diff --git a/doc/html/.buildinfo b/doc/html/.buildinfo index a4002c7c..a71db440 100644 --- a/doc/html/.buildinfo +++ b/doc/html/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 5c197f7d1a99bc4d9f1831306e12cc04 +config: 39df8dc76b5eba2fef9a1560a07e9143 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/doc/html/_sources/setup-dks.txt b/doc/html/_sources/setup-dks.txt index 70d9effd..0ea9328b 100644 --- a/doc/html/_sources/setup-dks.txt +++ b/doc/html/_sources/setup-dks.txt @@ -149,46 +149,6 @@ switch the working branch which is done by $ cd $HOME/Apps/musrfit $ git checkout dks6 -Install via automake -^^^^^^^^^^^^^^^^^^^^ - -.. note:: - - Currently ``automake`` is still supported but soon will be replaced by ``cmake``. Only follow - the ``automake`` procedure if you have good reasons. - -The configure script for musrfit has now a couple of more tags/options, which are: - -**- -enable-dks** - by default this is set to no, hence if you want to have GPU support you need to enable it. -**- -with-cuda** - with this tag you tell the configure script where it can find ``CUDA`` -**- -with-opencl** - with this tag you tell the configure script where it can find ``OpenCL`` -**- -with-dks** - with this tag you tell the configure script where it can find ``DKS`` - -For a typical setup on a RHEL system it could look like this - -.. code-block:: bash - - $ ./configure --enable-ASlibs --enable-BMWlibs --enable-NeXus --with-dks=$HOME/Apps/DKS/exec --enable-dks --prefix=$ROOTSYS - -After - -.. code-block:: bash - - $ make - $ make install - -and updating the shared library lookup table (*only* needed for Linux) - -.. code-block:: bash - - $ /sbin/ldconfig # as superuser / root - -you are done with the setup. - Install via cmake ^^^^^^^^^^^^^^^^^ @@ -201,7 +161,7 @@ For a typical setup on a RHEL or macOS system it could look like this .. code-block:: bash - $ cmake ../ -DCMAKE_INSTALL_PREFIX=$ROOTSYS -DASlibs=1 -DBMWlibs=1 -Dnexus=1 + $ cmake ../ -DCMAKE_INSTALL_PREFIX=$ROOTSYS -DASlibs=1 -DBMWlibs=1 -Dnexus=1 -Ddks=1 After diff --git a/doc/html/_sources/setup-standard.txt b/doc/html/_sources/setup-standard.txt index c2592605..a8dfab99 100644 --- a/doc/html/_sources/setup-standard.txt +++ b/doc/html/_sources/setup-standard.txt @@ -23,11 +23,9 @@ it can also be set up under **MS Windows** (cygwin, only for the *very brave*, p In case musrfit should be installed according to the description found on this page, the user is strongly encouraged to *read completely* each section dealing with the present installation step *before* starting the installation process! -Apart from `GCC, the GNU Compiler Collection `_ (``gcc``, ``g++``), the GNU build tools `autoconf `_, -`automake `_, and `libtool `_ are needed, if you want to build musrfit via the automake toolchain. -The ``automake`` toolchain will eventually be droped in upcoming releases. -If you plan to use the cmake toolchain (preferred way), `cmake `_. Furthermore the helper tool `pkg-config `_ is -needed and musrfit requires the installation of a few open-source libraries and programs including their header packages: +Apart from `GCC, the GNU Compiler Collection `_ (``gcc``, ``g++``), the build tool `cmake `_ is needed. Furthermore the helper +tool `pkg-config `_ needs to be in place, and musrfit requires the installation of a few open-source libraries and programs including +their header packages: .. index:: boost-c++ @@ -94,14 +92,15 @@ Before the installation procedure will be described, please note the following r **GNU/Linux** No serious problems are currently known. Tested distributions: `RHEL `_, `Fedora `_, - `Debian `_, `Ubuntu `_, `Mint `_, `openSUSE `_. + `Debian `_, `Ubuntu `_, `Mint `_, `openSUSE `_, + `manjaro `_, and `antergos `_. **Mac OS X/macOS** No serious problems are currently known for macOS ≥ 10.6. **MS Windows** Native *MS Windows* support is currently not available. Potential ways to get ``musrfit`` running are: * via installation of Linux via the Microsoft App store for Windows 10. - * via installation of the virtual machine on which you install Linux. + * via installation of the virtual machine on which you install Linux (probably the easiest for most Windows users). * via `cygwin`_. .. _cygwin: https://www.cygwin.com/ @@ -173,9 +172,18 @@ 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. *E.g.* on -Red Hat-like systems binary packages for ``MXML``, ``HDF4``, and ``HDF5`` might be called ``mxml``, ``mxml-devel``, -``hdf``, ``hdf-devel``, ``hdf5``, ``hdf5-devel``, on Debian-like systems ``libmxml1``, ``libmxml-dev``, ``libhdf4-dev``, ``libhdf5-dev``. +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: + + .. code-block:: bash + + $ yum install mxml-devel hdf-devel 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:: @@ -213,10 +221,8 @@ A brief instruction how to get ``NeXus`` compiled from source (lines starting wi ROOT ^^^^ -ROOT 5.34/xx is supported as legacy version *only*! **The default now will be ROOT 6.xx/yy!** - 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 ``musrfit``, though the situation is improving. If you are +manner incompatible with the way it is needed by ``musrfit``, 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). **One Warning:** if the ROOT packages are upgraded after a yum update (apt-get update; apt-get upgrade) you might need to recompile ``musrfit``. *If you are not sure about @@ -247,12 +253,12 @@ be added starting with a '#' which can be omitted. They are only there to explai $ # creat the Apps directory if not already present $ mkdir Apps $ cd Apps - $ git clone http://root.cern.ch/git/root.git + $ git clone http://github.com/root-project/root.git $ cd root $ git tag -l - $ # git tag -l will list all available tags. In the next command choose the tag v6-14-00 + $ # git tag -l will list all available tags. In the next command choose the tag v6-16-00 $ # or the latest official release number - $ git checkout -b v6-14-00 v6-14-00 + $ git checkout -b v6-16-00 v6-16-00 $ # now ROOT is ready to be configured. Below you will find the minimal ROOT configuration needed. $ # since we are using cmake build now, first we will need to create the build directory. $ mkdir root_build @@ -299,7 +305,7 @@ If an update of ROOT is needed, simple do the following: musrfit +++++++ -When all required software has been set up with the ``musrfit`` installation can be proceeded. First, the most +When all required software has been set up you can proceed with the ``musrfit`` installatio. First, the most recent source code should be downloaded. The preferred way of doing so is to clone the ``musrfit`` repository via git. Assuming the code should be located in ``$HOME/Apps`` this is achieved most easily calling from the terminal @@ -307,8 +313,7 @@ Assuming the code should be located in ``$HOME/Apps`` this is achieved most easi $ cd $HOME/Apps $ git clone https://bitbucket.org/muonspin/musrfit.git - $ # Only if legacy ROOT 5.xx.yy is used include the next line - $ cd musrfit; git checkout root5 + $ cd musrfit or @@ -316,8 +321,7 @@ or $ cd $HOME/Apps $ git clone git://gitlab.psi.ch/nemu/musrfit.git - $ # Only if legacy ROOT 5.xx.yy is used include the next line - $ cd musrfit; git checkout root5 + $ cd musrfit .. note:: @@ -331,24 +335,6 @@ or $ cd $HOME/Apps/musrfit $ git pull - -Now, depending whether you follow the ``automake`` or ``cmake`` tool chain you do - -**automake toolchain:** - -.. code-block:: bash - - $ make uninstall - $ make clean - $ make - $ make install - -or - -**cmake toolchain:** - -.. code-block:: bash - $ cd build $ xargs rm < install_manifest.txt $ cmake --build ./ --clean-first @@ -358,61 +344,6 @@ or As an alternative (if git is not available), the source code can also be downloaded from the following web-page: `musrfit at bitbucket`_ -.. index:: musrfit-build-automake-linux - -musrfit build with automake -^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -After the source-code extraction the ``autogen.sh`` script is called to prepare the build environment. -If it has been executed successfully the ``configure`` script should be ready to collect all the information needed -to create the Makefiles. If ``musrfit`` should support ``NeXus`` data files this has to be enabled by specifying the -``--enable-NeXus`` switch when calling configure. For an overview of all available options just call ``./configure --help``. -Besides the standard options there are a few special options which should be mentioned here: - -**- -prefix** - Specify the installation prefix, *e.g.* ``$ROOTSYS`` if already defined (by default: ``/usr/local``). -**- -with-rootsys** - Specify the top of the ``ROOT`` installation directory, *e.g.* ``$ROOTSYS`` if already defined. -**- -with-fftw3** - Specify the prefix of the ``FFTW3`` installation. *e.g.* ``/usr/local`` or ``/usr``. -**- -with-gsl** - Set the prefix of the ``GSL`` installation, *e.g.