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| <section id="python-package-management"> |
| <h1>Python Package Management<a class="headerlink" href="#python-package-management" title="Permalink to this headline">#</a></h1> |
| <p>When you want to run your PySpark application on a cluster such as YARN, Kubernetes, etc., you need to make |
| sure that your code and all used libraries are available on the executors.</p> |
| <p>As an example, let’s say you may want to run the <a class="reference internal" href="sql/arrow_pandas.html#series-to-scalar"><span class="std std-ref">Pandas UDF examples</span></a>. |
| As it uses pyarrow as an underlying implementation we need to make sure to have pyarrow installed on each executor |
| on the cluster. Otherwise you may get errors such as <code class="docutils literal notranslate"><span class="pre">ModuleNotFoundError:</span> <span class="pre">No</span> <span class="pre">module</span> <span class="pre">named</span> <span class="pre">'pyarrow'</span></code>.</p> |
| <p>Here is the script <code class="docutils literal notranslate"><span class="pre">app.py</span></code> from the previous example that will be executed on the cluster:</p> |
| <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span> |
| <span class="kn">from</span> <span class="nn">pyspark.sql.functions</span> <span class="kn">import</span> <span class="n">pandas_udf</span> |
| <span class="kn">from</span> <span class="nn">pyspark.sql</span> <span class="kn">import</span> <span class="n">SparkSession</span> |
| |
| <span class="k">def</span> <span class="nf">main</span><span class="p">(</span><span class="n">spark</span><span class="p">):</span> |
| <span class="n">df</span> <span class="o">=</span> <span class="n">spark</span><span class="o">.</span><span class="n">createDataFrame</span><span class="p">(</span> |
| <span class="p">[(</span><span class="mi">1</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">),</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mf">2.0</span><span class="p">),</span> <span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="mf">3.0</span><span class="p">),</span> <span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="mf">5.0</span><span class="p">),</span> <span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="mf">10.0</span><span class="p">)],</span> |
| <span class="p">(</span><span class="s2">"id"</span><span class="p">,</span> <span class="s2">"v"</span><span class="p">))</span> |
| |
| <span class="nd">@pandas_udf</span><span class="p">(</span><span class="s2">"double"</span><span class="p">)</span> |
| <span class="k">def</span> <span class="nf">mean_udf</span><span class="p">(</span><span class="n">v</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">)</span> <span class="o">-></span> <span class="nb">float</span><span class="p">:</span> |
| <span class="k">return</span> <span class="n">v</span><span class="o">.</span><span class="n">mean</span><span class="p">()</span> |
| |
| <span class="nb">print</span><span class="p">(</span><span class="n">df</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span><span class="s2">"id"</span><span class="p">)</span><span class="o">.</span><span class="n">agg</span><span class="p">(</span><span class="n">mean_udf</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="s1">'v'</span><span class="p">]))</span><span class="o">.</span><span class="n">collect</span><span class="p">())</span> |
| |
| |
| <span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">"__main__"</span><span class="p">:</span> |
| <span class="n">main</span><span class="p">(</span><span class="n">SparkSession</span><span class="o">.</span><span class="n">builder</span><span class="o">.</span><span class="n">getOrCreate</span><span class="p">())</span> |
| </pre></div> |
| </div> |
| <p>There are multiple ways to manage Python dependencies in the cluster:</p> |
| <ul class="simple"> |
| <li><p>Using PySpark Native Features</p></li> |
| <li><p>Using Conda</p></li> |
| <li><p>Using Virtualenv</p></li> |
| <li><p>Using PEX</p></li> |
| </ul> |
| <section id="using-pyspark-native-features"> |
