A high-performance computing framework for Monte Carlo ocean color simulations

This paper presents a high-performance computing (HPC) framework for Monte Carlo (MC) simulations in the ocean color (OC) application domain. The objective is to optimize a parallel MC radiative transfer code named MOX, developed by the authors to create a virtual marine environment for investigating the quality of OC data products derived from in situ measurements of in-water radiometric quantities. A consolidated set of solutions for performance modeling, prediction, and optimization is implemented to enhance the efficiency of MC OC simulations on HPC run-time infrastructures. HPC, machine learning, and adaptive computing techniques are applied taking into account a clear separation and systematic treatment of accuracy and precision requirements for large-scale MC OC simulations. The added value of the work is the integration of computational methods and tools for MC OC simulations in the form of an HPC-oriented problem-solving environment specifically tailored to investigate data acquisition and reduction methods for OC field measurements. Study results highlight the benefit of close collaboration between HPC and application domain researchers to improve the efficiency and flexibility of computer simulations in the marine optics application domain. (C) 2016 The Authors. Concurrency and Computation: Practice and Experience Published by John Wiley & Sons Ltd.Portuguese Foundation for Science and Technology (FCT/MEC) [PEst-OE/EEI/UI0527/2011]; ESA [22576/09/I-OL, ARG/003-025/1406/CIMA]; NOVA LINCS [UID/CEC/04516/2013]info:eu-repo/semantics/publishedVersio

Transistor scaled HPC application performance

We propose a radically new, biologically inspired, model of extreme scale computer on which ap- plication performance automatically scales with the transistor count even in the face of component failures. Today high performance computers are massively parallel systems composed of potentially hundreds of thousands of traditional processor cores, formed from trillions of transistors, consuming megawatts of power. Unfortunately, increasing the number of cores in a system, unlike increasing clock frequencies, does not automatically translate to application level improvements. No general auto-parallelization techniques or tools exist for HPC systems. To obtain application improvements, HPC application programmers must manually cope with the challenge of multicore programming and the significant drop in reliability associated with the sheer number of transistors. Drawing on biological inspiration, the basic premise behind this work is that computation can be dramatically accelerated by integrating a very large-scale, system-wide, predictive associative memory into the operation of the computer. The memory effectively turns computation into a form of pattern recognition and prediction whose result can be used to avoid significant fractions of computation. To be effective the expectation is that the memory will require billions of concurrent devices akin to biological cortical systems, where each device implements a small amount of storage, computation and localized communication. As typified by the recent announcement of the Lyric GP5 Probability Processor, very efficient scalable hardware for pattern recognition and prediction are on the horizon. One class of such devices, called neuromorphic, was pioneered by Carver Mead in the 80’s to provide a path for breaking the power, scaling, and reliability barriers associated with standard digital VLSI tech- nology. Recent neuromorphic research examples include work at Stanford, MIT, and the DARPA Sponsored SyNAPSE Project. These devices operate transistors as unclocked analog devices orga- nized to implement pattern recognition and prediction several orders of magnitude more efficiently than functionally equivalent digital counterparts. Abstractly, the devices can be used to implement modern machine learning or statistical inference. When exposed to data as a time-varying signal, the devices learn and store patterns in the data at multiple time scales and constantly provide predictions about what the signal will do in the future. This kind of function can be seen as a form of predictive associative memory. In this paper we describe our model and initial plans for exploring it.Department of Energy Office of Science (DE-SC0005365), National Science Foundation (1012798

Context adaptivity for selected computational kernels with applications in optoelectronics and in phylogenetics

