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
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
-
System76 Releases COSMIC Alpha 7
With scores of bug fixes and a really cool workspaces feature, COSMIC is looking to soon migrate from alpha to beta.
-
OpenMandriva Lx 6.0 Available for Installation
The latest release of OpenMandriva has arrived with a new kernel, an updated Plasma desktop, and a server edition.
-
TrueNAS 25.04 Arrives with Thousands of Changes
One of the most popular Linux-based NAS solutions has rolled out the latest edition, based on Ubuntu 25.04.
-
Fedora 42 Available with Two New Spins
The latest release from the Fedora Project includes the usual updates, a new kernel, an official KDE Plasma spin, and a new System76 spin.
-
So Long, ArcoLinux
The ArcoLinux distribution is the latest Linux distribution to shut down.
-
What Open Source Pros Look for in a Job Role
Learn what professionals in technical and non-technical roles say is most important when seeking a new position.
-
Asahi Linux Runs into Issues with M4 Support
Due to Apple Silicon changes, the Asahi Linux project is at odds with adding support for the M4 chips.
-
Plasma 6.3.4 Now Available
Although not a major release, Plasma 6.3.4 does fix some bugs and offer a subtle change for the Plasma sidebar.
-
Linux Kernel 6.15 First Release Candidate Now Available
Linux Torvalds has announced that the release candidate for the final release of the Linux 6.15 series is now available.
-
Akamai Will Host kernel.org
The organization dedicated to cloud-based solutions has agreed to host kernel.org to deliver long-term stability for the development team.