54 episodes

Find the latest information about the HDF file formats and new developments from The HDF Group and the HDF community.

The HDF Group's Call the Doctor The HDF Group

    • News

Find the latest information about the HDF file formats and new developments from The HDF Group and the HDF community.

    HDF5 in the Cloud tutorials - Matt Larson on Call the Doctor, February 13, 2024

    HDF5 in the Cloud tutorials - Matt Larson on Call the Doctor, February 13, 2024

    In this episode of Call the Doctor, The HDF Group’s Matt Larson will give an introduction to the HDF in the Cloud tutorials: 
    REST VOL, HSDS, ROS3. and H5Coro. If you’re an experienced HDF5 user, come to this Call the Doctor session, take a look at the tutorial content, and feel free to make improvements or let us know of any issues.
    Call the Doctor is a series of weekly, unscripted, live events! The HDF Group’s staff members will answer attendee questions and, for example, go over the previous week’s HDF Forum posts. The HDF Clinics are free sessions intended to help users tackle real-world HDF problems from a common cold to severe headaches and offer relief where that’s possible. As time permits, we will include how-tos, offer advice on tool usage, review your code samples, teach you survival in the documentation jungle, and discuss what’s new or just around the corner in the land of HDF.

    Join us every Tuesday at 12:20 p.m. central (US/Canada.) on Zoom!

    • 29 min
    Adding support for 16-bit floating point and complex number datatypes to HDF5 - Call the Doctor 2/6/24

    Adding support for 16-bit floating point and complex number datatypes to HDF5 - Call the Doctor 2/6/24

    For this week's Call the Doctor, The HDF Group's Jordan Henderson, author of the Adding support for 16-bit floating point and complex number datatypes to HDF5 RFC, briefly talked through that RFC and lead a community discussion for feedback on the concept and proposal.

    For more to discussion, and to participate in the discussion, please visit this forum post: https://forum.hdfgroup.org/t/hdf5-rfc-adding-support-for-16-bit-floating-point-and-complex-number-datatypes-to-hdf5/11975

    This session happened on February 6, 2024. You can also watch this session online.


    Call the Doctor is a series of weekly, unscripted, live events! The HDF Group’s staff members will answer attendee questions and, for example, go over the previous week’s HDF Forum posts. The HDF Clinics are free sessions intended to help users tackle real-world HDF problems from a common cold to severe headaches and offer relief where that’s possible. As time permits, we will include how-tos, offer advice on tool usage, review your code samples, teach you survival in the documentation jungle, and discuss what’s new or just around the corner in the land of HDF.

    Join us every Tuesday at 12:20 p.m. central (US/Canada.) on Zoom!

    • 35 min
    An HDF5 Tutorial Developed by the Community for the Community - Call the Doctor hosted by Gerd Heber

    An HDF5 Tutorial Developed by the Community for the Community - Call the Doctor hosted by Gerd Heber

    For an individual, creating an HDF5 tutorial is hard; making a good HDF5 tutorial is nearly impossible. There are many technical facets to cover; the global community it serves is phenomenally diverse, and so is its rich ecosystem. Wouldn’t it be great to have a tutorial that anyone could enjoy without pesky installation details, and everyone with an idea to improve upon it could contribute easily? Introducing the HDF5 Tutorial developed by the community for the community. Fork it on GitHub at https://github.com/HDFGroup/hdf5-tutorial.

    The HDF Group's Executive Director Gerd Heber will uses this session of Call the Doctor to give an overview of the tutorial and introduce the underpinnings so that everyone so inclined can contribute and help create the best possible HDF5 tutorial ever.

    Would you like to discuss this tutorial with Gerd and others? Come to the forum and let us know your thoughts.

    This session was recorded on January 30, 2024. You can also watch this episode online.
    Call the Doctor is a series of weekly, unscripted, live events! The HDF Group’s staff members will answer attendee questions and, for example, go over the previous week’s HDF Forum posts. The HDF Clinics are free sessions intended to help users tackle real-world HDF problems from a common cold to severe headaches and offer relief where that’s possible. As time permits, we will include how-tos, offer advice on tool usage, review your code samples, teach you survival in the documentation jungle, and discuss what’s new or just around the corner in the land of HDF.

    Join us every Tuesday at 12:20 p.m. central (US/Canada.) on Zoom!

