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<div class="section" id="setting-up-musrfit-on-different-platforms">
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<span id="musrfit-setup"></span><span id="index-0"></span><h1>Setting up <tt class="docutils literal"><span class="pre">musrfit</span></tt> on Different Platforms<a class="headerlink" href="#setting-up-musrfit-on-different-platforms" title="Permalink to this headline">¶</a></h1>
|
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<div class="section" id="supported-operating-systems-and-software-requirements">
|
||
<span id="supported-operating-systems"></span><span id="index-1"></span><h2>Supported Operating Systems and Software Requirements<a class="headerlink" href="#supported-operating-systems-and-software-requirements" title="Permalink to this headline">¶</a></h2>
|
||
<p>This page is intended to demonstrate for the interested user which steps are necessary to set up the <a class="reference external" href="http://www.gnu.org/philosophy/free-sw.html">free software</a>
|
||
μSR data analysis framework <a class="reference internal" href="user-manual.html#user-manual"><em>musrfit</em></a>. While the preferred way is to run the software on <strong>GNU/Linux</strong> or <strong>MacOS X/macOS</strong>, with some restrictions
|
||
it can also be set up under <strong>MS Windows</strong> (cygwin, only for the <em>very brave</em>, probably it is easier for most MS Windows users to install a Virtual Machine running Linux).</p>
|
||
<div class="admonition note">
|
||
<p class="first admonition-title">Note</p>
|
||
<p class="last">In case musrfit should be installed according to the description found on this page, the user is strongly encouraged to <em>read completely</em> each section dealing with the
|
||
present installation step <em>before</em> starting the installation process!</p>
|
||
</div>
|
||
<p>Apart from <a class="reference external" href="http://gcc.gnu.org/">GCC, the GNU Compiler Collection</a> (<tt class="docutils literal"><span class="pre">gcc</span></tt>, <tt class="docutils literal"><span class="pre">g++</span></tt>), the GNU build tools <a class="reference external" href="http://www.gnu.org/software/autoconf/">autoconf</a>,
|
||
<a class="reference external" href="http://www.gnu.org/software/automake/">automake</a>, and <a class="reference external" href="http://www.gnu.org/software/libtool/">libtool</a> are needed, if you want to build musrfit via the automake toolchain.
|
||
The <tt class="docutils literal"><span class="pre">automake</span></tt> toolchain will eventually be droped in upcoming releases.
|
||
If you plan to use the cmake toolchain (preferred way), <a class="reference external" href="https://cmake.org/">cmake</a>. Furthermore the helper tool <a class="reference external" href="http://pkg-config.freedesktop.org/wiki/">pkg-config</a> is
|
||
needed and musrfit requires the installation of a few open-source libraries and programs including their header packages:</p>
|
||
<dl class="docutils" id="index-2">
|
||
<dt><strong>boost C++ libraries</strong></dt>
|
||
<dd>The powerful Spirit parser framework used by musrfit is included in that collection of libraries. <em>Required version ≥ 1.33</em> (see <a class="reference external" href="http://www.boost.org/">boost C++ libraries</a>).</dd>
|
||
</dl>
|
||
<dl class="docutils" id="index-3">
|
||
<dt><strong>GNU Scientific Library</strong></dt>
|
||
<dd>A numerical <tt class="docutils literal"><span class="pre">C</span></tt> and <tt class="docutils literal"><span class="pre">C++</span></tt> library which provides efficient implementations of various mathematical routines. <em>Required version ≥ 1.9</em> (see <a class="reference external" href="http://www.gnu.org/software/gsl/">GNU Scientific Library</a>).</dd>
|
||
</dl>
|
||
<dl class="docutils" id="index-4">
|
||
<dt><strong>FFTW</strong></dt>
|
||
<dd>A <tt class="docutils literal"><span class="pre">C</span></tt> implementation for the fast computation of discrete Fourier transforms. <em>Required version ≥ 3.1</em> (see <a class="reference external" href="http://www.fftw.org/">FFTW</a>).</dd>
|
||
</dl>
|
||
<dl class="docutils" id="index-5">
|
||
<dt><strong>ROOT</strong></dt>
|
||
<dd>A C++ data analysis framework developed at <a class="reference external" href="http://www.cern.ch/">CERN</a>. <em>Required version ≥ 5.22</em> (see <a class="reference external" href="http://root.cern.ch/">ROOT</a>).</dd>
|
||
</dl>
|
||
<dl class="docutils" id="index-6">
|
||
<dt><strong>libxml2</strong></dt>
|
||
<dd>The <tt class="docutils literal"><span class="pre">XML</span> <span class="pre">C</span></tt> parser and toolkit of <a class="reference external" href="http://www.gnome.org/">gnome</a>. <em>Required version ≥ 2.0</em> (see <a class="reference external" href="http://xmlsoft.org/">libxml2</a>).</dd>
|
||
</dl>
|
||
<p>Additionally, <em>only</em> if <tt class="docutils literal"><span class="pre">musrfit</span></tt> should support reading of data files in the <cite>NeXus</cite> format the following libraries are needed:</p>
|
||
<dl class="docutils" id="index-7">
|
||
<dt><strong>HDF4</strong></dt>
|
||
<dd>A library and multi-object file format for storing and managing data (see <a class="reference external" href="http://www.hdfgroup.org/products/hdf4/">HDF4</a>). <tt class="docutils literal"><span class="pre">HDF4</span></tt> is “outdated” and its support will soon be dropped.</dd>
|
||
</dl>
|
||
<dl class="docutils" id="index-8">
|
||
<dt><strong>HDF5</strong></dt>
|
||
<dd>A data model, library, and file format for storing and managing data (see <a class="reference external" href="https://portal.hdfgroup.org/display/support">HDF5</a>).</dd>
|
||
</dl>
|
||
<dl class="docutils" id="index-9">
|
||
<dt><strong>minixml</strong></dt>
|
||
<dd>A small <tt class="docutils literal"><span class="pre">XML</span></tt> library that can be used to read and write <tt class="docutils literal"><span class="pre">XML</span></tt> and <tt class="docutils literal"><span class="pre">XML</span></tt>-like data files. <em>Required version ≥ 2.2</em> (see <a class="reference external" href="http://www.minixml.org/">minixml</a>).</dd>
|
||
</dl>
|
||
<dl class="docutils" id="index-10">
|
||
<dt><strong>NeXus</strong></dt>
|
||
<dd>A common data format for neutron, x-ray, and muon science. <em>Required version ≥ 4.4</em> (see <a class="reference external" href="http://www.nexusformat.org/">NeXus</a>).</dd>
|
||
</dl>
|
||
<p>If <em>optionally</em> the editor and graphical user interface <tt class="docutils literal"><span class="pre">musrgui</span></tt> / <tt class="docutils literal"><span class="pre">musredit</span></tt> is going to be installed there is one further requirement:</p>
|
||
<dl class="docutils" id="index-11">
|
||
<dt><strong>Qt</strong></dt>
|
||
<dd>A cross-platform application and user interface framework. <em>Required version ≥ 4.6</em> (musredit) (see <a class="reference external" href="http://qt.io/">Qt</a>).</dd>
|
||
</dl>
|
||
<p>Each of the following sections focusing on the installation of <tt class="docutils literal"><span class="pre">musrfit</span></tt> on the different operating systems will also give a brief introduction on the installation of the requirements before the actual musrfit installation is described.</p>
|
||
</div>
|
||
<div class="section" id="os-restrictions">
|
||
<span id="index-12"></span><h2>OS Restrictions<a class="headerlink" href="#os-restrictions" title="Permalink to this headline">¶</a></h2>
|
||
<p>Before the installation procedure will be described, please note the following restrictions:</p>
|
||
<dl class="docutils">
|
||
<dt><strong>GNU/Linux</strong></dt>
|
||
<dd>No serious problems are currently known. Tested distributions: <a class="reference external" href="https://www.redhat.com/de/technologies/linux-platforms/enterprise-linux">RHEL</a>, <a class="reference external" href="https://getfedora.org/">Fedora</a>,
|
||
<a class="reference external" href="https://www.debian.org/">Debian</a>, <a class="reference external" href="https://www.ubuntu.com/">Ubuntu</a>, <a class="reference external" href="https://linuxmint.com/">Mint</a>, <a class="reference external" href="https://en.opensuse.org/Main_Page">openSUSE</a>.</dd>
|
||
<dt><strong>Mac OS X/macOS</strong></dt>
|
||
<dd>No serious problems are currently known for macOS ≥ 10.6.</dd>
|
||
<dt><strong>MS Windows</strong></dt>
|
||
<dd><p class="first">Native <em>MS Windows</em> support is currently not available. Potential ways to get <tt class="docutils literal"><span class="pre">musrfit</span></tt> running are:</p>
|
||
<ul class="last simple">
|
||
<li>via installation of Linux via the Microsoft App store for Windows 10.</li>
|
||
<li>via installation of the virtual machine on which you install Linux.</li>
|
||
<li>via <a class="reference external" href="https://www.cygwin.com/">cygwin</a>.</li>
|
||
</ul>
|
||
</dd>
|
||
</dl>
|
||
</div>
|
||
<div class="section" id="gnu-linux">
|
||
<span id="index-13"></span><span id="id1"></span><h2>GNU/Linux<a class="headerlink" href="#gnu-linux" title="Permalink to this headline">¶</a></h2>
|
||
<div class="section" id="requirements">
|
||
<span id="gnu-linux-requirements"></span><span id="index-14"></span><h3>Requirements<a class="headerlink" href="#requirements" title="Permalink to this headline">¶</a></h3>
|
||
<div class="section" id="everything-but-root-and-nexus">
|
||
<h4>Everything but ROOT and NeXus<a class="headerlink" href="#everything-but-root-and-nexus" title="Permalink to this headline">¶</a></h4>
|
||
<p>Depending on the GNU/Linux distribution chosen, the above mentioned software – except <tt class="docutils literal"><span class="pre">ROOT/CERN</span></tt> and <tt class="docutils literal"><span class="pre">NeXus</span></tt> – should be available from
|
||
the distributor and could be easily installed in the form of binary packages. If done in this way there should be taken care of installing <em>both</em>,
|
||
the libraries and the header (dev, devel) files.</p>
|
||
<p>On a <a class="reference external" href="https://www.redhat.com/en">Red Hat Linux</a> (or other RPM-package base Linux distributions) system the following command executed as <em>superuser</em>
|
||
from the shell will do the trick (never type the ‘$’ it is the shell prompt of your system):</p>
|
||
<p>For <strong>Qt4</strong>:</p>
|
||
<blockquote>
|
||
<div><div class="highlight-bash"><div class="highlight"><pre><span></span>$ yum install git cmake boost-devel gsl-devel fftw-devel libxml2-devel qt-devel qtwebkit-devel
|
||
</pre></div>
|
||
</div>
|
||
</div></blockquote>
|
||
<p>For <strong>Qt5</strong>:</p>
|
||
<blockquote>
|
||
<div><div class="highlight-bash"><div class="highlight"><pre><span></span>$ yum install epel-release
|
||
$ yum install git cmake boost-devel gsl-devel fftw-devel libxml2-devel qt5-qtbase-devel qt5-qtsvg-devel qt5-qtwebkit-devel
|
||
</pre></div>
|
||
</div>
|
||
</div></blockquote>
|
||
<p>Depending on your distribution <strong>Qt4</strong> is still the default but is likely to be replaced by <strong>Qt5</strong> in the very near future.</p>
|
||
<p>When dealing with a distribution that uses the dpkg/apt package manager like <a class="reference external" href="https://www.debian.org/">Debian</a> or <a class="reference external" href="https://www.ubuntu.com/">Ubuntu</a>
|
||
the installation would look like:</p>
|
||
<p>For <strong>Qt4</strong>:</p>
|
||
<blockquote>
|
||
<div><div class="highlight-bash"><div class="highlight"><pre><span></span>$ apt-get install git cmake libboost-dev libgsl-dev libfftw3-dev libxml2-dev libqt4-dev libqtwebkit-dev
|
||
</pre></div>
|
||
</div>
|
||
</div></blockquote>
|
||
<p>For <strong>Qt5</strong>:</p>
|
||
<blockquote>
|
||
<div><div class="highlight-bash"><div class="highlight"><pre><span></span>$ apt-get install git cmake libboost-dev libgsl-dev libfftw3-dev libxml2-dev qt5-default qtbase5-dev libqt5svg5-dev libqt5webkit5-dev
|
||
</pre></div>
|
||
</div>
|
||
</div></blockquote>
|
||
<p>Everyone should know best himself which is the way to install distribution software on the chosen distribution.</p>
|
||
<p>In case the distribution does not include the required software it has to be compiled from the source files. This means either to download
|
||
the source code from the corresponding website, or to clone the git repo. If you need to follow this line, please check the install details of the corresponding package.</p>
|
||
<p>For any further information on the standard installation of software, please refer to the web search engine of choice and ask for “install software on linux”...</p>
|
||
</div>
|
||
<div class="section" id="installation-of-nexus-requirements-optional">
|
||
<span id="index-15"></span><h4>Installation of NeXus requirements (optional)<a class="headerlink" href="#installation-of-nexus-requirements-optional" title="Permalink to this headline">¶</a></h4>
|
||
<p><em>Only</em> if <tt class="docutils literal"><span class="pre">musrfit</span></tt> should support reading/writing data files in the <tt class="docutils literal"><span class="pre">NeXus</span></tt> format the further required
|
||
software has to be set up. The required libraries and header files could either be available through the user’s
|
||
GNU/Linux distribution or if this is not the case, the packages can be installed from the source code. <em>E.g.</em> on
|
||
Red Hat-like systems binary packages for <tt class="docutils literal"><span class="pre">MXML</span></tt>, <tt class="docutils literal"><span class="pre">HDF4</span></tt>, and <tt class="docutils literal"><span class="pre">HDF5</span></tt> might be called <tt class="docutils literal"><span class="pre">mxml</span></tt>, <tt class="docutils literal"><span class="pre">mxml-devel</span></tt>,
|
||
<tt class="docutils literal"><span class="pre">hdf</span></tt>, <tt class="docutils literal"><span class="pre">hdf-devel</span></tt>, <tt class="docutils literal"><span class="pre">hdf5</span></tt>, <tt class="docutils literal"><span class="pre">hdf5-devel</span></tt>, on Debian-like systems <tt class="docutils literal"><span class="pre">libmxml1</span></tt>, <tt class="docutils literal"><span class="pre">libmxml-dev</span></tt>, <tt class="docutils literal"><span class="pre">libhdf4-dev</span></tt>, <tt class="docutils literal"><span class="pre">libhdf5-dev</span></tt>.</p>
|
||
<div class="admonition note">
|
||
<p class="first admonition-title">Note</p>
|
||
<p class="last"><tt class="docutils literal"><span class="pre">HDF4</span></tt> support within <tt class="docutils literal"><span class="pre">NeXus</span></tt> will be dropped by <tt class="docutils literal"><span class="pre">musrfit</span></tt> in the near future. If you <em>not</em> urgently need
|
||
to read old <tt class="docutils literal"><span class="pre">ISIS</span> <span class="pre">NeXus</span></tt> files, you safely can drop it.</p>
|
||
</div>
|
||
<p><strong>Only NeXus Version ≥ 4.4 is support!</strong></p>
|
||
<p>Even though there might exist binary packages for the <tt class="docutils literal"><span class="pre">NeXus</span></tt> library, it is best to build and
|
||
install it directly from the source code which can be found <a class="reference external" href="https://github.com/nexusformat/code">here</a>.</p>
|
||
<p>A brief instruction how to get <tt class="docutils literal"><span class="pre">NeXus</span></tt> compiled from source (lines starting with ‘#’ are comments <em>only</em>):</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> Downloads
|
||
$ <span class="c1"># create a directory for the NeXus source code</span>
|
||
$ mkdir nexus
|
||
$ <span class="nb">cd</span> nexus
|
||
$ <span class="c1"># get the source code from the master repository</span>
|
||
$ git clone https://github.com/nexusformat/code.git
|
||
$ <span class="c1"># next we will build NeXus out-of-source</span>
|
||
$ mkdir build
|
||
$ <span class="nb">cd</span> build
|
||
$ <span class="c1"># The next line only if HDF4 support is needed</span>
|
||
$ cmake -DENABLE_HDF5<span class="o">=</span><span class="m">1</span> -DENABLE_HDF4<span class="o">=</span><span class="m">1</span> -DENABLE_MXML<span class="o">=</span><span class="m">1</span> ../code
|
||
$ <span class="c1"># The next line if HDF4 support is NOT needed</span>
|
||
$ cmake -DENABLE_HDF5<span class="o">=</span><span class="m">1</span> -DENABLE_MXML<span class="o">=</span><span class="m">1</span> ../code
|
||
$ cmake --build ./ --clean-first
|
||
$ <span class="c1"># make install needs either to be carried out as root or sudo depending on your linux flavour.</span>
|
||
$ sudo make install
|
||
</pre></div>
|
||
</div>
|
||
</div>
|
||
<div class="section" id="index-16">
|
||
<span id="id4"></span><h4>ROOT<a class="headerlink" href="#index-16" title="Permalink to this headline">¶</a></h4>
|
||
<p>ROOT 5.34/xx is supported as legacy version <em>only</em>! <strong>The default now will be ROOT 6.xx/yy!</strong></p>
|
||
<p>The ROOT framework may or may not be part of the GNU/Linux distribution. Some distributions are packing ROOT in a
|
||
manner incompatible with the way it is needed for <tt class="docutils literal"><span class="pre">musrfit</span></tt>, though the situation is improving. If you are
|
||
experienced enough you can try the packed ROOT version. Often ROOT is split in many sub-packages. Install the
|
||