* ``/usr/local`` or ``/usr``. -**- -with-boostinc** - Set the path to the header files of the ``Boost`` installation, *e.g.* ``/usr/local/include`` or ``/usr/include``. -**- -with-hdf4** - Set the prefix of the ``HDF4`` installation, *e.g.* ``/usr/local`` (only useful in conjunction with the ``NeXus`` support). -**- -with-hdf5** - Set the prefix of the ``HDF5`` installation, *e.g.* ``/usr`` (only useful in conjunction with the ``NeXus`` support). -**- -with-nexus** - Set the prefix of the ``NeXus`` installation, *e.g.* ``/usr/local`` (only useful in conjunction with the ``NeXus`` support). -**- -with-qt3** - Set the prefix of the ``Qt3`` installation, *e.g.* ``/usr/lib/qt-3.3`` (only useful in conjunction with building ``musrgui``). -**- -with-qt4** - Set the prefix of the ``Qt4`` installation, *e.g.* ``/usr/lib/qt47`` (only useful in conjunction with building ``musredit``). -**- -with-qt5** - Set the prefix of the ``Qt5`` installation, *e.g.* ``/usr/lib64`` (only useful in conjunction with building ``musredit``). -**- -enable-NeXus** - Enable the support of ``NeXus`` data files (requires the ``HDF4``, ``HDF5`` and ``NeXus`` libraries to be installed). -**- -disable-editor** - Disable the integrated building of ``musredit``/``musrgui``. -**- -disable-omp** - Switches off the `OpenMP `_ features of ``musrfit`` (parallelization of the :math:`\chi^2` calculation when compiled with GCC ≥ 4.2). - -Normally it should not be necessary to make use of any of the options except for specifying the installation path with ``--prefix``. 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 ``musrfit`` libraries and executables. -A standard installation sequence (without ``NeXus`` support) might then look like (In case the normal user has no write permissions to the -``$ROOTSYS`` and the installation path the "make install" commands have to be executed as superuser.): - -.. code-block:: bash - - $ cd $HOME/Apps/musrfit - $ sh autogen.sh - $ ./configure --prefix=$ROOTSYS - $ make - $ make install - $ /sbin/ldconfig # (as superuser) - .. index:: musrfit-build-cmake-linux musrfit build with cmake @@ -484,8 +415,7 @@ musredit ++++++++ In the latest version of ``musrfit`` the configure script tries to determine automatically the highest available ``Qt`` version. -In case this is found, the editor ``musredit`` is built already together with ``musrfit``. If not, one can try to call -the configure script with the **- -with-qt5** option (``automake``). ``cmake`` will determine everthing automatically. +In case this is found, the editor ``musredit`` is built already together with ``musrfit``. To install this editor separately, *i.e.* by "hand" do .. code-block:: bash @@ -739,61 +669,7 @@ If the repository had been checked out already before, one can update the local As an alternative (if git is not available), the source code can also be downloaded from the following web-page: `musrfit at bitbucket`_. - -.. index:: musrfit-build-automake-windows - -musrfit build with automake -^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -After the source-code extraction the ``autogen.sh`` script is called to prepare the build environment. -If it has been executed successfully the ``configure`` script should be ready to collect all the information -needed to create the Makefiles. If ``musrfit`` should support ``NeXus`` data files this has to be enabled by -specifying the ``--enable-static --enable-NeXus`` switches when calling configure. For an overview of all -available options just call ``./configure --help``. Besides the standard options there are a few special -options which should be mentioned here: - -**- -prefix** - Specify the installation prefix, *e.g.* ``/opt/root-system`` (by default: ``/usr/local``) -**- -with-rootsys** - Specify the top of the ``ROOT`` installation directory, *e.g.* ``/opt/root-system`` -**- -with-fftw3** - Specify the prefix of the ``FFTW3`` installation. *e.g.* ``/usr/local`` or ``/usr`` -**- -with-gsl** - Set the prefix of the ``GSL`` installation, *e.g.* ``/usr/local`` or ``/usr`` -**- -with-boostinc** - Set the path to the header files of the ``Boost`` installation, *e.g.* ``/usr/local/include`` or ``/usr/include`` -**- -with-hdf4** - Set the prefix of the ``HDF4`` installation, *e.g.* ``/usr/local`` (only useful in conjunction with the ``NeXus`` support) -**- -with-hdf5** - Set the prefix of the ``HDF5`` installation, *e.g.* ``/usr`` (only useful in conjunction with the ``NeXus`` support) -**- -with-nexus** - Set the prefix of the ``NeXus`` installation, *e.g.* ``/usr/local`` (only useful in conjunction with the ``NeXus`` support) -**- -with-qt3** - Set the prefix of the ``Qt3`` installation, *e.g.* ``/usr/lib/qt-3.3`` (only useful in conjunction with building ``musrgui``) -**- -with-qt4** - Set the prefix of the ``Qt4`` installation, *e.g.* ``/usr/lib/qt47`` (only useful in conjunction with building ``musredit``) -**- -with-qt5** - Set the prefix of the ``Qt5`` installation, *e.g.* ``/usr/lib/qt56`` (only useful in conjunction with building ``musredit``) -**- -enable-NeXus** - Enable the support of ``NeXus`` data files (requires the ``HDF4``, ``HDF5`` and ``NeXus`` libraries to be installed). -**- -disable-editor** - Disable the integrated building of ``musredit``/``musrgui``. -**- -disable-omp** - Switches off the ``OpenMP`` features of ``musrfit`` (parallelization of the :math:`\chi^2` calculation when compiled with ``GCC`` ≥ 4.2) - -Normally it should not be necessary to make use of any of the options except for specifying the installation path with ``--prefix``. -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 ``musrfit`` -libraries and executables. A standard installation sequence (without ``NeXus`` support) might then look like: - -.. code-block:: bash - - $ cd musrfit - $ sh autogen.sh - $ ./configure --prefix=$ROOTSYS - $ make - $ make install - + .. index:: musrfit-build-cmake-windows musrfit build with cmake @@ -847,8 +723,7 @@ musredit In the latest version of ``musrfit`` 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 ``musredit`` is built -readily with ``musrfit``. If not, one can either try to call the ``configure`` script with the -``--with-qt4`` option or install this editor separately, *.e.g.*: +readily with ``musrfit``. If not, try the following: .. code-block:: bash @@ -945,7 +820,7 @@ with OS X (on the installation DVD/CDs) should be installed: **X11** 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 `XQuartz `. If ``ROOT`` runs without ``XQuartz`` *do not* + will need to install `XQuartz `_. If ``ROOT`` runs without ``XQuartz`` *do not* install it. After installing the ``Xcode`` tools go to the `MacPorts install page `_, download @@ -1034,7 +909,7 @@ Only ``NeXus`` Version ≥ 4.4 is support!) this can be achieved for example by: ROOT ^^^^ -ROOT 5.34/xx is supported as legacy version only! **The default now will be ROOT 6.xx/yy!** +**The default ROOT version is based on ROOT 6.xx/yy!** ROOT installed via package installer """""""""""""""""""""""""""""""""""" @@ -1042,16 +917,16 @@ ROOT installed via package installer The lazy way to get ``ROOT`` installed is via package installer. If your macOS is directly supported by the ``ROOT`` people you can download the package installer from the ``ROOT`` `download page `_. Choose the latest ``ROOT`` release and download you macOS version dmg-file, *e.g.* for macOS 10.13 (High Sierra) -it is at the time of writting ``root_v6.14.00.macosx64-10.13-clang91.dmg``. After the installation +it is at the time of writting ``root_v6.16.00.macosx64-10.13-clang91.dmg``. After the installation ``ROOT`` will be installed under ``/Application`` 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 ``ROOT`` directory: .. code-block:: bash $ cd /Applications - $ sudo chown -R root_v6.14.00 - $ sudo chgrp -R staff root_v6.14.00 - $ sudo ln -s root_v6.14.00 root + $ sudo chown -R root_v6.16.00 + $ sudo chgrp -R staff root_v6.16.00 + $ sudo ln -s root_v6.16.00 root ROOT installed from source """""""""""""""""""""""""" @@ -1068,12 +943,12 @@ comments will be added starting with a '#' which can be omitted. They are only t .. code-block:: bash $ cd $HOME/Applications - $ git clone http://root.cern.ch/git/root.git + $ git clone http://github.com/root-project/root.git $ cd root $ git tag -l $ # git tag -l will list all available tags. In the next command choose the tag v6-10-xx - $ # where xx is the highest listed number, e.g. v6-14-00 - $ git checkout -b v6-14-00 v6-14-00 + $ # where xx is the highest listed number, e.g. v6-16-00 + $ git checkout -b v6-16-00 v6-16-00 $ # now ROOT is ready to be configured. Below you will find the minimal ROOT configuration needed. $ # We will use the cmake out-of-source approach here. $ mkdir root_build @@ -1158,7 +1033,7 @@ Before proceeding with the usage of the `Fink`_ system first a few useful tools **X11** 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 `XQuartz `. If ``ROOT`` runs without ``XQuartz`` *do not* + will need to install `XQuartz `_. If ``ROOT`` runs without ``XQuartz`` *do not* install it. After installing the ``Xcode`` tools go to the `Fink download page `_, @@ -1256,7 +1131,7 @@ this can be achieved for example by: ROOT ^^^^ -ROOT 5.34/xx is supported as legacy version only and will likely to be dropped in 2018. **The default now is ROOT 6.xx/yy!