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POSYDON-code / POSYDON

POSYDON is a next-generation single and binary-star population synthesis code incorporating full stellar structure and evolution modeling with the use of MESA.
BSD 3-Clause "New" or "Revised" License
29 stars 19 forks source link

kernel stopping when loading the h5 file #351

Open ezapartas opened 3 months ago

ezapartas commented 3 months ago

Hello all. Has anyone else experience a problem with their kernel when loading a h5 file (with pd.read_hdf) of a POSYDON population in jupyter notebook of their local setup? I get this error which I print screen below. In the beginning I thought it was a memory issues, but it is not, and the h5 file is ~tens of MB. Making a new conda environment from scratch in my local setup also does not work. Searching of the error, it seems that it is possibly connected with mismatch in libraries with the hdf5 creation and my jupyter. e.g. https://stackoverflow.com/questions/47022997/jupyter-the-kernel-appears-to-have-died-it-will-restart-automatically Does anyone have any suggestions? Also, is it something that we should have in mind for potential issues that a user may experience? image

maxbriel commented 3 months ago

@ezapartas Do you get a similar error when running the commands in a python shell/script? (from the command line) Or just with jupyter?

ezapartas commented 2 months ago

Update on this:

The issue is found and solved in MacOS if the conda install hdf5 pytables

is run in the environment before the posydon (re)installation, as mentioned in the installation guide

ezapartas commented 2 months ago

TODO:better to add it in the troubleshooting too!