| <h2>Using PySpark Native Features<a class="headerlink" href="#using-pyspark-native-features" title="Permalink to this headline">#</a></h2> |
| <p>PySpark allows to upload Python files (<code class="docutils literal notranslate"><span class="pre">.py</span></code>), zipped Python packages (<code class="docutils literal notranslate"><span class="pre">.zip</span></code>), and Egg files (<code class="docutils literal notranslate"><span class="pre">.egg</span></code>) |
| to the executors by one of the following:</p> |
| <ul class="simple"> |
| <li><p>Setting the configuration setting <code class="docutils literal notranslate"><span class="pre">spark.submit.pyFiles</span></code></p></li> |
| <li><p>Setting <code class="docutils literal notranslate"><span class="pre">--py-files</span></code> option in Spark scripts</p></li> |
| <li><p>Directly calling <a class="reference internal" href="../reference/api/pyspark.SparkContext.addPyFile.html#pyspark.SparkContext.addPyFile" title="pyspark.SparkContext.addPyFile"><code class="xref py py-meth docutils literal notranslate"><span class="pre">pyspark.SparkContext.addPyFile()</span></code></a> in applications</p></li> |
| </ul> |
| <p>This is a straightforward method to ship additional custom Python code to the cluster. You can just add individual files or zip whole |
| packages and upload them. Using <a class="reference internal" href="../reference/api/pyspark.SparkContext.addPyFile.html#pyspark.SparkContext.addPyFile" title="pyspark.SparkContext.addPyFile"><code class="xref py py-meth docutils literal notranslate"><span class="pre">pyspark.SparkContext.addPyFile()</span></code></a> allows you to upload code even after having started your job.</p> |
| <p>However, it does not allow to add packages built as <a class="reference external" href="https://www.python.org/dev/peps/pep-0427/">Wheels</a> and therefore |
| does not allow to include dependencies with native code.</p> |
| </section> |
| <section id="using-conda"> |
| <h2>Using Conda<a class="headerlink" href="#using-conda" title="Permalink to this headline">#</a></h2> |
| <p><a class="reference external" href="https://docs.conda.io/en/latest/">Conda</a> is one of the most widely-used Python package management systems. PySpark users can directly |
| use a Conda environment to ship their third-party Python packages by leveraging |
| <a class="reference external" href="https://conda.github.io/conda-pack/spark.html">conda-pack</a> which is a command line tool creating |
| relocatable Conda environments.</p> |
| <p>The example below creates a Conda environment to use on both the driver and executor and packs |
| it into an archive file. This archive file captures the Conda environment for Python and stores |
| both Python interpreter and all its relevant dependencies.</p> |
| <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>conda<span class="w"> </span>create<span class="w"> </span>-y<span class="w"> </span>-n<span class="w"> </span>pyspark_conda_env<span class="w"> </span>-c<span class="w"> </span>conda-forge<span class="w"> </span>pyarrow<span class="w"> </span>pandas<span class="w"> </span>conda-pack |
| conda<span class="w"> </span>activate<span class="w"> </span>pyspark_conda_env |
| conda<span class="w"> </span>pack<span class="w"> </span>-f<span class="w"> </span>-o<span class="w"> </span>pyspark_conda_env.tar.gz |
| </pre></div> |
| </div> |
| <p>After that, you can ship it together with scripts or in the code by using the <code class="docutils literal notranslate"><span class="pre">--archives</span></code> option |
| or <code class="docutils literal notranslate"><span class="pre">spark.archives</span></code> configuration (<code class="docutils literal notranslate"><span class="pre">spark.yarn.dist.archives</span></code> in YARN). It automatically unpacks the archive on executors.</p> |
| <p>In the case of a <code class="docutils literal notranslate"><span class="pre">spark-submit</span></code> script, you can use it as follows:</p> |
| <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">export</span><span class="w"> </span><span class="nv">PYSPARK_DRIVER_PYTHON</span><span class="o">=</span>python<span class="w"> </span><span class="c1"># Do not set in cluster modes.</span> |
| <span class="nb">export</span><span class="w"> </span><span class="nv">PYSPARK_PYTHON</span><span class="o">=</span>./environment/bin/python |
| spark-submit<span class="w"> </span>--archives<span class="w"> </span>pyspark_conda_env.tar.gz#environment<span class="w"> </span>app.py |
| </pre></div> |
| </div> |
| <p>Note that <code class="docutils literal notranslate"><span class="pre">PYSPARK_DRIVER_PYTHON</span></code> above should not be set for cluster modes in YARN or Kubernetes.</p> |
| <p>If you’re on a regular Python shell or notebook, you can try it as shown below:</p> |
| <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">os</span> |
| <span class="kn">from</span> <span class="nn">pyspark.sql</span> <span class="kn">import</span> <span class="n">SparkSession</span> |
| <span class="kn">from</span> <span class="nn">app</span> <span class="kn">import</span> <span class="n">main</span> |
| |
| <span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s1">'PYSPARK_PYTHON'</span><span class="p">]</span> <span class="o">=</span> <span class="s2">"./environment/bin/python"</span> |
| <span class="n">spark</span> <span class="o">=</span> <span class="n">SparkSession</span><span class="o">.</span><span class="n">builder</span><span class="o">.</span><span class="n">config</span><span class="p">(</span> |
| <span class="s2">"spark.archives"</span><span class="p">,</span> <span class="c1"># 'spark.yarn.dist.archives' in YARN.</span> |
| <span class="s2">"pyspark_conda_env.tar.gz#environment"</span><span class="p">)</span><span class="o">.</span><span class="n">getOrCreate</span><span class="p">()</span> |
| <span class="n">main</span><span class="p">(</span><span class="n">spark</span><span class="p">)</span> |
| </pre></div> |
| </div> |
| <p>For a pyspark shell:</p> |
| <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">export</span><span class="w"> </span><span class="nv">PYSPARK_DRIVER_PYTHON</span><span class="o">=</span>python |
| <span class="nb">export</span><span class="w"> </span><span class="nv">PYSPARK_PYTHON</span><span class="o">=</span>./environment/bin/python |
| pyspark<span class="w"> </span>--archives<span class="w"> </span>pyspark_conda_env.tar.gz#environment |
| </pre></div> |
| </div> |
| </section> |
| <section id="using-virtualenv"> |
| <h2>Using Virtualenv<a class="headerlink" href="#using-virtualenv" title="Permalink to this headline">#</a></h2> |
| <p><a class="reference external" href="https://virtualenv.pypa.io/en/latest/">Virtualenv</a> is a Python tool to create isolated Python environments. |
| Since Python 3.3, a subset of its features has been integrated into Python as a standard library under |
| the <a class="reference external" href="https://docs.python.org/3/library/venv.html">venv</a> module. PySpark users can use virtualenv to manage |
| Python dependencies in their clusters by using <a class="reference external" href="https://jcristharif.com/venv-pack/index.html">venv-pack</a> |
| in a similar way as conda-pack.</p> |
| <p>A virtual environment to use on both driver and executor can be created as demonstrated below. |
| It packs the current virtual environment to an archive file, and it contains both Python interpreter and the dependencies. |
| However, it requires all nodes in a cluster to have the same Python interpreter installed because |
| <a class="reference external" href="https://github.com/jcrist/venv-pack/issues/5">venv-pack packs Python interpreter as a symbolic link</a>.</p> |
| <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>python<span class="w"> </span>-m<span class="w"> </span>venv<span class="w"> </span>pyspark_venv |
| <span class="nb">source</span><span class="w"> </span>pyspark_venv/bin/activate |
| pip<span class="w"> </span>install<span class="w"> </span>pyarrow<span class="w"> </span>pandas<span class="w"> </span>venv-pack |
| venv-pack<span class="w"> </span>-o<span class="w"> </span>pyspark_venv.tar.gz |
| </pre></div> |
| </div> |
