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Low memory combine_rows #30
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dkoes
approved these changes
Aug 26, 2020
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Not sure how I missed this PR.
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The script
combine_rows.py
has a high memory consumption for large datasets (such as PDBbind18) and runs out of memory on a 64GB machine.This PR re-implements such script with a totally different approach, pre-allocating
pandas.DataFrame
s and populating them one row at a time. This approach consistently reduces the memory usage.The final check is also sped up using
numpy
instead of Python loops.Since the approach is completely different from the original script, I created a new script
combine_rows_lowmem.py
instead of modifying the original one.Small Test
Loading only rows 1-3 and printing a 5x5 sub-matrix with the new code:
Loading only rows 1-3 and printing a 5x5 sub-matrix with
combine_rows.py
: