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GettingStarted.html
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<div class="section" id="getting-started">
<span id="gettingstarted"></span><h1>Getting Started<a class="headerlink" href="#getting-started" title="Permalink to this headline">¶</a></h1>
<div class="contents local topic" id="contents">
<ul class="simple">
<li><a class="reference internal" href="#environment" id="id5">Environment</a><ul>
<li><a class="reference internal" href="#windows" id="id6">Windows</a><ul>
<li><a class="reference internal" href="#windows-subsystem-for-linux-wsl2" id="id7">Windows Subsystem for Linux (WSL2)</a></li>
</ul>
</li>
<li><a class="reference internal" href="#linux" id="id8">Linux</a><ul>
<li><a class="reference internal" href="#red-hat-cent-os-fedora" id="id9">Red Hat/Cent OS/Fedora</a></li>
<li><a class="reference internal" href="#ubuntu-18-04" id="id10">Ubuntu 18.04</a></li>
<li><a class="reference internal" href="#ubuntu-20-04" id="id11">Ubuntu 20.04</a></li>
</ul>
</li>
<li><a class="reference internal" href="#osx" id="id12">OSX</a></li>
<li><a class="reference internal" href="#docker" id="id13">Docker</a></li>
</ul>
</li>
<li><a class="reference internal" href="#getting-the-mantid-code" id="id14">Getting the Mantid code</a><ul>
<li><a class="reference internal" href="#custom-git-setup-for-inside-the-ornl-firewall" id="id15">Custom git setup for inside the ORNL firewall:</a></li>
</ul>
</li>
<li><a class="reference internal" href="#setting-up-github" id="id16">Setting up GitHub</a></li>
<li><a class="reference internal" href="#building-mantid" id="id17">Building Mantid</a></li>
<li><a class="reference internal" href="#archive-access-isis" id="id18">Archive access - ISIS</a><ul>
<li><a class="reference internal" href="#id3" id="id19">OSX</a></li>
<li><a class="reference internal" href="#id4" id="id20">Linux</a></li>
</ul>
</li>
</ul>
</div>
<div class="section" id="environment">
<h2><a class="toc-backref" href="#id5">Environment</a><a class="headerlink" href="#environment" title="Permalink to this headline">¶</a></h2>
<p>Some initial setup is required before being able to build the code. This is platform
specific and described here.</p>
<div class="section" id="windows">
<h3><a class="toc-backref" href="#id6">Windows</a><a class="headerlink" href="#windows" title="Permalink to this headline">¶</a></h3>
<p>Install the following:</p>
<ul class="simple">
<li><a class="reference external" href="https://visualstudio.microsoft.com/downloads/">Visual Studio 2019 Community Edition</a>.<ul>
<li>When asked about installation workloads choose <code class="docutils literal notranslate"><span class="pre">Desktop</span> <span class="pre">development</span> <span class="pre">with</span> <span class="pre">C++</span></code></li>
<li>Under the “Installation details” section verify that the following are checked:<ul>
<li><code class="docutils literal notranslate"><span class="pre">Windows</span> <span class="pre">Universal</span> <span class="pre">CRT</span> <span class="pre">SDK</span></code></li>
<li>The latest Windows 10 SDK</li>
</ul>
</li>
<li>If your machine has less than 32GB of memory Mantid may not build. If you have problems change the maximum number of parallel project builds to 1 in Visual Studio in Tools -> Options -> Projects and Solutions -> Build And Run.</li>
</ul>
</li>
<li><a class="reference external" href="https://git-scm.com/">Git</a>.<ul>
<li>install the latest version and ensure that Git LFS is checked to be included</li>
<li>when the install has completed create a directory for storage of the LFS objects, e.g. <code class="docutils literal notranslate"><span class="pre">C:\GitLFSStorage</span></code></li>
<li>open up Git Bash and run <code class="docutils literal notranslate"><span class="pre">git</span> <span class="pre">config</span> <span class="pre">--global</span> <span class="pre">lfs.storage</span> <span class="pre">C:/GitLFSStorage</span></code></li>