| <p>You can directly pass/unpack the archive file and enable the environment on executors by leveraging |
| the <code class="docutils literal notranslate"><span class="pre">--archives</span></code> option or <code class="docutils literal notranslate"><span class="pre">spark.archives</span></code> configuration (<code class="docutils literal notranslate"><span class="pre">spark.yarn.dist.archives</span></code> in YARN).</p> |
| <p>For <code class="docutils literal notranslate"><span class="pre">spark-submit</span></code>, you can use it by running the command as follows. Also, notice that |
| <code class="docutils literal notranslate"><span class="pre">PYSPARK_DRIVER_PYTHON</span></code> has to be unset in Kubernetes or YARN cluster modes.</p> |
| <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">export</span><span class="w"> </span><span class="nv">PYSPARK_DRIVER_PYTHON</span><span class="o">=</span>python<span class="w"> </span><span class="c1"># Do not set in cluster modes.</span> |
| <span class="nb">export</span><span class="w"> </span><span class="nv">PYSPARK_PYTHON</span><span class="o">=</span>./environment/bin/python |
| spark-submit<span class="w"> </span>--archives<span class="w"> </span>pyspark_venv.tar.gz#environment<span class="w"> </span>app.py |
| </pre></div> |
| </div> |
| <p>For regular Python shells or notebooks:</p> |
| <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>import<span class="w"> </span>os |
| from<span class="w"> </span>pyspark.sql<span class="w"> </span>import<span class="w"> </span>SparkSession |
| from<span class="w"> </span>app<span class="w"> </span>import<span class="w"> </span>main |
| |
| os.environ<span class="o">[</span><span class="s1">'PYSPARK_PYTHON'</span><span class="o">]</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"./environment/bin/python"</span> |
| <span class="nv">spark</span><span class="w"> </span><span class="o">=</span><span class="w"> </span>SparkSession.builder.config<span class="o">(</span> |
| <span class="w"> </span><span class="s2">"spark.archives"</span>,<span class="w"> </span><span class="c1"># 'spark.yarn.dist.archives' in YARN.</span> |
| <span class="w"> </span><span class="s2">"pyspark_venv.tar.gz#environment"</span><span class="o">)</span>.getOrCreate<span class="o">()</span> |
| main<span class="o">(</span>spark<span class="o">)</span> |
| </pre></div> |
| </div> |
| <p>In the case of a pyspark shell:</p> |
| <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">export</span><span class="w"> </span><span class="nv">PYSPARK_DRIVER_PYTHON</span><span class="o">=</span>python |
| <span class="nb">export</span><span class="w"> </span><span class="nv">PYSPARK_PYTHON</span><span class="o">=</span>./environment/bin/python |
| pyspark<span class="w"> </span>--archives<span class="w"> </span>pyspark_venv.tar.gz#environment |
| </pre></div> |
| </div> |
| </section> |
| <section id="using-pex"> |
| <h2>Using PEX<a class="headerlink" href="#using-pex" title="Permalink to this headline">#</a></h2> |
| <p>PySpark can also use <a class="reference external" href="https://github.com/pantsbuild/pex">PEX</a> to ship the Python packages |
| together. PEX is a tool that creates a self-contained Python environment. This is similar |
| to Conda or virtualenv, but a <code class="docutils literal notranslate"><span class="pre">.pex</span></code> file is executable by itself.</p> |
| <p>The following example creates a <code class="docutils literal notranslate"><span class="pre">.pex</span></code> file for the driver and executor to use. |
| The file contains the Python dependencies specified with the <code class="docutils literal notranslate"><span class="pre">pex</span></code> command.</p> |
| <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pip<span class="w"> </span>install<span class="w"> </span>pyarrow<span class="w"> </span>pandas<span class="w"> </span>pex |
| pex<span class="w"> </span>pyspark<span class="w"> </span>pyarrow<span class="w"> </span>pandas<span class="w"> </span>-o<span class="w"> </span>pyspark_pex_env.pex |
| </pre></div> |
| </div> |
| <p>This file behaves similarly with a regular Python interpreter.</p> |
