BISMG:SarahS/jules testing

JULES ROSE testing
Stuff to install for the VM
 * Install virtual box (https://www.virtualbox.org/) and vagrant 1.5 or later (https://www.vagrantup.com/)
 * Install cygwin (https://www.cygwin.com/). Select the xinit and xorg-server packages from the X11 section and the openssh and openssl packages from the Net section.

VM set up and run

 * Download VM from https://github.com/metomi/metomi-vms (the ubuntu-1404)
 * cd \cygwin\c\metomi-vms-master\ubuntu-1404
 * \cygwin\c\Vagrant\bin\vagrant.exe up
 * Enter password and user name. Make sure there is no % symbol in the password
 * sudo install-jules-extras installs netCDF libraries and utilities like ncdump, nccmp
 * Synphx is already installed on the VM but we need latex also to build the pdf containing the documentation. sudo apt-get install texlive-full
 * Note sure but might need to do this to install latex as well.  make latexpdf

Generate KGO data

 * install-jules-gswp2-data installs the forcing data
 * fcm co https://code.metoffice.gov.uk/svn/jules/main/trunk@793 jules-trunk (to check out version 4.2 trunk)
 * cd jules-trunk
 * rose stem --task=generate_kgo --source=. --new (this will create kgo data in /jules/rose-stem-kgo/vn4.2)
 * KGO will be written to ~jules/rose-stem-kgo

Run ROSE stem tests

 * Check out a copy of the code fcm co https://code.metoffice.gov.uk/svn/jules/main/trunk@793 jules_vn4.2
 * cd jules_vn4.2
 * rose stem --group=all --source=. --new (will run all the rose stem tests)
 * Check trac.log in ~/cycl_run/jules_vn4.2 for the results

Run JULES with ROSE

 * First create a rose suite from namelists. Go to ~/jules-doc/examples/pl where the namelists are
 * ~/jules-trunk/bin/create_rose_app vn4.2 vn4.2
 * cd rose-suite
 * rosie create save as tmp-aa004 (y)
 * cp -r rose-suite/* ~/roses/tmp-aa004
 * rose edit -M ~/jules-trunk/rose-meta -C ~/roses/tmp-aa004&

Editing the documentation
* Change jules_surf_hgt namelist stuff in model_grid.nml.rst
 * svn co https://code.metoffice.gov.uk/svn/jules/doc/branches/dev/sarahshannon/vn4.3_absoluteheight jules-doc-n4.3_absoluteheight
 * svn commit -m "Make documentation clearer." model_grid.nml.rst
 * make latexpdf
 * qpdfview build/latex/JULES_User_Guide.pdf
 * qpdfview JULES_User_Guide.pdf& to view the documentation

rose edit -M /home/vagrant/jules-trunk/rose-meta -C /home/vagrant/jules-trunk/rose-stem

svn copy -r 793 https://code.metoffice.gov.uk/svn/jules/main/trunk/ https://code.metoffice.gov.uk/svn/jules/main/branches/dev/sarahshannon/vn4.2_absoluteheight