physics (HEP) scientists could
be substantial as, ‘currently, most of the
LHC’s worldwide distributed CPU budget
– in the range of half a million CPU-years
equivalent – is dedicated to simulation’.
Dr Federico Carminati, CERN’s
project coordinator, explains: ‘This work
demonstrates the potential of machine
learning models in physics-based
simulations’.
Previously, AI models were excluded
because it was not possible for the data
scientist to guarantee the data-derived AI
model would not introduce non-physical
artifacts. As CERN’s Dr Sofia Vallecorsa
points out, ‘the data distributions coming
from the trained machine learning model
are effectively indistinguishable from real
and simulated data,’ so why not use the
faster computational version?
6 Scientific Computing World October/November 2018
Traditonal
HPC
systems
Scalable data
Large-scale
numerical
simulation
Deep
learning
 DOE objective: drive integration of simulation, data analytics and machine learning
“Our motivation is to
create increasingly rich
data services, so people
don’t just come to the
ALCF for simulation, but
for simulation and data-
centric activities,”
Ian Foster, Argonne Data
Science and Learning
division director and
distinguished fellow
The CERN work reflects a huge change
in thinking in the physics and modeling
simulation community – a change in
mindset that can benefit others in a wide
range of fields realise similar orders-
of-magnitude-faster speedups for
computationally expensive simulation
tasks.
The work is part of a CERN openlab
project in collaboration with Intel
Corporation, who partially funded the
endeavor through the Intel Parallel
Computing Center (IPCC) programme.
At Argonne National Laboratory,
researchers are exploring ways to improve
collaboration and eliminate barriers to
using next-generation exascale systems
like Aurora. However, the Argonne effort
is but one example of a number of efforts
being explored to help scientists exploit
the convergence of big data, machine
learning and extreme-scale HPC.
In particular, a team of researchers from
the ALCF and Argonne’s Data Science and
CORAL
Supercomputers
analytics and exascale
systems
ANLi
Learning Division is developing a service
that will make it easier for users to access,
share, analyse, and reuse both large-scale
datasets and associated data analysis and
learning methods. The service leverages
well-known tools including Globus for
research data management and Argonne’s
Petrel storage system.
‘Our motivation,’ Ian Foster (Argonne
Data Science and Learning Division
director and Distinguished Fellow)
explains, ‘is to create increasingly rich data
services, so people don’t just come to the
ALCF for simulation but for simulation and
data-centric activities.’
The ALCF is a US Department of Energy
Office of Science user facility.
Indirect impacts –
a huge change in mindset
The prevalence of AI-optimised hardware,
in particular the reduced-precision
convolutions used in image recognition
that have been added to CPUs and GPUs
plus expanding support for FPGAs, has
given the HPC community new hardware
capabilities to exploit for increased library
and application performance – including
new optimised versions of the workhorse
BLAS linear algebra libraries.
Reduced precision maths libraries
Of extreme interest to the HPC community
is work on optimised batched and reduced
precision BLAS libraries.
Over the past few decades there has
been a tremendous amount of work
performed by vendors and the HPC
community to create optimised libraries
that implement the BLAS specification.
The reason is, as Jack Dongarra noted
@scwmagazine | www.scientific-computing.com
 HIGH PERFORMANCE COMPUTING

in his ISC18 talk on NLAFET that, ecosystem of numerical tools. In among colleagues and between
‘Linear algebra is both fundamental and particular, the HiCMA linear algebra library disciplines, the potential for discovery
ubiquitous in computational science and can operate on billion by billion matrices, through the pragmatic application of
its vast application areas’. So many HPC in workstations containing only gigabytes new computational resources, coupled
applications heavily rely on BLAS that of memory. with unrestrained data flow, staggers the
even a small performance increment can imagination.’
translate into huge savings in runtime by Data flow architectures From new hardware to new approaches,
the aggregate HPC community. New ideas, numerical methods, and the true impact of deep and machine
The parallel Numerical Linear Algebra for programmable hardware devices such learning on HPC is yet to be seen.
Future Extreme Scale Systems (NLAFET) is as FPGAs opens the door to data flow In short, the biggest impact is not
a high-profile example where methods and architectures. Cloud providers such technological, but rather a change in
hardware popularised for AI applications as Microsoft Azure are already using mindset that is stimulating innovation
– including DAGs (directed acyclic graphs) persistent neural networks for inference. and new approaches to decade’s old
and reduced precision hardware, are In this case, the ANN is implemented technologies and problems. Thus, we are
used to map BLAS operations to various directly on the FPGA – there is no program at the start of a point of inflection brought
hardware platforms including CPUs, GPUs counter or executable like a conventional about by the popularity of AI hardware
and FPGAs. Similarly, Alexander Heinecke CPU or GPU. Instead, data ‘flows’ through that a host of bright and innovative
(research scientist, Intel Labs) has created the computational elements on the FPGA scientists are exploiting to bring about
the open-source libXSMM library that to produce the desired output. The result the convergence of AI and HPC. The
can speed batched small linear algebra is high performance, low latency and low ramifications are difficult to predict but will
operations, including techniques that use power consumption. be extraordinarily fun to see.
reduced-precision arithmetic operators, While there is speculation about the
while still preserving accuracy. adoption of non-von Neumann data A fully referenced version of this feature is
The advent of optimised reduced- flow architectures in HPC and exascale available online
precision hardware for AI has brought supercomputers, it is clear that scientists
the question of ‘how much numerical are currently laying the groundwork
precision is enough?’ to the attention for the use of data flow architectures . Rob Farber was a pioneer in the field of neural
of computer scientists and is in some This is a natural merging of the use of networks while on staff as a scientist in the
theoretical division at Los Alamos National
sense motivating the development of new DAGs in projects such as NLAFET and Laboratory. He works with companies and national
numerical approaches, such as the efforts programmable hardware such as FPGAs. laboratories as a consultant, and also teaches about
at King Abdullah University of Science and As the ALCF posted, ‘Because current HPC and AI technology worldwide. Rob can be
reached at info@techenablement.com
Technology (KAUST) to build an enhanced innovation is driven by collaboration

Visit the PRACE booth #2033 at SC18 from 12 to 15 November 2018. More information: www.prace-ri.eu/praceatsc18

SHAPE 8th CALL IS OPEN

1 OCTOBER – 1 DECEMBER 2018
Over 40 SMEs have already taken
advantage of the opportunities
opened up by being part of SHAPE
DON’T GET LEFT BEHIND!

YOU ARE: SUCCESSFUL APPLICANTS TO

Keen to enhance your software via more powerful computers THE SHAPE PROGRAMME GET:
A European Small to Medium-sized Enterprise
Individual support from a high performance computing expert
Interested in increasing your competitiveness Effort to develop and enhance your applications
SHAPE is an opportunity you should not miss Compute time on some of Europe’s most powerful computing systems

INTERESTED? TO IMPROVE YOUR:

Contact the SHAPE team at: shape@prace-ri.eu Time to solution Product quality Service innovation
or visit: www.prace-ri.eu/SHAPE

The Partnership for Advanced Computing in Europe (PRACE) is an international non-profit association with its seat in Brussels.
The PRACE Research Infrastructure provides a persistent world-class high performance computing service for scientists and
researchers from academia and industry in Europe. The computer systems and their operations accessible through PRACE are
provided by 5 PRACE members (BSC representing Spain, CINECA representing Italy, ETH Zurich/CSCS representing Switzerland, GCS
representing Germany and GENCI representing France). The Implementation Phase of PRACE receives funding from the EU’s Horizon
2020 Research and Innovation Programme (2014-2020) under grant agreement 730913. For more information, see www.prace-ri.eu Partnership for Advanced Computing in Europe
 HIGH PERFORMANCE COMPUTING

Exploring machine
learning with FPGAs
BILL JENKINS, OF INTEL
PROGRAMMABLE SYSTEMS
GROUP, LOOKS AT THE ROLE
OF FPGA TECHNOLOGY IN
MACHINE LEARNING

Machine learning is not a new

idea: computer scientists have
been developing algorithms
based on models of the way in which the
human brain works for decades. But if
you’ve recently been tagged in a photo on
social media, targeted by ads on an
e-commerce site, or curious about just
how autonomous vehicles are going to
drive themselves, then you’ll know that
machine learning is rapidly moving out of
the lab and into the real world.
This is driving a period of feverish
development in machine learning, within
which field-programmable gate arrays
(FPGAs) are already taking a starring role.
One approach to machine learning that
is currently getting a lot of attention is the  Figure 1: Intel PSG FPGAs offer fine-grained and low latency between compute and memory
convolutional neural network (CNN), widely
used in image-processing tasks such as example, cats have been tagged. Each done with much less processing power
object detection and classification. neuron ’decides’ on its output values and, often, using much less precise
A CNN is loosely based on the way that based on the input image, passing those number representations.
human vision works, and so is made up of values on as inputs to neurons lower down Object detection and classification is
artificial neurons, each with multiple inputs the network’s layers. The final layer of the such a useful skill that there’s an annual
and outputs. Each neuron takes its inputs, network delivers the network’s verdict. competition, the ImageNet Large Scale
applies a transform to them, and delivers Then, crucially, the error between the Visual Recognition Challenge, to test
an output value. The value of each input network’s decision and the right answer is the accuracy of new algorithms using
signal can be modified by a weighting calculated and used to propagate a series a standard dataset of tagged images.
factor, and the value that each neuron of adjustments to the weighting and bias This closely fought contest has seen
needs to reach before it will deliver an factors for each neuron back through each rapid improvements in accuracy using
output can be altered by a biasing factor. layer of the network, from the output to new algorithms or fresh adaptations of g
The neurons are arranged into a series the input.
of layers: an input layer that takes in the
raw data, an output layer that delivers
Repeat this process often enough,
with a large enough dataset of accurately
“One approach to machine
the network’s conclusion, and multiple tagged images, and the network will learning that is currently
‘hidden’ layers in between. These hidden
layers create intermediate results that help
adapt its weights and biases so that it can
‘recognise’, in this example, cats within an
getting a lot of attention
the network formulate a conclusion to the untagged image. is the convolutional
question it has been trained to answer, This training process is computationally neural network (CNN),
widely used in image-
such as ‘Is there a cat in this image?’ intensive – think days or weeks of
An untrained neural network begins dedicated computational effort in large
with random values for the weights and data centres. However, once the right processing tasks such
biasing factors attributed to each neuron,
and is trained to give the right answer by
set of weights and biases have emerged
from the training process, applying them,
as object detection and
being shown many images in which, for a process known as inferencing, can be classification”

8 Scientific Computing World October/November 2018 @scwmagazine | www.scientific-computing.com

 AN F
CE
ND S O
TE AR
AT YE
SC 30

Does your HPC deliver NAG HPC Consulting brings expertise,

experience, and impartiality to help
the best impact at the you deliver the best HPC Service,
best cost? evaluate technology options, acquire
HPC systems, make your applications
www.nag.com go faster, understand your competitive
position, train users and managers,
and ensure best impact at best cost.

