python_environment_set_up.md

install necessary software to cluster machine

pyenv

• download and install pyenv via github

$ git clone https://github.com/yyuu/pyenv.git ~/.pyenv

• add the following to ~/.bash_profile

export PYENV_ROOT="${HOME}/.pyenv"
if [ -d "${PYENV_ROOT}" ]; then
    export PATH=${PYENV_ROOT}/bin:${PYENV_ROOT}/shims:${PATH}
    eval "$(pyenv init -)"
fi

• reflect

$ source ~/.bash_profile

• download and install pyenv-virtualenv plug-in

$ git clone git://github.com/yyuu/pyenv-virtualenv.git ~/.pyenv/plugins/pyenv-virtualenv

Anaconda

• Anaconda comes with scientific packages
• install anaconda with pyenv

$ pyenv versions                 # List available python versions on the machine
$ pyenv install -l               # List available python versions for installation
$ pyenv install anaconda2-4.1.1  # Install a version whatever you'd like to work with
$ pyenv rehash

• swich python versions with pyenv

$ pyenv versions
$ pyenv global anaconda2-4.1.1
$ pyenv versions

virtualenvvwrapper

$ pip install virtualenvwrapper

Jupyter

$ pip install jupyter

connect to cluster machine (login node)

local$ ssh -L 8888:localhost:8888 servername

References

• http://www.pupha.net/archives/2213/
• http://www.task-notes.com/entry/20151116/1447642800
• http://www.alfredo.motta.name/create-isolated-jupyter-ipython-kernels-with-pyenv-and-virtualenv/