Installation guide

A step-by-step instructions to follow in order to install all the required packages and tools.
Example of installation in a Debian 8 as root:
  1. as root
    2. $ su
  2. install subversion, version control packaes
    3. # apt-get install subversion
  3. install GIT, different paradigm version control
    4. # apt-get install git
  4. get python and its necessary applications
    5. # apt-get install python python-scipy python-numpy cython cython-dbg
  5. get netcdf libraries tools and applications (cdo and nco are also installed maybe not required...)
    6. # apt-get install netcdf-bin netcdf-dbg libnetcdf-dev netcdf-doc ncview cdo nco
  6. get hdf5
    7. # apt-get install libhdf5-dev
  7. install matplotlib and basemap in order to plot and drow maps
    8. # apt-get install python-matplotlib python-matplotlib-data python-matplotlib-doc python-mpltoolkits.basemap python-mpltoolkits.basemap-data
  8. install system tools (Scripts use LATEX interface for titles and labels)
    9. # apt-get install dvipng
  9. install netcdf4, python API interface to netCDF files
    1. Some new linux distributions (at least Debian >8) provide the netcdf4 API in the package systems:
      2. # apt-get install python-netcdf4
    2. Otherwise, it can be manually done. Be careful with interferencies with anaconda (some issues on mixture of netcdf libraries have been detected).
      • Following https://github.com/Unidata/netcdf4-python)
        • # git clone https://github.com/Unidata/netcdf4-python.git
        cd netcdf4-python/
      • Editing `setup.cfg' to add/change some values (there are installation issues if `nc-config' is used along installation)
        • 
use_ncconfig=False
netCDF4_dir = /usr/local
HDF5_dir = /usr/local
HDF5_libdir = /usr/lib/x86_64-linux-gnu/hdf5/serial
HDF5_INCDIR = /usr/include/hdf5/serial
        # python setup.py build >& run_pysetup.log
        # python setup.py install >& run_pyinstall.log
  10. Getting the scripts, no need to be root:
    11. # exit
    $ cd $HOME
    $ svn co http://svn.lmd.jussieu.fr/LMDZ_WRF/trunk/tools PyNCplot
  11. Now all the scripts are held in ${HOME}/PyNCplot. It might be desirable to set an environment variable to make life easier:
    $ export pyHOME=${HOME}/PyNCplot
  12. Finally one need to compile the Fortran modules using the same python to run the scripts. This is done using a standard `Makefile' and the tool f2py to link Fortran compiled codes to python. There are different versions for different LMD/IPSL and French HPC machines. For a standard linux 64-bits machine (debain 7) there is one example as `Makefile.foudre'. Follow the instructions there in after linking the appropriated file:
    13. $ ln -s Makefile.[machine].[compiler] ./Makefile
    At the end one should have: 
    
      module_ForDiag.so
      module_ForInt.so