necessary ones (guess from the description below). <strong>One Warning:</strong> if the ROOT packages are upgraded after a
|
||
yum update (apt-get update; apt-get upgrade) you might need to recompile <tt class="docutils literal"><span class="pre">musrfit</span></tt>. <em>If you are not sure about
|
||
all this: install ROOT from source</em>. Before installing ROOT from source you will need to install some additional header packages.</p>
|
||
<p>For RPM based systems (RedHat, Fedora, <em>etc</em>) this will likely to be <tt class="docutils literal"><span class="pre">libX11-devel</span></tt>, <tt class="docutils literal"><span class="pre">libXft-devel</span></tt>, <tt class="docutils literal"><span class="pre">libXpm-devel</span></tt>, and <tt class="docutils literal"><span class="pre">libXext-devel</span></tt>:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ yum install libX11-devel libXft-devel libXpm-devel libXext-devel
|
||
</pre></div>
|
||
</div>
|
||
<p>For a dpkg/apt based system (Debian, Ubuntu, <em>etc</em>) this will likely to be <tt class="docutils literal"><span class="pre">libx11-dev</span></tt>, <tt class="docutils literal"><span class="pre">libxft-dev</span></tt>, <tt class="docutils literal"><span class="pre">libxpm-dev</span></tt>, and <tt class="docutils literal"><span class="pre">libxext-dev</span></tt>:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ apt-get install libx11-dev libxft-dev libxpm-dev libxext-dev
|
||
</pre></div>
|
||
</div>
|
||
<p>Also make sure that you have installed all required packages listed under <a class="reference internal" href="#gnu-linux-requirements"><em>Required Software</em></a> (<em>e.g.</em> fftw, gsl, <em>etc</em>).</p>
|
||
<p>In the following it is assumed that <tt class="docutils literal"><span class="pre">ROOT</span></tt> shall be installed under <tt class="docutils literal"><span class="pre">$HOME/Apps</span></tt>. If you want to install
|
||
it somewhere else, just systematically replace the related terms of the following description. For the
|
||
following list of commands the ‘$’ will be given, the command prompt. Do not enter it! Also some comments will
|
||
be added starting with a ‘#’ which can be omitted. They are only there to explain what is going on.</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> <span class="nv">$HOME</span>
|
||
$ <span class="c1"># creat the Apps directory if not already present</span>
|
||
$ mkdir Apps
|
||
$ <span class="nb">cd</span> Apps
|
||
$ git clone http://root.cern.ch/git/root.git
|
||
$ <span class="nb">cd</span> root
|
||
$ git tag -l
|
||
$ <span class="c1"># git tag -l will list all available tags. In the next command choose the tag v6-14-00</span>
|
||
$ <span class="c1"># or the latest official release number</span>
|
||
$ git checkout -b v6-14-00 v6-14-00
|
||
$ <span class="c1"># now ROOT is ready to be configured. Below you will find the minimal ROOT configuration needed.</span>
|
||
$ <span class="c1"># since we are using cmake build now, first we will need to create the build directory.</span>
|
||
$ mkdir root_build
|
||
$ <span class="nb">cd</span> root_build
|
||
$ cmake ../ -Dgminimal<span class="o">=</span>ON -Dasimage<span class="o">=</span>ON -Dmathmore<span class="o">=</span>On -Dminuit2<span class="o">=</span>ON -Dxml<span class="o">=</span>ON -DCMAKE_INSTALL_PREFIX<span class="o">=</span>../root_exec
|
||
$ <span class="c1"># next will be the make called via cmake. If running on a multicore CPU you can speed up tremendously by</span>
|
||
$ <span class="c1"># calling it with the option -j <number>, where <number> is the number of threads which you want to give,</span>
|
||
$ <span class="c1"># e.g. cmake --build ./ --clean-first -- -j8</span>
|
||
$ cmake --build ./ --clean-first
|
||
$ <span class="c1"># as a last step of the ROOT build process we need to install it</span>
|
||
$ make install
|
||
</pre></div>
|
||
</div>
|
||
<p>What is still missing is that the system should be told where to find the <tt class="docutils literal"><span class="pre">ROOT</span></tt> installation, therefore the following is suggested:</p>
|
||
<ul>
|
||
<li><p class="first">As superuser create a file <tt class="docutils literal"><span class="pre">/etc/ld.so.conf.d/cern-root.conf</span></tt> where the path to the lib directory of <tt class="docutils literal"><span class="pre">ROOT</span></tt> is
|
||
added and call <tt class="docutils literal"><span class="pre">/sbin/ldconfig</span></tt> afterwards. In the example mentioned above one way of doing this is
|
||
(<tt class="docutils literal"><span class="pre"><home></span></tt> has to be the path to your home, <em>e.g.</em> <tt class="docutils literal"><span class="pre">/home/luke_skywalker</span></tt>):</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">echo</span> <span class="s2">"<home>/Apps/root/root_exec/lib"</span> >> /etc/ld.so.conf.d/cern-root.conf
|
||
$ /sbin/ldconfig
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
<li><p class="first">Additionally, as normal user one should append the following lines to the <tt class="docutils literal"><span class="pre">~/.bashrc</span></tt> and/or <tt class="docutils literal"><span class="pre">~/.bash_profile</span></tt>
|
||
(<tt class="docutils literal"><span class="pre">~./profile</span></tt> on Debian like systems, and then either restart the shell or call the same commands once more from
|
||
the shell) in order to change some path-setting environment variables:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">export</span> <span class="nv">ROOTSYS</span><span class="o">=</span><span class="nv">$HOME</span>/Apps/root/root_exec
|
||
$ <span class="nb">export</span> <span class="nv">PATH</span><span class="o">=</span><span class="nv">$ROOTSYS</span>/bin:<span class="nv">$PATH</span>
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
</ul>
|
||
<p>If an update of ROOT is needed, simple do the following:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> <span class="nv">$HOME</span>/Apps/root
|
||
$ git pull
|
||
$ <span class="nb">cd</span> root_build
|
||
$ cmake --build ./ --clean-first
|
||
</pre></div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="section" id="musrfit">
|
||
<span id="index-17"></span><h3>musrfit<a class="headerlink" href="#musrfit" title="Permalink to this headline">¶</a></h3>
|
||
<p>When all required software has been set up with the <tt class="docutils literal"><span class="pre">musrfit</span></tt> installation can be proceeded. First, the most
|
||
recent source code should be downloaded. The preferred way of doing so is to clone the <tt class="docutils literal"><span class="pre">musrfit</span></tt> repository via git.
|
||
Assuming the code should be located in <tt class="docutils literal"><span class="pre">$HOME/Apps</span></tt> this is achieved most easily calling from the terminal</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> <span class="nv">$HOME</span>/Apps
|
||
$ git clone https://bitbucket.org/muonspin/musrfit.git
|
||
$ <span class="c1"># Only if legacy ROOT 5.xx.yy is used include the next line</span>
|
||
$ <span class="nb">cd</span> musrfit<span class="p">;</span> git checkout root5
|
||
</pre></div>
|
||
</div>
|
||
<p>or</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> <span class="nv">$HOME</span>/Apps
|
||
$ git clone git://gitlab.psi.ch/nemu/musrfit.git
|
||
$ <span class="c1"># Only if legacy ROOT 5.xx.yy is used include the next line</span>
|
||
$ <span class="nb">cd</span> musrfit<span class="p">;</span> git checkout root5
|
||
</pre></div>
|
||
</div>
|
||
<div class="admonition note">
|
||
<p class="first admonition-title">Note</p>
|
||
<p class="last">after cloning the <tt class="docutils literal"><span class="pre">musrfit</span></tt> repo you will automatically be on the
|
||
<tt class="docutils literal"><span class="pre">root6</span></tt> branch. If you want to get legacy ROOT 5.34.xx support, you
|
||
will needed to switch branches first.</p>
|
||
</div>
|
||
<p><strong>Update:</strong> If a local repository clone is already present (it needs to be newer than Dec. 2016), one can update it using:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> <span class="nv">$HOME</span>/Apps/musrfit
|
||
$ git pull
|
||
</pre></div>
|
||
</div>
|
||
<p>Now, depending whether you follow the <tt class="docutils literal"><span class="pre">automake</span></tt> or <tt class="docutils literal"><span class="pre">cmake</span></tt> tool chain you do</p>
|
||
<p><strong>automake toolchain:</strong></p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ make uninstall
|
||
$ make clean
|
||
$ make
|
||
$ make install
|
||
</pre></div>
|
||
</div>
|
||
<p>or</p>
|
||
<p><strong>cmake toolchain:</strong></p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> build
|
||
$ xargs rm < install_manifest.txt
|
||
$ cmake --build ./ --clean-first
|
||
$ make install
|
||
</pre></div>
|
||
</div>
|
||
<p>As an alternative (if git is not available), the source code can also be downloaded from the following web-page: <a class="reference external" href="https://bitbucket.org/muonspin/musrfit/downloads">musrfit at bitbucket</a></p>
|
||
<div class="section" id="musrfit-build-with-automake">
|
||
<span id="index-18"></span><h4>musrfit build with automake<a class="headerlink" href="#musrfit-build-with-automake" title="Permalink to this headline">¶</a></h4>
|
||
<p>After the source-code extraction the <tt class="docutils literal"><span class="pre">autogen.sh</span></tt> script is called to prepare the build environment.
|
||
If it has been executed successfully the <tt class="docutils literal"><span class="pre">configure</span></tt> script should be ready to collect all the information needed
|
||
to create the Makefiles. If <tt class="docutils literal"><span class="pre">musrfit</span></tt> should support <tt class="docutils literal"><span class="pre">NeXus</span></tt> data files this has to be enabled by specifying the
|
||
<tt class="docutils literal"><span class="pre">--enable-NeXus</span></tt> switch when calling configure. For an overview of all available options just call <tt class="docutils literal"><span class="pre">./configure</span> <span class="pre">--help</span></tt>.
|
||
Besides the standard options there are a few special options which should be mentioned here:</p>
|
||
<dl class="docutils">
|
||
<dt><strong>- -prefix</strong></dt>
|
||
<dd>Specify the installation prefix, <em>e.g.</em> <tt class="docutils literal"><span class="pre">$ROOTSYS</span></tt> if already defined (by default: <tt class="docutils literal"><span class="pre">/usr/local</span></tt>).</dd>
|
||
<dt><strong>- -with-rootsys</strong></dt>
|
||
<dd>Specify the top of the <tt class="docutils literal"><span class="pre">ROOT</span></tt> installation directory, <em>e.g.</em> <tt class="docutils literal"><span class="pre">$ROOTSYS</span></tt> if already defined.</dd>
|
||
<dt><strong>- -with-fftw3</strong></dt>
|
||
<dd>Specify the prefix of the <tt class="docutils literal"><span class="pre">FFTW3</span></tt> installation. <em>e.g.</em> <tt class="docutils literal"><span class="pre">/usr/local</span></tt> or <tt class="docutils literal"><span class="pre">/usr</span></tt>.</dd>
|
||
<dt><strong>- -with-gsl</strong></dt>
|
||
<dd>Set the prefix of the <tt class="docutils literal"><span class="pre">GSL</span></tt> installation, <em>e.g.</em> <tt class="docutils literal"><span class="pre">/usr/local</span></tt> or <tt class="docutils literal"><span class="pre">/usr</span></tt>.</dd>
|
||
<dt><strong>- -with-boostinc</strong></dt>
|
||
<dd>Set the path to the header files of the <tt class="docutils literal"><span class="pre">Boost</span></tt> installation, <em>e.g.</em> <tt class="docutils literal"><span class="pre">/usr/local/include</span></tt> or <tt class="docutils literal"><span class="pre">/usr/include</span></tt>.</dd>
|
||
<dt><strong>- -with-hdf4</strong></dt>
|
||
<dd>Set the prefix of the <tt class="docutils literal"><span class="pre">HDF4</span></tt> installation, <em>e.g.</em> <tt class="docutils literal"><span class="pre">/usr/local</span></tt> (only useful in conjunction with the <tt class="docutils literal"><span class="pre">NeXus</span></tt> support).</dd>
|
||
<dt><strong>- -with-hdf5</strong></dt>
|
||
<dd>Set the prefix of the <tt class="docutils literal"><span class="pre">HDF5</span></tt> installation, <em>e.g.</em> <tt class="docutils literal"><span class="pre">/usr</span></tt> (only useful in conjunction with the <tt class="docutils literal"><span class="pre">NeXus</span></tt> support).</dd>
|
||
<dt><strong>- -with-nexus</strong></dt>
|
||
<dd>Set the prefix of the <tt class="docutils literal"><span class="pre">NeXus</span></tt> installation, <em>e.g.</em> <tt class="docutils literal"><span class="pre">/usr/local</span></tt> (only useful in conjunction with the <tt class="docutils literal"><span class="pre">NeXus</span></tt> support).</dd>
|
||
<dt><strong>- -with-qt3</strong></dt>
|
||
<dd>Set the prefix of the <tt class="docutils literal"><span class="pre">Qt3</span></tt> installation, <em>e.g.</em> <tt class="docutils literal"><span class="pre">/usr/lib/qt-3.3</span></tt> (only useful in conjunction with building <tt class="docutils literal"><span class="pre">musrgui</span></tt>).</dd>
|
||
<dt><strong>- -with-qt4</strong></dt>
|
||
<dd>Set the prefix of the <tt class="docutils literal"><span class="pre">Qt4</span></tt> installation, <em>e.g.</em> <tt class="docutils literal"><span class="pre">/usr/lib/qt47</span></tt> (only useful in conjunction with building <tt class="docutils literal"><span class="pre">musredit</span></tt>).</dd>
|
||
<dt><strong>- -with-qt5</strong></dt>
|
||
<dd>Set the prefix of the <tt class="docutils literal"><span class="pre">Qt5</span></tt> installation, <em>e.g.</em> <tt class="docutils literal"><span class="pre">/usr/lib64</span></tt> (only useful in conjunction with building <tt class="docutils literal"><span class="pre">musredit</span></tt>).</dd>
|
||
<dt><strong>- -enable-NeXus</strong></dt>
|
||
<dd>Enable the support of <tt class="docutils literal"><span class="pre">NeXus</span></tt> data files (requires the <tt class="docutils literal"><span class="pre">HDF4</span></tt>, <tt class="docutils literal"><span class="pre">HDF5</span></tt> and <tt class="docutils literal"><span class="pre">NeXus</span></tt> libraries to be installed).</dd>
|
||
<dt><strong>- -disable-editor</strong></dt>
|
||
<dd>Disable the integrated building of <tt class="docutils literal"><span class="pre">musredit</span></tt>/<tt class="docutils literal"><span class="pre">musrgui</span></tt>.</dd>
|
||
<dt><strong>- -disable-omp</strong></dt>
|
||
<dd>Switches off the <a class="reference external" href="http://en.wikipedia.org/wiki/OpenMP">OpenMP</a> features of <tt class="docutils literal"><span class="pre">musrfit</span></tt> (parallelization of the <span class="math">\(\chi^2\)</span> calculation when compiled with GCC ≥ 4.2).</dd>
|
||
</dl>
|
||
<p>Normally it should not be necessary to make use of any of the options except for specifying the installation path with <tt class="docutils literal"><span class="pre">--prefix</span></tt>. The
|
||
other paths should be detected automatically. If this does not work for some reason the configure script will terminate and ask for the
|
||
information. When the configure script has been called successfully everything is ready for building the <tt class="docutils literal"><span class="pre">musrfit</span></tt> libraries and executables.
|
||
A standard installation sequence (without <tt class="docutils literal"><span class="pre">NeXus</span></tt> support) might then look like (In case the normal user has no write permissions to the
|
||
<tt class="docutils literal"><span class="pre">$ROOTSYS</span></tt> and the installation path the “make install” commands have to be executed as superuser.):</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> <span class="nv">$HOME</span>/Apps/musrfit
|
||
$ sh autogen.sh
|
||
$ ./configure --prefix<span class="o">=</span><span class="nv">$ROOTSYS</span>
|
||
$ make
|
||
$ make install
|
||
$ /sbin/ldconfig <span class="c1"># (as superuser)</span>
|
||
</pre></div>
|
||
</div>
|
||
</div>
|
||
<div class="section" id="musrfit-build-with-cmake">
|
||
<span id="index-19"></span><h4>musrfit build with cmake<a class="headerlink" href="#musrfit-build-with-cmake" title="Permalink to this headline">¶</a></h4>
|
||
<p>Currently the following configuration switches for <tt class="docutils literal"><span class="pre">musrfit</span></tt> are available:</p>
|
||
<dl class="docutils">
|
||
<dt><strong>-DCMAKE_INSTALL_PREFIX=<prefix-path></strong></dt>
|
||
<dd>Specify the installation prefix, <em>i.e.</em> the place where <tt class="docutils literal"><span class="pre">musrfit</span></tt> shall be installed, <em>e.g.</em> <tt class="docutils literal"><span class="pre">$ROOTSYS</span></tt> if already defined (by default: <tt class="docutils literal"><span class="pre">/usr/local</span></tt>).</dd>
|
||
<dt><strong>-Dnexus=<value></strong></dt>
|
||
<dd>enable/disable the support of <tt class="docutils literal"><span class="pre">NeXus</span></tt> data files (requires the <tt class="docutils literal"><span class="pre">HDF4</span></tt>, <tt class="docutils literal"><span class="pre">HDF5</span></tt> and <tt class="docutils literal"><span class="pre">NeXus</span></tt> libraries to be installed).
