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updated docu

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suter_a
2019-07-24 10:15:15 +02:00
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doc/html/_sources/setup-standard.txt
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@ -67,7 +67,8 @@ Additionally, *only* if ``musrfit`` should support reading of data files in the
.. index:: minixml
**minixml**
A small ``XML`` library that can be used to read and write ``XML`` and ``XML``-like data files. *Required version ≥ 2.2* (see `minixml <http://www.minixml.org/>`_).
A small ``XML`` library that can be used to read and write ``XML`` and ``XML``-like data files. *Required version ≥ 2.2* (see `minixml <http://www.minixml.org/>`_).
Currently the ``MXML`` support in ``NeXus`` is broken and hence you will **not** need to install ``minixml`` for the time being.
.. index:: nexus
@ -172,23 +173,20 @@ Installation of NeXus requirements (optional)
*Only* if ``musrfit`` should support reading/writing data files in the ``NeXus`` 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. The necessary
packages to build ``NeXus`` are ``MXML``, (``HDF4``), and ``HDF5``. This means, for a rpm-package based distro try something like:
GNU/Linux distribution or if this is not the case, the packages can be installed from the source code. In principle
NeXus should support ``MXML``, ``HDF4``, and ``HDF5``. At the time of this writing, the ``MXML`` support in the
NeXus project is broken, and ``HDF4`` is outdated on most platforms, hence currently only the ``HDF5`` binding is
used. Hence, the necessary package to build ``NeXus`` is ``HDF5``. This means, for a rpm-package based distro try something like:
.. code-block:: bash
$ yum install mxml-devel hdf-devel hdf5-devel
$ yum install hdf5-devel
and on a deb-package based distro try something like:
.. code-block:: bash
$ apt-get install libmxml-dev libhdf4-dev libhdf5-dev
.. note::
``HDF4`` support within ``NeXus`` will be dropped by ``musrfit`` in the near future. If you *not* urgently need
to read old ``ISIS NeXus`` files, you safely can drop it.
$ apt-get install libhdf5-dev
**Only NeXus Version ≥ 4.4 is support!**
@ -208,10 +206,7 @@ A brief instruction how to get ``NeXus`` compiled from source (lines starting wi
$ # next we will build NeXus out-of-source
$ mkdir build
$ cd build
$ # The next line only if HDF4 support is needed
$ cmake -DENABLE_HDF5=1 -DENABLE_HDF4=1 -DENABLE_MXML=1 ../code
$ # The next line if HDF4 support is NOT needed
$ cmake -DENABLE_HDF5=1 -DENABLE_MXML=1 ../code
$ cmake -DENABLE_HDF5=1 -DENABLE_HDF4=0 -DENABLE_MXML=0 ../code
$ cmake --build ./ --clean-first
$ # make install needs either to be carried out as root or sudo depending on your linux flavour.
$ sudo make install
@ -550,11 +545,7 @@ to be set up. Under ``Cygwin`` of all the required libraries only ``HDF5`` is av
``libhdf5-devel`` can be installed through the ``Cygwin`` setup. One should also make sure that ``bison``, ``flex``
and a package containing ``/usr/lib/librpc.a`` (*e.g.* ``sunrpc = 4.0-3``, but *not* ``sunrpc = 4.0-4``) are installed.
All other libraries have to be built from the sources. The following lines will track the installation of ``JPEG 6b``,
``MXML 2.9``, ``HDF 4.2.7-patch1``, and ``NeXus 4.3.2``. The version numbers and source-code locations might of
course change with time but should be easily adjustable.
*Only* ``NeXus`` version ≥ 4.4 is support!
**Only NeXus Version ≥ 4.4 is support!**
.. code-block:: bash
@ -567,18 +558,6 @@ course change with time but should be easily adjustable.
$ make
$ make install
$ cd ..
$ curl www.msweet.org/files/project3/mxml-2.9.tar.gz -G | tar xz
$ cd mxml-2.9
$ ./configure --prefix=/usr/local --enable-static
$ make
$ make install
$ cd ..
$ curl http://www.hdfgroup.org/ftp/HDF/HDF_Current/src/hdf-4.2.7-patch1.tar.gz -G | tar xz
$ cd hdf-4.2.7-patch1
$ ./configure --prefix=/usr/local --enable-static --disable-fortran --with-jpeg=/usr/local
$ make
$ make install
$ cd ..
$ # create a directory for the NeXus source code
$ mkdir nexus
$ cd nexus
@ -587,7 +566,7 @@ course change with time but should be easily adjustable.
$ # next we will build NeXus out-of-source
$ mkdir build
$ cd build
$ cmake -DENABLE_HDF5=1 -DENABLE_HDF4=1 -DENABLE_MXML=1 ../code
$ cmake -DENABLE_HDF5=1 -DENABLE_HDF4=0 -DENABLE_MXML=0 ../code
$ make
$ make install
@ -876,21 +855,14 @@ Installation of NeXus requirements (optional)
.. code-block:: bash
$ sudo port -v install hdf4 hdf5
$ sudo port -v install hdf5
Unfortunately, the ``minixml`` and ``NeXus`` 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 ``NeXus`` Version ≥ 4.4 is support!) this can be achieved for example by:
**Only NeXus Version ≥ 4.4 is support!**
To get things compiled do:
.. code-block:: bash
$ # get and instal Mini-XML
$ cd $HOME/Applications
$ git clone https://github.com/michaelrsweet/mxml.git
$ cd mxml
$ ./configure --prefix=/usr/local
$ make
$ sudo make install
$ # get and install NeXus
$ cd $HOME/Applications
$ # get the source code from the master repository
@ -899,7 +871,7 @@ Only ``NeXus`` Version ≥ 4.4 is support!) this can be achieved for example by:
$ cd nexus
$ mkdir build
$ cd build
$ cmake -DENABLE_HDF5=1 -DENABLE_HDF4=1 -DENABLE_MXML=1 ../code
$ cmake -DENABLE_HDF5=1 -DENABLE_HDF4=0 -DENABLE_MXML=0 ../code
$ make
$ sudo make install
@ -1101,27 +1073,20 @@ packages can be installed through Fink (check for the most recent versions):
libjpeg hdf hdf5-cpp11 hdf5-cpp11-shlibs
Unfortunately, the ``minixml`` and ``NeXus`` 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)
Unfortunately, the ``NeXus`` 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:
.. code-block:: bash
$ # first build Mini-XML
$ cd $HOME/Applications
$ git clone https://github.com/michaelrsweet/mxml.git
$ cd mxml
$ ./configure --prefix=/usr/local
$ make
$ sudo make install
$ # second build NeXus
$ # build NeXus
$ cd ..
$ git clone https://github.com/nexusformat/code.git nexus/code
$ cd nexus
$ # build NeXus out-of-source
$ mkdir build
$ cd build
$ cmake ../code -DENABLE_HDF4=1 -DENABLE_HDF5=1 -DENABLE_MXML=1
$ cmake ../code -DENABLE_HDF5=1 -DENABLE_HDF4=0 -DENABLE_MXML=0
$ cmake --build ./ --clean-first -- -j8
$ sudo make install