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Thank you for your answer Ronald.

Unfortunately ticking the ‘Remove all variable before execution’ box does not solve the issue, and neither I could solve it with magic commands. Deleting the Nazca arrays frees a bit of memory, but leaves the majority accumulating.

Indeed I reuse the same iPython console, i.e. I just rerun my script in Spyder. the only way I can free my RAM is by manually closing the console every few run.