|
||
<value>=1 enables <tt class="docutils literal"><span class="pre">NeXus</span></tt>, <value>=0 disables <tt class="docutils literal"><span class="pre">NeXus</span></tt>. The default setting, <em>i.e.</em> the switch is not provided is <tt class="docutils literal"><span class="pre">NeXus</span></tt> support is disabled.</dd>
|
||
<dt><strong>-DASlibs=<value></strong></dt>
|
||
<dd>enable/disable the <tt class="docutils literal"><span class="pre">ASlibs</span></tt>. <value>=1 enables the <tt class="docutils literal"><span class="pre">ASlibs</span></tt>, <value>=0 disables the <tt class="docutils literal"><span class="pre">ASlibs</span></tt>. The default setting, <em>i.e.</em> the
|
||
switch is not provided is <tt class="docutils literal"><span class="pre">ASlibs</span></tt> support is disabled. For details see Documentation of <a class="reference internal" href="user-libs.html#user-libs"><em>user libs</em></a>.</dd>
|
||
<dt><strong>-DBMWlibs=<value></strong></dt>
|
||
<dd>enable/disable the <tt class="docutils literal"><span class="pre">BMWlibs</span></tt>. <value>=1 enables the <tt class="docutils literal"><span class="pre">BMWlibs</span></tt>, <value>=0 disables the <tt class="docutils literal"><span class="pre">BMWlibs</span></tt>. The default setting, <em>i.e.</em> the
|
||
switch is not provided is <tt class="docutils literal"><span class="pre">BMWlibs</span></tt> support is disabled. For details see Documentation of <a class="reference internal" href="user-libs.html#user-libs"><em>user libs</em></a>.</dd>
|
||
<dt><strong>-DBNMRlibs=<value></strong></dt>
|
||
<dd>enable/disable the <tt class="docutils literal"><span class="pre">BNMRlibs</span></tt>. <value>=1 enables the <tt class="docutils literal"><span class="pre">BNMRlibs</span></tt>, <value>=0 disables the <tt class="docutils literal"><span class="pre">BNMRlibs</span></tt>. The default setting,
|
||
<em>i.e.</em> the switch is not provided is <tt class="docutils literal"><span class="pre">BNMRlibs</span></tt> support is disabled.</dd>
|
||
<dt><strong>-Dqt_based_tools=<value></strong></dt>
|
||
<dd>Will try to get <tt class="docutils literal"><span class="pre">musredit</span></tt>, <tt class="docutils literal"><span class="pre">musrWiz</span></tt>, <tt class="docutils literal"><span class="pre">musrStep</span></tt>, and <tt class="docutils literal"><span class="pre">mupp</span></tt> installed, if <tt class="docutils literal"><span class="pre">Qt</span></tt> is found.
|
||
By default this is enabled. Again <value>=0 means disabled, <value>=1 enabled.</dd>
|
||
<dt><strong>-Dqt_version=<value></strong></dt>
|
||
<dd>Allows to specify which <tt class="docutils literal"><span class="pre">Qt</span></tt> version shall be tried. <value> can take the values: <tt class="docutils literal"><span class="pre">AUTO,</span> <span class="pre">3,</span> <span class="pre">4,</span> <span class="pre">5</span></tt>.
|
||
If the value is set to <tt class="docutils literal"><span class="pre">AUTO</span></tt>, this highest installed version is chosen, otherwise the specified version is used.</dd>
|
||
<dt><strong>-Dtry_OpenMP=<value></strong></dt>
|
||
<dd>Will check if <tt class="docutils literal"><span class="pre">OpenMP</span></tt> support is possible, and if yes use it. The default is enabled</dd>
|
||
</dl>
|
||
<p>Normally it should not be necessary to make use of any of the options except for specifying the installation path with <tt class="docutils literal"><span class="pre">-DCMAKE_INSTALL_PREFIX</span></tt>.
|
||
<tt class="docutils literal"><span class="pre">musrfit</span></tt> build with <tt class="docutils literal"><span class="pre">cmake</span></tt> takes the <tt class="docutils literal"><span class="pre">out-of-source</span></tt> approach. Therefore a typical configuration / make / install process including
|
||
<tt class="docutils literal"><span class="pre">NeXus</span></tt> support would look like</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> <span class="nv">$HOME</span>/Apps/musrfit
|
||
$ mkdir build
|
||
$ <span class="nb">cd</span> build
|
||
$ cmake ../ -DCMAKE_INSTALL_PREFIX<span class="o">=</span><span class="nv">$ROOTSYS</span> -Dnexus<span class="o">=</span><span class="m">1</span>
|
||
<span class="c1"># below it is assumed that multiple cores are present, hence the -j8 option</span>
|
||
$ cmake --build ./ --clean-first -- -j8
|
||
$ make install
|
||
$ /sbin/ldconfig <span class="c1"># (as superuser)</span>
|
||
</pre></div>
|
||
</div>
|
||
</div>
|
||
<div class="section" id="musrfit-last-step-of-the-installation">
|
||
<span id="index-20"></span><h4>musrfit last step of the installation<a class="headerlink" href="#musrfit-last-step-of-the-installation" title="Permalink to this headline">¶</a></h4>
|
||
<p>In order to finish the installation of musrfit two more things should be done:</p>
|
||
<blockquote>
|
||
<div><ul>
|
||
<li><p class="first">Define the <em>MUSRFITPATH</em> environment variable containing the path to the <tt class="docutils literal"><span class="pre">musrfit</span></tt> executables and <tt class="docutils literal"><span class="pre">XML</span></tt> files.
|
||
<em>E.g.</em> if the location of the example above is used append the following line to the <tt class="docutils literal"><span class="pre">~/.bashrc</span></tt> and
|
||
<tt class="docutils literal"><span class="pre">~/.bash_profile</span></tt> (and then either restart the shell, source the file, or call the same commands once more from the shell):</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span><span class="nb">export</span> <span class="nv">MUSRFITPATH</span><span class="o">=</span><span class="nv">$ROOTSYS</span>/bin
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
<li><p class="first">Adjust the paths where <tt class="docutils literal"><span class="pre">musrfit</span></tt> will search for data files in the installed <tt class="docutils literal"><span class="pre">musrfit_startup.xml</span></tt>. For
|
||
detailed information on this XML file refer to the <a class="reference internal" href="user-manual.html#musrfit-startup"><em>manual</em></a>.</p>
|
||
</li>
|
||
</ul>
|
||
</div></blockquote>
|
||
</div>
|
||
</div>
|
||
<div class="section" id="musredit">
|
||
<span id="index-21"></span><h3>musredit<a class="headerlink" href="#musredit" title="Permalink to this headline">¶</a></h3>
|
||
<p>In the latest version of <tt class="docutils literal"><span class="pre">musrfit</span></tt> the configure script tries to determine automatically the highest available <tt class="docutils literal"><span class="pre">Qt</span></tt> version.
|
||
In case this is found, the editor <tt class="docutils literal"><span class="pre">musredit</span></tt> is built already together with <tt class="docutils literal"><span class="pre">musrfit</span></tt>. If not, one can try to call
|
||
the configure script with the <strong>- -with-qt5</strong> option (<tt class="docutils literal"><span class="pre">automake</span></tt>). <tt class="docutils literal"><span class="pre">cmake</span></tt> will determine everthing automatically.
|
||
To install this editor separately, <em>i.e.</em> by “hand” do</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> <span class="nv">$HOME</span>/Apps/musrfit/src/musredit_qt5
|
||
$ <span class="c1"># for some distributions you will need qmake-qt5 for the next command</span>
|
||
$ qmake musredit.pro
|
||
</pre></div>
|
||
</div>
|
||
<p>If everything went fine, <tt class="docutils literal"><span class="pre">musredit</span></tt> can be compiled and installed:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ make
|
||
$ make install
|
||
</pre></div>
|
||
</div>
|
||
<p>In case one does not like the executable <tt class="docutils literal"><span class="pre">musredit</span></tt> to be copied to the default installation directory <tt class="docutils literal"><span class="pre">$ROOTSYS/bin</span></tt>
|
||
the last <em>make install</em> can be skipped and the executable can be copied somewhere else instead.</p>
|
||
</div>
|
||
<div class="section" id="musrgui-obsolate">
|
||
<h3>musrgui (obsolate)<a class="headerlink" href="#musrgui-obsolate" title="Permalink to this headline">¶</a></h3>
|
||
<p>If <tt class="docutils literal"><span class="pre">Qt4.6</span></tt> or higher is not available but <tt class="docutils literal"><span class="pre">Qt3</span></tt> is set up <tt class="docutils literal"><span class="pre">musrgui</span></tt> can be installed. For this please
|
||
follow the instructions for the <tt class="docutils literal"><span class="pre">musredit</span></tt> installation where simply every <tt class="docutils literal"><span class="pre">musredit</span></tt> occurrence has to
|
||
be replaced by <tt class="docutils literal"><span class="pre">musrgui</span></tt>. If there are problems during the <tt class="docutils literal"><span class="pre">qmake</span></tt> step, <em>e.g.</em>
|
||
“uic: File generated with too old version of Qt Designer”, this most probably means the <tt class="docutils literal"><span class="pre">Qt4</span></tt> version of <tt class="docutils literal"><span class="pre">qmake</span></tt>
|
||
is being used. In order to use the <tt class="docutils literal"><span class="pre">Qt3</span></tt> version it should be enough to specify the full path to its location
|
||
when calling it. Within the most GNU/Linux distributions this location will be something like <tt class="docutils literal"><span class="pre">/usr/lib/qt-3.3/bin/qmake</span></tt>.</p>
|
||
</div>
|
||
<div class="section" id="check-the-installation">
|
||
<h3>Check the installation<a class="headerlink" href="#check-the-installation" title="Permalink to this headline">¶</a></h3>
|
||
<p>In order to perform a quick test for finding out if the installation has been completed successfully, a few msr files
|
||
together with the corresponding data files can be found in the <tt class="docutils literal"><span class="pre">musrfit</span></tt> source tree at <tt class="docutils literal"><span class="pre">doc/examples/</span></tt>.
|
||
If <tt class="docutils literal"><span class="pre">musrgui</span></tt> has been installed, just open one of the <tt class="docutils literal"><span class="pre">test-*.msr</span></tt> files in the editor and test the <tt class="docutils literal"><span class="pre">musrfit</span></tt>
|
||
functionalities. Otherwise, if only the terminal should be used, as an initial test for instance the following could be done:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> <span class="nv">$HOME</span>/Apps/musrfit/doc/examples
|
||
$ musrview test-histo-ROOT-NPP.msr
|
||
</pre></div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="section" id="ms-windows">
|
||
<h2>MS Windows<a class="headerlink" href="#ms-windows" title="Permalink to this headline">¶</a></h2>
|
||
<div class="admonition note">
|
||
<p class="first admonition-title">Note</p>
|
||
<p class="last">The description here is only for the very brave ones. It hasn’t been tested for quite a while and therefore gives you
|
||
rather a flavour of what needs to be done rather than a real instruction how to setup <tt class="docutils literal"><span class="pre">musrfit</span></tt>. If you just need
|
||
<tt class="docutils literal"><span class="pre">musrfit</span></tt> to work on a MS Windows platform, it is recommended to install it via a linux virtual machine!</p>
|
||
</div>
|
||
<div class="admonition note">
|
||
<p class="first admonition-title">Note</p>
|
||
<p class="last">For adventurous guys using Windows 10, there is the possibility to activate the built in Ubuntu bash-shell. It allows
|
||
to install <tt class="docutils literal"><span class="pre">musrfit</span></tt> as described in the Linux section.</p>
|
||
</div>
|
||
<div class="admonition note">
|
||
<p class="first admonition-title">Note</p>
|
||
<p class="last">One more advice: Please never try to install either <tt class="docutils literal"><span class="pre">ROOT</span></tt> or <tt class="docutils literal"><span class="pre">musrfit</span></tt> from or to a directory containing spaces
|
||
in the absolute path or in case you do, do not wonder if some errors occur! msr files, however, might be saved in such
|
||
directories like <tt class="docutils literal"><span class="pre">...\My</span> <span class="pre">Documents\...</span></tt></p>
|
||
</div>
|
||
<p>Under Windows a native installation is not supported but there is the possibility to run musrfit through <a class="reference external" href="https://www.cygwin.com/">cygwin</a>
|
||
which has the great advantage that one gains additionally various nice UNIX tools also for other purposes.
|
||
Please also be aware of the fact that the X server which is going to be installed with <tt class="docutils literal"><span class="pre">Cygwin</span></tt> has to be started
|
||
(<em>e.g.</em> by selecting it from the “Programs” folder) before any graphical application (<tt class="docutils literal"><span class="pre">musrview</span></tt>, <tt class="docutils literal"><span class="pre">musrgui</span></tt>, etc.) is started.</p>
|
||
<div class="section" id="id5">
|
||
<h3>Requirements<a class="headerlink" href="#id5" title="Permalink to this headline">¶</a></h3>
|
||
<div class="section" id="setting-up-cygwin">
|
||
<span id="index-22"></span><h4>Setting up Cygwin<a class="headerlink" href="#setting-up-cygwin" title="Permalink to this headline">¶</a></h4>
|
||
<p>For the start go to the Cygwin website, download the setup file and use it to install Cygwin 1.7 or newer. During the installation
|
||
process you will be asked where you want to install Cygwin and normally the default choice should just be fine. At some point you
|
||
will be asked which packages should be installed. Make sure that you choose at least the following (or packages with revisions close
|
||
to the following) in order to fulfill the <tt class="docutils literal"><span class="pre">musrfit</span></tt> requirements and be able to work with this base system:</p>
|
||
<div class="highlight-python"><div class="highlight"><pre><span></span>a2ps, alternatives, autoconf, automake, base-cygwin, base-files, base-passwd bash, bash-completion,
|
||
bc, binutils, bison, boost, boost-devel, bzip2, cmake, colorgcc, coreutils, curl, cygutils, cygwin,
|
||
editrights, fftw3, findutils, flex, font-adobe-dpi100, font-adobe-dpi75, font-alias,
|
||
font-bitstream-dpi100, font-bitstream-dpi75, font-encodings, font-ibm-type1, font-sun-misc, font-util,
|
||
font-xfree86-type1, fontconfig, freeglut, gawk, gcc-tools-autoconf, gcc-tools-automake, gcc4,
|
||
gcc4-core, gcc4-fortran, gcc4-g++, gccmakedep, gd, gettext, ghostscript, ghostscript-fonts-std,
|
||
giflib, gmp, grep, groff, gsl, gsl-apps, gsl-devel, gv, gzip, inputproto, jasper, jpeg, lapack,
|
||
less, libboost, libbz2_1, libcharset1, libcurl4, libfftw3-devel, libfftw3_3, libgcc1, libgd-devel,
|
||
libgif-devel, libGL-devel, libGL1, libGLU-devel, libGLU1, libglut-devel, libglut3, libgmp-devel,
|
||
libgmp3, libgomp1, libICE-devel, libICE6, libjpeg-devel, libjpeg62, liblapack-devel, libmpfr-devel,
|
||
libmpfr1, libncurses-devel, libncurses9, libOSMesa-devel, libOSMesa7, libpng, libpng14, libpng14-devel,
|
||
libreadline6, libSM-devel, libSM6, libssh2_1, libstdc++6, libstdc++6-devel, libtiff-devel, libtiff5,
|
||
libtool, libX11-devel, libX11_6, libXau-devel, libXau6, libXaw7, libxcb-devel, libxcb-xlib-devel,
|
||
libXcursor-devel, libXcursor1, libXdmcp-devel, libXdmcp6, libXext-devel, libXext6, libXfixes-devel,
|
||
libXfixes3, libXfont-devel, libXfont1, libXft-devel, libXft2, libXi-devel, libXi6, libxkbfile1,
|
||
libxml2, libxml2-devel, libXmu-devel, libXmu6, libXpm-devel, libXpm4, libXrender-devel, libXrender1,
|
||
libXt-devel, libXt6, login, m4, make, makedepend, man, mpfr, nano, opengl, openssh, openssl, pdftk,
|
||
perl, ping, pkg-config, psutils, python, qt3, qt3-bin, qt3-devel, readline, rebase, rgb, rsync, run,
|
||
screen, sed, subversion, tar, tcltk, terminfo, unzip, util-linux, vim, w32api, which,
|
||
X-start-menu-icons, xauth, xextproto, xfontsel, xinit, xkbcomp, xkeyboard-config, xkill, xlogo,
|
||
xlsfonts, xorg-cf-files, xorg-scripts, xorg-server, xproto, xrdb, xrefresh, xset, xterm, zip, zlib,
|
||
zlib-devel, zlib0, libQt3Support4-devel, libQtAssistantClient4-devel, libQtCore4-devel,
|
||
libQtDBus4-devel, libQtDesigner4-devel, libQtGui4-devel, libQtHelp4-devel, libQtNetwork4-devel,
|
||
libQtOpenGL4-devel, libQtScript4-devel, libQtScriptTools4-devel, libQtSql4-devel, libQtSvg4-devel,
|
||
libQtTest4-devel, libQtWebKit4-devel, libQtXml4-devel, libQtXmlPatterns4-devel
|
||
</pre></div>
|
||
</div>
|
||
<p>After these installations already most of the required software is present and the Cygwin shell can be started now for the further steps!
