Difference between revisions of "Installation linux"

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__TOC__
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== Installing the relax dependencies ==
 
== Installing the relax dependencies ==
  
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== Minfx and Bmrblib ==
 
== Minfx and Bmrblib ==
  
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Remember to check, if there are newer versions of [http://download.gna.org/minfx minfx] and [http://download.gna.org/bmrblib bmrblib]. <br>
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# [[Minfx#Install | Minfx]]
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The [https://gna.org/projects/minfx/ minfx] and [https://gna.org/projects/bmrblib/ bmrblib] libraries can be installed on all Linux systems by typing:
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# [[Bmrblib#Install | Bmrblib]]
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<source lang="bash">
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# [[mpi4py#Install | mpi4py]]
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cd $HOME/Downloads
 
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wget http://download.gna.org/minfx/minfx-1.0.6.tar.gz
 
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tar -xzf minfx-1.0.6.tar.gz
 
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cd minfx-1.0.6
 
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#Then either
 
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sudo pip install .
 
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# Or
 
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sudo python setup.py install
 
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cd ..
 
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wget http://download.gna.org/bmrblib/bmrblib-1.0.3.tar.gz
 
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tar -xzf bmrblib-1.0.3.tar.gz
 
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cd bmrblib-1.0.3
 
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#Then either
 
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sudo pip install .
 
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# Or
 
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sudo python setup.py install
 
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cd ..
 
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</source>
 
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== mpi4py ==
 
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For the model-free and relaxation dispersion analyses in relax, the optimisation can be speed up using Gary Thompson's multi-processor framework.  This allows the calculations to be run on a computer cluster.  This uses OpenMPI via the [[mpi4py]] Python package. [http://www.nmr-relax.com/manual/Usage_multi_processor.html See the manual].<br>
 
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It requires the installation of '''openmpi''' and the '''mpi4py''' Python package.<br>
 
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Remember to check if there are newer versions of [https://bitbucket.org/mpi4py/mpi4py/downloads mpi4py]. <br>
 
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The [https://code.google.com/p/mpi4py/ mpi4py] libraries can be installed on all Linux systems by typing [http://mpi4py.scipy.org/docs/usrman/install.html or check instructions here.]:
 
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<source lang="bash">
 
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# Install openmpi-devel, to get 'mpicc'
 
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sudo yum install openmpi-devel
 
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# Check for mpicc
 
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which mpicc
 
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# If not found, try this fix, ref: http://forums.fedoraforum.org/showthread.php?t=194688
 
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#For 32 computer.
 
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sudo ln -s /usr/lib/openmpi/bin/mpicc /usr/bin/mpicc
 
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# For 64 bit computer.
 
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sudo ln -s /usr/lib64/openmpi/bin/mpicc /usr/bin/mpicc
 
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# Source your shell settings, to find the executable,
 
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# or restart your terminal.
 
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source $HOME/.cshrc
 
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# Then install mpi4py
 
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cd $HOME/Downloads
 
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wget https://bitbucket.org/mpi4py/mpi4py/downloads/mpi4py-1.3.1.tar.gz
 
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tar -xzf mpi4py-1.3.1.tar.gz
 
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cd mpi4py-1.3.1
 
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#Then either
 
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sudo pip install .
 
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# Or
 
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python setup.py build
 
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sudo python setup.py install
 
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</source>
 
  
 
== Testing the Python installation ==
 
== Testing the Python installation ==
  
 
Before installing relax, it is best to be sure that the Python modules are functional by importing them:
 
Before installing relax, it is best to be sure that the Python modules are functional by importing them:
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<source lang="python">
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 +
{{collapsible script
 +
| type  = Python commands
 +
| title  = Testing modules by importing them.
 +
| lang   = python
 +
| script =
 
$ python
 
$ python
 
Python 2.6.6 (r266:84292, Oct 12 2012, 14:23:48)
 
Python 2.6.6 (r266:84292, Oct 12 2012, 14:23:48)
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>>> mpi4py.__file__
 
>>> mpi4py.__file__
 
'...'
 
'...'
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</source>
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}}
  
 
== Checking out a relax branch ==
 
== Checking out a relax branch ==
  
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If you would like to play with relax branch rather than the main [http://www.nmr-relax.com/download.html relax downloads], the [http://subversion.tigris.org/ Subversion] program should first be installed. <br>
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If you would like to play with relax branch rather than the main [http://www.nmr-relax.com/download.html relax downloads], the [https://git-scm.com/ Git] program should first be installed. <br>
−
You can see the different branches [http://svn.gna.org/viewcvs/relax/ here.] <br>
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You can see the different branches {{relax source|text=here}}. <br>
 
First the relax sources can be checked out of the source code repository and the C modules compiled:
 
First the relax sources can be checked out of the source code repository and the C modules compiled:
  
