Software for Exascale Computing - SPPEXA 2016-2019

This open access book summarizes the research done and results obtained in the second funding phase of the Priority Program 1648 "Software for Exascale Computing" (SPPEXA) of the German Research Foundation (DFG) presented at the SPPEXA Symposium in Dresden during October 21-23, 2019. In that respect, it both represents a continuation of Vol. 113 in Springer’s series Lecture Notes in Computational Science and Engineering, the corresponding report of SPPEXA’s first funding phase, and provides an overview of SPPEXA’s contributions towards exascale computing in today's sumpercomputer technology. The individual chapters address one or more of the research directions (1) computational algorithms, (2) system software, (3) application software, (4) data management and exploration, (5) programming, and (6) software tools. The book has an interdisciplinary appeal: scholars from computational sub-fields in computer science, mathematics, physics, or engineering will find it of particular interest

Fast algorithm for real-time rings reconstruction

The GAP project is dedicated to study the application of GPU in several contexts in which real-time response is important to take decisions. The definition of real-time depends on the application under study, ranging from answer time of μs up to several hours in case of very computing intensive task. During this conference we presented our work in low level triggers [1] [2] and high level triggers [3] in high energy physics experiments, and specific application for nuclear magnetic resonance (NMR) [4] [5] and cone-beam CT [6]. Apart from the study of dedicated solution to decrease the latency due to data transport and preparation, the computing algorithms play an essential role in any GPU application. In this contribution, we show an original algorithm developed for triggers application, to accelerate the ring reconstruction in RICH detector when it is not possible to have seeds for reconstruction from external trackers

