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slsDetectorPackage 9.1.1
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<p class="caption" role="heading"><span class="caption-text">Installation:</span></p>
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<li class="toctree-l2"><a class="reference internal" href="#install-binaries-using-conda">Install binaries using conda</a></li>
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<section id="installation">
<span id="id1"></span><h1>Installation<a class="headerlink" href="#installation" title="Link to this heading"></a></h1>
<p>One can either install pre-built binaries using conda or build from source.</p>
<div class="admonition warning">
<p class="admonition-title">Warning</p>
<p>Before building from source make sure that you have the
<a class="reference internal" href="dependencies.html"><span class="doc">dependencies</span></a> installed. If installing using conda, conda will
manage the dependencies. Avoid also installing packages with pip.</p>
</div>
<section id="install-binaries-using-conda">
<h2>Install binaries using conda<a class="headerlink" href="#install-binaries-using-conda" title="Link to this heading"></a></h2>
<p>Conda is not only useful to manage python environments but can also
be used as a user space package manager. Dates in the tag (for eg. 2020.07.23.dev0)
are from the developer branch. Please use released tags for stability.</p>
<dl>
<dt>We have four different packages available:</dt><dd><table class="docutils align-default">
<thead>
<tr class="row-odd"><th class="head"><p>Package</p></th>
<th class="head"><p>Description</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>slsdetlib</p></td>
<td><p>shared libraries and command line utilities</p></td>
</tr>
<tr class="row-odd"><td><p>slsdetgui</p></td>
<td><p>GUI</p></td>
</tr>
<tr class="row-even"><td><p>slsdet</p></td>
<td><p>Python bindings</p></td>
</tr>
<tr class="row-odd"><td><p>moenchzmq</p></td>
<td><p>moench</p></td>
</tr>
</tbody>
</table>
</dd>
</dl>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1">#Add channels for dependencies and our library</span>
conda<span class="w"> </span>config<span class="w"> </span>--add<span class="w"> </span>channels<span class="w"> </span>conda-forge
conda<span class="w"> </span>config<span class="w"> </span>--add<span class="w"> </span>channels<span class="w"> </span>slsdetectorgroup
conda<span class="w"> </span>config<span class="w"> </span>--set<span class="w"> </span>channel_priority<span class="w"> </span>strict
<span class="c1">#create and activate an environment with our library</span>
<span class="c1">#replace 6.1.1 with the required tag</span>
conda<span class="w"> </span>create<span class="w"> </span>-n<span class="w"> </span>myenv<span class="w"> </span><span class="nv">slsdetlib</span><span class="o">=</span><span class="m">6</span>.1.1
conda<span class="w"> </span>activate<span class="w"> </span>myenv
<span class="c1">#ready to use</span>
sls_detector_get<span class="w"> </span>exptime
...
</pre></div>
</div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1">#List available versions</span>
<span class="c1"># lib and binaries</span>
conda<span class="w"> </span>search<span class="w"> </span>slsdetlib
<span class="c1"># python</span>
conda<span class="w"> </span>search<span class="w"> </span>slsdet
<span class="c1"># gui</span>
conda<span class="w"> </span>search<span class="w"> </span>slsdetgui
<span class="c1"># moench</span>
conda<span class="w"> </span>search<span class="w"> </span>moenchzmq
</pre></div>
</div>
</section>
<section id="build-from-source">
<h2>Build from source<a class="headerlink" href="#build-from-source" title="Link to this heading"></a></h2>
<section id="download-source-code-from-github">
<h3>1. Download Source Code from github<a class="headerlink" href="#download-source-code-from-github" title="Link to this heading"></a></h3>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/slsdetectorgroup/slsDetectorPackage.git<span class="w"> </span>--branch<span class="w"> </span><span class="m">6</span>.1.1
</pre></div>
</div>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>For v6.x.x of slsDetectorPackage and older, refer <a class="reference internal" href="#pybind-for-different-slsdetectorpackage-versions"><span class="std std-ref">pybind11 notes on cloning.</span></a></p>
</div>
</section>
<section id="build-from-source-using-cmake">
<span id="id2"></span><h3>2. Build from Source<a class="headerlink" href="#build-from-source-using-cmake" title="Link to this heading"></a></h3>
<p>One can either build using cmake or use the in-built cmk.sh script.</p>
</section>
<section id="build-using-cmake">
<h3>Build using CMake<a class="headerlink" href="#build-using-cmake" title="Link to this heading"></a></h3>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># outside slsDetecorPackage folder</span>
mkdir<span class="w"> </span>build<span class="w"> </span><span class="o">&amp;&amp;</span><span class="w"> </span><span class="nb">cd</span><span class="w"> </span>build
<span class="c1"># configure &amp; generate Makefiles using cmake</span>
<span class="c1"># by listing all your options (alternately use ccmake described below)</span>
<span class="c1"># cmake3 for some systems</span>
cmake<span class="w"> </span>../slsDetectorPackage<span class="w"> </span>-DCMAKE_INSTALL_PREFIX<span class="o">=</span>/your/install/path
<span class="c1"># compiled to the build/bin directory</span>
make<span class="w"> </span>-j12<span class="w"> </span><span class="c1">#or whatever number of cores you are using to build</span>
<span class="c1"># install headers and libs in /your/install/path directory</span>
make<span class="w"> </span>install
</pre></div>
</div>
<p>Instead of the cmake command, one can use ccmake to get a list of options to configure and generate Makefiles at ease.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># ccmake3 for some systems</span>
ccmake<span class="w"> </span>..
