Selected publications

When writing an HPC compute time application, you can strengthen your case by citing papers that have used your software on a cluster or in a HPC facility (with number of node hours, particles, etc.) to show its relevance to the HPC field. When applying for benchmark or development access, it can be beneficial to cite prior HPC work carried out with the software outlined in the proposal.

The following sections list relevant HPC literature filtered by topics.

Software

HPC method development: ESPResSo

[esDev-1]

Jean-Noël Grad, Alexander Reinauer, Christian Holm, and Rudolf Weeber. Pathway to exascale: experiences in adopting more scalable algorithms in ESPResSo. In deRSE24 – 4^th conference for Research Software Engineering in Germany. Zenodo, March 2024. doi:10.5281/zenodo.10806020.

[esDev-2]

Jean-Noël Grad and Rudolf Weeber. Report on the current scalability of ESPResSo and the planned work to extend it. MultiXscale Deliverable 2.1, EuroHPC Centre of Excellence MultiXscale, September 2023. doi:10.5281/zenodo.8420222.

[esDev-3]

Steffen Hirschmann. Load-Balancing for Scalable Simulations with Large Particle Numbers. PhD thesis, University of Stuttgart, July 2021. doi:10.18419/opus-11796.

[esDev-4]

Steffen Hirschmann, Malte Brunn, Michael Lahnert, Colin W. Glass, Miriam Mehl, and Dirk Pflüger. Load balancing with p4est for short-range molecular dynamics with ESPResSo. In Sanzio Bassini, Marco Danelutto, Patrizio Dazzi, Gerhard R. Joubert, and Frans Peters, editors, Parallel Computing is Everywhere, volume 32 of Advances in Parallel Computing, pages 455–464. IOS Press, Amsterdam, Netherlands, March 2018. doi:10.3233/978-1-61499-843-3-455.

[esDev-5]

Steffen Hirschmann, Colin W. Glass, and Dirk Pflüger. Enabling unstructured domain decompositions for inhomogeneous short-range molecular dynamics in ESPResSo. The European Physical Journal Special Topics, 227(14):1779–1788, March 2019. doi:10.1140/epjst/e2019-800159-0.

[esDev-6]

Steffen Hirschmann, Michael Lahnert, Carolin Schober, Malte Brunn, Miriam Mehl, and Dirk Pflüger. Load-balancing and spatial adaptivity for coarse-grained molecular dynamics applications. In Wolfgang E. Nagel, Dietmar H. Kröner, and Michael M. Resch, editors, High Performance Computing in Science and Engineering '18, pages 409–423. Springer International Publishing, Cham, Switzerland, June 2019. doi:10.1007/978-3-030-13325-2_26.

[esDev-7]

Steffen Hirschmann, Dirk Pflüger, and Colin W. Glass. Towards understanding optimal load-balancing of heterogeneous short-range molecular dynamics. In Proceedings of the IEEE 23^rd International Conference on High Performance Computing Workshops (HiPCW), 130–141. Los Alamitos, California, USA, 2016. IEEE. doi:10.1109/HiPCW.2016.027.

[esDev-8]

Michael Lahnert, Carsten Burstedde, Christian Holm, Miriam Mehl, Georg Rempfer, and Florian Weik. Towards lattice-Boltzmann on dynamically adaptive grids — minimally-invasive grid exchange in ESPResSo. In M. Papadrakakis, V. Papadopoulos, G. Stefanou, and V. Plevris, editors, Proceedings of the ECCOMAS Congress, 2566–2590. 2016. doi:10.7712/100016.1982.4659.

HPC simulations: ESPResSo

[esHPC-1]

Steffen Hirschmann, Andreas Kronenburg, Colin W. Glass, and Dirk Pflüger. Load-balancing for large-scale soot particle agglomeration simulations. In Ian Foster, Gerhard R. Joubert, Luděk Kučera, Wolfgang E. Nagel, and Frans Peters, editors, Parallel Computing: Technology Trends, volume 36 of Advances in Parallel Computing, pages 147–156. IOS Press, Amsterdam, Netherlands, March 2020. doi:10.3233/APC200035.

