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

Posted by Vedran Miletić on 2025-04-28 11:15:13 UTC

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


human statues near white building

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.

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

Posted by Vedran Miletić on 2025-04-28 11:15:13 UTC

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


a fountain in the middle of a town square

Photo source: Jahanzeb Ahsan (@jahan_photobox) | Unsplash


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.

Should I do a Ph.D.?

Posted by Vedran Miletić on 2025-04-28 11:15:13 UTC

Should I do a Ph.D.?


a bike is parked in front of a building

Photo source: Santeri Liukkonen (@iamsanteri) | Unsplash


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.

Don't use RAR

Posted by Vedran Miletić on 2025-04-28 11:15:13 UTC

Don't use RAR


a large white tank

Photo source: Tim Mossholder (@ctimmossholder) | Unsplash


I sometimes joke with my TA Milan Petrović that his usage of RAR does not imply that he will be driving a rari. After all, he is not Devito rapping^Wsinging Uh 😤. Jokes aside, if you search for "should I use RAR" or a similar phrase on your favorite search engine, you'll see articles like 2007 Don't Use ZIP, Use RAR and 2011 Why RAR Is Better Than ZIP & The Best RAR Software Available.

Markdown vs reStructuredText for teaching materials

Posted by Vedran Miletić on 2025-04-28 11:15:13 UTC

Markdown vs reStructuredText for teaching materials


blue wooden door surrounded by book covered wall

Photo source: Eugenio Mazzone (@eugi1492) | Unsplash


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.

Mirroring free and open-source software matters

Posted by Vedran Miletić on 2025-04-28 11:15:13 UTC

Mirroring free and open-source software matters


gold and silver steel wall decor

Photo source: Tuva Mathilde Løland (@tuvaloland) | Unsplash


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.

Fly away, little bird

Posted by Vedran Miletić on 2025-04-28 11:15:13 UTC

Fly away, little bird


macro-photography blue, brown, and white sparrow on branch

Photo source: Vincent van Zalinge (@vincentvanzalinge) | Unsplash


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.

Why we use reStructuredText and Sphinx static site generator for maintaining teaching materials

Posted by Vedran Miletić on 2025-04-28 11:15:13 UTC

Why we use reStructuredText and Sphinx static site generator for maintaining teaching materials


open book lot

Photo source: Patrick Tomasso (@impatrickt) | Unsplash


Yesterday I was asked by Edvin Močibob, a friend and a former student teaching assistant of mine, the following question:

You seem to be using Sphinx for your teaching materials, right? As far as I can see, it doesn't have an online WYSIWYG editor. I would be interested in comparison of your solution with e.g. MediaWiki.

While the advantages and the disadvantages of static site generators, when compared to content management systems, have been written about and discussed already, I will outline our reasons for the choice of Sphinx below. Many of the points have probably already been presented elsewhere.

Enabling HTTP/2, HTTPS, and going HTTPS-only on inf2

Posted by Vedran Miletić on 2025-04-28 11:15:13 UTC

Enabling HTTP/2, HTTPS, and going HTTPS-only on inf2


an old padlock on a wooden door

Photo source: Arkadiusz Gąsiorowski (@ambuscade) | Unsplash


Inf2 is a web server at University of Rijeka Department of Informatics, hosting Sphinx-produced static HTML course materials (mirrored elsewhere), some big files, a WordPress instance (archived elsewhere), and an internal instance of Moodle.

HTTPS was enabled on inf2 for a long time, albeit using a self-signed certificate. However, with Let's Encrpyt coming into public beta, we decided to join the movement to HTTPS.

Celebrating Graphics and Compute Freedom Day

Posted by Vedran Miletić on 2025-04-28 11:15:13 UTC

Celebrating Graphics and Compute Freedom Day


stack of white and brown ceramic plates

Photo source: Elena Mozhvilo (@miracleday) | Unsplash


Hobbyists, activists, geeks, designers, engineers, etc have always tinkered with technologies for their purposes (in early personal computing, for example). And social activists have long advocated the power of giving tools to people. An open hardware movement driven by these restless innovators is creating ingenious versions of all sorts of technologies, and freely sharing the know-how through the Internet and more recently through social media. Open-source software and more recently hardware is also encroaching upon centers of manufacturing and can empower serious business opportunities and projects.

The free software movement is cited as both an inspiration and a model for open hardware. Free software practices have transformed our culture by making it easier for people to become involved in producing things from magazines to music, movies to games, communities to services. With advances in digital fabrication making it easier to manipulate materials, some now anticipate an analogous opening up of manufacturing to mass participation.

