---
title: Python
#tags:
last_updated: 28 September 2020
keywords: [python, anaconda, conda, jupyter, numpy]
summary: Running Python on Merlin
sidebar: merlin6_sidebar
permalink: /merlin6/python.html
---

PSI provides a variety of ways to execute python code.

1. **psi-python modules** - Central installation with common packages pre-installed
2. **Anaconda** - Custom environments for using installation and development
3. **Jupyterhub** - Execute Jupyter notebooks on the cluster
4. **System Python** - Do not use! Only for OS applications.

## `psi-python` modules

The easiest way to use python is using the centrally maintained psi-python modules:

```
~ $ module avail psi-python
------------------------------------- Programming:  ------------------------------

psi-python27/2.3.0              psi-python27/2.2.0              psi-python27/2.4.1
psi-python27/4.4.0              psi-python34/2.1.0              psi-python35/4.2.0
psi-python36/4.4.0

~ $ module load psi-python36/4.4.0
~ $ python --version
Python 3.6.1 :: Anaconda 4.4.0 (64-bit)
```

These include over 250 common packages from the
[Anaconda](https://docs.anaconda.com/anaconda/) software distribution, including
numpy, pandas, requests, flask, hdf5, and more.

{% include callout.html type="warning" content="
**Caution**{: .text-warning}
Do not use `module load python`. These modules are minimal installs intended as
dependencies for other modules that embed python.
"%}

## Anaconda

[Anaconda](https://www.anaconda.com/) ("conda" for short) is a package manager with
excellent python integration. Using it you can create isolated environments for each
of your python applications, containing exactly the dependencies needed for that app.
It is similar to the [virtualenv](http://virtualenv.readthedocs.org/) python package,
but can also manage non-python requirements.

### Loading conda

Conda is loaded from the module system:

```
module load anaconda
```

### Using pre-made environments

Loading the module provides the `conda` command, but does not otherwise change your
environment. First an environment needs to be activated. Available environments can
be seen with `conda info --envs` and include many specialized environments for
software installs. After activating you should see the environment name in your
prompt:

```
~ $ conda activate datascience_py37
(datascience_py37) ~ $
```

### CondaRC file

Creating a `~/.condarc` file is recommended if you want to create new environments on
merlin. Environments can grow quite large, so you will need to change the default
storage location from the default (your home directory) to a larger volume (usually
`/data/user/$USER`).

Save the following as `$HOME/.condarc` (update USERNAME and module version as
necessary):

```
always_copy: true

envs_dirs:
  - /data/user/USERNAME/conda/envs

pkgs_dirs:
  - /data/user/USERNAME/conda/pkgs
  - /opt/psi/Programming/anaconda/2019.07/conda/pkgs

channels:
  - http://conda-pkg.intranet.psi.ch
  - conda-forge
  - defaults
```

Run `conda info` to check that the variables are being set correctly.

### Creating environments

We will create an environment named `myenv` which uses an older version of numpy, e.g. to test for backwards compatibility of our code (the `-q` and `--yes` switches are just for not getting prompted and disabling the progress bar). The environment will be created in the default location as defined by the `.condarc` configuration file (see above).

```
~ $ conda create -q --yes -n 'myenv1' numpy=1.8 scipy ipython

Fetching package metadata: ...
Solving package specifications: .
Package plan for installation in environment /gpfs/home/feichtinger/conda-envs/myenv1:

The following NEW packages will be INSTALLED:

    ipython:    2.3.0-py27_0
    numpy:      1.8.2-py27_0
    openssl:    1.0.1h-1
    pip:        1.5.6-py27_0
    python:     2.7.8-1
    readline:   6.2-2
    scipy:      0.14.0-np18py27_0
    setuptools: 5.8-py27_0
    sqlite:     3.8.4.1-0
    system:     5.8-1
    tk:         8.5.15-0
    zlib:       1.2.7-0

To activate this environment, use:
$ source activate myenv1

To deactivate this environment, use:
$ source deactivate
```

The created environment contains **just the packages that are needed to satisfy the
requirements** and it is local to your installation. The python installation is even
independent of the central installation, i.e. your code will still work in such an
environment, even if you are offline or AFS is down. However, you need the central
installation if you want to use the `conda` command itself.

Packages for your new environment will be either copied from the central one into
your new environment, or if there are newer packages available from anaconda and you
did not specify exactly the version from our central installation, they may get
downloaded from the web. **This will require significant space in the `envs_dirs`
that you defined in `.condarc`. If you create other environments on the same local
disk, they will share the packages using hard links.

We can switch to the newly created environment with the `conda activate` command.

```
$ conda activate myenv1
```

{% include callout.html type="info" content="Note that anaconda's activate/deactivate
scripts are compatible with the bash and zsh shells but not with [t]csh." %}

Let's test whether we indeed got the desired numpy version:

```
$ python -c 'import numpy as np; print np.version.version'

1.8.2
```

You can install additional packages into the active environment using the `conda
install` command.

```
$ conda install --yes -q bottle

Fetching package metadata: ...
Solving package specifications: .
Package plan for installation in environment /gpfs/home/feichtinger/conda-envs/myenv1:

The following NEW packages will be INSTALLED:

    bottle: 0.12.5-py27_0
```

## Jupyterhub

Jupyterhub is a service for running code notebooks on the cluster, particularly in
python. It is a powerful tool for data analysis and prototyping. For more infomation
see the [Jupyterhub documentation]({{"jupyterhub.html"}}).

## Pythons to avoid

Avoid using the system python (`/usr/bin/python`). It is intended for OS software and
may not be up to date.

Also avoid the 'python' module (`module load python`). This is a minimal install of
python intended for embedding in other modules.
