software: add conda

index.rst

@@ -4,6 +4,9 @@ Welcome to Tardis's documentation!
 Changelog
 =========
 
+3.6.1 (19.09.2019)
+  + added minimal howto for Conda
+
 3.6.1 (19.09.2019)
   + updated SPM12 section (env modules)
 

software/python.rst

@@ -158,6 +158,75 @@ directly. It is much more convenient to use the wrapper functions though.
    :file:`source /etc/bash_completion` **or** :file:`module load virtualenvwrapper`
 
 
+Conda
+-----
+
+Another approach to virtual environments (and a whole virtual operating system
+in fact) is provided by a third party, commercial python distribution called
+`Anaconda`_ (:file:`conda`). Though discouraged for smaller projects, you can
+use an environment module to load and activate a (mini)conda distribution on the
+Tardis:
+
+
+.. code-block:: bash
+
+   [krause@master ~] module avail conda
+
+   -------- /opt/environment/modules --------
+   conda/4.7.10
+   [krause@master ~] module load conda
+   [krause@master ~] conda -V
+   conda 4.7.10
+
+Once loaded, just like with `pyvenv` or `virtualenv`, you can create and manage
+multiple conda environments and keep specific python versions and their library
+dependencies in it. Note however, that conda will also download and manage
+a large number of system libraries, which *may* make bugs very hard to debug
+and could lead to unexpected reproducibility issues. Some software however can
+only be installed with conda and I strongly recommend to limit the use of conda
+for those specific projects.
+
+One example of those projects is Theano and its optional dependency pygpu. To
+install Theano (or other conda-only packages) you can create a new environment:
+
+.. code-block:: bash
+
+   [krause@master ~] module load conda                  # activate conda itself
+   [krause@master ~] conda create --yes --name theano
+   Collecting package metadata (current_repodata.json): done
+   Solving environment: done
+   [...]
+
+   [krause@master ~] conda activate theano              # activate a conda env
+   (theano) [krause@master ~] # now you can install packages into the env
+   (theano) [krause@master ~] conda install --yes numpy scipy mkl
+   [...]
+   (theano) [krause@master ~] conda install --yes theano pygpu
+   (theano) [krause@master ~] which python
+   /home/beegfs/krause/.conda/envs/theano/bin/python
+   (theano) [krause@master ~] python
+   Python 3.7.4 (default, Aug 13 2019, 20:35:49)
+   [GCC 7.3.0] :: Anaconda, Inc. on linux
+   Type "help", "copyright", "credits" or "license" for more information.
+   >>> import theano as t
+   WARNING (theano.tensor.blas): Using NumPy C-API based implementation for BLAS functions.
+   >>>
+
+
+To deactivate (and possibly remove) an existing conda environment, run:
+
+.. code-block:: bash
+
+   (theano) [krause@master ~] conda deactivate
+   [krause@master ~] # deactivated, safe to remove
+
+   [krause@master ~] conda remove --yes --name theano --all
+    Remove all packages in environment /home/beegfs/krause/.conda/envs/theano:
+	[...]
+
+
 .. _PyPI: https://pypi.python.org/pypi
 .. _pyvenv: https://virtualenvwrapper.readthedocs.io/en/latest
 .. _virtualenvwrapper: https://packaging.python.org/installing/#creating-virtual-environments
+.. _Anaconda: https://docs.conda.io/projects/conda
+