[esHPC-2]

Roman Staňo, Jéré van Lente, Saskia Lindhoud, and Peter Košovan. Sequestration of small ions, weak acids and bases by polyelectrolyte complex studied by simulation and experiment. ChemRxiv, June 2023. doi:10.26434/chemrxiv-2023-6q159.

HPC simulations: GROMACS

[gmxHPC-1]

Simon Gravelle, Christian Holm, and Alexander Schlaich. Transport of thin water films: from thermally activated random walks to hydrodynamics. The Journal of Chemical Physics, 157(10):104702, September 2022. doi:10.1063/5.0099646.

[gmxHPC-2]

Johannes Zeman, Svyatoslav Kondrat, and Christian Holm. Bulk ionic screening lengths from extremely large-scale molecular dynamics simulations. Chemical Communications, 56(100):15635–15638, December 2020. doi:10.1039/d0cc05023g.

[gmxHPC-3]

Johannes Zeman, Svyatoslav Kondrat, and Christian Holm. Ionic screening in bulk and under confinement. The Journal of Chemical Physics, 155(20):204501, November 2021. doi:10.1063/5.0069340.

HPC simulations: LAMMPS

[lammpsHPC-1]

Simon Gravelle, Christian Holm, and Alexander Schlaich. Transport of thin water films: from thermally activated random walks to hydrodynamics. The Journal of Chemical Physics, 157(10):104702, September 2022. doi:10.1063/5.0099646.

Institutes

HPC at the ICP

[ICP-1]

Jean-Noël Grad, Alexander Reinauer, Christian Holm, and Rudolf Weeber. Pathway to exascale: experiences in adopting more scalable algorithms in ESPResSo. In deRSE24 – 4^th conference for Research Software Engineering in Germany. Zenodo, March 2024. doi:10.5281/zenodo.10806020.

[ICP-2]

Jean-Noël Grad and Rudolf Weeber. Report on the current scalability of ESPResSo and the planned work to extend it. MultiXscale Deliverable 2.1, EuroHPC Centre of Excellence MultiXscale, September 2023. doi:10.5281/zenodo.8420222.

[ICP-3]

Simon Gravelle, Christian Holm, and Alexander Schlaich. Transport of thin water films: from thermally activated random walks to hydrodynamics. The Journal of Chemical Physics, 157(10):104702, September 2022. doi:10.1063/5.0099646.

[ICP-4]

Michael Kuron, Philipp Stärk, Christian Holm, and Joost de Graaf. Hydrodynamic mobility reversal of squirmers near flat and curved surfaces. Soft Matter, 15(29):5908–5920, July 2019. doi:10.1039/C9SM00692C.

[ICP-5]

Michael Lahnert, Carsten Burstedde, Christian Holm, Miriam Mehl, Georg Rempfer, and Florian Weik. Towards lattice-Boltzmann on dynamically adaptive grids — minimally-invasive grid exchange in ESPResSo. In M. Papadrakakis, V. Papadopoulos, G. Stefanou, and V. Plevris, editors, Proceedings of the ECCOMAS Congress, 2566–2590. 2016. doi:10.7712/100016.1982.4659.

[ICP-6]

Arndt Wagner, Elissa Eggenweiler, Felix Weinhardt, Zubin Trivedi, David Krach, Christoph Lohrmann, Kartik Jain, Nikolaos Karadimitriou, Carina Bringedal, Paul Voland, Christian Holm, Holger Class, Holger Steeb, and Iryna Rybak. Permeability estimation of regular porous structures: a benchmark for comparison of methods. Transport in Porous Media, 138(1):1–23, April 2021. doi:10.1007/s11242-021-01586-2.

[ICP-7]

Johannes Zeman, Svyatoslav Kondrat, and Christian Holm. Bulk ionic screening lengths from extremely large-scale molecular dynamics simulations. Chemical Communications, 56(100):15635–15638, December 2020. doi:10.1039/d0cc05023g.

