Dr. Iain Bethune
HPC Project Manager

Contact Details

Email:	iain@thebethunes.com
Mob:	+44 (0) 7598317015
Twitter:	@IainBethune
Skype:	iainbethune

Overview

Iain is an HPC Project Manager at Atos, managing delivery of High Performance Computing systems to customers across the Northern Europe region. He holds a PhD in Physics from the University of Edinburgh.

From January 2020 to February 2022, Iain was Head of Software Development at WRLD3D Ltd, a Scottish software company which provides a platform for building dynamic 3D mapping web, mobile and AR/VR apps for smart buildings and smart cities.

Between June 2017 and December 2019 Iain was Technical Programme Manager for the STFC Hartree Centre's Innovation Return on Research (IROR) programme. IROR was a 5 year joint research and development programme with IBM Research, aiming to produce an 18-24 month competitive advantage for UK industry, and to develop digital assets which can be exploited as part of other Hartree projects and collaborations.

From 2008 to 2017, Iain worked at EPCC, specialising in performance analysis and optimization of HPC applications. He collaborated with a range of researchers around the UK and Europe in fields as diverse as Computational Chemistry, Mathematics, Fluid Mechanics and Biomechanical Engineering, developing 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 Atomistic Simulation, 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.

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 ultra-marathon / trail running and is an avid space exploration and research enthusiast.

Previous Projects

• MIST - the Molecular Integration Simulation Toolkit is a software library which provides an API to several Molecular Dynamics codes, allowing simpler development of new integration algorithms for MD while still achieving good performance. Iain developed the library as part of his PhD.
• IROR - Innovation Return on Research is a 5-year collaborative research programme between STFC and IBM Research, with the goal of providing an 18-24 month competitive advantage to UK industry and developing a range of digital assets which can be deployed in future projects at the Hartree Centre. The programme engages with a wide range of companies in the broad areas of Chemistry, Life Sciences and Science, Engineering and Manufacturing.
• PrimeGrid - a volunteer computing project which promotes mass participation in the solution of mathematical problems, as well as finding very large - million digit - prime numbers.
• CP2K-UK - an EPSRC-funded 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. Iain leads the work, in collaboration with KCL, UCL, University of Lincoln and EPCC, in addition to many more group involved in the wider network.
• ARCHER eCSE: MIST - developing an MPI-parallel version of the Molecular Integration Simulation Toolkit.
• TPLS - collaboration with Dr. Prash Valluri (UoE Engineering) and Dr. Lennon O Naraigh (UCD) to implement more scalable solvers in their TPLS (Two-Phase Level Set) fluid dynamics code, which models the interface between two phases of a fluid using ultra-high resolution DNS. Various funding sources including HECToR dCSE / ARCHER eCSE, EPSRC grants and Impact Acceleration funding. Iain is a member of the Edinburgh Fluid Dynamics Group.
• 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.
• MSc in HPC - teaching Fast Fourier Transforms as part of 'Parallel Numerical Algorithms' and supervising dissertation projects.
• EPCC 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.
• ExTASY - we are developing an "Extensible Toolkit for Advanced Samping and analYsis" to couple novel algorithms for large time-step molecular dynamics, advanced analysis tools, and large scale ensemble calculations in order to overcome the Grand Challenge of effective sampling of complex macro-molecules. 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.
• CP2K-NSF - supporting UK-US 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 eCSE: LAMMPS - working with Prof. Jon Essex's group to implement their ELBA dual-resolution forcefield into LAMMPS.
• Greenhouse-GPU - a collaboration with University of Edinburgh and Bristol 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 auto-tuning and accelerator hardware.
• PRACE - as part of the Applications work package of PRACE, we are porting and optimisng CP2K for the Intel Xeon Phi co-processor architecture. Three previous projects under PRACE have also extended mixed-mode OpenMP parallelism in CP2K, and developed an auto-tuning framework for key computational kernels, to support efficient massively parallel MP2 calculations on the PRACE Tier-0 HPC resources.
• Novel Asynchronous Algorithms and Software for Large Sparse Systems - an EPSRC-funded 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 Heriot-Watt and Edinburgh Universties formed as a result of winning the Heriot-Watt Crucible in May 2012 to develop software for in-silico design and optimisation of micro-fluidic 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: VOX-FE - 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

