Tips for ABINIT users and developers

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====== Tips and tricks ======

===== 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>