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Minor documentation update

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Bastian M. Wojek
2011-08-28 10:00:40 +00:00
parent d201408728
commit a3bfa4e70b
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doc/html/user/MUSR/MusrFitSetup.html
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@ -1,7 +1,7 @@
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@ -21,7 +21,7 @@
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@ -190,7 +190,7 @@ Additionally, <font color="#ff0000">only if</font> <code>musrfit</code> should s
</dd></dl>
<p></p>
If optionally the editor and graphical user interface <code><a href="MusrGui.html">musrgui</a></code> / <code><a href="MusrGui.html">musredit</a></code> is going to be installed there is one further requirement: <dl>
<dt> <a href="http://www.qtsoftware.com/" target="_top">Qt</a> </dt><dd> A cross-platform application and user interface framework. <em>Required version &#8805; 3.3 &#38; &#8810; 4.0 (<code>musrgui</code>) <strong>OR</strong> &#8805; 4.6 (<code>musredit</code>)</em>
<dt> <a href="http://qt.nokia.com/" target="_top">Qt</a> </dt><dd> A cross-platform application and user interface framework. <em>Required version &#8805; 3.3 &#38; &#8810; 4.0 (<code>musrgui</code>) <strong>OR</strong> &#8805; 4.6 (<code>musredit</code>)</em>
</dd></dl>
<p></p>
Each of the following sections focusing on the installation of <code>musrfit</code> on the different operating systems will also give a brief introduction on the installation of the requirements before the actual <code>musrfit</code> installation is described.
@ -234,7 +234,7 @@ Even though there might exist binary packages for the <code>NeXus</code> library
The <code>ROOT</code> system may or may not be part of the GNU/Linux distribution. If it is, it should be checked that the provided binaries are of a recent version and then these in principle can be installed using a package manager as described above. <br>
In case the distribution provides no or only outdated binary packages there are the following possibilities: <ul>
<li> Visit the <code>ROOT</code> <a href="http://root.cern.ch/drupal/content/downloading-root" target="_top">web page</a> and download the packed precompiled binary version matching best the GNU/Linux distribution. Then unpack the bundle to its final destination.
</li> <li> If there is no precompiled binary version of <code>ROOT</code> available for your system or e.g. <code>ROOT</code> should be compiled with another version of <code>GCC</code> visit the <a href="http://root.cern.ch/drupal/content/downloading-root" target="_top">web page</a> and download the 'complete source tree for all systems'. Then unpack this source tree to its destination (e.g. /opt/root-system)<a name="FootNote1text"></a><span class="FootNoteTextLink" title="In case only a single user is working at the machine it might be considerable to change the ownership of the &#61;ROOT&#61; folder so that the user has easy write access to this directory&#58; &#60;&#33;&#45;&#45;&#0;verbatim3506&#0;&#45;&#45;&#62;"><a href="#FootNote1note" class="foswikiCurrentTopicLink">(1)</a></span>, configure<a name="FootNote2text"></a><span class="FootNoteTextLink" title=" When using &#61;GCC&#61; &#38;&#35;8805&#59; 4&#46;2 please make sure that the environment variables &#42;USE_PARALLEL_MINUIT2&#42; and &#42;USE_OPENMP&#42; are <em>not</em> set&#33; Otherwise &#61;MINUIT2&#61; will be compiled with parallelization support and cannot be used together with &#61;musrfit&#61; afterwards since the &#61;musrfit&#61; code is <em>not</em> fully thread&#45;safe&#33; When compiled with &#61;GCC&#61; &#38;&#35;8805&#59; 4&#46;2 &#61;musrfit&#61; itself will parallelize the &#38;chi&#59;&#60;sup&#62;2&#60;&#47;sup&#62; calculation&#46;"><a href="#FootNote2note" class="foswikiCurrentTopicLink">(2)</a></span> it (here using the minimal set of options) and compile it as follows right below: <pre class="bash">
