Prerequisites and Installation

Prerequisites

To run LATTIN, you need

The main Python packages that must be installed are the following:

  • time

  • struct

  • datetime

  • functools

  • pathlib

  • gzip

  • shutil

  • math

  • fnmatch

  • sys

  • os

  • imp

  • aiohttp==3.9.5

  • dask==2023.9.2

  • mpi4py==3.1.4

  • netcdf4==1.7.2

  • numpy==1.26.4

  • pandas==2.2.3

  • psutil==7.0.0

  • requests==2.32.2

  • scipy==1.12.0

  • setuptools==65.5.0

  • tenacity==9.1.2

  • tqdm==4.67.1

  • xarray==2023.6.0

  • zarr==3.0.5

  • matplotlib==3.10.3

  • FORTRAN 90 Compiler

Installation

1 - First Method

conda install -c tramo-ephyslab lattin

If you install LATTIN using conda, the first time you import lattin, it automatically will compile the FORTRAN subroutines. Therefore, we strongly recommend typing the following sentences in terminal after the LATTIN installation.

python
import lattin

If you have problems compiling FORTRAN subroutines when importing lattin` the first time, you can manually compile these subroutines. Go to your Anaconda installation and run the build_lattin_so.sh script.

cd  patho_to_anaconda_installation/.../site-packages/lattin
sh build_lattin_so.sh

To knnow the exactly path of your Anaconda installation (patho_to_anaconda_installation/…/site-packages/), you can follow these instructions:

python
from distutils.sysconfig import get_python_lib
print(get_python_lib())

2- Second Method

You must check that all the packages are installed and that there is no error message when they are imported.

  • Clone the repository:

git git clone https://github.com/apalarcon/LATTIN.git

  • Verify you have installed all packages requiered for LATTIN (see LATTIN requirements section). If you use an Anaconda environment, please be sure you have activated the environment.

Note

From now on it should be installed in the python environment and can be used like any other Python package.

Possible problems with python packages:

If you have a problem with the mpi4py library, try these steps:

  • Remove the mpi4py library conda remove mpi4py

  • Install the openmpi library conda install conda-forge::openmpi

  • Install again the mpi4py library conda install mpi4py

  • If the problem continue (the problem is frequently related with the libmpi.so.12 or similar), you can also try

Search the mising library on your system and link it to your Anaconda lib path.

ln -s path_to_missing_library/libmpi.so.12 patho_to_anaconda_installation/lib/

or

Contact your system administrator

If you have a problem compiling the FORTRAN package in Python 3.12+, the error is caused by the shift in how Python and NumPy handle compilation in newer versions.

The Problem:

  • Python 3.12+ removed the distutils package.

  • f2py (part of NumPy) now defaults to using Meson as the build backend instead of distutils.

Try these steps to solve it:

  • Install meson and ninja

conda install meson ninja

  • Install gcc_linux-64 and gfortran_linux-64

conda install -c conda-forge gcc_linux-64 gfortran_linux-64