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<h1 id="python">Python<a class="headerlink" href="#python" title="Permanent link"></a></h1>
<p>PSI provides a variety of ways to execute python code.</p>
<ol>
<li><strong>Anaconda</strong> - Custom environments for using installation and development</li>
<li><strong>Jupyterhub</strong> - Execute Jupyter notebooks on the cluster</li>
<li><strong>System Python</strong> - Do not use! Only for OS applications.</li>
</ol>
<h2 id="anaconda">Anaconda<a class="headerlink" href="#anaconda" title="Permanent link"></a></h2>
<p><a href="https://www.anaconda.com/">Anaconda</a> ("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
<a href="http://virtualenv.readthedocs.org/">virtualenv</a> python package, but can also
manage non-python requirements.</p>
<h3 id="loading-conda">Loading conda<a class="headerlink" href="#loading-conda" title="Permanent link"></a></h3>
<p>Conda is loaded from the module system:</p>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-0-1"><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>module<span class="w"> </span>load<span class="w"> </span>anaconda
</span></code></pre></div>
<h3 id="using-pre-made-environments">Using pre-made environments<a class="headerlink" href="#using-pre-made-environments" title="Permanent link"></a></h3>
<p>Loading the module provides the <code>conda</code> command, but does not otherwise change your
environment. First an environment needs to be activated. Available environments can
be seen with <code>conda info --envs</code> and include many specialized environments for
software installs. After activating you should see the environment name in your
prompt:</p>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-1-1"><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>conda<span class="w"> </span>activate<span class="w"> </span>datascience_py37
</span></code></pre></div>
<h3 id="condarc-file">CondaRC file<a class="headerlink" href="#condarc-file" title="Permanent link"></a></h3>
<p>Creating a <code>~/.condarc</code> 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
<code>/data/user/$USER</code>).</p>
<p>Save the following as <code>$HOME/.condarc</code>:</p>
<div class="language-yaml highlight"><span class="filename">YAML</span><pre><span></span><code><span id="__span-2-1"><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a><span class="nt">always_copy</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">true</span>
</span><span id="__span-2-2"><a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>
</span><span id="__span-2-3"><a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a><span class="nt">envs_dirs</span><span class="p">:</span>
</span><span id="__span-2-4"><a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a><span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">/data/user/$USER/conda/envs</span>
</span><span id="__span-2-5"><a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a>
</span><span id="__span-2-6"><a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></a><span class="nt">pkgs_dirs</span><span class="p">:</span>
</span><span id="__span-2-7"><a id="__codelineno-2-7" name="__codelineno-2-7" href="#__codelineno-2-7"></a><span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">/data/user/$USER/conda/pkgs</span>
</span><span id="__span-2-8"><a id="__codelineno-2-8" name="__codelineno-2-8" href="#__codelineno-2-8"></a><span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">$ANACONDA_PREFIX/conda/pkgs</span>
</span><span id="__span-2-9"><a id="__codelineno-2-9" name="__codelineno-2-9" href="#__codelineno-2-9"></a>
</span><span id="__span-2-10"><a id="__codelineno-2-10" name="__codelineno-2-10" href="#__codelineno-2-10"></a><span class="nt">channels</span><span class="p">:</span>
</span><span id="__span-2-11"><a id="__codelineno-2-11" name="__codelineno-2-11" href="#__codelineno-2-11"></a><span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">conda-forge</span>
</span><span id="__span-2-12"><a id="__codelineno-2-12" name="__codelineno-2-12" href="#__codelineno-2-12"></a><span class="w"> </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">nodefaults</span>
</span></code></pre></div>
<p>Run <code>conda info</code> to check that the variables are being set correctly.</p>
<h3 id="creating-environments">Creating environments<a class="headerlink" href="#creating-environments" title="Permanent link"></a></h3>