• "MIST: A Simple and Efficient Molecular Dynamics Abstraction Library for Integrator Development", I. Bethune, R. Banisch, E. Breitmoser, A. B. K. Collis, G. Gibb, G. Gobbo, C. Matthews, G. J. Ackland, B. J. Leimkuhler, Computer Physics Communications Volume 236, March 2019, Pages 224-236 (arXiv)
• "CoCo-MD: A Simple and Effective Method for the Enhanced Sampling of Conformational Space", A. Shkurti, I. Styliari, V. Balasubramanian, I. Bethune, C. Pedebos, S. Jha, C. Laughton, ASAP in Journal of Chemical Theory and Computation
• How does blood regulate cerebral temperatures during hypothermia?", S. Blowers, I. Marshall, M. Thrippleton, P. J. Andrews, B. Harris, I. Bethune, P. Valluri, Scientific Reports 8, Article number 7877, May 2018
• "pyPcazip: a PCA-based Toolkit for Compression and Analysis of Molecular Simulation Data", A. Shkurti, R. Goni, P. Andrio, E. Breitmoser, I. Bethune, M. Orozco, C. Laughton, SoftwareX, Vol. 5, 2016, Pages 44–50
• "High-performance computational fluid dynamics: a custom-code approach", J. Fannon, J-C. Louiseau, P. Valluri, I. Bethune, L. O Naraigh, European Journal of Physics 37 045001, Apr 2016
• "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 three-dimensional laminar two-layer liquid/liquid flows", L. O Naraigh, P. Valluri, D. Scott, I. Bethune, P. Spelt, Journal of Fluid Mechanics, Jul 2014, 750: 464-506
• "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: 97-111
• "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. Steenman-Clark, B. Ralston, C. Laughton, Comp. Phys. Comm. Volume 183, Issue 3, March 2012, Pages 520-529

PhD Thesis

• "MIST: A Portable and Efficient Toolkit for Molecular Dynamics Integration Algorithm Development", I. Bethune, Aug 2020

Conference Papers / talks

• I. Bethune, Business Models for Materials Modelling Software, May 2019 * Invited Talk *
• "Two approaches to healthcare virtual agents", I. Bethune, D. Meredith, Think London 2018, Nov 2018 * Invited Talk *
• "CP2K-UK: EPSRC investment with international impact", I. Bethune, L. Kantorovich, M. Watkins, B. Slater, SSI Workshop: Impact of international research software collaboration, Apr 2018 (Slides)
• "HPC in the UK: a changing landscape?", I. Bethune, University of Hull HPC Symposium, Sep 2017 (Slides) * Invited Talk *
• "Porting of the DBCSR library for Sparse Matrix-Matrix Multiplications to Intel Xeon Phi systems", I. Bethune, A. Gloess, J. Hutter, A. Lazzaro, H. Pabst, F. Reid, International Conference on Parallel Computing (ParCo) 2017, Sep 2017 (Preprint)
• "CP2K-UK: Supporting Advances in Atomistic Simulation Capability", I. Bethune, New Approaches to Atomistic and Quantum Simulation of Materials, Jan 2017 (Slides)
• "Molecular Integration Simulation Toolkit - interfacing novel integrators with Molecular Dynamics codes", I. Bethune, Condensed Phase Simulations: Recent Advances in Theory and Applications - CCP5 Annual Conference 2016, Sep 2016 (Slides)
• "Molecular Integration Simulation Toolkit - interfacing novel integrators with Molecular Dynamics codes", I. Bethune, International Society of Quantum Biology and Pharmacology (ISQBP) President's Meeting 2016, Jun 2016 (Slides)
• "ExTASY: Scalable and Flexible Coupling of MD Simulations and Advanced Sampling Techniques", V. Balasubramanian, I. Bethune, A. Shkurti, E. Breitmoser, E. Hruska, C. Clementi, C. Laughton, S. Jha, IEEE 12th International Conference on eScience, 2016
• "Executing dynamic heterogeneous workloads on Blue Waters with RADICAL-Pilot", M. Santcroos, R. Castain, A. Merzky, I. Bethune, S. Jha, Cray User Group 2016
• "Interfacing novel integrators and existing Molecular Dynamics codes with the MIST library", I. Bethune, E. Breitmoser, A. B. K. Collis, G. Gobbo, B. J. Leimkuhler, Producing High Performance and Sustainable Software for Molecular Simulation Workshop, Supercomputing 2015, Nov 2015
• "Developing a scalable and flexible code for high-resolution DNS of two-phase flows", I. Bethune, 2nd ThermaPOWER Mini-symposium, 14th UK Heat Transfer Conference 2015, Sep 2015 * Invited Talk *
• "Developing a scalable and flexible high-resolution DNS code for two-phase flows", I. Bethune, T. Collis, L. O Naraigh, D. Scott, P. Valluri, in Parallel Computing: On the Road to Exascale, Advances in Parallel Computing Volume 27, Proceedings of the International Conference on Parallel Computing (ParCo) 2015, May 2016 (PDF version)
• "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. 95-98
• "Linear and nonlinear instability and ligament dynamics in 3D laminar two-layer 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, 106-113, 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 43-60
• "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

