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
-
AUR Repository Still Under DDoS Attack
Arch User Repository continues to be under a DDoS attack that has been going on for two weeks.
-
RingReaper Malware Poses Danger to Linux Systems
A new kind of malware exploits modern Linux kernels for I/O operations.
-
Happy Birthday, Linux
On August 25, Linux officially turns 34.
-
VirtualBox 7.2 Has Arrived
With early support for Linux kernel 6.17 and other new additions, VirtualBox 7.2 is a must-update for users.
-
Linux Mint 22.2 Beta Available for Testing
Some interesting new additions and improvements are coming to Linux Mint. Check out the Linux Mint 22.2 Beta to give it a test run.
-
Debian 13.0 Officially Released
After two years of development, the latest iteration of Debian is now available with plenty of under-the-hood improvements.
-
Upcoming Changes for MXLinux
MXLinux 25 has plenty in store to please all types of users.
-
A New Linux AI Assistant in Town
Newelle, a Linux AI assistant, works with different LLMs and includes document parsing and profiles.
-
Linux Kernel 6.16 Released with Minor Fixes
The latest Linux kernel doesn't really include any big-ticket features, just a lot of lines of code.
-
EU Sovereign Tech Fund Gains Traction
OpenForum Europe recently released a report regarding a sovereign tech fund with backing from several significant entities.