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AI coding agents and a rerun of the operating-system wars

Photo source: Rod Long (@rodlong) | Unsplash

Attending the Agentic AI for Science workshop at MPCDF in Garching got me thinking about the platforms we are starting to build our scientific workflows around. The workshop programme brings together hands-on work with agents, examples from scientific software development and materials simulations, and perspectives from industry. For someone interested in free and open-source software, this raises some familiar questions: who controls those platforms, what can we change ourselves, and how much of our work can we take elsewhere?

What interests me here is the software around the model. An agent harness gives the model tools, supplies context, and controls what it can do. The flagship GPT, Claude, and Gemini models are proprietary, but the software using them does not have to be (and often isn't). We can use the same model through different harnesses, with different licenses, tools, and restrictions. Choosing the model, deciding where it runs, and choosing the harness are separate decisions, even when a product offering bundles them together.

A few harnesses and development environments for programming, scientific workflows, and other tasks illustrate these differences. This is only part of the picture: agents embedded in enterprise applications bring their own integrations and dependencies.

This led me to a somewhat loose comparison: Claude Code reminds me of Windows, Codex CLI of BSD, OpenCode and the like of Linux, and Antigravity of the Macintosh. Each comparison emphasizes something different: compatibility, permissive reuse, independence from suppliers, or the appeal of an integrated experience.

If you have used Claude Code in a terminal, the first part probably sounds wrong already. How does a program that reads files, invokes shell tools, and fits into a Unix workflow resemble Windows? Bear with me. The resemblance is in how people build tools and workflows around the software, rather than how its interface looks.

The future of MkDocs: ProperDocs and Zensical

Photo source: Roman Synkevych (@synkevych) | Unsplash

The slow collapse of MkDocs is, by now, well documented and worth reading if you are interested in the details of it.

In summary, MkDocs is unlikely to get future releases compatible with its current version, which makes the instructions for setting up a GitHub Action for MkDocs deployment in need of an update. Without further ado, here are two good options to move forward.

OpenSSH connections with post-quantum key exchange through WireGuard tunnel

Photo source: Bozhin Karaivanov (@murrayc) | Unsplash

The other day, I set up a machine using a fairly standard Fedora 43 Server installation with a WireGuard VPN tunnel to another machine running a fairly standard Arch Linux installation (of course).

When I tried to SSH from the Arch machine to the Fedora machine, the OpenSSH client would hang.

Reproducibility of scientific career paths over time

Photo source: Murray Campbell (@murrayc) | Unsplash

Klara Filek, a postdoctoral researcher at the Medical University of Graz, recently wrote an article about career orientation for young scientists for the Penkala Association blog. She makes many great points through the article, and I heartily recommend reading it, especially to current PhD students seeking future opportunities.

I would like to emphasize the two reasons that she mentioned why career guidance is so difficult in Croatian academia (translation mine):

• Limited experience of the mentors: Many mentors rely on their own experience in a system they are part of and know very well, and outside of which they often cannot help us much (depending, of course, on the field and personal affinities).
• The “academia-only” narrative: Continuing higher education and a doctorate seem to presuppose a postdoc position and a teaching career. In addition, a good number of academics I was (and still am) surrounded by are convinced that academia is the only place where you can be creative and flexible, which is not true and makes it difficult to explore other possibilities.

I thought quite a bit about both of these points, given that I am guiding Matea Turalija through her PhD journey and I am eager to help her with my acquired experience as much as I can. However, as Klara explained above, this is far from a trivial endeavor.

Cross-building and cross-testing GROMACS for Windows on Linux with MinGW and Wine

Photo source: Katerina (@kat_katerina) | Unsplash

GROMACS 2025.1 (doi:10.5281/zenodo.15006630) bugfix release came out on Tuesday with a few bugfixes. Among them is a fix for energy correction map (CMAP) parsing code, a feature which I introduced in 2025 release in preparation for adding a converted version of Amber ff19SB force field (doi:10.1021/acs.jctc.9b00591) to GROMACS.

The fix for the issue also added several tests to avoid future regressions. I like developing free and open-source software in general and GROMACS in particular; it feels a lot like the postdoc years in Heidelberg again. However, that was not the only change I proposed that got merged for the bugfix release.

The unfortunate state of early-career scientist funding in Croatia

Photo source: Markus Spiske (@markusspiske) | Unsplash

Over the last couple of weeks, there has been a lot of discussion about scientific research funding in the US. There are many changes, and it remains to be seen what will come out of it in the end. If some of the new policies stick around for a longer time, I have no doubt they will inspire discussions and considerations in the rest of the world, including Europe, as many of them in the US tend to do.

While science funding in the US is an important and interesting topic, I would like to say a couple of words regarding science funding that hits closer to home, namely in Croatia. Earlier this week, the Croatian Science Foundation (HrZZ) closed the project call for Installation Research Projects UIP-2025-02. This was the first project call of this type after 5 years, which is possibly the reason why the usual range of eligible scientists with a maximum of 7 years after obtaining the PhD degree was extended to a maximum of 10 years after it. The call still requires a minimum of 2 years of experience after the degree.

How to run Visual Studio (VS) Code Remote over SSH on FreeBSD 13 and 14

Photo source: Lemon Pepper Pictures (@lemonpepperpictures) | Unsplash

FreeBSD Ports provide editors/vscode with the latest stable version of Visual Studio Code and the FreeBSD Foundation provides an excellent guide how to install and use it. Unfortunately, the latest stable version of Visual Studio Code Remote - SSH still does not officially support FreeBSD, but only Linux, Windows, and macOS.

Serverless URL redirects using JavaScript on GitHub Pages

Photo source: Lautaro Andreani (@lautaroandreani) | Unsplash

As many readers of this blog are already aware, we make great use of GitHub Pages for hosting this website and several others. In particular, after FIDIT's inf2 server was finally decomissioned, Pages was the obvious choice for replacing the remaining services it offered.

Since the number and variety of applications and services hosted on inf2 server grew and diminished organically over time, what remained afterward was a collection of complex, but unrelated link hierarchies that had to be redirected to new locations (remember that Cool URIs don't change).

Coming /home

Photo source: Julian Hochgesang (@julianhochgesang) | Unsplash

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.

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

Photo source: Darran Shen (@darranshen) | Unsplash

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.