If you require python modules on farm machines that are not yet available there are 3 possible ways to get this fixed:

  1. Check if the module has been packaged by Debian and if it is available for the current release.
  2. Install it in your home directory.
  3. Use Python VirtualEnvs to install your modules independently from the ones already available on your Linux installation.

Checking if the module is available as Debian package

Python module packages in Debian are named python-MODULENAME, e.g. for sphinx the Debian package is DebPkg:python-sphinxdebian. As a general rule we can only provide modules and versions that are available in the official Debian package repositories since we lack the man power to build and maintain other ones.

If the module you want is available as a Debian package you can check the available version by runningn apt-cache policy PACKAGENAME:
$ apt-cache policy python-sphinx
  Installed: 1.1.3+dfsg-4
  Candidate: 1.1.3+dfsg-4
  Version table:
 *** 1.1.3+dfsg-4 0
        500 wheezy/main amd64 Packages
        100 /var/lib/dpkg/status

The output of the command states that Debian package version 1.1.3+dfsg-4 of python-sphinx is currently installed which corresponds to upstream version 1.1.3.

$ apt-cache policy python-sphinx-issuetracker
  Installed: (none)
  Candidate: 0.8-1
  Version table:
     0.8-1 0
        500 wheezy/main amd64 Packages

In this case Debian package version 0.8-1 is available but not installed; 0.8-1 corresponds to upstream 0.8.

If you require a python library that is available but not installed, create a ticket to including the name of the package and your local machine.

Installing modules into your home directory

Setting environment variables

If you decide to install python libraries to your home directory you will probably need to extend your python load path. This can be done via the environment variable PYTHONPATH which by default is not set. As long as it is not set, your python interpretet will usually only look for modules in certain system directories. You can find out what these are by running the following command:

$ python -c "import sys; print sys.path"
['', '/usr/lib/python2.7', '/usr/lib/python2.7/plat-linux2', '/usr/lib/python2.7/lib-tk', '/usr/lib/python2.7/lib-old', '/usr/lib/python2.7/lib-dynload', '/usr/local/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages/PIL', '/usr/lib/python2.7/dist-packages/gtk-2.0', '/usr/lib/pymodules/python2.7']

If you e.g. install modules to ~/mypythonmodules and want them to be included in your load path you can do it like this:
$ PYTHONPATH=~/mypythonmodules python -c "import sys; print sys.path"
['', '/u/yourusername/mypythonmodules', '/usr/lib/python2.7', '/usr/lib/python2.7/plat-linux2', '/usr/lib/python2.7/lib-tk', '/usr/lib/python2.7/lib-old', '/usr/lib/python2.7/lib-dynload', '/usr/local/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages/PIL', '/usr/lib/python2.7/dist-packages/gtk-2.0', '/usr/lib/pymodules/python2.7']

Since setting the variable each time you run python is annoying you can either export this variable in your current shell by running
$ export PYTHONPATH=~/mypythonmodules

or set it for every new shell by adding that line to your ~/.profile or ~/.bashrc.

If you install modules in your home dir and forget to set PYTHONPATH you might experience errors like
ImportError: No module named mymodule

Installing via pip

The default way to run pip would be to execute pip install MODULENAME however this will probably fail because without further options pip will try to mess with system directories.

Instead think about where in your home directory you would like to store your python stuff and pass this location as a prefix option like this (example installs sphinxcontrib-bibtex +dependencies to ~/python):

$ pip install --install-option="--prefix=~/python" sphinxcontrib-bibtex
Downloading/unpacking sphinxcontrib-bibtex
  Downloading sphinxcontrib-bibtex-0.3.4.tar.gz (50Kb): 50Kb downloaded
  Running egg_info for package sphinxcontrib-bibtex

...skipped output ...

Requirement already satisfied (use --upgrade to upgrade): PyYAML >=3.01 in /usr/lib/python2.7/dist-packages (from pybtex>=0.17->sphinxcontrib-bibtex)

...skipped output ...