** +**The default ROOT version is based on ROOT 6.xx/yy!** ROOT installed via package installer """""""""""""""""""""""""""""""""""" @@ -1264,16 +1139,16 @@ ROOT installed via package installer The lazy way to get ``ROOT`` installed is via package installer. If your macOS is directly supported by the ``ROOT`` people you can download the package installer from the ``ROOT`` `download page `_. Choose the latest ``ROOT`` release and download you macOS version dmg-file, *e.g.* for macOS 10.13 (High Sierra) -it is at the time of writting ``root_v6.14.00.macosx64-10.13-clang91.dmg``. After the installation +it is at the time of writting ``root_v6.16.00.macosx64-10.13-clang91.dmg``. After the installation ``ROOT`` will be installed under ``/Application`` 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 ``ROOT`` directory: .. code-block:: bash $ cd /Applications - $ sudo chown -R root_v6.14.00 - $ sudo chgrp -R staff root_v6.14.00 - $ sudo ln -s root_v6.14.00 root + $ sudo chown -R root_v6.16.00 + $ sudo chgrp -R staff root_v6.16.00 + $ sudo ln -s root_v6.16.00 root ROOT installed from source """""""""""""""""""""""""" @@ -1290,12 +1165,12 @@ comments will be added starting with a '#' which can be omitted. They are only t .. code-block:: bash $ cd $HOME/Applications - $ git clone http://root.cern.ch/git/root.git + $ git clone http://github.com/root-project/root.git $ cd root $ git tag -l $ # git tag -l will list all available tags. In the next command choose the tag v6-10-xx - $ # where xx is the highest listed number, e.g. v6-14-00 - $ git checkout -b v6-14-00 v6-14-00 + $ # where xx is the highest listed number, e.g. v6-16-00 + $ git checkout -b v6-16-00 v6-16-00 $ # now ROOT is ready to be configured. Below you will find the minimal ROOT configuration needed. $ # We will use the cmake out-of-source approach here. $ mkdir root_build @@ -1374,8 +1249,7 @@ in ``~/Applications/musrfit`` this is achieved most easily calling from the term $ cd ~/Applications $ git clone https://bitbucket.org/muonspin/musrfit.git - $ # Only if legacy ROOT 5.xx.yy is used include the next line - $ cd musrfit; git checkout root5 + $ cd musrfit or @@ -1383,8 +1257,7 @@ or $ cd ~/Applications $ git clone git://gitlab.psi.ch/nemu/musrfit.git - $ # Only if legacy ROOT 5.xx.yy is used include the next line - $ cd musrfit; git checkout root5 + $ cd musrfit If a local repository clone is already present, one can update it using: @@ -1395,63 +1268,7 @@ If a local repository clone is already present, one can update it using: As an alternative (*if git is not available*), the source code can also be downloaded from the following web-page: `musrfit at bitbucket`_. - -.. index:: musrfit-build-automake-macos - -musrfit build with automake -^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -After the source-code extraction the ``autogen.sh`` script is called to prepare the build environment. -If it has been executed successfully the ``configure`` script should be ready to collect all the information needed -to create the Makefiles. If ``musrfit`` should support ``NeXus`` data files this has to be enabled by specifying the -``--enable-NeXus`` switch when calling configure. For an overview of all available options just call ``./configure --help``. -Besides the standard options there are a few special options which should be mentioned here: - -**- -prefix** - Specify the installation prefix, *e.g.* ``$ROOTSYS`` if already defined (by default: ``/usr/local``). -**- -with-rootsys** - Specify the top of the ``ROOT`` installation directory, *e.g.* ``$ROOTSYS`` if already defined. -**- -with-fftw3** - Specify the prefix of the ``FFTW3`` installation. *e.g.* ``/usr/local`` or ``/usr``. -**- -with-gsl** - Set the prefix of the ``GSL`` installation, *e.g.* ``/usr/local`` or ``/usr``. -**- -with-boostinc** - Set the path to the header files of the ``Boost`` installation, *e.g.* ``/usr/local/include`` or ``/usr/include``. -**- -with-hdf4** - Set the prefix of the ``HDF4`` installation, *e.g.* ``/usr/local`` (only useful in conjunction with the ``NeXus`` support). -**- -with-hdf5** - Set the prefix of the ``HDF5`` installation, *e.g.* ``/usr`` (only useful in conjunction with the ``NeXus`` support). -**- -with-nexus** - Set the prefix of the ``NeXus`` installation, *e.g.* ``/usr/local`` (only useful in conjunction with the ``NeXus`` support). -**- -with-qt3** - Set the prefix of the ``Qt3`` installation, *e.g.* ``/usr/lib/qt-3.3`` (only useful in conjunction with building ``musrgui``). -**- -with-qt4** - Set the prefix of the ``Qt4`` installation, *e.g.* ``/usr/lib/qt47`` (only useful in conjunction with building ``musredit``). -**- -with-qt5** - Set the prefix of the ``Qt5`` installation, *e.g.* ``/usr/lib64`` (only useful in conjunction with building ``musredit``). -**- -enable-NeXus** - Enable the support of ``NeXus`` data files (requires the ``HDF4``, ``HDF5`` and ``NeXus`` libraries to be installed). -**- -disable-editor** - Disable the integrated building of ``musredit``/``musrgui``. -**- -disable-omp** - Switches off the `OpenMP `_ features of ``musrfit`` (parallelization of the :math:`\chi^2` calculation when compiled with GCC ≥ 4.2). - -Normally it should not be necessary to make use of any of the options except for specifying the installation path with ``--prefix``. 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 ``musrfit`` libraries and executables. -A standard installation sequence (without ``NeXus`` support) might then look like (In case the normal user has no write permissions to the -``$ROOTSYS`` and the installation path the "make install" commands have to be executed as superuser.): - -.. code-block:: bash - - $ cd $HOME/Apps/musrfit - $ sh autogen.sh - $ ./configure --prefix=$ROOTSYS - $ make - $ make install - $ /sbin/ldconfig # (as superuser) - - + .. index:: musrfit-build-cmake-macos musrfit build with cmake @@ -1521,8 +1338,7 @@ musredit In the latest version of ``musrfit`` the configure script tries to determine automatically the highest available Qt version. In case this is found, the editor ``musredit`` is built already together with ``musrfit``. -If not, one can try to call the configure script with the **--with-qt5** option (``automake``). ``cmake`` will -determine everthing automatically. To install this editor separately, *i.e.* by “hand” do +If not, try the following: .. code-block:: bash diff --git a/doc/html/acknowledgement.html b/doc/html/acknowledgement.html index 7ec06c40..d9bc68bb 100644 --- a/doc/html/acknowledgement.html +++ b/doc/html/acknowledgement.html @@ -6,7 +6,7 @@ - Acknowledgements — musrfit 1.4.1 documentation + Acknowledgements — musrfit 1.4.2 documentation @@ -14,7 +14,7 @@ - + @@ -41,7 +41,7 @@
  • previous |
  • -
  • musrfit 1.4.1 documentation »
  • +
  • musrfit 1.4.2 documentation »
  • @@ -108,12 +108,12 @@ extremely competent way to deal with his projects as well as to deal with the ch
  • previous |
  • -
  • musrfit 1.4.1 documentation »
  • +
  • musrfit 1.4.2 documentation »
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  • diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js index 058381e2..b403ced5 100644 --- a/doc/html/searchindex.js +++ b/doc/html/searchindex.js @@ -1 +1 @@ -Search.setIndex({filenames:["acknowledgement","any2many","bugtracking","cite","index","msr2data","mupp","musr-root","musredit","setup-dks","setup-standard","tutorial","user-libs","user-manual"],titles:["Acknowledgements","any2many - a Universal \u03bcSR-file-format converter","Bugtracking","How to Cite musrfit?","Welcome to the musrfit documentation!","msr2data - A Program for Automatically Processing Multiple musrfit msr Files","mupp - \u03bcSR Parameter Plotter","MusrRoot - an Extensible Open File Format for \u03bcSR","musredit: the GUI Based Interface to musrfit","Setting up musrfit / DKS: High Speed Fitting with GPU’s","Setting up musrfit on Different Platforms","Tutorial for musrfit","Documentation of user libs (user functions)","User 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\ No newline at end of file diff --git a/doc/html/setup-dks.html b/doc/html/setup-dks.html index bd141748..5ee2ebcc 100644 --- a/doc/html/setup-dks.html +++ b/doc/html/setup-dks.html @@ -6,7 +6,7 @@ - Setting up musrfit / DKS: High Speed Fitting with GPU’s — musrfit 1.4.1 documentation + Setting up musrfit / DKS: High Speed Fitting with GPU’s — musrfit 1.4.2 documentation @@ -14,7 +14,7 @@ - + @@ -41,7 +41,7 @@
  • previous |
  • -
  • musrfit 1.4.1 documentation »
  • +
  • musrfit 1.4.2 documentation »
  • @@ -160,39 +160,6 @@ switch the working branch which is done by

