I need to go with the "big fat monster table". This is how relational databases should work, although you must normalize them (create one table for users, another for datasets, and another for data points). Having multiple tables with the same layouts is a bad idea from all sides - design, management, security, and even queries; Are you sure you will never want to combine information from two data sets?
If you are really sure that each data set will be completely isolated, you can also not use SQL at all. HDF (hierarchical data format) was literally built for this purpose, the effective storage and retrieval of "sets of scientific data", which are often very serial data. “Tables” in HDF are literally called datasets, they can share definitions, they can be multidimensional (for example, one dimension for a day, one at a time), and they are much cheaper than SQL tables.
I usually don’t try to push people away from SQL, but unusual situations sometimes require unusual solutions. If you are faced with billions of rows in an SQL table (or more), and you have virtually no other data to store, then SQL may not be the best solution for you.
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