<li>run <code class="docutils literal notranslate"><span class="pre">git</span> <span class="pre">lfs</span> <span class="pre">install</span></code> to initialize Git LFS. (Note that if you miss this step you may get errors due to the third party libraries not checking out properly. This can be fixed later by running <code class="docutils literal notranslate"><span class="pre">git</span> <span class="pre">lfs</span> <span class="pre">fetch</span></code> and <code class="docutils literal notranslate"><span class="pre">git</span> <span class="pre">lfs</span> <span class="pre">checkout</span></code> in the <code class="docutils literal notranslate"><span class="pre">external\src\ThirdParty</span></code> directory.)</li>
</ul>
</li>
<li><a class="reference external" href="https://cmake.org/download/">CMake</a> >= 3.15</li>
<li><a class="reference external" href="https://miktex.org/download">MiKTeX</a>. Installation instructions are <a class="reference external" href="https://miktex.org/howto/install-miktex">available here</a>. Once installed:<ul>
<li>open the MikTeX console from the start menu</li>
<li>switch to administrator mode</li>
<li>settings -> select “Always install missing packages on-the-fly”</li>
</ul>
</li>
<li><a class="reference external" href="http://nsis.sourceforge.net/Download">NSIS</a> (optional). Used for building packages</li>
</ul>
<p><a class="reference external" href="http://graphviz.org/download/">Graphviz</a> is required to generate the workflow diagrams in the documentation.
Unfortunately CMake can’t find it out of the box and the following steps are required to make this link</p>
<ul class="simple">
<li>open regedit</li>
<li>add a new key <code class="docutils literal notranslate"><span class="pre">[HKEY_LOCAL_MACHINE\\SOFTWARE\\ATT\\Graphviz]</span></code></li>
<li>create a new string value named <code class="docutils literal notranslate"><span class="pre">InstallPath</span></code> within this key and set the value
to point to the install directory of Graphviz.</li>
</ul>
<div class="section" id="windows-subsystem-for-linux-wsl2">
<h4><a class="toc-backref" href="#id7">Windows Subsystem for Linux (WSL2)</a><a class="headerlink" href="#windows-subsystem-for-linux-wsl2" title="Permalink to this headline">¶</a></h4>
<p>It is also possible to install a Linux subsystem within Windows by following <a class="reference internal" href="WindowsSubsystemForLinux.html#windowssubsystemforlinux"><span class="std std-ref">these</span></a> instructions. This step is optional.</p>
</div>
</div>
<div class="section" id="linux">
<h3><a class="toc-backref" href="#id8">Linux</a><a class="headerlink" href="#linux" title="Permalink to this headline">¶</a></h3>
<div class="section" id="red-hat-cent-os-fedora">
<h4><a class="toc-backref" href="#id9">Red Hat/Cent OS/Fedora</a><a class="headerlink" href="#red-hat-cent-os-fedora" title="Permalink to this headline">¶</a></h4>
<ul class="simple">
<li>Follow the <a class="reference external" href="https://fedoraproject.org/wiki/EPEL">instructions here</a> to enable the EPEL repository
for RHEL7</li>
<li>Run the following to install the mantid-developer package</li>
</ul>
<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span><span class="c1"># Install copr plugin</span>
yum install yum-plugin-copr
<span class="c1"># Enable the mantid repo from copr</span>
yum copr <span class="nb">enable</span> mantid/mantid
<span class="c1"># Install dependencies</span>
yum install mantid-developer
<span class="c1"># Install pre-commit</span>
pip3 install pre-commit --user
</pre></div>
</div>
<p>On fedora, the <code class="docutils literal notranslate"><span class="pre">yum</span></code> commands should be replaced with <code class="docutils literal notranslate"><span class="pre">dnf</span></code>.