    $ git checkout dks6 -
    -

    Install via automake

    -
    -

    Note

    -

    Currently automake is still supported but soon will be replaced by cmake. Only follow -the automake procedure if you have good reasons.

    -
    -

    The configure script for musrfit has now a couple of more tags/options, which are:

    -
    -
    - -enable-dks
    -
    by default this is set to no, hence if you want to have GPU support you need to enable it.
    -
    - -with-cuda
    -
    with this tag you tell the configure script where it can find CUDA
    -
    - -with-opencl
    -
    with this tag you tell the configure script where it can find OpenCL
    -
    - -with-dks
    -
    with this tag you tell the configure script where it can find DKS
    -
    -

    For a typical setup on a RHEL system it could look like this

    -
    $ ./configure --enable-ASlibs --enable-BMWlibs --enable-NeXus --with-dks=$HOME/Apps/DKS/exec --enable-dks --prefix=$ROOTSYS
    -
    -
    -

    After

    -
    $ make
    -$ make install
    -
    -
    -

    and updating the shared library lookup table (only needed for Linux)

    -
    $ /sbin/ldconfig # as superuser / root
    -
    -
    -

    you are done with the setup.

    -

    Install via cmake

    There is on more configuration switch

    @@ -201,7 +168,7 @@ $ make install
    it allows to enable/disable DKS support. The default is <value>=1, i.e. enabled. To disable use <value>=0.