</li> <li> If there is no precompiled binary version of <code>ROOT</code> available for your system or e.g. <code>ROOT</code> should be compiled with another version of <code>GCC</code> visit the <a href="http://root.cern.ch/drupal/content/downloading-root" target="_top">web page</a> and download the 'complete source tree for all systems'. Then unpack this source tree to its destination (e.g. /opt/root-system)<a name="FootNote1text"></a><span class="FootNoteTextLink" title="In case only a single user is working at the machine it might be considerable to change the ownership of the &#61;ROOT&#61; folder so that the user has easy write access to this directory&#58; &#60;&#33;&#45;&#45;&#0;verbatim3192&#0;&#45;&#45;&#62;"><a href="#FootNote1note" class="foswikiCurrentTopicLink">(1)</a></span>, configure<a name="FootNote2text"></a><span class="FootNoteTextLink" title=" When using &#61;GCC&#61; &#38;&#35;8805&#59; 4&#46;2 please make sure that the environment variables &#42;USE_PARALLEL_MINUIT2&#42; and &#42;USE_OPENMP&#42; are <em>not</em> set&#33; Otherwise &#61;MINUIT2&#61; will be compiled with parallelization support and cannot be used together with &#61;musrfit&#61; afterwards since the &#61;musrfit&#61; code is <em>not</em> fully thread&#45;safe&#33; When compiled with &#61;GCC&#61; &#38;&#35;8805&#59; 4&#46;2 &#61;musrfit&#61; itself will parallelize the &#38;chi&#59;&#60;sup&#62;2&#60;&#47;sup&#62; calculation&#46;"><a href="#FootNote2note" class="foswikiCurrentTopicLink">(2)</a></span> it (here using the minimal set of options) and compile it as follows right below: <pre class="bash">
cd /opt/root-system
./configure linux --gminimal --enable-asimage --enable-mathmore --enable-minuit2 --enable-xml
(or in case of a 64 bit installation: ./configure linuxx8664gcc --gminimal --enable-asimage --enable-mathmore --enable-minuit2 --enable-xml)
@ -283,6 +283,10 @@ After the source-code extraction the <strong>autogen.sh</strong> script is calle
</dd> <dt> --with-hdf4 </dt><dd> Set the prefix of the <code>HDF4</code> installation, e.g. /usr/local (<em>only useful in conjunction with the <code>NeXus</code> support</em>)
</dd> <dt> --with-hdf5 </dt><dd> Set the prefix of the <code>HDF5</code> installation, e.g. /usr (<em>only useful in conjunction with the <code>NeXus</code> support</em>)
</dd> <dt> --with-nexus </dt><dd> Set the prefix of the <code>NeXus</code> installation, e.g. /usr/local (<em>only useful in conjunction with the <code>NeXus</code> support</em>)
</dd> <dt> --with-qt3 </dt><dd> Set the prefix of the <code>Qt3</code> installation, e.g. /usr/lib/qt-3.3 (<em>only useful in conjunction with building <code>musrgui</code></em>)
</dd> <dt> --with-qt4 </dt><dd> Set the prefix of the <code>Qt4</code> installation, e.g. /usr/lib/qt47 (<em>only useful in conjunction with building <code>musredit</code></em>)
</dd> <dt> --enable-NeXus </dt><dd> Enable the support of <code>NeXus</code> data files (<em>requires the <code>HDF4</code>, <code>HDF5</code> and <code>NeXus</code> libraries to be installed</em>).
</dd> <dt> --disable-editor </dt><dd> Disable the integrated building of <code>musredit</code>/<code>musrgui</code>.
