ASTRA kernelkit: GPU-accelerated projectors for computed tomography using cupy
A. Graas, W. J. Palenstijn, B. van Werkhoven, F. Lucka
Applied Mathematics for Modern Challenges 2024
FAIR Sharing of Data in Autotuning Research (Vision Paper)
J. Hozzová, J. O. Tørring, B. van Werkhoven, D. Střelák, R. Vuduc
International Conference on Performance Engineering (ICPE) 2024
Kernel Launcher: C++ library for creating optimal-performance portable CUDA applications
S. Heldens, B. van Werkhoven
International Workshop on Automatic Performance Tuning (iWAPT2023) co-located with IPDPS 2023
Towards a Benchmarking Suite for Kernel Tuners
J. Odgård Tørring, B. van Werkhoven, F. Petrovič, F.J. Willemsen, J. Filipovič, A. C. Elster
International Workshop on Automatic Performance Tuning (iWAPT2023) co-located with IPDPS 2023
Optimization Techniques for GPU Programming
P. Hijma, A. Sclocco, S. Heldens, B. van Werkhoven, H.E. Bal
ACM Computing Surveys 2023
Going green: optimizing GPUs for energy efficiency through model-steered auto-tuning
R. Schoonhoven, B. Veenboer, B. van Werkhoven, K. J. Batenburg
International Workshop on Performance Modeling, Benchmarking and Simulation of High Performance Computer Systems (PMBS) at Supercomputing (SC22) 2022
Benchmarking optimization algorithms for auto-tuning GPU kernels
R. Schoonhoven, B. van Werkhoven, K. J. Batenburg
IEEE Transactions on Evolutionary Computation 2022
litstudy: A Python package for literature reviews
S. Heldens, A. Sclocco, H. Dreuning, B. van Werkhoven, P. Hijma, J. Maassen, R. V. van Nieuwpoort
SoftwareX 2022
Lightning: Scaling the GPU Programming Model Beyond a Single GPU
S. Heldens, P. Hijma, B. van Werkhoven, J. Maassen, R. V. van Nieuwpoort
International Parallel and Distributed Processing Symposium (IPDPS) 2022
The eWaterCycle platform for open and FAIR hydrological collaboration
Rolf Hut, Niels Drost, Nick van de Giesen, Ben van Werkhoven, Banafsheh Abdollahi, Jerom Aerts, Thomas Albers, Fakhereh Alidoost, Bouwe Andela, Jaro Camphuijsen, Yifat Dzigan, Ronald van Haren, Eric Hutton, Peter Kalverla, Maarten van Meersbergen, Gijs van den Oord, Inti Pelupessy, Stef Smeets, Stefan Verhoeven, Martine de Vos, and Berend Weel
Geoscientific Model Development 2022
Bayesian Optimization for auto-tuning GPU kernels
F.J. Willemsen, R.V. van Nieuwpoort, B. van Werkhoven
International Workshop on Performance Modeling, Benchmarking and Simulation of High Performance Computer Systems (PMBS) at Supercomputing (SC21) 2021
3D particle averaging and detection of macromolecular symmetry in localization microscopy
H. Heydarian, M. Joosten, A. Przybylski, F. Schueder, R. Jungmann, B. van Werkhoven, J. Keller-Findeisen, J. Ries, S. Stallinga, M. Bates, B. Rieger
Nature Communications 2021
Rocket: Efficient and Scalable All-Pairs Computations on Heterogeneous Platforms
S. Heldens, P. Hijma, B. van Werkhoven, J. Maassen, H.E. Bal, and R.V. van Nieuwpoort
Supercomputing (SC20) 2020
The Landscape of Exascale Research: A Data-Driven Literature Analysis
S. Heldens, P. Hijma, B. van Werkhoven, J. Maassen, A.S.Z. Belloum, and R.V. van Nieuwpoort
ACM Computing Surveys (CSUR) 2020
Lessons learned in a decade of research software engineering GPU applications
B. van Werkhoven, W.J. Palenstijn, and A. Sclocco
SE4Science workshop at ICCS 2020
AMBER: A real-time pipeline for the detection of single pulse astronomical transients
A. Sclocco, S. Heldens, and B. van Werkhoven
SoftwareX 2020
ESiWACE2 Services: RSE collaborations in Weather and Climate
G. van den Oord, V. Azizi, A. Sclocco, G.E. Moulard, D. Guibert, J. Attema, E. Raffin, and B. van Werkhoven
Research Software Engineers in HPC (RSE-HPC-2020) Workshop at Supercomputing (SC20) 2020
Kernel Tuner: A search-optimizing GPU code auto-tuner
B. van Werkhoven
Future Generation Computer Systems 2019
