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Installation mac

282 bytes added, 11:49, 27 October 2017
→‎Check out a relax branch: Transclusion of the {{historical svn}} template.
How to install relax on Mac OS X systems.
 
== Installing the relax dependencies ==
The [http://plasma-gate.weizmann.ac.il/Grace/ Grace] software is used for visualisation of 2D data sets.
== The official way == The most reliable way to install relax on your system is to use the official way Python releases. The steps are: === Python === First check if you have the latest Python 2.7 installed, before installing the newest. Search in Spotlight for '''Terminal''', and write here<source lang="bash">which pythonpython --version</source>If needed, download the latest 2.7 version from the [http://www.python.org/download/ Official Python website].<br>This should be the DMG file labelled as '''Python 2.7.x Mac OS X 64-bit/32-bit x86-64/i386 Installer (for Mac OS X 10.6 and later)'''.<br>Open the DMG file, double click on the '''Python.mpkg''' file, and follow the instructions.<br>The Python binary should now be located at '''/usr/local/bin/python'''. This is actually a symbolic link pointing to '''/Library/Frameworks/Python.framework/Versions/2.7/bin/python'''. === Check out a relax branch ==={{historical svn}}You can see the different relax branches [http://svn.gna.org/viewcvs/relax/ here.]. '''Subversion''' is necessary, and should be shipped with [ http://subversion.apache.org/packages.html#osx OS X].<source lang="bash">which svnsvn --versioncd $HOME/Downloads</source>To check out trunk using the subversion client, simply type:<source lang="bash">svn co svn://svn.gna.org/svn/relax/trunk relax_trunk</source>If this svn command does not work, try:<source lang="bash">svn co http://svn.gna.org/svn/relax/trunk relax_trunk</source> === SCons - building relax=== This is required to build the relax C modules. Download the file form the [http://www.scons.org/download.php SCons download site].** Download the file called '''scons-2.x.x.tar.gz'''. <br>** Open this through the Finder to unpackage the archive into the '''~/Downloads/scons-2.x.x/''' directory. <br>** Open a terminal and type, replacing the x's with the current version, the following to get into the correct directory:<source lang="bash">cd $HOME/Downloads/scons-2.x.x</source>Then compile by:<source lang="bash">sudo python setup.py install</source>If you have several Python versions, then compile with the wished python interpreter by typing:<source lang="bash">sudo /Library/Frameworks/Python.framework/Versions/2.7/bin/python setup.py install</source>This should install scons into '''/usr/local/bin/scons'''. <br><source lang="bash">which scons</source> === First try to build relax ===To compile the C modules in relax, several packages must be in place, including the minfx package.<br>But we can just try to build relax now, and then solve the dependencies.<source lang="bash">cd $HOME/Downloads/relax_trunk# Then buildscons</source>You should get the message: '''The dependency 'minfx' has not been installed''' === Minfx and Bmrblib === # [[Minfx#Install | Minfx]]# [[Bmrblib#Install | Bmrblib]] Let's try to build again<source lang="bash">cd $HOME/Downloads/relax_trunkscons</source>If you get the message '''-bash: gcc: command not found''', you need to install [https://developer.apple.com/xcode/ Apple Xcode]. === Numpy ===First check if you have numpy installed in the current python installation.<source lang="bash">pythonimport numpynumpy.__version__; numpy.__file__# Exit python with: Ctrl+d</source>If needed, download the latest Numpy DMG file from the [http://sourceforge.net/projects/numpy/files/NumPy/ sourceforge download site].<br>This should be the DMG file '''numpy-1.x.x-py2.7-python.org-macosx10.x.dmg'''.<br>Open the DMG file, double click on the '''numpy-1.x.x-py2.7.mpkg''' file, and follow the instructions. === Scipy ===First check if you have scipy installed in the current python installation.<source lang="bash">pythonimport scipyscipy.__version__; scipy.__file__# Exit python with: Ctrl+d</source>If needed, download the latest Scipy DMG file from the [http://sourceforge.net/projects/scipy/files/scipy/ sourceforge download site].<br>This should be the DMG file '''scipy-0.xx.x-py2.7-python.org-macosx10.3.dmg'''.<br>Open the DMG file, double click on the '''scipy-0.xx.x-py2.7.mpkg''' file or equivalent, and follow the instructions.