|
||
Inside the shell the POSIX naming convention applies, therefore, paths will be given with separating “/” instead of “” in DOS. The file
|
||
structure accessible through this shell can also be accessed through the Windows Explorer — just go to the directory which you specified
|
||
as “cygwin root” during the installation: this is the equivalent to “/” in the shell. By default, the different hard drives or network shares
|
||
like <tt class="docutils literal"><span class="pre">C:\</span></tt> can be found at <tt class="docutils literal"><span class="pre">/cygdrive/c/</span></tt> in the shell — the cygdrive prefix can in principle also be changed but for now we stick to the default.</p>
|
||
<p>Since later on the boost header files should be used and in the standard Cygwin installation these are found at a version specific location,
|
||
the later handling will be easier if a symbolic link to these files is created now in the terminal (in case it had not been present before):</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ ln -sf /usr/include/boost-x_yy_z/boost /usr/include/boost
|
||
</pre></div>
|
||
</div>
|
||
<p>where <tt class="docutils literal"><span class="pre">x_yy_z</span></tt> has to be substituted by the correct version number, <em>e.g.</em> <tt class="docutils literal"><span class="pre">1_33_1</span></tt>.</p>
|
||
</div>
|
||
<div class="section" id="id6">
|
||
<h4>Everything but ROOT and NeXus<a class="headerlink" href="#id6" title="Permalink to this headline">¶</a></h4>
|
||
</div>
|
||
<div class="section" id="index-23">
|
||
<span id="id7"></span><h4>Installation of NeXus requirements (optional)<a class="headerlink" href="#index-23" title="Permalink to this headline">¶</a></h4>
|
||
<p>Only if <tt class="docutils literal"><span class="pre">musrfit</span></tt> should support reading data files in the <tt class="docutils literal"><span class="pre">NeXus</span></tt> format the further required software has
|
||
to be set up. Under <tt class="docutils literal"><span class="pre">Cygwin</span></tt> of all the required libraries only <tt class="docutils literal"><span class="pre">HDF5</span></tt> is available. The packages <tt class="docutils literal"><span class="pre">hdf5</span></tt> and
|
||
<tt class="docutils literal"><span class="pre">libhdf5-devel</span></tt> can be installed through the <tt class="docutils literal"><span class="pre">Cygwin</span></tt> setup. One should also make sure that <tt class="docutils literal"><span class="pre">bison</span></tt>, <tt class="docutils literal"><span class="pre">flex</span></tt>
|
||
and a package containing <tt class="docutils literal"><span class="pre">/usr/lib/librpc.a</span></tt> (<em>e.g.</em> <tt class="docutils literal"><span class="pre">sunrpc</span> <span class="pre">=</span> <span class="pre">4.0-3</span></tt>, but <em>not</em> <tt class="docutils literal"><span class="pre">sunrpc</span> <span class="pre">=</span> <span class="pre">4.0-4</span></tt>) are installed.</p>
|
||
<p>All other libraries have to be built from the sources. The following lines will track the installation of <tt class="docutils literal"><span class="pre">JPEG</span> <span class="pre">6b</span></tt>,
|
||
<tt class="docutils literal"><span class="pre">MXML</span> <span class="pre">2.9</span></tt>, <tt class="docutils literal"><span class="pre">HDF</span> <span class="pre">4.2.7-patch1</span></tt>, and <tt class="docutils literal"><span class="pre">NeXus</span> <span class="pre">4.3.2</span></tt>. The version numbers and source-code locations might of
|
||
course change with time but should be easily adjustable.</p>
|
||
<p><em>Only</em> <tt class="docutils literal"><span class="pre">NeXus</span></tt> version ≥ 4.4 is support!</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span>
|
||
$ mkdir nexus
|
||
$ <span class="nb">cd</span> nexus
|
||
$ curl http://www.hdfgroup.org/ftp/lib-external/jpeg/src/jpegsrc.v6b.tar.gz -G <span class="p">|</span> tar xz
|
||
$ <span class="nb">cd</span> jpeg-6b
|
||
$ ./configure --prefix<span class="o">=</span>/usr/local --enable-static
|
||
$ make
|
||
$ make install
|
||
$ <span class="nb">cd</span> ..
|
||
$ curl www.msweet.org/files/project3/mxml-2.9.tar.gz -G <span class="p">|</span> tar xz
|
||
$ <span class="nb">cd</span> mxml-2.9
|
||
$ ./configure --prefix<span class="o">=</span>/usr/local --enable-static
|
||
$ make
|
||
$ make install
|
||
$ <span class="nb">cd</span> ..
|
||
$ curl http://www.hdfgroup.org/ftp/HDF/HDF_Current/src/hdf-4.2.7-patch1.tar.gz -G <span class="p">|</span> tar xz
|
||
$ <span class="nb">cd</span> hdf-4.2.7-patch1
|
||
$ ./configure --prefix<span class="o">=</span>/usr/local --enable-static --disable-fortran --with-jpeg<span class="o">=</span>/usr/local
|
||
$ make
|
||
$ make install
|
||
$ <span class="nb">cd</span> ..
|
||
$ <span class="c1"># create a directory for the NeXus source code</span>
|
||
$ mkdir nexus
|
||
$ <span class="nb">cd</span> nexus
|
||
$ <span class="c1"># get the source code from the master repository</span>
|
||
$ git clone https://github.com/nexusformat/code.git
|
||
$ <span class="c1"># next we will build NeXus out-of-source</span>
|
||
$ mkdir build
|
||
$ <span class="nb">cd</span> build
|
||
$ cmake -DENABLE_HDF5<span class="o">=</span><span class="m">1</span> -DENABLE_HDF4<span class="o">=</span><span class="m">1</span> -DENABLE_MXML<span class="o">=</span><span class="m">1</span> ../code
|
||
$ make
|
||
$ make install
|
||
</pre></div>
|
||
</div>
|
||
</div>
|
||
<div class="section" id="index-24">
|
||
<span id="id8"></span><h4>ROOT<a class="headerlink" href="#index-24" title="Permalink to this headline">¶</a></h4>
|
||
<p>In order to install the <tt class="docutils literal"><span class="pre">ROOT</span></tt> system, there are two possibilities:</p>
|
||
<ul>
|
||
<li><p class="first">Download the precompiled Cygwin GCC 4.3 (or newer) package of the most recent <tt class="docutils literal"><span class="pre">ROOT</span></tt> version
|
||
from the <a class="reference external" href="https://root.cern.ch/downloading-root">web page</a> and unpack it in a <tt class="docutils literal"><span class="pre">Cygwin</span></tt> shell
|
||
(in order to get the line endings correctly) at the final location. Suppose the package has been
|
||
downloaded to <tt class="docutils literal"><span class="pre">C:\</span></tt> and the <tt class="docutils literal"><span class="pre">ROOT</span></tt> tree should be in <tt class="docutils literal"><span class="pre">C:\root</span></tt>, this is achieved by:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> /cygdrive/c
|
||
$ tar xzf root_v5.xx.yy.win32gcc-gcc-4.3.tar.gz
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
<li><p class="first">If due to some reason there was no precompiled Cygwin GCC 4.3 package available or <tt class="docutils literal"><span class="pre">ROOT</span></tt> should
|
||
be built from source, one has to visit the <a class="reference external" href="https://root.cern.ch/downloading-root">web page</a>,
|
||
download the ‘complete source tree for all systems’ and save it for instance in <tt class="docutils literal"><span class="pre">C:\</span></tt>.
|
||
Then go to the Cygwin shell and unpack this source tree, configure it (here using the minimal set of options)
|
||
and compile it as follows right below:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> /cygdrive/c
|
||
$ tar xzf root_v5.xx.yy.source.tar.gz
|
||
$ <span class="nb">cd</span> root
|
||
$ ./configure win32gcc --gminimal --enable-asimage --enable-mathmore --enable-minuit2 --enable-xml
|
||
$ make
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
<li><p class="first">In order to finalize the <tt class="docutils literal"><span class="pre">ROOT</span></tt> installation and to prepare already the installation of <tt class="docutils literal"><span class="pre">musrfit</span></tt> and
|
||
<tt class="docutils literal"><span class="pre">musredit</span></tt> this is a good time for setting necessary environment variables for the use in Cygwin. For
|
||
accomplishing that put the following lines at the end of the <tt class="docutils literal"><span class="pre">/home/Username/.bashrc</span></tt> (<tt class="docutils literal"><span class="pre">C:\cygwin\home\Username\.bashrc</span></tt>
|
||
for the user <tt class="docutils literal"><span class="pre">Username</span></tt> and the <tt class="docutils literal"><span class="pre">cygwin</span> <span class="pre">root</span></tt> at <tt class="docutils literal"><span class="pre">C:\cygwin</span></tt>):</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span><span class="nb">export</span> <span class="nv">DISPLAY</span><span class="o">=</span>:0.0
|
||
<span class="nb">export</span> <span class="nv">QTDIR</span><span class="o">=</span>/usr/lib/qt4
|
||
<span class="nb">export</span> <span class="nv">ROOTSYS</span><span class="o">=</span>/cygdrive/c/root
|
||
<span class="nb">export</span> <span class="nv">PATH</span><span class="o">=</span><span class="nv">$ROOTSYS</span>/bin:<span class="nv">$QTDIR</span>/bin:/usr/i686-pc-cygwin/bin:<span class="nv">$PATH</span>
|
||
<span class="nb">export</span> <span class="nv">MUSRFITPATH</span><span class="o">=</span><span class="nv">$ROOTSYS</span>/bin
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
</ul>
|
||
<p>Afterwards close the Cygwin shell and reopen it again for the installation of <tt class="docutils literal"><span class="pre">musrfit</span></tt>.</p>
|
||
</div>
|
||
</div>
|
||
<div class="section" id="index-25">
|
||
<span id="id9"></span><h3>musrfit<a class="headerlink" href="#index-25" title="Permalink to this headline">¶</a></h3>
|
||
<p>First, the most recent source code should be downloaded. The preferred way of doing so is to clone the <tt class="docutils literal"><span class="pre">musrfit</span></tt>
|
||
repository via git. Assuming the code should be located in <tt class="docutils literal"><span class="pre">~/musrfit</span></tt> this is achieved most easily calling from the terminal</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span>
|
||
$ git clone https://bitbucket.org/muonspin/musrfit.git
|
||
</pre></div>
|
||
</div>
|
||
<p>or</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span>
|
||
$ git clone git://gitlab.psi.ch/nemu/musrfit.git
|
||
</pre></div>
|
||
</div>
|
||
<p>If the repository had been checked out already before, one can update the local copy using:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> musrfit
|
||
$ git pull
|
||
</pre></div>
|
||
</div>
|
||
<p>As an alternative (if git is not available), the source code can also be downloaded from the following
|
||
web-page: <a class="reference external" href="https://bitbucket.org/muonspin/musrfit/downloads">musrfit at bitbucket</a>.</p>
|
||
<div class="section" id="index-26">
|
||
<span id="id10"></span><h4>musrfit build with automake<a class="headerlink" href="#index-26" title="Permalink to this headline">¶</a></h4>
|
||
<p>After the source-code extraction the <tt class="docutils literal"><span class="pre">autogen.sh</span></tt> script is called to prepare the build environment.
|
||
If it has been executed successfully the <tt class="docutils literal"><span class="pre">configure</span></tt> script should be ready to collect all the information
|
||
needed to create the Makefiles. If <tt class="docutils literal"><span class="pre">musrfit</span></tt> should support <tt class="docutils literal"><span class="pre">NeXus</span></tt> data files this has to be enabled by
|
||
specifying the <tt class="docutils literal"><span class="pre">--enable-static</span> <span class="pre">--enable-NeXus</span></tt> switches when calling configure. For an overview of all
|
||
available options just call <tt class="docutils literal"><span class="pre">./configure</span> <span class="pre">--help</span></tt>. Besides the standard options there are a few special
|
||
options which should be mentioned here:</p>
|
||
<dl class="docutils">
|
||
<dt><strong>- -prefix</strong></dt>
|
||
<dd>Specify the installation prefix, <em>e.g.</em> <tt class="docutils literal"><span class="pre">/opt/root-system</span></tt> (by default: <tt class="docutils literal"><span class="pre">/usr/local</span></tt>)</dd>
|
||
<dt><strong>- -with-rootsys</strong></dt>
|
||
<dd>Specify the top of the <tt class="docutils literal"><span class="pre">ROOT</span></tt> installation directory, <em>e.g.</em> <tt class="docutils literal"><span class="pre">/opt/root-system</span></tt></dd>
|
||
<dt><strong>- -with-fftw3</strong></dt>
|
||
<dd>Specify the prefix of the <tt class="docutils literal"><span class="pre">FFTW3</span></tt> installation. <em>e.g.</em> <tt class="docutils literal"><span class="pre">/usr/local</span></tt> or <tt class="docutils literal"><span class="pre">/usr</span></tt></dd>
|
||
<dt><strong>- -with-gsl</strong></dt>
|
||
<dd>Set the prefix of the <tt class="docutils literal"><span class="pre">GSL</span></tt> installation, <em>e.g.</em> <tt class="docutils literal"><span class="pre">/usr/local</span></tt> or <tt class="docutils literal"><span class="pre">/usr</span></tt></dd>
|
||
<dt><strong>- -with-boostinc</strong></dt>
|
||
<dd>Set the path to the header files of the <tt class="docutils literal"><span class="pre">Boost</span></tt> installation, <em>e.g.</em> <tt class="docutils literal"><span class="pre">/usr/local/include</span></tt> or <tt class="docutils literal"><span class="pre">/usr/include</span></tt></dd>
|
||
<dt><strong>- -with-hdf4</strong></dt>
|
||
<dd>Set the prefix of the <tt class="docutils literal"><span class="pre">HDF4</span></tt> installation, <em>e.g.</em> <tt class="docutils literal"><span class="pre">/usr/local</span></tt> (only useful in conjunction with the <tt class="docutils literal"><span class="pre">NeXus</span></tt> support)</dd>
|
||
<dt><strong>- -with-hdf5</strong></dt>
|
||
<dd>Set the prefix of the <tt class="docutils literal"><span class="pre">HDF5</span></tt> installation, <em>e.g.</em> <tt class="docutils literal"><span class="pre">/usr</span></tt> (only useful in conjunction with the <tt class="docutils literal"><span class="pre">NeXus</span></tt> support)</dd>
|
||
<dt><strong>- -with-nexus</strong></dt>
|
||
<dd>Set the prefix of the <tt class="docutils literal"><span class="pre">NeXus</span></tt> installation, <em>e.g.</em> <tt class="docutils literal"><span class="pre">/usr/local</span></tt> (only useful in conjunction with the <tt class="docutils literal"><span class="pre">NeXus</span></tt> support)</dd>
|
||
<dt><strong>- -with-qt3</strong></dt>
|
||
<dd>Set the prefix of the <tt class="docutils literal"><span class="pre">Qt3</span></tt> installation, <em>e.g.</em> <tt class="docutils literal"><span class="pre">/usr/lib/qt-3.3</span></tt> (only useful in conjunction with building <tt class="docutils literal"><span class="pre">musrgui</span></tt>)</dd>
|
||
<dt><strong>- -with-qt4</strong></dt>
|
||
<dd>Set the prefix of the <tt class="docutils literal"><span class="pre">Qt4</span></tt> installation, <em>e.g.</em> <tt class="docutils literal"><span class="pre">/usr/lib/qt47</span></tt> (only useful in conjunction with building <tt class="docutils literal"><span class="pre">musredit</span></tt>)</dd>
|
||
<dt><strong>- -with-qt5</strong></dt>
|
||
<dd>Set the prefix of the <tt class="docutils literal"><span class="pre">Qt5</span></tt> installation, <em>e.g.</em> <tt class="docutils literal"><span class="pre">/usr/lib/qt56</span></tt> (only useful in conjunction with building <tt class="docutils literal"><span class="pre">musredit</span></tt>)</dd>
|
||
<dt><strong>- -enable-NeXus</strong></dt>
|
||
<dd>Enable the support of <tt class="docutils literal"><span class="pre">NeXus</span></tt> data files (requires the <tt class="docutils literal"><span class="pre">HDF4</span></tt>, <tt class="docutils literal"><span class="pre">HDF5</span></tt> and <tt class="docutils literal"><span class="pre">NeXus</span></tt> libraries to be installed).</dd>
|
||
<dt><strong>- -disable-editor</strong></dt>
|
||
<dd>Disable the integrated building of <tt class="docutils literal"><span class="pre">musredit</span></tt>/<tt class="docutils literal"><span class="pre">musrgui</span></tt>.</dd>
|
||
<dt><strong>- -disable-omp</strong></dt>
|
||
<dd>Switches off the <tt class="docutils literal"><span class="pre">OpenMP</span></tt> features of <tt class="docutils literal"><span class="pre">musrfit</span></tt> (parallelization of the <span class="math">\(\chi^2\)</span> calculation when compiled with <tt class="docutils literal"><span class="pre">GCC</span></tt> ≥ 4.2)</dd>
|
||
</dl>
|
||
<p>Normally it should not be necessary to make use of any of the options except for specifying the installation path with <tt class="docutils literal"><span class="pre">--prefix</span></tt>.