Lattice Boltzmann Methods for Fluid-Dynamics in Relativistic Regimes

In this thesis work we present the algorithmic derivation of a new class of Lattice Boltzmann Methods appropriate for the study of dissipative relativistic fluids. While previous models were restricted to the use of massless particles, implying ultra-relativistic equations of state, this work provides a significant step towards the formulation of a unified relativistic lattice kinetic scheme, covering ideal gases of both massive and near-massless particles, seamlessly bridging the gap between relativistic and low-speed non-relativistic fluid regimes. In a first important application of this novel numerical tool, we present results bringing new insight in the long standing problem of understanding the pathway from relativistic kinetic theory to relativistic hydrodynamics. We conduct an accurate analysis of the relativistic transport coefficients in the relaxation time approximation, providing numerical evidence that the Chapman Enskog expansion correctly relates kinetic transport coefficients and macroscopic hydrodynamics parameters in dissipative relativistic fluid dynamics, confirming recent theoretical results. This analysis, in turn, can be seen as an accurate calibration of this class of numerical solvers, making them suitable to deliver improved physical accuracy in the simulation of realistic systems. To give an example, we present results of simulations solving the Riemann problem for a quark-gluon plasma, showing good agreement with previous results obtained using other solvers present in the literature. As a further application we study the transport properties of electrons in ultra-clean graphene samples, for which a hydrodynamic description is appropriate due to the predominance of electron-electron scattering over electron-phonon interactions. Using appropriate 2D formulations, enriched to describe the effects of the external electrostatic drive, and to capture the interactions with phonons and impurities, we present simulations of laminar flows taking into consideration geometrical setups used in actual experiments. Furthermore, we also consider electronic systems where nonlinear effects start becoming relevant. Basing on extensive numerical simulations, we identify transport parameters which could be used to trigger and observe preturbulent signals in a hydrodynamic region as close as possible to those within reach of current experimental conditions. As a closing note, we remark that the numerical methods described in this thesis work retains the main computational advantages of standard Lattice Boltzmann Methods, offering high amenability to parallelization, that can be exploited to write efficient codes. These aspects are covered in the last chapter of the thesis, in which we summarize the best practices in the development of a performance portable code targeting modern high performance computing accelerators.In questo lavoro di tesi viene presentata la derivazione algoritmica di una nuova classe di metodi reticolari di Boltzmann per lo studio di fluidi relativistici. Se da un lato i modelli sin'ora presenti in letteratura consideravano solo particelle a massa nulla ed equazioni di stato ultra-relativistiche, questo lavoro rappresenta un significativo passo in avanti verso la formulazione di un metodo cinetico unificato, in grado di trattare gas relativistici ideali, sia massivi sia a massa trascurabile, spaziando tra regimi relavitistici e regimi classici. Come primo esempio di applicazione viene presentato uno studio atto a chiarire la problematica connessione tra teoria cinetica e teoria idrodinamica relativistica: a seguito di un'accurata analisi dei coefficienti di trasporto relativistici, vengono presentati dati numerici che evidenziano come l'espansione di Chapman Enskog leghi correttamente i coefficienti di trasporto cinetici con i parametri macroscopici idrodinamici relativistici, andando a confermare recenti studi teorici. D'altro canto, l'analisi in questione può essere interpretata come un' accurata calibrazione di questa nuova classe di algoritmi, il che li candida ad affidabili strumenti per l'implementazione di simulazioni numeriche di sistemi fisici reali. Come esempio viene preso in considerazione lo studio del problema di Riemann per un quark-gluon plasma. I risultati ottenuti sono validati tramite confronto con simulazioni ottenute utilizzando altri risolutori numerici presenti in letteratura. Come ulteriore applicazione, viene condotto uno studio sulle proprietà di trasporto degli elettroni nel grafene, in cui una descrizione idrodinamica è giustificata dal fatto che il moto collettivo degli elettroni risulta dominante rispetto a interazioni tra elettroni e fononi. Utilizzando una formulazione numerica bidimensionale, arricchita per inglobare effetti elettrostatici e interazioni con fononi e impurità, vengono presentati risultati di simulazioni di flussi laminari in cui vengono riprodotte condizioni sperimentali simili a quelle reali. Successivamente sono stati presi in considerazione sistemi in cui termini non-lineari sono rilevanti. I risultati di un estensivo lavoro numerico hanno permesso di identificare parametri di trasporto che consentano l'osservazione di segnali preturbolenti in una regione idrodinamica quanto più simile a quella accessibile nelle attuali condizioni sperimentali. Per finire, va sottolineato che i metodi numerici descritti in questo lavoro di tesi preservano dal punto di vista computazionale gli stessi vantaggi rispetto ai classici metodi reticolari di Boltzmann. Questi metodi numerici si prestano infatti a efficienti implementazioni altamente parallele. Questi aspetti sono dettagliati nell'ultimo capitolo di questa tesi, dove vengono riassunti gli elementi più rilevanti nello sviluppo di codici in grado di offrire non solo portabilità, ma anche portabilità delle prestazioni, su varie moderne architetture altamente parallele.In der vorliegenden Arbeit wird die algorithmische Entwicklung einer neuen Klasse von Lattice Boltzmann Methoden dargestellt, die zur Anwendung und Untersuchung von dissipativen, relativistischen Fluiden geeignet ist. Vorangehende Arbeiten sind eingeschränkt auf masselose Teilchen und damit auf ultrarelativistische Zustandsgleichungen. Im Gegensatz dazu werden in dieser Arbeit signifikante Fortschritte zur Formulierung einer einheitlichen, kinetischen Lattice Methode gemacht, die ideale Gase aus sowohl massiven wie auch fast masselosen Teilchen abdeckt und nahtlos auf den gesamten Bereich von nicht-relativistischen zu relativistischen Fluidregimen anwendbar ist. Der Übergang von der relativistischen, kinetischen Theorie zur relativistischen Hydrodynamik ist ein altes Problem. Eine erste, wichtige Anwendung der neuartigen, numerischen Methode dieser Arbeit führt hier zu neuen Erkenntnissen. Eine präzise Analyse der relativistischen Transportkoeffizienten unter Verwendung der Zeitrelaxationsnäherung ist durchgeführt worden. Damit konnte numerisch nachgewiesen werden, dass die Chapman-Enskog-Entwicklung die kinetischen Transportkoeffizienten und die makroskopischen, hydrodynamischen Parameter in der dissipativen, relativistischen Fluiddynamik korrekt in Beziehung setzt. Dies bestätigt neuere, theoretische Resultate. Umgekehrt kann diese Analyse als präzise Kalibrierung dieser Klasse von numerischen Lösern verstanden werden, um so die Genauigkeit für Berechnungen im relativistischen Regime zu erhöhen. Anhand des Riemann Problems für ein Quark-Gluon-Plasma vergleichen wir Simulationsergebnisse unserer Methode mit bekannten Ergebnissen von anderen Lösern aus der Literatur. In einer weiteren Anwendung untersuchen wir die Transporteigenschaften von Elektronen in extrem reinen Graphen-Proben. Hierbei ist eine hydrodynamische Beschreibung geeignet, da die Elektron-Elektron-Streuung die Elektron-Phonon-Interaktion dominiert. Basierend auf 2D-Formulierungen, einem externen elektrostatischen Antrieb und der Erfassung von Wechselwirkungen von Phononen mit Verunreinigungen präsentieren wir Simulationen einer laminaren Strömung. Dabei berücksichtigen wir die Geometrie des zugrundeliegenden physikalischen Experiments. Ferner betrachten wir elektrische Systeme, in denen nichtlineare Effekte an Bedeutung gewinnen. Auf der Grundlage einer umfassenden Menge von numerischen Simulationen identifizieren wir Transportparameter, welche man verwenden könnte, um präturbulente Signale auszulösen bzw. zu beobachten. Dabei sind entsprechende hydrodynamische Regime so nah wie möglich an den aktuellen Bedingungen der Experimente. Abschliessend sei angemerkt, dass die numerischen Methoden dieser Arbeit die rechentechnischen Vorzüge der standard Lattice Boltzmann Methode erhalten. Dies schliesst insbesondere ein hohes Mass an Parallelisierbarkeit ein, welche genutzt werden kann, um effiziente Löser zu programmieren. Diesen Aspekten ist das letzte Kapitel der Arbeit gewidmet. Hierbei fassen wir beste Verfahren zur Entwicklung von performanten, portablen Programmen im Kontext von modernen Hochleistungsrechenbeschleunigern zusammen

