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installation-slides.html
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<!DOCTYPE html><html lang="en-US"><head><meta charset="UTF-8"><meta name="viewport" content="width=device-width,height=device-height,initial-scale=1.0"><meta name="apple-mobile-web-app-capable" content="yes"><meta http-equiv="X-UA-Compatible" content="ie=edge"><meta property="og:type" content="website"><meta name="twitter:card" content="summary"><style>@media screen{body[data-bespoke-view=""] .bespoke-marp-parent>.bespoke-marp-osc>button,body[data-bespoke-view=next] .bespoke-marp-parent>.bespoke-marp-osc>button,body[data-bespoke-view=presenter] .bespoke-marp-presenter-container .bespoke-marp-presenter-info-container button,body[data-bespoke-view=presenter] .bespoke-marp-presenter-container .bespoke-marp-presenter-note-container button{-webkit-tap-highlight-color:transparent;-webkit-appearance:none;appearance:none;background-color:initial;border:0;color:inherit;cursor:pointer;font-size:inherit;opacity:.8;outline:none;padding:0;transition:opacity .2s linear}body[data-bespoke-view=""] .bespoke-marp-parent>.bespoke-marp-osc>button:disabled,body[data-bespoke-view=next] .bespoke-marp-parent>.bespoke-marp-osc>button:disabled,body[data-bespoke-view=presenter] .bespoke-marp-presenter-container .bespoke-marp-presenter-info-container button:disabled,body[data-bespoke-view=presenter] .bespoke-marp-presenter-container .bespoke-marp-presenter-note-container button:disabled{cursor:not-allowed;opacity:.15!important}body[data-bespoke-view=""] .bespoke-marp-parent>.bespoke-marp-osc>button:hover,body[data-bespoke-view=next] .bespoke-marp-parent>.bespoke-marp-osc>button:hover,body[data-bespoke-view=presenter] .bespoke-marp-presenter-container .bespoke-marp-presenter-info-container button:hover,body[data-bespoke-view=presenter] .bespoke-marp-presenter-container .bespoke-marp-presenter-note-container button:hover{opacity:1}body[data-bespoke-view=""] .bespoke-marp-parent>.bespoke-marp-osc>button:hover:active,body[data-bespoke-view=next] 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/*!
* Marp default theme.
*
* @theme default
* @author Yuki Hattori
*
* @auto-scaling true
* @size 16:9 1280px 720px
* @size 4:3 960px 720px
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.pl-c2{background-color:var(--color-prettylights-syntax-carriage-return-bg);color:var(--color-prettylights-syntax-carriage-return-text)}div#\:\$p>svg>foreignObject>section .pl-sr .pl-cce{color:var(--color-prettylights-syntax-string-regexp);font-weight:700}div#\:\$p>svg>foreignObject>section .pl-ml{color:var(--color-prettylights-syntax-markup-list)}div#\:\$p>svg>foreignObject>section .pl-mh,div#\:\$p>svg>foreignObject>section .pl-mh .pl-en,div#\:\$p>svg>foreignObject>section .pl-ms{color:var(--color-prettylights-syntax-markup-heading);font-weight:700}div#\:\$p>svg>foreignObject>section .pl-mi{color:var(--color-prettylights-syntax-markup-italic);font-style:italic}div#\:\$p>svg>foreignObject>section .pl-mb{color:var(--color-prettylights-syntax-markup-bold);font-weight:700}div#\:\$p>svg>foreignObject>section .pl-md{background-color:var(--color-prettylights-syntax-markup-deleted-bg);color:var(--color-prettylights-syntax-markup-deleted-text)}div#\:\$p>svg>foreignObject>section .pl-mi1{background-color:var(--color-prettylights-syntax-markup-inserted-bg);color:var(--color-prettylights-syntax-markup-inserted-text)}div#\:\$p>svg>foreignObject>section .pl-mc{background-color:var(--color-prettylights-syntax-markup-changed-bg);color:var(--color-prettylights-syntax-markup-changed-text)}div#\:\$p>svg>foreignObject>section .pl-mi2{background-color:var(--color-prettylights-syntax-markup-ignored-bg);color:var(--color-prettylights-syntax-markup-ignored-text)}div#\:\$p>svg>foreignObject>section .pl-mdr{color:var(--color-prettylights-syntax-meta-diff-range);font-weight:700}div#\:\$p>svg>foreignObject>section .pl-ba{color:var(--color-prettylights-syntax-brackethighlighter-angle)}div#\:\$p>svg>foreignObject>section .pl-sg{color:var(--color-prettylights-syntax-sublimelinter-gutter-mark)}div#\:\$p>svg>foreignObject>section .pl-corl{color:var(--color-prettylights-syntax-constant-other-reference-link);text-decoration:underline}div#\:\$p>svg>foreignObject>section g-emoji{display:inline-block;font-family:Apple Color Emoji,Segoe UI Emoji,Segoe UI Symbol;font-size:1em;font-style:normal!important;font-weight:var(--base-text-weight-normal,400);line-height:1;min-width:1ch;vertical-align:-.075em}div#\:\$p>svg>foreignObject>section g-emoji img{height:1em;width:1em}div#\:\$p>svg>foreignObject>section .task-list-item{list-style-type:none}div#\:\$p>svg>foreignObject>section .task-list-item label{font-weight:var(--base-text-weight-normal,400)}div#\:\$p>svg>foreignObject>section .task-list-item.enabled label{cursor:pointer}div#\:\$p>svg>foreignObject>section .task-list-item+.task-list-item{margin-top:4px}div#\:\$p>svg>foreignObject>section .task-list-item .handle{display:none}div#\:\$p>svg>foreignObject>section .task-list-item-checkbox{margin:0 .2em .25em -1.4em;vertical-align:middle}div#\:\$p>svg>foreignObject>section .contains-task-list:dir(rtl) .task-list-item-checkbox{margin:0 -1.6em .25em .2em}div#\:\$p>svg>foreignObject>section 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<h2 id="installation-guide-for-ehep-2023"><strong>Installation guide for EHEP 2023</strong></h2>
<p>Deepak Samuel<br />
Central University of Karnataka</p>
</section>
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<h2 id="download-links">Download links</h2>
<table>
<thead>
<tr>
<th>Software</th>
<th>Download Link (tested for Ubuntu)</th>
<th>Size (approx)</th>
<th>Install command</th>
</tr>
</thead>
<tbody>
<tr>
<td>Anaconda</td>
<td><a href="https://repo.anaconda.com/archive/Anaconda3-2023.07-2-Linux-x86_64.sh">https://repo.anaconda.com/archive/Anaconda3-2023.07-2-Linux-x86_64.sh</a> Refer <a href="https://www.anaconda.com/download">https://www.anaconda.com/download</a> for other OS</td>
<td>1 GB</td>
<td><code>chmod +x Anaconda3-2023.07-2-Linux-x86_64.sh</code> <code>./Anaconda3-2023.07-2-Linux-x86_64.sh</code></td>
</tr>
<tr>
<td>Snap</td>
<td>Direct install Refer <a href="https://snapcraft.io/docs/installing-snap-on-ubuntu">https://snapcraft.io/docs/installing-snap-on-ubuntu</a> for other OS</td>
<td>5 MB</td>
<td><code>sudo apt update</code> <code>sudo apt install snapd</code></td>
</tr>
<tr>
<td>VSCode</td>
<td>Direct install Refer <a href="https://code.visualstudio.com/">https://code.visualstudio.com/</a> for more information</td>
<td>70 MB</td>
<td><code>sudo snap install code --classic</code></td>
</tr>
<tr>
<td>Git</td>
<td>Direct install</td>
<td>20 MB</td>
<td><code>sudo snap install git-ubuntu --classic</code></td>
</tr>
<tr>
<td>CMake</td>
<td>Direct Install</td>
<td>5 MB</td>
<td><code>sudo snap install cmake --classic</code></td>
</tr>
<tr>
<td>ROOT</td>
<td><a href="https://root.cern/download/root_v6.28.06.source.tar.gz">https://root.cern/download/root_v6.28.06.source.tar.gz</a></td>
<td>200 MB</td>
<td>To be discussed, refer to <a href="https://root.cern/install/">https://root.cern/install/</a> for requirements for your system</td>
</tr>
<tr>
<td>Geant4</td>
<td><a href="https://gitlab.cern.ch/geant4/geant4/-/archive/v11.1.2/geant4-v11.1.2.tar.gz">https://gitlab.cern.ch/geant4/geant4/-/archive/v11.1.2/geant4-v11.1.2.tar.gz</a></td>
<td>450 MB</td>
<td>To be discussed …</td>
</tr>
</tbody>
</table>
</section>
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<h2 id="geant4-datasets">Geant4 datasets</h2>
