Optimisation of the first principle code Octopus for massive parallel architectures: application to light harvesting complexes Thesis Dissertation April 23, 2015 Joseba Alberdi-Rodriguez (
[email protected]) Supervisors: Dr. Javier Muguerza Rivero Department of Computer Architecture and Technology Faculty of Computer Science Prof. Angel Rubio Secades Department of Materials Physics Faculty of Chemistry eman ta zabal zazu Universidad Euskal Herriko del País Vasco Unibertsitatea Servicio Editorial de la Universidad del País Vasco (UPV/EHU) - Euskal Herriko Unibertsitateko (UPV/EHU) Argitalpen Zerbitzua - University of the Basque Country (UPV/EHU) Press - ISBN: 978-84-9082-371-2 Knows no end Jakintzak ez duelako inoiz mugarik Familiari Abstract Computer simulation has become a powerful technique for assisting scientists in developing novel insights into the basic phenomena underlying a wide variety of complex physical systems. The work reported in this thesis is concerned with the use of massively parallel computers to simulate the fundamental features at the electronic structure level that control the initial stages of harvesting and transfer of solar energy in green plants which initiate the photosynthetic process. Currently available supercomputer facilities offer the possibility of using hundred of thousands of computing cores. However, obtaining a linear speed-up from HPC systems is far from trivial. Thus, great efforts must be devoted to understand the nature of the scientific code, the methods of parallel execution, data communication requirements in multi-process calculations, the efficient use of available memory, etc. This thesis deals with all of these themes, with a clear objective in mind: the electronic structure simulation of complete macro-molecular complexes, namely the Light Harvesting Complex II, with the aim of understanding its physical behaviour.