Tools for Biomolecular Modeling and Simulation

Electrostatic interactions play a pivotal role in understanding biomolecular systems, influencing their structural stability and functional dynamics. The Poisson-Boltzmann (PB) equation, a prevalent implicit solvent model that treats the solvent as a continuum while describes the mobile ions using the Boltzmann distribution, has become a standard tool for detailed investigations into biomolecular electrostatics. There are two primary methodologies: grid-based finite difference or finite element methods and body-fitted boundary element methods. This dissertation focuses on developing fast and accurate PB solvers, leveraging both methodologies, to meet diverse scientific needs and overcome various obstacles in the field

Efficient algorithms for the fast computation of space charge effects caused by charged particles in particle accelerators

In this dissertation, a Poisson solver is improved with three parts: the efficient integrated Green's function; the discrete cosine transform of the efficient integrated Green's function values; the implicitly zero-padded fast Fourier transform for charge density. In addition, the high performance computing technology is utilized for the further improvement of efficiency, such as: OpenMP API, OpenMP+CUDA, MPI, and MPI+OpenMP parallelizations. The examples and simulation results are matched with the results of the commonly used Poisson solver to demonstrate the accuracy performance

Roadmap on Electronic Structure Codes in the Exascale Era

Electronic structure calculations have been instrumental in providing many important insights into a range of physical and chemical properties of various molecular and solid-state systems. Their importance to various fields, including materials science, chemical sciences, computational chemistry and device physics, is underscored by the large fraction of available public supercomputing resources devoted to these calculations. As we enter the exascale era, exciting new opportunities to increase simulation numbers, sizes, and accuracies present themselves. In order to realize these promises, the community of electronic structure software developers will however first have to tackle a number of challenges pertaining to the efficient use of new architectures that will rely heavily on massive parallelism and hardware accelerators. This roadmap provides a broad overview of the state-of-the-art in electronic structure calculations and of the various new directions being pursued by the community. It covers 14 electronic structure codes, presenting their current status, their development priorities over the next five years, and their plans towards tackling the challenges and leveraging the opportunities presented by the advent of exascale computing.Comment: Submitted as a roadmap article to Modelling and Simulation in Materials Science and Engineering; Address any correspondence to Vikram Gavini ([email protected]) and Danny Perez ([email protected]

Computational Methods in Science and Engineering : Proceedings of the Workshop SimLabs@KIT, November 29 - 30, 2010, Karlsruhe, Germany

In this proceedings volume we provide a compilation of article contributions equally covering applications from different research fields and ranging from capacity up to capability computing. Besides classical computing aspects such as parallelization, the focus of these proceedings is on multi-scale approaches and methods for tackling algorithm and data complexity. Also practical aspects regarding the usage of the HPC infrastructure and available tools and software at the SCC are presented

Roadmap on Electronic Structure Codes in the Exascale Era

Electronic structure calculations have been instrumental in providing many important insights into a range of physical and chemical properties of various molecular and solid-state systems. Their importance to various fields, including materials science, chemical sciences, computational chemistry and device physics, is underscored by the large fraction of available public supercomputing resources devoted to these calculations. As we enter the exascale era, exciting new opportunities to increase simulation numbers, sizes, and accuracies present themselves. In order to realize these promises, the community of electronic structure software developers will however first have to tackle a number of challenges pertaining to the efficient use of new architectures that will rely heavily on massive parallelism and hardware accelerators. This roadmap provides a broad overview of the state-of-the-art in electronic structure calculations and of the various new directions being pursued by the community. It covers 14 electronic structure codes, presenting their current status, their development priorities over the next five years, and their plans towards tackling the challenges and leveraging the opportunities presented by the advent of exascale computing

Roadmap on Electronic Structure Codes in the Exascale Era

Electronic structure calculations have been instrumental in providing many important insights into a range of physical and chemical properties of various molecular and solid-state systems. Their importance to various fields, including materials science, chemical sciences, computational chemistry and device physics, is underscored by the large fraction of available public supercomputing resources devoted to these calculations. As we enter the exascale era, exciting new opportunities to increase simulation numbers, sizes, and accuracies present themselves. In order to realize these promises, the community of electronic structure software developers will however first have to tackle a number of challenges pertaining to the efficient use of new architectures that will rely heavily on massive parallelism and hardware accelerators. This roadmap provides a broad overview of the state-of-the-art in electronic structure calculations and of the various new directions being pursued by the community. It covers 14 electronic structure codes, presenting their current status, their development priorities over the next five years, and their plans towards tackling the challenges and leveraging the opportunities presented by the advent of exascale computing