The academic and the free software community ideals

Posted by Vedran Miletić on 2025-04-28 11:15:13 UTC

The academic and the free software community ideals


book lot on black wooden shelf

Photo source: Giammarco Boscaro (@giamboscaro) | Unsplash


Today I vaguely remembered there was one occasion in 2006 or 2007 when some guy from the academia doing something with Java and Unicode posted on some mailing list related to the free and open-source software about a tool he was developing. What made it interesting was that the tool was open source, and he filed a patent on the algorithm.

Free to know: Open access and open source

Posted by Vedran Miletić on 2025-04-28 11:15:13 UTC

Free to know: Open access and open source


yellow and black come in we're open sign

Photo source: Álvaro Serrano (@alvaroserrano) | Unsplash


!!! info Reposted from Free to Know: Open access & open source, originally posted by STEMI education on Medium.

Q&A with Vedran Miletić

In June 2014, Elon Musk opened up all Tesla patents. In a blog post announcing this, he wrote that patents "serve merely to stifle progress, entrench the positions of giant corporations and enrich those in the legal profession, rather than the actual inventors." In other words, he joined those who believe that free knowledge is the prerequisite for a great society -- that it is the vibrancy of the educated masses that can make us capable of handling the strange problems our world is made of.

The movements that promote and cultivate this vibrancy are probably most frequently associated with terms "Open access" and "open source". In order to learn more about them, we Q&A-ed Vedran Miletić, the Rocker of Science -- researcher, developer and teacher, currently working in computational chemistry, and a free and open source software contributor and activist. You can read more of his thoughts on free software and related themes on his great blog, Nudged Elastic Band. We hope you will join him, us, and Elon Musk in promoting free knowledge, cooperation and education.

I am still not buying the new-open-source-friendly-Microsoft narrative

Posted by Vedran Miletić on 2025-04-28 11:15:13 UTC

I am still not buying the new-open-source-friendly-Microsoft narrative


black framed window

Photo source: Patrick Bellot (@pbellot) | Unsplash


This week Microsoft released Computational Network Toolkit (CNTK) on GitHub, after open sourcing Edge's JavaScript engine last month and a whole bunch of projects before that.

Even though the open sourcing of a bunch of their software is a very nice move from Microsoft, I am still not convinced that they have changed to the core. I am sure there are parts of the company who believe that free and open source is the way to go, but it still looks like a change just on the periphery.

All the projects they have open-sourced so far are not the core of their business. Their latest version of Windows is no more friendly to alternative operating systems than any version of Windows before it, and one could argue it is even less friendly due to more Secure Boot restrictions. Using Office still basically requires you to use Microsoft's formats and, in turn, accept their vendor lock-in.

Put simply, I think all the projects Microsoft has opened up so far are a nice start, but they still have a long way to go to gain respect from the open-source community. What follows are three steps Microsoft could take in that direction.

AMD and the open-source community are writing history

Posted by Vedran Miletić on 2025-04-28 11:15:13 UTC

AMD and the open-source community are writing history


a close up of a cpu chip on top of a motherboard

Photo source: Andrew Dawes (@andrewdawes) | Unsplash


Over the last few years, AMD has slowly been walking the path towards having fully open source drivers on Linux. AMD did not walk alone, they got help from Red Hat, SUSE, and probably others. Phoronix also mentions PathScale, but I have been told on Freenode channel #radeon this is not the case and found no trace of their involvement.

AMD finally publically unveiled the GPUOpen initiative on the 15th of December 2015. The story was covered on AnandTech, Maximum PC, Ars Technica, Softpedia, and others. For the open-source community that follows the development of Linux graphics and computing stack, this announcement comes as hardly surprising: Alex Deucher and Jammy Zhou presented plans regarding amdgpu on XDC2015 in September 2015. Regardless, public announcement in mainstream media proves that AMD is serious about GPUOpen.

I believe GPUOpen is the best chance we will get in this decade to open up the driver and software stacks in the graphics and computing industry. I will outline the reasons for my optimism below. As for the history behind open-source drivers for ATi/AMD GPUs, I suggest the well-written reminiscence on Phoronix.

On having leverage and using it for pushing open-source software adoption

Posted by Vedran Miletić on 2025-04-28 11:15:13 UTC

On having leverage and using it for pushing open-source software adoption


Open 24 Hours neon signage

Photo source: Alina Grubnyak (@alinnnaaaa) | Unsplash


Back in late August and early September, I attended 4th CP2K Tutorial organized by CECAM in Zürich. I had the pleasure of meeting Joost VandeVondele's Nanoscale Simulations group at ETHZ and working with them on improving CP2K. It was both fun and productive; we overhauled the wiki homepage and introduced acronyms page, among other things. During a coffee break, there was a discussion on the JPCL viewpoint that speaks against open-source quantum chemistry software, which I countered in the previous blog post.