    Skipping installation of /u/yourusername/python/lib/python2.7/site-packages/sphinxcontrib/ (namespace package)

...skipped output ...

Successfully installed sphinxcontrib-bibtex latexcodec pybtex pybtex-docutils six oset
Cleaning up...

I chose this example and these excerpt of the output to highlight a few things:
  • pip will start downloading the package and then check its dependencies
  • If pip recognized that some dependencies are already available (in the example PyYAML) it will skip installation
  • pip will not not install files for so called namespace packages. This will cause import sphinxcontrib.bibtex to fail, since sphinxcontrib which includes a directory bibtex does not have a file and will therefore not be recognized as a module
  • /u/yourusername/python/lib/python2.7/site-packages is the directory you will need to add to your PYTHONPATH

After installation you will need to do the following steps:
  • Set your PYTHONPATH
  • Add an empty file for all namespace modules
  • (Optional) If your python modules also install scripts to ~/python/bin you might want to extend your PATH

In the example above this is achieved by running the following commands:

$ export PYTHONPATH=~/python/lib/python2.7/site-packages
$ touch $PYTHONPATH/sphinxcontrib/
$ # optional: set PATH
$ export PATH=~/python/bin:$PATH
$ # optional: set PYTHONPATH in your .bashrc.
$ echo export PYTHONPATH=~/python/lib/python2.7/site-packages >> ~/.bashrc

Use Python VirtualEnvs

What is a Python virtual environment?

At its core, the main purpose of Python virtual environments is to create an isolated environment for Python projects. This means that each project can have its own dependencies, regardless of what dependencies every other project has.

On the GSI Linux desktops the virtualenv command is available for Python version 2 and version 3. In particular, the following three packages should be installed on your machine:
  • python-virtualenv
  • python3-virtualenv
  • virtualenv

An example: install Tensorflow

The following is an example on how to install the Tensorflow framework from Google using Python VirtualEnvs.
  1. mkdir /data.local1/tensorflow
  2. virtualenv --system-site-packages /data.local1/tensorflow
  3. source /data.local1/tensorflow/bin/activate (for Bash or Zsh). You should see that the previous command has modified your shell prompt into something like: (tensorflow)$
  4. pip install --upgrade tensorflow
The step '4' will take a while because pip has to download all the dependencies and compile everything.

NOTE: in order to use Tensorflow you'll always has to use the command specified at step 3.

If you wish to leave the Python virtual environment you'll just need to issue the following command: deactivate


A short list of references about Python virtual environments:

Use a Python software distribution (Anaconda/Miniconda)

When it's not possible to install new version of modules due to an old version of the interpreter, the only remaining possibility is to use a Python distribution like Anaconda

Anaconda basically provide an archive distribution comprising of the latest version of Python (both 3.x and 2.x tree), multiple modules and a package management system called Conda

We highly recommend to use a reduced version of Anaconda, called Miniconda which just include the Python interpreter and the Conda package manager.

Install Miniconda

The following steps can be followed to install Miniconda with Python 3.7 and create your virtual environments with it.

0. Download the Miniconda environment installer (for Linux) from here

1. Start the installer on your terminal: bash (and accept the license agreement)

2.By default,the installer will install Miniconda under $HOME/miniconda3 (you are free to choose another path, for example /data.local if available on your desktop).

2a. NOTE: if possible, avoid to install conda and related modules under your Lustre directory. Depending on the modules needed, the installation will be broken down in hundred, sometimes thousands of small files and this will greatly hamper the performance of Lustre for all the users.

3.The installer will then proceed to install additional packages into the destination directory chosen at point 2 .It will then ask if you want to initialize your environment. If you choose to do so, the installer will add the following lines at the very end of your .bashrc file:

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/home/myuser/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
    if [ -f "/home/myuser/miniconda3/etc/profile.d/" ]; then
        . "/home/myuser/miniconda3/etc/profile.d/"
        export PATH="/home/myuser/miniconda3/bin:$PATH"
unset __conda_setup
# <<< conda initialize <<<

4. For the changes to take effect, it's better if you close your terminal window and open a new one. A simple test would be to run the conda package manager on the command line in the new terminal session:

:~$ conda --version
conda 4.7.12

NOTE: the version may change for newer version of the conda package manager.