[ICP-8]

Johannes Zeman, Svyatoslav Kondrat, and Christian Holm. Ionic screening in bulk and under confinement. The Journal of Chemical Physics, 155(20):204501, November 2021. doi:10.1063/5.0069340.

HPC at the IPVS

[IPVS-1]

Naveen Himthani, Malte Brunn, Jae-Youn Kim, Miriam Schulte, Andreas Mang, and George Biros. CLAIRE—parallelized diffeomorphic image registration for large-scale biomedical imaging applications. Journal of Imaging, 8(9):251, September 2022. doi:10.3390/jimaging8090251.

[IPVS-2]

Steffen Hirschmann. Load-Balancing for Scalable Simulations with Large Particle Numbers. PhD thesis, University of Stuttgart, July 2021. doi:10.18419/opus-11796.

[IPVS-3]

Steffen Hirschmann, Malte Brunn, Michael Lahnert, Colin W. Glass, Miriam Mehl, and Dirk Pflüger. Load balancing with p4est for short-range molecular dynamics with ESPResSo. In Sanzio Bassini, Marco Danelutto, Patrizio Dazzi, Gerhard R. Joubert, and Frans Peters, editors, Parallel Computing is Everywhere, volume 32 of Advances in Parallel Computing, pages 455–464. IOS Press, Amsterdam, Netherlands, March 2018. doi:10.3233/978-1-61499-843-3-455.

[IPVS-4]

Steffen Hirschmann, Colin W. Glass, and Dirk Pflüger. Enabling unstructured domain decompositions for inhomogeneous short-range molecular dynamics in ESPResSo. The European Physical Journal Special Topics, 227(14):1779–1788, March 2019. doi:10.1140/epjst/e2019-800159-0.

[IPVS-5]

Steffen Hirschmann, Michael Lahnert, Carolin Schober, Malte Brunn, Miriam Mehl, and Dirk Pflüger. Load-balancing and spatial adaptivity for coarse-grained molecular dynamics applications. In Wolfgang E. Nagel, Dietmar H. Kröner, and Michael M. Resch, editors, High Performance Computing in Science and Engineering '18, pages 409–423. Springer International Publishing, Cham, Switzerland, June 2019. doi:10.1007/978-3-030-13325-2_26.

[IPVS-6]

Steffen Hirschmann, Dirk Pflüger, and Colin W. Glass. Towards understanding optimal load-balancing of heterogeneous short-range molecular dynamics. In Proceedings of the IEEE 23^rd International Conference on High Performance Computing Workshops (HiPCW), 130–141. Los Alamitos, California, USA, 2016. IEEE. doi:10.1109/HiPCW.2016.027.

HPC at SimTech

[SimTech-1]

Simon Gravelle, Christian Holm, and Alexander Schlaich. Transport of thin water films: from thermally activated random walks to hydrodynamics. The Journal of Chemical Physics, 157(10):104702, September 2022. doi:10.1063/5.0099646.

[SimTech-2]

Steffen Hirschmann. Load-Balancing for Scalable Simulations with Large Particle Numbers. PhD thesis, University of Stuttgart, July 2021. doi:10.18419/opus-11796.

Clusters

Bee

Ehlers

bwUniCluster

[bwHPC-1]

Michael Kuron, Philipp Stärk, Christian Holm, and Joost de Graaf. Hydrodynamic mobility reversal of squirmers near flat and curved surfaces. Soft Matter, 15(29):5908–5920, July 2019. doi:10.1039/C9SM00692C.

Vulcan

[Vulcan-1]

Li Zhong, Oleksandr Shcherbakov, Dennis Hoppe, Michael Resch, and Bastian Koller. Towards seamless execution of deep learning application on heterogeneous HPC systems. In Gintautas Dzemyda, Jolita Bernatavičienė, and Janusz Kacprzyk, editors, Data Science in Applications, volume 1084 of Studies in Computational Intelligence, pages 233–252. Springer International Publishing, Cham, Switzerland, 2023. doi:10.1007/978-3-031-24453-7_11.

