Optimisation of the first principle code Octopus for massive parallel architectures: application to light harvesting complexes

Abstract

[EN]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. In order to simulate this complex, we have used (with the assistance of the PRACE consortium) some of the most powerful supercomputers in Europe to runOctopus, a scientific software package for Density Functional Theory and Time-Dependent Density Functional Theory calculations. Results obtained with Octopus have been analysed in depth in order to identify the main obstacles to optimal scaling using thousands of cores. Many problems have emerged, mainly the poor performance of the Poisson solver, high memory requirements, the transfer of high quantities of complex data structures among processes, and so on. Finally, all of these problems have been overcome, and the new version reaches a very high performance in massively parallel systems. Tests run efficiently up to 128K processors and thus we have been able to complete the largest TDDFT calculations performed to date. At the conclusion of this work it has been possible to study the Light Harvesting Complex II as originally envisioned.

[EU]Konputagailu bidezko simulazioa da, gaur egun, zientzialariek eskura duten tresnarik ahaltsuenetako bat sistema fisiko konplexuen portaera ulertzen saiatzeko. Oinarrizko fenomeno fisiko horiek simulatzeko superkonputagailuak erabili dira tesi honetan aurkezten den lanean. Konkretuki, punta-puntako konputagailuak erabili dira fotosintesiaren lehen urratsak ulertzeko, landare berdeetan eguzki-energiaren xurgatze-prozesua kontrolatzen duen molekula simulatuz. Superkonputazio-zentroek ehunka milaka prozesatze-nukleo dituzten makinak erabiltzeko aukera eskaintzen dute, baina ez da batere erraza azelerazio-faktore linealak lortzea halako konputagailuetan. Hori dela eta, ahalegin handiak egin behar dira, informatikaren ikuspegitik, sistema osoaren ezagutza ahalik eta sakonena lortzeko: kode zientifikoen izaera, beraren exekuzio paraleloen aukerak, prozesuen arteko datu-transmisioaren beharrak, sistemaren memoriaren erabilera eraginkorrena, eta abar. Tesi honek aurreko arazo guztiei aurre egiten die, helburu argi batekin: konplexu makromolekular osoen simulazioa, konkretuki Light Harvesting Complex II sistemaren egitura elektronikoaren simulazioa, beraren portaera fisikoa ulertu ahal izateko. Sistema hori simulatu ahal izateko bidean, Europako superkonputagailu azkarrenak erabili dira (PRACE partzuergoari esker) Octopus software-paketea exekutatzeko, zeina Density Functional Theory eta Time-Dependent Density Functional Theory izeneko teorien araberako simulazio elektronikoak egiten baititu. Lortutako emaitzak sakonki analizatu dira, milaka konputazio-nukleo eraginkorki erabiltzea oztopatzen zuten arazoak aurkitzeko. Problema ugari azaldu dira bide horretan, nagusiki Poisson ebazlearen errendimendu baxua, memoria eskaera handiak, datu-egitura konplexuen kopuru handiko transferentziak, eta abar. Azkenean, problema horiek guztiak ebatzi dira, eta bertsio berriak errendimendu handia lortu du superkonputagailu paraleloetan. Exekuzio eraginkorrak frogatu ahal izan ditugu 128K prozesadorera arte eta, ondorioz, inoizko TDDFT simulaziorik handienak egin ahal izan ditugu. Hala, lan honen amaieran, hasierako helburua bete ahal izan da: Light Harvesting Complex II sistema molekularraren azterketa egitea.