PaNOSC at the HDF5 User Group Meeting 2020

The HDF Group and the Lawrence Berkeley National Lab (LBNL) have organized a virtual HDF5 User Group Meeting to be held from October 13th to October 16th, 2020.

Loïc Huder from the European Synchrotron Radiation Facility (ESRF), and Thomas Kluyver from the European XFEL will represent PaNOSC with the following presentations:

Loïc Huderh5web: a web-based viewer of HDF5 files


HDF5 (with Nexus) is becoming the de facto standard in most X-ray facilities. However, it is not always easy to navigate such files to get quick feedback on the data, due to the peculiar structure of Nexus files. HDF5 file viewers are one way to solve this issue. They allow for the browsing and inspecting of the hierarchical structure of HDF5 files, as well as visualising the datasets they contain as basic plots (1D, 2D, 3D).
This presentation will focus on  h5web, the open-source web-based viewer being developed at the European Synchrotron Radiation Facility. The intent is to provide synchrotron users with an easy-to-use application and to make open-source components available for other similar web applications. `h5web` is built with React, a front-end web development library. It supports the exploration of HDF5 files, requested from a separate back-end (e.g. HSDS) for modularity, and the visualisation of datasets using performant WebGL-based visualisations.

Thomas Kluyver – H5Glance: Explore HDF5 files in a terminal or a notebook


There’s HDFview, vitables, h5web, and more. Who needs yet another tool for viewing HDF5 files? Well, it was done so at European XFEL. We often work with HDF5 files in an SSH session or a Jupyter notebook, and we wanted to explore the files without leaving those contexts. So we made H5Glance, which works both as a shell command and a Python library to use with h5py. What H5Glance can do in both contexts will be shown, and some of the specific features that help it to fit in to our workflows will be explained.

Thomas Kluyver – h5py: A bridge between HDF5 and Python


HDF5 and the Python language, both popular tools in science and data analysis, are ideal partners. The popular NumPy library, which provides multidimensional arrays in Python, closely matches the core features of HDF5 datatypes & dataspaces. It will be shown how the h5py bindings, built on the HDF5 C API, let you read & write HDF5 files with a convenient, high-level interface. This includes advanced HDF5 features such as creating virtual datasets.

The events’ presentations and discussions will cover the topics listed below:

  • Updates on The HDF Group and HDF5
  • HDF5 for Exascale and HPC
  • HDF5 VOL connectors and VFDs
  • HDF5 use cases in sciences
  • HDF5 language bindings
  • HDF5 Cloud solutions
  • HDF5 Industry use cases

A hands-on tutorial on HDF5 performance tuning techniques will also take place on October 13th, followed by technical and invited talks on October 14-16.

For further questions, please contact the organisers via email or via Slack.