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H5Record

codecov PyPI version

Large dataset ( > 100G, <= 1T) storage format for Pytorch (wip)

Support python 3

pip install h5record

Why?

  • Writing large dataset is still a wild west in pytorch. Approaches seen in the wild include:

    • large directory with lots of small files : slow IO when complex file is fetched, deserialized frequently
    • database approach : depend on what kind of database engine used, usually multi-process read is not supported
    • the above method scale non linear in terms of data - storage size

  • TFRecord solved the above problems well ( multiprocess fetch, (de)compression ), fast serialization ( protobuf )

  • However TFRecord port does not support data size evaluation (used frequently by Dataloader ), no index level access available ( important for data evaluation or verification )

H5Record aim to tackle TFRecord problems by compressing the dataset into HDF5 file with an easy to use interface through predefined interfaces ( String, Image, Sequences, Integer).

Some advantage of using H5Record

  • Support multi-process read

  • Relatively simple to use and low technical debt

  • Support compression/de-compression on the fly

  • Quick load to memory if required

Simple usage

pip install h5record
  1. Sentence Similarity
from h5record import H5Dataset, Float, String

schema = (
    String(name='sentence1'),
    String(name='sentence2'),
    Float(name='label')
)
data = [
    ['Sent 1.', 'Sent 2', 0.1],
    ['Sent 3', 'Sent 4', 0.2],
]

def pair_iter():
    for row in data:
        yield {
            'sentence1': row[0],
            'sentence2': row[1],
            'label': row[2]
        }

dataset = H5Dataset(schema, './question_pair.h5', pair_iter())
for idx in range(len(dataset)):
    print(dataset[idx])

Note

Due to in progress development, this package should be use in care in storage with FAT, FAT-32 format

Comparison between different compression algorithm

No chunking is used

Compression Type File size Read speed row/second
no compression 2.0G 2084.55 it/s
lzf 1.7G 1496.14 it/s
gzip 1.1G 843.78 it/s

benchmarked in i7-9700, 1TB NVMe SSD

If you are interested to learn more feel free to checkout the note as well!