Iain Bethune
EPCC Project Manager
Contact Details
Address:

2404 James Clerk Maxwell Building, The King's Buildings, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK


Email:

ibethune@epcc.ed.ac.uk

Tel/Fax:

+44 (0) 131 650 5201 / 6555

Mob:

+44 (0) 7598317015

Twitter:

@IainBethune 
Skype:

iainbethune

Overview
Since 2008, Iain has worked at EPCC, specialising in performance analysis and optimization of HPC applications. He collaborates with a range of researchers around the UK and Europe in fields as diverse as Computational Chemistry, Mathematics and Biomechanical Engineering. He develops scalable software to allow researchers to harness HPC resources such as HECToR and ARCHER  the UK National HPC Services  and the European PRACE infrastructure. Most of his work has been in the area of Materials Science, and he is a developer on the CP2K project  a powerful program enabling Density Functional Theory and other atomistic modelling techniques to be applied a diverse range of systems using tens of thousands of CPU cores at a time.
Iain has a wideranging interest in high performance computing architectures and programming models including MPI, OpenMP, CUDA and OpenCL. He teaches several classes on EPCC's MSc in HPC on Numerical Algorithms and Performance Optimisation.
Believing that outreach to the public about scientific research is an important part of science itself, Iain is a developer for the PrimeGrid volunteer computing project, which promotes mass participation in the solution of mathematical problems, as well as finding very large  million digit  prime numbers.
Prior to joining EPCC, Iain earned a First Class BSc. (Hons) in Computer Science & Physics from Edinburgh University in 2005 before spending two and a half years working for IBM on SAN storage virtualization.
In his limited spare time, Iain enjoys white water kayaking, hill walking and is an avid space exploration and research enthusiast.
Current Projects
 CP2KUK  an EPSRCfunded project to improve the usability of CP2K, support the growth of the CP2K user and developer community in the UK via networking activities, improved software engineering, and new algorithm development. EPCC leads the work, in collaboration with KCL and UCL, in addition to many more group involved in the wider network.
 CP2KNSF  supporting UKUS project led by Prof. Ilja Siepmann (University of Minnesota) and Dr. Ben Slater (UCL) to develop new Monte Carlo methods in CP2K to allow the study of reactive phase and sorption equilibria.
 ARCHER  the new UK National HPC Service based on the Cray XC30 platform. Supporting CP2K usage and acting as liaison to the UK Materials Chemistry HPC Consortium.
 LAMMPS eCSE  working with Prof. Jon Essex's group to implement their ELBA dualresolution forcefield into LAMMPS.
 ExTASY  we are developing an "Extensible Toolkit for Advanced Samping and analYsis" to couple novel algorithms for large timestep molecular dynamics, advanced analysis tools, and large scale ensemble calculations in order to overcome the Grand Challenge of effective sampling of complex macromolecules. Funded jointly by EPSRC and NSF, the project team comprises Rice U., Rutgers U., Duke U., U. of Edinburgh, U. of Nottingham and Imperial College London.
 PhD  Iain is studying parttime towards a PhD in materials physics, supervised by Prof. Graeme Ackland at the University of Edinburgh, to investigate the properties and structure of silicate melts found at high temperature and pressure in the Earth's mantle
 MSc in HPC  teaching Fast Fourier Transforms as part of 'Parallel Numerical Algorithms' and supervising dissertation projects.
 TPLS  collaboration with Dr. Prash Valluri (UoE Engineering) and Dr. Lennon O Naraigh (UCD) to implement more scalable solvers in their TPLS (TwoPhase Level Set) fluid dynamics code, which models the interface between two phases of a fluid using ultrahigh resolution DNS.