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=== Using subversion ===
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=== Using git ===
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To check out the relax_disp or trunk branch using the subversion client, simply type:
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To check out the relax trunk using the git client, simply type:
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<source lang="bash">
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{{#tag:source|
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svn co svn://svn.gna.org/svn/relax/branches/relax_disp relax_disp
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{{relax clone}}
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svn co svn://svn.gna.org/svn/relax/trunk relax_trunk
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| lang="bash"
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</source>
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}}
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If this svn command does not work, try:
 
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<source lang="bash">
 
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svn co http://svn.gna.org/svn/relax/branches/relax_disp relax_disp
 
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svn co http://svn.gna.org/svn/relax/trunk relax_trunk
 
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</source>
 
  
 
=== Compilation of the C modules ===
 
=== Compilation of the C modules ===
  
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For the R1 and R2 and relaxation dispersion analyses, the relax C modules must be compiled.  This is done using the scons program, by simply typing:
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For the {{:R1}} and {{:R2}} and relaxation dispersion analyses, the relax C modules must be compiled.  This is done using the scons program, by simply typing:
 
<source lang="bash">
 
<source lang="bash">
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cd relax_disp
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cd relax_trunk
 
scons
 
scons
 
</source>
 
</source>
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<source lang="bash">
 
<source lang="bash">
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cd relax_disp
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cd relax_trunk
 
echo "setenv PATH $PWD"':$PATH' >> $HOME/.cshrc
 
echo "setenv PATH $PWD"':$PATH' >> $HOME/.cshrc
 
</source>
 
</source>
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</source>
 
</source>
  
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=== In multiprocessor mode ===
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== Test installation ==
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<source lang="bash">
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{{caution|After an installation you should really run an [[Installation_test]].}}
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set RELAX=`which relax`
 
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# Normal
 
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mpirun -np N+1 $RELAX --multi='mpi4py'
 
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# In gui
 
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mpirun -np N+1 $RELAX --multi='mpi4py' -g
 
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</source>
 
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where N is the number of slaves you have.  See the mpirun documentation for details - this is not part of relax.  <br>
 
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This code runs in the GUI, the script UI and the prompt UI, i.e. everywhere.
 
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== Helper start scripts ==
 
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If you have several versions or development branches of relax installed, you could probably use some of these scripts, and put them in your PATH.
 
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=== Script for force running the disp branch of relax on server computer ===
 
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This script exemplifies a setup, where the above installation requirements is met on one server computer ''haddock'', and where satellite computers
 
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are forced to run on this computer.  
 
  
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The file '''relax_disp''' is made executable (''chmod +x relax_disp''), and put in a PATH, known by all satellite computers.
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== Trouble shooting ==
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<source lang="bash">
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=== The menu icons are missing in Linux. ===
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#!/bin/tcsh -f
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On some Linux systems, the icons for the menu items are not shown. This was a decision taken by the Gnome developers at some point to keep the GUI minimal, though in recent versions this behaviour has been reverted. <br>
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If you suffer from this problem, to reactive the icons simply type in the shell:
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# Set the lax version used for this script.
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gconftool-2 --get /desktop/gnome/interface/menus_have_icons
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set RELAX=/network_drive/software_user/software/NMR-relax/relax_disp/relax
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gconftool-2 --type boolean --set /desktop/gnome/interface/menus_have_icons true
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# Check machine, since only machine haddock have correct packages installed.
 
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if ( $HOST != "haddock") then
 
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        echo "You have to run on haddock. I do it for you"
 
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        ssh haddock -Y -t "cd $PWD; $RELAX $argv; /bin/tcsh"
 
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else
 
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        $RELAX $argv
 
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endif
 
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</source>
 
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=== Script for running the disp branch of relax with maximum number of processors available ===
 
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This script exemplifies a setup, to test the running relax with maximum number of processors.
 
  
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The file '''relax_test''' is made executable, and put in a PATH, known by all satellite computers.
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For GNOME 3
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<source lang="bash">
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# Get schemas
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#!/bin/tcsh -fe
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gsettings list-schemas
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gsettings list-schemas | grep org.gnome.desktop
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gsettings list-schemas | grep org.gnome.desktop.interface
  
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# Set the relax version used for this script.
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# Get keys
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set RELAX=/sbinlab2/tlinnet/software/NMR-relax/relax_disp/relax
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gsettings list-keys org.gnome.desktop.interface
 +
gsettings list-keys org.gnome.desktop.interface | grep icon
 +
gsettings list-keys org.gnome.desktop.interface | grep desktop
  
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# Set number of available CPUs.
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# Get value
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set NPROC=`nproc`
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gsettings get org.gnome.desktop.interface icon-theme
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set NP=`echo $NPROC + 1 | bc `
 
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echo "Running relax with NP=$NP in multi-processor mode"
 
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# Run relax in multi processor mode.
 