<p>We will create an environment named <code>myenv</code> which uses an older version of
numpy, e.g. to test for backwards compatibility of our code (the <code>-q</code> and
<code>--yes</code> switches are just for not getting prompted and disabling the progress
bar). The environment will be created in the default location as defined by the
<code>.condarc</code> configuration file (see above).</p>
<div class="language-console highlight"><span class="filename">Bash Session</span><pre><span></span><code><span id="__span-3-1"><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a><span class="gp">$ </span>conda<span class="w"> </span>create<span class="w"> </span>-q<span class="w"> </span>--yes<span class="w"> </span>-n<span class="w"> </span><span class="s1">'myenv1'</span><span class="w"> </span><span class="nv">numpy</span><span class="o">=</span><span class="m">1</span>.8<span class="w"> </span>scipy<span class="w"> </span>ipython
</span><span id="__span-3-2"><a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>
</span><span id="__span-3-3"><a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a><span class="go">Fetching package metadata: ...</span>
</span><span id="__span-3-4"><a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a><span class="go">Solving package specifications: .</span>
</span><span id="__span-3-5"><a id="__codelineno-3-5" name="__codelineno-3-5" href="#__codelineno-3-5"></a><span class="go">Package plan for installation in environment /gpfs/home/feichtinger/conda-envs/myenv1:</span>
</span><span id="__span-3-6"><a id="__codelineno-3-6" name="__codelineno-3-6" href="#__codelineno-3-6"></a>
</span><span id="__span-3-7"><a id="__codelineno-3-7" name="__codelineno-3-7" href="#__codelineno-3-7"></a><span class="go">The following NEW packages will be INSTALLED:</span>
</span><span id="__span-3-8"><a id="__codelineno-3-8" name="__codelineno-3-8" href="#__codelineno-3-8"></a>
</span><span id="__span-3-9"><a id="__codelineno-3-9" name="__codelineno-3-9" href="#__codelineno-3-9"></a><span class="go"> ipython: 2.3.0-py27_0</span>
</span><span id="__span-3-10"><a id="__codelineno-3-10" name="__codelineno-3-10" href="#__codelineno-3-10"></a><span class="go"> numpy: 1.8.2-py27_0</span>
</span><span id="__span-3-11"><a id="__codelineno-3-11" name="__codelineno-3-11" href="#__codelineno-3-11"></a><span class="go"> openssl: 1.0.1h-1</span>
</span><span id="__span-3-12"><a id="__codelineno-3-12" name="__codelineno-3-12" href="#__codelineno-3-12"></a><span class="go"> pip: 1.5.6-py27_0</span>
</span><span id="__span-3-13"><a id="__codelineno-3-13" name="__codelineno-3-13" href="#__codelineno-3-13"></a><span class="go"> python: 2.7.8-1</span>
</span><span id="__span-3-14"><a id="__codelineno-3-14" name="__codelineno-3-14" href="#__codelineno-3-14"></a><span class="go"> readline: 6.2-2</span>
</span><span id="__span-3-15"><a id="__codelineno-3-15" name="__codelineno-3-15" href="#__codelineno-3-15"></a><span class="go"> scipy: 0.14.0-np18py27_0</span>
</span><span id="__span-3-16"><a id="__codelineno-3-16" name="__codelineno-3-16" href="#__codelineno-3-16"></a><span class="go"> setuptools: 5.8-py27_0</span>
</span><span id="__span-3-17"><a id="__codelineno-3-17" name="__codelineno-3-17" href="#__codelineno-3-17"></a><span class="go"> sqlite: 3.8.4.1-0</span>
</span><span id="__span-3-18"><a id="__codelineno-3-18" name="__codelineno-3-18" href="#__codelineno-3-18"></a><span class="go"> system: 5.8-1</span>
</span><span id="__span-3-19"><a id="__codelineno-3-19" name="__codelineno-3-19" href="#__codelineno-3-19"></a><span class="go"> tk: 8.5.15-0</span>
</span><span id="__span-3-20"><a id="__codelineno-3-20" name="__codelineno-3-20" href="#__codelineno-3-20"></a><span class="go"> zlib: 1.2.7-0</span>
</span><span id="__span-3-21"><a id="__codelineno-3-21" name="__codelineno-3-21" href="#__codelineno-3-21"></a>
</span><span id="__span-3-22"><a id="__codelineno-3-22" name="__codelineno-3-22" href="#__codelineno-3-22"></a><span class="go">To activate this environment, use:</span>
</span><span id="__span-3-23"><a id="__codelineno-3-23" name="__codelineno-3-23" href="#__codelineno-3-23"></a><span class="gp">$ </span><span class="nb">source</span><span class="w"> </span>activate<span class="w"> </span>myenv1
</span><span id="__span-3-24"><a id="__codelineno-3-24" name="__codelineno-3-24" href="#__codelineno-3-24"></a>