Creating a Reusable Cross-Disciplinary Multi-scale and Multi-physics Framework: From AMUSE to OMUSE and Beyond
F.I. Pelupessy, S. Portegies Zwart, A. van Elteren, H.A. Dijkstra, F. Jansson, D. Crommelin, P. Siebesma, B. van Werkhoven, G. van den Oord
International Conference on Computational Science (ICCS) 2019
Template-Free 2D Particle Fusion in Localization Microscopy
H. Heydarian, F. Schueder, M.T. Strauss, B. van Werkhoven, M. Fazel, K.A. Lidke, R. Jungmann, S. Stallinga, and B. Rieger
Nature Methods 2018
Painting the Picture of Software Impact with the Research Software Directory
J. Spaaks, T. Klaver, S. Verhoeven, J. Maassen, T. Bakker, A. van der Ploeg, B. van Werkhoven, W. van Hage and R. van Nieuwpoort
9th International Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE6.1) 2018
Survey on Research Software Engineering in the Netherlands
B. van Werkhoven, T. Bakker, O. Philippe, and S. Hettrick
9th International Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE6.1) 2018
A Jungle Computing approach to common image source identification in large collections of images
B. van Werkhoven, P. Hijma, C.J.H. Jacobs, J. Maassen, Z.J.M.H. Geradts, and H.E. Bal
Digital Investigation 2018
The Oceanographic Multipurpose Software Environment (OMUSE v1.0)
I. Pelupessy, B. van Werkhoven, A.K. van Elteren, J. Viebahn, A. Candy, S.F. Portegies Zwart, and H.A. Dijkstra
Geoscientific Model Development 2017
Clustering image noise patterns by embedding and visualization for common source camera detection
S. Georgievska, R. Bakhshi, A. Gavai, A. Sclocco, and B. van Werkhoven
Digital Investigation 2017
Changes in extreme regional sea level under global warming
S.E. Brunnabend, H.A. Dijkstra, M.A. Kliphuis, H.E Bal, F.J. Seinstra, B. van Werkhoven, J. Maassen, M. van Meersbergen
Ocean Science 2017
On the complexities of utilizing large-scale lightpath-connected distributed cyberinfrastructure
J. Maassen, B. van Werkhoven, M. van Meersbergen, H.E Bal, M. Kliphuis, S.E. Brunnabend, H.A. Dijkstra, et al.
Concurrency and Computation: Practice and Experience 2016
An integrated approach to porting large scientific applications to GPUs
B. van Werkhoven, P. Hijma
11th IEEE International Conference on eScience 2015
Performance models for CPU-GPU data transfers
B. van Werkhoven, J. Maassen, F.J. Seinstra, H.E. Bal
14th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGRID) 2014
Optimizing convolution operations on GPUs using adaptive tiling
B. van Werkhoven, J. Maassen, H.E. Bal, F.J. Seinstra
Future Generation Computer Systems 2014
A distributed computing approach to improve the performance of the Parallel Ocean Program (v2. 1)
B. van Werkhoven, J. Maassen, M. Kliphuis, H.A. Dijkstra, S.E. Brunnabend, M. van Meersbergen, F. J. Seinstra, H.E. Bal
Geoscientific Model Development 2014
Changes in extreme regional sea surface height due to an abrupt weakening of the Atlantic meridional overturning circulation
S.E. Brunnabend, H.A. Dijkstra, M.A Kliphuis, B. van Werkhoven, H.E. Bal, F.J. Seinstra, J. Maassen, M. van Meersbergen
Ocean Science 2014
User transparent data and task parallel multimedia computing with Pyxis-DT
T. van Kessel, B. van Werkhoven, N. Drost, J. Maassen, H.E. Bal, F.J. Seinstra
Future Generation Computer Systems 2013
Jungle computing: Distributed supercomputing beyond clusters, grids, and clouds
F.J. Seinstra, J. Maassen, R.V. van Nieuwpoort, N. Drost, T. van Kessel, B. van Werkhoven, J. Urbani, C. Jacobs, T. Kielmann, H.E. Bal
Grids, Clouds and Virtualization 2011
Optimizing Convolution Operations in CUDA with Adaptive Tiling
B. van Werkhoven, J. Maassen, F.J. Seinstra
2nd Workshop on Applications for Multi and Many Core Processors (A4MMC 2011) 2011
Towards user transparent parallel multimedia computing on GPU-clusters
B. van Werkhoven, J. Maassen, F.J. Seinstra
1st Workshop on Applications for Multi and Many Core Processors (A4MMC 2010) 2010