Installation instructions

Disclaimer

MolMod is developed and tested on modern Linux environments. The installation and usage will therefore be relatively easy on Linux. If you want to use MolMod on other operating systems such as Windows or OSX, you should have a minimal computer geek status to get it working. We are always interested in hearing from your installation adventures.

External dependencies

Some software packages should be installed before MolMod can be installed or used. It is recommended to use the software package management of your Linux distribution to install these dependencies.

The following software must be installed for MolMod:

Most Linux distributions can install this software with just a single command:

  • Ubuntu 12.4:

    sudo apt-get install python python-dev python-numpy gfortran gcc git-core python-nose python-sphinx
    
  • Debian 5. You first have to become root because the sudo program is not configured by default.

    su -
    apt-get install python python-dev python-numpy gfortran gcc git-core python-nose python-sphinx
    exit
    
  • Fedora 17:

    sudo yum install python-devel numpy numpy-f2py gcc-gfortran gcc git python-nose sphinx
    
  • Suse 11.2:

    sudo zypper install python-devel python-numpy gcc gcc-fortran git python-nose sphinx
    

Download MolMod

Stable release

The latest stable release of MolMod can be downloaded here:

Choose a suitable directory, e.g. ~/build, download and unpack the archive:

mkdir -p ~/build
cd ~/build
wget http://github.com/molmod/molmod/releases/download/v1.1/molmod-1.1.tar.gz
tar -xvzf molmod-1.1.tar.gz
cd molmod-1.1

Latest development code (experts only)

In order to get the latest development version of the source code, and to upload your own changes, you need to work with git. Git is a version control system that makes life easy when a group of people are working on a common source code. All information about git (including downloads and tutorials) can be found here: http://git-scm.com/. The official git URL of MolMod is: git://github.com/molmod/molmod.git. In order to clone the public MolMod repository, run this command:

git clone git://github.com/molmod/molmod.git
cd molmod

The version history can be updated with the latest patches with the following command:

git pull

There is also a web interface to MolMod’s git repository: https://github.com/molmod/molmod

Install MolMod

The following series of commands will download the latest versions of the MolMod package, and will then install it into your home directory.

./setup.py install --user

You are now ready to start using MolMod!

A few quick checks

It may be interesting to double check your installation before proceeding, unless you feel lucky.

The MolMod modules should be accessible from any Python session. This can be checked by starting Python interactively and loading the modules manually. There should be no errors when importing the modules. Just, make sure that you change your current directory to something else than the MolMod source tree before trying this test, e.g. as follows:

$ cd
$ python
Python 2.6.5 (r265:79063, Apr 16 2010, 13:57:41)
[GCC 4.4.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import molmod
>>> quit()

Testing your installation

The installation can be tested outside the source tree as follows:

cd
nosetests -v molmod

This will run a series of tests to check the validity of the outcomes generated by MolMod. If some tests fail, post the output of the tests on the MolMod mailing list. (There are currently three test that are skipped.)