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2019-07-24 10:15:15 +02:00
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@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>Setting up musrfit on Different Platforms &mdash; musrfit 1.5.0 documentation</title>
<title>Setting up musrfit on Different Platforms &mdash; musrfit 1.5.1 documentation</title>
<link rel="stylesheet" href="_static/nature.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
VERSION: '1.5.0',
VERSION: '1.5.1',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@ -24,7 +24,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
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</head>
@ -41,7 +41,7 @@
<li class="right" >
<a href="user-libs.html" title="Documentation of user libs (user functions)"
accesskey="P">previous</a> |</li>
<li><a href="index.html">musrfit 1.5.0 documentation</a> &raquo;</li>
<li><a href="index.html">musrfit 1.5.1 documentation</a> &raquo;</li>
</ul>
</div>
@ -96,7 +96,8 @@ their header packages:</p>
</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>
<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>).
Currently the <tt class="docutils literal"><span class="pre">MXML</span></tt> support in <tt class="docutils literal"><span class="pre">NeXus</span></tt> is broken and hence you will <strong>not</strong> need to install <tt class="docutils literal"><span class="pre">minixml</span></tt> for the time being.</dd>
</dl>
<dl class="docutils" id="index-10">
<dt><strong>NeXus</strong></dt>
@ -177,24 +178,21 @@ the source code from the corresponding website, or to clone the git repo. If you
<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&#8217;s
GNU/Linux distribution or if this is not the case, the packages can be installed from the source code. The necessary
packages to build <tt class="docutils literal"><span class="pre">NeXus</span></tt> are <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>. This means, for a rpm-package based distro try something like:</p>
GNU/Linux distribution or if this is not the case, the packages can be installed from the source code. In principle
NeXus should support <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>. At the time of this writing, the <tt class="docutils literal"><span class="pre">MXML</span></tt> support in the
NeXus project is broken, and <tt class="docutils literal"><span class="pre">HDF4</span></tt> is outdated on most platforms, hence currently only the <tt class="docutils literal"><span class="pre">HDF5</span></tt> binding is
used. Hence, the necessary package to build <tt class="docutils literal"><span class="pre">NeXus</span></tt> is <tt class="docutils literal"><span class="pre">HDF5</span></tt>. This means, for a rpm-package based distro try something like:</p>
<blockquote>
<div><div class="highlight-bash"><div class="highlight"><pre><span></span>$ yum install mxml-devel hdf-devel hdf5-devel
<div><div class="highlight-bash"><div class="highlight"><pre><span></span>$ yum install hdf5-devel
</pre></div>
</div>
</div></blockquote>
<p>and on a deb-package based distro try something like:</p>
<blockquote>
<div><div class="highlight-bash"><div class="highlight"><pre><span></span>$ apt-get install libmxml-dev libhdf4-dev libhdf5-dev
<div><div class="highlight-bash"><div class="highlight"><pre><span></span>$ apt-get install libhdf5-dev
</pre></div>
</div>
</div></blockquote>
<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>
@ -208,10 +206,7 @@ $ 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 -DENABLE_HDF5<span class="o">=</span><span class="m">1</span> -DENABLE_HDF4<span class="o">=</span><span class="m">0</span> -DENABLE_MXML<span class="o">=</span><span class="m">0</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
@ -500,10 +495,7 @@ the later handling will be easier if a symbolic link to these files is created n
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>
<p><strong>Only NeXus Version ≥ 4.4 is support!</strong></p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span>
$ mkdir nexus
$ <span class="nb">cd</span> nexus
@ -513,18 +505,6 @@ $ ./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
@ -533,7 +513,7 @@ $ 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
$ cmake -DENABLE_HDF5<span class="o">=</span><span class="m">1</span> -DENABLE_HDF4<span class="o">=</span><span class="m">0</span> -DENABLE_MXML<span class="o">=</span><span class="m">0</span> ../code
$ make
$ make install
</pre></div>
@ -770,20 +750,12 @@ please change over to <tt class="docutils literal"><span class="pre">musredit</s
<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>
<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
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ sudo port -v install 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>
<p><strong>Only NeXus Version ≥ 4.4 is support!</strong></p>
<p>To get things compiled do:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <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
@ -791,7 +763,7 @@ $ <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
$ cmake -DENABLE_HDF5<span class="o">=</span><span class="m">1</span> -DENABLE_HDF4<span class="o">=</span><span class="m">0</span> -DENABLE_MXML<span class="o">=</span><span class="m">0</span> ../code
$ make
$ sudo make install
</pre></div>
@ -956,24 +928,17 @@ 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)
<p>Unfortunately, the <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 number 4.4 (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>
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="c1"># 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 ../code -DENABLE_HDF5<span class="o">=</span><span class="m">1</span> -DENABLE_HDF4<span class="o">=</span><span class="m">0</span> -DENABLE_MXML<span class="o">=</span><span class="m">0</span>
$ cmake --build ./ --clean-first -- -j8
$ sudo make install
</pre></div>
@ -1315,12 +1280,12 @@ $ musrview test-histo-ROOT-NPP.msr
<li class="right" >
<a href="user-libs.html" title="Documentation of user libs (user functions)"
>previous</a> |</li>
<li><a href="index.html">musrfit 1.5.0 documentation</a> &raquo;</li>
<li><a href="index.html">musrfit 1.5.1 documentation</a> &raquo;</li>
</ul>
</div>
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&copy; Copyright 2019, Andreas Suter.
Last updated on May 15, 2019.
Last updated on Jul 24, 2019.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
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