 EPCC Publicity & Outreach  taking EPCC to other departments, universities and science fairs (e.g. British Science Festival, Bang Goes The Borders). Developing publicity videos for EPCC projects. Iain is a STEM Ambassador and part of the RSE@Schools programme.
Previous Projects
 GreenhouseGPU  a collaboration with University of Edinburgh and Britol geochemistry researchers to investigate the benefits of using Nvidia GPUs for their calculations
 NAIS  as part of the Centre for Numerical Algorithms and Intelligent
Software, Iain developed improved programs for primality testing using autotuning and accelerator hardware.
 PRACE  as part of the Applications work package of PRACE, we are porting and optimisng CP2K for the Intel Xeon Phi coprocessor architecture. Three previous projects under PRACE have also extended mixedmode OpenMP parallelism in CP2K, and developed an autotuning framework for key computational kernels, to support efficient massively parallel MP2 calculations on the PRACE Tier0 HPC resources.
 Novel Asynchronous Algorithms and Software for Large Sparse Systems  an EPSRCfunded collaboration with Universities of Manchester, Leeds, Hull and Strathclyde to develop the next generation of methods for solving linear algebra problems with billions of unknowns using tens of thousands of CPU cores.
 HPC Simulations of complex solids and clusters using static lattice techniques  EPSRC Software Development project with UCL and Curtin University (Australia) to integrate GULP, the 'General Utility Lattice Program' with a new controller code in order to support a wide range of materials science applications.
 ChipSHOP  a collaboration with biological scientists and engineers from HeriotWatt and Edinburgh Universties formed as a result of winning the HeriotWatt Crucible in May 2012 to develop software for insilico design and optimisation of microfluidic devices for applications in separation of biological fluids such as DNA/blood plasma, and cells/buffer solution.
 TEXT "Towards EXaflop applicaTions"  an EU FP7 research project exploring the use of the MPI and SMPSs as a hybrid programming model to allow high productivity and efficient use of current and future HPC architectures.
 Commercial Projects  optimised use of FFT in a key code for a Scottish Oil & Gas services SME.
 HECToR dCSE: VOXFE  implemented parallel I/O for improved scalability and performance.
 HECToR dCSE: Quantum Espresso  modified FFT schemes for SMP cluster systems.
 HECToR dCSE: CP2K  three projects improving MPI and OpenMP parallelisation in all key areas of the code including grid operations, FFT, sparse matrix multiplication
 ACE "Architecture Comparison Exercise"  benchmarking and performance analysis on 5 representative UK codes on a range of HPC architectures, to understand the links between hardware characteristics and application performance.
 HPCx  supporting the 'Complementary Capability Computing' initiative: parallel visualisation, interactive MD, job submission portlets.
Publications
Journal Articles
 "pyPcazip: a PCAbased Toolkit for Compression and Analysis of Molecular Simulation Data", A. Shkurti, R. Goni, P. Andrio, E. Breitmoser, I. Bethune, M. Orozco, C. Laughton, submitted
 "Simplified TPLS as a learning tool for highperformance computational fluid dynamics (preprint)", J. Fannon, JC. Louiseau, P. Valluri, I. Bethune, L. O Naraigh, Submitted
 "Genefer: Programs for finding large probable generalized Fermat primes.", I. Bethune, Y. Gallot, Journal of Open Research Software, 3: e10, Nov 2015
 "Linear instability, nonlinear instability, and ligament dynamics in threedimensional laminar twolayer liquid/liquid flows", L. O Naraigh, P. Valluri, D. Scott, I. Bethune, P. Spelt, Journal of Fluid Mechanics, Jul 2014, 750: 464506