<p>For Geant4 simulations to run, you need to download the datasets on to your computer:</p>
<p>Go to: <a href="https://geant4.web.cern.ch/download/11.1.2.html">https://geant4.web.cern.ch/download/11.1.2.html</a></p>
<p>Download all the datasets therein into the ‘data’ folder inside g4</p>
</section>
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<h2 id="dependencies">Dependencies</h2>
<p>To install the dependencies, use the following commands</p>
<ul>
<li>ROOT
<ul>
<li><code>sudo apt-get install dpkg-dev cmake g++ gcc binutils libx11-dev libxpm-dev libxft-dev libxext-dev python libssl-dev</code></li>
<li><code>sudo apt-get install gfortran libpcre3-dev xlibmesa-glu-dev libglew-dev libftgl-dev libmysqlclient-dev libfftw3-dev libcfitsio-dev graphviz-dev libavahi-compat-libdnssd-dev libldap2-dev python-dev python-numpy libxml2-dev libkrb5-dev libgsl0-dev qtwebengine5-dev</code></li>
</ul>
</li>
</ul>
</section>
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<ul>
<li>Geant4
<ul>
<li>GDML: <code>sudo apt-get install -y libxerces-c-dev</code></li>
<li>libXMu: <code>sudo apt-get install -y libxmu-dev</code></li>
<li>Qt:
<ul>
<li><code>sudo apt-get install qtbase5-dev</code></li>
<li><code>sudo apt-get install qtdeclarative5-dev</code></li>
</ul>
</li>
<li>OpenSSL: <code>sudo apt-get -y install build-essential openssl libssl-dev libssl1.0 libgl1-mesa-dev libqt5x11extras5</code></li>
</ul>
</li>
</ul>
</section>
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<h2 id="folder-structure">Folder structure</h2>
<p>For the sake of this preschool, we propose to use this folder structure:</p>
<ul>
<li>Create a main directory called <code>ehep</code>, preferably on the Desktop</li>
<li>Inside of ehep, create three directories (along with the subdirectories as shown below
<ul>
<li><code>downloads</code></li>
<li><code>g4</code>
<ul>
<li><code>build</code></li>
<li><code>install</code></li>
<li><code>data</code></li>
</ul>
</li>
<li><code>root</code>
<ul>
<li><code>build</code></li>
<li><code>install</code></li>
</ul>
</li>
</ul>
</li>
</ul>
</section>
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<h2 id="easy-download-script">Easy download script</h2>
<p>I have written a script which will do all of the above in one go, the script named <code>ehep.sh</code> is found in this repository, you can download it on your Desktop:</p>
<p><a href="https://raw.githubusercontent.com/deepaksamuel/ehep-2023/main/ehep.sh">https://raw.githubusercontent.com/deepaksamuel/ehep-2023/main/ehep.sh</a></p>
<p>Right click and save link as ehep.sh on your Desktop</p>
<p>Once saved, on your terminal execute the command <code>source ehep.sh</code></p>
<p>Please note that this script will also download the Geant4 datasets which may be extremely time consuming. However, as soon as the datasets downloading begins, parallely you can compile other codes.</p>
<p>Do not close the terminal in which the ehep.sh script is running. Open a new terminal for parallely compiling the other programmes.</p>
</section>
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<h2 id="instructions-for-installing-anaconda">Instructions for installing Anaconda</h2>
<p>Please invoke these commands from the terminal after <code>cd</code> ing to the location where the binary was downloaded:</p>
<ul>
<li><code>cd ehep/downloads</code></li>
<li><code>chmod +x Anaconda3-2023.07-2-Linux-x86_64.sh</code></li>
<li><code>./Anaconda3-2023.07-2-Linux-x86_64.sh</code></li>
</ul>
</section>
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<p>Please watch out for these screens:</p>
<p><img src="img/anaconda-installation.png" alt="" title="a title" style="width:650px;" /></p>
</section>