    For a typical setup on a RHEL or macOS system it could look like this

    -
    $ cmake ../ -DCMAKE_INSTALL_PREFIX=$ROOTSYS -DASlibs=1 -DBMWlibs=1 -Dnexus=1
    +
    $ cmake ../ -DCMAKE_INSTALL_PREFIX=$ROOTSYS -DASlibs=1 -DBMWlibs=1 -Dnexus=1 -Ddks=1
     

    After

    @@ -354,12 +321,12 @@ The only thing you need DKS previous | -
  • musrfit 1.4.1 documentation »
  • +
  • musrfit 1.4.2 documentation »
  • diff --git a/doc/html/setup-standard.html b/doc/html/setup-standard.html index e64c9cb0..c077e111 100644 --- a/doc/html/setup-standard.html +++ b/doc/html/setup-standard.html @@ -6,7 +6,7 @@ - Setting up musrfit on Different Platforms — musrfit 1.4.1 documentation + Setting up musrfit on Different Platforms — musrfit 1.4.2 documentation @@ -14,7 +14,7 @@ - + @@ -41,7 +41,7 @@
  • previous |
  • -
  • musrfit 1.4.1 documentation »
  • +
  • musrfit 1.4.2 documentation »
  • @@ -62,11 +62,9 @@ it can also be set up under MS Windows (cygwin, only for the In case musrfit should be installed according to the description found on this page, the user is strongly encouraged to read completely each section dealing with the present installation step before starting the installation process!

    -

    Apart from GCC, the GNU Compiler Collection (gcc, g++), the GNU build tools autoconf, -automake, and libtool are needed, if you want to build musrfit via the automake toolchain. -The automake toolchain will eventually be droped in upcoming releases. -If you plan to use the cmake toolchain (preferred way), cmake. Furthermore the helper tool pkg-config is -needed and musrfit requires the installation of a few open-source libraries and programs including their header packages:

    +

    Apart from GCC, the GNU Compiler Collection (gcc, g++), the build tool cmake is needed. Furthermore the helper +tool pkg-config needs to be in place, and musrfit requires the installation of a few open-source libraries and programs including +their header packages:

    boost C++ libraries
    The powerful Spirit parser framework used by musrfit is included in that collection of libraries. Required version ≥ 1.33 (see boost C++ libraries).
    @@ -117,14 +115,15 @@ needed and musrfit requires the installation of a few open-source libraries and
    GNU/Linux
    No serious problems are currently known. Tested distributions: RHEL, Fedora, -Debian, Ubuntu, Mint, openSUSE.
    +Debian, Ubuntu, Mint, openSUSE, +manjaro, and antergos.
    Mac OS X/macOS
    No serious problems are currently known for macOS ≥ 10.6.
    MS Windows

    Native MS Windows support is currently not available. Potential ways to get musrfit running are:

    • via installation of Linux via the Microsoft App store for Windows 10.
    • -
    • via installation of the virtual machine on which you install Linux.
    • +
    • via installation of the virtual machine on which you install Linux (probably the easiest for most Windows users).
    • via cygwin.
    @@ -178,9 +177,19 @@ the source code from the corresponding website, or to clone the git repo. If you

    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. E.g. on -Red Hat-like systems binary packages for MXML, HDF4, and HDF5 might be called mxml, mxml-devel, -hdf, hdf-devel, hdf5, hdf5-devel, on Debian-like systems libmxml1, libmxml-dev, libhdf4-dev, libhdf5-dev.

    +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:

    +
    +
    $ yum install mxml-devel hdf-devel hdf5-devel
    +
    +
    +
    +

    and on a deb-package based distro try something like:

    +
    +
    $ 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 @@ -211,9 +220,8 @@ $ sudo make install

    ROOT

    -

    ROOT 5.34/xx is supported as legacy version only! The default now will be ROOT 6.xx/yy!

    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 musrfit, though the situation is improving. If you are +manner incompatible with the way it is needed by musrfit, 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). One Warning: if the ROOT packages are upgraded after a yum update (apt-get update; apt-get upgrade) you might need to recompile musrfit. If you are not sure about @@ -235,12 +243,12 @@ be added starting with a ‘#’ which can be omitted. They are only the $ # creat the Apps directory if not already present $ mkdir Apps $ cd Apps -$ git clone http://root.cern.ch/git/root.git +$ git clone http://github.com/root-project/root.git $ cd root $ git tag -l -$ # git tag -l will list all available tags. In the next command choose the tag v6-14-00 +$ # git tag -l will list all available tags. In the next command choose the tag v6-16-00 $ # or the latest official release number -$ git checkout -b v6-14-00 v6-14-00 +$ git checkout -b v6-16-00 v6-16-00 $ # now ROOT is ready to be configured. Below you will find the minimal ROOT configuration needed. $ # since we are using cmake build now, first we will need to create the build directory. $ mkdir root_build @@ -284,20 +292,18 @@ $ cmake --build ./ --clean-first

    musrfit

    -

    When all required software has been set up with the musrfit installation can be proceeded. First, the most +

    When all required software has been set up you can proceed with the musrfit installatio. First, the most recent source code should be downloaded. The preferred way of doing so is to clone the musrfit repository via git. Assuming the code should be located in $HOME/Apps this is achieved most easily calling from the terminal

    $ cd $HOME/Apps
     $ git clone https://bitbucket.org/muonspin/musrfit.git
    -$ # Only if legacy ROOT 5.xx.yy is used include the next line
    -$ cd musrfit; git checkout root5
    +$ cd musrfit
     

    or

    $ cd $HOME/Apps
     $ git clone git://gitlab.psi.ch/nemu/musrfit.git
    -$ # Only if legacy ROOT 5.xx.yy is used include the next line
    -$ cd musrfit; git checkout root5
    +$ cd musrfit
     
    @@ -309,78 +315,15 @@ will needed to switch branches first.

    Update: If a local repository clone is already present (it needs to be newer than Dec. 2016), one can update it using:

    $ cd $HOME/Apps/musrfit
     $ git pull
    -
    -
    -

    Now, depending whether you follow the automake or cmake tool chain you do

    -

    automake toolchain:

    -
    $ make uninstall
    -$ make clean
    -$ make
    -$ make install
    -
    -
    -

    or

    -

    cmake toolchain:

    -
    $ cd build
    +$ cd build
     $ xargs rm < install_manifest.txt
     $ cmake --build ./ --clean-first
     $ make install
     

    As an alternative (if git is not available), the source code can also be downloaded from the following web-page: musrfit at bitbucket

    -
    -

    musrfit build with automake

    -

    After the source-code extraction the autogen.sh script is called to prepare the build environment. -If it has been executed successfully the configure script should be ready to collect all the information needed -to create the Makefiles. If musrfit should support NeXus data files this has to be enabled by specifying the ---enable-NeXus switch when calling configure. For an overview of all available options just call ./configure --help. -Besides the standard options there are a few special options which should be mentioned here:

