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<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
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<li class="toctree-l1 current"><a class="current reference internal" href="#"> Jobrunner</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#installation">Installation</a></li>
<li class="toctree-l2"><a class="reference internal" href="#dependencies">Dependencies</a></li>
<li class="toctree-l2"><a class="reference internal" href="#writing-a-jobfile">Writing a Jobfile</a></li>
<li class="toctree-l2"><a class="reference internal" href="#jobrunner-commands">Jobrunner commands</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#setup">Setup</a></li>
<li class="toctree-l3"><a class="reference internal" href="#submit">Submit</a></li>
<li class="toctree-l3"><a class="reference internal" href="#archive">Archive</a></li>
<li class="toctree-l3"><a class="reference internal" href="#export">Export</a></li>
<li class="toctree-l3"><a class="reference internal" href="#clean">Clean</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#examples">Examples</a></li>
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<div class="section" id="icon-jobrunner">
<h1><a class="reference internal" href="proxy.php?url=https%3A%2F%2Fgithub.com%2F_images%2Ficon.svg"><img alt="icon" src="proxy.php?url=https%3A%2F%2Fgithub.com%2F_images%2Ficon.svg" width="50" /></a> Jobrunner<a class="headerlink" href="#icon-jobrunner" title="Permalink to this headline"></a></h1>
<p><a class="reference external" href="proxy.php?url=https%3A%2F%2Fgithub.com%2F%3Ca+href%3D"https://github.com/psf/black"><img">https://github.com/psf/black"><img alt="Code style: black" src="proxy.php?url=https%3A%2F%2Fgithub.com%2F%3Ca+href%3D"https://img.shields.io/badge/code%20style-black-000000.svg" rel="nofollow">https://img.shields.io/badge/code%20style-black-000000.svg" /></a></p>
<p>Jobrunner is a command line tool to manage and deploy computing jobs,
organize complex workloads, and enforce a directory based hierarchy to
enable reuse of files and bash scripts within a project. Organization
details of a directory tree are encoded in Jobfiles which serve as an
index of files/scripts, and indicate their purpose when deploying or
setting up a job. It is a flexible tool that allows users to design
their own directory structure, perserve their design, and maintain
consistency with increase in complexity of the project.</p>
<div class="section" id="installation">
<h2>Installation<a class="headerlink" href="#installation" title="Permalink to this headline"></a></h2>
<p>Stable releases of Jobrunner are hosted on Python Package Index website
(<a class="reference external" href="proxy.php?url=https%3A%2F%2Fgithub.com%2F%3Ca+href%3D"https://pypi.org/project/PyJobRunner/">https://pypi.org/project/PyJobRunner/</a" rel="nofollow">https://pypi.org/project/PyJobRunner/">https://pypi.org/project/PyJobRunner/</a>) and can be installed by
executing,</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="n">PyJobrunner</span>
</pre></div>
</div>
<p>Note that <code class="docutils literal notranslate"><span class="pre">pip</span></code> should point to <code class="docutils literal notranslate"><span class="pre">python3+</span></code> installation package
<code class="docutils literal notranslate"><span class="pre">pip3</span></code>.</p>
<p>Upgrading and uninstallation is easily managed through this interface
using,</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">upgrade</span> <span class="n">PyJobrunner</span>
<span class="n">pip</span> <span class="n">uninstall</span> <span class="n">PyJobRunner</span>
</pre></div>
</div>
<p>There maybe situations where users may want to install Jobrunner in
development mode $\textemdash$ to design new features, debug, or
customize options/commands to their needs. This can be easily
accomplished using the <code class="docutils literal notranslate"><span class="pre">setup</span></code> script located in the project root
directory and executing,</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">./</span><span class="n">setup</span> <span class="n">develop</span>
</pre></div>
</div>
<p>Development mode enables testing of features/updates directly from the
source code and is an effective method for debugging. Note that the
<code class="docutils literal notranslate"><span class="pre">setup</span></code> script relies on <code class="docutils literal notranslate"><span class="pre">click</span></code>, which can be installed using,</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="n">click</span>
</pre></div>
</div>