NAG is a
No other consulting group in the UK, USA or worldwide has the experience,
WHPC Chapter expertise, independence and track record that NAG brings to you

COMPUTING
INSIGHT UK 2018

12-13 DECEMBER 2018 SHOWCASE

YOUR
MANCHESTER, UK BUSINESS

EXHIBITORS WELCOME
Want a presence at the UK conference for
HPC, big data analytics and cognitive technologies?
Stand spaces are allocated on a first come, first
served basis - so snap yours up quick!

www.scd.stfc.ac.uk/ciuk
@CompInsightUK #ciuk
 HIGH PERFORMANCE COMPUTING
g existing approaches over the past five
years. There’s similarly rapid progress in
other machine-learning fields, such as
autonomous driving, and the semantic
analysis of text to enable services such as
online chatbots.
The FPGA advantage
A lot of machine-learning work to date
has been done using CPUs, or GPUs
whose architectures happen to match the
computational requirements of algorithms
such as CNNs, so where do FPGAs fit?
The answer is that FPGAs have a unique
set of attributes that give them particular
advantages for the implementation of
machine-learning algorithms.
The first of these is the flexibility that
comes with the fact that FPGAs are simply
reconfigurable hardware. This means
that as algorithms change, so can the
hardware. It also means that FPGA users
can control the whole datapath of their
application, from input through processing
to output. This sounds obvious, but
many comparisons of machine-learning
performance look at how fast a CPU runs
an algorithm, rather than how fast the
algorithm works in its systemic context.
An FPGA implementation, however, can
be programmed to achieve the greatest
systemic performance – and will deliver it
in a highly deterministic way, unlike a CPU-
based approach subject to interrupts.
The structure of FPGAs is also a
good match for many machine-learning
algorithms, with highly distributed logic
resources, rich interconnect schemes
and plenty of distributed local memory.
This is important because neural network
implementations usually involve many
distributed computations to mimic
the neurons, lots of local storage to
hold intermediate values, and rich
interconnections to pass the outputs
of one layer of neurons to the inputs of
the next, or among neurons in the same
layer. This improves performance and
reduces power consumption by cutting
the amount of off-chip memory accesses
necessary to implement machine-learning
algorithms.
The highly parallel hardware of an
“FPGAs have a unique
set of attributes that
give them particular
advantages for the
implementation of
machine-learning
algorithms”
10 Scientific Computing World October/November 2018
FPGA also promises low latency and high
throughput, essential characteristics in
applications such as advanced driver
assistance systems. And the performance
and programmability of an FPGA’s I/O
capabilities also makes it easier to
integrate the devices into a system, and
adapt the implementation for different
markets or evolving I/O standards. It would
be possible, for example, to use FPGAs to
apply machine-learning strategies to pre-
process data as it came off disc storage in
a large data centre, before it even reached
the server farm.
Applying FPGAs to machine learning
Many developers working on machine
learning are used to implementing their
algorithms by writing software in relatively
high-level languages and then running
it on CPUs or GPUs, with compilers and
related tools doing the job of parallelising
the task across multiple processor
execution threads, cores or even CPUs.
Making the move to running algorithms
directly on hardware, even if it is
reprogrammable, may seem alien to their
software-centric outlook.
This needn’t be so. The history of
software development has been one of
a steady rise in the level of abstraction
at which developers have expressed
themselves. This is also true in the field
of machine learning: Google, for example,
has released TensorFlow, an open-
source software library for ‘numerical
computation using data-flow graphs’, in
other words, neural networks and related
algorithms. Nodes in the graph represent
mathematical operations, such as the
transfer functions of the neurons we
described above, while the graph edges
represent the multidimensional data arrays
 Intel programmable
acceleration card (PAC) with
Intel Stratix 10 SX FPGA
(tensors in Google’s terms, weighted
values in ours) that are communicated
between them.
Intel PSG is implementing some of the
key primitives used in common machine-
learning algorithms so that developers
who are used to working at the level of
abstraction of the TensorFlow library,
can also do so when FPGAs are the
implementation target. One way in which
this is delivered is as a Deep Learning
Accelerator, which enables users to
implement the key primitives on an FPGA
in such a way that they can then configure
various network topologies within the
FPGA, without having to reprogram its
hardware.
If this is too constricting, Intel
PSG is also implementing a software
development kit for OpenCL, a common
platform for parallel programming various
types of processor to work together, so
that users can customise and extend the
facilities of the Deep Learning Accelerator.
They might do this, for example, by
changing primitives or adding custom
accelerators. The solution is available
today for Intel PSG’s Arria 10 PCIe cards.
Interest in machine learning is growing
very rapidly at the moment. Although
some very successful approaches have
emerged over the past five years, it is
clear that there’s still room for enormous
amounts of innovation in both algorithms
and implementations. FPGAs can bring
the advantages of dedicated hardware
to machine-learning developers, as well
as offering a flexible path to efficient
systemic implementations once an
algorithm has been finalised.
Bill Jenkins is a senior product specialist in artificial
intelligence at Intel Programmable Systems group
@scwmagazine | www.scientific-computing.com
 ISC
HIGH
PERFORMANCE
2019 FUELING
INNOVATION

CALL FOR ACTION

RESEARCH PAPERS JUNE 16 – 20

2019
Submission Deadline
December 12, 2018

TUTORIALS
Submission Deadline FRANKFURT, GERMANY
February 6, 2019

WORKSHOPS
Submission Deadline
February 13, 2019 SAVE THE DATE!

Platinum Sponsors:

Next-Generation High Performance Components | Exascale Systems | Extreme-Scale Applications | HPC and Advanced
Environmental Engineering Projects | Parallel Ray Tracing -- Visualization at its Best | Blockchain Technology and
Cryptocurrency | Parallel Processing in Life Science | Quantum Computers / Computing | What´s New with Cloud Computing
for HPC | Parallel Programming Models for Extreme-Scale Computing | Workflow Management | Machine Learning and
Big Data Analytics | Deep Learning and HPC – State of the Art

isc-hpc.com
 HIGH PERFORMANCE COMPUTING
OPENMP 5.0 is changing
the landscape
Matthijs van Waveren, coordinator at the OpenMP ARB, shares
highlights of the latest iteration of the parallel computing API
The OpenMP API is an
application programming
interface (API) that gives
parallel programmers a
simple and flexible interface
for developing parallel
applications. The OpenMP
community has made a
multitude of requests since the
OpenMP language introduced
version 4.5 in 2015, and as a
result, OpenMP 5.0 adds many
new features that will be useful
for highly parallel and complex
applications. With version
5.0, the OpenMP API now
covers the whole hardware
spectrum from embedded
systems and accelerator
devices to multicore systems
and shared-memory systems.
Vendors have started releasing
reference implementations of
parts of the standard, and user
courses will soon be given at
OpenMP workshops and major
conferences. The OpenMP
specification version 5.0 has
been released at SC18.
OpenMP users are in a
wide range of fields, from
automotive and aeronautics
to biotech, automation,
robotics, and financial analysis.
There were user requests
to bring OpenMP to the
embedded system space
and the accelerator space.
Also, there was an urgent
need to bring OpenMP to the
latest levels of the C, C++,
and Fortran standards, and to
have a standard interface for
debugging and performance
tools. Finally, there were
user requests for improved
portability and usability.
The OpenMP ARB, a group
of major computer hardware
and software vendors, as well
12 Scientific Computing World October/November 2018
as users, jointly developed
version 5.0 of the OpenMP
specification to fulfil these
requests. In addition to
several minor and major
improvements, the updated
specification includes the
following features:
Full support for accelerator
devices. With the latest
additions, the OpenMP
specification has full support
for accelerator devices.
These include mechanisms to
require unified shared memory
between hosts system and
coprocessor devices, the
ability to use device-specific
function implementations,
better control of implicit data
mapping, and the ability to
override device offload at
runtime. Reverse offload,
implicit function generation,
and the ability to easily
copy object-oriented data
structures are also supported.
Improved debugging
and performance analysis.
Two new tools interfaces
enabling intuitive debugging
and support for deeper
performance analysis.
Support for the latest
versions of C, C++, and
Fortran. The OpenMP API now
supports important features of
Fortran 2008, C11, C++14, and
C++17.
Multilevel memory
systems. Memory allocation
mechanisms are available
that place data in different
types of memory, such as
high-bandwidth. New OpenMP
features also make it easier
to deal with the NUMAness of
modern HPC systems.
Greater memory flexibility.
Support for acquire/release
semantics to optimise low-
level memory synchronisation.
Enhanced portability.
Declare variant directive and
”The OpenMP
community has
made a multitude
of requests since
the OpenMP
language
introduced version
4.5 in 2015”
a new meta-directive for
performance portability by
compile-time adaptation of
OpenMP pragmas.
The specifications can be
downloaded from the OpenMP
website, and it is possible to
participate in the discussions
on the OpenMP Forum!
Implementations
The major vendors have
implemented parts of the
OpenMP 5.0 specification in
their compiler products. GNU
is the furthest along, with
their implementation of GCC.
They plan to have quite a few
features in the next release of
GCC, viz GCC 9. In addition, the
debugging and performance
tools of the vendors are being
@scwmagazine | www.scientific-computing.com
Arbi Studio/Shutterstock.com
extended with OpenMP 5.0
features. More information can
be found on the Resources
page of the OpenMP website,
where you can also find links
for OpenMP benchmarks, and
OpenMP research projects.
The OpenMP YouTube
channel is a great place to find
education videos, from basic
entry-level videos to advanced
videos treating the different
OpenMP 5.0 features. On the
OpenMP website, you find links
to tutorials. Advanced OpenMP
courses treating elements
of OpenMP 5.0 are being
given at OpenMP workshops
and the SC conferences
(SC18 & SC19). The OpenMP
workshops, where courses on
OpenMP 5.0 can be followed,
are the International Workshop
on OpenMP (IWOMP), the
OpenMP Users’ Conference
(OpenMPCon) and the UK
OpenMP Users’ Conference.
Once OpenMP 5.0 has been
released, the basic OpenMP
courses given at universities
and other venues will be
updated. In addition, a guide
with OpenMP examples is
available for download from
the OpenMP website.
REGISTER TODAY! Enjoy substantial savings by joining
ACM, IEEE, or SIGHPC during your registration process. sc18.supercomputing.org

Discover a broad program
of HPC-focused technical
presentations, papers, workshops,
informative tutorials, timely
research posters, and more.
Explore exhibits showcasing
the latest HPC technologies
from the world’s leading
vendors, universities, and
research organizations.
Enjoy several days in Dallas,
one of the country’s top tech
cities, and home to great
amenities, food, and nightlife.
Bring the family!

November 11–16, 2018

The International Conference for High Performance
Computing, Networking, Storage, and Analysis

Sponsored by:
 HIGH PERFORMANCE COMPUTING
Scaling up computing capacity
Wim Slagter highlights the importance of HPC for engineering
simulation – whether on premise or in the cloud
Ansys has developed a free benchmark
tool that allows users to test their own
simulation model on a small HPC cluster to
demonstrate the benefits of scaling up an
organisation’s computing infrastructure.
This tool is aimed at driving adoption of
HPC resources through HPC appliances
and cloud-based solutions that Ansys
offers in collaboration with its partners.
This can benefit organisations that require
HPC but do not have the time or inclination
to set up, configure and operate an
in-house cluster.
‘I personally have never come across
an engineer yet who does not want more
compute power. But many of them want
to see proof that using more CPU cores
on a more powerful machine is worth the
investment,’ said Wim Slagter, director of
HPC and cloud alliances at Ansys.
‘Engineers need to convince their
boss, and possibly the purchaser of the
organisation, and they can now get that
proof for free through our benchmark
program,’ said Slagter. ‘It was designed
as an easy way for an engineer to see
proof that their own Ansys model can be
14 Scientific Computing World August/September 2018
significantly sped up by using more CPU
cores.’
Slagter noted that the concept came
from a survey of more than 1,800 Ansys
users. From the survey Ansys found
that ‘customers said how often they are
constrained by turnaround limitations.
It was striking to me that a really large
percentage of the respondents limit the
size or amount of detail for nearly every
simulation model,’ added Slagter.
According to the survey, 40 per cent
of respondents limit detail in simulation
models due to time constraints. The
survey also reflects that, in many cases,
limiting the size or amount of detail can
result in lower-fidelity results less useful to
respondents’ design experiments.
“According to the survey
of customers, 40 per
cent of the more than
1,800 respondents
limit the size or amount
of detail in simulation
models because of time
constraints”
Master3D/Shutterstock.com
‘Engineers are running bigger models,
bigger in terms of size and complexity, and
they also have to run an increasing number
of design variants to ensure product
integrity and robustness. But customers
and engineers are compute bound and
constrained by their compute capacity.
That is why we have established this
free benchmark programme. Customers
wonder about the performance of their
simulation model. No matter how many
HPC benchmarks we produce, engineers
still want to know the performance of their
own model,’ Slagter stated.
While limiting a model’s size or scale
can help to reduce the simulation
time, engineering organisations must
compete in highly competitive markets
which require a careful balance between
performance, innovation and time-to-
market for new products or components.
The benchmark tool allows users to look
at their own workloads to see how their
current projects could be accelerated
through the application of HPC resources,
either on premise or in the cloud.
If engineers have to limit the size of a
model ‘then they are almost wasting their
time because they have to change and
re-mesh the model in order to be able
to squeeze it onto the machine or to get g
@scwmagazine | www.scientific-computing.com
Bigger, Better, Faster Simulations:
HPC TECHNOLOGY LEADERSHIP
Intense focus on HPC software development and strategic
partnerships enables breakthrough productivity on current
and emerging HPC systems - on premise and in the cloud.

