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add option to musrfit that the user can choose from the command line the number of threads to be used for OpenMP. Updated the docu accordingly.

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suter_a
2021-10-02 19:41:45 +02:00
parent 251cf6b6f8
commit 1341cfb8fe
32 changed files with 142 additions and 965 deletions
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doc/html/setup-standard.html
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@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
VERSION: '1.7.1',
VERSION: '1.7.4',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@ -117,9 +117,9 @@ Currently the <tt class="docutils literal"><span class="pre">MXML</span></tt> su
<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>,
<a class="reference external" href="https://de.manjaro.org/">manjaro</a>, and <a class="reference external" href="https://antergos.com/">antergos</a>.</dd>
and <cite>manjaro &lt;https://de.manjaro.org/&gt;</cite>.</dd>
<dt><strong>Mac OS X/macOS</strong></dt>
<dd>No serious problems are currently known for macOS ≥ 10.6.</dd>
<dd>No serious problems are currently known for macOS ≥ 10.6. <tt class="docutils literal"><span class="pre">musrfit</span></tt> is ARM M1 ready.</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">
@ -141,34 +141,35 @@ the distributor and could be easily installed in the form of binary packages. If
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 &#8216;$&#8217; it is the shell prompt of your system):</p>
<p>For <strong>Qt4</strong>:</p>
<p>For <strong>Qt4</strong> (deprecated):</p>
<blockquote>
<div><div class="highlight-bash"><div class="highlight"><pre><span></span>$ 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>
<p>For <strong>Qt5/Qt6</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
</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>If using <tt class="docutils literal"><span class="pre">Qt6</span></tt> replace <tt class="docutils literal"><span class="pre">qt5-qtbase-devel</span> <span class="pre">qt5-qtsvg-devel</span></tt> by <tt class="docutils literal"><span class="pre">qt6-qtbase-devel</span> <span class="pre">qt6-qtsvg-devel</span></tt></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>
<p>For <strong>Qt4</strong> (deprecated):</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
<div><div class="highlight-bash"><div class="highlight"><pre><span></span>$ apt-get install git cmake libboost-dev libboost-filesystem-dev libboost-system-dev libgsl-dev libfftw3-dev libxml2-dev libqt4-dev libqtwebkit-dev
</pre></div>
</div>
</div></blockquote>
<p>For <strong>Qt5</strong>:</p>
<p>For <strong>Qt5/Qt6</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
<div><div class="highlight-bash"><div class="highlight"><pre><span></span>$ apt-get install git cmake libboost-dev libboost-filesystem-dev libboost-system-dev libgsl-dev libfftw3-dev libxml2-dev qt5-default qtbase5-dev libqt5svg5-dev
</pre></div>
</div>
</div></blockquote>
<p>If using <tt class="docutils literal"><span class="pre">Qt6</span></tt> replace <tt class="docutils literal"><span class="pre">qt5-default</span> <span class="pre">qtbase5-dev</span> <span class="pre">libqt5svg5-dev</span></tt> by <tt class="docutils literal"><span class="pre">qt6-default</span> <span class="pre">qtbase6-dev</span> <span class="pre">libqt6svg6-dev</span></tt></p>
<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>
@ -382,8 +383,8 @@ detailed information on this XML file refer to the <a class="reference internal"
<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>.</p>
</div>
<div class="section" id="musrgui-depreciated">
<h3>musrgui (depreciated)<a class="headerlink" href="#musrgui-depreciated" title="Permalink to this headline"></a></h3>
<div class="section" id="musrgui-deprecated">
<h3>musrgui (deprecated)<a class="headerlink" href="#musrgui-deprecated" 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>
@ -638,14 +639,14 @@ musredit <span class="p">&amp;</span>
</pre></div>
</div>
</div>
<div class="section" id="id12">
<h3>musrgui (depreciated)<a class="headerlink" href="#id12" title="Permalink to this headline"></a></h3>
<div class="section" id="musrgui-depreciated">
<h3>musrgui (depreciated)<a class="headerlink" href="#musrgui-depreciated" 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="id13">
<h3>Check the installation<a class="headerlink" href="#id13" title="Permalink to this headline"></a></h3>
<div class="section" id="id12">
<h3>Check the installation<a class="headerlink" href="#id12" 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/.