</dd> <dt> --disable-omp </dt><dd> Switches off the <a href="http://en.wikipedia.org/wiki/OpenMP" target="_top">OpenMP</a> features of <code>musrfit</code> (parallelization of the &chi;<sup>2</sup> calculation when compiled with GCC &ge; 4.2)
</dd></dl>
<p></p>
@ -305,7 +309,7 @@ export MUSRFITPATH&#61;/opt/root-system/bin
<p></p>
<a name="MusrGuiInstallLinux"></a>
<h2><a name="A_3.3_61_61musredit_61_61"></a> 3.3 <code><b>musredit</b></code> </h2>
If <code>Qt4.6</code> or higher is set up on the machine the installation of the <code>musrfit</code> editor is also straight forward:
<font color="#0000ff">In the latest version of <code>musrfit</code> the configure script tries to determine automatically if <code>Qt4.6</code> or higher is set up on the machine. In case this is found, the editor <code>musredit</code> is built already together with <code>musrfit</code>. <em>If not</em>, one can either try to call the configure script with the "--with-qt4" option or install this editor separately:</font>
<pre class="bash">
cd src/musredit
qmake musredit.pro
@ -454,6 +458,10 @@ After the source-code extraction the <strong>autogen.sh</strong> script is calle
</dd> <dt> --with-hdf4 </dt><dd> Set the prefix of the <code>HDF4</code> installation, e.g. /usr/local (<em>only useful in conjunction with the <code>NeXus</code> support</em>)
</dd> <dt> --with-hdf5 </dt><dd> Set the prefix of the <code>HDF5</code> installation, e.g. /usr (<em>only useful in conjunction with the <code>NeXus</code> support</em>)
</dd> <dt> --with-nexus </dt><dd> Set the prefix of the <code>NeXus</code> installation, e.g. /usr/local (<em>only useful in conjunction with the <code>NeXus</code> support</em>)
</dd> <dt> --with-qt3 </dt><dd> Set the prefix of the <code>Qt3</code> installation, e.g. /usr/lib/qt-3.3 (<em>only useful in conjunction with building <code>musrgui</code></em>)
</dd> <dt> --with-qt4 </dt><dd> Set the prefix of the <code>Qt4</code> installation, e.g. /usr/lib/qt47 (<em>only useful in conjunction with building <code>musredit</code></em>)
</dd> <dt> --enable-NeXus </dt><dd> Enable the support of <code>NeXus</code> data files (<em>requires the <code>HDF4</code>, <code>HDF5</code> and <code>NeXus</code> libraries to be installed</em>).
</dd> <dt> --disable-editor </dt><dd> Disable the integrated building of <code>musredit</code>/<code>musrgui</code>.
</dd> <dt> --disable-omp </dt><dd> Switches off the <a href="http://en.wikipedia.org/wiki/OpenMP" target="_top">OpenMP</a> features of <code>musrfit</code> (parallelization of the &chi;<sup>2</sup> calculation when compiled with GCC &ge; 4.2)
</dd></dl>
<p></p>
@ -470,7 +478,7 @@ In order to finish the installation of <code>musrfit</code> the paths where <cod
<p></p>
<a name="MusrEditInstallCygwin"></a>
<h2><a name="A_4.3_61_61musredit_61_61"></a> 4.3 <code><b>musredit</b></code> </h2>
If <code>Qt4.5</code> is set up on the machine the installation of the <code>musrfit</code> editor is also straight forward:
<font color="#0000ff">In the latest version of <code>musrfit</code> the configure script tries to determine automatically if <code>Qt4.5</code> or higher is set up on the machine. In case this is found, the editor <code>musredit</code> is built already together with <code>musrfit</code>. <em>If not</em>, one can either try to call the configure script with the "--with-qt4" option or install this editor separately:</font>
<pre class="bash">
cd src/musredit
qmake-qt4 musredit.pro
@ -725,6 +733,10 @@ After the source-code extraction the <strong>autogen.sh</strong> script is calle
</dd> <dt> --with-hdf4 </dt><dd> Set the prefix of the <code>HDF4</code> installation, e.g. /sw (<em>only useful in conjunction with the <code>NeXus</code> support</em>)
</dd> <dt> --with-hdf5 </dt><dd> Set the prefix of the <code>HDF5</code> installation, e.g. /sw (<em>only useful in conjunction with the <code>NeXus</code> support</em>)
</dd> <dt> --with-nexus </dt><dd> Set the prefix of the <code>NeXus</code> installation, e.g. /usr/local (<em>only useful in conjunction with the <code>NeXus</code> support</em>)
</dd> <dt> --with-qt3 </dt><dd> Set the prefix of the <code>Qt3</code> installation, e.g. /opt/local/lib/qt-3.3 (<em>only useful in conjunction with building <code>musrgui</code></em>)
</dd> <dt> --with-qt4 </dt><dd> Set the prefix of the <code>Qt4</code> installation, e.g. /opt/local/lib/qt-4.7 (<em>only useful in conjunction with building <code>musredit</code></em>)
</dd> <dt> --enable-NeXus </dt><dd> Enable the support of <code>NeXus</code> data files (<em>requires the <code>HDF4</code>, <code>HDF5</code> and <code>NeXus</code> libraries to be installed</em>).