For systems with default python3 the <code class="docutils literal notranslate"><span class="pre">pip3</span></code> command can be replaced with <code class="docutils literal notranslate"><span class="pre">pip</span></code>, but it should work either way.</p>
<p>Make sure you install <a class="reference external" href="https://developer.mantidproject.org/BuildingWithCMake.html#from-the-command-line">devtoolset-7</a> as described in the link.</p>
<p>Now you can <a class="reference external" href="https://developer.mantidproject.org/GettingStarted.html#getting-the-mantid-code">get the mantid code</a>, and build it:</p>
<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>mkdir build
<span class="nb">cd</span> build
scl <span class="nb">enable</span> devtoolset-7 <span class="s2">"cmake3 [mantid source]"</span>
cmake3 --build .
</pre></div>
</div>
<p>See the instructions on <a class="reference internal" href="RunningTheUnitTests.html#runningtheunittests"><span class="std std-ref">this</span></a> page to run the Mantid unit tests.</p>
</div>
<div class="section" id="ubuntu-18-04">
<h4><a class="toc-backref" href="#id10">Ubuntu 18.04</a><a class="headerlink" href="#ubuntu-18-04" title="Permalink to this headline">¶</a></h4>
<ul class="simple">
<li>Setup the Kitware APT repository to get a recent version of CMake by
following <a class="reference external" href="https://apt.kitware.com/">these instructions</a></li>
<li>Follow the <a class="reference external" href="http://download.mantidproject.org/ubuntu.html">Ubuntu instructions</a>
to add the stable release repository and mantid ppa and</li>
<li>Download the latest
<a class="reference external" href="https://sourceforge.net/projects/mantid/files/developer">mantid-developer</a>
package and install it:</li>
</ul>
<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>apt install gdebi-core
gdebi ~/Downloads/mantid-developer.X.Y.Z.deb
</pre></div>
</div>
<p>where <code class="docutils literal notranslate"><span class="pre">X.Y.Z</span></code> should be replaced with the version that was downloaded.</p>
<p>Install pre-commit for use in our current developer workflow</p>
<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>pip install pre-commit --user
</pre></div>
</div>
<p>if you wish to setup eclipse for use developing mantid, then instructions can be found <a class="reference internal" href="Eclipse.html#eclipse"><span class="std std-ref">here</span></a>.</p>
<p>Now you can <a class="reference external" href="https://developer.mantidproject.org/GettingStarted.html#getting-the-mantid-code">get the mantid code</a>, and build it:</p>
<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>mkdir build
<span class="nb">cd</span> build
cmake -GNinja <span class="o">[</span>mantid source<span class="o">]</span>
cmake --build .
</pre></div>
</div>
<p>See the instructions on <a class="reference internal" href="RunningTheUnitTests.html#runningtheunittests"><span class="std std-ref">this</span></a> page to run the Mantid unit tests.</p>
</div>
<div class="section" id="ubuntu-20-04">
<h4><a class="toc-backref" href="#id11">Ubuntu 20.04</a><a class="headerlink" href="#ubuntu-20-04" title="Permalink to this headline">¶</a></h4>
<ul class="simple">
<li>Mantid uses <cite>qtpy</cite> to talk to Python bindings of Qt. It is recommended to have the _
environment var <cite>QT_API=pyqt5</cite> exported to the shell before building with CMake.</li>
<li>The header and lib shipped with Anaconda (if installed) could interfere with Mantid building _
process. It is highly recommended to remove Anaconda Python from your env prior to building _
using <cite>conda deactivate</cite>.</li>
<li>Mantid is not yet officially supported on Ubuntu 20.04, but mantid-developer package (see Ubuntu 18.04 instructions) has been modified to support it.</li>
<li>Install pre-commit for use in our current developer workflow</li>
</ul>
<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>pip install pre-commit --user
</pre></div>
</div>
</div>
</div>
<div class="section" id="osx">
<h3><a class="toc-backref" href="#id12">OSX</a><a class="headerlink" href="#osx" title="Permalink to this headline">¶</a></h3>
<p>The build environment on OS X is described here <a class="reference internal" href="BuildingOnOSX.html#buildingonosx"><span class="std std-ref">Building on OS X</span></a>.</p>
<p>Install pre-commit for use in our current developer workflow</p>
<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>brew install pre-commit
</pre></div>
</div>
</div>
<div class="section" id="docker">
<h3><a class="toc-backref" href="#id13">Docker</a><a class="headerlink" href="#docker" title="Permalink to this headline">¶</a></h3>
<p>On Docker supported systems you may use the <a class="reference external" href="https://github.com/mantidproject/dockerfiles/tree/master/development">mantid-development</a>