@ -673,8 +674,8 @@ and <tt class="docutils literal"><span class="pre">C:\cygwin\bin\bash.exe</span>
<h2>Mac OS X / macOS<a class="headerlink" href="#mac-os-x-macos" title="Permalink to this headline"></a></h2>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">macOS 11 alias <strong>Big Sur</strong>: <tt class="docutils literal"><span class="pre">musrfit</span></tt> is ready for <strong>Big Sur</strong> on Intel based macs. The <tt class="docutils literal"><span class="pre">DKS</span></tt> version of
<tt class="docutils literal"><span class="pre">musrfit</span></tt> for macOS <strong>Big Sur</strong> is ready as well.</p>
<p class="last">macOS 11.3 alias <strong>Big Sur</strong>: <tt class="docutils literal"><span class="pre">musrfit</span></tt> is ready for <strong>Big Sur</strong> on Intel <strong>and</strong> M1 (Apple Silicon) based macs, both running natively.
The <tt class="docutils literal"><span class="pre">DKS</span></tt> version of <tt class="docutils literal"><span class="pre">musrfit</span></tt> for macOS <strong>Big Sur</strong> is ready as well.</p>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
@ -751,7 +752,7 @@ add a new line pointing to your local copy, <em>e.g.</em></p>
<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-28">
<span id="id14"></span><h4>Installation of NeXus requirements (optional)<a class="headerlink" href="#index-28" title="Permalink to this headline"></a></h4>
<span id="id13"></span><h4>Installation of NeXus requirements (optional)<a class="headerlink" href="#index-28" 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>
@ -773,7 +774,7 @@ $ sudo make install
</div>
</div>
<div class="section" id="index-29">
<span id="id15"></span><h4>ROOT<a class="headerlink" href="#index-29" title="Permalink to this headline"></a></h4>
<span id="id14"></span><h4>ROOT<a class="headerlink" href="#index-29" title="Permalink to this headline"></a></h4>
<p><strong>The default ROOT version is based on 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>
@ -943,7 +944,7 @@ specific location, the later handling will be easier if a symbolic link to this
</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-31">
<span id="id17"></span><h4>Installation of NeXus requirements (optional)<a class="headerlink" href="#index-31" title="Permalink to this headline"></a></h4>
<span id="id16"></span><h4>Installation of NeXus requirements (optional)<a class="headerlink" href="#index-31" 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
@ -966,10 +967,10 @@ $ sudo make install
</div>
</div>
<div class="section" id="index-32">
<span id="id18"></span><h4>ROOT<a class="headerlink" href="#index-32" title="Permalink to this headline"></a></h4>
<span id="id17"></span><h4>ROOT<a class="headerlink" href="#index-32" title="Permalink to this headline"></a></h4>
<p><strong>The default ROOT version is based on 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>
<div class="section" id="id18">
<h5>ROOT installed via package installer<a class="headerlink" href="#id18" 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)
@ -983,8 +984,8 @@ $ sudo ln -s root_v6.16.00 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>
<div class="section" id="id20">
<h5>ROOT installed from source<a class="headerlink" href="#id20" 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>
@ -1014,8 +1015,8 @@ $ make install
</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>
<div class="section" id="id22">
<h5>Setting up Environment Variables for ROOT and musrfit<a class="headerlink" href="#id22" 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 &lt; 10.8:</strong></p>
@ -1059,7 +1060,7 @@ launchctl setenv LD_LIBRARY_PATH <span class="nv">$LD_LIBRARY_PATH</span>
</div>
</div>
<div class="section" id="index-33">
<span id="id24"></span><h3>musrfit<a class="headerlink" href="#index-33" title="Permalink to this headline"></a></h3>
<span id="id23"></span><h3>musrfit<a class="headerlink" href="#index-33" 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>
@ -1082,7 +1083,7 @@ $ git pull
<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-34">
<span id="id25"></span><h4>musrfit build with cmake<a class="headerlink" href="#index-34" title="Permalink to this headline"></a></h4>
<span id="id24"></span><h4>musrfit build with cmake<a class="headerlink" href="#index-34" 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=&lt;prefix-path&gt;</strong></dt>
@ -1122,8 +1123,8 @@ $ /sbin/ldconfig <span class="c1"># (as superus
</pre></div>
</div>
</div>
<div class="section" id="id26">
<h4>musrfit last step of the installation<a class="headerlink" href="#id26" title="Permalink to this headline"></a></h4>
<div class="section" id="id25">
<h4>musrfit last step of the installation<a class="headerlink" href="#id25" 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.
