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BUILD-Ubuntu.md

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Building Puffin on Ubuntu and other similar Linux

The below instruction of Puffin install is meant for Ubuntu, however it can be successfully applied on other Linux branches (e.g. Manjaro). The packages required by Ubuntu (and other Linux) include:

  • gfortran (gfortran)
  • OpenMPI (libopenmpi-dev, openmpi-bin - for Ubuntu, other distributions often use different package names)
  • Cmake (cmake)

In general, you need to be able to issue commands like: mpirun, mpicc, mpif90, cmake. When trying to issue such command you should only see message that the source input file is missing but the command should execute. Some version of Ubuntu have precompiled HDF5 nad FFTW3 libraries. However, the libraries are often not fully compatibile with Puffin. The most general approach to build Puffin is to build first your own HDF5 and FFTW3 libraries. Whatever the reason, we must build our own versions of FFTW3 and HDF5.

Fortunately, building both FFTW3 and HDF5 is relatively simple. Grab the sources (FFTW3 and HDF5) then configure, make, and make install. For FFTW3, go into the top-level of the unzipped source and do:

./configure --prefix=$/my_home_directory/my_fftw3_install_directory --enable-mpi --enable-openmp
make
make install

This will build the FFTW3 libraries in your /my_home_directory/my_fftw3_install_directory directory. Similarly, do

./configure --enable-parallel --enable-fortran --prefix=/my_home_directory/my_hdf5_install_directory
make
make install

for HDF5, in the root of its unzipped source.

Fetch Puffin to <path to Puffin source root>. To clone from Github, do

git clone git@github.com:UKFELs/Puffin.git <path to Puffin source root>

where <path to Puffin source root> is where you want the top level of the Puffin source to be downloaded to.

Then to build Puffin, we do the usual CMake and build commands (outlined here):

cmake <path to Puffin source root> -DENABLE_PARALLEL:BOOL=1 -DCMAKE_PREFIX_PATH:FILEPATH="/my_home_directory/my_hdf5_install_directory;/my_home_directory/my_fftw3_install_directory" -DCMAKE_INSTALL_PREFIX:FILEPATH=/my_home_directory/my_puffin_install_directory
make
make install

which builds Puffin in the /my_home_directory/my_puffin_install_directory directory.