images to develop Mantid without having to configure your system as a suitable
build environment. This will give you an out of the box working build
environment, Python 3 (where available) and ccache.</p>
<p>More details and instructions can be found at the GitHub link above.</p>
</div>
</div>
<div class="section" id="getting-the-mantid-code">
<h2><a class="toc-backref" href="#id14">Getting the Mantid code</a><a class="headerlink" href="#getting-the-mantid-code" title="Permalink to this headline">¶</a></h2>
<p>We use <a class="reference external" href="https://git-scm.com/">Git</a> as our version control system (VCS). The master copies of our repositories are located at <a class="reference external" href="http://github.com/mantidproject">GitHub</a>. We have a number of repositories, of which the main one (the one containing all the source code for Mantid itself) is called simply <a class="reference external" href="http://github.com/mantidproject/mantid">mantid</a>.</p>
<p>If you are not already set up with Git, you can follow these <a class="reference external" href="https://git-scm.com/book/en/v2/Getting-Started-First-Time-Git-Setup">instructions</a>.</p>
<p>There are a number of URLs via which the code can be checked out using various protocols. The easiest way to get the one you want is to select the protocol you want on the right side of the <a class="reference external" href="http://github.com/mantidproject/mantid">mantid</a> repository page on github and copy the url into your clipboard. The way to clone the repository via ssh on the command line, into a directory called Mantid, is:</p>
<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>git clone git@github.com:mantidproject/mantid.git
</pre></div>
</div>
<p>Alternatively, one can use the <code class="docutils literal notranslate"><span class="pre">https</span></code> protocol for cloning the repository.
This requires one to supply an authentication token when pushing or re-type their password.</p>
<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>git clone https://github.com/mantidproject/mantid.git
</pre></div>
</div>
<div class="section" id="custom-git-setup-for-inside-the-ornl-firewall">
<h3><a class="toc-backref" href="#id15">Custom git setup for inside the ORNL firewall:</a><a class="headerlink" href="#custom-git-setup-for-inside-the-ornl-firewall" title="Permalink to this headline">¶</a></h3>
<p>Due to security configuration at ORNL one needs to do additional configuration to access github from within the lab.
One option is to use the <code class="docutils literal notranslate"><span class="pre">https</span></code> protocol listed above
The alternative is to “corkscrew the snowman” which allows for using the <code class="docutils literal notranslate"><span class="pre">git</span></code> protocol by modifying the ssh configuration.
Corkscrew can be installed from your package manager, or it is a single <code class="docutils literal notranslate"><span class="pre">c</span></code> file found on github.
Add the following lines to <code class="docutils literal notranslate"><span class="pre">~/.ssh/config</span></code>:</p>
<div class="code bash highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">ProxyCommand</span> <span class="n">corkscrew</span> <span class="n">snowman</span><span class="o">.</span><span class="n">ornl</span><span class="o">.</span><span class="n">gov</span> <span class="mi">3128</span> <span class="o">%</span><span class="n">h</span> <span class="o">%</span><span class="n">p</span>
<span class="n">Host</span> <span class="n">github</span><span class="o">.</span><span class="n">com</span>
</pre></div>
</div>
<p>If you need further help, ask another developer at the facility how to configure the corkscrew option.</p>
</div>
</div>
<div class="section" id="setting-up-github">
<h2><a class="toc-backref" href="#id16">Setting up GitHub</a><a class="headerlink" href="#setting-up-github" title="Permalink to this headline">¶</a></h2>
<p>Please install the ZenHub Browser extension from this <a class="reference external" href="https://www.zenhub.com/extension">page</a>.</p>
</div>
<div class="section" id="building-mantid">
<h2><a class="toc-backref" href="#id17">Building Mantid</a><a class="headerlink" href="#building-mantid" title="Permalink to this headline">¶</a></h2>
<p>See <a class="reference internal" href="BuildingWithCMake.html#buildingwithcmake"><span class="std std-ref">Building with CMake</span></a> for information about building Mantid.</p>
</div>
<div class="section" id="archive-access-isis">
<h2><a class="toc-backref" href="#id18">Archive access - ISIS</a><a class="headerlink" href="#archive-access-isis" title="Permalink to this headline">¶</a></h2>
<p>It is very convenient to be able to access the data archive directly.