To learn more visit ansys.com/hpc

ANS107
 HIGH PERFORMANCE COMPUTING
g acceptable run times,’ said Slagter. ‘This
is not what they want. They clearly want to
solve their engineering problem and not
unnecessarily to spend time adapting the
model to suit the computing resources
available.’
Selecting the right technology
Once the performance benchmark
has been run on a user’s model, Ansys
engineers will produce a report that
highlights performance on a small
HPC cluster compared to their existing
infrastructure and simulation timings over
a number of CPU cores.
‘We want to demonstrate that, if they
were to run their model on a more powerful
machine, you can get time savings in a
certain order of magnitude. On average we
have shown a six-times shorter runtime
using a small cluster, when compared to a
customer’s current configuration. This is
across the board, across different models
that we have received so far,’ said Slagter.
With this jump in performance, an
organisation ‘can increase their simulation
throughput, tack on more complex
models, larger models with more complex
physics, or create more design variants
to demonstrate the performance or make
product trade-off studies.
The benefits of using HPC for simulation
are well understood, yet the technology
has not been adopted by some
engineering organisations. This can be
for a number of reasons but generally it
comes down to two primary factors; lack
of expertise or a reluctance to invest in a
new technology.
In Slagter’s experience, it is often that
companies lack the expertise or the staff
to set up and manage an HPC cluster.
‘Proper sizing of an HPC cluster involves
more than just choosing the processor,
core count or memory. People need to
consider storage, remote visualisation,
job scheduling and possibly workload
management software, and that is not
what these engineers want to do,’ said
Slagter.
‘We do not want to put a burden on their
IT department either. We propose two
options: one is an on-premise deployment
option and the other is off-premise
deployment in the cloud,’ said Slagter.
HPC in the cloud
Ansys has developed cloud-based
solutions with a number of cloud-hosting
partners who provide HPC infrastructure
and IT services to cater for either
burst capacity, or as an extension of
an organisation’s in-house computing
capacity. Slagter noted that flexibility can
be a key factor when talking to customers.
16 Scientific Computing World August/September 2018
“This allows the
customers to stay more
focussed on their core
engineering competence
rather than spending
time on IT”
This relates not only to flexibility on
compute capacity, but also the ability to
scale the number of software licenses an
organisation is using.
Cloud hosting offers a platform to
expand computing capacity or a way of
trying HPC on-demand before bringing
a cluster in-house. It can also be used to
provide burst capacity for users with an
existing HPC system.
‘We have developed an ecosystem of
cloud-hosting partners such as Rescale,
Gompute (Gridcore) and Ubercloud, which
provide HPC infrastructure and IT services
for customers,’ said Slagter. ‘This allows
the customers to stay more focussed on
their core engineering competence, rather
than spending time on IT. Many of those
engineer organisations lack good IT staff
or even an IT department. Sometimes
they have to manage the computer
themselves.’
These products – developed by Ansys
partners – offer a solution to a challenge
that faces many HPC users. While large
automotive and aerospace companies
have been using HPC simulation for
some time, many smaller enterprises
are much less experienced. Without the
infrastructure and expertise to configure
DRN Studio/Shutterstock.com
and manage an HPC cluster, the barrier to
entry can be too large, which discourages
organisations from taking the first step.
HPC out of the box
For enterprises that prefer an on premise
solution, Ansys has partnered with Hewlett
Packard Enterprise (HPE), to offer an out-
of-the box solution for users that want
a fully managed cluster, optimised for
Ansys software and pre-configured with
Ansys engineering and job management
software.
This system has been designed to shift
simulation jobs off local workstations
to a central cluster resource, enabling
users to increase resource utilisation. The
appliance reduces the time and cost of
acquisition and aims to make it easier to
adopt and maintain HPC, even if you don’t
have IT support and resources. Ansys
offers several different appliances for
different application workloads, with each
optimised for a specific set of workflows.
‘Not everybody is ready for cloud
computing yet, but we want to give people
the choice. Either they choose to adopt
cloud or continue to invest in on premise
hardware.
‘We need to make it much simpler to
acquire a system and to reduce the risk
of acquiring a new cluster that may not
be balanced or optimised for engineering
workloads,’ added Slagter.
‘Simulation is a different application,
a more computationally demanding
application than any other enterprise
application. Even different Ansys products
have different requirements for hardware,’
Slagter concluded.
@scwmagazine | www.scientific-computing.com

White Papers
now available online
Data integrity: Audit tails with ease of review
By Thermo Fischer Scientific
Learn about the Thermo Scientific™ Chromeleon™ CDS
audit trail controls, the regulatory requirements and
guidance that they pertain to, and how Chromeleon CDS
will ease the review of audit trails.
Enabling data integrity from drug discovery
through manufacturing
By Thermo Fisher Scientific
There’s no aspect of quality control quite as complex as
keeping up with regulatory guidelines.
ADAS Simulation Under Severe Vibrations
By Altair
Automotive radars are becoming standard equipment on
vehicles, with several antenna architectures being used
to cover the different safety functions in complex chassis
environments and where the side effects become more
significant on radar performance.
*Registration required
www.scientific-computing.com/white-papers
VIEW
FOR *
FREE
Ultra-Fast, High-Fidelity Computational Fluid
Dynamics on GPUs for Automotive Aerodynamics
By Altair
Altair ultraFluidX™ is a simulation tool for ultra-fast
prediction of the aerodynamic properties of passenger
and heavy-duty vehicles as well as for the evaluation of
building and environmental aerodynamics.
How the Internet of Things Validates
the Lab of the Future
By BIOVIA
Imagine a laboratory in the future where all devices and
instruments communicate their status, activities and data
with each other and with enterprise information systems.
Data would be acquired without manual intervention.
SCIENTIFIC
COMPUTING
WORLD
 LABORATORY INFORMATICS
Big data opens
new avenues
for genomics
research
CLARE SANSOM LOOKS
AT THE IMPACT BIG DATA
IS HAVING ON GENOMICS
RESEARCH
What was the earliest example of
digital data? The answer is
surprisingly clear and probably
earlier than you think. Some 30,000 years
ago, in the Palaeolithic era, someone put
57 scratches on a wolf bone. These are
arranged in groups of five, making the first
known example of something that is still
used from time to time: a tally stick. It is
also an example of digital data. For almost
all human history, however, such data was
scarce, relatively few people handled it and
it was easy to manage. Only half a century
ago the Moon landings were controlled by
banks of computers that together held
less data than one of today’s iPhones.
More than 200 million of these were sold in
2017 alone.
So we are now in an age of big data,
but what makes it big? The term was
coined in 2006, but five years earlier an
analyst called Doug Laney had described
the growing complexity of data through
‘three Vs’: volume, velocity and variety.
That is, there is a lot of data, there are a
lot of different kinds and it is growing very
fast. Two more Vs have been added since:
veracity (i.e. data can somehow be verified)
and value (it can and should be useful).
The 57 scratches on that Palaeolithic
wolf bone form one byte of data, as does
any integer up to 255. If you are interested
18 Scientific Computing World October/November 2018
enough to be reading this, you probably
own at least one device with a hard drive
with a capacity of at least 1TB. You could
fit one trillion virtual wolf bones, or, only
just less implausibly, almost 20,000 copies
of the complete works of Shakespeare
onto such a hard drive.
Scientific data is a few orders of
magnitude further on. Within the sciences,
particle physics is at the top of the
data league; the data centre at CERN,
home of the Large Hadron Collider,
processes about 1PB (1,000TB, or 20
million Shakespeares) of data every day.
Biomedicine may be some way behind,
but it is fast catching up, driven first and
foremost by genomics.
Sequencing the human genome
The first human genome sequence
was completed in 2003, after 15 years’
research and an investment of about $3bn.
The same task today takes less than a day
and costs less than a thousand dollars.
There is probably no tally of the number
of human genomes now known, but
Genomics England’s project to sequence
100,000 genomes from people with
cancer and rare disease and their close
“Data analysis on the
fly is commonly used
in some disciplines,
including particle physics
and crystallography,
but it is only recently
becoming common in
bioinformatics, which is a
younger science”
relatives within a few years gives an idea
of what is now possible. The raw sequence
data for a single genome will occupy about
30GB (30 x 109 bytes) of storage, and the
processed data about 1GB, so you could
theoretically fit a thousand on your home
hard drive (if with little space for anything
else).
About a third of that first human genome
was sequenced at the Wellcome Trust
Sanger Institute, south of Cambridge.
This is now one of the largest repositories
of gene sequences and associated data
in the world, and possibly the largest
in Europe. Data in the form of DNA
sequences – As, Cs, Gs, and Ts – pours off
its sequencers at an unprecedented rate,
initially destined for the Sanger Institute’s
private cloud and massive data centre.
This centre was extended from three
‘quadrants’ to four in the summer of 2018,
giving the Institute a massive 50PB in
storage space. ‘We now generate raw
data at the rate of about 6PB per year,
but even keeping scratch space free
for processing, we should have enough
capacity for the next few years’, says the
Institute’s director of ICT, Paul Woobey.
The data is managed using an open
source data management system, iRODS,
which is becoming a favourite of research
funding bodies in the UK and elsewhere.
‘One benefit of iRODS is that it is highly
queryable’, adds Woobey. ‘This makes it
easy to locate, for instance, all the data
produced by a particular sequencer on a
particular day.’
By itself, DNA sequence data means
very little; like almost any form of data,
it only becomes meaningful once it is
analysed. Much of this analysis is done
in-house, but many researchers worldwide
need access to the Sanger data.
@scwmagazine | www.scientific-computing.com