|
||
The other paths should be detected automatically. If this does not work for some reason the <tt class="docutils literal"><span class="pre">configure</span></tt> script will terminate and
|
||
ask for the information. When the <tt class="docutils literal"><span class="pre">configure</span></tt> script has been called successfully everything is ready for building the <tt class="docutils literal"><span class="pre">musrfit</span></tt>
|
||
libraries and executables. A standard installation sequence (without <tt class="docutils literal"><span class="pre">NeXus</span></tt> support) might then look like:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> musrfit
|
||
$ sh autogen.sh
|
||
$ ./configure --prefix<span class="o">=</span><span class="nv">$ROOTSYS</span>
|
||
$ make
|
||
$ make install
|
||
</pre></div>
|
||
</div>
|
||
</div>
|
||
<div class="section" id="index-27">
|
||
<span id="id11"></span><h4>musrfit build with cmake<a class="headerlink" href="#index-27" title="Permalink to this headline">¶</a></h4>
|
||
<p>Currently the following configuration switches for <tt class="docutils literal"><span class="pre">musrfit</span></tt> are available:</p>
|
||
<dl class="docutils">
|
||
<dt><strong>-DCMAKE_INSTALL_PREFIX=<prefix-path></strong></dt>
|
||
<dd>Specify the installation prefix, <em>i.e.</em> the place where <tt class="docutils literal"><span class="pre">musrfit</span></tt> shall be installed, <em>e.g.</em> <tt class="docutils literal"><span class="pre">$ROOTSYS</span></tt> if already defined (by default: <tt class="docutils literal"><span class="pre">/usr/local</span></tt>)</dd>
|
||
<dt><strong>-Dnexus=<value></strong></dt>
|
||
<dd>enable/disable the support of <tt class="docutils literal"><span class="pre">NeXus</span></tt> data files (requires the <tt class="docutils literal"><span class="pre">HDF4</span></tt>, <tt class="docutils literal"><span class="pre">HDF5</span></tt> and <tt class="docutils literal"><span class="pre">NeXus</span></tt> libraries to be installed).
|
||
<value>=1 enables <tt class="docutils literal"><span class="pre">NeXus</span></tt>, <value>=0 disables <tt class="docutils literal"><span class="pre">NeXus</span></tt>. The default setting, <em>i.e.</em> the switch is not provided is <tt class="docutils literal"><span class="pre">NeXus</span></tt> support is disabled.</dd>
|
||
<dt><strong>-DASlibs=<value></strong></dt>
|
||
<dd>enable/disable the <tt class="docutils literal"><span class="pre">ASlibs</span></tt>. <value>=1 enables the <tt class="docutils literal"><span class="pre">ASlibs</span></tt>, <value>=0 disables the <tt class="docutils literal"><span class="pre">ASlibs</span></tt>.
|
||
The default setting, <em>i.e.</em> the switch is not provided is <tt class="docutils literal"><span class="pre">ASlibs</span></tt> support is <em>disabled</em>. For details see Documentation of <a class="reference internal" href="user-libs.html#user-libs"><em>user libs</em></a>.</dd>
|
||
<dt><strong>-DBMWlibs=<value></strong></dt>
|
||
<dd>enable/disable the <tt class="docutils literal"><span class="pre">BMWlibs</span></tt>. <value>=1 enables the <tt class="docutils literal"><span class="pre">BMWlibs</span></tt>, <value>=0 disables the <tt class="docutils literal"><span class="pre">BMWlibs</span></tt>.
|
||
The default setting, <em>i.e.</em> the switch is not provided is <tt class="docutils literal"><span class="pre">BMWlibs</span></tt> support is <em>disabled</em>. For details see Documentation of <a class="reference internal" href="user-libs.html#user-libs"><em>user libs</em></a>.</dd>
|
||
<dt><strong>-DBNMRlibs=<value></strong></dt>
|
||
<dd>enable/disable the <tt class="docutils literal"><span class="pre">BNMRlibs</span></tt>. <value>=1 enables the <tt class="docutils literal"><span class="pre">BNMRlibs</span></tt>, <value>=0 disables the <tt class="docutils literal"><span class="pre">BNMRlibs</span></tt>.
|
||
The default setting, <em>i.e.</em> the switch is not provided is <tt class="docutils literal"><span class="pre">BNMRlibs</span></tt> support is <em>disabled</em>.</dd>
|
||
<dt><strong>-Dqt_based_tools=<value></strong></dt>
|
||
<dd>Will try to get <tt class="docutils literal"><span class="pre">musredit</span></tt>, <tt class="docutils literal"><span class="pre">musrWiz</span></tt>, <tt class="docutils literal"><span class="pre">musrStep</span></tt>, and <tt class="docutils literal"><span class="pre">mupp</span></tt> installed, if <tt class="docutils literal"><span class="pre">Qt</span></tt> is found.
|
||
By default this is <em>enabled</em>. Again <value>=0 means disabled, <value>=1 enabled.</dd>
|
||
<dt><strong>-Dqt_version=<value></strong></dt>
|
||
<dd>Allows to specify which <tt class="docutils literal"><span class="pre">Qt</span></tt> version shall be tried. <value> can take the values: <tt class="docutils literal"><span class="pre">AUTO,</span> <span class="pre">3,</span> <span class="pre">4,</span> <span class="pre">5</span></tt>.
|
||
If the value is set to <tt class="docutils literal"><span class="pre">AUTO</span></tt>, this highest installed version is chosen, otherwise the specified version is used.</dd>
|
||
<dt><strong>-Dtry_OpenMP=<value></strong></dt>
|
||
<dd>Will check if <tt class="docutils literal"><span class="pre">OpenMP</span></tt> support is possible, and if yes use it. The default is <em>enabled</em>.</dd>
|
||
</dl>
|
||
<p>Normally it should not be necessary to make use of any of the options except for specifying the installation path with
|
||
<tt class="docutils literal"><span class="pre">-DCMAKE_INSTALL_PREFIX</span></tt>. <tt class="docutils literal"><span class="pre">musrfit</span></tt> build with <tt class="docutils literal"><span class="pre">cmake</span></tt> takes the out-of-source approach. Therefore a typical
|
||
configuration / make / install process including <tt class="docutils literal"><span class="pre">NeXus</span></tt> support would look like</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> <span class="nv">$HOME</span>/Apps/musrfit
|
||
$ mkdir build
|
||
$ <span class="nb">cd</span> build
|
||
$ cmake ../ -DCMAKE_INSTALL_PREFIX<span class="o">=</span><span class="nv">$ROOTSYS</span> -Dnexus<span class="o">=</span><span class="m">1</span>
|
||
<span class="c1"># below it is assumed that multiple cores are present, hence the -j8 option</span>
|
||
$ cmake --build ./ --clean-first -- -j8
|
||
$ make install
|
||
$ /sbin/ldconfig <span class="c1"># (as superuser)</span>
|
||
</pre></div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="section" id="index-28">
|
||
<span id="id12"></span><h3>musredit<a class="headerlink" href="#index-28" title="Permalink to this headline">¶</a></h3>
|
||
<p>In the latest version of <tt class="docutils literal"><span class="pre">musrfit</span></tt> the configure script tries to determine automatically if
|
||
Qt4.5 or higher is set up on the machine. In case this is found, the editor <tt class="docutils literal"><span class="pre">musredit</span></tt> is built
|
||
readily with <tt class="docutils literal"><span class="pre">musrfit</span></tt>. If not, one can either try to call the <tt class="docutils literal"><span class="pre">configure</span></tt> script with the
|
||
<tt class="docutils literal"><span class="pre">--with-qt4</span></tt> option or install this editor separately, <em>.e.g.</em>:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> src/musredit
|
||
$ qmake-qt4 musredit.pro
|
||
</pre></div>
|
||
</div>
|
||
<p>If everything went fine <tt class="docutils literal"><span class="pre">musredit</span></tt> can be compiled and installed:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ make
|
||
$ make install
|
||
</pre></div>
|
||
</div>
|
||
<p>In case one likes to get the editor started just with starting the X server from the Windows start
|
||
menu the file <tt class="docutils literal"><span class="pre">~/.startxwinrc</span></tt> with the following contents can be created:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span><span class="ch">#!/bin/sh</span>
|
||
|
||
<span class="nb">export</span> <span class="nv">DISPLAY</span><span class="o">=</span>:0.0
|
||
<span class="nb">export</span> <span class="nv">QTDIR</span><span class="o">=</span>/usr/lib/qt4
|
||
<span class="nb">export</span> <span class="nv">ROOTSYS</span><span class="o">=</span>/cygdrive/c/root
|
||
<span class="nb">export</span> <span class="nv">PATH</span><span class="o">=</span><span class="nv">$ROOTSYS</span>/bin:<span class="nv">$QTDIR</span>/bin:/usr/i686-pc-cygwin/bin:<span class="nv">$PATH</span>
|
||
<span class="nb">export</span> <span class="nv">MUSRFITPATH</span><span class="o">=</span><span class="nv">$ROOTSYS</span>/bin
|
||
|
||
musredit <span class="p">&</span>
|
||
</pre></div>
|
||
</div>
|
||
</div>
|
||
<div class="section" id="id13">
|
||
<h3>musrgui (obsolate)<a class="headerlink" href="#id13" title="Permalink to this headline">¶</a></h3>
|
||
<p>If <tt class="docutils literal"><span class="pre">Qt4.5</span></tt> or higher is not available but <tt class="docutils literal"><span class="pre">Qt3</span></tt> is set up <tt class="docutils literal"><span class="pre">musrgui</span></tt> can be installed. For this
|
||
please follow the instructions for the <tt class="docutils literal"><span class="pre">musredit</span></tt> installation where simply every <tt class="docutils literal"><span class="pre">musredit</span></tt> occurrence
|
||
has to be replaced by <tt class="docutils literal"><span class="pre">musrgui</span></tt>, and <tt class="docutils literal"><span class="pre">qt4</span></tt> is replaced by <tt class="docutils literal"><span class="pre">qt3</span></tt>.</p>
|
||
</div>
|
||
<div class="section" id="id14">
|
||
<h3>Check the installation<a class="headerlink" href="#id14" title="Permalink to this headline">¶</a></h3>
|
||
<p>In order to perform a quick test for finding out if the installation has been completed successfully,
|
||
a few msr files together with the corresponding data files can be found in the <tt class="docutils literal"><span class="pre">musrfit</span></tt> source tree
|
||
at doc/examples/.
|
||
If <tt class="docutils literal"><span class="pre">musrgui</span></tt> has been installed, just open one of the <tt class="docutils literal"><span class="pre">test-*.msr</span></tt> files in the editor and test
|
||
the <tt class="docutils literal"><span class="pre">musrfit</span></tt> functionalities. Otherwise, if only the terminal should be used, as an initial test
|
||
for instance the following could be done:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> doc/examples
|
||
$ musrview test-histo-ROOT-NPP.msr
|
||
</pre></div>
|
||
</div>
|
||
</div>
|
||
<div class="section" id="potential-problems">
|
||
<h3>Potential Problems<a class="headerlink" href="#potential-problems" title="Permalink to this headline">¶</a></h3>
|
||
<p>It might be that especially when running on Windows 7 <tt class="docutils literal"><span class="pre">musredit</span></tt> and <tt class="docutils literal"><span class="pre">musrgui</span></tt> produce errors like a
|
||
“STATUS_ACCESS_VIOLATION”. In this case, try to do the following: Close all Cygwin programs (including
|
||
the terminals and X server) and run from a Windows command prompt (cmd)</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ C:<span class="se">\c</span>ygwin<span class="se">\b</span>in<span class="se">\a</span>sh.exe /bin/rebaseall
|
||
</pre></div>
|
||
</div>
|
||
<p>If this does not resolve the problem, try to change the compatibility settings of <tt class="docutils literal"><span class="pre">C:\cygwin\bin\sh.exe</span></tt>
|
||
and <tt class="docutils literal"><span class="pre">C:\cygwin\bin\bash.exe</span></tt> so that they are executed with administrator privileges.</p>
|
||
</div>
|
||
</div>
|
||
<div class="section" id="mac-os-x-macos">
|
||
<h2>Mac OS X / macOS<a class="headerlink" href="#mac-os-x-macos" title="Permalink to this headline">¶</a></h2>
|
||
<p>With Mac OS X / macOS the situation is up to some extent similar like on MS Windows but still different since
|
||
Mac OS X is a UNIX system. The similarity is that also on OS X a helping framework — either <a class="reference external" href="https://www.macports.org/">MacPorts</a>
|
||
or <a class="reference external" href="http://www.finkproject.org/">Fink</a> — which provides open-source software is employed to fulfill the basic software requirements of <tt class="docutils literal"><span class="pre">musrfit</span></tt>.
|
||
In the following, both possibilities (using MacPorts or Fink) are described but it is emphasized here that
|
||
it should be followed only <em>one</em> of the possible routes .</p>
|
||
<div class="section" id="requirements-macports">
|
||
<span id="index-29"></span><h3>Requirements (MacPorts)<a class="headerlink" href="#requirements-macports" title="Permalink to this headline">¶</a></h3>
|
||
<p>Before proceeding with the usage of the <tt class="docutils literal"><span class="pre">MacPorts</span></tt> system first a few useful tools provided by Apple together
|
||
with OS X (on the installation DVD/CDs) should be installed:</p>
|
||
<blockquote>
|
||
<div><dl class="docutils">
|
||
<dt><strong>Xcode</strong></dt>
|
||
<dd><p class="first">Useful developer tools including for instance the GNU compiler collection. It can be installed via the Apple App store.
|
||
Starting from <tt class="docutils literal"><span class="pre">XCode</span></tt> ≥ 4.3 the command line tools need to be installed manually. The necessary command line tools
|
||
can be installed via the following commands entered in the terminal</p>
|
||
<div class="last highlight-bash"><div class="highlight"><pre><span></span>$ xcode-select --install
|
||
$ sudo xcodebuild -license
|
||
</pre></div>
|
||
</div>
|
||
</dd>
|
||
</dl>
|
||
</div></blockquote>
|
||
<dl class="docutils">
|
||
<dt><strong>X11</strong></dt>
|
||
<dd>The X-window system is automatically installed on 10.5 Leopard and 10.6 Snow Leopard. For some other versions you also
|
||
will need to install <cite>XQuartz <http://xquartz.macosforge.org/trac></cite>. If <tt class="docutils literal"><span class="pre">ROOT</span></tt> runs without <tt class="docutils literal"><span class="pre">XQuartz</span></tt> <em>do not</em>
|
||
install it.</dd>
|
||
</dl>
|
||
<p>After installing the <tt class="docutils literal"><span class="pre">Xcode</span></tt> tools go to the <a class="reference external" href="http://www.macports.org/install.php">MacPorts install page</a>, download
|
||
the installer for your system and follow the installation instructions on the page. By default the MacPorts system will be
|
||
installed in <tt class="docutils literal"><span class="pre">/opt/local</span></tt>. To be sure that the newest version of the software is used a MacPorts upgrade should be performed
|
||
by typing in a terminal:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ sudo port -v selfupdate
|
||
</pre></div>
|
||
</div>
|
||
<p><strong>Remark:</strong> MacPorts uses <a class="reference external" href="http://rsync.samba.org/">rsync</a> in order to synchronize the list of available packages. It frequently
|
||
happens that this service is blocked by firewalls. In this case it should be possible to download a local version of the package
|
||
repository and do the synchronization. If this step becomes necessary (<em>and only then</em>) it can be done in the following way:</p>
|
||
<ol class="arabic">
|
||
<li><p class="first">Get a local version of the repository:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ svn co http://svn.macports.org/repository/macports/trunk/dports ~/dports
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
<li><p class="first">Edit the file <tt class="docutils literal"><span class="pre">/opt/local/etc/macports/sources.conf</span></tt>: At the end of the file, comment the line beginning with <tt class="docutils literal"><span class="pre">rsync://</span></tt> and
|
||
add a new line pointing to your local copy, <em>e.g.</em></p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>file:///Users/username/dports
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
<li><p class="first">Synchronize the packages:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ sudo port -v -d sync
|
||
</pre></div>
|
||
</div>
|
||
</li>
|
||
</ol>
|
||
<p>Then the MacPorts system should be set up and can be used to install additional software.</p>
|
||
<p>The installation of the software mentioned above is then done in the terminal:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ sudo port -v install pkgconfig autoconf automake libtool cmake fftw-3 fftw-3-single gsl boost libxml2 qt5 qt5-qtsvg qt5-qtwebengine
|
||
</pre></div>
|
||
</div>
|
||
<p>With <tt class="docutils literal"><span class="pre">Qt5</span></tt>, <tt class="docutils literal"><span class="pre">musredit</span></tt> will be installed. If it happens that you used <tt class="docutils literal"><span class="pre">musrgui</span></tt> in the past,
|
||
please change over to <tt class="docutils literal"><span class="pre">musredit</span></tt> since there will be no further development for <tt class="docutils literal"><span class="pre">musrgui</span></tt> anymore!</p>
|
||
<div class="section" id="index-30">
|
||
<span id="id15"></span><h4>Installation of NeXus requirements (optional)<a class="headerlink" href="#index-30" title="Permalink to this headline">¶</a></h4>
|
||
<p><em>Only</em> if <tt class="docutils literal"><span class="pre">musrfit</span></tt> should support reading data files in the <tt class="docutils literal"><span class="pre">NeXus</span></tt> format the further required packages are set up:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ sudo port -v install hdf4 hdf5
|
||
</pre></div>
|
||
</div>
|
||
<p>Unfortunately, the <tt class="docutils literal"><span class="pre">minixml</span></tt> and <tt class="docutils literal"><span class="pre">NeXus</span></tt> libraries have to be compiled and installed directly from the source code.
|
||
Given the respective version numbers of 2.9 and 4.4.2 (which are subject to change with time.