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<h3 id="python-libraries-required-for-ehep-2023-can-be-installed-using-conda-or-pip-the-commands-for-conda-are-given-below">Python libraries required for EHEP 2023 can be installed using conda or pip. The commands for conda are given below:</h3>
<pre is="marp-pre" data-auto-scaling="downscale-only"><code> conda install -c anaconda jupyter
conda install -c conda-forge jupyter-lsp
conda install -c conda-forge nbdime
conda install -c conda-forge jupyterlab-git
conda install -c conda-forge scikit-learn
conda install -c conda-forge seaborn
conda install -c conda-forge tensorflow
conda install -c conda-forge keras
conda install -c pytorch pytorch
conda install -c conda-forge dask
conda install -c conda-forge libxgboost
conda install -c conda-forge qutip
conda install -c conda-forge qiskit-terra
conda install -c conda-forge qiskit-metal
</code></pre>
<h3 id="important-do-not-mix-pip-install-and-conda-install-as-they-will-result-in-conflicts">Important: Do not mix <code>pip install</code> and <code>conda install</code> as they will result in conflicts.</h3>
</section>
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<h2 id="instructions-for-installing-root">Instructions for installing ROOT</h2>
<h3 id="invoking-cmake-gui">Invoking CMake-GUI</h3>
<p>Most often, softwares used in HEP are distributed as source codes than binaries. In such a case, you will have to use CMake to generate your build files and then compile your code to generate the binary.<br />
There is a command line way to work with CMake but just to make things easier, we will use the cmake gui.<br />
You can call the gui by typing <code>cmake3-gui</code> on the terminal.</p>
</section>
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<p><img src="img/cmake-root.png" alt="Alt text" title="a title" /></p>
</section>
</foreignObject></svg><svg data-marpit-svg="" viewBox="0 0 1280 720"><foreignObject width="1280" height="720"><section id="13">
<p>The first three steps are generic whenever you compile from sources (you will do the same for Geant4 as well).</p>
<ol>
<li>Choosing the location where your source code resides: The easy download script places the source code in the root folder</li>
<li>Choosing the location for your build files: The build folder inside root folder is used for this purpose</li>
<li>Choosing the location for your install files: The install folder inside root folder is used for this purpose</li>
</ol>
<p>The fourth step is where you choose additional options for your root installation. If you scroll down you will see options like <code>pyroot</code> and <code>roofit</code> which you should enable as they will be used in the school.</p>
</section>
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<h3 id="important">Important:</h3>
<p>It is often the case that the python installed by Anaconda distribution conflicts with your many other python distributions on your computer. If you want your ROOT to be compiled with the python from Anaconda distribution, you may have to set the CMake variable appropriately. For example, I have set <code>CMAKE_INSTALL_PYTHONDIR</code> to <code>/home/samuel/anaconda3/bin/python</code>.</p>
</section>
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<p>The fifth step is clicking on the <code>configure</code> button which leads you to another popup asking you to choose the compiler and so on. The default option is <code>use default native compilers</code> with <code>Unix Makefiles</code> in the dropdown. Unless you know what you are doing, accept the defaults. If you see no erros reported in the log, you can go on to the next step. In case of errors, you may have to install additional dependencies reported therein.</p>
<p>The final step is clicking on the <code>Generate</code> button. Once again, you may have to check for any errors reported at this stage.</p>
