HDF5 for efficient I/O
Fast Containers
© Lead Image © Kirsty Pargeter, 123RF.com
HDF5 is a flexible, self-describing, and portable hierarchical filesystem supported by a number of languages and tools, with the ability to run processes in parallel.
Input/output operations are a very important part of many applications, sometimes involving a huge amount of data and a large number of reads and writes. Therefore, applications can use a very significant portion of their total run time to perform I/O, which becomes critical in Big Data, machine learning, and high-performance computing (HPC).
In a previous article [1], I discussed options for improving I/O performance, focusing on parallel I/O. One of the options mentioned was to use a high-level library to perform the I/O. A great example of such a library is the Hierarchical Data Format (HDF) [2], a standard library used primarily for scientific computing.
In this article, I introduce HDF5 and focus on the concepts and its strengths in performing I/O; then, I look at some simple Python and Fortran code examples, before ending with an example of parallel I/O with HDF5 and Fortran.
[...]
Buy this article as PDF
(incl. VAT)
Buy Linux Magazine
US / Canada
UK / Australia
Subscribe to our Linux Newsletters
Find Linux and Open Source Jobs
Subscribe to our ADMIN Newsletters
Support Our Work
Linux Magazine content is made possible with support from readers like you. Please consider contributing when you’ve found an article to be beneficial.
News
-
Linux Mint 22.3 Now Available with New Tools
Linux Mint 22.3 has been released with a pair of new tools for system admins and some pretty cool new features.
-
New Linux Malware Targets Cloud-Based Linux Installations
VoidLink, a new Linux malware, should be of real concern because of its stealth and customization.
-
Say Goodbye to Middle-Mouse Paste
Both Gnome and Firefox have proposed getting rid of a long-time favorite Linux feature.
-
Manjaro 26.0 Primary Desktop Environments Default to Wayland
If you want to stick with X.Org, you'll be limited to the desktop environments you can choose.
-
Mozilla Plans to AI-ify Firefox
With a new CEO in control, Mozilla is doubling down on a strategy of trust, all the while leaning into AI.
-
Gnome Says No to AI-Generated Extensions
If you're a developer wanting to create a new Gnome extension, you'd best set aside that AI code generator, because the extension team will have none of that.
-
Parrot OS Switches to KDE Plasma Desktop
Yet another distro is making the move to the KDE Plasma desktop.
-
TUXEDO Announces Gemini 17
TUXEDO Computers has released the fourth generation of its Gemini laptop with plenty of updates.
-
Two New Distros Adopt Enlightenment
MX Moksha and AV Linux 25 join ranks with Bodhi Linux and embrace the Enlightenment desktop.
-
Solus Linux 4.8 Removes Python 2
Solus Linux 4.8 has been released with the latest Linux kernel, updated desktops, and a key removal.