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build:install_netcdf [2017/05/25 10:06] (current)
Matthieu Verstraete created
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 +===== How to link netCDF 4 with Abinit =====
 +
 +First create a directory where you are going to store all you libraries. It is common to create this directory under /​local/​name_of_the_compiler. In my case I want to compile using Intel 13 compiler and therefore I will issue:
 +
 +<​code>​
 +cd local
 +mkdir Intel13
 +</​code>​
 +
 +  - **Install zlib** \\ Go on the Zlib website [[http://​zlib.net/​|http://​zlib.net/​]] and download the latest version and then untar it e.g.: <​code>​
 +wget http://​zlib.net/​zlib-1.2.8.tar.gz
 +tar -xvf zlib-1.2.8.tar.gz
 +</​code>​ Then go into the folder and issue: <​code>​
 +./configure --prefix='/​home/​ucl/​naps/​sponce/​local/​Intel13'​
 +make 
 +make install
 +</​code>​
 +  - **Install HDF5** \\ Go on the HDF5 website [[http://​www.hdfgroup.org/​HDF5/​]] and download it, e.g.:<​code>​
 +wget http://​www.hdfgroup.org/​ftp/​HDF5/​current/​src/​hdf5-1.8.11.tar
 + tar -xvf hdf5-1.8.11.tar
 +</​code>​ Then go into the folder and issue:<​code>​
 +./configure --with-zlib=/​home/​ucl/​naps/​sponce/​local/​Intel13 --prefix=/​home/​ucl/​naps/​sponce/​local/​Intel13 --enable-fortran --enable-cxx
 +make 
 +make install
 +</​code>​
 +  - **Install netCDF4** \\ Go on the netcdf4 website [[http://​www.unidata.ucar.edu/​downloads/​netcdf/​netcdf-4_0/​index.jsp]] and download it, e.g. :<​code>​
 +wget http://​www.unidata.ucar.edu/​downloads/​netcdf/​ftp/​netcdf-4.1.3.tar.gz
 +tar -xvf netcdf-4.1.3.tar.gz
 +</​code>​ Because the --with-hdf5= option does not work for necdf-4.1.3,​ you will need to export HDF5 location paths as follows: <​code>​
 +export CPPFLAGS=-I/​home/​ucl/​naps/​sponce/​local/​Intel13/​include/​
 +export LDFLAGS=-L/​home/​ucl/​naps/​sponce/​local/​Intel13/​lib
 +export LD_LIBRARY_PATH=/​home/​ucl/​naps/​sponce/​local/​Intel13/​lib
 +export FC=ifort
 +export CC=icc
 +</​code>​
 +Then issue:
 +<​code>​
 +./configure --enable-netcdf4 --prefix=/​home/​ucl/​naps/​sponce/​local/​Intel13 ​ --enable-dap --enable-shared
 +make 
 +make install
 +</​code>​
 +  - **Install Abinit with netCDF4**\\ ​
 +Be careful if you have set flags into you .ac file. You should unset the variable first: ​
 +<​code>​
 +unset FC
 +unset CC
 +</​code> ​
 +You should then add the following lines into your .ac configuration file:
 +<​code>​
 +with_netcdf_incs="​-I/​home/​ucl/​naps/​sponce/​local/​Intel13/​include"​
 +with_netcdf_libs="​-L/​home/​ucl/​naps/​sponce/​local/​Intel13/​lib -lnetcdf -lnetcdff"​
 +with_trio_flavor="​netcdf+etsf_io"​
 +</​code>​
 +For some mpi-io parallel I/O fancy stuff you may need to add the hdf5 explicitly ​
 +<​code> ​
 +with_netcdf_incs="​-I/​home/​ucl/​naps/​sponce/​local/​Intel13/​include "
 +with_netcdf_libs="​-L/​home/​ucl/​naps/​sponce/​local/​Intel13/​lib -lnetcdf -lnetcdff -lhdf5_fortran -lhdf5_hl -lhdf5"​
 +with_trio_flavor="​netcdf+etsf_io"​
 +</​code>​
 +Note that here all of the libraries have been put in the same lib and include directories for convenience (otherwise you need to add the corresponding -I<​path>/​include and -L<​path>/​lib statements)
 +
 +Then you should make a build directory into Abinit and issue: ​
 +<​code>​
 +../​configure --with-config-file='​./​name_of_your_ac_file.ac'​
 +make mj4
 +</​code>​
 +
 +
 +
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build/install_netcdf.txt ยท Last modified: 2017/05/25 10:06 by Matthieu Verstraete