Einrichtungen und Anlagen (Raumfahrt)

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Synergia: Driving Massively Parallel Particle Accelerator Simulations with Python

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Simulations of beam dynamics in particle accelerators have a wide range of computational requirements. The simplest calculations involve independent-particle tracking of a few thousand particles which can easily be accomplished on modern desktop computers. Calculations involving collective effects may require millions or even billions of particles and push the limits of modern supercomputers. We describe Synergia, a hybrid Python/C++ accelerator simulation package capable of dealing with the entire spectrum of beam dynamics simulations. We describe the motivations for the hybrid language design and discuss the issues that arise in the implementation. We also describe the most novel feature of our code, a hybrid C++/Python object serialization system, in detail. The same techniques are of general use in any domain by providing data and computationally intensive C++ frameworks with the advanced programming and user-friendly features of Python.
Verwandte Themen: Physik der Elementarteilchen und Felder Strukturmechanik Elektronik und Elektrotechnik Einrichtungen und Anlagen (Raumfahrt) Energieproduktion und Konversion

Compiling Python Modules to Native Parallel Modules Using Pythran and OpenMP Annotations

(0,24 MB)

High Performance Computing users traditionally rely on low-level, compiled language such as C or FORTRAN to perform compute-intensive tasks. As a consequence, it is a common situation to have High Performance Computing application written in a high-level language such as Python, calling native routines for compute-intensive tasks. To improve development speed and reduce maintenance costs, using a higher-level language like Python seems attractive. While it is usually associated with low performance, several solutions such as Cython, Numba, Parakeet or Pythran offer to automatically or semi-automatically turn Python functions into native ones. One of the key points required to match the performance of native applications is the ability to write parallel applications. This paper studies the addition of OpenMP directives, a popular model to describe parallelism in C/C++/FORTRAN applications, to Pythran, an automatic compiler from a subset of Python to C++. It shows that scientific Python applications annotated with OpenMP directives can be turned by an automatic compiler into native applications that run within the same order of magnitude than manually-written ones.
Verwandte Themen: Elektronik und Elektrotechnik Einrichtungen und Anlagen (Raumfahrt) Numerische Analyse

A Problem Solving Environment for Stochastic Biological Simulations

(11,56 MB)

Stochastic simulations of biological systems vary widely in scope from reaction modules, to single cells, to cell colonies. While the same techniques for sampling the stochastic equations governing cellular processes apply to all these systems, the setup of the simulation volume and initial state for the simulations differ significantly. Lattice Microbes is a GPU accelerated stochastic biological problem solving environment with a general interface that meets the diverse requirements of these types of biological simulations. The software includes a Python interface that allows facile customization of the simulation setup and on-the-fly modification of the simulation state with access to highly optimized, compiled algorithms for solving the stochastic equations. Here we describe the interface to Lattice Microbes and present several examples of very different simulations that were rapidly prototyped in Python. Two examples show standard stochastic biochemical problems. As an example of the true utility of the Python interface, the highly optimized method for sampling the reaction-diffusion master equation in Lattice Microbes is coupled to the COBRA toolbox, a Python package that solves a linear programming problem representing the steady-state reaction flux through the full metabolic model of the cell. This final example shows how the Python interface allows the GPU optimized code to be used to interface with other methods.
Verwandte Themen: Systemanalyse Numerische Analyse Exobiology Physik der Elementarteilchen und Felder Elektronik und Elektrotechnik Einrichtungen und Anlagen (Raumfahrt) Luft- und Raumfahrtmedizin
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