Computational Kernels sind der kritische Teil rechenintensiver Software, wofür der größte Rechenaufwand anfällt; daher müssen deren Design und Implementierung sorgfältig vorgenommen werden. Zwei wissenschaftliche Anwendungsprobleme aus der Optoelektronik und aus der Phylogenetik, sowie dazugehörige Computational Kernels motivieren diese Arbeit. Im ersten Anwendungsproblem werden Komponenten zur Berechnung komplex-symmetrischer Eigenwertprobleme diskutiert, welche in der Simulation von Wellenleitern in der Optoelektronik auftreten. LAPACK und ScaLAPACK beinhalten sehr leistungsfähige Referenzimplementierungen für bestimmte Problemstellungen der linearen Algebra. In Bezug auf Eigenwertprobleme werden ausschließlich reell-symmetrische und komplex-hermitesche Varianten angeboten, daher sind effiziente Codes für komplex-symmetrische (nicht-hermitesche) Eigenwertprobleme sehr wünschenswert. Das zweite Anwendungsproblem behandelt einen parallelen, wissenschaftlichen Workflow zur Rekonstruktion von Phylogenien, welcher entworfen, umgesetzt und evaluiert wird. Die Rekonstruktion von phylogenetischen Bäumen ist ein NP-hartes Problem, welches äußerst viel Rechenkapazität benötigt, wodurch ein paralleler Ansatz erforderlich ist. Die grundlegende Idee dieser Arbeit ist die Untersuchung der Wechselbeziehung zwischen dem Kontext der behandelten Kernels und deren Effizienz. Ein Kontext eines Computational Kernels beinhaltet Modellaspekte (z.B. Struktur der Eingabedaten), Softwareaspekte (z.B. rechenintensive Bibliotheken), Hardwareaspekte (z.B. verfügbarer Hauptspeicher und unterstützte darstellbare Genauigkeit), sowie weitere Anforderungen bzw. Einschränkungen. Einschränkungen sind hinsichtlich Laufzeit, Speicherverbrauch, gelieferte Genauigkeit usw., möglich. Das Konzept der Kontextadaptivität wird für ausgewählte Anwendungsprobleme in Computational Science gezeigt. Die vorgestellte Methode ist ein Meta-Algorithmus, der Aspekte des Kontexts verwendet, um optimale Leistung hinsichtlich der angewandten Metrik zu erzielen. Es ist wichtig, den Kontext einzubeziehen, weil Anforderungen gegeneinander ausgetauscht werden könnten, resultierend in einer höheren Leistung. Zum Beispiel kann im Falle einer niedrigen benötigten Genauigkeit ein schnellerer Algorithmus einer bewährten, aber langsameren, Methode vorgezogen werden. Speziell für komplex-symmetrische Eigenwertprobleme zugeschnittene Codes zielen darauf ab, Genauigkeit gegen Geschwindigkeit einzutauschen. Die Innovation wird durch neue algorithmische Ansätze belegt, welche die algebraische Struktur ausnutzen. Bezüglich der Berechnung von phylogenetischen Bäumen wird die Abbildung eines Workflows auf ein Campusgrid-System gezeigt. Die Innovation besteht in der anpassungsfähigen Implementierung des Workflows, der nebenläufige Instanzen von Computational Kernels in einem verteilten System darstellt. Die Adaptivität bezeichnet hier die Fähigkeit des Workflows, die Rechenlast hinsichtlich verfügbarer Rechner, Zeit und Qualität der phylogenetischen Bäume anzupassen. Kontextadaptivität wird durch die Implementierung und Evaluierung von wissenschaftlichen Problemstellungen aus der Optoelektronik und aus der Phylogenetik gezeigt. Für das Fachgebiet der Optoelektronik zielt eine Familie von Algorithmen auf die Lösung von verallgemeinerten komplex-symmetrischen Eigenwertproblemen ab. Unser alternativer Ansatz nutzt die symmetrische Struktur aus und spielt günstigere Laufzeit gegen eine geringere Genauigkeit aus. Dieser Ansatz ist somit schneller, jedoch (meist) ungenauer als der konventionelle Lösungsweg. Zusätzlich zum sequentiellen Löser wird eine parallele Variante diskutiert und teilweise auf einem Cluster mit bis zu 1024 CPU-Cores evaluiert. Die erzielten Laufzeiten beweisen die Überlegenheit unseres Ansatzes -- allerdings sind weitere Untersuchungen zur Erhöhung der Genauigkeit notwendig. Für das Fachgebiet der Phylogenetik zeigen wir, dass die phylogenetische Baum-Rekonstruktion mittels eines Condor-basierten Campusgrids effizient parallelisiert werden kann. Dieser parallele wissenschaftliche Workflow weist einen geringen parallelen Overhead auf, resultierend in exzellenter Effizienz.Computational kernels are the crucial part of computationally intensive software, where most of the computing time is spent; hence, their design and implementation have to be accomplished carefully. Two scientific application problems from optoelectronics and from phylogenetics and corresponding computational kernels are motivating this thesis. In the first application problem, components for the computational solution of complex symmetric EVPs are discussed, arising in the simulation of waveguides in optoelectronics. LAPACK and ScaLAPACK contain highly effective reference implementations for certain numerical problems in linear algebra. With respect to EVPs, only real symmetric and complex Hermitian codes are available, therefore efficient codes for complex symmetric (non-Hermitian) EVPs are highly desirable. In the second application problem, a parallel scientific workflow for computing phylogenies is designed, implemented, and evaluated. The reconstruction of phylogenetic trees is an NP-hard problem that demands huge scale computing capabilities, and therefore a parallel approach is necessary. One idea underlying this thesis is to investigate the interaction between the context of the kernels considered and their efficiency. The context of a computational kernel comprises model aspects (for instance, structure of input data), software aspects (for instance, computational libraries), hardware aspects (for instance, available RAM and supported precision), and certain requirements or constraints. Constraints may exist with respect to runtime, memory usage, accuracy required, etc.. The concept of context adaptivity is demonstrated to selected computational problems in computational science. The method proposed here is a meta-algorithm that utilizes aspects of the context to result in an optimal performance concerning the applied metric. It is important to consider the context, because requirements may be traded for each other, resulting in a higher performance. For instance, in case of a low required accuracy, a faster algorithmic approach may be favored over an established but slower method. With respect to EVPs, prototypical codes that are especially targeted at complex symmetric EVPs aim at trading accuracy for speed. The innovation is evidenced by the implementation of new algorithmic approaches exploiting structure. Concerning the computation of phylogenetic trees, the mapping of a scientific workflow onto a campus grid system is demonstrated. The adaptive implementation of the workflow features concurrent instances of a computational kernel on a distributed system. Here, adaptivity refers to the ability of the workflow to vary computational load in terms of available computing resources, available time, and quality of reconstructed phylogenetic trees. Context adaptivity is discussed by means of computational problems from optoelectronics and from phylogenetics. For the field of optoelectronics, a family of implemented algorithms aim at solving generalized complex symmetric EVPs. Our alternative approach exploiting structural symmetry trades runtime for accuracy, hence, it is faster but (usually) features a lower accuracy than the conventional approach. In addition to a complete sequential solver, a parallel variant is discussed and partly evaluated on a cluster utilizing up to 1024 CPU cores. Achieved runtimes evidence the superiority of our approach, however, further investigations on improving accuracy are suggested. For the field of phylogenetics, we show that phylogenetic tree reconstruction can efficiently be parallelized on a campus grid infrastructure. The parallel scientific workflow features a moderate parallel overhead, resulting in an excellent efficiency

