Tools for Simulation Study

A collection of freely available tools．

The explanations below for setting up tools are for Unix-like environments, such as Linux or Mac OS. On these environments, software settings are written in configuration files in the user's home directory (given by ~ / or ${HOME}/).

• FFTW

  Type

  Programming

  Description

  Library for fast Fourier transform

  Version

  Version 3 is recommended (Version 2 is incompatible with version 3.)

• GIMP

  Type

  Graphics

  Description

  Image manipulation

• GNU Compiler Collection

  Type

  Programming

  Description

  Compiler

• git

  Type

  Tool

  Description

  version control

  Memo

  To use proxy, configure the proxy server setting by git config command. The setting is stored in ~/.gitconfig.

  git config --global http.proxy http://<IP ADDRESS>:<PORT NUMBER>
  git config --global https.proxy http://<IP ADDRESS>:<PORT NUMBER>

• gnuplot

  Type

  Visualization and data processing

  Description

  Data plot, graphing

  Version

  Version 5 or higher is recommended

  Memo

  The configuration file is ~/.gnuplot．To enable Fortran output format (use of the D and Q format descriptors), and make the default terminal x11

  set datafile fortran
  set terminal x11

• HDF5

  Type

  Programming

  Description

  Library for data format

  Version

  The latest version is 1.10, but ver. 1.8 is used in many sites. (as of 2016/11/20)
  Parallel I/O capability is recommended to be activated．

• Inkscape

  Type

  Graphics

  Description

  Vector graphics editor

• JupyterLab

  Type

  Integrated development environment，Visualization and data processing

  Description

  Code editor, data plot, graphing

• MPICH

  Type

  Programming

  Description

  Implementation of MPI standard (Library)

• NetCDF

  Type

  Programming

  Description

  Library for data format

  Version

  Parallel I/O capability is recommended to be activated. It depends on HDF5.

• Octave

  Type

  Visualization and data processing

  Description

  Data plot, graphing

  Version

  Version 4 or higher is recommended

  Memo

  GNU Octave supports the installation of extra packages to add extra functionalities. For example, netcdf to support I/O for NetCDF data or io to support I/O for various data formats (including Fortran namelists). To use packages, install required packages, and load them by the 'pkg' command or load them at startup by setting up the start-up file. The start-up file for octave is ~/.octaverc. Like configuring the shell, the commands written in this file are executed at startup.

  pkg load pkgname
  addpath('path_to_script');
  graphics_toolkit('gnuplot');

  'graphics_toolkit' is a command to setup graphics engine. By using gnuplot as a graphics engine, you can you symbols available in gnuplot. The available toolkis are shown by the available_graphics_toolkits.

• VS Code

  Type

  Integrated development environment

  Description

  Code editor

• Wolfram Engine

  Type

  Visualization and data processing

  Description

  Formulae manipulation