== Why would I want to install another netcdf library? ==
You don't want to install another netcdf library. In general all is taken care of by the TCCG and the libIGCM team. Nevertheless, there was a netcdf-related problem in March 2015 and this was the procedure to load a different netcdf library, use it for the compilation and use it for running the model.
 
Check which modules are loaded
{{{
module list
}}}

Unload the module you no longer want to use, i.e., netcdf/4.2_hdf5_parallel. Note that there could be dependencies between modules. If so, unload whatever needs to be unloaded.
{{{
module unload netcdf/4.2_hdf5_parallel (NetCDF)
}}}

and load the new module
{{{
module load netcdf/4.3.3.1_hdf5_parallel
}}}

Check if the new module was loaded
{{{
module list
}}}

Check for the library paths in the module
{{{
module show netcdf/4.3.3.1_hdf5_parallel
}}}

for this example you will get the follow output
{{{
...
setenv		NETCDF_ROOT	/usr/local/netcdf-4.3.3.1_hdf5_parallel
setenv		NETCDF_EXEDIR	/usr/local/netcdf-4.3.3.1_hdf5_parallel/bin
setenv		NETCDF_INCDIR	/usr/local/netcdf-4.3.3.1_hdf5_parallel/include
setenv		NETCDF_LIBDIR	/usr/local/netcdf-4.3.3.1_hdf5_parallel/lib
...
}}}

Make sure that these paths are used in
{{{
../../modeles/IOIPSL/src/Makefile
../../modeles/ORCHIDEE/arch.path
../../modeles/LMDZ/arch.path
../../modeles/XIOS/arch/arch-X64_CURIE.path
}}}

When you change from library 4.2 to 4.3.3.1 you will have to change NETCDF_INC_DIR to NETCDF_INCDIR and NETCDF_LIB_DIR to NETCDF_LIBDIR in files above. 

Make sure that the correct modules are loaded in XIOS .env file : (you can empty this file as you already loaded the netcdf and hdf5): 
{{{
../../modeles/XIOS/arch/arch-X64_CURIE.env
}}}

After doing so do a make clean and compile (it worked for me with fcm). If you want that these changes are permanent, remember to also change the paths in the AA_make file, that way the new path will be used when doing an ins_make.  

Now the model is compiled with the new libraries but the libIGCM is not aware of that, so you will have to make some changes to libIGCM as well.
{{{
emacs ../../../libIGCM/libIGCM_sys/libIGCM_sys_curie.ksh &
}}}

Add the module load and unload statements as follows. If this should become a lasting change you will have to change the modules in /ccc/cont003/home/dsm/p86ipsl/.atlas_env_netcdf4_curie_ks rather than in libIGCM_sys_curie.ksh

{{{
#====================================================
# Set environment tools (ferret, nco, cdo)
#====================================================
if [ X${TaskType} = Xcomputing ] ; then
  . /ccc/cont003/home/dsm/p86ipsl/.atlas_env_netcdf4_curie_ksh > /dev/null 2>&1
# to run with netcdf 3.6.3 ie compilation done before 17/2/2014
# uncomment 2 lines :
#  module unload netcdf
#  module load netcdf/3.6.3
module unload nco/4.1.0
module unload netcdf/4.2_hdf5_parallel
module load netcdf/4.3.3.1_hdf5_parallel
module list

  export PATH=${PATH}:/ccc/cont003/home/dsm/p86ipsl/AddNoise/src_X64_CURIE/bin
  export PATH=${PATH}:/ccc/cont003/home/dsm/p86ipsl/AddPerturbation/src_X64_CURIE/bin
else
  . /ccc/cont003/home/dsm/p86ipsl/.atlas_env_netcdf4_curie_ksh > /dev/null 2>&1
  PCMDI_MP=/ccc/work/cont003/dsm/p86ipsl/PCMDI-MP
fi
}}}

Use libIGCM to launch the model, you can check the Script-file to see whether the modules were indeed loaded.