How to download and install Abinit code

 

First we need to add the path to the ~/.bashrc  file

#---------Abinit path----------------------------------
export ABINITROOT=/home/algerien/abinitio/abinit-7.10.5/bin

export PATH=$PATH:$ABINITROOT

#---------------------------------------------------------

$ source ~/.bashrc

 

NB: It's better to create a bin directory and copy all the executables and tools inside it 

 

Prerequisites

For Ubuntu

# 1 # compiler
sudo apt install gfortran

# 2 # MPI libraries - choice for Open MPI
sudo apt install libopenmpi-dev

# 3 # math libraries - choice for lapack and blas
sudo apt install liblapack-dev libblas-dev

# 4 # mandatory libraries
sudo apt install libhdf5-dev libnetcdf-dev libnetcdff-dev libpnetcdf-dev libxc-dev

 

For Opensuse

# 1 # GCC compilers
sudo zypper install gcc gcc-c++ gcc-fortran

# 2 # MPI libraries - choice for Open MPI
sudo zypper install openmpi openmpi-devel openmpi-libs


# 3 # math libraries - choice for lapack and blas
sudo zypper install liblapack3 libblas3

# 4 # mandatory libraries

sudo zypper install hdf5 hdf5-devel libhdf5

sudo zypper install fftw3 fftw3-devel

sudo zypper install netcdf netcdff libnetcdf libnetcdff

sudo zypper install libxc

 

Compiling ABINIT

Downloading the version abinit.7.10.5

wget https://www.abinit.org/sites/default/files/packages/abinit-9.0.4.tar.gz
tar xzf abinit-7.10.5.tar.gz
cd abinit-7.10.5

Create a working directory:

mkdir build && cd build

To configure, use:

../configure --with-config-file='my_config_file.ac9'

where ‘my_config_file.ac9’ is a configuration file that is discussed in more details in the next section.

 

Compile with:

make -j4

Install (optional):

make install

 

The configuration file¶

The configure script accepts variables and flags to customize the configuration. For example

../configure FC=mpifort --with-mpi="yes"

tells ABINIT to configure for a MPI build with the mpifort MPI wrapper. To obtain the documentation for the different variables and flags, use:

../configure --help

Most configuration options are detected automatically by configure. For example, if with_mpi is set to ‘yes’, configure will try to use the parallel fortran compiler (mpifort) and automatically detect the MPI installation with libraries (.so) and header (.h) files. When you install the Open MPI package via apt, these directories can be printed to terminal by using dpkg -L 'libopenmpi-dev'.

When a lot of options must be passed to configure, it is advised to use an external configuration file with the syntax:

../configure --with-config-file='my_config_file.ac9'

An example of configuration file my_config_file.ac9 to build abinit with MPI, lapack and blas and automatic detection for libxc, hdf5, and netcdf:

prefix="$HOME/local"

enable_mpi="no"
enable_mpi_io="no"
#with_mpi_prefix="/usr/bin"

with_trio_flavor="netcdf+fox"

#with_netcdf_incs="-I/usr/include"
#with_netcdf_libs="-L/usr/lib -lnetcdf -lnetcdff"
#with_etsf_io_incs="-I/usr/include"
#with_etsf_io_libs="-L/usr/lib -letsf_io_low_level -letsf_io_utils -letsf_io"

with_fft_flavor="fftw3"
with_fft_incs="-I/usr/include"
with_fft_libs="-L/usr/lib -lfftw3 -lfftw3f"

with_linalg_flavor="atlas"
with_linalg_libs="-L/usr/lib/atlas-base -llapack_atlas -lf77blas -lcblas -latlas -L/usr/lib/atlas-base/atlas -llapack -lblas"

#with_dft_flavor="atompaw+bigdft+libxc+wannier90"

Note that:

• one uses ‘-‘ when typing a flag but ‘_’ inside the config file, e.g. --with-mpi="yes" becomes with_mpi="yes".

• the LINALG_LIBS variable was explicitly set for this linux distrubution. The directory was extracted via dpkg -L liblapack-dev and dpkg -L libblas-dev.

• when fine tuning variables and flags for a particular linux distribution, it is advised to take a look at the template file ~abinit/doc/build/config-template.ac9. For example, the setting of LINALG_LIBS in this template file is given by the line #LINALG_LIBS="-L/usr/local/lib -llapack -lblas".

More specialized libraries might be harder to detect. For example, the following section was added to the config file to detect customized FFT and XML libraries. These libraries are available via apt (libfftw3-devand libxml2-dev). The directories for the corresponding library and header files can be found by using dpkg -L [package] and other flags can be extracted from the ~abinit/doc/build/config-template.ac9 template

# fast fourier settings
with_fft_flavor="fftw3"
FFTW3_CPPFLAGS="-I/usr/include"
FFTW3_FCFLAGS="-I/usr/include"
FFTW3_LIBS="-L/usr/lib/x86_64-linux-gnu -lfftw3 -lfftw3f"

# XML2 library (used by multibinit)
with_libxml2="yes"
LIBXML2_FCFLAGS="-I/usr/lib/x86_64-linux-gnu/"
LIBXML2_LIBS="-L/usr/include/libxml2/libxml/ -lxmlf90"

 

The output of configuration is:

Summary of important options:

  * C compiler      : gnu version 6.2
  * Fortran compiler: gnu version 6.2
  * architecture    : unknown unknown (64 bits)

  * debugging       : basic
  * optimizations   : standard

  * OpenMP enabled  : yes (collapse: yes)
  * MPI    enabled  : no
  * MPI-IO enabled  : no
  * GPU    enabled  : no (flavor: none)

  * TRIO   flavor = netcdf-fallback+fox-fallback
  * TIMER  flavor = abinit (libs: ignored)
  * LINALG flavor = netlib-fallback (libs: ignored)
  * ALGO   flavor = none (libs: ignored)
  * FFT    flavor = fftw3 (libs: user-defined)
  * MATH   flavor = none (libs: ignored)
  * DFT    flavor = none

Configuration complete.
You may now type "make" to build ABINIT.
(or, on a SMP machine, "make mj4", or "make multi multi_nprocs=<n>")

Compile 

make mj4

 

After compilation we need to install all the executables in the created bin directory

$ cp /home/algerien/abinitio/abinit-7.10.5/build/src/98_main/abinit $ABINITROOT 

 

Reference: https://docs.abinit.org/INSTALL_Ubuntu/

For more information check the following links:

 https://forum.abinit.org/viewtopic.php?f=3&t=2807

https://docs.abinit.org/INSTALL_Ubuntu/ 

https://docs.abinit.org/installation/ 

https://pitp.phas.ubc.ca/confs/sherbrooke2018/archives/gonze.pdf