PFFT - An Extension of FFTW to Massively Parallel Architectures

We present a MPI based software library for computing the fast Fourier transforms on massively parallel, distributed memory architectures. Similar to established transpose FFT algorithms, we propose a parallel FFT framework that is based on a combination of local FFTs, local data permutations and global data transpositions. This framework can be generalized to arbitrary multi-dimensional data and process meshes. All performance relevant building blocks can be implemented with the help of the FFTW software library. Therefore, our library offers great flexibility and portable performance. Likewise FFTW, we are able to compute FFTs of complex data, real data and even- or odd-symmetric real data. All the transforms can be performed completely in place. Furthermore, we propose an algorithm to calculate pruned FFTs more efficiently on distributed memory architectures. For example, we provide performance measurements of FFTs of size 512^3 and 1024^3 up to 262144 cores on a BlueGene/P architecture

Massively Parallel, Fast Fourier Transforms and Particle-Mesh Methods: Massiv parallele schnelle Fourier-Transformationen und Teilchen-Gitter-Methoden

The present thesis provides a modularized view on the structure of fast numerical methods for computing Coulomb interactions between charged particles in three-dimensional space. Thereby, the common structure is given in terms of three self-contained algorithmic frameworks that are built on top of each other, namely fast Fourier transform (FFT), nonequispaced fast Fourier transform (NFFT) and NFFT based particle-mesh methods (P²NFFT). For each of these frameworks algorithmic enhancement and parallel implementations are presented with special emphasis on scalability up to hundreds of thousands of parallel processes. In the context of FFT massively parallel algorithms are composed from hardware adaptive low level modules provided by the FFTW software library. The new algorithmic NFFT concepts include pruned NFFT, interlacing, analytic differentiation, and optimized deconvolution in Fourier space with respect to a mean square aliasing error. Enabled by these generalized concepts it is shown that NFFT provides a unified access to particle-mesh methods. Especially, mixed-periodic boundary conditions are handled in a consistent way and interlacing can be incorporated more efficiently. Heuristic approaches for parameter tuning are presented on the basis of thorough error estimates.Die vorliegende Dissertation beschreibt einen modularisierten Blick auf die Struktur schneller numerischer Methoden für die Berechnung der Coulomb-Wechselwirkungen zwischen Ladungen im dreidimensionalen Raum. Die gemeinsame Struktur ist geprägt durch drei selbstständige und auf einander aufbauenden Algorithmen, nämlich der schnellen Fourier-Transformation (FFT), der nicht äquidistanten schnellen Fourier-Transformation (NFFT) und der NFFT-basierten Teilchen-Gitter-Methode (P²NFFT). Für jeden dieser Algorithmen werden Verbesserungen und parallele Implementierungen vorgestellt mit besonderem Augenmerk auf massiv paralleler Skalierbarkeit. Im Kontext der FFT werden parallele Algorithmen aus den Hardware adaptiven Modulen der FFTW Softwarebibliothek zusammengesetzt. Die neuen NFFT-Konzepte beinhalten abgeschnittene NFFT, Versatz, analytische Differentiation und optimierte Entfaltung im Fourier-Raum bezüglich des mittleren quadratischen Aliasfehlers. Mit Hilfe dieser Verallgemeinerungen bietet die NFFT einen vereinheitlichten Zugang zu Teilchen-Gitter-Methoden. Insbesondere gemischt periodische Randbedingungen werden einheitlich behandelt und Versatz wird effizienter umgesetzt. Heuristiken für die Parameterwahl werden auf Basis sorgfältiger Fehlerabschätzungen angegeben

PARALLEL THREE-DIMENSIONAL NONEQUISPACED FAST FOURIER TRANSFORMS AND THEIR APPLICATION TO PARTICLE SIMULATION

Abstract. In this paper we describe a parallel algorithm for calculating nonequispaced fast Fourier transforms on massively parallel distributed memory architectures. These algorithms are implemented in an open source software library called PNFFT. Furthermore, we derive a parallel fast algorithm for the computation of the Coulomb potentials and forces in a charged particle system, which is based on the parallel nonequispaced fast Fourier transform. To prove the high scalability of our algorithms we provide performance results on a BlueGene/P system using up to 65536 cores. Key words and phrases: parallel nonequispaced fast Fourier transform, parallel fast summation, parallel particle mesh methods, NFF

rainwoodman/pfft-python 0.1.13

python binding of pff

Tumor Necrosis Factor Receptor/Tumor Necrosis Factor Family Members in Antiviral CD8 T-Cell Immunity

CD8 memory T cells can play a critical role in protection against repeated exposure to infectious agents such as viruses, yet can also contribute to the immunopathology associated with these pathogens. Understanding the mechanisms that control effective memory responses has important ramifications for vaccine design and in the management of adverse immune reactions. Recent studies have implicated several members of the tumor necrosis factor receptor (TNFR) family as key stimulatory and inhibitory molecules involved in the regulation of CD8 T cells. In this review, we discuss their control of the generation, persistence, and reactivation of CD8 T cells during virus infection