<span class="c1"># choose the options</span>
<span class="c1"># first press [c] - configure (until you see [g])</span>
<span class="c1"># then press [g] - generate</span>
</pre></div>
</div>
<table class="docutils align-default">
<thead>
<tr class="row-odd"><th class="head"><p>Example cmake options</p></th>
<th class="head"><p>Comment</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>-DSLS_USE_PYTHON=ON</p></td>
<td><p>Python</p></td>
</tr>
<tr class="row-odd"><td><p>-DPython_FIND_VIRTUALENV=ONLY</p></td>
<td><p>Python from the conda env</p></td>
</tr>
<tr class="row-even"><td><p>-DSLS_USE_GUI=ON</p></td>
<td><p>GUI</p></td>
</tr>
<tr class="row-odd"><td><p>-DSLS_USE_HDF5=ON</p></td>
<td><p>HDF5</p></td>
</tr>
<tr class="row-even"><td><p>-DSLS_USE_SIMULATOR=ON</p></td>
<td><p>Simulator</p></td>
</tr>
</tbody>
</table>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>For v7.x.x of slsDetectorPackage and older, refer <a class="reference internal" href="#zeromq-for-different-slsdetectorpackage-versions"><span class="std std-ref">zeromq notes for cmake option to hint library location.</span></a></p>
</div>
</section>
<section id="build-using-in-built-cmk-sh-script">
<h3>Build using in-built cmk.sh script<a class="headerlink" href="#build-using-in-built-cmk-sh-script" title="Link to this heading"></a></h3>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>The<span class="w"> </span>binaries<span class="w"> </span>are<span class="w"> </span>generated<span class="w"> </span><span class="k">in</span><span class="w"> </span>slsDetectorPackage/build/bin<span class="w"> </span>directory.
Usage:<span class="w"> </span><span class="nv">$0</span><span class="w"> </span><span class="o">[</span>-b<span class="o">]</span><span class="w"> </span><span class="o">[</span>-c<span class="o">]</span><span class="w"> </span><span class="o">[</span>-d<span class="w"> </span>&lt;HDF5<span class="w"> </span>directory&gt;<span class="o">]</span><span class="w"> </span><span class="o">[</span>-e<span class="o">]</span><span class="w"> </span><span class="o">[</span>-g<span class="o">]</span><span class="w"> </span><span class="o">[</span>-h<span class="o">]</span><span class="w"> </span><span class="o">[</span>-i<span class="o">]</span>
<span class="o">[</span>-j<span class="w"> </span>&lt;Number<span class="w"> </span>of<span class="w"> </span>threads&gt;<span class="o">]</span><span class="w"> </span><span class="o">[</span>-k<span class="w"> </span>&lt;CMake<span class="w"> </span>command&gt;<span class="o">]</span><span class="w"> </span><span class="o">[</span>-l<span class="w"> </span>&lt;Install<span class="w"> </span>directory&gt;<span class="o">]</span>
<span class="o">[</span>-m<span class="o">]</span><span class="w"> </span><span class="o">[</span>-n<span class="o">]</span><span class="w"> </span><span class="o">[</span>-p<span class="o">]</span><span class="w"> </span><span class="o">[</span>-r<span class="o">]</span><span class="w"> </span><span class="o">[</span>-s<span class="o">]</span><span class="w"> </span><span class="o">[</span>-t<span class="o">]</span><span class="w"> </span><span class="o">[</span>-u<span class="o">]</span><span class="w"> </span><span class="o">[</span>-z<span class="o">]</span>
-<span class="o">[</span>no<span class="w"> </span>option<span class="o">]</span>:<span class="w"> </span>only<span class="w"> </span>make
-b:<span class="w"> </span>Builds/Rebuilds<span class="w"> </span>CMake<span class="w"> </span>files<span class="w"> </span>normal<span class="w"> </span>mode
-c:<span class="w"> </span>Clean
-d:<span class="w"> </span>HDF5<span class="w"> </span>Custom<span class="w"> </span>Directory
-e:<span class="w"> </span>Debug<span class="w"> </span>mode
-g:<span class="w"> </span>Build/Rebuilds<span class="w"> </span>gui