    -
    -
    - -prefix
    -
    Specify the installation prefix, e.g. $ROOTSYS if already defined (by default: /usr/local).
    -
    - -with-rootsys
    -
    Specify the top of the ROOT installation directory, e.g. $ROOTSYS if already defined.
    -
    - -with-fftw3
    -
    Specify the prefix of the FFTW3 installation. e.g. /usr/local or /usr.
    -
    - -with-gsl
    -
    Set the prefix of the GSL installation, e.g. /usr/local or /usr.
    -
    - -with-boostinc
    -
    Set the path to the header files of the Boost installation, e.g. /usr/local/include or /usr/include.
    -
    - -with-hdf4
    -
    Set the prefix of the HDF4 installation, e.g. /usr/local (only useful in conjunction with the NeXus support).
    -
    - -with-hdf5
    -
    Set the prefix of the HDF5 installation, e.g. /usr (only useful in conjunction with the NeXus support).
    -
    - -with-nexus
    -
    Set the prefix of the NeXus installation, e.g. /usr/local (only useful in conjunction with the NeXus support).
    -
    - -with-qt3
    -
    Set the prefix of the Qt3 installation, e.g. /usr/lib/qt-3.3 (only useful in conjunction with building musrgui).
    -
    - -with-qt4
    -
    Set the prefix of the Qt4 installation, e.g. /usr/lib/qt47 (only useful in conjunction with building musredit).
    -
    - -with-qt5
    -
    Set the prefix of the Qt5 installation, e.g. /usr/lib64 (only useful in conjunction with building musredit).
    -
    - -enable-NeXus
    -
    Enable the support of NeXus data files (requires the HDF4, HDF5 and NeXus libraries to be installed).
    -
    - -disable-editor
    -
    Disable the integrated building of musredit/musrgui.
    -
    - -disable-omp
    -
    Switches off the OpenMP features of musrfit (parallelization of the \(\chi^2\) calculation when compiled with GCC ≥ 4.2).
    -
    -

    Normally it should not be necessary to make use of any of the options except for specifying the installation path with --prefix. 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 musrfit libraries and executables. -A standard installation sequence (without NeXus support) might then look like (In case the normal user has no write permissions to the -$ROOTSYS and the installation path the “make install” commands have to be executed as superuser.):

    -
    $ cd $HOME/Apps/musrfit
    -$ sh autogen.sh
    -$ ./configure --prefix=$ROOTSYS
    -$ make
    -$ make install
    -$ /sbin/ldconfig     # (as superuser)
    -
    -
    -
    -

    musrfit build with cmake

    +

    musrfit build with cmake

    Currently the following configuration switches for musrfit are available:

    -DCMAKE_INSTALL_PREFIX=<prefix-path>
    @@ -421,7 +364,7 @@ $ /sbin/ldconfig # (as superus
    -

    musrfit last step of the installation

    +

    musrfit last step of the installation

    In order to finish the installation of musrfit two more things should be done:

      @@ -440,10 +383,9 @@ detailed information on this XML file refer to the
    -

    musredit

    +

    musredit

    In the latest version of musrfit the configure script tries to determine automatically the highest available Qt version. -In case this is found, the editor musredit is built already together with musrfit. If not, one can try to call -the configure script with the - -with-qt5 option (automake). cmake will determine everthing automatically. +In case this is found, the editor musredit is built already together with musrfit. To install this editor separately, i.e. by “hand” do

    $ cd $HOME/Apps/musrfit/src/musredit_qt5
     $ # for some distributions you will need qmake-qt5 for the next command
    @@ -505,7 +447,7 @@ Please also be aware of the fact that the X server which is going to be installe
     

    Requirements

    -

    Setting up Cygwin

    +

    Setting up Cygwin

    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 @@ -552,8 +494,8 @@ the later handling will be easier if a symbolic link to these files is created n

    Everything but ROOT and NeXus

    -
    -

    Installation of NeXus requirements (optional)

    +
    +

    Installation of NeXus requirements (optional)

    Only if musrfit should support reading data files in the NeXus format the further required software has to be set up. Under Cygwin of all the required libraries only HDF5 is available. The packages hdf5 and libhdf5-devel can be installed through the Cygwin setup. One should also make sure that bison, flex @@ -597,8 +539,8 @@ $ make install

    -
    -

    ROOT

    +
    +

    ROOT

    In order to install the ROOT system, there are two possibilities:

    • Download the precompiled Cygwin GCC 4.3 (or newer) package of the most recent ROOT version @@ -639,8 +581,8 @@ for the user Username

      Afterwards close the Cygwin shell and reopen it again for the installation of musrfit.

    -
    -

    musrfit

    +
    +

    musrfit

    First, the most recent source code should be downloaded. The preferred way of doing so is to clone the musrfit repository via git. Assuming the code should be located in ~/musrfit this is achieved most easily calling from the terminal

    $ cd
    @@ -659,58 +601,8 @@ $ git pull
     

    As an alternative (if git is not available), the source code can also be downloaded from the following web-page: musrfit at bitbucket.

    -
    -

    musrfit build with automake

    -

    After the source-code extraction the autogen.sh script is called to prepare the build environment. -If it has been executed successfully the configure script should be ready to collect all the information -needed to create the Makefiles. If musrfit should support NeXus data files this has to be enabled by -specifying the --enable-static --enable-NeXus switches when calling configure. For an overview of all -available options just call ./configure --help. Besides the standard options there are a few special -options which should be mentioned here:

    -
    -
    - -prefix
    -
    Specify the installation prefix, e.g. /opt/root-system (by default: /usr/local)
    -
    - -with-rootsys
    -
    Specify the top of the ROOT installation directory, e.g. /opt/root-system
    -
    - -with-fftw3
    -
    Specify the prefix of the FFTW3 installation. e.g. /usr/local or /usr
    -
    - -with-gsl
    -
    Set the prefix of the GSL installation, e.g. /usr/local or /usr
    -
    - -with-boostinc
    -
    Set the path to the header files of the Boost installation, e.g. /usr/local/include or /usr/include
    -
    - -with-hdf4
    -
    Set the prefix of the HDF4 installation, e.g. /usr/local (only useful in conjunction with the NeXus support)
    -
    - -with-hdf5
    -
    Set the prefix of the HDF5 installation, e.g. /usr (only useful in conjunction with the NeXus support)
    -
    - -with-nexus
    -
    Set the prefix of the NeXus installation, e.g. /usr/local (only useful in conjunction with the NeXus support)
    -
    - -with-qt3
    -
    Set the prefix of the Qt3 installation, e.g. /usr/lib/qt-3.3 (only useful in conjunction with building musrgui)
    -
    - -with-qt4
    -
    Set the prefix of the Qt4 installation, e.g. /usr/lib/qt47 (only useful in conjunction with building musredit)
    -
    - -with-qt5
    -
    Set the prefix of the Qt5 installation, e.g. /usr/lib/qt56 (only useful in conjunction with building musredit)
    -
    - -enable-NeXus
    -
    Enable the support of NeXus data files (requires the HDF4, HDF5 and NeXus libraries to be installed).
    -
    - -disable-editor
    -
    Disable the integrated building of musredit/musrgui.
    -
    - -disable-omp
    -
    Switches off the OpenMP features of musrfit (parallelization of the \(\chi^2\) calculation when compiled with GCC ≥ 4.2)
    -
    -

    Normally it should not be necessary to make use of any of the options except for specifying the installation path with --prefix. -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 musrfit -libraries and executables. A standard installation sequence (without NeXus support) might then look like:

    -
    $ cd musrfit
    -$ sh autogen.sh
    -$ ./configure --prefix=$ROOTSYS
    -$ make
    -$ make install
    -
    -
    -
    -
    -

    musrfit build with cmake

    +
    +

    musrfit build with cmake

    Currently the following configuration switches for musrfit are available:

    -DCMAKE_INSTALL_PREFIX=<prefix-path>
    @@ -751,12 +643,11 @@ $ /sbin/ldconfig # (as superus
    -
    -

    musredit

    +
    +

    musredit

    In the latest version of musrfit 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 musredit is built -readily with musrfit. If not, one can either try to call the configure script with the ---with-qt4 option or install this editor separately, .e.g.:

    +readily with musrfit. If not, try the following:

    $ cd src/musredit
     $ qmake-qt4 musredit.pro
     
    @@ -780,14 +671,14 @@ musredit &
    -
    -

    musrgui (obsolate)

    +
    +

    musrgui (obsolate)

    If Qt4.5 or higher is not available but Qt3 is set up musrgui can be installed. For this please follow the instructions for the musredit installation where simply every musredit occurrence has to be replaced by musrgui, and qt4 is replaced by qt3.