|
||
Only <tt class="docutils literal"><span class="pre">NeXus</span></tt> Version ≥ 4.4 is support!) this can be achieved for example by:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="c1"># get and instal Mini-XML</span>
|
||
$ <span class="nb">cd</span> <span class="nv">$HOME</span>/Applications
|
||
$ git clone https://github.com/michaelrsweet/mxml.git
|
||
$ <span class="nb">cd</span> mxml
|
||
$ ./configure --prefix<span class="o">=</span>/usr/local
|
||
$ make
|
||
$ sudo make install
|
||
$ <span class="c1"># get and install NeXus</span>
|
||
$ <span class="nb">cd</span> <span class="nv">$HOME</span>/Applications
|
||
$ <span class="c1"># get the source code from the master repository</span>
|
||
$ git clone https://github.com/nexusformat/code.git nexus/code
|
||
$ <span class="c1"># next we will build NeXus out-of-source</span>
|
||
$ <span class="nb">cd</span> nexus
|
||
$ mkdir build
|
||
$ <span class="nb">cd</span> build
|
||
$ cmake -DENABLE_HDF5<span class="o">=</span><span class="m">1</span> -DENABLE_HDF4<span class="o">=</span><span class="m">1</span> -DENABLE_MXML<span class="o">=</span><span class="m">1</span> ../code
|
||
$ make
|
||
$ sudo make install
|
||
</pre></div>
|
||
</div>
|
||
</div>
|
||
<div class="section" id="index-31">
|
||
<span id="id16"></span><h4>ROOT<a class="headerlink" href="#index-31" title="Permalink to this headline">¶</a></h4>
|
||
<p>ROOT 5.34/xx is supported as legacy version only! <strong>The default now will be ROOT 6.xx/yy!</strong></p>
|
||
<div class="section" id="root-installed-via-package-installer">
|
||
<h5>ROOT installed via package installer<a class="headerlink" href="#root-installed-via-package-installer" title="Permalink to this headline">¶</a></h5>
|
||
<p>The lazy way to get <tt class="docutils literal"><span class="pre">ROOT</span></tt> installed is via package installer. If your macOS is directly supported
|
||
by the <tt class="docutils literal"><span class="pre">ROOT</span></tt> people you can download the package installer from the <tt class="docutils literal"><span class="pre">ROOT</span></tt> <a class="reference external" href="https://root.cern.ch/downloading-root">download page</a>.
|
||
Choose the latest <tt class="docutils literal"><span class="pre">ROOT</span></tt> release and download you macOS version dmg-file, <em>e.g.</em> for macOS 10.13 (High Sierra)
|
||
it is at the time of writting <tt class="docutils literal"><span class="pre">root_v6.14.00.macosx64-10.13-clang91.dmg</span></tt>. After the installation
|
||
<tt class="docutils literal"><span class="pre">ROOT</span></tt> will be installed under <tt class="docutils literal"><span class="pre">/Application</span></tt> as owner root. In order to ease your life for the
|
||
steps to follow and assuming you are the only guy working on your Mac, you could change the owner and group of the <tt class="docutils literal"><span class="pre">ROOT</span></tt> directory:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> /Applications
|
||
$ sudo chown -R <username> root_v6.14.00
|
||
$ sudo chgrp -R staff root_v6.14.00
|
||
$ sudo ln -s root_v6.14.00 root
|
||
</pre></div>
|
||
</div>
|
||
</div>
|
||
<div class="section" id="root-installed-from-source">
|
||
<h5>ROOT installed from source<a class="headerlink" href="#root-installed-from-source" title="Permalink to this headline">¶</a></h5>
|
||
<p>The best way to get <tt class="docutils literal"><span class="pre">ROOT</span></tt> exactly the way needed for <tt class="docutils literal"><span class="pre">musrfit</span></tt> is to install it from source.
|
||
Before describing it, please make sure that you have installed all required packages listed under
|
||
<a class="reference internal" href="#supported-operating-systems"><em>Requested Software</em></a> (<em>e.g.</em> <tt class="docutils literal"><span class="pre">fftw</span></tt>, <tt class="docutils literal"><span class="pre">gsl</span></tt>, etc).</p>
|
||
<p>For the following it is assumed that <tt class="docutils literal"><span class="pre">ROOT</span></tt> shall be installed under <tt class="docutils literal"><span class="pre">$HOME/Applications</span></tt>. If you want
|
||
to install it somewhere else, just systematically replace the related terms of the following description.
|
||
For the following list of commands the ‘$’ will be given, the command prompt. Do not enter it! Also some
|
||
comments will be added starting with a ‘#’ which can be omitted. They are only there to explain what is going on.</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> <span class="nv">$HOME</span>/Applications
|
||
$ git clone http://root.cern.ch/git/root.git
|
||
$ <span class="nb">cd</span> root
|
||
$ git tag -l
|
||
$ <span class="c1"># git tag -l will list all available tags. In the next command choose the tag v6-10-xx</span>
|
||
$ <span class="c1"># where xx is the highest listed number, e.g. v6-14-00</span>
|
||
$ git checkout -b v6-14-00 v6-14-00
|
||
$ <span class="c1"># now ROOT is ready to be configured. Below you will find the minimal ROOT configuration needed.</span>
|
||
$ <span class="c1"># We will use the cmake out-of-source approach here.</span>
|
||
$ mkdir root_build
|
||
$ <span class="nb">cd</span> root_build
|
||
$ cmake ../ -Dgminimal<span class="o">=</span>ON -Dasimage<span class="o">=</span>ON -Dmathmore<span class="o">=</span>ON -Dminuit2<span class="o">=</span>ON -Dxml<span class="o">=</span>ON -DCMAKE_INSTALL_PREFIX<span class="o">=</span><span class="nv">$HOME</span>/Applications/root/root_exec
|
||
$ <span class="c1"># next will be the make. If running on a multicore CPU you can speed up tremendously by calling</span>
|
||
$ <span class="c1"># make with the option -j <number>, where <number> is the number of threads which you want to give,</span>
|
||
$ <span class="c1"># e.g. make -j8</span>
|
||
$ cmake --build ./ --clean-first -- -j8
|
||
$ <span class="c1"># make will take quite a while</span>
|
||
$ make install
|
||
</pre></div>
|
||
</div>
|
||
<p>For further details see <a class="reference external" href="https://root.cern.ch/building-root">Installing ROOT from Source</a>.</p>
|
||
</div>
|
||
<div class="section" id="setting-up-environment-variables-for-root-and-musrfit">
|
||
<h5>Setting up Environment Variables for ROOT and musrfit<a class="headerlink" href="#setting-up-environment-variables-for-root-and-musrfit" title="Permalink to this headline">¶</a></h5>
|
||
<p>Since Apple in its wisdom decided that programs started from a shell are treated differently than Apps if it is coming to
|
||
system variables, we need to work harder compared to a Linux system.</p>
|
||
<p><strong>For Mac OS X < 10.8:</strong></p>
|
||
<p>In order to finalize the <tt class="docutils literal"><span class="pre">ROOT</span></tt> installation and to prepare already the installation of <tt class="docutils literal"><span class="pre">musrfit</span></tt> and <tt class="docutils literal"><span class="pre">musredit</span></tt>
|
||
this is a good time for setting necessary environment variables for the use in Mac OS X. Here it assumed that you
|
||
installed <tt class="docutils literal"><span class="pre">ROOT</span></tt> from source. If you downloaded the binary package, you will need to adopt the paths accordingly.
|
||
Put the following lines (without the comments in parentheses and with the paths adjusted to your local installation)
|
||
into the file <tt class="docutils literal"><span class="pre">~/.MacOSX/environment.plist</span></tt> and re-login:</p>
|
||
<div class="highlight-xml"><div class="highlight"><pre><span></span><span class="cp"><?xml version="1.0" encoding="UTF-8"?></span>
|
||
<span class="cp"><!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd"></span>
|
||
<span class="nt"><plist</span> <span class="na">version=</span><span class="s">"1.0"</span><span class="nt">></span>
|
||
<span class="nt"><dict></span>
|
||
<span class="nt"><key></span>MUSRFITPATH<span class="nt"></key></span>
|
||
<span class="nt"><string></span>$HOME/Applications/root/root_exec/bin<span class="nt"></string></span> (where to find the musrfit executables)
|
||
<span class="nt"><key></span>QTDIR<span class="nt"></key></span>
|
||
<span class="nt"><string></span>/opt/local/lib/qt3mac<span class="nt"></string></span> (where to find Qt3 (for musrgui) or Qt4 (for musredit))
|
||
<span class="nt"><key></span>ROOTSYS<span class="nt"></key></span>
|
||
<span class="nt"><string></span>$HOME/Applications/root/root_exec<span class="nt"></string></span> (where to find the ROOT system)
|
||
<span class="nt"></dict></span>
|
||
<span class="nt"></plist></span>
|
||
</pre></div>
|
||
</div>
|
||
<p><strong>For Mac OS X ≥ 10.8:</strong></p>
|
||
<p>One needs to add some system variables in <tt class="docutils literal"><span class="pre">~/.profile</span></tt>:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span><span class="nb">export</span> <span class="nv">ROOTSYS</span><span class="o">=</span><span class="nv">$HOME</span>/Applications/root/root_exec
|
||
<span class="nb">export</span> <span class="nv">MUSRFITPATH</span><span class="o">=</span><span class="nv">$ROOTSYS</span>/bin
|
||
<span class="nb">export</span> <span class="nv">PATH</span><span class="o">=</span><span class="nv">$ROOTSYS</span>/bin:<span class="nv">$QTDIR</span>/bin:<span class="nv">$PATH</span>
|
||
<span class="nb">export</span> <span class="nv">LD_LIBRARY_PATH</span><span class="o">=</span><span class="nv">$ROOTSYS</span>/lib:<span class="nv">$LD_LIBRARY_PATH</span>
|
||
|
||
launchctl setenv ROOTSYS <span class="nv">$ROOTSYS</span>
|
||
launchctl setenv MUSRFITPATH <span class="nv">$MUSRFITPATH</span>
|
||
launchctl setenv PATH <span class="nv">$PATH</span>
|
||
launchctl setenv LD_LIBRARY_PATH <span class="nv">$LD_LIBRARY_PATH</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>After this you will need to “execute” <tt class="docutils literal"><span class="pre">.profile</span></tt> before proceeding:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">source</span> <span class="nv">$HOME</span>/.profile
|
||
</pre></div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="section" id="requirements-fink">
|
||
<span id="index-32"></span><h3>Requirements (Fink)<a class="headerlink" href="#requirements-fink" title="Permalink to this headline">¶</a></h3>
|
||
<p>Before proceeding with the usage of the <a class="reference external" href="http://www.finkproject.org/">Fink</a> system first a few useful tools provided by Apple together with OS X (on the installation DVD/CDs) should be installed:</p>
|
||
<dl class="docutils">
|
||
<dt><strong>Xcode</strong></dt>
|
||
<dd><p class="first">Useful developer tools including for instance the GNU compiler collection. It can be installed via the Apple App store.
|
||
Starting from <tt class="docutils literal"><span class="pre">XCode</span></tt> ≥ 4.3 the command line tools need to be installed manually. The necessary command line tools
|
||
can be installed via the following commands entered in the terminal</p>
|
||
<div class="last highlight-bash"><div class="highlight"><pre><span></span>$ xcode-select --install
|
||
$ sudo xcodebuild -license
|
||
</pre></div>
|
||
</div>
|
||
</dd>
|
||
<dt><strong>X11</strong></dt>
|
||
<dd>The X-window system is automatically installed on 10.5 Leopard and 10.6 Snow Leopard. For some other versions you also
|
||
will need to install <cite>XQuartz <http://xquartz.macosforge.org/trac></cite>. If <tt class="docutils literal"><span class="pre">ROOT</span></tt> runs without <tt class="docutils literal"><span class="pre">XQuartz</span></tt> <em>do not</em>
|
||
install it.</dd>
|
||
</dl>
|
||
<p>After installing the <tt class="docutils literal"><span class="pre">Xcode</span></tt> tools go to the <a class="reference external" href="http://www.finkproject.org/download/index.php?phpLang=en">Fink download page</a>,
|
||
download the installer for your system and follow the installation instructions on the page. By default the Fink system is
|
||
installed under <tt class="docutils literal"><span class="pre">/sw</span></tt>. After the basic setup make sure that in <tt class="docutils literal"><span class="pre">/sw/etc/fink.conf</span></tt> the line starting with Trees reads like:</p>
|
||
<div class="highlight-python"><div class="highlight"><pre><span></span>Trees: local/main stable/main stable/crypto unstable/main
|
||
</pre></div>
|
||
</div>
|
||
<p>After applying the changes above to the configuration file, the Fink core system should be upgraded to its newest version by typing in a terminal:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ sudo fink selfupdate
|
||
</pre></div>
|
||
</div>
|
||
<p>Then the Fink system should be set up and can be used to install additional software.
|
||
The Fink installer package also contains a graphical user interface called FinkCommander and it is
|
||
suggested to use that for installing the following packages (or packages with revisions close to the following) — it
|
||
is necessary to compile a few packages from source since no binary packages are available, however, this is done
|
||
automatically by the FinkCommander after you have chosen the software packages for installation:</p>
|
||
<div class="highlight-python"><div class="highlight"><pre><span></span>autoconf automake cmake boost1.63-nopython boost1.63.nopython-shlibs fftw3 fftw3-shlibs gsl gsl-shlibs
|
||
libtool2 libtool2-shlibs libxml2 libxml2-bin libxml2-shlibs pkgconfig qt5-mac-qtbase qt5-mac-qtbase-dev-tools
|
||
qt5-mac-qtsvg qt5-mac-qtsvg-shlibs qt5-mac-qtwebengine qt5-mac-qtwebengine-shlibs qt5-mac-qtwebenginecore-shlibs
|
||
qt5-mac-qtwebenginewidgets-shlibs
|
||
</pre></div>
|
||
</div>
|
||
<p>Under OS X 10.6 Snow Leopard it will <em>not</em> be possible to install <tt class="docutils literal"><span class="pre">qt3mac</span></tt> since the system is by default a 64-bit
|
||
system and the old <tt class="docutils literal"><span class="pre">qt3-mac</span></tt> depends on software which is only available for 32-bit systems. It is suggested to
|
||
install <tt class="docutils literal"><span class="pre">qt5-mac</span></tt> instead and use <tt class="docutils literal"><span class="pre">musredit</span></tt>.</p>
|
||
<p>Also, due to some not fulfilled dependencies, it might not be possible to install FFTW3 through Fink. In this case
|
||
(<em>and ONLY in THIS case</em>) simply download the FFTW3 source code from its download page and install it from a terminal
|
||
using the following commands (for the FFTW version 3.x.y):</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ tar xz fftw-3.x.y
|
||
$ <span class="nb">cd</span> fftw-3.x.y
|
||
$ ./configure --enable-single --enable-shared --enable-threads --prefix<span class="o">=</span>/usr/local
|
||
$ make
|
||
$ sudo make install
|
||
</pre></div>
|
||
</div>
|
||
<p>Since later on the boost header files should be used and in the standard Fink installation these are found at a version
|
||
specific location, the later handling will be easier if a symbolic link to this files is created now in the terminal
|
||
(if it did not exist earlier), <em>e.g.</em>:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ ln -sf /sw/include/boost-x_yy_z/boost /sw/include/boost
|
||
</pre></div>
|
||
</div>
|
||
<p>where <tt class="docutils literal"><span class="pre">x_yy_z</span></tt> has to be substituted by the correct version number, <em>e.g.</em> <tt class="docutils literal"><span class="pre">1_63_0</span></tt>.</p>
|
||
<div class="section" id="index-33">
|
||
<span id="id17"></span><h4>Installation of NeXus requirements (optional)<a class="headerlink" href="#index-33" title="Permalink to this headline">¶</a></h4>
|
||
<p><em>Only</em> if <tt class="docutils literal"><span class="pre">musrfit</span></tt> should support reading data files in the <tt class="docutils literal"><span class="pre">NeXus</span></tt> format the further required
|
||
packages can be installed through Fink (check for the most recent versions):</p>
|
||
<div class="highlight-python"><div class="highlight"><pre><span></span>libjpeg hdf hdf5-cpp11 hdf5-cpp11-shlibs
|
||
</pre></div>
|
||
</div>
|
||
<p>Unfortunately, the <tt class="docutils literal"><span class="pre">minixml</span></tt> and <tt class="docutils literal"><span class="pre">NeXus</span></tt> libraries have to be compiled and installed directly from
|
||
the source code. Given the respective version numbers of 2.9 and 4.3.2 (which are subject to change with time)
|
||
this can be achieved for example by:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="c1"># first build Mini-XML</span>
|
||
$ <span class="nb">cd</span> <span class="nv">$HOME</span>/Applications
|
||
$ git clone https://github.com/michaelrsweet/mxml.git
|
||
$ <span class="nb">cd</span> mxml
|
||
$ ./configure --prefix<span class="o">=</span>/usr/local
|
||
$ make
|
||
$ sudo make install
|
||
$ <span class="c1"># second build NeXus</span>
|
||
$ <span class="nb">cd</span> ..