</span><span id="__span-3-25"><a id="__codelineno-3-25" name="__codelineno-3-25" href="#__codelineno-3-25"></a><span class="go">To deactivate this environment, use:</span>
</span><span id="__span-3-26"><a id="__codelineno-3-26" name="__codelineno-3-26" href="#__codelineno-3-26"></a><span class="gp">$ </span><span class="nb">source</span><span class="w"> </span>deactivate
</span></code></pre></div>
<p>The created environment contains <strong>just the packages that are needed to satisfy the
requirements</strong> 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 <code>conda</code> command itself.</p>
<p>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. <strong>This will require significant space in the <code>envs_dirs</code>
that you defined in <code>.condarc</code></strong>. If you create other environments on the same local
disk, they will share the packages using hard links.</p>
<p>We can switch to the newly created environment with the <code>conda activate</code> command.</p>
<div class="language-bash highlight"><span class="filename">Bash</span><pre><span></span><code><span id="__span-4-1"><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>conda<span class="w"> </span>activate<span class="w"> </span>myenv1
</span></code></pre></div>
<div class="admonition info">
<p class="admonition-title">Info</p>
<p>Note that anaconda's activate/deactivate scripts are compatible with the
bash and zsh shells but not with [t]csh.</p>
</div>
<p>Let's test whether we indeed got the desired numpy version:</p>
<div class="language-console highlight"><span class="filename">Bash Session</span><pre><span></span><code><span id="__span-5-1"><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a><span class="gp">$ </span>python<span class="w"> </span>-c<span class="w"> </span><span class="s1">'import numpy as np; print np.version.version'</span>
</span><span id="__span-5-2"><a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a>
</span><span id="__span-5-3"><a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a><span class="go">1.8.2</span>
</span></code></pre></div>
<p>You can install additional packages into the active environment using the <code>conda
install</code> command.</p>
<div class="language-console highlight"><span class="filename">Bash Session</span><pre><span></span><code><span id="__span-6-1"><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a><span class="gp">$ </span>conda<span class="w"> </span>install<span class="w"> </span>--yes<span class="w"> </span>-q<span class="w"> </span>bottle
</span><span id="__span-6-2"><a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a>
</span><span id="__span-6-3"><a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a><span class="go">Fetching package metadata: ...</span>
</span><span id="__span-6-4"><a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a><span class="go">Solving package specifications: .</span>
</span><span id="__span-6-5"><a id="__codelineno-6-5" name="__codelineno-6-5" href="#__codelineno-6-5"></a><span class="go">Package plan for installation in environment /gpfs/home/feichtinger/conda-envs/myenv1:</span>
</span><span id="__span-6-6"><a id="__codelineno-6-6" name="__codelineno-6-6" href="#__codelineno-6-6"></a>
</span><span id="__span-6-7"><a id="__codelineno-6-7" name="__codelineno-6-7" href="#__codelineno-6-7"></a><span class="go">The following NEW packages will be INSTALLED:</span>
</span><span id="__span-6-8"><a id="__codelineno-6-8" name="__codelineno-6-8" href="#__codelineno-6-8"></a>
</span><span id="__span-6-9"><a id="__codelineno-6-9" name="__codelineno-6-9" href="#__codelineno-6-9"></a><span class="go"> bottle: 0.12.5-py27_0</span>
</span></code></pre></div>
<h2 id="jupyterhub">Jupyterhub<a class="headerlink" href="#jupyterhub" title="Permanent link"></a></h2>
<p>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 <a href="../../jupyterhub/jupyterhub/">Jupyterhub documentation</a>.</p>
<h2 id="pythons-to-avoid">Pythons to avoid<a class="headerlink" href="#pythons-to-avoid" title="Permanent link"></a></h2>
<p>Avoid using the system python (<code>/usr/bin/python</code>). It is intended for OS
software and may not be up to date.</p>
<p>Also avoid the 'python' module (<code>module load python</code>). This is a minimal
install of python intended for embedding in other modules.</p>
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