<p>The <code class="docutils literal notranslate"><span class="pre">jobrunner</span></code> script is installed in <code class="docutils literal notranslate"><span class="pre">$HOME/.local/bin</span></code> directory
and therfore the environment variable, <code class="docutils literal notranslate"><span class="pre">PATH</span></code>, should be updated to
include this location for command line use.</p>
</div>
<div class="section" id="dependencies">
<h2>Dependencies<a class="headerlink" href="#dependencies" title="Permalink to this headline"></a></h2>
<p><code class="docutils literal notranslate"><span class="pre">python3.8+</span></code> <code class="docutils literal notranslate"><span class="pre">click</span></code> <code class="docutils literal notranslate"><span class="pre">toml</span></code> <code class="docutils literal notranslate"><span class="pre">pyyaml</span></code></p>
</div>
<div class="section" id="writing-a-jobfile">
<h2>Writing a Jobfile<a class="headerlink" href="#writing-a-jobfile" title="Permalink to this headline"></a></h2>
<p>A Jobfile provides details on functionality of each file in a directory
tree along with schedular configuration. Consider the following
directory tree for a project,</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ tree Project
├── Jobfile
├── environment.sh
├── JobObject1
├── JobObject2
├── Jobfile
├── application.input
├── application.exe
├── setupScript.sh
├── submitScript.sh
├── preProcess.sh
├── Config1
├── Config2
├── Jobfile
├── application.input
</pre></div>
</div>
<p>The base directory <code class="docutils literal notranslate"><span class="pre">Project</span></code> contains two different job object
subdirectories <code class="docutils literal notranslate"><span class="pre">/Project/JobObject1</span></code> and <code class="docutils literal notranslate"><span class="pre">/Project/JobObject2</span></code> which
share a common environment defined in <code class="docutils literal notranslate"><span class="pre">environment.sh</span></code>,</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># module for OpenMPI</span>
module load openmpi
<span class="c1"># environment variables common to different job objects</span>
<span class="nb">export</span> <span class="nv">COMMON_ENV_VARIABLE_1</span><span class="o">=</span>/path/to/a/library
<span class="nb">export</span> <span class="nv">COMMON_ENV_VARIABLE_2</span><span class="o">=</span><span class="s2">"value"</span>
</pre></div>
</div>
<p>It makes sense to places this file at the level of project home
directory and define it in <code class="docutils literal notranslate"><span class="pre">Jobfile</span></code> as given below, indicating that
<code class="docutils literal notranslate"><span class="pre">environment.sh</span></code> should be included when executing both <code class="docutils literal notranslate"><span class="pre">jobrunner</span>
<span class="pre">setup</span></code> and <code class="docutils literal notranslate"><span class="pre">jobrunner</span> <span class="pre">submit</span></code> commands. Details regarding the job
schedular are also defined at this level. The schedular command
$\textemdash$ <code class="docutils literal notranslate"><span class="pre">slurm</span></code> in this case $\textemdash$ is used to dispatch
the jobs with desired options.</p>
<div class="highlight-YAML notranslate"><div class="highlight"><pre><span></span><span class="c1"># scripts to include during jobrunner setup and submit commands</span>
<span class="nt">job</span><span class="p">:</span>
<span class="nt">setup</span><span class="p">:</span>
<span class="p p-Indicator">-</span> <span class="l l-Scalar l-Scalar-Plain">environment.sh</span>
<span class="nt">submit</span><span class="p">:</span>
<span class="p p-Indicator">-</span> <span class="l l-Scalar l-Scalar-Plain">environment.sh</span>
<span class="c1"># schedular command and options to dispatch jobs</span>
<span class="nt">schedular</span><span class="p">:</span>
<span class="nt">command</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">slurm</span>
<span class="nt">options</span><span class="p">:</span>
<span class="p p-Indicator">-</span> <span class="s">"#SBATCH</span><span class="nv"> </span><span class="s">-t</span><span class="nv"> </span><span class="s">0-30:00"</span>
<span class="p p-Indicator">-</span> <span class="s">"#SBATCH</span><span class="nv"> </span><span class="s">--job-name=myjob"</span>
<span class="p p-Indicator">-</span> <span class="s">"#SBATCH</span><span class="nv"> </span><span class="s">--ntasks=5"</span>
</pre></div>
</div>
<p>At the level of subdirectory <code class="docutils literal notranslate"><span class="pre">/Project/JobObject2</span></code> more files are