• "Implementation of Dual Resolution Simulation Methodology in LAMMPS", I. Bethune, S. Wheeler, S. Genheden, J. Essex, ARCHER white paper, Aug 2016
• "VOX-FE: New functionality for new communities", N. Banglawala, I. Bethune, M. Fagan, R. Holbrey, ARCHER white paper, Jun 2016
• "Voxel-based finite element modelling with VOX-FE2", 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 Two-Phase 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 PARA-BMU", 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 KS-DFT with CP2K", I. Bethune, A. Carter, X. Guo, P. Korosoglou, PRACE White Paper, 2011
• "Improving the scalability of CP2K on multi-core 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

• "CP2K-UK: EPSRC investment with international impact", I. Bethune, L. Kantorovich, M. Watkins, B. Slater, SSI Workshop: Impact of international research software collaboration, Apr 2018
• "CP2K: Highly scalable atomistic simulation for all", I. Bethune, G. Gibb, L. Kantorovich, M. Watkins, S. Chulkov, B. Slater, Exascale Applications and Software Conference (EASC) 2018, Apr 2018 (Lightning Talk)
• "Molecular Integration Simulation Toolkit: Interfacing novel integrators with Molecular Dynamics codes", I. Bethune, E. Breitmoser, A. Martinsson, Z. Trstanova, B. Leimkuhler, Computational Molecular Science (CMS) 2017, Mar 2017
• "CP2K-UK: Supporting Advances in Atomistic Simulation Capability", I. Bethune, G. Gibb, L. Kantorovich, M. Watkins, S. Chulkov, B. Slater, Computational Molecular Science (CMS) 2017, Mar 2017
• "CP2K-UK: Supporting Advances in Atomistic Simulation Capability", I. Bethune, L. Kantorovich, L. Tong, M. Watkins, S. Chulkov, B. Slater, New Approaches to Atomistic and Quantum Simulation of Materials, Jan 2017
• "Implementation of Dual Resolution Simulation Methodology in LAMMPS", I. Bethune, S. Wheeler, S. Genheden, J. Essex, New Approaches to Atomistic and Quantum Simulation of Materials, Jan 2017
• "Bespoke bone modelling with VOX-FE", N. Banglawala, I. Bethune, R. Holbrey, M. Fagan, Women in HPC Workshop, Supercomputing 2016, Nov 2016
• "CP2K-UK: Supporting Advances in Atomistic Simulation Capability", I. Bethune, L. Kantorovich, L. Tong, M. Watkins, S. Chulkov, B. Slater, Condensed Phase Simulations: Recent Advances in Theory and Applications - CCP5 Annual Conference 2016, Sep 2016
• "Implementation of Dual Resolution Simulation Methodology in LAMMPS", I. Bethune, S. Wheeler, S. Genheden, J. Essex, Condensed Phase Simulations: Recent Advances in Theory and Applications - CCP5 Annual Conference 2016, Sep 2016
• "Molecular Integration Simulation Toolkit - interfacing novel integrators with Molecular Dynamics codes", I. Bethune, E. Breitmoser, B. Leimkuhler, International Society of Quantum Biology and Pharmacology (ISQBP) President's Meeting 2016, Jun 2016
• "ExTASY: A python-based 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 high-resolution DNS of two-phase 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, AS-SIMEX 2015, Jun 2015
• "Developing a scalable and flexible code for high-resolution DNS of two-phase flows", I. Bethune, T. Collis, M. Jackson, L. O Naraigh, P. Valluri, D. Scott, PRACE Scientific and Industrial Conference 2015, May 2015
• "CP2K-UK: 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 high-resolution DNS of two-phase 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
• "CP2K-UK: 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 User-Centric 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
• Heriot-Watt Crucible Bio Poster, I. Bethune, Feb 2012