-h:<span class="w"> </span>Builds/Rebuilds<span class="w"> </span>Cmake<span class="w"> </span>files<span class="w"> </span>with<span class="w"> </span>HDF5<span class="w"> </span>package
-i:<span class="w"> </span>Builds<span class="w"> </span>tests
-j:<span class="w"> </span>Number<span class="w"> </span>of<span class="w"> </span>threads<span class="w"> </span>to<span class="w"> </span>compile<span class="w"> </span>through
-k:<span class="w"> </span>CMake<span class="w"> </span><span class="nb">command</span>
-l:<span class="w"> </span>Install<span class="w"> </span>directory
-m:<span class="w"> </span>Manuals
-n:<span class="w"> </span>Manuals<span class="w"> </span>without<span class="w"> </span>compiling<span class="w"> </span>doxygen<span class="w"> </span><span class="o">(</span>only<span class="w"> </span>rst<span class="o">)</span>
-p:<span class="w"> </span>Builds/Rebuilds<span class="w"> </span>Python<span class="w"> </span>API
-r:<span class="w"> </span>Build/Rebuilds<span class="w"> </span>only<span class="w"> </span>receiver
-s:<span class="w"> </span>Simulator
-t:<span class="w"> </span>Build/Rebuilds<span class="w"> </span>only<span class="w"> </span>text<span class="w"> </span>client
-u:<span class="w"> </span>Chip<span class="w"> </span>Test<span class="w"> </span>Gui
-z:<span class="w"> </span>Moench<span class="w"> </span>zmq<span class="w"> </span>processor
<span class="c1"># display all options</span>
./cmk.sh<span class="w"> </span>-?
<span class="c1"># new build and compile in parallel (recommended basic option):</span>
./cmk.sh<span class="w"> </span>-cbj5
<span class="c1"># new build, python and compile in parallel:</span>
./cmk.sh<span class="w"> </span>-cbpj5
<span class="c1">#For rebuilding only certain sections</span>
./cmk.sh<span class="w"> </span>-tg<span class="w"> </span><span class="c1">#only text client and gui</span>
./cmk.sh<span class="w"> </span>-r<span class="w"> </span><span class="c1">#only receiver</span>
</pre></div>
</div>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>For v7.x.x of slsDetectorPackage and older, refer <a class="reference internal" href="#zeromq-for-different-slsdetectorpackage-versions"><span class="std std-ref">zeromq notes for cmk script option to hint library location.</span></a></p>
</div>
</section>
<section id="build-on-old-distributions">
<h3>Build on old distributions<a class="headerlink" href="#build-on-old-distributions" title="Link to this heading"></a></h3>
<p>If your linux distribution doesn’t come with a C++11 compiler (gcc&gt;4.8) then
it’s possible to install a newer gcc using conda and build the slsDetectorPackage
using this compiler</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1">#Create an environment with the dependencies</span>
conda<span class="w"> </span>create<span class="w"> </span>-n<span class="w"> </span>myenv<span class="w"> </span>gxx_linux-64<span class="w"> </span>cmake
conda<span class="w"> </span>activate<span class="w"> </span>myenv
<span class="c1"># outside slsDetecorPackage folder</span>
mkdir<span class="w"> </span>build<span class="w"> </span><span class="o">&amp;&amp;</span><span class="w"> </span><span class="nb">cd</span><span class="w"> </span>build
cmake<span class="w"> </span>../slsDetectorPackage<span class="w"> </span>-DCMAKE_PREFIX_PATH<span class="o">=</span><span class="nv">$CONDA_PREFIX</span>
make<span class="w"> </span>-j12
</pre></div>
</div>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>For v7.x.x of slsDetectorPackage and older, refer <a class="reference internal" href="#zeromq-for-different-slsdetectorpackage-versions"><span class="std std-ref">zeromq notes for dependencies for conda.</span></a></p>
</div>
</section>
<section id="build-slsdetectorgui-qt5">
<h3>Build slsDetectorGui (Qt5)<a class="headerlink" href="#build-slsdetectorgui-qt5" title="Link to this heading"></a></h3>
<ol class="arabic">