added and lead to a Jobfile that looks like,</p>
<div class="highlight-yaml notranslate"><div class="highlight"><pre><span></span><span class="nt">job</span><span class="p">:</span>
<span class="c1"># list of scripts and input files that need to execute during setup command</span>
<span class="nt">setup</span><span class="p">:</span>
<span class="p p-Indicator">-</span> <span class="l l-Scalar l-Scalar-Plain">setupScript.sh</span>
<span class="c1"># input for the job</span>
<span class="nt">input</span><span class="p">:</span>
<span class="p p-Indicator">-</span> <span class="l l-Scalar l-Scalar-Plain">application.input</span>
<span class="c1"># target file/executable for the job</span>
<span class="nt">target</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">application.exe</span>
<span class="c1"># list of scripts that need to execute when running submit command</span>
<span class="nt">submit</span><span class="p">:</span>
<span class="p p-Indicator">-</span> <span class="l l-Scalar l-Scalar-Plain">preProcess.sh</span>
<span class="p p-Indicator">-</span> <span class="l l-Scalar l-Scalar-Plain">submitScript.sh</span>
</pre></div>
</div>
<p>The field, <code class="docutils literal notranslate"><span class="pre">job:input</span></code>, refers to the inputs required to run
<code class="docutils literal notranslate"><span class="pre">job:target</span></code> executable common for configurations
<code class="docutils literal notranslate"><span class="pre">/Project/JobObject2/Config1</span></code> and <code class="docutils literal notranslate"><span class="pre">/Project/JobObject2/Config2</span></code>.
Each configuration contains additional input files with values that are
appended to the ones provided at the current level. The Jobfile at
<code class="docutils literal notranslate"><span class="pre">/Project/JobObject2/Config2</span></code> becomes,</p>
<div class="highlight-YAML notranslate"><div class="highlight"><pre><span></span><span class="nt">job</span><span class="p">:</span>
<span class="c1"># append to input file</span>
<span class="nt">input</span><span class="p">:</span>
<span class="p p-Indicator">-</span> <span class="l l-Scalar l-Scalar-Plain">application.input</span>
<span class="c1"># list of file/patterns to archive</span>
<span class="nt">archive</span><span class="p">:</span>
<span class="p p-Indicator">-</span> <span class="s">"*_hdf5_*"</span>
<span class="p p-Indicator">-</span> <span class="s">"*.log"</span>
</pre></div>
</div>
<p>The field, <code class="docutils literal notranslate"><span class="pre">job.archive</span></code>, provides a list of file/patterns that are
moved over to the
<code class="docutils literal notranslate"><span class="pre">/Project/JobObject2/Config2/jobnode.archive/<tagID></span></code> directory when
running <code class="docutils literal notranslate"><span class="pre">jobrunner</span> <span class="pre">archive</span> <span class="pre">--tag=<tagID></span></code>. This feature is provided to
store results before cleaning up working directory for fresh runs</p>
</div>
<div class="section" id="jobrunner-commands">
<h2>Jobrunner commands<a class="headerlink" href="#jobrunner-commands" title="Permalink to this headline"></a></h2>
<div class="section" id="setup">
<h3>Setup<a class="headerlink" href="#setup" title="Permalink to this headline"></a></h3>
<p><code class="docutils literal notranslate"><span class="pre">jobrunner</span> <span class="pre">setup</span> <span class="pre"><JobWorkDir></span></code> creates a <code class="docutils literal notranslate"><span class="pre">job.setup</span></code> file in
<code class="docutils literal notranslate"><span class="pre"><workdir></span></code> using <code class="docutils literal notranslate"><span class="pre">job.setup</span></code> scripts defined in Jobfiles along the
directory tree. Jobrunner executes each script serially by changing the
working directory to the location of the script. A special environment
variable <code class="docutils literal notranslate"><span class="pre">JobWorkDir</span></code> provides the value of <code class="docutils literal notranslate"><span class="pre"><JobWorkDir></span></code> supplied
during invocation of the command.</p>
<p>The <code class="docutils literal notranslate"><span class="pre">--show</span></code> option can be used to check which bash scripts will be
included during invocation. Following is the result of <code class="docutils literal notranslate"><span class="pre">jobrunner</span> <span class="pre">setup</span>