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/usr/lib64/openmpi/bin/mpirun -np $NP $RELAX --multi='mpi4py' $argv
 
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</source>
 
  
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== TEST INSTALLATION ==
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# https://wiki.archlinux.org/index.php/GNOME/Tips_and_tricks#Enable_button_and_menu_icons
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After an installation you should really run an [[Installation_test]]
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# Since GTK+ 3.10, the GSettings key 'menus-have-icons' has been deprecated. Icons in buttons and menus can still be enabled by setting the following overrides:
 +
gsettings set org.gnome.settings-daemon.plugins.xsettings overrides "{'Gtk/ButtonImages': <1>, 'Gtk/MenuImages': <1>}"
  
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== Trouble shooting ==
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# Check
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=== The menu icons are missing in Linux. ===
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gsettings list-keys org.gnome.settings-daemon.plugins.xsettings
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On some Linux systems, the icons for the menu items are not shown. This was a decision taken by the Gnome developers at some point to keep the GUI minimal, though in recent versions this behaviour has been reverted. <br>
+
  gsettings get org.gnome.settings-daemon.plugins.xsettings overrides
−
If you suffer from this problem, to reactive the icons simply type in the shell:
 
−
  gconftool-2 --type boolean --set /desktop/gnome/interface/menus_have_icons true
 
  
 
== See also ==
 
== See also ==
 
[[Category:Installation]]
 
[[Category:Installation]]

Latest revision as of 20:42, 27 October 2017

Installing the relax dependencies

The python-devel and scons packages are only required if the C modules need to be compiled for your system.

  • Grace software is used for visualisation of 2D data sets.
  • subversion is only if you wan't to checkout the source code.
  • matplotlib is not a necessity, but is likely to be implemented later for extended plotting.

RHEL 5 and compatible distributions

For RPM-based Linux distributions with access to the YUM installer, first install the relax dependencies with: 

yum install python
yum install python-devel
yum install numpy
yum install scipy
yum install scons
yum install wxPython
yum install grace
yum install subversion
yum install python-matplotlib

# We can manage python package installations with pip
sudo easy_install pip

If you do not have root access but are in the sudo group, then add a sudo before each of the above commands.

Minfx and Bmrblib

  1. Minfx
  2. Bmrblib
  3. mpi4py

Testing the Python installation

Before installing relax, it is best to be sure that the Python modules are functional by importing them:

Python commands: Testing modules by importing them.

Checking out a relax branch

If you would like to play with relax branch rather than the main relax downloads, the Git program should first be installed.
You can see the different branches here.
First the relax sources can be checked out of the source code repository and the C modules compiled:

Using git

To check out the relax trunk using the git client, simply type: 

git clone git://git.code.sf.net/p/nmr-relax/code/ relax

Compilation of the C modules

For the R1 and R2 and relaxation dispersion analyses, the relax C modules must be compiled. This is done using the scons program, by simply typing: 

cd relax_trunk
scons

You must be in the base relax directory for this to work.

In addition, if you would like to compile the relax user manual via LaTeX, you can also use scons. See the wiki page manual.:

Add to path - C_shell / Tcsh

cd relax_trunk
echo "setenv PATH $PWD"':$PATH' >> $HOME/.cshrc

Restart the terminal, to load the new variables.

Start relax

Normal

# Normal
relax
# See help
relax -h
# In GUI mode
relax -g
# Execute script
relax -g

Test installation

Caution  After an installation you should really run an Installation_test.

Trouble shooting

The menu icons are missing in Linux.

On some Linux systems, the icons for the menu items are not shown. This was a decision taken by the Gnome developers at some point to keep the GUI minimal, though in recent versions this behaviour has been reverted.
If you suffer from this problem, to reactive the icons simply type in the shell: 

gconftool-2 --get /desktop/gnome/interface/menus_have_icons
gconftool-2 --type boolean --set /desktop/gnome/interface/menus_have_icons true

For GNOME 3 

# Get schemas
gsettings list-schemas
gsettings list-schemas | grep org.gnome.desktop
gsettings list-schemas | grep org.gnome.desktop.interface

# Get keys
gsettings list-keys org.gnome.desktop.interface 
gsettings list-keys org.gnome.desktop.interface | grep icon
gsettings list-keys org.gnome.desktop.interface | grep desktop

# Get value
gsettings get org.gnome.desktop.interface icon-theme

# https://wiki.archlinux.org/index.php/GNOME/Tips_and_tricks#Enable_button_and_menu_icons
# Since GTK+ 3.10, the GSettings key 'menus-have-icons' has been deprecated. Icons in buttons and menus can still be enabled by setting the following overrides: 
gsettings set org.gnome.settings-daemon.plugins.xsettings overrides "{'Gtk/ButtonImages': <1>, 'Gtk/MenuImages': <1>}"

# Check
gsettings list-keys org.gnome.settings-daemon.plugins.xsettings
gsettings get org.gnome.settings-daemon.plugins.xsettings overrides

See also

Retrieved from "http://wiki.nmr-relax.com/wiki/index.php?title=Installation_linux&oldid=7295"