The growth in genomics data
Some years ago, scientists would routinely
download Sanger datasets, but this is
not always possible now because of their
sheer size. Tim Cutts, head of scientific
computing at the Institute, explains: ‘In
an extreme scenario, it would take a user
a year and cost a fortune to download
all our data, even over the fastest
commodity networks in the world’. This
is clearly impossible, so the default now
is for researchers to login to a server and
analyse the data onsite or in the cloud.
Another approach is to perform an initial
analysis as soon as data is generated,
save that and throw the raw stuff away.
‘Data analysis on the fly is commonly
used in some disciplines, including
www.scientific-computing.com | @scwmagazine
LABORATORY INFORMATICS
Zita/Shutterstock.com
particle physics and crystallography, but
it is only recently becoming common
in bioinformatics, which is a younger
science’, adds Cutts.
Cutts expects that the sequencing
capacity of the Sanger Institute will grow
further over the next few years, putting
further demands on its data storage and
analysis capacity. However, the most
significant growth is likely to be in another
of big data’s Vs: variety. Increasingly,
genomic data will be integrated with
physiological and pathological data from
individuals’ health records, accelerating
the growth of personalised medicine.
‘We are developing datasets and
analysis tools for integrating these diverse
data types, so they can be used for drug
“We are developing
datasets and analysis
tools for integrating these
diverse data types, so
they can be used for drug
discovery. But we have
no ambition to become
involved in this ourselves”
discovery’, says Cutts. ‘But we have
no ambition to become involved in this
ourselves.’ BenevolentAI, headquartered in
London and New York, is one of a new type
of bioinformatics company that is using
machine learning to look for patterns in
such diverse data and to discover or re-
purpose ‘the right drug for the right patient
at the right time’.
The unique reputation of the Sanger
Institute and, by association, the University
of Cambridge in genetics and genomics, is
matched at the ‘other place’ by a similarly
high one in other data-rich biomedical
sciences: epidemiology and population
health.
The pioneering British Doctors’
Smoking Study began in Oxford in 1951
when academics Richard Doll and Austin
Bradford Hill, both later knighted, sent a
survey of smoking habits to almost 60,000
registered British doctors. Over two-thirds
of the doctors returned questionnaires,
and the data gathered was of sufficient
statistical power to demonstrate smokers’
increased risk of death from lung cancer
and from heart and lung disease within five
and seven years respectively.
Over 60 years later, research in these
disciplines has been integrated with the g
October/November 2018 Scientific Computing World 19
 LABORATORY INFORMATICS
g rest of Oxford’s biomedical research in a
new Big Data Institute, part-funded with
a generous donation from one of Asia’s
richest and most influential entrepreneurs,
the Hong Kong billionaire Li Ka-Shing.
This institute hosts the single biggest
computer centre in Oxford and takes
in data from all over the world. ‘Our
largest datasets come from imaging
and genomics, but we also hold gene
expression and proteomics data, as well
as consumer data and NHS records’,
says the Institute’s director, Gil McVean.
‘And ‘imaging data’ itself covers a huge
variety of modalities and therefore of
image types, from whole-body imaging
and functional MRI brain scans to digital
pathology slides’.
The Big Data Institute holds all the
data collected through one of the largest
epidemiology initiatives yet launched: the
UK Biobank, designed to track diseases
of middle and old age in the general
population. This recruited half a million
middle-aged British individuals between
2006 and 2010. Initially, they provided
demographic and health information,
blood, saliva and urine samples, and
consented to long-term health follow-up.
This information, including universal
genome-wide genotyping of all
participants, is being combined with health
records including primary and secondary
care and national death and cancer
registries, to link genetics, physiology,
lifestyle and disease.
Many participants have also been to
answer further web-based questionnaires
or to wear activity trackers for a given
period, and the genetic part of the study
is still being extended, as its senior
epidemiologist Naomi Allen explains. ‘A
consortium of pharma companies, led by
Regeneron, has funded exome sequencing
– that is, sequencing the two per cent
of the genome that actually codes for
functional genes – of all participants. They
hope to complete the sequencing by the
end of 2019 and UKB will make the data
20 Scientific Computing World October/November 2018
“Some datasets,
particularly those
including genomic
data, are so rich that it
becomes possible – if very
hard – to track down an
individual from their data,
even if all identification
has been removed”
publicly available to the wider research
community a year later.’ The eventual,
if ambitious, aim of UK Biobank is to
sequence all 500,000 complete genomes
over the next few years and release that
data, too, to the research community.
Ensuring data access and anonymity
All academic and even some commercial
biomedical research is now carried out
under open access principles. These can
be hard to apply to human health data,
however, as issues of privacy are also
important. The UK Biobank restricts its
data to bona fide scientists seeking to use
the data in the interest of public health; as
such, the type of research projects varies
widely. All the data are ‘pseudonymised’ by
using encrypted identifiers that are unique
to each research project, before being
made available to researchers.
However, with the amount of detailed
data available nowadays, it is becoming
harder to guarantee anonymity. ‘Some
datasets, particularly those including
genomic data, are so rich that it becomes
possible – if very hard – to track down
an individual from their data, even if all
identification has been removed’, explains
McVean.
One perhaps drastic solution is the
creation of artificial data records. These
have similar characteristics to patient
records and can be fully analysed but
represent no individuals. Edwin Morley-
Fletcher, CEO of Rome-based technology
consultancy, Lynkeus, has pioneered
machine learning methods for creating
this type of data for e-clinical trials. ‘We
use a method called recursive conditional
parameter aggregation to create data for a
set of artificial patients that is statistically
indistinguishable from the real patient data
it was derived from,’ he explains.
Any health study that depends on
volunteers providing data can also suffer
from the problem of volunteer bias: people
interested enough in their health to join
such studies are generally likely to be
healthier than the population as a whole. It
is possible to collect data directly from the
millions of Fitbit fitness trackers in regular
use, but this would represent an even more
biased dataset, as most people who own
Fitbits are richer and more tech-savvy,
as well as more health-conscious than
average.
Martin Landray, deputy director of the
Big Data Institute, was involved in the
Biobank study of exercise and health,
which overcame some of this bias by
sending accelerometers to 100,000
volunteers and asking them to wear them
for a week.
Each one returned 100 data-points per
second, generating a huge dataset. ‘This
presented a big data challenge in three
ways: in logistics, in ‘cleaning’ the raw
data for analysis and in machine learning:
picking out movement patterns associated
with each type of activity,’ he says. ‘Only
then could we – after discarding outliers –
detect any relationship between actual (as
opposed to self-reported) activity levels
and health outcomes’.
But whose data is it anyway? All
biomedical data, including ‘omics data,
is derived from one or more individuals,
and much of the data collection depends
on willing volunteers. And, particularly as
anonymisation cannot be fully guaranteed
in all circumstances, all these individuals
as ‘data subjects’ must have some rights
over their data.
Anna Middleton, head of society and
ethics research at the Wellcome Trust
Genome Campus (the home of the Sanger
Institute), leads a global project called
‘Your DNA Your Say’ that aims to discover
how willing people are to donate and
share their genomic and other biomedical
data. ‘We are finding that people are
more willing to share their data if they
understand what it means, and if they trust
the scientists who will be using it,’ she
says. ‘Unfortunately, levels of knowledge
and trust are low in many countries, and
scientists must do more to communicate
the meaning and value of our big data and
how it drives our work.’
@scwmagazine | www.scientific-computing.com

AI advances
healthcare research
SOPHIA KTORI EXPLORES
THE ROLE OF AI AND DEEP
LEARNING IN HEALTHCARE
– IN THE FIRST OF A TWO
PART SERIES
Harnessing AI for drug discovery
applications will significantly
speed the identification of
promising drug candidates, believes Matt
Segall, CEO at Optibrium. The UK-based
firm, together with partners Intellegens
and Medicines Discovery Catapult,
recently received a grant from Innovate UK
to help fund a £1 million project focussed
on combining Optibrium’s existing
StarDrop software for small molecule
design, optimisation and data analysis,
and Intellegens’ deep learning platform
Alchemite.
The aim is to develop a novel, deep
learning AI-based method for predicting
the ADMET (absorption, distribution,
metabolism, excretion and toxicity)
properties of new drugs candidates.
Ultimately, the platform could help to guide
the selection and design of more effective,
safer compounds earlier in the discovery
process, Segall states.
‘The pharma industry is increasingly
leveraging quantitative structure-activity
relationship [QSAR] models to help predict
the biological activity and toxicity of drug
compounds, based on their structure,’
he explains. ‘People have been applying
deep learning techniques to datasets to
build these QSAR models, but frankly, they
often add very little new insight. Published
data suggests that using conventional
deep learning algorithms to build QSAR
models adds very little extra intelligence,
compared with random forest and other
algorithms that are commonly used.’
The reason for this is that deep learning
methods are designed to deal with very
large, but complete datasets, whereas the
pharmaceutical sector commonly deals
with very sparse and incomplete data,
Segall continues.
www.scientific-computing.com | @scwmagazine
LABORATORY INFORMATICS
“The platform combines
two-dimensional and
three-dimensional
structure activity
relationships with de
novo design, to help
explore new strategies
for optimisation”
‘A big pharma company might have one
to two million compounds and thousands
of assays, but there’s no way that every
compound will have been through every
type of assay. Their overall pot of data may
only be a few per cent complete and most
of the information that they would ideally
have for every compound, or for every
assay, is actually missing. Conventional
deep learning methods really can’t work
with that sort of data input,’ said Segall.
The Intellegens’ platform is designed to
be able to bridge these gaps, by learning
underlying correlations and relationships
between different bioactivities and
different assay endpoints, so that missing
properties, relationships and activities can
be predicted. ‘The platform is a unique
approach to deep learning, based on
sparse and uncertain data, but it’s also
very generic and can be applied in almost
any vertical,’ Segall notes. ‘Intellegens’
Panuwatccn/ WhiteMocca/Shutterstock.com
algorithms are already being exploited
with commercial success in the materials
science space.’ Optibrium’s own StarDrop
software is a very comprehensive platform
for small molecule design optimisation
and data analysis.
‘StarDrop combines conventional data
visualisation techniques with a unique
decision analysis algorithm to tackle
multi-parameter optimisation challenges,
and also a very comprehensive suite of
computational chemistry capabilities
for understanding the structure activity
relationships within existing projects, and
applying those to guide the design of new
compounds,’ Segall comments.
‘The platform combines two-
dimensional and three-dimensional
structure activity relationships with
de novo design, to help explore new
strategies for optimisation. Our platform
is an ideal fit with Intellegens’ deep
learning capabilities for the compound
optimisation space.’
The third partner in the funded project,
Medicines Discovery Catapult, is providing
specialist expertise in data curation, to
increase the amount of data available to
the algorithms.
New avenues for research
‘We have some data that we have
generated over the years, and the
companies who we are working with have
big datasets of their own based on their g
October/November 2018 Scientific Computing World 21
 LABORATORY INFORMATICS

g own compounds and assays, but we also

believe that there is a treasure trove of
hard to find, but valuable data in the public
domain,’ Segall notes, and that is where
the expertise of Medicines Discovery
Catapult – a national, Innovate UK-funded
scientific gateway to specialist expertise –
comes into its own.
‘Medicines Discovery Catapult is using
natural language processing machine
learning technology to find published
papers with relevant data on compounds
and structures, which can be used to build
on what we already have and what our
customers have, and provide a really rich
source of data for these more hard-to-find
targets,’ Segall added. ‘We have presented
some early proof-of-concept work
demonstrating that by combining all this
expertise we can significantly outperform
conventional QSAR approaches.’
The new machine learning technology
for ADMET is also versatile, and can be
tuned to select results with a greater
or lesser confidence. ‘We can ask the
algorithm to present only those activities
that can be predicted with the highest
confidence. It’ll be a smaller number of
Tex vector/Shutterstock.com

results, but the data will be more reliable

for decision making,’ stated Segall.
Turn the predictive power dial the other
way and it is possible to take a bit more
risk and include some more uncertain
data, but you then get a bigger pot of
compounds for selection. ‘Putting it all
together, we believe this platform will be
able to make more accurate predictions
across a broader range of important
endpoints for making decisions, and also
learn in real time from new data as it is
generated by our customers or in the
literature,’ said Segall.
While the pharmaceutical industry is
embracing deep learning technologies for
discovery and development, a tendency
towards ‘overhype’ of some research
means that not all algorithms are created
equal, Segall adds.
‘One needs to be very careful, because
“The companies who we
in the drug optimisation space, for
example, some of the new methods
emerging are really more like conventional
QSAR machine-learning based methods
rebranded through good marketing. But
the industry needs much more than just
the same old stuff in a different box of
tricks,’ said Segall.
This new platform is designed to
represent the next step forward in being
able to answer questions intuitively
using the data already available, however
fragmented. ‘Our goal is to give scientists
the power to help make informed
decisions on which compounds they can
test, but also provide insight into the most
appropriate assays for the next round of
effects of potential drug compounds on
individual cells.
While traditional high content screening
(HCS) methods rely on teams of scientists
laboriously setting up the image analysis
to identify and quantify compound-related
phenotypic changes, Imagence takes this
processing time down to literally seconds,
explains Professor Stephan Steigele, head
of science at Genedata.
‘The software uses machine learning
technology to understand, and then
rapidly detect and extract cellular
phenotypes that provide quantitative
insight into the effects of an individual
compound,’ he states. ‘Importantly, the
software can be applied to a wide range of

are working with have

screening, to move promising compounds
forwards towards optimised clinical
big datasets of their candidates,’ Segall added.
own, based on their own Rapid detection
compounds and assays, Genedata is poised to launch an AI-based
but we also believe phenotypic image analysis software,
Imagence, which has been developed
that there is a treasure to automate the workflows and analysis
trove of hard to find, but of otherwise massively time-consuming
phenotypic assay formats and workflows.
For the pharma industry, this means
it is now possible to conduct massive
screens involving millions of different
chemical substances, in microtiter plate
format, and generate far more consistent,
reproducible and high-quality data for the
discovery workflow than with classical
computer vision,’ stated Steigele.
So, traditional HCS approaches tie up

valuable data in the public

high-content screening data. Typically, weeks of time as technicians, IT scientists
this analysis is carried out during and biologists must define and set up
domain” pharmaceutical R&D to evaluate the the screens and the image analysis

22 Scientific Computing World October/November 2018 @scwmagazine | www.scientific-computing.com


parameters, run the workflows, and then
capture and analyse the images. ‘But using
Imagence, one single biologist can now
run the complete workflow from image
production to the interpretation of results,’
Dr Steigele says.
‘It saves time, money, resources, and
a multidisciplinary workforce. Labs can
now effectively scale-up throughput
and data output massively; and whereas
classical approaches to HCS require major
computing clusters to analyse huge sets
of images, we use some essentially very
primitive hardware setups,’ he adds.
Imagence is the result of collaborations
between Genedata and leaders in
the biopharmaceutical industry. It
was the basis for a Genedata project
with AstraZeneca, Deep Learning for
Phenotypic Image Analysis, which won
the 2018 Bio-IT World Best Practices
Award. ‘We wanted to remove the burden
of classical analysis, in which humans
have to think about, recognise and then
handcraft features covering relevant
phenotypic information from the cell
images,’ Dr Steigele notes. ‘For AI-based
approaches, the biologist just provides the
algorithm with a curated training set, and
the software can then learn by itself which
features to extract and are best suited to
differentiate between the existing trainings
classes (eg, images of dogs vs cats or
different cellular states in the applied
example of high-content screening). It’s
the expertise of the biologist that drives
the whole process, but the underlying
complexity is hidden.’
Efficient generation of training data is
key. As Genedata explains, the process
involves generation of interactive, human
readable maps from images in which
similar responding cells present in the
images co-cluster and thereby allow a
very fast exploration of the phenotypic
space and the collection of training data
for all phenotype classes of interest; a
process typically applied during assay
development and via deep learning, which
is capable of detecting even very subtle
differences. It’s then over to the biologist,
who has the expertise to understand
which phenotypes are important for the
assay in development. Relevant training
data are then curated in just a very few
hours to train networks for production
application on quantities of screening
data (typically 50,000 to 2.5 million tested
substances per screening campaign).
Advancing healthcare
The ability to apply deep learning
techniques to typically workforce-
intensive tasks in discovery and preclinical
R&D will have important knock-on effects
www.scientific-computing.com | @scwmagazine
LABORATORY INFORMATICS
for personalised medicine and other areas
of clinical practice, Dr Steigele believes.
Large-scale assays using low-volume
clinical samples, coupled with more
consistent data extraction and analysis,
will help to identify which and how drugs
impact on subsets of patients, and make
it faster and more cost-effective to apply
technologies, such as HCS, for the fast-
developing field of personalised medicine.
Come out of the lab and into the clinic
and healthcare environment, and artificial
intelligence is being harnessed to aid and
speed diagnosis at the patient bedside.
Transformative AI is harnessing artificial
intelligence and analytical techniques
developed at CERN and Cambridge
University to generate predictive
monitoring tools that they hope will
ultimately save patients’ lives.
‘We believe that predictive analytics
hold the key to transforming healthcare,’
states Dr Marek Sirendi, CEO and co-
“We believe that
predictive analytics hold
the key to transforming
healthcare. We aim to
transform the emergency
medicine paradigm
from rapid response to
personalised preparation
and prevention”
founder at Transformative AI. ‘We aim
to transform the emergency medicine
paradigm from rapid response to
personalised preparation and prevention.’
The firm’s first product, designed for
use in hospitals, analyses data from
monitors to warn doctors in advance
that the patient may be likely to suffer
deadly cardiac arrhythmias. The algorithm
detects tiny changes in physiology that
are predictive of sudden cardiac death,
triggering an alarm that gives doctors the
opportunity to prepare for, and potentially
prevent the episode, explains Dr Sirendi.
Perhaps surprisingly, the Transformative
AI algorithm used for predictive monitoring
in hospital settings is based on decision
algorithms developed and used at CERN’s
large hadron collider, which detect exotic
proton-proton collision events in real time.
‘The algorithm employs a number of state-
of-the-art deep learning models along with
other machine learning frameworks. We
present it with examples, and ask it to learn
to recognise the cases of interest.’
This basic AI approach can thus be
used in multiple fields, from business
analytics, to physics or even predictive
medicine. ‘AI is best thought of as an
optimiser and a mathematical learning
machine,’ Dr Sirendi continues. ‘It can
streamline many processes encountered
in the modern workplace, which can
boost the productivity of existing
business activities. But AI can also reveal
unexpected insights from large messy
datasets, which opens up entirely new
product categories. Our AI is designed to
accomplish both tasks. It will make alarms
more actionable and clinically relevant,
while identifying something the human
eye is unable to spot – subtle changes in
human physiology that precede the onset
of sudden cardiac arrest.’
And that predictive capacity can save
lives, the company believes. Although
doctors can give lifesaving CPR and
defibrillation to patients already in cardiac
arrest, the arrest occurs suddenly and
there is no warning, so treatment is started
only after blood has stopped flowing
to the brain. This increases mortality
rates and can have damaging effects on
long-term neurological function among
survivors, Dr Sirendi states. AI could be
used to warn doctors in advance of a
cardiac event. ‘Telemetry monitoring only
identifies arrhythmias after they have
started. Our algorithm can potentially
predict deadly arrhythmias up to an hour
before they begin, giving doctors a chance
to proactively manage this life-threatening
condition.’
Importantly, the algorithm also reduces
the number of false alarms. ‘Nurses are
frustrated by an abundance of alarms,
rather than a lack of them,’ Dr Sirendi
adds. We cut out 54 per cent of irrelevant
alarms while making the remaining more
clinically relevant. The key is to make
technology smarter, so that people (the
nurses, doctors, technicians) can rely on it
to a greater extent.’
Ultimately, the decision on whether to
act on a machine-derived prediction is up
to the clinician, who will also have blood
test and potentially other clinical data and
results to inform their course of action.
‘We’re working with a number of hospitals,
cardiologists and electrophysiologists,’ Dr
Sirendi notes.
Engaging clinicians and healthcare
providers will be key if AI is to be
accepted into mainstream healthcare,
the company believes. ‘To get healthcare
providers excited about integrating AI
into healthcare, new tools shouldn’t just
replicate tasks that human healthcare
workers are capable of. Rather, AI tools
should provide novel insights that elevate
the standard of clinical care.’
October/November 2018 Scientific Computing World 23
 LABORATORY INFORMATICS
Data ecosystems in the cloud
Faisal Mushtaq explains the role of cloud informatics in overcoming the
challenges associated with modern pharmaceutical R&D
Increased automation and powerful
bioinformatics have created a
pharmaceutical R&D landscape where
data can be rapidly generated on a truly
remarkable scale.
Take genome sequencing, for example.
Not long ago, mapping gigabase-sized
sequences took scientists years to
complete using traditional techniques.
Today, this can be accomplished in a
matter of hours with next-generation
sequencing (NGS) technologies(1). Similar
advances in mass spectrometry, synthetic
biology and quantitative polymerase
chain reaction approaches mean today’s
R&D pipelines are bursting at the seams
with complex, multi-dimensional data.
24 Scientific Computing World October/November 2018
However, the sustained growth in
the volume of information generated
by modern R&D workflows presents a
challenge for biotech and pharmaceutical
companies, in terms of organising and
utilising these vast datasets. To truly
capitalise on the value of these datasets,
information management tools must
support integrative thinking and enable
fast, informed decision-making by these
organisations. Moreover, these tools must
not only support innovation today – they
must be sufficiently flexible and scalable
to adapt to tomorrow’s R&D landscape.
Increasingly, forward-thinking biotech
and pharmaceutical firms are turning to
cloud-based informatics platforms, which
overcome data management challenges
by integrating R&D streams and centrally
organising the information they generate.
In particular, platform solutions are gaining
Phipatbig/Shutterstock.com
traction as a scalable and cost-effective
approach to help laboratories connect
individual processes to achieve end-
to-end visibility of R&D pipelines. In this
article, we look at how these cloud-based
tools are ideally placed to help businesses
take back control of their data and meet
the needs of modern pharmaceutical R&D.
The challenge of managing increasingly
complex R&D data
Drug discovery today is as challenging
as it’s ever been. R&D budgets may
be squeezed, yet industry players are
under continued pressure to bring
safe and effective medicines to market
against accelerated timeframes.
Meanwhile, regulatory authorities are
turning their attention to the integrity of
pharmaceutical data, putting additional
demands on laboratories to demonstrate
@scwmagazine | www.scientific-computing.com

compliance quickly and cost-effectively.
Against this backdrop, biotech and
pharmaceutical organisations need an
integrated, open and secure informatics
platform to utilise their growing volumes
of R&D data in the most efficient way.
However, for many organisations, this
isn’t the reality. While large numbers
of biotech and pharmaceutical firms
have made the leap from paper-based
workflows to laboratory information
management systems (LIMS) and
electronic laboratory notebooks (ELNs),
for a significant proportion, these tools
are not used in a joined-up, integrated
way.
Instead, they’re employed as point
solutions or assigned to specific
workflows or departments – resulting in
poor visibility over the full R&D pipeline,
and severely limiting organisational
output. Most importantly, when new
technologies are brought on-line, these
fragmented systems are often unable to
cope. So, what’s the solution?
Cloud-based informatics: The solution
to expanding R&D pipelines
Cloud-based laboratory informatics
platforms bring together R&D data,
creating a single connected digital
ecosystem for drug discovery,
development and manufacture. In
doing so, these systems make end-
to-end pipeline data fully searchable,
sharable, accessible and actionable,
freeing organisations from the technical
challenges associated with fragmented
approaches. And because these tools
are deployed through cloud-based
architecture, they offer much greater
flexibility and scalability compared to
traditional in-house set-ups. In short, they
offer the perfect solution to the challenge
of managing an expanding information
pipeline.
What’s more, because cloud-based
platforms are developed and maintained
by independent software vendors, many
boast innovative workflow support tools
that would be unfeasible to develop
in-house. For instance, some of the
latest platforms incorporate artificial
intelligence (AI) functionality, empowering
organisations with highly-effective
reporting and trending capabilities. AI
algorithms can, for example, analyse
complex unstructured biological data in
real-time using machine learning, natural
language processing and text analytics,
enabling faster and smarter decision-
making. Additionally, AI frees experienced
scientists from some of the more routine
and time-consuming data analysis
responsibilities, so they can put their
www.scientific-computing.com | @scwmagazine
LABORATORY INFORMATICS
expertise to better use driving innovation
– within the R&D pipeline.
Cloud-based solutions also offer
enhanced data sharing functionality, an
increasingly important requirement for
modern pharmaceutical data and analytics
platforms. The last decade has witnessed
a tangible shift towards more collaborative
working practices, as stakeholders
recognise that many of today’s most
pressing healthcare challenges require
knowledge and expertise from across the
industry. Equally, growth in the contract
research and manufacturing sector means
that organisational partnerships are
becoming the new norm.
To thrive, biotech and pharmaceutical
companies need platform-based
approaches that make securely sharing
large datasets as simple as sending
an email. Cloud-based platforms make
“The sustained growth in
the volume of information
generated by modern
R&D workflows presents
a challenge for biotech
and pharmaceutical
companies, in terms of
organising and utilising
these vast datasets”
data retrieval and distribution fast
and straightforward, providing a solid
framework on which to build successful
partnerships. By giving authorised
users real-time access to pipeline data
– from genomics datasets through to
chromatography method parameters –
these platforms can streamline workflows,
improve communication and accelerate
R&D innovation at the click of a button.
Managing the R&D pipelines
of tomorrow
Developing, implementing and validating
new IT infrastructure in-house can often
be complex, expensive and resource-
intensive.
In contrast, the latest solutions make
migrating to a cloud-based informatics
platform simple and straightforward. In
particular, systems based on modular
frameworks, such as Thermo Fisher
Platform for Science software, offer
additional flexibility and are capable of
seamlessly integrating data from existing
LIMS and ELN systems in a way that is
consistent with an organisation’s growth
needs. Even when a complete system
re-design is needed, data can be carried
over in full from the previous framework.
Alternatively, if partial upgrades to an
existing platform are required to bring
additional capabilities on-stream, new
features can be added on without
fundamental IT infrastructure having to be
replaced.
One of the most important features of
cloud-based platforms is the ability to
scale and adapt to users’ needs. Some
providers offer application libraries that
allow laboratories to install new features,
tools and interfaces as their needs evolve
and their pipelines grow. Because these
pre-configured modular applications
are designed to comply with the latest
industry best practice and regulatory
requirements, they are ready to be
used alongside existing LIMS and ELNs
from the moment they are installed. By
supporting organisations through this
flexible approach, cloud-based platform
solutions can help laboratories tackle the
R&D challenges that are most relevant
to them, in the most cost-effective and
scalable way.
Biotech and pharmaceutical companies
are under continued pressure to find
informatics solutions to manage the
mountains of multi-dimensional data
generated by their R&D workflows. To
maintain the competitive advantage
moving forwards, these platforms must
make searching, sharing and manipulating
large datasets quick and efficient, and
above all, they must be capable of
evolving with the rapidly changing drug
development landscape.
As a result, many future-savvy
organisations are implementing cloud-
based informatics platforms to create
a single, integrated digital ecosystem
for their R&D data and analytics. These
modern tools for data and analytics
are bringing together R&D streams and
overcoming the limitations associated
with fragmented approaches, helping
organisations to achieve greater pipeline
oversight, boost efficiency and drive
faster, more effective decision-making.
Faisal Mushtaq is the Vice President and General
Manager of the Digital Science business unit at
Thermo Fisher Scientific. Faisal began his career
developing software solutions for healthcare
providers. In recent years, Faisal has transitioned
to executive management roles at firms that deliver
focussed, software-as-a-service solutions
Reference
[1]
 K Kulski. Next-Generation Sequencing – An
J
Overview of the History, Tools, and “Omic”
Applications, in Next Generation Sequencing –
Advances, Applications and Challenges, 2016, Ed.
JK Kulski, IntechOpen, DOI: 10.5772/61964.
October/November 2018 Scientific Computing World 25
 MODELLING AND SIMULATION
Decentralised systems
buck data-sharing trend
ADRIAN GIORDANI REPORTS
ON THE USE OF BLOCKCHAIN
IN THE AUTOMOTIVE
INDUSTRY
Until the first half of 2018
automotive manufacturers
struggled to integrate a
smartphone-based system into their new
car models. Communication between an
external network and a car would only
work if the manufacturer’s central
database was always online. However,
systems that increase trust and remove
the concept of third parties within a
network, known as distributed ledger
technologies, are growing at a fast pace.
This is disrupting centralised data
management approaches, both at a
commercial and academic level.
In July at the international exhibition
for global microelectronics industries:
SEMICON West in San Francisco, US,
analysts touted that the automotive sector
– particularly self-driving cars, in addition
to artificial intelligence and high-powered
computing – is driving the next boom in
semiconductors. Car chips, for example,
use the same amount of silicon as five to
15 iPhones.
In addition to a rise in computational
demand, players in the decentralised data
movement are working in partnerships to
solve problems and explore opportunities.
This year XAIN, based near Berlin in
Germany, solved trust between a database
of its automotive client Porsche and its
26 Scientific Computing World October/November 2018
car model application. This was done
using a complex machine learning network
to enable a four-door sedan Porsche
Panamera to act as the software client
independently of backend database
support, with overall control managed
by the driver through a blockchain
application, a type of distributed ledger
technology.
XAIN successfully tested their
technology to remotely open and close
the Panamera up to six times faster than
before (1.6 seconds).
‘However, we need to differentiate here
that other automotive manufacturers
were previously integrating a blockchain
wallet into a car; which only stores private
[cryptographic] keys so that the car can,
for example, pursue payments,’ said
Leif-Nissen Lundbæk, CEO, chairman
and co-founder of XAIN. ‘In our case, we
integrated a full client in a car that also
verifies all communication, so that the
blockchain is not part of the backend
system, but actually the car itself is the
blockchain.’
His work focuses on AI algorithms for
distributed cryptographic systems. In
fact, XAIN originated as a spin-off from his
academic work at Oxford University and
Imperial College London.
His firm’s mission is an eXpandable
Artificial Intelligence Network (XAIN),
using blockchain systems as an open or
permission-based system that enables
connectivity to Internet-connected
devices. These include electronic control
units (ECU) in cars to control electrical
systems or subsystems. XAIN cooperates
with semiconductors and integrates them
with automotive microcontrollers from
other vendors.
Smart contracts are used by the
network to bypass the need for
middlemen between permitted parties
within the network, saving time. It
algorithmically decides on the contents
of the next ‘block’ in the blockchain
with a proprietary-created consensus
mechanism called a ‘Proof of Kernel Work’
(PoKW). Only specific users or drivers
are given rights to the car for opening or
locking the doors or starting the engine.
XAIN’s network runs on the Ethereum
Blockchain, an open-source distributed
computing platform. Its uses range from
decentralised video streaming services
to helping distribute food vouchers and
mobile banking in third world countries.
‘Here security and incentivisation are
really the key points. The most powerful
technique are open consensus methods,
that protect from changes, while also
allowing for incentivising all sorts of
processes, ranging from the consensus
itself to standardisation processes,’ said
Lundbæk.
The key layer of XAIN’s novel approach
is the distributed ledger technology or
DLT protocol. It enables a special form of
electronic data processing and storage.
Importantly, a DLT is a database that
exists across several locations, nodes
“We integrated a
full client in a car
that also verifies all
communication, so that
the blockchain is not part
of the backend system,
but actually the car itself
is the blockchain”
@scwmagazine | www.scientific-computing.com

