Frequently Asked Questions

What dependency versions should I use?

The species package is kept reasonably well up to date with recent dependency versions. If you encounter an error then try to update the dependencies.

For example, in your local folder where you may have cloned the repository:

pip install --upgrade -e .

Which tools support multiprocessing?

The parameter inference tools in FitModel, FitEvolution, EmissionLine, and AtmosphericRetrieval that make use of MultiNest, UltraNest, and Dynesty.

How do I run my code on multiple CPUs?

First, make sure to install mpi4py:

pip install mpi4py

Then, to execute you species script with MPI, for example using 8 CPUs:

mpirun -n 8 python run_species.py

Important

Writing to the HDF5 database is not possible with multiprocessing, whereas reading data is. It is important to store any needed data (e.g. companion data, atmospheric models) in the HDF5 database using a single CPU, before running a fit. Next, it is recommended to execute a minimal code with multiprocessing, e.g. only SpeciesInit, FitModel, and run_multinest. The results from the fit will get stored in the database.