 "Performance analysis of asynchronous Jacobi's methods implemented in MPI, SHMEM and OpenMP", I. Bethune, M. Bull, N. Dingle, N. Higham, International Journal of High Performance Computing Applications, Feb 2014, 28: 97111
 "Mapping application performance to HPC architecture", A. Gray, I. Bethune, R. Kenway, L. Smith, M. Guest, C. Kitchen, P. Calleja, A. Korzynski, S. Rankin, M. Ashworth, A. Porter, I. Todorov, M. Plummer, E. Jones, L. SteenmanClark, B. Ralston, C. Laughton, Comp. Phys. Comm. Volume 183, Issue 3, March 2012, Pages 520529
Conference Papers / talks
 "Developing a scalable and flexible code for highresolution DNS of twophase flows", I. Bethune, 2nd ThermaPOWER Minisymposium, 14th UK Heat Transfer Conference 2015, Sep 2015 * Invited Talk *
 "Developing a scalable and flexible highresolution DNS code for
twophase flows", I. Bethune, T. Collis, L. O Naraigh, D. Scott, P. Valluri, International Conference on Parallel Computing (ParCo) 2015, Sep 2015, to appear ASAP (Preprint)
 "PrimeGrid: a Volunteer Computing Platform for Number Theory", I. Bethune, International Conference on Computational Mathematics, Computational Geometry & Statistics (CMCGS) 2015, Jan 2015
 "CP2K Performance from Cray XT3 to XC30", I. Bethune, F. Reid, A. Lazzaro, Cray User Group 2014
 "Automated regression testing and code coverage analysis of the CP2K application", M. Misic, I. Bethune, M. Tomasevic, IEEE Seventh International Conference on Software Testing, Verification and Validation (ICST) 2014, p. 9598
 "Linear and nonlinear instability and ligament dynamics in 3D laminar twolayer liquid/liquid flows", L. O Naraigh, P. Valluri, D. Scott, I. Bethune, P. Spelt, Bulletin of the American Physical Society, Vol 58, 18, Nov 2013
 "A hybrid approach for extreme scalability when solving linear systems", N. Brown, M. Bull, I. Bethune, Exascale Applications and Software Conference (EASC), 2013
 "Extending the generalized Fermat prime search beyond one million digits using GPUs", I. Bethune, M. Goetz, Proceedings of the 10th International Conference on Parallel Processing and Applied Mathematics, PPAM 2013, Lecture Notes in Computer Science 8384, 106113, 2014 (Slides)
 "PRACE DECI (Distributed European Computing Initiative) Minisymposium, C. Johnson, A. Carter, I. Bethune, K. Stratford, M. Alava, V. Cardoso, M. Asif, B. S. A. Schuberth, T. Weinzierl, Applied Parallel and Scientific Computing Lecture Notes in Computer Science Volume 7782, 2013, pp 4360
 "Improving the performance of CP2K on the Cray XT", I. Bethune, Proceedings of the Cray User Group (2010), May 2010 (Slides)
Technical Reports & White Papers
 "Voxelbased finite element modelling with VOXFE2", N. Banglawala, I. Bethune, M. Fagan, R. Holbrey, ARCHER white paper, May 2015
 "Using RSIP Networking with Parallel Applications on ARCHER Phase 2", I. Bethune, ARCHER White Paper, Apr 2015
 "Optimising CP2K for the Intel Xeon Phi", F. Reid, I. Bethune, PRACE White Paper, 2013
 "Evaluating CP2K on Exascale Hardware: Intel Xeon Phi", F. Reid, I. Bethune, PRACE White Paper, 2013
 "Solving Large Sparse Linear Systems using Asynchronous Multisplitting", N. Brown, J. M. Bull, I. Bethune, PRACE White Paper, 2013
 "Performance Enhancement and Optimization of the TPLS and DIM TwoPhase Flow Solvers", D. Scott, L O Naraigh, I. Bethune, P. Valluri, P. Spelt, HECToR dCSE Report, Jun 2013
 "High Performance MP2 for Condensed Phase Simulations", R. Reyes, I. Bethune, PRACE White Paper, 2013
 "Adding Parallel I/O to PARABMU", N. Johnson, I. Bethune, HECToR dCSE Report, Oct 2012
 "Application Porting from External Developers", J. Labarta, I. Bethune, M. Garcia, V. Lopez. G. Rilley, TEXT Project Deliverable, Aug 2012
 "CP2K  Scalable Atomistic Simulations for the PRACE Community", I. Bethune, A. Carter, K. Stratford, P. Korosoglou, PRACE White Paper, 2012