|
||
$ git clone https://github.com/nexusformat/code.git nexus/code
|
||
$ <span class="nb">cd</span> nexus
|
||
$ <span class="c1"># build NeXus out-of-source</span>
|
||
$ mkdir build
|
||
$ <span class="nb">cd</span> build
|
||
$ cmake ../code -DENABLE_HDF4<span class="o">=</span><span class="m">1</span> -DENABLE_HDF5<span class="o">=</span><span class="m">1</span> -DENABLE_MXML<span class="o">=</span><span class="m">1</span>
|
||
$ cmake --build ./ --clean-first -- -j8
|
||
$ sudo make install
|
||
</pre></div>
|
||
</div>
|
||
</div>
|
||
<div class="section" id="index-34">
|
||
<span id="id18"></span><h4>ROOT<a class="headerlink" href="#index-34" title="Permalink to this headline">¶</a></h4>
|
||
<p>ROOT 5.34/xx is supported as legacy version only and will likely to be dropped in 2018. <strong>The default now is ROOT 6.xx/yy!</strong></p>
|
||
<div class="section" id="id19">
|
||
<h5>ROOT installed via package installer<a class="headerlink" href="#id19" title="Permalink to this headline">¶</a></h5>
|
||
<p>The lazy way to get <tt class="docutils literal"><span class="pre">ROOT</span></tt> installed is via package installer. If your macOS is directly supported
|
||
by the <tt class="docutils literal"><span class="pre">ROOT</span></tt> people you can download the package installer from the <tt class="docutils literal"><span class="pre">ROOT</span></tt> <a class="reference external" href="https://root.cern.ch/downloading-root">download page</a>.
|
||
Choose the latest <tt class="docutils literal"><span class="pre">ROOT</span></tt> release and download you macOS version dmg-file, <em>e.g.</em> for macOS 10.13 (High Sierra)
|
||
it is at the time of writting <tt class="docutils literal"><span class="pre">root_v6.14.00.macosx64-10.13-clang91.dmg</span></tt>. After the installation
|
||
<tt class="docutils literal"><span class="pre">ROOT</span></tt> will be installed under <tt class="docutils literal"><span class="pre">/Application</span></tt> as owner root. In order to ease your life for the
|
||
steps to follow and assuming you are the only guy working on your Mac, you could change the owner and group of the <tt class="docutils literal"><span class="pre">ROOT</span></tt> directory:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> /Applications
|
||
$ sudo chown -R <username> root_v6.14.00
|
||
$ sudo chgrp -R staff root_v6.14.00
|
||
$ sudo ln -s root_v6.14.00 root
|
||
</pre></div>
|
||
</div>
|
||
</div>
|
||
<div class="section" id="id21">
|
||
<h5>ROOT installed from source<a class="headerlink" href="#id21" title="Permalink to this headline">¶</a></h5>
|
||
<p>The best way to get <tt class="docutils literal"><span class="pre">ROOT</span></tt> exactly the way needed for <tt class="docutils literal"><span class="pre">musrfit</span></tt> is to install it from source.
|
||
Before describing it, please make sure that you have installed all required packages listed under
|
||
<a class="reference internal" href="#supported-operating-systems"><em>Requested Software</em></a> (<em>e.g.</em> <tt class="docutils literal"><span class="pre">fftw</span></tt>, <tt class="docutils literal"><span class="pre">gsl</span></tt>, etc).</p>
|
||
<p>For the following it is assumed that <tt class="docutils literal"><span class="pre">ROOT</span></tt> shall be installed under <tt class="docutils literal"><span class="pre">$HOME/Applications</span></tt>. If you want
|
||
to install it somewhere else, just systematically replace the related terms of the following description.
|
||
For the following list of commands the ‘$’ will be given, the command prompt. Do not enter it! Also some
|
||
comments will be added starting with a ‘#’ which can be omitted. They are only there to explain what is going on.</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> <span class="nv">$HOME</span>/Applications
|
||
$ git clone http://root.cern.ch/git/root.git
|
||
$ <span class="nb">cd</span> root
|
||
$ git tag -l
|
||
$ <span class="c1"># git tag -l will list all available tags. In the next command choose the tag v6-10-xx</span>
|
||
$ <span class="c1"># where xx is the highest listed number, e.g. v6-14-00</span>
|
||
$ git checkout -b v6-14-00 v6-14-00
|
||
$ <span class="c1"># now ROOT is ready to be configured. Below you will find the minimal ROOT configuration needed.</span>
|
||
$ <span class="c1"># We will use the cmake out-of-source approach here.</span>
|
||
$ mkdir root_build
|
||
$ <span class="nb">cd</span> root_build
|
||
$ cmake ../ -Dgminimal<span class="o">=</span>ON -Dasimage<span class="o">=</span>ON -Dmathmore<span class="o">=</span>ON -Dminuit2<span class="o">=</span>ON -Dxml<span class="o">=</span>ON -DCMAKE_INSTALL_PREFIX<span class="o">=</span><span class="nv">$HOME</span>/Applications/root/root_exec
|
||
$ <span class="c1"># next will be the make. If running on a multicore CPU you can speed up tremendously by calling</span>
|
||
$ <span class="c1"># make with the option -j <number>, where <number> is the number of threads which you want to give,</span>
|
||
$ <span class="c1"># e.g. make -j8</span>
|
||
$ cmake --build ./ --clean-first -- -j8
|
||
$ <span class="c1"># make will take quite a while</span>
|
||
$ make install
|
||
</pre></div>
|
||
</div>
|
||
<p>For further details see <a class="reference external" href="https://root.cern.ch/building-root">Installing ROOT from Source</a>.</p>
|
||
</div>
|
||
<div class="section" id="id23">
|
||
<h5>Setting up Environment Variables for ROOT and musrfit<a class="headerlink" href="#id23" title="Permalink to this headline">¶</a></h5>
|
||
<p>Since Apple in its wisdom decided that programs started from a shell are treated differently than Apps if it is coming to
|
||
system variables, we need to work harder compared to a Linux system.</p>
|
||
<p><strong>For Mac OS X < 10.8:</strong></p>
|
||
<p>In order to finalize the <tt class="docutils literal"><span class="pre">ROOT</span></tt> installation and to prepare already the installation of <tt class="docutils literal"><span class="pre">musrfit</span></tt> and <tt class="docutils literal"><span class="pre">musredit</span></tt>
|
||
this is a good time for setting necessary environment variables for the use in Mac OS X. Here it assumed that you
|
||
installed <tt class="docutils literal"><span class="pre">ROOT</span></tt> from source. If you downloaded the binary package, you will need to adopt the paths accordingly.
|
||
Put the following lines (without the comments in parentheses and with the paths adjusted to your local installation)
|
||
into the file <tt class="docutils literal"><span class="pre">~/.MacOSX/environment.plist</span></tt> and re-login:</p>
|
||
<div class="highlight-xml"><div class="highlight"><pre><span></span><span class="cp"><?xml version="1.0" encoding="UTF-8"?></span>
|
||
<span class="cp"><!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd"></span>
|
||
<span class="nt"><plist</span> <span class="na">version=</span><span class="s">"1.0"</span><span class="nt">></span>
|
||
<span class="nt"><dict></span>
|
||
<span class="nt"><key></span>MUSRFITPATH<span class="nt"></key></span>
|
||
<span class="nt"><string></span>$HOME/Applications/root/root_exec/bin<span class="nt"></string></span> (where to find the musrfit executables)
|
||
<span class="nt"><key></span>QTDIR<span class="nt"></key></span>
|
||
<span class="nt"><string></span>/opt/local/lib/qt3mac<span class="nt"></string></span> (where to find Qt3 (for musrgui) or Qt4 (for musredit))
|
||
<span class="nt"><key></span>ROOTSYS<span class="nt"></key></span>
|
||
<span class="nt"><string></span>$HOME/Applications/root/root_exec<span class="nt"></string></span> (where to find the ROOT system)
|
||
<span class="nt"></dict></span>
|
||
<span class="nt"></plist></span>
|
||
</pre></div>
|
||
</div>
|
||
<p><strong>For Mac OS X ≥ 10.8:</strong></p>
|
||
<p>One needs to add some system variables in <tt class="docutils literal"><span class="pre">~/.profile</span></tt>:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span><span class="nb">export</span> <span class="nv">ROOTSYS</span><span class="o">=</span><span class="nv">$HOME</span>/Applications/root/root_exec
|
||
<span class="nb">export</span> <span class="nv">MUSRFITPATH</span><span class="o">=</span><span class="nv">$ROOTSYS</span>/bin
|
||
<span class="nb">export</span> <span class="nv">PATH</span><span class="o">=</span><span class="nv">$ROOTSYS</span>/bin:<span class="nv">$QTDIR</span>/bin:<span class="nv">$PATH</span>
|
||
<span class="nb">export</span> <span class="nv">LD_LIBRARY_PATH</span><span class="o">=</span><span class="nv">$ROOTSYS</span>/lib:<span class="nv">$LD_LIBRARY_PATH</span>
|
||
|
||
launchctl setenv ROOTSYS <span class="nv">$ROOTSYS</span>
|
||
launchctl setenv MUSRFITPATH <span class="nv">$MUSRFITPATH</span>
|
||
launchctl setenv PATH <span class="nv">$PATH</span>
|
||
launchctl setenv LD_LIBRARY_PATH <span class="nv">$LD_LIBRARY_PATH</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>After this you will need to “execute” <tt class="docutils literal"><span class="pre">.profile</span></tt> before proceeding:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">source</span> <span class="nv">$HOME</span>/.profile
|
||
</pre></div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="section" id="index-35">
|
||
<span id="id24"></span><h3>musrfit<a class="headerlink" href="#index-35" title="Permalink to this headline">¶</a></h3>
|
||
<p>First, the most recent source code should be downloaded. First, the most recent source code should be downloaded.
|
||
The preferred way of doing so is to clone the <tt class="docutils literal"><span class="pre">musrfit</span></tt> repository via git. Assuming the code should be located
|
||
in <tt class="docutils literal"><span class="pre">~/Applications/musrfit</span></tt> this is achieved most easily calling from the termin</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> ~/Applications
|
||
$ git clone https://bitbucket.org/muonspin/musrfit.git
|
||
$ <span class="c1"># Only if legacy ROOT 5.xx.yy is used include the next line</span>
|
||
$ <span class="nb">cd</span> musrfit<span class="p">;</span> git checkout root5
|
||
</pre></div>
|
||
</div>
|
||
<p>or</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> ~/Applications
|
||
$ git clone git://gitlab.psi.ch/nemu/musrfit.git
|
||
$ <span class="c1"># Only if legacy ROOT 5.xx.yy is used include the next line</span>
|
||
$ <span class="nb">cd</span> musrfit<span class="p">;</span> git checkout root5
|
||
</pre></div>
|
||
</div>
|
||
<p>If a local repository clone is already present, one can update it using:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> ~/Applications/musrfit
|
||
$ git pull
|
||
</pre></div>
|
||
</div>
|
||
<p>As an alternative (<em>if git is not available</em>), the source code can also be downloaded from the following
|
||
web-page: <a class="reference external" href="https://bitbucket.org/muonspin/musrfit/downloads">musrfit at bitbucket</a>.</p>
|
||
<div class="section" id="index-36">
|
||
<span id="id25"></span><h4>musrfit build with automake<a class="headerlink" href="#index-36" title="Permalink to this headline">¶</a></h4>
|
||
<p>After the source-code extraction the <tt class="docutils literal"><span class="pre">autogen.sh</span></tt> script is called to prepare the build environment.
|
||
If it has been executed successfully the <tt class="docutils literal"><span class="pre">configure</span></tt> script should be ready to collect all the information needed
|
||
to create the Makefiles. If <tt class="docutils literal"><span class="pre">musrfit</span></tt> should support <tt class="docutils literal"><span class="pre">NeXus</span></tt> data files this has to be enabled by specifying the
|
||
<tt class="docutils literal"><span class="pre">--enable-NeXus</span></tt> switch when calling configure. For an overview of all available options just call <tt class="docutils literal"><span class="pre">./configure</span> <span class="pre">--help</span></tt>.
|
||
Besides the standard options there are a few special options which should be mentioned here:</p>
|
||
<dl class="docutils">
|
||
<dt><strong>- -prefix</strong></dt>
|
||
<dd>Specify the installation prefix, <em>e.g.</em> <tt class="docutils literal"><span class="pre">$ROOTSYS</span></tt> if already defined (by default: <tt class="docutils literal"><span class="pre">/usr/local</span></tt>).</dd>
|
||
<dt><strong>- -with-rootsys</strong></dt>
|
||
<dd>Specify the top of the <tt class="docutils literal"><span class="pre">ROOT</span></tt> installation directory, <em>e.g.</em> <tt class="docutils literal"><span class="pre">$ROOTSYS</span></tt> if already defined.</dd>
|
||
<dt><strong>- -with-fftw3</strong></dt>
|
||
<dd>Specify the prefix of the <tt class="docutils literal"><span class="pre">FFTW3</span></tt> installation. <em>e.g.</em> <tt class="docutils literal"><span class="pre">/usr/local</span></tt> or <tt class="docutils literal"><span class="pre">/usr</span></tt>.</dd>
|
||
<dt><strong>- -with-gsl</strong></dt>
|
||
<dd>Set the prefix of the <tt class="docutils literal"><span class="pre">GSL</span></tt> installation, <em>e.g.</em> <tt class="docutils literal"><span class="pre">/usr/local</span></tt> or <tt class="docutils literal"><span class="pre">/usr</span></tt>.</dd>
|
||
<dt><strong>- -with-boostinc</strong></dt>
|
||
<dd>Set the path to the header files of the <tt class="docutils literal"><span class="pre">Boost</span></tt> installation, <em>e.g.</em> <tt class="docutils literal"><span class="pre">/usr/local/include</span></tt> or <tt class="docutils literal"><span class="pre">/usr/include</span></tt>.</dd>
|
||
<dt><strong>- -with-hdf4</strong></dt>
|
||
<dd>Set the prefix of the <tt class="docutils literal"><span class="pre">HDF4</span></tt> installation, <em>e.g.</em> <tt class="docutils literal"><span class="pre">/usr/local</span></tt> (only useful in conjunction with the <tt class="docutils literal"><span class="pre">NeXus</span></tt> support).</dd>
|
||
<dt><strong>- -with-hdf5</strong></dt>
|
||
<dd>Set the prefix of the <tt class="docutils literal"><span class="pre">HDF5</span></tt> installation, <em>e.g.</em> <tt class="docutils literal"><span class="pre">/usr</span></tt> (only useful in conjunction with the <tt class="docutils literal"><span class="pre">NeXus</span></tt> support).</dd>
|
||
<dt><strong>- -with-nexus</strong></dt>
|
||
<dd>Set the prefix of the <tt class="docutils literal"><span class="pre">NeXus</span></tt> installation, <em>e.g.</em> <tt class="docutils literal"><span class="pre">/usr/local</span></tt> (only useful in conjunction with the <tt class="docutils literal"><span class="pre">NeXus</span></tt> support).</dd>
|
||
<dt><strong>- -with-qt3</strong></dt>
|
||
<dd>Set the prefix of the <tt class="docutils literal"><span class="pre">Qt3</span></tt> installation, <em>e.g.</em> <tt class="docutils literal"><span class="pre">/usr/lib/qt-3.3</span></tt> (only useful in conjunction with building <tt class="docutils literal"><span class="pre">musrgui</span></tt>).</dd>
|
||
<dt><strong>- -with-qt4</strong></dt>
|
||
<dd>Set the prefix of the <tt class="docutils literal"><span class="pre">Qt4</span></tt> installation, <em>e.g.</em> <tt class="docutils literal"><span class="pre">/usr/lib/qt47</span></tt> (only useful in conjunction with building <tt class="docutils literal"><span class="pre">musredit</span></tt>).</dd>
|
||
<dt><strong>- -with-qt5</strong></dt>
|
||
<dd>Set the prefix of the <tt class="docutils literal"><span class="pre">Qt5</span></tt> installation, <em>e.g.</em> <tt class="docutils literal"><span class="pre">/usr/lib64</span></tt> (only useful in conjunction with building <tt class="docutils literal"><span class="pre">musredit</span></tt>).</dd>
|
||
<dt><strong>- -enable-NeXus</strong></dt>
|
||
<dd>Enable the support of <tt class="docutils literal"><span class="pre">NeXus</span></tt> data files (requires the <tt class="docutils literal"><span class="pre">HDF4</span></tt>, <tt class="docutils literal"><span class="pre">HDF5</span></tt> and <tt class="docutils literal"><span class="pre">NeXus</span></tt> libraries to be installed).</dd>
|
||
<dt><strong>- -disable-editor</strong></dt>
|
||
<dd>Disable the integrated building of <tt class="docutils literal"><span class="pre">musredit</span></tt>/<tt class="docutils literal"><span class="pre">musrgui</span></tt>.</dd>
|
||
<dt><strong>- -disable-omp</strong></dt>
|
||
<dd>Switches off the <a class="reference external" href="http://en.wikipedia.org/wiki/OpenMP">OpenMP</a> features of <tt class="docutils literal"><span class="pre">musrfit</span></tt> (parallelization of the <span class="math">\(\chi^2\)</span> calculation when compiled with GCC ≥ 4.2).</dd>
|
||
</dl>
|
||
<p>Normally it should not be necessary to make use of any of the options except for specifying the installation path with <tt class="docutils literal"><span class="pre">--prefix</span></tt>. The
|
||
other paths should be detected automatically. If this does not work for some reason the configure script will terminate and ask for the
|
||
information. When the configure script has been called successfully everything is ready for building the <tt class="docutils literal"><span class="pre">musrfit</span></tt> libraries and executables.