[Vulcan-2]

Huan Zhou, José Gracia, and Ralf Schneider. MPI collectives for multi-core clusters: optimized performance of the hybrid MPI+MPI parallel codes. In Workshop Proceedings of the 48^th International Conference on Parallel Processing. New York, New York, USA, August 2019. ACM. doi:10.1145/3339186.3339199.

[Vulcan-3]

HPCG. June 2020 HPCG results (High Performance Conjugate Gradients Benchmark project). In High Performance Computing 35^th International Conference, ISC High Performance 2020. June 2020. URL: https://www.hpcg-benchmark.org/custom/index.html%3Flid=155&slid=303.html.

HPE Hawk

Hazel Hen

[Hazel-1]

Steffen Hirschmann, Malte Brunn, Michael Lahnert, Colin W. Glass, Miriam Mehl, and Dirk Pflüger. Load balancing with p4est for short-range molecular dynamics with ESPResSo. In Sanzio Bassini, Marco Danelutto, Patrizio Dazzi, Gerhard R. Joubert, and Frans Peters, editors, Parallel Computing is Everywhere, volume 32 of Advances in Parallel Computing, pages 455–464. IOS Press, Amsterdam, Netherlands, March 2018. doi:10.3233/978-1-61499-843-3-455.

[Hazel-2]

Steffen Hirschmann, Colin W. Glass, and Dirk Pflüger. Enabling unstructured domain decompositions for inhomogeneous short-range molecular dynamics in ESPResSo. The European Physical Journal Special Topics, 227(14):1779–1788, March 2019. doi:10.1140/epjst/e2019-800159-0.

[Hazel-3]

Steffen Hirschmann, Michael Lahnert, Carolin Schober, Malte Brunn, Miriam Mehl, and Dirk Pflüger. Load-balancing and spatial adaptivity for coarse-grained molecular dynamics applications. In Wolfgang E. Nagel, Dietmar H. Kröner, and Michael M. Resch, editors, High Performance Computing in Science and Engineering '18, pages 409–423. Springer International Publishing, Cham, Switzerland, June 2019. doi:10.1007/978-3-030-13325-2_26.

[Hazel-4]

Steffen Hirschmann, Dirk Pflüger, and Colin W. Glass. Towards understanding optimal load-balancing of heterogeneous short-range molecular dynamics. In Proceedings of the IEEE 23^rd International Conference on High Performance Computing Workshops (HiPCW), 130–141. Los Alamitos, California, USA, 2016. IEEE. doi:10.1109/HiPCW.2016.027.

[Hazel-5]

Johannes Zeman, Svyatoslav Kondrat, and Christian Holm. Bulk ionic screening lengths from extremely large-scale molecular dynamics simulations. Chemical Communications, 56(100):15635–15638, December 2020. doi:10.1039/d0cc05023g.

[Hazel-6]

Johannes Zeman, Svyatoslav Kondrat, and Christian Holm. Ionic screening in bulk and under confinement. The Journal of Chemical Physics, 155(20):204501, November 2021. doi:10.1063/5.0069340.

[Hazel-7]

Huan Zhou, José Gracia, and Ralf Schneider. MPI collectives for multi-core clusters: optimized performance of the hybrid MPI+MPI parallel codes. In Workshop Proceedings of the 48^th International Conference on Parallel Processing. New York, New York, USA, August 2019. ACM. doi:10.1145/3339186.3339199.

Vega

[Vega-1]

Jean-Noël Grad, Alexander Reinauer, Christian Holm, and Rudolf Weeber. Pathway to exascale: experiences in adopting more scalable algorithms in ESPResSo. In deRSE24 – 4^th conference for Research Software Engineering in Germany. Zenodo, March 2024. doi:10.5281/zenodo.10806020.

[Vega-2]

Jean-Noël Grad and Rudolf Weeber. Report on the current scalability of ESPResSo and the planned work to extend it. MultiXscale Deliverable 2.1, EuroHPC Centre of Excellence MultiXscale, September 2023. doi:10.5281/zenodo.8420222.