<span class="pre">--show</span> <span class="pre">JobObject2</span></code> for the example above,</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">Working</span> <span class="n">directory</span><span class="p">:</span> <span class="o">/</span><span class="n">Project</span><span class="o">/</span><span class="n">JobObject2</span>
<span class="n">Parsing</span> <span class="n">Jobfiles</span> <span class="ow">in</span> <span class="n">directory</span> <span class="n">tree</span>
<span class="n">job</span><span class="o">.</span><span class="n">setup</span><span class="p">:</span> <span class="p">[</span>
<span class="o">/</span><span class="n">Project</span><span class="o">/</span><span class="n">environment</span><span class="o">.</span><span class="n">sh</span>
<span class="o">/</span><span class="n">Project</span><span class="o">/</span><span class="n">JobObject2</span><span class="o">/</span><span class="n">setupScript</span><span class="o">.</span><span class="n">sh</span>
<span class="p">]</span>
</pre></div>
</div>
</div>
<div class="section" id="submit">
<h3>Submit<a class="headerlink" href="#submit" title="Permalink to this headline"></a></h3>
<p><code class="docutils literal notranslate"><span class="pre">jobrunner</span> <span class="pre">submit</span> <span class="pre"><JobWorkDir></span></code> creates a <code class="docutils literal notranslate"><span class="pre">job.submit</span></code> file in
<code class="docutils literal notranslate"><span class="pre"><JobWorkDir></span></code> using <code class="docutils literal notranslate"><span class="pre">job.submit</span></code> scripts and <code class="docutils literal notranslate"><span class="pre">schedular.options</span></code>
values defined in Jobfiles along the directory tree.
<code class="docutils literal notranslate"><span class="pre">schedular.command</span></code> is used to dispatch the result script.</p>
<p>The <code class="docutils literal notranslate"><span class="pre">--show</span></code> option can be used to check schedular configuration and
list of bash scripts that will be included during invocation. Following
is the result of <code class="docutils literal notranslate"><span class="pre">jobrunner</span> <span class="pre">submit</span> <span class="pre">--show</span> <span class="pre">JobObject2/Config2</span></code> for the
example above,</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">Working</span> <span class="n">directory</span><span class="p">:</span> <span class="o">/</span><span class="n">Project</span><span class="o">/</span><span class="n">JobObject2</span><span class="o">/</span><span class="n">Config2</span>
<span class="n">Parsing</span> <span class="n">Jobfiles</span> <span class="ow">in</span> <span class="n">directory</span> <span class="n">tree</span>
<span class="n">schedular</span><span class="o">.</span><span class="n">command</span><span class="p">:</span>
<span class="n">slurm</span>
<span class="n">schedular</span><span class="o">.</span><span class="n">options</span><span class="p">:</span> <span class="p">[</span>
<span class="c1">#SBATCH -t 0-30:00</span>
<span class="c1">#SBATCH --job-name=myjob</span>
<span class="c1">#SBATCH --ntasks=5</span>
<span class="p">]</span>
<span class="n">job</span><span class="o">.</span><span class="n">input</span><span class="p">:</span> <span class="p">[</span>
<span class="o">/</span><span class="n">Project</span><span class="o">/</span><span class="n">JobObject2</span><span class="o">/</span><span class="n">flash</span><span class="o">.</span><span class="n">par</span>
<span class="o">/</span><span class="n">Project</span><span class="o">/</span><span class="n">JobObject2</span><span class="o">/</span><span class="n">Config2</span><span class="o">/</span><span class="n">flash</span><span class="o">.</span><span class="n">par</span>
<span class="p">]</span>
<span class="n">job</span><span class="o">.</span><span class="n">target</span><span class="p">:</span>
<span class="o">/</span><span class="n">Project</span><span class="o">/</span><span class="n">JobObject2</span><span class="o">/</span><span class="n">flashx</span>
<span class="n">job</span><span class="o">.</span><span class="n">submit</span><span class="p">:</span> <span class="p">[</span>
<span class="o">/</span><span class="n">Project</span><span class="o">/</span><span class="n">environment</span><span class="o">.</span><span class="n">sh</span>
<span class="o">/</span><span class="n">Project</span><span class="o">/</span><span class="n">JobObject2</span><span class="o">/</span><span class="n">preProcess</span><span class="o">.</span><span class="n">sh</span>
<span class="o">/</span><span class="n">Project</span><span class="o">/</span><span class="n">JobObject2</span><span class="o">/</span><span class="n">submitScript</span><span class="o">.</span><span class="n">sh</span>
