Prerequisites and Installation

Prerequisites

To run CyTRACK, you need

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

- netCDF4
- numpy
- scipy
- mpi4py
- time
- datetime
- functools
- math
- sys
- os
- matplotlib
- imp
- xarray
- sklearn
- argparse

1 - First Method

conda install -c tramo-ephyslab cytrack

or

conda install -c apa_py cytrack

2 - Second Method

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

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

Verify you have installed all packages requiered for CyTRACK. If you use an Anaconda environment, please be sure you have activated the environment
Copy the src/cytrack directory to your Anaconda installation

cp -r src/cytrack path_to_anaconda_installation/lib/python3.x/site-packages/

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

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

3 - Third Method

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

Verify you have installed all packages requiered for CyTRACK. If you use an Anaconda environment, please be sure you have activated the environment.
Go to src directory

run install_CyTRACK.sh.

Note

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

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