Other

• "Crowdsourced prime number could help solve a 50-year-old problem", Newscientist.com, Nov 2016
• "Modelling the Universe with Supercomputers: From nanometers to light-years", Dundee Science Festival, Nov 2015
• "Seventeen or Bust: Solving hard mathematical problems with your help!", British Science Festival, Sep 2014 (Video)
• "High-Performance 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, 250-251
• "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)
• "Mixed-mode Parallelism in CP2K: A Case Study", DEISA/PRACE Spring School, Mar 2011, (Slides)
• Project highlights videos, 2011 - HPC Europa, OGSA-DAI
• "Improving the scalability of Domain Decomposition within CP2K", HECToR dCSE Technical Meeting, Sep 2009 (Slides)
• "Simulation of Radiation Damage to Metals", BSc. Dissertation Project Report, Mar 2005

Supervision of Research Projects

• "Assessing the Performance of Optimised Primality Tests", C. Curry, MSc in HPC, 2016
• "Porting the Essential Dynamics/Molecular Dynamics method for large-scale nucleic acid simulations to ARCHER", J. Si, MSc in HPC, 2016
• "Data Intensive Analysis on ARCHER and on Amazon Web Services: A case study of DNA Trajectory", K.Y. Tey, MSc in HPC, 2016
• "Porting of GHG-CUDA over GPU", S. Tiwari, MSc in HPC, 2015
• "Dynamic Load Balancing in CP2K", P. Shividasan, MSc in HPC, 2014
• "Multi-platform 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

• AP26 - Programs for finding large chains of primes in arithmetic progression. Developed by Bryan Little and others, and used by PrimeGrid.
• BOINC - the Berkeley Open Infrastructure for Network Computing. Used by PrimeGrid and many other projects.
• CP2K - Highly scalable, modular, open source molecular dynamics program, featuring wide range of force evaluation methods including classical potentials, linear scaling DFT, Hartree-Fock, MP2 and GW. Large, distributed developer community led by Prof. Joost VandeVondele (ETH Zurich) and Prof. Jurg Hutter (University of Zurich).
• GCWSieve - Fixed-b sieving code for Generalised Cullen and Woodall numbers n*b^n+/-1. Originally developed by Geoffrey Reynolds, maintained and update for PrimeGrid's current GCW prime search.
• Genefer - Programs for finding large Generalized Fermat Primes. Developed in collaboration with Yves Gallot and various others from the PrimeGrid project.
• GULP - Lattice dynamics code development by Julian Gale, Curtin University
• LAMMPS - the Large-scale Atomic/Molecular Massively Parallel Simulator, a classical molecular dynamics code.
• 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.
• LSDMap - Analysis software for automatic determination of collective variables for MD trajectory data. Developed by Prof. Cecilia Clementi's group, Rice University
• PRPNet - A client/server application for prime search projects, developed by Mark Rodenkirch and used by PrimeGrid.
• TPLS - CFD software for ultra-high resolution DNS of turbulent two-phase flows, developed by Dr. Prash Valluri and Dr. Lennon O Naraigh.
• Quantum Espresso - Popular suite of open source codes for materials science. Mainly developed in Italy (DEMOCRITOS, SISSA, CINECA).
• VOX-FE - 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.

Funding

Employment & Education