=== wxPython ===First check if you have wxPzthon installed in the current python installation.<source lang="bash">pythonimport wxwx.__version__; wx.__file__# Exit python with: Ctrl+d</source>If needed, download the wxPython Development 2.9 DMG file from the [http://wxpython.org/download.php#unstable official wxPython website].<br>The most reliable way to install relax link should be called '''wxPython2.9-osx-cocoa-py2.7'''.<br>Open the DMG file, double click on your system is to use the official Python releases'''wxPython2.9-osx-cocoa-py2.7.pkg''' file, and follow the instructions. The steps are:
* '''Python:''' First download the latest 2.7 version from the [http://www.python.org/download/ Official Python website].** This should be the DMG file labelled as '''Python 2.7.x Mac OS X 64-bit/32-bit x86-64/i386 Installer (for Mac OS X 10.6 and later)'''.** Open the DMG file, double click on the '''Python.mpkg''' file, and follow the instructions.** The Python binary should now be located at '''/usr/local/bin/python'''. This is actually a symbolic link pointing to '''/Library/Frameworks/Python.framework/Versions/2.7/bin/python'''.* '''wxPython:''' Download the wxPython Development 2.9 DMG file from the [http://wxpython.org/download.php#unstable official wxPython website].** The link should be called '''wxPython2.9-osx-cocoa-py2.7'''.** Open the DMG file, double click on the '''wxPython2.9-osx-cocoa-py2.7.pkg''' file, and follow the instructions.* '''Numpy:''' Download the latest Numpy DMG file from the [http://sourceforge.net/projects/numpy/files/NumPy/ sourceforge download site].** This should be the DMG file '''numpy-1.x.x-py2.7-python.org-macosx10.3.dmg'''.** Open the DMG file, double click on the '''numpy-1.x.x-py2.7.mpkg''' file, and follow the instructions.* '''Scipy:''' Download the latest Scipy DMG file from the [http://sourceforge.net/projects/scipy/files/scipy/ sourceforge download site].=== Mpi4py ===** {{note|This should be the DMG file '''scipy-0.xx.x-py2.7-python.org-macosx10.3.dmg'''.** Open the DMG file, double click on the '''scipy-0.xx.x-py2.7.mpkg''' file or equivalent, and follow the instructions.* '''Mpi4py:''' This is for running on multi-processor machines, for the analyses in relax which support it. Download the file from the [https://code.google.com/p/mpi4py/downloads/list mpi4py download site].** Note, this will require an up to date version of XCode installed on your system, as the code will be compiled.** Download the file labelled as '''mpi4py-1.x.x.tar.gz'''.** Open this through the Finder to unpackage the archive into the '''~/Downloads/mpi4py-1.x.x/''' directory.** Open a terminal and type, replacing the x's with the current version, the following to get into the correct directory: <source lang="bash">$ cd ~/Downloads/mpi4py-1.x.x </source>** Then to be sure the correct Python version is being used, type: <source lang="bash">$ sudo /Library/Frameworks/Python.framework/Versions/2.7/bin/python setup.py install </source>* '''SCons:''' This is required to build the relax C modules. Download the file form the [http://www.scons.org/download.php SCons download site].** Download the file called '''scons-2.x.x.tar.gz'''.** Open this through the Finder to unpackage the archive into the '''~/Downloads/scons-2.x.x/''' directory.** Open a terminal and type, replacing the x's with the current version, the following to get into the correct directory: <source lang="bash">$ cd ~/Downloads/scons-1.x.x </source>** Then to be sure the correct Python version is being used, type: <source lang="bash">$ sudo /Library/Frameworks/Python.framework/Versions/2.7/bin/python setup.py install</source>** This will install scons into '''/usr/local/bin/scons'''.** To compile the C modules, the minfx package must be installed first. Please see below.** You may still have 'minfx' installation problems when compiling the C modules if multiple Python version are present. So it is recommended to open the '''/usr/local/bin/scons''' file and change the first line from '''/usr/bin/env python''' to '''/usr/local/bin/python''' so that the correct Python version is used. Alternatively you change your PATH environmental variable to have '''/usr/local/bin/''' at the start. SCons is always an issue when multiple Python versions are installed.}}
==== Multiple Python versions ====This is for running on multi-processor machines, for the analyses in relax which support it.
