MIT

Green Research Group

Fundamental and Applied Chemical Kinetics

RPMDrate Installation

2.1. Installation

There are multiple ways to download RPMDrate to your computer:

2.2. Dependencies

RPMDrate depends on several other packages in order to provide its full functional capabilities. The following dependencies are required to compile and run RPMDrate:

  • Python (version 2.6.x or later, including any version of Python 3, is recommended)
  • NumPy (version 1.5.0 or later is recommended)
  • FFTW (version 3.3 or later is recommended)
  • A standard Fortran 90/95 compiler (e.g. gfortran, g95, ifort, etc.)

2.3. Compilation

Once you have obtained a copy of RPMDrate, either from a released package or from cloning the git repository, RPMDrate can be installed by invoking the setup.py script as usual:

$ python setup.py install

This will compile the Fortran source and Python wrapper code, which may take some time. Note that you may need administrator privileges to install RPMDrate.

If you wish to use RPMDrate without installing, simply add the folder containing this file to your PYTHONPATH environment variable and compile the source code in-place using the command

$ python setup.py build_ext --inplace

A Makefile that wraps these commands has been provided. The Makefile also provides a clean target for deleting all files created during compilation.

RPMDrate uses the f2py tool (bundled with NumPy) to expose its Fortran code to Python. The default compiling option for the FFTW library (which is required to link against when building Fortran extension modules using f2py) is “-lfftw3”. These options can be modified at the end of the setup.py file as the libraries options of the rpmdrate._main Fortran extension module. The libraries are assumed to be located in the standard library search path on target systems. If you need to link with these libraries in a non-standard location, you’ll have to specify the directories to search for those libraries. The library_dirs option is a list of directories to search for libraries at link-time, and the runtime_library_dirs option – for shared (dynamically loaded) libraries at run-time. (More information is available at http://docs.python.org/distutils.)

2.4. Local installation of Python

Below is the procedure to install Python 2.7 to your local account. This will place Python 2.7 in $HOME/local directory (e.g. /home/username/local). The whole procedure should not take more than 10-15 minutes.

  1. Install Python 2.7
$ mkdir $HOME/local

$ wget http://python.org/ftp/python/2.7.3/Python-2.7.3.tar.bz2

$ tar -xjvf Python-2.7.3.tar.bz2

$ cd Python-2.7.3

$ ./configure --prefix=$HOME/local

$ make

$ make install
  1. Edit .bash_profile to add these lines
$ export PATH=$HOME/local/bin:$PATH

$ export LD_LIBRARY_PATH=$HOME/local/lib:$LD_LIBRARY_PATH
  1. Log out and in again so modified .bash_profile takes effect
  2. Run Python once to ensure default is 2.7 3. Install setuptools
$ wget http://pypi.python.org/packages/source/s/setuptools/setuptools-0.6c11.tar.gz

$ tar -xzvf setuptools-0.6c11.tar.gz

$ cd setuptools-0.6c11

$ python setup.py install
  1. Install pip
$ wget http://pypi.python.org/packages/source/p/pip/pip-1.1.tar.gz

$ tar -xzvf pip-1.1.tar.gz

$ cd pip-1.1

$ python setup.py install
  1. Install numpy (and f2py)
$ pip install numpy
2.4.1. Developing for RPMDrate

If you would like to follow along with the bleeding-edge development of RPMDrate, the best way to do so is to clone the repository using our version control system, git:

$ git clone git://github.com/YurySuleymanov/RPMDrate_v2.0.git

This enables you to easy update your local copy with the latest changes. If you intend to contribute to RPMDrate – and you are welcome to do so! – you should fork the project on GitHub first, and clone from your fork.

Once you have cloned the repository, follow the compilation instructions for building RPMDrate in-place. You may also wish to add the folder containing the RPMDrate repository to your PYTHONPATH environment variable.