@ -1140,7 +1141,7 @@ detailed information on this XML file refer to the <a class="reference internal"
</div>
</div>
<div class="section" id="index-35">
<span id="id27"></span><h3>musredit<a class="headerlink" href="#index-35" title="Permalink to this headline"></a></h3>
<span id="id26"></span><h3>musredit<a class="headerlink" href="#index-35" 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, try the following:</p>
@ -1176,8 +1177,8 @@ accomplish that, add the following lines to <tt class="docutils literal"><span c
</pre></div>
</div>
</div>
<div class="section" id="id28">
<h3>Check the installation<a class="headerlink" href="#id28" title="Permalink to this headline"></a></h3>
<div class="section" id="id27">
<h3>Check the installation<a class="headerlink" href="#id27" 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>
@ -1214,7 +1215,7 @@ $ musrview test-histo-ROOT-NPP.msr
</ul>
</li>
<li><a class="reference internal" href="#musredit">musredit</a></li>
<li><a class="reference internal" href="#musrgui-depreciated">musrgui (depreciated)</a></li>
<li><a class="reference internal" href="#musrgui-deprecated">musrgui (deprecated)</a></li>
<li><a class="reference internal" href="#check-the-installation">Check the installation</a></li>
</ul>
</li>
@ -1231,8 +1232,8 @@ $ musrview test-histo-ROOT-NPP.msr
</ul>
</li>
<li><a class="reference internal" href="#index-26">musredit</a></li>
<li><a class="reference internal" href="#id12">musrgui (depreciated)</a></li>
<li><a class="reference internal" href="#id13">Check the installation</a></li>
<li><a class="reference internal" href="#musrgui-depreciated">musrgui (depreciated)</a></li>
<li><a class="reference internal" href="#id12">Check the installation</a></li>
<li><a class="reference internal" href="#potential-problems">Potential Problems</a></li>
</ul>
</li>
@ -1250,12 +1251,12 @@ $ musrview test-histo-ROOT-NPP.msr
</li>
<li><a class="reference internal" href="#index-33">musrfit</a><ul>
<li><a class="reference internal" href="#index-34">musrfit build with cmake</a></li>
<li><a class="reference internal" href="#id26">musrfit last step of the installation</a></li>
<li><a class="reference internal" href="#id25">musrfit last step of the installation</a></li>
</ul>
</li>
<li><a class="reference internal" href="#index-35">musredit</a></li>
<li><a class="reference internal" href="#musrgui-obsolete">musrgui (obsolete)</a></li>
<li><a class="reference internal" href="#id28">Check the installation</a></li>
<li><a class="reference internal" href="#id27">Check the installation</a></li>
</ul>
</li>
</ul>
@ -1307,8 +1308,8 @@ $ musrview test-histo-ROOT-NPP.msr
</div>
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&copy; Copyright 2021, Andreas Suter.
Last updated on Apr 09, 2021.
Last updated on Aug 10, 2021.
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