python - Incremental writes to hdf5 with h5py

Question

I have got a question about how best to write to hdf5 files with python / h5py.

I have data like:

-----------------------------------------
| timepoint | voltage1 | voltage2 | ...
-----------------------------------------
| 178       | 10       | 12       | ...
-----------------------------------------
| 179       | 12       | 11       | ...
-----------------------------------------
| 185       | 9        | 12       | ...
-----------------------------------------
| 187       | 15       | 12       | ...
                    ...

with about 10^4 columns, and about 10^7 rows. (That's about 10^11 (100 billion) elements, or ~100GB with 1 byte ints).

With this data, typical use is pretty much write once, read many times, and the typical read case would be to grab column 1 and another column (say 254), load both columns into memory, and do some fancy statistics.

I think a good hdf5 structure would thus be to have each column in the table above be a hdf5 group, resulting in 10^4 groups. That way we won't need to read all the data into memory, yes? The hdf5 structure isn't yet defined though, so it can be anything.

Now the question: I receive the data ~10^4 rows at a time (and not exactly the same numbers of rows each time), and need to write it incrementally to the hdf5 file. How do I write that file?

I'm considering python and h5py, but could another tool if recommended. Is chunking the way to go, with e.g.

dset = f.create_dataset("voltage284", (100000,), maxshape=(None,), dtype='i8', chunks=(10000,))

and then when another block of 10^4 rows arrives, replace the dataset?

Or is it better to just store each block of 10^4 rows as a separate dataset? Or do I really need to know the final number of rows? (That'll be tricky to get, but maybe possible).

I can bail on hdf5 if it's not the right tool for the job too, though I think once the awkward writes are done, it'll be wonderful.

unutbu unutbu · Accepted Answer · 2014-09-04T01:53:18

Per the FAQ, you can expand the dataset using dset.resize. For example,

import os
import h5py
import numpy as np
path = '/tmp/out.h5'
os.remove(path)
with h5py.File(path, "a") as f:
    dset = f.create_dataset('voltage284', (10**5,), maxshape=(None,),
                            dtype='i8', chunks=(10**4,))
    dset[:] = np.random.random(dset.shape)        
    print(dset.shape)
    # (100000,)

    for i in range(3):
        dset.resize(dset.shape[0]+10**4, axis=0)   
        dset[-10**4:] = np.random.random(10**4)
        print(dset.shape)
        # (110000,)
        # (120000,)
        # (130000,)

python - Incremental writes to hdf5 with h5py

2 Answers