or participants. A blockchain is just one
specific type of DLT. Not all DLTs use a
chain of blocks, for example, and not all
distributed databases are DLTs – the trust
boundaries are different.
A DLT delegates access to functions and
data over multiple parties through secure
cryptographic principles. This platform
works in tandem with Porsche’s traditional
centralised servers, but the novel network
becomes part of the backend with better
trust and security, and gives network users
a new level of access between ‘read’ and
‘write’ permissions and more.
DLTs are most famously known for
underpinning the digital currency Bitcoin.
In 2018, Bitcoin mining represented
roughly 0.6% of global energy demand –
equivalent to Argentina’s consumption.
Even though Bitcoin mining consumes
lots of energy, a DLT network controlled
algorithmically does not necessarily have
to consume more energy per node.
‘First of all, I think blockchain is
outdated. Blockchain became a buzzword,
we even used it on our company name,’
said Robert Küfner, advisor to Advanced
Blockchain, a German publicly listed
company focusing on the design,
development and deployment of DLTs.
‘Using more energy in order to solve a
problem is simply wrong,’ said Küfner. ‘All
www.scientific-computing.com | @scwmagazine
MODELLING AND SIMULATION
“The most powerful
techniques are open
consensus methods, that
protect from changes,
while also allowing for
incentivising all sorts
of processes, ranging
from the consensus
itself to standardisation
processes”
August, researchers at the San Diego
Supercomputer Center (SDSC), of the
Piusillu/WhiteMocca/Shutterstock.com
University of California San Diego, US,
were awarded a three-year National
Science Foundation grant of $818,000
to design and develop an infrastructure
of open-source distributed ledger
technologies to enable researchers to
efficiently share information about their
scientific data, while preserving the
original information. The hope is that
of this will be obsolete because code can researchers will be able to efficiently
replace the work that currently requires access and securely verify data, according
lots of energy. This goes back to what we to the SDSC press release.
are doing in Advanced Blockchain. Known as the Open Science Chain, this
‘If we look at distributed ledger is not a supercomputer-related project
technology, blockchain is just one... the according to Subhashini Sivagnanam,
majority of people and start-ups are principal investigator for the grant and
focussing on Fintech, everything around a scientific computing specialist with
finance and money. But there are a few SDSC’s data-enabled scientific computing
industries with a higher potential that division. This infrastructure will be
will disrupt sooner than others; those integrated with actual scientific datasets.
industries that involve a middle party The Open Science Chain aims to
have a problem with the decentralised increase productivity, security and
movement,’ said Küfner. reproducibility. As the datasets change
The automotive sector is one such area. over time, new information will be
It can enable better oversight of odometer appended to the chain.
fraud to car buyers, such as clocking or ‘My first impressions are that it may
busting miles, which is the illegal practice help part of the problem – validating
of rolling back odometers to make it and verifying the data,’ said Les Hatton,
appear that vehicles have lower distances emeritus professor of forensic software
travelled, costing millions. engineering at Kingston University,
‘The vehicle identification number, the London, UK.
time stamp and actual mileage of the Hatton, who is not involved in this
vehicle will be uploaded and stored to research, said: ‘However, nothing is said
a ledger,’ said Küfner; ‘which cannot be about the software which analyses that
compromised. By doing so, you have a data. Full computational reproducibility
digital twin logbook of the car.’ depends on the whole package: data,
analysis software, glue software and
Opening up to more reproducible testing software.’
scientific research However, the large-scale challenge of
A distributed approach to data also reproducing scientific data is bigger than
opens up possibilities for academia. In just one technical approach, Hatton states.g
October/November 2018 Scientific Computing World 27
 MODELLING AND SIMULATION
g More education for researchers about
computational reproducibility and the
basic techniques, rather than something
sophisticated, may prove more fruitful.
Enhanced security
Advocates of DLTs say that they enable
better security between parties in the
network by decreasing the chances of a
malicious outside attack. For example, an
automotive manufacturer stops becoming
a single entry point; but, DLTs are not a
panacea and must not be used in isolation.
‘It would be wrong to use a blockchain
to store data, for reasons of scalability and
post-quantum security, so it is used rather
as a synchronisation proof mechanism
and user registry,’ said Lundbæk.
These architectures can be used with
traditional centralised or decentralised
databases to enhance resilience to
hacks. However, any executable program
running within that network could also be a
security risk open to hackers.
‘A lot of the most impactful advances
are algorithmic in nature, instead of a
matter of scale,’ said André Platzer, an
associate professor in the computer
science department at Carnegie Mellon
University, Pennsylvania, US. His work
focusses on the general principles for
designing motion or other physical
processes in cyber-physical systems,
such as surgical robots, aircraft or self-
driving car applications.
‘The most subtle but impactful
challenges in all these systems is the
identification of which actions can safely
be taken under what circumstance and
why,’ said Platzer. ‘For example, when
should an aircraft climb and when it should
descend instead; or, when can a car
accelerate or coast, or even brake.’
Platzer and his colleagues develop
methods that enforce safety in
reinforcement learning algorithms. For
example, they use programming principles
with an automated pipeline approach
called ‘VeriPhy’ (verified controller
executables from verified cyber-physical
system models).
It provides a safe interaction between
the code and actual physics to generate
executables that perform exactly in the
same way that the original models and
algorithms were supposed to execute.
Platzer says that this is a more disciplined
approach to address security concerns.
‘Privacy is another matter and, indeed,
it’s not clear if the world is better off
favouring privacy over exchange of
information – in case only the latter can
prevent collisions of cars. Privacy clearly
is something to be thought about
carefully,’ said Platzer.
28 Scientific Computing World October/November 2018
spainter_vfx/Shutterstock.com
“If we look at distributed
ledger technology,
blockchain is just one...
the majority of people
and start-ups are
focussing on Fintech,
everything around
finance and money. But
there are a few industries
with a higher potential
that will disrupt sooner
than others”
Privacy in a networked world
The growth of automation and distributed
data exchanges heightens the concerns
of personal data threats and control. The
European Union’s General Data Protection
Regulation (GDPR) came into effect in May
2018 for 28 member states, including
businesses. The GDPR’s main goals are
stronger rules on data protection, so
individuals have more control over their
personal data and businesses have a level
playing field on processing private data.
The use of cryptography within DLTs can
also support GDPR principles. All personal
data is encrypted and can be stored on
individual file storage.
‘A GDPR-compliant process – specific
to a given use case – can then be defined,
individualised and built into the user
interface by mapping out or combining
processes for consent, access, update
and erasure policy,’ said Lundbæk.
‘The user can then decide whether or
not to grant access of this data to the
manufacturer or other parties.’
Now XAIN is testing other applications
with Porsche vehicles. These include
real-time notifications for drivers about a
third-party car access, granting remote
access of a parked car for secure delivery
of packages and unlocking or locking a
car with a blockchain-powered offline
connection, with no server connection.
Porsche benefits from increased trust
in vehicle data, audited information for
reports, local data access for predictive
maintenance and training of distributed
machine learning for autonomous driving.
‘We are working with Daimler and other
automotive manufacturers, representing
roughly 39 per cent of the world’s vehicle
production, on integrations in their
cars,’ said Lundbæk. ‘We are working
with Infineon, a leading microcontroller
manufacturer, to embed our protocol
on their devices to make our solution
easier to adapt in vehicles, and more
secure using the trusted microcontroller
environment as an accelerator.’
Based on these early adopters, could
a DLT approach make centralised
approaches go the way of the minidisc or
eight-track tape?
‘Traditional database will likely continue
to be the standard and have their role until
these protocols are tested at production
level,’ said Lundbæk.
‘This process has just started and it
is still very challenging for centralised
businesses to think this way, but it is
mostly the case that they fear that their
business will end if they don’t change.’
According to Küfner, the rise of DLTs
compare with the TCP/IP protocol that
underpins email exchanges. In the 90s,
when people tried to explain to others how
to create and use an email address, there
was little knowledge available. Küfner sees
DLTs moving much faster.
As it progresses, blockchain suffers
from issues such as block response times
and block sizes. Advanced Blockchain is
focussed on implementing another type of
DLT that is practical and scalable, called a
Directed Acyclic Graph (DAG).
‘These issues are not sustainable and
blockchain will be replaced by a better
version called DAG,’ said Küfner. ‘If you
have a fully functional DAG, imagine all
the energy that you can save. So DLT will
be fantastic for climate change because
it will reduce the amount of energy that is
consumed by all the processes that are
currently running.’
Large organisations or companies, like
large cruise ships or tankers, are floating
on an ocean of possibilities. Some are
actively directing their paths straight
into the currents of decentralised data
management streams more than others.
The market is ambitious.
‘There is no one in DLT who is a
professional and has proven themselves
to know what they are doing, because
the industry is so young,’ Küfner said.
‘In fact, I would not call this an industry,
rather a movement. Because it affects
human interactions; that is why it is not a
business. It is a beginning of a change to
social-economic behaviour and will involve
in the near future.’
@scwmagazine | www.scientific-computing.com
 Subscribe
for free*
Do you compute?
The only global
publication for scientists
and engineers using
computing and software
in their daily work

*Registration required

Do you subscribe? Register for free now! SCIENTIFIC

COMPUTING
scientific-computing.com/subscribe WORLD
 MODELLING AND SIMULATION

Intelligent
Optimisation
GEMMA CHURCH LOOKS AT
THE ROLE OF OPTIMSATION
SOFTWARE IN MODERN
ENGINEERING PRACTICES
Optimisation is everywhere. It’s
prevalent in our day-to-day
decisions as we choose the
fastest route to work, the cheapest
product or service for our needs, or the
healthiest snack (or, maybe, the tastiest)
when hunger arises.
It’s also inherent to optimise the
designs, processes and services that
shape our lives through a range of evolving
simulation techniques and applications.
As such, optimisation is finding a new
place in the additive manufacturing market
and is helping manufacturers meet rising
demands for lighter and more energy
However, tolerances and precision in the
aerospace industry (where optimisation is
an established tool) are astoundingly tight
because of the high degree of regulation
and safety required. As a result, errors
and deformation from thermal cycling
that occur on the micron scale during
manufacturing processes can render a
part unusable.
Manufacturing Technology Centre
(MTC) is working to optimise the achieved
precision in its additive processes and
overcome this challenge. Using Comsol
Multiphysics modeling and simulation
apps, MTC has created an app that
predicts the deformation of parts and
allows designers to build deformations
directly into their designs.
The implications of such apps are wider
reaching, according to Sjodin, who added:
‘The field of simulation apps also opens
up the door for a variety of optimisation
opportunities, such as supporting a sales
“3D printing or additive
team, or product optimisation with non-
simulation experts, to name a few.’
Digital twins
Optimisation is now helping companies
create digital twins with the integration
of machine learning techniques. Brennan
explained: ‘As things mature, optimisation
algorithms will combine with learning
algorithms to improve product design.
‘For example, if we have a product out
in the field such as a wind turbine, data
will be gathered on its performance in
various conditions. This puts a load on that
device, which starts to make the baseline
design struggle for its normal longevity
of product duration, particularly during
adverse conditions.’
Brennan added: ‘That data can be
used the next time a structure needs to
be placed in that same place, under the
same conditions. That new structure will
then withstand that environment better
because of the information provided to the
digital twin version with data from the field.
That’s a form of optimisation that takes

efficient products by optimising mass
distributions.
Bjorn Sjodin, VP of product
management at Comsol, explained: ‘3D
printing, or additive manufacturing, is
probably the current strongest trend
within the optimisation space. Here,
shape and topology optimisation are
manufacturing is
place over years – after the product leaves
the manufacturing plant and is in service.
probably the current Product improvement still hasn’t stopped
strongest trend within because the data is taken from the
environment of true operation to inform
the optimisation space” the next generation of that product.’

Altair
important methods, and they result in new
shapes and designs that the human mind
could never envision without the help of
computational tools. It is an exciting area
that we are very active in, with respect to
customer interactions and implementation
of new tools for the future.’
Consequently, topology optimisation is
finding a new lease of life in the 3D printing
and additive manufacturing markets.
Jeffrey Brennan, chief marketing officer at
Altair, explained: ‘Topology optimisation,
with its generation of efficient, non-
traditional, organic-like designs, serves
as a perfect complement for 3D printing,
given the manufacturing flexibility that it
offers. But it goes beyond that to include
the design and optimisation of even
complex lattice structures using different
optimisation disciplines.’  The latest Altair 365 and Altair Inspire platform images