 "CP2K  Sparse Linear Algebra on 1000s of Cores", I. Bethune, HECToR dCSE Report, Jan 2012
 "Million Atom KSDFT with CP2K", I. Bethune, A. Carter, X. Guo, P. Korosoglou, PRACE White Paper, 2011
 "Improving the scalability of CP2K on multicore systems", I. Bethune, HECToR dCSE Report, Sep 2010
 "Improving the performance of GWW", I. Bethune, HECToR dCSE Report, Aug 2009
 "Improving the performance of CP2K on HECToR", I. Bethune, HECToR dCSE Report, Jul 2009
 "Parallel Visualisation on HPCx", I. Bethune, HPCx Technical Report, Apr 2008
Posters
 "ExTASY: A pythonbased Extensible Toolkit for Advanced Sampling and Analysis in Biomolecular Simulation", A. Shkurti, C. Laughton, R. Goni, I. Bethune, E. Breitmoser, S. Jha, V. Balasubramanian, C. Clementi, B. Leimkuhler, P. Parpas, M. Maggioni, EuroSciPy 2015, Aug 2015
 "Developing a scalable and flexible code for highresolution DNS of twophase flows", I. Bethune, T. Collis, M. Jackson, L. O Naraigh, P. Valluri, 14th UK Heat Transfer Conference 2015, Sep 2015
 "Introduction to CP2K: a first principles electronic structure simulation package", L. Tong, M. Watkins, I. Bethune, L. Kantorovich, ASSIMEX 2015, Jun 2015
 "Developing a scalable and flexible code for highresolution DNS of twophase flows", I. Bethune, T. Collis, M. Jackson, L. O Naraigh, P. Valluri, D. Scott, PRACE Scientific and Industrial Conference 2015, May 2015
 "CP2KUK: Supporting Advances in Atomistic Simulation Capability", I. Bethune, J. Nowell, F. Reid, L. Kantorovich, L. Tong, M. Watkins, B. Slater, Exascale Applications and Software Conference (EASC) 2015, Apr 2015
 "Developing a scalable and flexible code for highresolution DNS of twophase flows", I. Bethune, T. Collis, M. Jackson, L. O Naraigh, P. Valluri, D. Scott, Exascale Applications and Software Conference (EASC) 2015, Apr 2015 * Poster Prize Winner *
 "MIST: Molecular Integration Simulation Toolkit", I. Bethune, E. Breitmoser, G. Gobbo, C. Matthews, B. Leimkuhler, Computational Molecular Science 2015, Mar 2015
 "CP2KUK: Supporting Advances in Atomistic Simulation Capability", I. Bethune, J. Nowell, F. Reid, L. Kantorovich, L. Tong, M. Watkins, B. Slater, Computational Molecular Science 2015, Mar 2015
 "Putting ExTASY in charge of an arduous computational challenge", A. Shkurti, C. Laughton, R. Goni, I. Bethune, E. Breitmoser, S. Jha, C. Clementi, B. Leimkuhler, P. Parpas, M. Maggioni, Women in HPC Workshop, Supercomputing 2014, Nov 2014
 "Implementation of Filter Matrix Diagonalisation", L. Tong, M. Watkins, I. Bethune, L. Kantorovich, CompMat2014, Sep 2014
 "Acceleration of Diagrammatic Determinantal Quantum Monte Carlo Calculations using GPUs", M. Schmitt, I. Bethune, P. Haase, T. Pruschke, DPG Fruhjahrstagung, Apr 2014
 "Developing a UserCentric CP2K Benchmark Suite", F. Reid, I. Bethune, CSC Spring School in Computational Chemistry, Feb 2014
 "CP2K: Capability and Scalability", I. Bethune, Exascale Applications and Software Conference (EASC) 2013, Apr 2013
 "High Performance Computing with CP2K", I. Bethune, CAMD Summer School on Electronic Structure Theory and Materials Design, Aug 2012
 "High Performance Computing with CP2K", I. Bethune, CCP5 Summer School in Molecular Simulation, Jul 2012
 HeriotWatt Crucible Bio Poster, I. Bethune, Feb 2012
Other
 "Modelling the Universe with Supercomputers: From nanometers to lightyears", Dundee Science Festival, Nov 2015
 "Seventeen or Bust: Solving hard mathematical problems with your help!", British Science Festival, Sep 2014 (Video)
 "HighPerformance Computing", Omega Tau Podcast Episode, Aug 2014
 "Porting CP2K to the Intel Xeon Phi", ARCHER Technical Forum Webinar, July 2014, (Slides)
 "CP2K: Scalable atomistic simulation on HECToR", HECToR dCSE Technical Meeting, Mar 2014, (Slides)
 "PrimeGrid: Searching for a New World Record Prime Number", Mathematics Today, Vol: 49 No. 6 Dec 2013, 250251