<li><p>Using pre-built binary on conda</p>
<blockquote>
<div><div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>conda<span class="w"> </span>create<span class="w"> </span>-n<span class="w"> </span>myenv<span class="w"> </span><span class="nv">slsdetgui</span><span class="o">=</span><span class="m">7</span>.0.0
conda<span class="w"> </span>activate<span class="w"> </span>myenv
</pre></div>
</div>
</div></blockquote>
</li>
<li><p>Using system installation on RHEL7</p>
<blockquote>
<div><div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>yum<span class="w"> </span>install<span class="w"> </span>qt5-qtbase-devel.x86_64
yum<span class="w"> </span>install<span class="w"> </span>qt5-qtsvg-devel.x86_64
</pre></div>
</div>
</div></blockquote>
</li>
<li><p>Using system installation on RHEL8</p>
<blockquote>
<div><div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>yum<span class="w"> </span>install<span class="w"> </span>qt5-qtbase-devel.x86_64
yum<span class="w"> </span>install<span class="w"> </span>qt5-qtsvg-devel.x86_64
yum<span class="w"> </span>install<span class="w"> </span>expat-devel.x86_64
</pre></div>
</div>
</div></blockquote>
</li>
<li><p>Using conda</p>
<blockquote>
<div><div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1">#Add channels for dependencies and our library</span>
conda<span class="w"> </span>config<span class="w"> </span>--add<span class="w"> </span>channels<span class="w"> </span>conda-forge
conda<span class="w"> </span>config<span class="w"> </span>--add<span class="w"> </span>channels<span class="w"> </span>slsdetectorgroup
conda<span class="w"> </span>config<span class="w"> </span>--set<span class="w"> </span>channel_priority<span class="w"> </span>strict
<span class="c1"># create environment to compile</span>
<span class="c1"># on rhel7</span>
conda<span class="w"> </span>create<span class="w"> </span>-n<span class="w"> </span>slsgui<span class="w"> </span>gxx_linux-64<span class="w"> </span>gxx_linux-64<span class="w"> </span>mesa-libgl-devel-cos6-x86_64<span class="w"> </span>qt
<span class="c1"># on fedora or newer systems</span>
conda<span class="w"> </span>create<span class="w"> </span>-n<span class="w"> </span>slsgui<span class="w"> </span>qt
<span class="c1"># when using conda compilers, would also need libgl, but no need for it on fedora unless maybe using it with ROOT</span>
<span class="c1"># activate environment</span>
conda<span class="w"> </span>activate<span class="w"> </span>slsgui
<span class="c1"># compile with cmake outside slsDetecorPackage folder</span>
mkdir<span class="w"> </span>build<span class="w"> </span><span class="o">&amp;&amp;</span><span class="w"> </span><span class="nb">cd</span><span class="w"> </span>build
cmake<span class="w"> </span>../slsDetectorPackage<span class="w"> </span>-DSLS_USE_GUI<span class="o">=</span>ON
make<span class="w"> </span>-j12
<span class="c1"># or compile with cmk.sh</span>
<span class="nb">cd</span><span class="w"> </span>slsDetectorPackage
./cmk.sh<span class="w"> </span>-cbgj9
</pre></div>
</div>
</div></blockquote>
</li>
</ol>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>For v7.x.x of slsDetectorPackage and older, refer <a class="reference internal" href="#zeromq-for-different-slsdetectorpackage-versions"><span class="std std-ref">zeromq notes for dependencies for conda.</span></a></p>
</div>
</section>
<section id="build-this-documentation">
<h3>Build this documentation<a class="headerlink" href="#build-this-documentation" title="Link to this heading"></a></h3>
<p>The documentation for the slsDetectorPackage is build using a combination
of Doxygen, Sphinx and Breathe. The easiest way to install the dependencies