</section>
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<h3 id="using-cmake-command-line">Using CMake command line</h3>
<p>If you want know how to invoke cmake steps that you did in the earlier step using GUI, using the command line, here it is:<br />
First cd to the build folder inside root directory:</p>
<ul>
<li><code>cd ehep/root/build</code><br />
and then</li>
<li><code>cmake -DCMAKE_INSTALL_PREFIX=../install ../root-6.28.06/ -Dpyroot=ON -Drootfit=ON -DPython3_EXECUTABLE=/home/codespace/anaconda3/bin/python</code></li>
</ul>
<p>Note that the above step has to be done only if you are not using the Cmake-Gui.</p>
</section>
</foreignObject></svg><svg data-marpit-svg="" viewBox="0 0 1280 720"><foreignObject width="1280" height="720"><section id="17">
<h3 id="compiling-the-code">Compiling the code</h3>
<p>Now that the build files are created, you are now ready to compile your code.</p>
<ul>
<li>
<p>On a terminal window, cd to <code>build</code> folder inside <code>ehep/root</code></p>
</li>
<li>
<p>type <code>make -j4</code> to begin compiling</p>
</li>
<li>
<p>wait for 30 - 45 minutes</p>
</li>
<li>
<p>If the compiling is successful, type <code>make install</code></p>
</li>
</ul>
</section>
</foreignObject></svg><svg data-marpit-svg="" viewBox="0 0 1280 720"><foreignObject width="1280" height="720"><section id="18">
<h3 id="running-root">Running ROOT</h3>
<p>If everything is done, you should be able to run ROOT. For this, on a terminal cd to <code>ehep/root/install/bin</code> and type:</p>
<p><code>source thisroot.sh</code></p>
<p>Then type,</p>
<p><code>root</code></p>
<p>You should see the ROOT command prompt coming up.</p>
</section>
</foreignObject></svg><svg data-marpit-svg="" viewBox="0 0 1280 720"><foreignObject width="1280" height="720"><section id="19">
<p><img src="img/root-prompt.png" alt="Alt text" title="a title" /></p>
</section>
</foreignObject></svg><svg data-marpit-svg="" viewBox="0 0 1280 720"><foreignObject width="1280" height="720"><section id="20">
<p>You must source thisroot.sh every time you open a new terminal. In case you intend to use ROOT frequently, this may be inconvenient. You should instead add this line to your bash.rc file.</p>
</section>
</foreignObject></svg><svg data-marpit-svg="" viewBox="0 0 1280 720"><foreignObject width="1280" height="720"><section id="21">
<h3 id="other-ways-to-install--run-root">Other ways to install / run ROOT</h3>
<ul>
<li>To know more about build ROOT from source and other options, please go to: <a href="https://root.cern/install/build_from_source/">https://root.cern/install/build_from_source/</a></li>
<li>Other ways to install: <a href="https://root.cern/install/">https://root.cern/install/</a></li>
</ul>
</section>
</foreignObject></svg><svg data-marpit-svg="" viewBox="0 0 1280 720"><foreignObject width="1280" height="720"><section id="22">
<h2 id="instructions-for-installing-geant4">Instructions for installing Geant4</h2>
<h3 id="invoking-cmake-gui-1">Invoking CMake-GUI</h3>
<p>We will follow the same instructions as used for root installation<br />
Call <code>cmake3-gui</code> on the terminal.</p>
</section>
</foreignObject></svg><svg data-marpit-svg="" viewBox="0 0 1280 720"><foreignObject width="1280" height="720"><section id="23">
<p><img src="img/cmake-geant4.png" alt="Alt text" title="a title" /></p>
</section>
</foreignObject></svg><svg data-marpit-svg="" viewBox="0 0 1280 720"><foreignObject width="1280" height="720"><section id="24">
<p>The steps are as follows:</p>
<ol>
<li>Set the source location</li>
<li>Set the location for your build files: The build folder inside g4 folder is used for this purpose</li>
<li>Set the location for your install files: The install folder inside g4 folder is used for this purpose</li>