    • 40 min
    Issues writing results in the CGNS (CFD General Notation System) format - Scot Breitenfeld

    Issues writing results in the CGNS (CFD General Notation System) format - Scot Breitenfeld

    In this episode of "Call the Doctor," Scot Breitenfeld of The HDF Group hosted an open help session for your HPC HDF5 questions. (Questions are welcome at any session, but we knew we had some community members with specific needs for this session.)

    A research engineer working on open-source thermohydraulics code discusses issues with writing results in the CGNS (CFD General Notation System) format. The engineer explores different approaches, including writing the CGNS skeleton on the master processor and distributing data writing on multiple nodes. However, there are concerns about the slowdown when increasing time steps, possibly due to opening and closing the HDF file at each time step. The discussion also touches on options like sub-filing and using the core file driver to eliminate the file system component. Additionally, there's a brief inquiry about compressing large strings in HDF5. See this forum post for details. Overall, the episode addresses technical challenges in parallel file writing and optimization strategies.

    This session happened on January 23, 2024. You can also watch this episode online.
    Call the Doctor is a series of weekly, unscripted, live events! The HDF Group’s staff members will answer attendee questions and, for example, go over the previous week’s HDF Forum posts. The HDF Clinics are free sessions intended to help users tackle real-world HDF problems from a common cold to severe headaches and offer relief where that’s possible. As time permits, we will include how-tos, offer advice on tool usage, review your code samples, teach you survival in the documentation jungle, and discuss what’s new or just around the corner in the land of HDF.

    Join us every Tuesday at 12:20 p.m. central (US/Canada.) on Zoom!

    • 25 min
    Exploring and comparing performance between original and cloud-optimized HDF5 files

    Exploring and comparing performance between original and cloud-optimized HDF5 files

    In this episode of "Call the Doctor," Aleksandar Jelenak delves into recent work on analyzing Earth science HDF5 files, comparing their original versions with cloud-optimized versions. Using data from the Global Ecosystem Dynamics Investigation Instrument (GEDI) on the International Space Station, he showcases the instrument's laser beams mapping Earth's vegetation. Aleksandar discusses the challenges of optimizing HDF5 files for cloud usage, emphasizing the need for user-friendly data for scientists worldwide. He presents a detailed analysis of chunk data sets, storage settings, and statistics, highlighting the potential benefits of cloud-optimized files. The episode concludes with performance comparisons between original and cloud-optimized files, shedding light on the advantages of efficient data storage and access.

    This session was recorded on January 16, 2024. You can also watch it online.
    Call the Doctor is a series of weekly, unscripted, live events! The HDF Group’s staff members will answer attendee questions and, for example, go over the previous week’s HDF Forum posts. The HDF Clinics are free sessions intended to help users tackle real-world HDF problems from a common cold to severe headaches and offer relief where that’s possible. As time permits, we will include how-tos, offer advice on tool usage, review your code samples, teach you survival in the documentation jungle, and discuss what’s new or just around the corner in the land of HDF.

    Join us every Tuesday at 12:20 p.m. central (US/Canada.) on Zoom!

    • 33 min
    New HSDS Features Coming Soon and a Design Proposal for Long Running Tasks - John Readey

    New HSDS Features Coming Soon and a Design Proposal for Long Running Tasks - John Readey

    In this episode of Call the Doctor, The HDF Group's John Readey discusses upcoming features in the HSDS release. Since John is in China, the session is pre-recorded, with software engineer Matt Larson available to answer questions. The discussed features include shape reduction, broadcasting, UTF-8 fixed strings, quick scan, N-bit and scale offset filters, enhanced array type support, field ops for compound types, support for long attribute names, non-UTF-8 encodable attributes, multi-op attributes, long link names, and hyper chunking. John also introduces the concepts of async tasks for long-running operations and using Parquet for encoding chunks with variable-length types.  The design doc for async tasks can be viewed on github.  The episode includes a demonstration of the attribute multi-op feature, showcasing its efficiency compared to a serial approach.

    You can participate in the discussion of features for HSDS 0.9 on the forum.

    This session happened on January 9, 2024. You can also watch this episode.
    Call the Doctor is a series of weekly, unscripted, live events! The HDF Group’s staff members will answer attendee questions and, for example, go over the previous week’s HDF Forum posts. The HDF Clinics are free sessions intended to help users tackle real-world HDF problems from a common cold to severe headaches and offer relief where that’s possible. As time permits, we will include how-tos, offer advice on tool usage, review your code samples, teach you survival in the documentation jungle, and discuss what’s new or just around the corner in the land of HDF.

    Join us every Tuesday at 12:20 p.m. central (US/Canada.) on Zoom!

    • 26 min

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