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  • 6 minut(a/e) čitanja

Coming /home

FreeBSD 14.0-RELEASE annoucement is immiment. Due to faster (re)boot and related improvements by Colin Percival, this version made headlines in tech media even before it got released, which got me interested in trying it out on some of our machines. I installed the first beta on one of our servers and shortly afterward reported an upgrade bug, which got fixed during the beta cycle and was shipped as an errata in 13.2-RELEASE-p4 and 12.4-RELEASE-p6.

I was following the subsequent pre-releases with great interest as well. The final FreeBSD 14.0-RELEASE brings Clang/LLVM 16.0 (which we use in scientific software development and course teaching), OpenSSL 3.0, OpenZFS 2.2, Lua configuration support in the boot loader, upgraded WireGuard in the kernel wg driver, and plenty of other changes that are relevant to our usage. I found it well worth the time it took to go through these changes and learn what to expect from the release.

  • 7 minut(a/e) čitanja

My perspective after two years as a research and teaching assistant at FIDIT

My employment as a research and teaching assistant at Faculty of Informatics and Digital Technologies (FIDIT for short), University of Rijeka (UniRi) ended last month with the expiration of the time-limited contract I had. This moment has marked almost two full years I spent in this institution and I think this is a good time to take a look back at everything that happened during that time. Inspired by the recent posts by the PI of my group, I decided to write my perspective on the time that I hope is just the beginning of my academic career.

  • 5 minut(a/e) čitanja

Alumni Meeting 2023 at HITS and the reminiscence of the postdoc years

This month we had Alumni Meeting 2023 at the Heidelberg Institute for Theoretical Studies, or HITS for short. I was very glad to attend this whole-day event and reconnect with my former colleagues as well as researchers currently working in the area of computational biochemistry at HITS. After all, this is the place and the institution where I worked for more than half of my time as a postdoc, where I started regularly contributing code to GROMACS molecular dynamics simulator, and published some of my best papers.

  • 7 minut(a/e) čitanja

Should I do a Ph.D.?

Tough question, and the one that has been asked and answered over and over. The simplest answer is, of course, it depends on many factors.

As I started blogging at the end of my journey as a doctoral student, the topic of how I selected the field and ultimately decided to enroll in the postgraduate studies never really came up. In the following paragraphs, I will give a personal perspective on my Ph.D. endeavor. Just like other perspectives from doctors of not that kind, it is specific to the person in the situation, but parts of it might apply more broadly.

  • 5 minut(a/e) čitanja

Publishing (Material for) MkDocs website to GitHub Pages using custom Actions workflow

As you can probably see, this website is built using the Material theme for MkDocs, which we have been happily using for over one year after using Sphinx for many years prior to that. GitHub Pages offers built-in support for Jekyll, but not for MkDocs and therefore it requires the manual building and deployment of our website. However, it automates many other things, including HTTPS certificate provisioning on our domain via Let's Encrypt.

There are several somewhat related approaches using GitHub Actions for automating the deployment of MkDocs-generated sites, usually with the Material theme, to GitHub Pages. These guides are not only found on blogs written by enthusiasts; the official Getting started section of the Material for MkDocs documentation describes the usage of GitHub Actions for deployment and provides a generic YAML file for that purpose.

  • 5 minut(a/e) čitanja

Markdown vs reStructuredText for teaching materials

Back in summer 2017. I wrote an article explaining why we used Sphinx and reStructuredText to produce teaching materials and not a wiki. In addition to recommending Sphinx as the solution to use, it was general praise for generating static HTML files from Markdown or reStructuredText.

This summer I made the conversion of teaching materials from reStructuredText to Markdown. Unfortunately, the automated conversion using Pandoc didn't quite produce the result I wanted so I ended up cooking my own Python script that converted the specific dialect of reStructuredText that was used for writing the contents of the group website and fixing a myriad of inconsistencies in the writing style that accumulated over the years.

  • 3 minut(a/e) čitanja

Mirroring free and open-source software matters

Post theme song: Mirror mirror by Blind Guardian

A mirror is a local copy of a website that's used to speed up access for the users residing in the area geographically close to it and reduce the load on the original website. Content distribution networks (CDNs), which are a newer concept and perhaps more familiar to younger readers, serve the same purpose, but do it in a way that's transparent to the user; when using a mirror, the user will see explicitly which mirror is being used because the domain will be different from the original website, while, in case of CDNs, the domain will remain the same, and the DNS resolution (which is invisible to the user) will select a different server.

Free and open-source software was distributed via (FTP) mirrors, usually residing in the universities, basically since its inception. The story of Linux mentions a directory on ftp.funet.fi (FUNET is the Finnish University and Research Network) where Linus Torvalds uploaded the sources, which was soon after mirrored by Ted Ts'o on MIT's FTP server. The GNU Project's history contains an analogous process of making local copies of the software for faster downloading, which was especially important in the times of pre-broadband Internet, and it continues today.

  • 3 minut(a/e) čitanja

Fly away, little bird

The last day of July happened to be the day that Domagoj Margan, a former student teaching assistant and a great friend of mine, set up his own DigitalOcean droplet running a web server and serving his professional website on his own domain domargan.net. For a few years, I was helping him by providing space on the server I owned and maintained, and I was always glad to do so. Let me explain why.