|
||
A standard installation sequence (without <tt class="docutils literal"><span class="pre">NeXus</span></tt> support) might then look like (In case the normal user has no write permissions to the
|
||
<tt class="docutils literal"><span class="pre">$ROOTSYS</span></tt> and the installation path the “make install” commands have to be executed as superuser.):</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> <span class="nv">$HOME</span>/Apps/musrfit
|
||
$ sh autogen.sh
|
||
$ ./configure --prefix<span class="o">=</span><span class="nv">$ROOTSYS</span>
|
||
$ make
|
||
$ make install
|
||
$ /sbin/ldconfig <span class="c1"># (as superuser)</span>
|
||
</pre></div>
|
||
</div>
|
||
</div>
|
||
<div class="section" id="index-37">
|
||
<span id="id27"></span><h4>musrfit build with cmake<a class="headerlink" href="#index-37" title="Permalink to this headline">¶</a></h4>
|
||
<p>Currently the following configuration switches for <tt class="docutils literal"><span class="pre">musrfit</span></tt> are available:</p>
|
||
<dl class="docutils">
|
||
<dt><strong>-DCMAKE_INSTALL_PREFIX=<prefix-path></strong></dt>
|
||
<dd>Specify the installation prefix, <em>i.e.</em> the place where <tt class="docutils literal"><span class="pre">musrfit</span></tt> shall be installed, <em>e.g.</em> <tt class="docutils literal"><span class="pre">$ROOTSYS</span></tt> if already defined (by default: <tt class="docutils literal"><span class="pre">/usr/local</span></tt>).</dd>
|
||
<dt><strong>-Dnexus=<value></strong></dt>
|
||
<dd>enable/disable the support of <tt class="docutils literal"><span class="pre">NeXus</span></tt> data files (requires the <tt class="docutils literal"><span class="pre">HDF4</span></tt>, <tt class="docutils literal"><span class="pre">HDF5</span></tt> and <tt class="docutils literal"><span class="pre">NeXus</span></tt> libraries to be installed).
|
||
<value>=1 enables <tt class="docutils literal"><span class="pre">NeXus</span></tt>, <value>=0 disables <tt class="docutils literal"><span class="pre">NeXus</span></tt>. The default setting, <em>i.e.</em> the switch is not provided is <tt class="docutils literal"><span class="pre">NeXus</span></tt> support is disabled.</dd>
|
||
<dt><strong>-DASlibs=<value></strong></dt>
|
||
<dd>enable/disable the <tt class="docutils literal"><span class="pre">ASlibs</span></tt>. <value>=1 enables the <tt class="docutils literal"><span class="pre">ASlibs</span></tt>, <value>=0 disables the <tt class="docutils literal"><span class="pre">ASlibs</span></tt>. The default setting, <em>i.e.</em> the
|
||
switch is not provided is <tt class="docutils literal"><span class="pre">ASlibs</span></tt> support is disabled. For details see Documentation of <a class="reference internal" href="user-libs.html#user-libs"><em>user libs</em></a>.</dd>
|
||
<dt><strong>-DBMWlibs=<value></strong></dt>
|
||
<dd>enable/disable the <tt class="docutils literal"><span class="pre">BMWlibs</span></tt>. <value>=1 enables the <tt class="docutils literal"><span class="pre">BMWlibs</span></tt>, <value>=0 disables the <tt class="docutils literal"><span class="pre">BMWlibs</span></tt>. The default setting, <em>i.e.</em> the
|
||
switch is not provided is <tt class="docutils literal"><span class="pre">BMWlibs</span></tt> support is disabled. For details see Documentation of <a class="reference internal" href="user-libs.html#user-libs"><em>user libs</em></a>.</dd>
|
||
<dt><strong>-DBNMRlibs=<value></strong></dt>
|
||
<dd>enable/disable the <tt class="docutils literal"><span class="pre">BNMRlibs</span></tt>. <value>=1 enables the <tt class="docutils literal"><span class="pre">BNMRlibs</span></tt>, <value>=0 disables the <tt class="docutils literal"><span class="pre">BNMRlibs</span></tt>. The default setting,
|
||
<em>i.e.</em> the switch is not provided is <tt class="docutils literal"><span class="pre">BNMRlibs</span></tt> support is disabled.</dd>
|
||
<dt><strong>-Dqt_based_tools=<value></strong></dt>
|
||
<dd>Will try to get <tt class="docutils literal"><span class="pre">musredit</span></tt>, <tt class="docutils literal"><span class="pre">musrWiz</span></tt>, <tt class="docutils literal"><span class="pre">musrStep</span></tt>, and <tt class="docutils literal"><span class="pre">mupp</span></tt> installed, if <tt class="docutils literal"><span class="pre">Qt</span></tt> is found.
|
||
By default this is enabled. Again <value>=0 means disabled, <value>=1 enabled.</dd>
|
||
<dt><strong>-Dqt_version=<value></strong></dt>
|
||
<dd>Allows to specify which <tt class="docutils literal"><span class="pre">Qt</span></tt> version shall be tried. <value> can take the values: <tt class="docutils literal"><span class="pre">AUTO,</span> <span class="pre">3,</span> <span class="pre">4,</span> <span class="pre">5</span></tt>.
|
||
If the value is set to <tt class="docutils literal"><span class="pre">AUTO</span></tt>, this highest installed version is chosen, otherwise the specified version is used.</dd>
|
||
<dt><strong>-Dtry_OpenMP=<value></strong></dt>
|
||
<dd>Will check if <tt class="docutils literal"><span class="pre">OpenMP</span></tt> support is possible, and if yes use it. The default is enabled</dd>
|
||
</dl>
|
||
<p>Normally it should not be necessary to make use of any of the options except for specifying the installation path with <tt class="docutils literal"><span class="pre">-DCMAKE_INSTALL_PREFIX</span></tt>.
|
||
<tt class="docutils literal"><span class="pre">musrfit</span></tt> build with <tt class="docutils literal"><span class="pre">cmake</span></tt> takes the <tt class="docutils literal"><span class="pre">out-of-source</span></tt> approach. Therefore a typical configuration / make / install process including
|
||
<tt class="docutils literal"><span class="pre">NeXus</span></tt> support would look like</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> <span class="nv">$HOME</span>/Apps/musrfit
|
||
$ mkdir build
|
||
$ <span class="nb">cd</span> build
|
||
$ cmake ../ -DCMAKE_INSTALL_PREFIX<span class="o">=</span><span class="nv">$ROOTSYS</span> -Dnexus<span class="o">=</span><span class="m">1</span>
|
||
<span class="c1"># below it is assumed that multiple cores are present, hence the -j8 option</span>
|
||
$ cmake --build ./ --clean-first -- -j8
|
||
$ make install
|
||
$ /sbin/ldconfig <span class="c1"># (as superuser)</span>
|
||
</pre></div>
|
||
</div>
|
||
</div>
|
||
<div class="section" id="id28">
|
||
<h4>musrfit last step of the installation<a class="headerlink" href="#id28" title="Permalink to this headline">¶</a></h4>
|
||
<p>In order to finish the installation of <tt class="docutils literal"><span class="pre">musrfit</span></tt> two more things should be done:</p>
|
||
<ul class="simple">
|
||
<li>Define the <tt class="docutils literal"><span class="pre">MUSRFITPATH</span></tt> environment variable containing the path to the <tt class="docutils literal"><span class="pre">musrfit</span></tt> executables and <tt class="docutils literal"><span class="pre">XML</span></tt> files.
|
||
<em>E.g.</em> if the location of the example above is used append the following line to the <tt class="docutils literal"><span class="pre">~/.bashrc</span></tt> and <tt class="docutils literal"><span class="pre">~/.bash_profile</span></tt>
|
||
(and then either restart the shell or call the same commands once more from the shell):</li>
|
||
</ul>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span><span class="nb">export</span> <span class="nv">MUSRFITPATH</span><span class="o">=</span><span class="nv">$ROOTSYS</span>/bin
|
||
</pre></div>
|
||
</div>
|
||
<ul class="simple">
|
||
<li>Adjust the paths where <tt class="docutils literal"><span class="pre">musrfit</span></tt> will search for data files in the installed <tt class="docutils literal"><span class="pre">musrfit_startup.xml</span></tt>. For
|
||
detailed information on this XML file refer to the <a class="reference internal" href="user-manual.html#musrfit-startup"><em>manual</em></a>.</li>
|
||
</ul>
|
||
</div>
|
||
</div>
|
||
<div class="section" id="index-38">
|
||
<span id="id29"></span><h3>musredit<a class="headerlink" href="#index-38" title="Permalink to this headline">¶</a></h3>
|
||
<p>In the latest version of <tt class="docutils literal"><span class="pre">musrfit</span></tt> the configure script tries to determine automatically the highest
|
||
available Qt version. In case this is found, the editor <tt class="docutils literal"><span class="pre">musredit</span></tt> is built already together with <tt class="docutils literal"><span class="pre">musrfit</span></tt>.
|
||
If not, one can try to call the configure script with the <strong>–with-qt5</strong> option (<tt class="docutils literal"><span class="pre">automake</span></tt>). <tt class="docutils literal"><span class="pre">cmake</span></tt> will
|
||
determine everthing automatically. To install this editor separately, <em>i.e.</em> by “hand” do</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> <span class="nv">$HOME</span>/Apps/musrfit/src/musredit_qt5
|
||
$ <span class="c1"># for some distributions you will need qmake-qt5 for the next command</span>
|
||
$ qmake musredit.pro
|
||
</pre></div>
|
||
</div>
|
||
<p>If everything went fine, <tt class="docutils literal"><span class="pre">musredit</span></tt> can be compiled and installed:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ make
|
||
$ make install
|
||
</pre></div>
|
||
</div>
|
||
<p>In case one does not like the executable <tt class="docutils literal"><span class="pre">musredit</span></tt> to be copied to the default installation directory
|
||
<tt class="docutils literal"><span class="pre">$ROOTSYS/bin</span></tt> the last make install can be skipped and the executable can be copied somewhere else instead.</p>
|
||
</div>
|
||
<div class="section" id="musrgui-obsolete">
|
||
<h3>musrgui (obsolete)<a class="headerlink" href="#musrgui-obsolete" title="Permalink to this headline">¶</a></h3>
|
||
<p>If Qt3 is set up the installation of the <tt class="docutils literal"><span class="pre">musrfit</span></tt> editor can be done as follows from within the shell:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> ~/Applications/musrfit/src/musrgui
|
||
$ qmake musrgui.pro
|
||
$ make
|
||
$ make install
|
||
</pre></div>
|
||
</div>
|
||
<p>The last command copies <tt class="docutils literal"><span class="pre">musrgui.app</span></tt> to the standard program directory <tt class="docutils literal"><span class="pre">/Applications</span></tt>.</p>
|
||
<p>Under some circumstances it might happen, that if <tt class="docutils literal"><span class="pre">musrgui</span></tt> was called from Finder the necessary libraries
|
||
for executing <tt class="docutils literal"><span class="pre">musrfit</span></tt> could not be found. In that case, the only workaround for the moment is to export
|
||
the environment variable <tt class="docutils literal"><span class="pre">DYLD_LIBRARY_PATH</span></tt> in the shell and call <tt class="docutils literal"><span class="pre">musrgui</span></tt> from a terminal! In order to
|
||
accomplish that, add the following lines to <tt class="docutils literal"><span class="pre">~/.profile</span></tt> and call <tt class="docutils literal"><span class="pre">musrgui</span></tt> with the specified command:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span><span class="nb">export</span> <span class="nv">DYLD_LIBRARY_PATH</span><span class="o">=</span>/opt/root-system/lib:/sw/lib:<span class="nv">$DYLD_LIBRARY_PATH</span>
|
||
<span class="nb">alias</span> <span class="nv">mgui</span><span class="o">=</span><span class="s1">'/Applications/musrgui.app/Contents/MacOS/musrgui'</span>
|
||
</pre></div>
|
||
</div>
|
||
</div>
|
||
<div class="section" id="id30">
|
||
<h3>Check the installation<a class="headerlink" href="#id30" title="Permalink to this headline">¶</a></h3>
|
||
<p>In order to perform a quick test for finding out if the installation has been completed successfully, a few msr
|
||
files together with the corresponding data files can be found in the musrfit source tree at <tt class="docutils literal"><span class="pre">doc/examples/</span></tt>.
|
||
If <tt class="docutils literal"><span class="pre">musrgui</span></tt> has been installed, just open one of the <tt class="docutils literal"><span class="pre">test-*.msr</span></tt> files in the editor and test the <tt class="docutils literal"><span class="pre">musrfit</span></tt>
|
||
functionalities. Otherwise, if only the terminal should be used, as an initial test for instance the following could be done:</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> ~/Applications/musrfit/doc/examples
|
||
$ musrview test-histo-ROOT-NPP.msr
|
||
</pre></div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="sphinxsidebar">
|
||
<div class="sphinxsidebarwrapper">
|
||
<h3><a href="index.html">Table Of Contents</a></h3>
|
||
<ul>
|
||
<li><a class="reference internal" href="#">Setting up <tt class="docutils literal"><span class="pre">musrfit</span></tt> on Different Platforms</a><ul>
|
||
<li><a class="reference internal" href="#supported-operating-systems-and-software-requirements">Supported Operating Systems and Software Requirements</a></li>
|
||
<li><a class="reference internal" href="#os-restrictions">OS Restrictions</a></li>
|
||
<li><a class="reference internal" href="#gnu-linux">GNU/Linux</a><ul>
|
||
<li><a class="reference internal" href="#requirements">Requirements</a><ul>
|
||
<li><a class="reference internal" href="#everything-but-root-and-nexus">Everything but ROOT and NeXus</a></li>
|
||
<li><a class="reference internal" href="#installation-of-nexus-requirements-optional">Installation of NeXus requirements (optional)</a></li>
|
||
<li><a class="reference internal" href="#index-16">ROOT</a></li>
|
||
</ul>
|
||
</li>
|
||
<li><a class="reference internal" href="#musrfit">musrfit</a><ul>
|
||
<li><a class="reference internal" href="#musrfit-build-with-automake">musrfit build with automake</a></li>
|
||
<li><a class="reference internal" href="#musrfit-build-with-cmake">musrfit build with cmake</a></li>
|
||
<li><a class="reference internal" href="#musrfit-last-step-of-the-installation">musrfit last step of the installation</a></li>
|
||
</ul>
|
||
</li>
|
||
<li><a class="reference internal" href="#musredit">musredit</a></li>
|
||
<li><a class="reference internal" href="#musrgui-obsolate">musrgui (obsolate)</a></li>
|
||
<li><a class="reference internal" href="#check-the-installation">Check the installation</a></li>
|
||
</ul>
|
||
</li>
|
||
<li><a class="reference internal" href="#ms-windows">MS Windows</a><ul>
|
||
<li><a class="reference internal" href="#id5">Requirements</a><ul>
|
||
<li><a class="reference internal" href="#setting-up-cygwin">Setting up Cygwin</a></li>
|
||
<li><a class="reference internal" href="#id6">Everything but ROOT and NeXus</a></li>
|
||
<li><a class="reference internal" href="#index-23">Installation of NeXus requirements (optional)</a></li>
|
||
<li><a class="reference internal" href="#index-24">ROOT</a></li>
|
||
</ul>
|
||
</li>
|
||
<li><a class="reference internal" href="#index-25">musrfit</a><ul>
|
||
<li><a class="reference internal" href="#index-26">musrfit build with automake</a></li>
|
||
<li><a class="reference internal" href="#index-27">musrfit build with cmake</a></li>
|
||
</ul>
|
||
</li>
|
||
<li><a class="reference internal" href="#index-28">musredit</a></li>
|
||
<li><a class="reference internal" href="#id13">musrgui (obsolate)</a></li>
|
||
<li><a class="reference internal" href="#id14">Check the installation</a></li>
|
||
<li><a class="reference internal" href="#potential-problems">Potential Problems</a></li>
|
||
</ul>
|
||
</li>
|
||
<li><a class="reference internal" href="#mac-os-x-macos">Mac OS X / macOS</a><ul>
|
||
<li><a class="reference internal" href="#requirements-macports">Requirements (MacPorts)</a><ul>
|
||
<li><a class="reference internal" href="#index-30">Installation of NeXus requirements (optional)</a></li>
|
||
<li><a class="reference internal" href="#index-31">ROOT</a></li>
|
||
</ul>
|
||
</li>
|
||
<li><a class="reference internal" href="#requirements-fink">Requirements (Fink)</a><ul>
|
||
<li><a class="reference internal" href="#index-33">Installation of NeXus requirements (optional)</a></li>
|
||
<li><a class="reference internal" href="#index-34">ROOT</a></li>
|
||
</ul>
|
||
</li>
|
||
<li><a class="reference internal" href="#index-35">musrfit</a><ul>
|
||
<li><a class="reference internal" href="#index-36">musrfit build with automake</a></li>
|
||
<li><a class="reference internal" href="#index-37">musrfit build with cmake</a></li>
|
||
<li><a class="reference internal" href="#id28">musrfit last step of the installation</a></li>
|
||
</ul>
|
||
</li>
|
||
<li><a class="reference internal" href="#index-38">musredit</a></li>
|
||
<li><a class="reference internal" href="#musrgui-obsolete">musrgui (obsolete)</a></li>
|
||
<li><a class="reference internal" href="#id30">Check the installation</a></li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
|
||
<h4>Previous topic</h4>
|
||
<p class="topless"><a href="user-libs.html"
|
||
title="previous chapter">Documentation of user libs (user functions)</a></p>
|
||
<h4>Next topic</h4>
|
||
<p class="topless"><a href="setup-dks.html"
|
||
title="next chapter">Setting up <tt class="docutils literal"><span class="pre">musrfit</span></tt> / <tt class="docutils literal"><span class="pre">DKS</span></tt>: High Speed Fitting with GPU’s</a></p>
|
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© Copyright 2018, Andreas Suter.
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Last updated on Oct 15, 2018.
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