</dd> <dt> --disable-editor </dt><dd> Disable the integrated building of <code>musredit</code>/<code>musrgui</code>.
</dd> <dt> --disable-omp </dt><dd> Switches off the <a href="http://en.wikipedia.org/wiki/OpenMP" target="_top">OpenMP</a> features of <code>musrfit</code> (parallelization of the &chi;<sup>2</sup> calculation when compiled with GCC &ge; 4.2)
</dd></dl>
<p></p>
@ -741,7 +753,7 @@ In order to finish the installation of <code>musrfit</code> the paths where <cod
<p></p>
<a name="MusrGuiInstall"></a>
<h2><a name="A_5.4_61_61musredit_61_61"></a> 5.4 <code><b>musredit</b></code> </h2>
If <code>Qt4.6</code> or higher is set up on the machine the installation of the <code>musrfit</code> editor is also straight forward:
<font color="#0000ff">In the latest version of <code>musrfit</code> the configure script tries to determine automatically if <code>Qt4.5</code> or higher is set up on the machine. In case this is found, the editor <code>musredit</code> is built already together with <code>musrfit</code>. <em>If not</em>, one can either try to call the configure script with the "--with-qt4" option or install this editor separately:</font>
<pre class="bash">
cd src/musredit
qmake musredit.pro
@ -794,7 +806,7 @@ musrview test-histo-ROOT-NPP.msr
</div><!-- /patternContent-->
<hr />
This topic: MUSR<span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span><a href="WebHome.html" class="foswikiCurrentWebHomeLink">WebHome</a> &gt; <a href="MusrFit.html">MusrFit</a><span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span>MusrFitSetup <br />
Topic revision: r47 - 07 Aug 2011 - 16:10:00 - <a href="https://intranet.psi.ch/Main/BastianWojek">BastianWojek</a>
Topic revision: r50 - 28 Aug 2011 - 11:56:04 - <a href="https://intranet.psi.ch/Main/BastianWojek">BastianWojek</a>
</div>
</div>
</div>
@ -810,6 +822,6 @@ Topic revision: r47 - 07 Aug 2011 - 16:10:00 - <a href="https://intranet.psi.ch/
<p></p>
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4
src/external/nexus/PNeXus.cpp vendored
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@ -1648,7 +1648,7 @@ vector<unsigned int>* PNeXus::GetGroupedHisto(unsigned int idx)
* <p>Read the NeXus file 'fileName'.
*
* <b>return:</b>
* - NX_OK on successfull reading
* - NX_OK on successful reading
* - NX_ERROR on error. The error code/message will give the details.
*
* \param fileName file name of the nexus file to be read
@ -2555,7 +2555,7 @@ int PNeXus::ReadFileIdf1()
attlen = VGNAMELENMAX - 1;
atttype = NX_CHAR;
status = NXgetattr(fFileHandle, "units", data_value, &attlen, &atttype);
status = NXgetattr(fFileHandle, const_cast<char*>("units"), data_value, &attlen, &atttype);
if (status == NX_OK) {
for (i = 0; i < attlen; i++)
cstr[i] = *(data_value + i);