I have a hdf5 file, and I want to extract a part of the data and save it as the same format.

The data type is


So far I have successfully extracted the data using h5dump but it is in ascii format. I couldn't save it as the same hdf5 format. I saw there are several flags for saving as xml formats, but it doesn't work for me. I have tried using flags like -x or -d such as

h5dump -d variable -s 1 10 -X output.file  input.file

It creates the output file, but it is an empty file.

edit: I need to do it using h5dump.

  • $\begingroup$ I think you must use small x instead of capital X. try with small -x and don't mention the output.file. if you can have the proper output in the stdout, simply redirect it to a file. $\endgroup$
    – Kasra
    Mar 8, 2022 at 18:52

1 Answer 1


You can always try using the h5py module in Python.

import h5py

# Load existing file
filename = "myfile.hdf5"
dataset = h5py.File(filename, "r")

# Show keys
print(*[item for item in dataset.items()],sep="\n")

# Assuming that you want to select the first 10 rows of key "A"
data = dataset["A"][:10]
# Create the new dataset / file
dataset2 = h5py.File("myfile2.hdf5", "w")
dataset2.create_dataset("A", data)
  • $\begingroup$ thank you for your answer, but unfortunately I cannot use python at the moment. I need to do it using h5dump. It wasn't very clear in the question, I'll edit it. $\endgroup$
    – atrlrgn
    Apr 2, 2019 at 8:40

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