For more details, see # [[Multiple Python versionsMpi4py#Install | Mpi4py]].
Now you will need to check that the correct Python and SCons versions are used when running relax or compiling the C modules. This can be checked by typing the following:
<source lang="bash">
$ sudo /usrLibrary/libexecFrameworks/locatePython.updatedb$ which python$ locate python | grep '\framework/python$\|\Versions/python2...$' | grep 7/bin | xargs ls -alh$ which scons$ locate python | grep '\/python$\|\/pythonsetup...$' | grep bin | xargs ls -alhpy install
</source>
The first command updates the locate database, the '''which''' commands show which version == Use of Python and SCons will be executed if '''python''' or '''scons''' are typed at the prompt, and the locate commands will show all installed versions of Python and SCons.repositories ==
=== macports ===
pip install numpy
=== Minfx and Bmrblib ===
Remember to check if there are newer versions of # [http://download.gna.org/minfx minfx[Minfx#Install | Minfx] and [http://download.gna.org/bmrblib bmrblib]. <br>The # [https://gna.org/projects/minfx/ minfx[Bmrblib#Install | Bmrblib] and [https://gna.org/projects/bmrblib/ bmrblib] libraries can be installed on all Linux systems by typing:<source lang="bash">wget http://download.gna.org/minfx/minfx-1.0.5.tar.gztar -xzf minfx-1.0.5.tar.gzcd minfx-1.0.5python setup.py installcd .. wget http://download.gna.org/bmrblib/bmrblib-1.0.3.tar.gztar -xzf bmrblib-1.0.3.tar.gzcd bmrblib-1.0.3python setup.py installcd ..</source>
Note that if you have multiple Python versions, the correct one must be specified. It is best to use the full Python path, for example:
>>> import wx
>>> wx.__version__; wx.__file__
'...'
>>> import bmrblib
>>> bmrblib.__version__; bmrblib.__file__
'...'
>>> import minfx
>>> minfx.__version__; minfx.__file__
'...'
</source>
== Checking out a relax branch Test Installation ==If {{tip|After an installation you would like to play with relax branch rather than the main should really run an [http://www.nmr-relax.com/download.html relax downloads], the [http://subversion.tigris.org/ SubversionInstallation_test] program should first be installed. <br>You can see the different branches [http://svn.gna.org/viewcvs/relax/ here.] <br>First the relax sources can be checked out of the source code repository and the C modules compiled:<source lang="bash">cd /usr/local/svn co svn://svn.gna.org/svn/relax/branches/relax_disp relax_dispcd relax_dispscons # Optional building of the user manual, if a LaTeX installation is available.scons user_manual_pdf</source>}}
If the svn command does not work, try:<source lang="bash">svn co http://svn.gna.org/svn/relax/branches/relax_disp relax_disp</source>= Trouble shooting ==
=== Multiple Python versions ===
For more details, see [[Multiple Python versions]].
=== Add You will need to check that the correct Python and SCons versions are used when running relax to path ===or compiling the C modules. This can be checked by typing the following:
<source lang="bash">
cd $ sudo /usr/locallibexec/binlocate.updatedb$ which pythonln -s $ locate python | grep '\/usrpython$\|\/local/relax_disp/relax python..</source>Restart the terminal, to load the new variables.$' | grep bin | xargs ls -alh$ which sconsStart relax in GUI mode<source lang="bash">relax $ locate scons | grep '\/scons$' | grep bin | xargs ls -galh
</source>
The first command updates the locate database, the '''which''' commands show which version of Python and SCons will be executed if '''python''' or '''scons''' are typed at the prompt, and the locate commands will show all installed versions of Python and SCons.
= TEST INSTALLATION =You may still have 'minfx' installation problems when compiling the C modules if multiple Python version are present. <br>So it is recommended to open the '''/usr/local/bin/scons''' file and change the first line from '''/usr/bin/env python''' to '''/usr/local/bin/python''' so that the correct Python version is used.<br>After an installation Alternatively you should really run change your PATH environmental variable to have '''/usr/local/bin/''' at the start. SCons is always an [[Installation_test]]issue when multiple Python versions are installed.
== See also ==
[[Category:Installation]]
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