<span class="p">]</span>
</pre></div>
</div>
<p>Along with the <code class="docutils literal notranslate"><span class="pre">job.submit</span></code> script, <code class="docutils literal notranslate"><span class="pre">job.input</span></code> and <code class="docutils literal notranslate"><span class="pre">job.target</span></code>
files are also created in <code class="docutils literal notranslate"><span class="pre"><JobWorkDir></span></code> and created using values
defined in Jobfiles.</p>
</div>
<div class="section" id="archive">
<h3>Archive<a class="headerlink" href="#archive" title="Permalink to this headline"></a></h3>
<p><code class="docutils literal notranslate"><span class="pre">jobrunner</span> <span class="pre">archive</span> <span class="pre">--tag=<tagID></span> <span class="pre"><JobWorkDir></span></code> creates archives along
the directory tree using the list of values defined <code class="docutils literal notranslate"><span class="pre">job.archive</span></code>. The
archives are created under the sub-directory <code class="docutils literal notranslate"><span class="pre">jobnode.archive/<tagID></span></code>
and represent the state of the directory tree during the invocation.</p>
</div>
<div class="section" id="export">
<h3>Export<a class="headerlink" href="#export" title="Permalink to this headline"></a></h3>
<p><code class="docutils literal notranslate"><span class="pre">jobrunner</span> <span class="pre">export</span> <span class="pre">--tag=<pathToArchive></span> <span class="pre"><JobWorkDir></span></code> exports
directory tree and archives objects to an external directory
<code class="docutils literal notranslate"><span class="pre"><pathToArchive></span></code> to preserve state and curate execution environment.</p>
</div>
<div class="section" id="clean">
<h3>Clean<a class="headerlink" href="#clean" title="Permalink to this headline"></a></h3>
<p><code class="docutils literal notranslate"><span class="pre">jobrunner</span> <span class="pre">clean</span> <span class="pre"><JobWorkDir></span></code> removes Jobrunner artifacts from the
working directory</p>
</div>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<p>Functionality of Jobrunner is best understood through example projects
which can be found in following repositories:</p>
<ul class="simple">
<li><p><a class="reference external" href="proxy.php?url=https%3A%2F%2Fgithub.com%2F%3Ca+href%3D"https://github.com/akashdhruv/Multiphase-Simulations">akashdhruv/Multiphase-Simulations</a">https://github.com/akashdhruv/Multiphase-Simulations">akashdhruv/Multiphase-Simulations</a>: A
collection of high-fidelity flow/pool boiling simulations</p></li>
</ul>
</div>
<div class="section" id="citation">
<h2>Citation<a class="headerlink" href="#citation" title="Permalink to this headline"></a></h2>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="nd">@software</span><span class="p">{</span><span class="n">akash_dhruv_2022_7255620</span><span class="p">,</span>
<span class="n">author</span> <span class="o">=</span> <span class="p">{</span><span class="n">Akash</span> <span class="n">Dhruv</span><span class="p">},</span>
<span class="n">title</span> <span class="o">=</span> <span class="p">{</span><span class="n">akashdhruv</span><span class="o">/</span><span class="n">Jobrunner</span><span class="p">:</span> <span class="n">October</span> <span class="mi">2022</span><span class="p">},</span>
<span class="n">month</span> <span class="o">=</span> <span class="nb">oct</span><span class="p">,</span>
<span class="n">year</span> <span class="o">=</span> <span class="mi">2022</span><span class="p">,</span>
<span class="n">publisher</span> <span class="o">=</span> <span class="p">{</span><span class="n">Zenodo</span><span class="p">},</span>
<span class="n">version</span> <span class="o">=</span> <span class="p">{</span><span class="mf">22.10</span><span class="p">},</span>
<span class="n">doi</span> <span class="o">=</span> <span class="p">{</span><span class="mf">10.5281</span><span class="o">/</span><span class="n">zenodo</span><span class="mf">.7255620</span><span class="p">},</span>
<span class="n">url</span> <span class="o">=</span> <span class="p">{</span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">doi</span><span class="o">.</span><span class="n">org</span><span class="o">/</span><span class="mf">10.5281</span><span class="o">/</span><span class="n">zenodo</span><span class="mf">.7255620</span><span class="p">}</span>
<span class="p">}</span>
</pre></div>
</div>
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