is to use conda</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>conda<span class="w"> </span>create<span class="w"> </span>-n<span class="w"> </span>myenv<span class="w"> </span><span class="nv">python</span><span class="o">=</span><span class="m">3</span>.12<span class="w"> </span>sphinx<span class="w"> </span>sphinx_rtd_theme<span class="w"> </span>breathe<span class="w"> </span>doxygen<span class="w"> </span>numpy
</pre></div>
</div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># using cmake or ccmake to enable DSLS_BUILD_DOCS</span>
<span class="c1"># outside slsDetecorPackage folder</span>
mkdir<span class="w"> </span>build<span class="w"> </span><span class="o">&amp;&amp;</span><span class="w"> </span><span class="nb">cd</span><span class="w"> </span>build
cmake<span class="w"> </span>../slsDetectorPackage<span class="w"> </span>-DSLS_BUILD_DOCS<span class="o">=</span>ON
make<span class="w"> </span>docs<span class="w"> </span><span class="c1"># generate API docs and build Sphinx RST</span>
make<span class="w"> </span>rst<span class="w"> </span><span class="c1"># rst only, saves time in case the API did not change</span>
</pre></div>
</div>
</section>
<section id="pybind-and-zeromq">
<h3>Pybind and Zeromq<a class="headerlink" href="#pybind-and-zeromq" title="Link to this heading"></a></h3>
<div class="line-block" id="pybind-for-different-slsdetectorpackage-versions">
<div class="line"><strong>Pybind11 for Python</strong></div>
<div class="line">v8.0.0+:</div>
<div class="line-block">
<div class="line">pybind11 is built</div>
<div class="line">* by default from tar file in repo (libs/pybind/v2.1x.0.tar.gz)</div>
<div class="line">* or use advanced option SLS_FETCH_PYBIND11_FROM_GITHUB [<a class="reference external" href="https://github.com/pybind/pybind11">link</a>].</div>
<div class="line-block">
<div class="line">* v9.0.0+: pybind11 (v2.13.6)</div>
<div class="line">* v8.x.x : pybind11 (v2.11.0)</div>
<div class="line"><br /></div>
</div>
</div>
<div class="line">v7.x.x:</div>
<div class="line-block">
<div class="line">pybind11 packaged into ‘libs/pybind’. No longer a submodule. No need for “recursive” or “submodule update”.</div>
<div class="line"><br /></div>
</div>
<div class="line">Older versions:</div>
<div class="line-block">
<div class="line">pybind11 is a submodule. Must be cloned using “recursive” and updated when switching between versions using the following commands.</div>
</div>
</div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Note: Only for v6.x.x versions and older</span>
<span class="c1"># clone using recursive to get pybind11 submodule</span>
git<span class="w"> </span>clone<span class="w"> </span>--recursive<span class="w"> </span>https://github.com/slsdetectorgroup/slsDetectorPackage.git
<span class="c1"># update submodule when switching between releases</span>
<span class="nb">cd</span><span class="w"> </span>slsDetectorPackage
git<span class="w"> </span>submodule<span class="w"> </span>update<span class="w"> </span>--init
</pre></div>
</div>
<div class="line-block" id="zeromq-for-different-slsdetectorpackage-versions">
<div class="line"><strong>Zeromq</strong></div>
<div class="line">v8.0.0+:</div>
<div class="line-block">
<div class="line">zeromq (v4.3.4) is built</div>
<div class="line">* by default from tar file in repo (libs/libzmq/libzmq-4.3.4.tar.gz)</div>
<div class="line">* or use advanced option SLS_FETCH_ZMQ_FROM_GITHUB [<a class="reference external" href="https://github.com/zeromq/libzmq.git">link</a>].</div>
<div class="line"><br /></div>
</div>
<div class="line">v7.x.x and older:</div>
<div class="line-block">
<div class="line">zeromq-devel must be installed and one can hint its location using</div>
<div class="line">* cmake option:’-DZeroMQ_HINT=/usr/lib64’ or</div>
<div class="line">* option ‘-q’ in cmk.sh script: : ./cmk.sh -cbj5 -q /usr/lib64</div>
<div class="line">* ‘zeromq’ dependency added when installing using conda</div>
</div>
</div>
</section>
</section>
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