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For HPC you probably want to avoid OO. As for Python speed it should be fine. You can use numba https://numba.pydata.org/ to speed up your non-standard functions.
If possible, try to monitor your memory usage during execution and if you see that you are consistently exceeding ~50% (my own rule of thumb, though you may want to discuss this with others as well) of what's available. If you are consistently using most of the available memory, then it's likely worth taking a moment to evaluate whether you can operate on subsets of the data from start to finish, and leave the rest of the data on disk until you are almost ready to use it. Tools like h5py are very helpful in these kinds of situations.