    -
    -

    Check the installation

    +
    +

    Check the installation

    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 doc/examples/. @@ -819,7 +710,7 @@ or Fink — In the following, both possibilities (using MacPorts or Fink) are described but it is emphasized here that it should be followed only one of the possible routes .

    -

    Requirements (MacPorts)

    +

    Requirements (MacPorts)

    Before proceeding with the usage of the MacPorts system first a few useful tools provided by Apple together with OS X (on the installation DVD/CDs) should be installed:

    @@ -838,7 +729,7 @@ $ sudo xcodebuild -license
    X11
    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 XQuartz <http://xquartz.macosforge.org/trac>. If ROOT runs without XQuartz do not +will need to install XQuartz. If ROOT runs without XQuartz do not install it.

    After installing the Xcode tools go to the MacPorts install page, download @@ -876,8 +767,8 @@ add a new line pointing to your local copy, e.g.

    With Qt5, musredit will be installed. If it happens that you used musrgui in the past, please change over to musredit since there will be no further development for musrgui anymore!

    -
    -

    Installation of NeXus requirements (optional)

    +
    +

    Installation of NeXus requirements (optional)

    Only if musrfit should support reading data files in the NeXus format the further required packages are set up:

    $ sudo port -v install hdf4 hdf5
     
    @@ -906,21 +797,21 @@ $ sudo make install
    -
    -

    ROOT

    -

    ROOT 5.34/xx is supported as legacy version only! The default now will be ROOT 6.xx/yy!

    +
    +

    ROOT

    +

    The default ROOT version is based on ROOT 6.xx/yy!

    ROOT installed via package installer

    The lazy way to get ROOT installed is via package installer. If your macOS is directly supported by the ROOT people you can download the package installer from the ROOT download page. Choose the latest ROOT release and download you macOS version dmg-file, e.g. for macOS 10.13 (High Sierra) -it is at the time of writting root_v6.14.00.macosx64-10.13-clang91.dmg. After the installation +it is at the time of writting root_v6.16.00.macosx64-10.13-clang91.dmg. After the installation ROOT will be installed under /Application 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 ROOT directory:

    $ cd /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
    +$ sudo chown -R <username> root_v6.16.00
    +$ sudo chgrp -R staff root_v6.16.00
    +$ sudo ln -s root_v6.16.00 root
     
    @@ -934,12 +825,12 @@ to install it somewhere else, just systematically replace the related terms of t 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.

    $ cd $HOME/Applications
    -$ git clone http://root.cern.ch/git/root.git
    +$ git clone http://github.com/root-project/root.git
     $ cd root
     $ git tag -l
     $ # git tag -l will list all available tags. In the next command choose the tag v6-10-xx
    -$ # where xx is the highest listed number, e.g. v6-14-00
    -$ git checkout -b v6-14-00 v6-14-00
    +$ # where xx is the highest listed number, e.g. v6-16-00
    +$ git checkout -b v6-16-00 v6-16-00
     $ # now ROOT is ready to be configured. Below you will find the minimal ROOT configuration needed.
     $ # We will use the cmake out-of-source approach here.
     $ mkdir root_build
    @@ -1000,7 +891,7 @@ launchctl setenv LD_LIBRARY_PATH $LD_LIBRARY_PATH
     
    -

    Requirements (Fink)

    +

    Requirements (Fink)

    Before proceeding with the usage of the Fink system first a few useful tools provided by Apple together with OS X (on the installation DVD/CDs) should be installed:

    Xcode
    @@ -1014,7 +905,7 @@ $ sudo xcodebuild -license
    X11
    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 XQuartz <http://xquartz.macosforge.org/trac>. If ROOT runs without XQuartz do not +will need to install XQuartz. If ROOT runs without XQuartz do not install it.

    After installing the Xcode tools go to the Fink download page, @@ -1058,8 +949,8 @@ specific location, the later handling will be easier if a symbolic link to this

    where x_yy_z has to be substituted by the correct version number, e.g. 1_63_0.

    -
    -

    Installation of NeXus requirements (optional)

    +
    +

    Installation of NeXus requirements (optional)

    Only if musrfit should support reading data files in the NeXus format the further required packages can be installed through Fink (check for the most recent versions):

    libjpeg hdf hdf5-cpp11 hdf5-cpp11-shlibs
    @@ -1088,21 +979,21 @@ $ sudo make install
     
    -
    -

    ROOT

    -

    ROOT 5.34/xx is supported as legacy version only and will likely to be dropped in 2018. The default now is ROOT 6.xx/yy!

    +
    +

    ROOT

    +

    The default ROOT version is based on ROOT 6.xx/yy!

    ROOT installed via package installer

    The lazy way to get ROOT installed is via package installer. If your macOS is directly supported by the ROOT people you can download the package installer from the ROOT download page. Choose the latest ROOT release and download you macOS version dmg-file, e.g. for macOS 10.13 (High Sierra) -it is at the time of writting root_v6.14.00.macosx64-10.13-clang91.dmg. After the installation +it is at the time of writting root_v6.16.00.macosx64-10.13-clang91.dmg. After the installation ROOT will be installed under /Application 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 ROOT directory:

    $ cd /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
    +$ sudo chown -R <username> root_v6.16.00
    +$ sudo chgrp -R staff root_v6.16.00
    +$ sudo ln -s root_v6.16.00 root
     
    @@ -1116,12 +1007,12 @@ to install it somewhere else, just systematically replace the related terms of t 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.

    $ cd $HOME/Applications
    -$ git clone http://root.cern.ch/git/root.git
    +$ git clone http://github.com/root-project/root.git
     $ cd root
     $ git tag -l
     $ # git tag -l will list all available tags. In the next command choose the tag v6-10-xx
    -$ # where xx is the highest listed number, e.g. v6-14-00
    -$ git checkout -b v6-14-00 v6-14-00
    +$ # where xx is the highest listed number, e.g. v6-16-00
    +$ git checkout -b v6-16-00 v6-16-00
     $ # now ROOT is ready to be configured. Below you will find the minimal ROOT configuration needed.
     $ # We will use the cmake out-of-source approach here.
     $ mkdir root_build
    @@ -1181,22 +1072,20 @@ launchctl setenv LD_LIBRARY_PATH $LD_LIBRARY_PATH
     
    -
    -

    musrfit

    +
    +

    musrfit

    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 musrfit repository via git. Assuming the code should be located in ~/Applications/musrfit this is achieved most easily calling from the termin

    $ cd ~/Applications
     $ git clone https://bitbucket.org/muonspin/musrfit.git
    -$ # Only if legacy ROOT 5.xx.yy is used include the next line
    -$ cd musrfit; git checkout root5
    +$ cd musrfit
     

    or

    $ cd ~/Applications
     $ git clone git://gitlab.psi.ch/nemu/musrfit.git
    -$ # Only if legacy ROOT 5.xx.yy is used include the next line
    -$ cd musrfit; git checkout root5
    +$ cd musrfit
     

    If a local repository clone is already present, one can update it using:

    @@ -1206,59 +1095,8 @@ $ git pull

    As an alternative (if git is not available), the source code can also be downloaded from the following web-page: musrfit at bitbucket.