 "PrimeGrid: Join in the search for a world record prime number", British Science Festival, Sep 2013 (Slides, Audio)
 "Density Functional Theory for Dummies", EPCC Seminar, Jun 2013, (Slides)
 "Research in a Nutshell", 1 minute Video, Feb 2012
 "Prime Numbers, Large Integer Arithmetic, and a 2PF Task Farm", EPCC Seminar, Sep 2011, (Slides, Audio)
 "Mixedmode Parallelism in CP2K: A Case Study", DEISA/PRACE Spring School, Mar 2011, (Slides)
 Project highlights videos, 2011  HPC Europa, OGSADAI
 "Improving the scalability of Domain Decomposition within CP2K", HECToR dCSE Technical Meeting, Sep 2009 (Slides)
Supervision of Research Projects
 "Porting of GHGCUDA over GPU", S. Tiwari, MSc in HPC, 2015
 "Dynamic Load Balancing in CP2K", P. Shividasan, MSc in HPC, 2014
 "Multiplatform parallel code coverage and regression testing with CP2K", M. Misic, PRACE Summer of HPC, 2013 (Video)
 "Diagrammatic Determinantal Quantum Monte Carlo Calculations on GPUs", M. Schmitt, MSc in HPC, 2013
 "Accelerated Primality Testing Using GPUs", D. McBain, MSc in HPC, 2013
 "Improving the Computing Efficiency of the Regional Genomic Relationship Mapping Approach", J. C. Ortuno, MSc in HPC, 2012
 "Optimising the DBCSR GPU Implementation", J. Chetty, MSc in HPC, 2011
 "Getting to know the LLVM compiler", G. Ye, MSc in HPC, 2011
 "Investigation into hardware acceleration of HPC kernels, within a cross platform OpenCL environment", S. Fraser, MSc in HPC, 2010
 "GPU Acceleration of HPC Applications", A. Richardson, MSc in HPC, 2009
 "Optimising EM", J. Read, MSc in HPC, 2009
Software
A list of programs which Iain has contributed to the development of:
 CP2K  Highly scalable, modular, open source molecular dynamics program, featuring wide range of force evaluation methods from potentials, linear scaling DFT, HartreeFock and MP2. Large, distributed developer community led by Prof. Joost VandeVondele (ETH Zurich) and Prof. Jurg Hutter (University of Zurich).
 TPLS  CFD software for ultrahigh resolution DNS of turbulent twophase flows, developed by Dr. Prash Valluri and Dr. Lennon O Naraigh.
 VOXFE  Finite Element Analysis software for voxel data sets. Targetted at mechanical properties of bones. Developed in collaboration with Prof. Michael Fagan's group at University of Hull.
 Quantum Espresso  Popular suite of open source codes for materials science. Mainly developed in Italy (DEMOCRITOS, SISSA, CINECA).
 GULP  Lattice dynamics code development by Julian Gale, Curtin University
 LSDMap  Analysis software for automatic determination of collective variables for MD trajectory data. Developed by Prof. Cecilia Clementi's group, Rice University
 Genefer  Programs for finding large Generalized Fermat Primes. Developed in collaboration with Yves Gallot and various others from the PrimeGrid project.
 PRPNet  A client/server application for prime search projects, developed by Mark Rodenkirch and used by PrimeGrid
 LLR  A program for perfoming efficient LLR, Proth, N+/1 and similar tests on x86 CPUs. Developed by Jean Penne and used by PrimeGrid. BOINC wrappers for LLR provided by Iain Bethune
Funding
A list of grants which Iain has held:
Project Name  Role  Source  Start  End  Value 
CP2K  scalable Density Functional Theory  Coproposer  ARCHER eCSE  Dec15    £87,000 
VOXFE  new functionality for new communities  Coproposer  ARCHER eCSE  Apr15    £21,700 
Local excitement in CP2K  Coproposer  ARCHER eCSE  Dec15    £120,000 
Large scale voxel based modelling  Coproposer  ARCHER eCSE  May14  Mar15  £50,700 
TPLS: Optimised Parallel I/O and Visualisation  Coproposer  ARCHER eCSE  Apr14  Jan15  £57,900 
SI2CHE: Collaborative Research: Developing First Principles Monte Carlo Methods for Reactive Phase and Sorption Equilibria in the CP2K Software Suite  CoI  EPSRC  Sep13    £15,000 
CP2KUK  PI  EPSRC  Jul13    £247,000 