30 Scientific Computing World October/November 2018 @scwmagazine | www.scientific-computing.com


 Optimised,
varying density,
lattice geometry
created using Ansys
Mechanical showing
displacement
Lightweight designs
Altair was the first company to implement
and commercialise topology optimisation.
Now, its primary optimisation focus is
simulation and the use of digital tools
for design improvement, specifically to
reduce component complexity, weight
and consequently simplify the resulting
manufacturing processes. For example, it
recently developed a 3D printed bracket
for the BMW i8 Roadster with the help
of optimisation techniques that realised
44 per cent component weight savings
compared to the previous car model.
Altair also worked with Sogeclair
Aerospace to find a new development
and manufacturing approach to reduce
the weight of its components, while
ensuring the safety of the designs. A CAE-
driven design process was developed,
which combined topology optimisation
using the optistruct and additive layer
manufacturing (ALM) tools.
As a result, a greater degree of design
freedom was realised, weight savings
were maximised while retaining the parts’
stiffness. The overall number of system
parts was reduced, which reduced the
assembly time.
Altair customer Rolo Bikes also applied
CAE techniques to optimise carbon fibre
structures with the objective of optimising
a new bike frame to achieve world-leading
performance for weight, stiffness and
comfort. ‘Composites materials are an
emerging technology as well. Given the
focus on lightweight designs, composite
www.scientific-computing.com | @scwmagazine
MODELLING AND SIMULATION
materials are increasingly gaining
prominence. And this trend extends
beyond aerospace to other industries
as well, including automotive,’ Brennan
added.
Changing times
Ansys is another established name in the
optimisation space. DesignXplorer, which
is part of Ansys Workbench. It has been
around for more than 15 years and makes
parametric optimisation in any simulation
area easy for engineers of all levels of
experience. More recently, Ansys released
a new topology optimisation capability
within Ansys Mechanical.
The company is noticing real change in
the optimisation space. Richard Mitchell,
lead product marketing manager for
structures at Ansys, said: ‘There are
definite moves to adopt new technologies
and to innovate faster. The trends I see
becoming less common are building
models entirely with scripts. We do
still have a good number of engineers
who are well versed in working this way,
moving optimisation closer to the user
and opening up new methods, meaning
that more users can get to better designs
faster.’
Challenges remain as optimisation
naturally leads to more solution runs,
according to Mitchell, who explained:
‘There are two main obvious obstacles
here. The first is, will the runs be carried
out successfully? A 99 per cent automatic
process is as effective as a 10 per cent
Ansys
“This type of
optimisation - based
on the management
of ‘free’, user-defined
parameters - allows
to apply the same
techniques to a
significantly more vast
spectrum of problems,
compared to topological
optimisation, which
remains limited to
geometry problems”
automatic one. In order to carry out
optimisation effectively, a process must be
100 per cent automatic.’
‘Optimisation inside of Ansys
Workbench is built to be robust and
reliable, even if solutions fail. A user is still
able to make choices though, that cause
issues with things like geometry updates
(from a CAD system) or exploring the edge
of viable solution sets.
‘The other challenge is to find the
optimised result in as few iterations as
possible without missing the target.
Ansys has numerous optimisation tools
that include single and multi-objective
algorithms, as well as reducing domain
algorithms,’ he added. g
October/November 2018 Scientific Computing World 31
 MODELLING AND SIMULATION
g Engineering expertise
Esteco has been working in the
optimisation field for nearly two decades,
with a focus on real-life engineering
problems. It promotes an approach based
on ‘optimisation driven design’, where
users can advance their design process
with intelligent algorithms, which utilise
machine learning techniques. These
algorithms ‘understand’ each specific
problem and find optimal designs in
less time, at lower cost and using fewer
computational resources than traditional
techniques.
Matteo Nicolich, Volta product manager
at Esteco, explained: ‘When building
workflows composed of complex software
chains, having a tool that automates all the
repetitive work needed to interface one
software with the other, or to interface the
output of one software with the input of
the following one is essential.’
Esteco also focuses on parametric
optimisation. ‘This type of optimisation
– based on the management of ‘free’, user-
defined parameters – allows to apply the
same techniques to a significantly more
vast spectrum of problems compared to
topological optimisation, which remains
limited to geometry problems,’ Nicolich
added.
Esteco’s optimisation tools have been
used as part of the GasVessel project in
Cyprus, where researchers are developing
a prototype tank containment system,
which will be installed on a vessel and
used to transport compressed natural gas
(CNG).
The Volta platform has incorporated
a deterministic simulation to generate
results as cost per cubic unit. Athos
Kleanthous, commercial analyst at Cyprus
Hydrocarbons Company (CHC), explained:
‘More specifically, we are running a
simulation of a vessel, which lifts a cargo
from point A and has to travel a certain
number of nautical miles to point B, where
it should discharge the cargo.’
The simulation needs a number
“We provide our
customers with
algorithms that are
not only able to deploy
multiple strategies
at once to the same
engineering problem, but
are also able to learn from
the problem itself and
adapt accordingly”
32 Scientific Computing World October/November 2018
 Shape optimisation analysis of a mounting bracket created using Comsol Multiphysics software
of variables, which will be used by
Volta, either as range limits or specific
predetermined sets. Kleanthous said:
‘Volta has incorporated those variables
into easily editable number sets. Volta
has given us the opportunity to run
optimisation and sensitivity analysis for
the various scenarios our vessel was
tested on.’
The cargo capacity, vessel’s speed,
distance travelled, supply and demand
variables have all been optimised using
the Volta platform. CHC is working with
Esteco to add new features or change
specific processes in the simulation
algorithm. It also expects to integrate Volta
with its other projects.
Kleanthous said: ‘Volta has helped
identify the smallest vessel capacity
possible for a specific route, less number
of ships employed in the specific supply
chain and optimal speed to achieve on-
time deliveries of the cargo in transit.’
‘The results Volta has returned have
shed light to the development team for the
directions to follow, in order to deliver a
viable project.
‘Besides the algorithm and the results
itself, Volta is a web-based tool, which is
easily accessible through any internet
browser, having inputs in a simple format
and also offers an extremely simple user
interface,’ Kleanthous added.
Autonomous future
Esteco is now focusing on its optimisation
automation tools. Nicolich explained the
reasoning for this approach: ‘One of the
biggest issues can be finding the most
effective strategy to tackle the problem
at hand. This is why we invested in
researching and developing a whole new
COMSOL
set of smart algorithms that come with a
possibility to run in ‘autonomous’ mode.’
‘We provide our customers with
algorithms that are not only able to deploy
multiple strategies at once to the same
engineering problem, but are also able to
learn from the problem itself and adapt
accordingly.
‘This is not about optimisation for
dummies, but it is about obtaining viable
and accurate insights with little time or
information about the product at hand.’
However, such automation opens up
another can of worms: management of the
huge swathes of data that result. ‘Together
with the management of simulation
processes, there is the big issue of
managing the data and all the work in
progress that is related to the construction
and creation of process automation, and
all the data that are generated upon the
execution of these processes,’ Nicolich
added.
Esteco has developed a Simulation Data
Management tool, which allows users to
keep track of all the information related
to a simulation process, so they can cycle
back along the history to see how a single
piece of information was created, by which
data and which model.
Nicolich said: ‘With the Engineering
Data Intelligence tool, we want the set
of functionalities to understand and
mine information in this potentially huge
amount of engineering data, and extract
information on how to predict the next
step of the design iteration.’
It’s an innovative approach and one
that should help Esteco future proof its
optimisation tools as automation and the
resulting reams of big data start to impact
the simulation and modelling space.
@scwmagazine | www.scientific-computing.com
 VIEW
FOR *
FREE

*Registration required

Webcasts
now available online
Sponsored by
Creating a connected ecosystem to gain insights across R&D

As data continues to increase exponentially, many organisations are turning to

the latest advancements in digital technology to respond to the evolving needs
of R&D scientists. For many organisations, a key challenge is managing the
complexity and the number of systems in place that generate multiple types of
complex data.

Sponsored by
Ensuring Data Integrity & Facilitating Compliance with ISO 17025

Today’s quality landscape is incredibly complex with multiple data analysis,

informatics, and enterprise systems. To ensure quality results, regulators
across industries are focusing on data integrity, data security and consistent
laboratory practices.

Laboratory 4.0: Moving Beyond Digitalization in the Lab Sponsored by

Today’s laboratories are becoming increasingly complex, with ever more

data being generated and captured. At the same time, regulatory oversight
is stronger than ever and places new compliance burdens on everyday
operations.

Leveraging Machine Learning for Decision Making in the Materials Sciences Sponsored by

Machine learning and Big Data analytics offer asignificant opportunities to

improve R&D in the materials sciences, providing scientists with a new set of
tools to analyze their data.

SCIENTIFIC
COMPUTING
www.scientific-computing.com/webcasts WORLD
 RESOURCES

Suppliers’ Directory
Find the suppliers you need quickly and easily
www.scientific-computing.com/suppliers

HIGH-PERFORMANCE LABORATORY Biovia Siemens

COMPUTING INFORMATICS
+ 1 858 799 5000 +1 322 536 2139
Altair Engineering, Inc www.3ds.com/products-services/ industrial-it.swe@siemens.com
Abbott Informatics biovia www.siemens.com/
(248) 614-2400
info@altair.com +44 (0)161 711 0340 n LIMS simaticit-rdsuite
www.altair.com AISalesUK@abbott.com n Electronic Laboratory www.siemens.com/industrial-it/lims
n Software www.abbottinformatics.com Notebooks n Electronic Laboratory
n LIMS Notebooks
Boston Limited n Scientific Document n LIMS
Eusoft
+44 (0)1727 876 100 Management Systems
sales@boston.co.uk +39 080 5426799
www.boston.co.uk info@eusoft.it Thermo Fisher
n Systems Integrator Accelerated Technology www.eusoft.it Scientific
Laboratories n LIMS +44 (0)161 942 3000
Calyos SA +1 910 673 8165 (outside of US) marketing.informatics@
0032 4 75 73 54 65 800 565 LIMS (5467) US and IDBS thermofisher.com
newbusiness@calyos-tm.com Canada info@idbs.com www.thermoscientific.com/
www.calyos-tm.com www.idbs.com informatics
info@atlab.com
n Cooling n LIMS
www.atlab.com n Electronic Laboratory
Notebooks n Scientific Document
Cluster Vision n Bioinformatics
Management Systems
+31 20 407 7550 n LIMS
marketing@clustervision.com InfoChem n Chromatography Data Systems
www.clustervision.com +49 (0)8958 3002 n Spectroscopy Software
Amphora Research Systems
n Software info@infochem.de
+44 (0)845 230 0160
info@amphora-research.com www.infochem.de MODELLING
Eurotech Spa n Cheminformatics
www.amphora-research.com AND SIMULATION
+39 0433 485 411
welcome@eurotech.com n Electronic Laboratory
www.eurotech.com LabWare Altair Engineering, Inc
Notebooks
n Systems Integrator infoEU@labware.com (248) 614-2400
www.labware.com info@altair.com
Autoscribe
Numerical Algorithms Group (NAG) n LIMS www.altair.com
+44 (0)1865 511 245 +44 (0) 118 984 0610
n Software
katie.ohare@nag.co.uk info@autoscribeinformatics.com
Osthus GmbH
www.nag.co.uk www.autoscribeinformatics.com +49 241 943 140 Integrated Engineering
n Software n Data Management office@osthus.de Software
n Electronic Laboratory www.osthus.de +1 204 632 5636
OCF Notebooks
+44 (0) 114 257 2200 n Electronic Laboratory info@integratedsoft.com
scw@ocf.co.uk n LIMS Notebooks www.integratedsoft.com
www.ocf.co.uk n Scientific Document n Cheminformatics n Mathematics, Simulation and
n Systems Integrator Management Systems n LIMS Modelling

Integrated Engineering Eurotech Spa Osthus GmbH OCF

Software +39 0433 485 411 +49 241 943 140 +44 (0) 114 257 2200
+1 204 632 5636 welcome@eurotech.com office@osthus.de scw@ocf.co.uk
info@integratedsoft.com www.eurotech.com www.osthus.de www.ocf.co.uk
www.integratedsoft.com

Integrated Engineering
Software is a leading
developer of hybrid simulation
tools for electromagnetic,
thermal and structural design
analysis.
Eurotech high-performance
computing solutions help
universities, research centres,
companies and governments
to excel in their field.
Our experts in life science
and industrial R&D help you
to transform information into
knowledge by custom data
integration projects for LIMS/
ELN/Bio&Chem Informatics.
At OCF we work with you to
meet your high performance
data processing, data
management and data storage
needs

34 Scientific Computing World October/November 2018 @scwmagazine | www.scientific-computing.com

 PARTNERSHIP FOR
ADVANCED COMPUTING
IN EUROPE

12–15 November 2018

Visit PRACE at
BOOTH
2033 PRACE BOOTH

PRACE HOSTING MEMBERS

JULIOT CURIE HAZEL HEN JUWELS SUPERMUC MARCONI MARENOSTRUM 4 PIZ DAINT
@ GENCI @ CEA, France @ GCS @ HLRS, Germany @ GCS @ FZJ, Germany @ GCS @ LRZ, Germany @ CINECA, Italy @ BSC, Spain @ CSCS, Switzerland

Drop by the PRACE booth 2033 and speak to our experts about:
• PRACE Project and Preparatory Access
• PRACE Industry Access and SHAPE (SME HPC Adoption Programme in Europe)
• PRACE Training & Education
• PRACE White Papers & Best Practice Guides EXDCI-2 PROJECT
• PRACE MOOCs, CodeVault IS PRESENTED TOO!

Call 18: 4 September – 30 October 2018

The PRACE Research Infrastructure provides a persistent world-class high performance computing service for
scientists and researchers from academia and industry in Europe. The computer systems and their operations
accessible through PRACE are provided by 5 PRACE members (BSC representing Spain, CINECA representing
Italy, ETH Zurich/CSCS representing Switzerland, GCS representing Germany and GENCI representing France).
The Implementation Phase of PRACE receives funding from the EU’s Horizon 2020 Research and Innovation
Programme (2014-2020) under grant agreement 730913. For more information, see www.prace-ri.eu
LABWARE 7
LIMS and ELN together in a single
integrated software platform.
A laboratory automation solution
for the entire enterprise.

Offices worldwide supporting customers

in more than 100 countries

www.labware.com