At ISIS, this is automatically done on the Windows machines, however OSX and Linux
require some extra setup.</p>
<div class="section" id="id3">
<h3><a class="toc-backref" href="#id19">OSX</a><a class="headerlink" href="#id3" title="Permalink to this headline">¶</a></h3>
<ul class="simple">
<li>In Finder “command”+k opens a mounting dialogue</li>
<li>For <cite>Server address</cite> enter <cite>smb://isisdatar80/inst$/</cite> hit Connect</li>
<li>This should prompt you for federal ID <cite>clrc….</cite> and password</li>
<li>After completing this the drive is now mounted</li>
<li>It can be found at <cite>/Volumes/inst$</cite></li>
</ul>
<p><strong>NB</strong> the address in step 2 sometimes changes - if it does not work, replace <cite>80</cite> with <cite>55</cite> or <cite>3</cite>.</p>
</div>
<div class="section" id="id4">
<h3><a class="toc-backref" href="#id20">Linux</a><a class="headerlink" href="#id4" title="Permalink to this headline">¶</a></h3>
<ol class="arabic simple">
<li>Install packages:</li>
</ol>
<p><code class="docutils literal notranslate"><span class="pre">sudo</span> <span class="pre">apt-get</span> <span class="pre">install</span> <span class="pre">-y</span> <span class="pre">autofs</span> <span class="pre">cifs-utils</span> <span class="pre">keyutils</span></code></p>
<ol class="arabic simple" start="2">
<li>Create an <code class="docutils literal notranslate"><span class="pre">/archive.creds</span></code> file in the root directory containing this, filling in the relevant details:</li>
</ol>
<p>This should only be done if full disk encryption is enabled or if the <code class="docutils literal notranslate"><span class="pre">archive.creds</span></code> file is stored in a secure (encrypted) location; to ensure passwords are kept safe.</p>
<div class="highlight-text notranslate"><div class="highlight"><pre><span></span>username=FEDERAL_ID_HERE
password=FED_PASSWD_HERE
domain=CLRC
</pre></div>
</div>
<ol class="arabic simple" start="3">
<li>Edit <code class="docutils literal notranslate"><span class="pre">/etc/auto.master</span></code> and add the line:</li>
</ol>
<div class="highlight-text notranslate"><div class="highlight"><pre><span></span>/archive /etc/auto.archive
</pre></div>
</div>
<ol class="arabic simple" start="4">
<li>Create <code class="docutils literal notranslate"><span class="pre">/etc/auto.archive</span></code> and add the single line:</li>
</ol>
<div class="highlight-text notranslate"><div class="highlight"><pre><span></span>* -fstype=cifs,ro,credentials=/archive.creds,file_mode=0444,dir_mode=0555,vers=3.0,noserverino,nounix ://isis.cclrc.ac.uk/inst\$/&
</pre></div>
</div>
<ol class="arabic simple" start="5">
<li>Enter the following commands:</li>
</ol>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo chmod <span class="m">400</span> /archive.creds
sudo mkdir /archive
service autofs restart
</pre></div>
</div>
<p>Done. You can now access directories in the archive. Test it by doing:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>ls /archive/ndxalf
</pre></div>
</div>
<p>If it’s working the command should return <code class="docutils literal notranslate"><span class="pre">ls:</span> <span class="pre">cannot</span> <span class="pre">access</span> <span class="pre">'/archive/ndxalf/DfsrPrivate':</span> <span class="pre">Permission</span> <span class="pre">denied</span></code></p>
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