Self adapting numerical software (SANS) effort

The challenge for the development of next generation software is the successful management of the complex computational environment while delivering to the scientist the full power of flexible compositions of the available algorithmic alternatives. Self-Adapting Numerical Software (SANS) systems are intended to meet this significant challenge. The process of arriving at an efficient numerical solution of problems in computational science involves numerous decisions by a numerical expert. Attempts to automate such decisions distinguish three levels: • Algorithmic decision; • Management of the parallel environment; • Processor-specific tuning of kernels. Additionally, at any of these levels we can decide to rearrange the user’s data. In this paper we look at a number of efforts at the University of Tennessee that are investigating these areas.

A Recommendation System for Preconditioned Iterative Solvers

Solving linear systems of equations is an integral part of most scientific simulations. In recent years, there has been a considerable interest in large scale scientific simulation of complex physical processes. Iterative solvers are usually preferred for solving linear systems of such magnitude due to their lower computational requirements. Currently, computational scientists have access to a multitude of iterative solver options available as "plug-and- play" components in various problem solving environments. Choosing the right solver configuration from the available choices is critical for ensuring convergence and achieving good performance, especially for large complex matrices. However, identifying the "best" preconditioned iterative solver and parameters is challenging even for an expert due to issues such as the lack of a unified theoretical model, complexity of the solver configuration space, and multiple selection criteria. Therefore, it is desirable to have principled practitioner-centric strategies for identifying solver configuration(s) for solving large linear systems. The current dissertation presents a general practitioner-centric framework for (a) problem independent retrospective analysis, and (b) problem-specific predictive modeling of performance data. Our retrospective performance analysis methodology introduces new metrics such as area under performance-profile curve and conditional variance-based finetuning score that facilitate a robust comparative performance evaluation as well as parameter sensitivity analysis. We present results using this analysis approach on a number of popular preconditioned iterative solvers available in packages such as PETSc, Trilinos, Hypre, ILUPACK, and WSMP. The predictive modeling of performance data is an integral part of our multi-stage approach for solver recommendation. The key novelty of our approach lies in our modular learning based formulation that comprises of three sub problems: (a) solvability modeling, (b) performance modeling, and (c) performance optimization, which provides the flexibility to effectively target challenges such as software failure and multiobjective optimization. Our choice of a "solver trial" instance space represented in terms of the characteristics of the corresponding "linear system", "solver configuration" and their interactions, leads to a scalable and elegant formulation. Empirical evaluation of our approach on performance datasets associated with fairly large groups of solver configurations demonstrates that one can obtain high quality recommendations that are close to the ideal choices