Install Python Modules

A list of conda commands to list, install and remove Python modules:

* List all installed packages in current virtual environment:

:~$ conda list

* Install or uninstall modules

:~$ conda install numpy
:~$ conda uninstall flask

* Update and search for a specific module:

:~$ conda update sqlite
:~$ conda search bottle

Use environments with Conda

By default, when Miniconda is installed, it will automatically define a Python environment called base (which you should also see added to your linux prompt in the console window, unless you have customized it in a different way). To avoid polluting your miniconda environment, it would be easy to create a separated one with the following commands. Instead of mytest, you are of course free of using whichever name you saw fit. Again, the versions reported below may change depending on the version of conda you are using.

:~$ conda create --name mytest python=3.7
Collecting package metadata (current_repodata.json): done           
Solving environment: done

## Package Plan ##                                                                                                                                                                                                                                            
  environment location: /home/myuser/miniconda3/envs/mytest                                                                                                                                                                                                 
  added / updated specs:                                                                                                                                                                                                                                      
    - python=3.7                                                                                                                                                                                                                                              

The following packages will be downloaded:
    package                    |            build                                                                                                                                                                                                            
    ca-certificates-2019.11.27 |                0         124 KB                                                                                                                                                                                             
    certifi-2019.11.28         |           py37_0         153 KB                                                                                                                                                                                             
    ld_impl_linux-64-2.33.1    |       h53a641e_7         568 KB                                                                                                                                                                                             
    openssl-1.1.1d             |       h7b6447c_3         2.5 MB                                                                                                                                                                                             
    pip-19.3.1                 |           py37_0         1.6 MB                                                                                                                                                                                             
    python-3.7.6               |       h0371630_2        44.9 MB                                                                                                                                                                                             
    setuptools-44.0.0          |           py37_0         520 KB                                                                                                                                                                                             
    sqlite-3.30.1              |       h7b6447c_0         1.1 MB
    wheel-0.33.6               |           py37_0          42 KB
                                           Total:        51.4 MB
The following NEW packages will be INSTALLED:
  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  ca-certificates    pkgs/main/linux-64::ca-certificates-2019.11.27-0
  certifi            pkgs/main/linux-64::certifi-2019.11.28-py37_0
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7
  libedit            pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
  libffi             pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
  ncurses            pkgs/main/linux-64::ncurses-6.1-he6710b0_1
  openssl            pkgs/main/linux-64::openssl-1.1.1d-h7b6447c_3
  pip                pkgs/main/linux-64::pip-19.3.1-py37_0
  python             pkgs/main/linux-64::python-3.7.6-h0371630_2
  readline           pkgs/main/linux-64::readline-7.0-h7b6447c_5
  setuptools         pkgs/main/linux-64::setuptools-44.0.0-py37_0
  sqlite             pkgs/main/linux-64::sqlite-3.30.1-h7b6447c_0
  tk                 pkgs/main/linux-64::tk-8.6.8-hbc83047_0
  wheel              pkgs/main/linux-64::wheel-0.33.6-py37_0
  xz                 pkgs/main/linux-64::xz-5.2.4-h14c3975_4
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3

Proceed ([y]/n)? y

Downloading and Extracting Packages

The new environment is now installed but it's not activated yet. In order to so:

conda activate mytest

Deactivation (and coming back to the base environment) is also a simple command:

conda deactivate

Remove an environment and all its installed modules:

conda remove --name mytest --all

Installing and removing modules works with the same conda commands explained in the previous section but they will just be confined in the environment.


* Conda commands reference

* Conda vs pip vs virtualenv

-- MatteoDessalvi - 28 Feb 2020

-- BastianNeuburger - 19 Jul 2016
Topic revision: r8 - 2020-02-28, MatteoDessalvi - This page was cached on 2021-10-22 - 21:49.

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