hdfgroup/h5pyd repository overview

Ingredients:

Python 3.7 HDF5 Library HDF5 Tools (h5dump, h5ls, h5repack, etc.) h5py (Python package for HDF5) h5pyd (Python SDK for HDF REST API) s3fs (for reading hdf5 files stored in S3) Instructions Launch the container interactively.

Example:

$ docker run --rm -v ${HOME}/.hscfg:/root/.hscfg
--env AWS_SECRET_ACCESS_KEY=$AWS_SECRET_ACCESS_KEY
--env AWS_ACCESS_KEY_ID=${AWS_ACCESS_KEY_ID}
-it hdfgroup/h5pyd bash

Where:

• .hscfg is the HSDS configuration file (optional)
• AWS_SECRET_ACCESS_KEY is you AWS secret key (optional - used for hsload with the --s3link option)
• AWS_ACCESS_KEY_ID is you AWS access key id (optional - used for hsload with the --s3link option)

Rather than mounting the .hscfg file you an provide these additional environment variables:

• HS_ENDPOINT -- server endpoint
• HS_USERNAME -- server username
• HS_PASSWORD -- server password

From the bash prompt you should then be able to use tools such as hsls or hsload on any mounted data files.

See Also: https://www.hdfgroup.org/HDF5⁠ for information on how to use HDF5 https://docs.h5py.org/en/stable/⁠ for information on using h5py https://github.com/HDFGroup/h5pyd⁠ for information on using h5pyd