| <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>./pyspark_pex_env.pex<span class="w"> </span>-c<span class="w"> </span><span class="s2">"import pandas; print(pandas.__version__)"</span> |
| <span class="m">1</span>.1.5 |
| </pre></div> |
| </div> |
| <p>However, <code class="docutils literal notranslate"><span class="pre">.pex</span></code> file does not include a Python interpreter itself under the hood so all |
| nodes in a cluster should have the same Python interpreter installed.</p> |
| <p>In order to transfer and use the <code class="docutils literal notranslate"><span class="pre">.pex</span></code> file in a cluster, you should ship it via the |
| <code class="docutils literal notranslate"><span class="pre">spark.files</span></code> configuration (<code class="docutils literal notranslate"><span class="pre">spark.yarn.dist.files</span></code> in YARN) or <code class="docutils literal notranslate"><span class="pre">--files</span></code> option because they are regular files instead |
| of directories or archive files.</p> |
| <p>For application submission, you run the commands as shown below. |
| Note that <code class="docutils literal notranslate"><span class="pre">PYSPARK_DRIVER_PYTHON</span></code> should not be set for cluster modes in YARN or Kubernetes.</p> |
| <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">export</span><span class="w"> </span><span class="nv">PYSPARK_DRIVER_PYTHON</span><span class="o">=</span>python<span class="w"> </span><span class="c1"># Do not set in cluster modes.</span> |
| <span class="nb">export</span><span class="w"> </span><span class="nv">PYSPARK_PYTHON</span><span class="o">=</span>./pyspark_pex_env.pex |
| spark-submit<span class="w"> </span>--files<span class="w"> </span>pyspark_pex_env.pex<span class="w"> </span>app.py |
| </pre></div> |
| </div> |
| <p>For regular Python shells or notebooks:</p> |
| <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">os</span> |
| <span class="kn">from</span> <span class="nn">pyspark.sql</span> <span class="kn">import</span> <span class="n">SparkSession</span> |
| <span class="kn">from</span> <span class="nn">app</span> <span class="kn">import</span> <span class="n">main</span> |
| |
| <span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s1">'PYSPARK_PYTHON'</span><span class="p">]</span> <span class="o">=</span> <span class="s2">"./pyspark_pex_env.pex"</span> |
| <span class="n">spark</span> <span class="o">=</span> <span class="n">SparkSession</span><span class="o">.</span><span class="n">builder</span><span class="o">.</span><span class="n">config</span><span class="p">(</span> |
| <span class="s2">"spark.files"</span><span class="p">,</span> <span class="c1"># 'spark.yarn.dist.files' in YARN.</span> |
| <span class="s2">"pyspark_pex_env.pex"</span><span class="p">)</span><span class="o">.</span><span class="n">getOrCreate</span><span class="p">()</span> |
| <span class="n">main</span><span class="p">(</span><span class="n">spark</span><span class="p">)</span> |
| </pre></div> |
| </div> |
| <p>For the interactive pyspark shell, the commands are almost the same:</p> |
| <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">export</span><span class="w"> </span><span class="nv">PYSPARK_DRIVER_PYTHON</span><span class="o">=</span>python |
| <span class="nb">export</span><span class="w"> </span><span class="nv">PYSPARK_PYTHON</span><span class="o">=</span>./pyspark_pex_env.pex |
| pyspark<span class="w"> </span>--files<span class="w"> </span>pyspark_pex_env.pex |
| </pre></div> |
| </div> |
| <p>An end-to-end Docker example for deploying a standalone PySpark with <code class="docutils literal notranslate"><span class="pre">SparkSession.builder</span></code> and PEX |
| can be found <a class="reference external" href="https://github.com/criteo/cluster-pack/blob/master/examples/spark-with-S3/README.md">here</a> |
| - it uses cluster-pack, a library on top of PEX that automatizes the intermediate step of having |
| to create & upload the PEX manually.</p> |
| </section> |
| </section> |
| |
| |
| </article> |
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