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How to sort a HDF5 file
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How to sort a HDF5 file
Hey everyone,

I am storing a large data file (10 GBs, N rows and 4 columns) in an HDF5 file using h5py package. Primarily because I do not want to use my RAM.

I would like to sort the items in the file based on second column. Any suggestions on how to do that?

Chunks | Sort | Merge

Split the data of the hdf5 file into chunks.
Then sort this chunks and write the sorted chunks to disk.
Then open all chunk files and merge them.
Write the output into a different file.

You need heapq.merge which return a generator.

Here an example how it could work.
import os
import heapq
import random
from contextlib import ExitStack
from pathlib import Path

def producer(size):
    Return some random integers between 0 and < 1024
    return [random.randint(0, 1024) for _ in range(size)]

# you could use chunked from more_itertools
def chunker(iterable, chunksize):
    Split a iterable into smaller chunks
    return zip(*[iter(iterable)] * chunksize)

def sorter(iterable, filename):
    Sort the chunks and save them into a files
    The files are defined by filename
    for n, chunk in enumerate(iterable):
        chunk = "\n".join(map(str, sorted(chunk)))
        with open(f"{filename}_{n}", "w") as fd:

def merger(filename, output):
    Find all files related to filename_*
    Sort the files by last number
    Then open the files
    Merge the chunks and write it to output
    key = lambda x: int("{filename}_", ""))
    files = sorted(Path(filename).parent.glob(f"{filename}_*"), key=key)
    with ExitStack() as stack, open(output, "w") as fd_out:
        files = [stack.enter_context( for file in files]
        map_to_int = [map(int, fd) for fd in files]
        for number in map(str, heapq.merge(*map_to_int)):

sorter(chunker(producer(100), 10), "sorting")
merger("sorting", "result.txt")
By the way, do not try to save the output data into the source hdf5 file.
Make a new hdf5 file.
My code examples are always for Python >=3.6.0
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