SI2CHE: ExTASY: Extensible Tools for Advanced Sampling and analYsis  CoI  EPSRC  Jul13    £277,000 
Modelling Complex Oxides using CP2K on Intel Xeon Phi  Proposer  PRACE1IP Ext.  Jul13  Dec13  6 personmonths 
Boiling in microchannels: integrated design of closedloop cooling system for devices operating at high heat fluxes  Project Partner  EPSRC  May13  Oct13  £23,000 
Evaluating CP2K on Exascale Hardware: Intel Xeon Phi  Proposer  PRACE3IP  Jan13  Jun13  6 personmonths 
Performance enhancement and optimization of the TPLS and DIM twophase flow solvers  Coproposer  HECToR dCSE  Sep12  Apr13  £75,000 
High Performance MP2 for Condensed Phase Simulations  Coproposer  PRACE2IP  Apr12  Oct12  6 personmonths 
Adding Parallel I/O to PARABMU  Coproposer  HECToR dCSE  Feb12  Sep12  £39,000 
HPC simulations of complex solids and clusters using static lattice techniques  CoI  EPSRC  Oct11  Sep13  £75,000 
CP2K: Scalable Atomistic Simulation for the PRACE community  Coproposer  PRACE1IP  Jun11  Jun12  10 personmonths 
Million Atom KSDFT with CP2K  Coproposer  PRACE1IP  Dec10  May11  6 personmonths 
CP2K  Sparse Linear Algebra on 1000s of cores  Coproposer  HECToR dCSE  Oct10  Dec11  £56,000 
Improving the performance of GWW  Coproposer  HECToR dCSE  Feb10  May10  £38,000 
Improving the scalability of CP2K on multicore systems  Coproposer  HECToR dCSE  Sep09  Sep10  £56,000 
Impacts
A nonexhaustive list of research highlights from Iain's collaborators:
 Dr. Ben Slater and others at UCL use CP2K to study the properties of ice crystasl surfaces e.g. Large variation of vacancy formation energies in the surface of crystalline ice", Watkins, Pan, Wang, Michaelides, VandeVondele and Slater, Nature Materials 10, 794798 (2011), "Point defects at the ice (0001) surface", Watkins, VandeVondele and Slater, Proceedings of the National Academy of Sciences of the USA 107(28), 1242912434 (2010)
 Prof. Joost VandeVondele and colleagues in Zurich found a mechaism for regeneration of coatings of dyesensitised solar cells using atomistic simulation with CP2K  "An atomistic picture of the regeneration process in dye sensitized solar cells"  Shiffmann, VandeVondele, Hutter, Urakawa, Wirz and Baiker, Proceedings of the National Academy of Sciences of the USA 107(11), 48304833 (2010)
 Dr. Carole Morrison from Edinburgh University's School of Chemisty studies proton transport through pores in biological membranes using CP2K  Simulating Proton Transport through a Simplified Model for TransMembrane Proteins, Shepherd and Morrison, J. Phys. Chem. B 114(20), 70477055 (2010)
 Prof. Michael Fagan's group use VOXFE to study the biomechanical properties of bones  "Why do humans have chins? Testing the mechanical significance of modern human symphyseal morphology with finite element analysis.", Groning, Liu, Fagan and O'Higgins, Americal Journal of Physics Anthropology 144, 593606 (2011)
 Prof. Merlyne De Souza uses Quantum Espresso to calculate the electronic structure and properties of carbon nanotubes, with applications in device electronics  "Role of hybridization on the Schottky barrier height of carbon nanotube field effect transistors", Casterman, De Souza, Tahraoui, Durkan and Milne, Phys. Rev. B 79 (2009)
 Prof. Cecilia Clementi's research group are applying the Locallyscaled Diffusion Map method using LSDMap to determine the fundamental dynamics of a wide variety of macromolecular systems e.g. "Polymer reversal rate calculated via locally scaled diffusion map", Zheng, Rohrdanz, Maggioni and Clementi, J. Chem Phys. 134 (2011)
Employment & Education
2012  Present 
Project Manager, EPCC, The University of Edinburgh 
2008  2012 
HPC Applications Consultant, EPCC, The University of Edinburgh 
2005  2008 
Software Engineer, IBM United Kingdom Ltd. 
2001  2005 
BSc. (Hons) 1st Class, Computer Science and Physics, The University of Edinburgh 