<li>Set the location for the data files: The data folder inside g4 folder is used for this purpose</li>
</ol>
</section>
</foreignObject></svg><svg data-marpit-svg="" viewBox="0 0 1280 720"><foreignObject width="1280" height="720"><section id="25">
<p>The fifth step is where you choose additional options for your Geant4 installation. Please make sure that the following options are checked:</p>
<ul>
<li>GEANT4_BUILD_MULTITHREADED</li>
<li>GEANT4_USE_GDML</li>
<li>GEANT4_USE_OPENGL_X11</li>
<li>GEANT4_USE_QT</li>
</ul>
<p>IMPORTANT: Please uncheck the <code>GEANT4_INSTALL_DATA</code> or else the datasets will be automatically downloaded again</p>
</section>
</foreignObject></svg><svg data-marpit-svg="" viewBox="0 0 1280 720"><foreignObject width="1280" height="720"><section id="26">
<p>The sixth step is clicking on the <code>configure</code> button which leads you to another popup asking you to choose the compiler and so on. The default option is <code>use default native compilers</code> with <code>Unix Makefiles</code> in the dropdown. Unless you know what you are doing, accept the defaults. If you see no erros reported in the log, you can go on to the next step. In case of errors, you may have to install additional dependencies reported therein.</p>
<p>The sevent step is clicking on the <code>Generate</code> button. Once again, you may have to check for any errors reported at this stage.</p>
</section>
</foreignObject></svg><svg data-marpit-svg="" viewBox="0 0 1280 720"><foreignObject width="1280" height="720"><section id="27">
<h3 id="compiling-geant4-using-cmake-command-line">Compiling Geant4 using CMake command line</h3>
<ul>
<li><code>cmake -DCMAKE_INSTALL_PREFIX=../install ../geant4-v11.1.2/ -DGEANT4_USE_GDML=ON -DGEANT4_INSTALL_DATADIR=../data -DGEANT4_USE_OPENGL_X11=ON -DGEANT4_USE_QT=ON</code></li>
</ul>
</section>
</foreignObject></svg><svg data-marpit-svg="" viewBox="0 0 1280 720"><foreignObject width="1280" height="720"><section id="28">
<h3 id="compiling-the-code-1">Compiling the code</h3>
<p>Now that the build files are created, you are now ready to compile your code.</p>
<ul>
<li>
<p>On a terminal window, cd to <code>build</code> folder inside <code>ehep/g4</code></p>
</li>
<li>
<p>type <code>make -j4</code> to begin compiling</p>
</li>
<li>
<p>wait for 45 - 60 minutes</p>
</li>
<li>
<p>If the compiling is successful, type <code>make install</code></p>
</li>
</ul>
</section>
</foreignObject></svg><svg data-marpit-svg="" viewBox="0 0 1280 720"><foreignObject width="1280" height="720"><section id="29">
<h3 id="setting-the-geant4-environment">Setting the Geant4 environment</h3>
<p>Every time you run a Geant4 code, you must source this script <code>geant4.sh</code> will is found in the <code>ehep/g4/install/bin folder</code></p>
<ul>
<li><code>source ehep/g4/install/bin/geant4.sh</code></li>
</ul>
<p>failing which, you will not be able to compile the code successfully. If you are frequently developing Geant4 code, it is best to source this in your .bashrc file.</p>
</section>
</foreignObject></svg><svg data-marpit-svg="" viewBox="0 0 1280 720"><foreignObject width="1280" height="720"><section id="30">
<h3 id="more-compile-options-for-geant4">More compile options for Geant4</h3>
<p>Please go to this link for more build options in Geant4:</p>
<ul>
<li><a href="https://geant4-userdoc.web.cern.ch/UsersGuides/InstallationGuide/html/installguide.html#geant4-build-options">https://geant4-userdoc.web.cern.ch/UsersGuides/InstallationGuide/html/installguide.html#geant4-build-options</a></li>
</ul>
</section>
</foreignObject></svg><svg data-marpit-svg="" viewBox="0 0 1280 720"><foreignObject width="1280" height="720"><section id="31"></section>
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