Changes

Remember to check, if there are newer versions of # [http://download.gna.org/minfx minfx] and [http://download.gna.org/bmrblib bmrblib]. <br>The [https://gna.org/projects/minfx/ minfxMinfx#Install | Minfx] and [https://gna.org/projects/bmrblib/ bmrblib] libraries can be installed on all Linux systems by typing:<source lang="bash">cd $HOME/Downloads wget http://download.gna.org/minfx/minfx-1.0.5.tar.gztar -xzf minfx-1.0.5.tar.gzcd minfx-1.0.5#Then eithersudo pip install .# Orsudo python setup.py installcd .. wget http://download.gna.org/bmrblib/bmrblib-1.0.3.tar.gztar -xzf bmrblib-1.0.3.tar.gzcd bmrblib-1.0.3#Then eithersudo pip install .# Orsudo python setup.py installcd ..</source> == mpi4py ==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 [[mpi4pyBmrblib#Install | Bmrblib]] Python package. [http://www.nmr-relax.com/manual/Usage_multi_processor.html See the manual].<br>It requires the installation of '''openmpi''' and the '''mpi4py''' Python package.<br> Remember to check if there are newer versions of [https://bitbucket.org/mpi4py/mpi4py/downloads mpi4py]. <br>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.]:<source lang="bash"># Install openmpi-devel, to get 'mpicc'sudo yum install openmpi-devel# Check for mpiccwhich mpicc# If not found, try this fix, ref: http://forums.fedoraforum.org/showthread.php?t=194688#For 32 computer.sudo ln -s /usr/lib/openmpi/bin/mpicc /usr/bin/mpicc# For 64 bit computer.sudo ln -s /usr/lib64/openmpi/bin/mpicc /usr/bin/mpicc# Source your shell settings, to find the executable, # or restart your terminal.source $HOME/.cshrc # Then install | mpi4pycd $HOME/Downloadswget https://bitbucket.org/mpi4py/mpi4py/downloads/mpi4py-1.3.1.tar.gztar -xzf mpi4py-1.3.1.tar.gzcd mpi4py-1.3.1python setup.py buildsudo python setup.py install</source>]]

<source {{collapsible script| type = Python commands| title = Testing modules by importing them.| lang ="python">| script =

If you would like to play with relax branch rather than the main [http://www.nmr-relax.com/download.html relax downloads], the [httphttps://subversiongit-scm.tigris.orgcom/ SubversionGit] program should first be installed. <br>You can see the different branches [http://svn.gna.org/viewcvs/{{relax/ source|text=here}}.] <br>

=== Using subversion git ===To check out the relax_disp or relax trunk branch using the subversion git client, simply type:<{{#tag:source lang="bash">|svn co svn://svn.gna.org/svn/{{relax/branches/relax_disp relax_dispclone}}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/branches/relax_disp relax_dispsvn co http://svn.gna.org/svn/relax/trunk relax_trunk</source>}}

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_disprelax_trunk

cd relax_disprelax_trunk

=== In multiprocessor mode =Test installation ==<source lang="bash">set RELAX=`which relax`# Normalmpirun -np N+1 $RELAX --multi='mpi4py'# In guimpirun -np N+1 $RELAX --multi='mpi4py' -g</source>where N is the number of slaves {{caution|After an installation you have. See the mpirun documentation for details - this is not part of relax. <br>This code runs in the GUI, the script UI and the prompt UI, i.e. everywhere. == Helper start scripts ==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.=== Script for force running the disp branch of relax on server computer ===This script exemplifies a setup, where the above installation requirements is met on one server computer ''haddock'', and where satellite computersare forced to should really run on this computeran [[Installation_test]]. }}

== Trouble shooting ===== The file '''relax_disp''' is made executable (''chmod +x relax_disp'')menu icons are missing in Linux. ===On some Linux systems, and put in the icons for the menu items are not shown. This was a PATHdecision taken by the Gnome developers at some point to keep the GUI minimal, known by all satellite computersthough in recent versions this behaviour has been reverted.<source lang="bash"br>#!/bin/tcsh -f # Set If you suffer from this problem, to reactive the icons simply type in the lax version used for this script.shell:set RELAX= gconftool-2 --get /network_drivedesktop/software_usergnome/softwareinterface/NMRmenus_have_icons gconftool-2 --relax/relax_disp/relax # Check machine, since only machine haddock have correct packages installed.if ( $HOST != "haddock") then echo "You have to run on haddock. I do it for you" ssh haddock type boolean -Y -t "cd $PWD; $RELAX $argv; set /bindesktop/tcsh"else $RELAX $argvendif<gnome/interface/source> === Script for running the disp branch of relax with maximum number of processors available ===This script exemplifies a setup, to test the running relax with maximum number of processors. menus_have_icons true

The file '''relax_test''' is made executable, and put in a PATH, known by all satellite computersFor GNOME 3 # Get schemas gsettings list-schemas gsettings list-schemas | grep org.gnome.desktop<source lang="bash">#!/bin/tcsh gsettings list-feschemas | grep org.gnome.desktop.interface

# Set the relax version used for this scriptGet keys gsettings list-keys org.gnome.desktop.interface gsettings list-keys org.gnome.desktop.interface | grep iconset RELAX=/sbinlab2/tlinnet/software/NMR gsettings list-relax/relax_disp/relaxkeys org.gnome.desktop.interface | grep desktop

# Set number of available CPUsGet value gsettings get org.gnome.set NPROC=`nproc`set NP=`echo $NPROC + 1 | bc ` echo "Running relax with NP=$NP in multi-processor mode" # Run relax in multi processor modedesktop./usr/lib64/openmpi/bin/mpirun interface icon-np $NP $RELAX --multi='mpi4py' $argv</source>theme

== Trouble shooting == # Check=== The menu icons are missing in Linux gsettings list-keys org. ===On some Linux systems, the icons for the menu items are not showngnome.settings-daemon. 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 revertedplugins. <br>If you suffer from this problem, to reactive the icons simply type in the shell:xsettings gconftoolgsettings get org.gnome.settings-2 --type boolean --set /desktop/gnome/interface/menus_have_icons truedaemon.plugins.xsettings overrides