    -
    -

    musrfit build with automake

    -

    After the source-code extraction the autogen.sh script is called to prepare the build environment. -If it has been executed successfully the configure script should be ready to collect all the information needed -to create the Makefiles. If musrfit should support NeXus data files this has to be enabled by specifying the ---enable-NeXus switch when calling configure. For an overview of all available options just call ./configure --help. -Besides the standard options there are a few special options which should be mentioned here:

    -
    -
    - -prefix
    -
    Specify the installation prefix, e.g. $ROOTSYS if already defined (by default: /usr/local).
    -
    - -with-rootsys
    -
    Specify the top of the ROOT installation directory, e.g. $ROOTSYS if already defined.
    -
    - -with-fftw3
    -
    Specify the prefix of the FFTW3 installation. e.g. /usr/local or /usr.
    -
    - -with-gsl
    -
    Set the prefix of the GSL installation, e.g. /usr/local or /usr.
    -
    - -with-boostinc
    -
    Set the path to the header files of the Boost installation, e.g. /usr/local/include or /usr/include.
    -
    - -with-hdf4
    -
    Set the prefix of the HDF4 installation, e.g. /usr/local (only useful in conjunction with the NeXus support).
    -
    - -with-hdf5
    -
    Set the prefix of the HDF5 installation, e.g. /usr (only useful in conjunction with the NeXus support).
    -
    - -with-nexus
    -
    Set the prefix of the NeXus installation, e.g. /usr/local (only useful in conjunction with the NeXus support).
    -
    - -with-qt3
    -
    Set the prefix of the Qt3 installation, e.g. /usr/lib/qt-3.3 (only useful in conjunction with building musrgui).
    -
    - -with-qt4
    -
    Set the prefix of the Qt4 installation, e.g. /usr/lib/qt47 (only useful in conjunction with building musredit).
    -
    - -with-qt5
    -
    Set the prefix of the Qt5 installation, e.g. /usr/lib64 (only useful in conjunction with building musredit).
    -
    - -enable-NeXus
    -
    Enable the support of NeXus data files (requires the HDF4, HDF5 and NeXus libraries to be installed).
    -
    - -disable-editor
    -
    Disable the integrated building of musredit/musrgui.
    -
    - -disable-omp
    -
    Switches off the OpenMP features of musrfit (parallelization of the \(\chi^2\) calculation when compiled with GCC ≥ 4.2).
    -
    -

    Normally it should not be necessary to make use of any of the options except for specifying the installation path with --prefix. 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 musrfit libraries and executables. -A standard installation sequence (without NeXus support) might then look like (In case the normal user has no write permissions to the -$ROOTSYS and the installation path the “make install” commands have to be executed as superuser.):

    -
    $ cd $HOME/Apps/musrfit
    -$ sh autogen.sh
    -$ ./configure --prefix=$ROOTSYS
    -$ make
    -$ make install
    -$ /sbin/ldconfig     # (as superuser)
    -
    -
    -
    -
    -

    musrfit build with cmake

    +
    +

    musrfit build with cmake

    Currently the following configuration switches for musrfit are available:

    -DCMAKE_INSTALL_PREFIX=<prefix-path>
    @@ -1298,8 +1136,8 @@ $ /sbin/ldconfig # (as superus
    -
    -

    musrfit last step of the installation

    +
    +

    musrfit last step of the installation

    In order to finish the installation of musrfit two more things should be done:

    • Define the MUSRFITPATH environment variable containing the path to the musrfit executables and XML files. @@ -1315,12 +1153,11 @@ detailed information on this XML file refer to the
    -
    -

    musredit

    +
    +

    musredit

    In the latest version of musrfit the configure script tries to determine automatically the highest available Qt version. In case this is found, the editor musredit is built already together with musrfit. -If not, one can try to call the configure script with the –with-qt5 option (automake). cmake will -determine everthing automatically. To install this editor separately, i.e. by “hand” do

    +If not, try the following:

    $ cd $HOME/Apps/musrfit/src/musredit_qt5
     $ # for some distributions you will need qmake-qt5 for the next command
     $ qmake musredit.pro
    @@ -1353,8 +1190,8 @@ accomplish that, add the following lines to 
    -
    -

    Check the installation

    +
    +

    Check the installation

    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 doc/examples/. If musrgui has been installed, just open one of the test-*.msr files in the editor and test the musrfit @@ -1386,7 +1223,6 @@ $ musrview test-histo-ROOT-NPP.msr

  • musrfit @@ -1400,41 +1236,39 @@ $ musrview test-histo-ROOT-NPP.msr
  • Requirements
  • -
  • musrfit
  • Mac OS X / macOS @@ -1481,12 +1315,12 @@ $ musrview test-histo-ROOT-NPP.msr
  • previous |
  • -
  • musrfit 1.4.1 documentation »
  • +
  • musrfit 1.4.2 documentation »
  • diff --git a/doc/html/tutorial.html b/doc/html/tutorial.html index 14bc3db4..fea64867 100644 --- a/doc/html/tutorial.html +++ b/doc/html/tutorial.html @@ -6,7 +6,7 @@ - Tutorial for musrfit — musrfit 1.4.1 documentation + Tutorial for musrfit — musrfit 1.4.2 documentation @@ -14,7 +14,7 @@ - + @@ -41,7 +41,7 @@
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  • @@ -443,12 +443,12 @@ For a complete description please refer to the manuals of previous | -
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  • diff --git a/doc/html/user-libs.html b/doc/html/user-libs.html index 5dddef1f..0b91497e 100644 --- a/doc/html/user-libs.html +++ b/doc/html/user-libs.html @@ -6,7 +6,7 @@ - Documentation of user libs (user functions) — musrfit 1.4.1 documentation + Documentation of user libs (user functions) — musrfit 1.4.2 documentation @@ -14,7 +14,7 @@ - + @@ -41,7 +41,7 @@
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  • @@ -662,12 +662,12 @@ K(m)&=\int_0^{\pi/2}\frac{\mathrm d\varphi}{\sqrt{1-m^2\sin^2{\varphi}}},\en
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  • diff --git a/doc/html/user-manual.html b/doc/html/user-manual.html index 25a0005f..5b10f3a7 100644 --- a/doc/html/user-manual.html +++ b/doc/html/user-manual.html @@ -6,7 +6,7 @@ - User manual — musrfit 1.4.1 documentation + User manual — musrfit 1.4.2 documentation @@ -14,7 +14,7 @@ - + @@ -41,7 +41,7 @@
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  • @@ -2238,12 +2238,12 @@ In case this cannot be ensured, the parallelization can be disabled by ̵
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