Profile
Dr Pedro Gonnet
Lecturer in the School of Engineering and Computing Sciences
Telephone: +44 (0) 191 33 42519
Room number: E113
(email at pedro.gonnet@durham.ac.uk)
Bibliometric Information
- ISI ResearcherID A-6935-2008
- Google Scholar entry
Biography
Pedro Gonnet is a Lecturer in Computer Science in the School of Engineering and Computing Sciences at Durham University. He recieved a Diploma from the Department of Computer Science at the ETH Zürich in 2003 and later a PhD in Computer Science, under the supervision of Prof. Walter Gander, in 2009.
Following his PhD, he worked as a Post-Doctoral researcher in the group of Prof. Jörg Stelling at the ETH Zürich before moving to Oxford University, to work with Prof. L. N. Trefethen as a member of the Chebfun development team with funding from the Swiss National Science Foundation.
Research
My research, in a nutshell, focuses on new algorithms for scientific computing on massively parallel shared-memory architectures.
In the past few years, we have witnessed an important paradigm shift in computer architecture: Although Moore's Law is still in effect, instead of getting faster, computers are getting more parallel. Most methods and algorithms in the computational sciences, however, were designed for single-processor machines or clusters thereof and do not readily lend themselves for shared-memory multi/many-core parallelization, SIMD-vectorization or GPU computing. In order to exploit this new paradigm, algorithms and methods designed specifically for these new architectures are urgently needed.
My research is centered around generalized approaches to shared-memory parallelization which avoid concurrency implicitly. More specifically, this is applied to Molecular Dynamics and Smoothed-Particle Hydrodynamics (SPH) simulations on multi-core and GPU architectures, and Numerical Linear Algebra on GPUs.
For more information, please visit the Desktop-HPC Group page here.
Software
- mdcore: A platform-independent, Open-Source library for Molecular Dynamics simulations on shared-memory and GPU architectures.
- odeSD: Second-Derivative ODE Integrator with parameter sensitivity analysis.
- quadcc: Robust, doubly-adaptive quadrature routine using Clenshaw-Curtis rules with an improved error estimate.
- Chebfun: I am a member of the Chebfun Developer Team.
Research Groups
School of Engineering and Computing Sciences
- Innovative Computing Research Group
Department of Computer Science
- Innovative Computing
Research Interests
- Algorithms for Systems Biology
- GPU Computing
- High-Performance Computing
- Hybrid Shared/Distributed-Memory Parallelism
- Numerical Algorithms for Interpolation and Approximation
- Particle-Based Simulations
Selected Publications
Books: sections
- Friberg, Markus T., Gonnet, Pedro, Barral, Yves, Schraudolph, Nicol N. & Gonnet, Gaston H. (2006). Measures of codon bias in yeast, the tRNA Pairing Index and possible DNA repair mechanisms. In Algorithms in Bioinformatics. Bucher, P & Moret, BME 4175: 1.
Conference papers
- Gonnet, Pedro (2010), Efficient Algorithms for Molecular Dynamics Simulations on the Cell Broadband Engine Architecture, in Psihoyios, G & Tsitouras, C eds, 1281: NUMERICAL ANALYSIS AND APPLIED MATHEMATICS. Rhodes, Greece, AIP, 1305.
Journal papers: academic
- Gonnet, P. (2013). Pseudo-Verlet lists: a new, compact neighbour list representation. Molecular Simulation 1.
- Gonnet, Pedro (2012). A Review of Error Estimation in Adaptive Quadrature. ACM Computing Surveys 44(4): 1.
- Gonnet, P. (2012). A short note on the fast evaluation of dihedral angle potentials and their derivatives. Journal of Computational Physics 231(7): 2691.
- Gonnet, P., Dimopoulos, S., Widmer, L. & Stelling, J. (2012). A Specialized ODE Integrator for Efficient Computation of Parameter Sensitivities. BMC Systems Biology 6: 46.
- Pachón, R., Gonnet, P. & van Deun, J. (2012). Fast and Stable Rational Interpolation in Roots of Unity and Chebyshev Points. SIAM Journal on Numerical Analysis 50(3): 1713-1734.
- Gonnet, Pedro (2012). Pairwise Verlet Lists: Combining Cell Lists and Verlet Lists to Improve Memory Locality and Parallelism. Journal of Computational Chemistry 33(1): 76-81.
- Gonnet, Pedro, Güttel, Stefan & Trefethen, Lloyd N (2012). Robust Padé approximation via SVD. SIAM Review 55(1): 101-117.
- Webb, Marcus, Trefethen, Lloyd N. & Gonnet, Pedro (2012). Stability of Barycentric Interpolation Formulas for Extrapolation. SIAM Journal on Scientific Computing 34(6): A3009-A3015.
- Gonnet, P., Pachón, R. & Trefethen, L.N. (2011). Robust Rational Interpolation and Least-Squares. Electronic Transactions on Numerical Analysis 38: 146-167.
- Cannarrozzi, Gina, Schraudolph, Nicol N., Faty, Mahamadou, von Rohr, Peter, Friberg, Markus T., Roth, Alexander C., Gonnet, Pedro, Gonnet, Gaston & Barral, Yves (2010). A Role for Codon Order in Translation Dynamics. Cell 141(2): 355-367.
- Gonnet, Pedro (2010). Increasing the Reliability of Adaptive Quadrature Using Explicit Interpolants. ACM Transactions on Mathematical Software 37(3): 26.
- Gonnet, P. (2010). Using piecewise polynomials for faster potential function evaluation. Journal of Computational Physics 229(2): 313.
- Gonnet, P., Walther, J.H. & Koumoutsakos, P. (2009). theta-SHAKE: An extension to SHAKE for the explicit treatment of angular constraints. Computer Physics Communications 180(3): 360.
- Gonnet, Pedro (2007). P-SHAKE: A quadratically convergent SHAKE in O(n(2). Journal of Computational Physics 220(2): 740.
- Gonnet, Pedro (2006). A simple algorithm to accelerate the computation of non-bonded interactions in cell-based molecular dynamics simulations. Journal of Computational Chemistry 28(2): 570.
- Zimmerli, Urs, Gonnet, Pedro, Walther, Jens & Koumoutsakos, Petros (2005). Curvature induced L-defects in water conduction in carbon nanotubes. Nano Letters 5(6): 1017.
- Gonnet, P., Rudd, KE. & Lisacek, F. (2004). Fine-tuning the prediction of sequences cleaved by signal peptidase II: A curated set of proven and predicted lipoproteins of Escherichia coli K-12. PROTEOMICS 4(6): 1597.
- Lisacek, F, Chichester, C, Gonnet, P, Jaillet, O, Kappus, S, Nikitin, F, Roland, P, Rossier, G, Truong, L & Appel, R (2004). Shaping biological knowledge: applications in proteomics. Comparative and Functional Genomics 5(2): 190.
- Jaffe, Richard L., Gonnet, Pedro, Werder, Thomas, Walther, Jens H. & Koumoutsakos, Petros (2004). Water-carbon interactions - 2: Calibration of potentials using contact angle data for different interaction models. Molecular Simulation 30(4): 205.
- Walther, JH., Werder, T., Jaffe, RL., Gonnet, P., Bergdorf, M., Zimmerli, U. & Koumoutsakos, P. (2004). Water-carbon interactions III: The influence of surface and fluid impurities. Physical Chemistry Chemical Physics 6(8): 1988.
- Gonnet, P. & Lisacek, F. (2002). Probabilistic alignment of motifs with sequences. Bioinformatics 18(8): 1091.