But there is a story from the workshop which somehow remained untold, and I wanted to tell it at some point. One of the attendants, Valérie Vaissier, told me how she used proprietary quantum chemistry software during her Ph.D.; if I recall correctly, it was Gaussian. Eventually, she decided to learn CP2K and made the switch. She liked CP2K better than the proprietary software package because it is available free of charge, the reported bugs get fixed quicker, and the group of developers behind it is very enthusiastic about their work and open to outsiders who want to join the development.

What is the price of open-source fear, uncertainty, and doubt?

Posted by Vedran Miletić on 2025-04-28 11:15:13 UTC

What is the price of open-source fear, uncertainty, and doubt?


turned on red open LED signage

Photo source: j (@janicetea) | Unsplash


The Journal of Physical Chemistry Letters (JPCL), published by American Chemical Society, recently put out two Viewpoints discussing open-source software:

  1. Open Source and Open Data Should Be Standard Practices by J. Daniel Gezelter, and
  2. What Is the Price of Open-Source Software? by Anna I. Krylov, John M. Herbert, Filipp Furche, Martin Head-Gordon, Peter J. Knowles, Roland Lindh, Frederick R. Manby, Peter Pulay, Chris-Kriton Skylaris, and Hans-Joachim Werner.

Viewpoints are not detailed reviews of the topic, but instead, present the author's view on the state-of-the-art of a particular field.

The first of two articles stands for open source and open data. The article describes Quantum Chemical Program Exchange (QCPE), which was used in the 1980s and 1990s for the exchange of quantum chemistry codes between researchers and is roughly equivalent to the modern-day GitHub. The second of two articles questions the open-source software development practice, advocating the usage and development of proprietary software. I will dissect and counter some of the key points from the second article below.

Joys and pains of interdisciplinary research

Posted by Vedran Miletić on 2025-04-28 11:15:13 UTC

Joys and pains of interdisciplinary research


white and black coffee maker

Photo source: Trnava University (@trnavskauni) | Unsplash


In 2012 University of Rijeka became NVIDIA GPU Education Center (back then it was called CUDA Teaching Center). For non-techies: NVIDIA is a company producing graphical processors (GPUs), the computer chips that draw 3D graphics in games and the effects in modern movies. In the last couple of years, NVIDIA and other manufacturers allowed the usage of GPUs for general computations, so one can use them to do really fast multiplication of large matrices, finding paths in graphs, and other mathematical operations.

Browser wars

Posted by Vedran Miletić on 2025-04-28 11:15:13 UTC

Browser wars


brown fox on snow field

Photo source: Ray Hennessy (@rayhennessy) | Unsplash


Last week in Rijeka we held Science festival 2015. This is the (hopefully not unlucky) 13th instance of the festival that started in 2003. Popular science events were organized in 18 cities in Croatia.

I was invited to give a popular lecture at the University departments open day, which is a part of the festival. This is the second time in a row that I got invited to give popular lecture at the open day. In 2014 I talked about The Perfect Storm in information technology caused by the fall of economy during 2008-2012 Great Recession and the simultaneous rise of low-cost, high-value open-source solutions. Open source completely changed the landscape of information technology in just a few years.

The follow-up

Posted by Vedran Miletić on 2025-04-28 11:15:13 UTC

The follow-up


people watching concert

Photo source: Andre Benz (@trapnation) | Unsplash


When Linkin Park released their second album Meteora, they had a quote on their site that went along the lines of

Musicians have their entire lives to come up with a debut album, and only a very short time afterward to release a follow-up.

Open-source magic all around the world

Posted by Vedran Miletić on 2025-04-28 11:15:13 UTC

Open-source magic all around the world


woman blowing sprinkle in her hand

Photo source: Almos Bechtold (@almosbech) | Unsplash


Last week brought us two interesting events related to open-source movement: 2015 Red Hat Summit (June 23-26, Boston, MA) and Skeptics in the pub (June 26, Rijeka, Croatia).

Posted by Mohammadreza Hendiani on 2025-04-28 06:01:54 UTC

Can't believe one of the biggest YouTubers ever just switched to Linux! :allthethings: Check it out: youtube.com/watch?v=pVI_smLgTY

WebKitGTK API Versions Demystified

Posted by Michael Catanzaro on 2025-04-28 05:00:00 UTC

WebKitGTK has a bunch of different confusing API versions. Here are the three API versions that are currently supported by upstream:

  • webkitgtk-6.0: This is WebKitGTK for GTK 4 (and libsoup 3), introduced in WebKitGTK 2.40. This is what’s built by default if you build WebKit with -DPORT=GTK.
  • webkit2gtk-4.1: This is WebKitGTK for GTK 3 and libsoup 3, introduced in WebKitGTK 2.32. Get this by building with -DPORT=GTK -DUSE_GTK3=ON.
  • webkit2gtk-4.0: This is WebKitGTK for GTK 3 and libsoup 2, introduced in WebKitGTK 2.6. Get this by building with -DPORT=GTK -DUSE_GTK3=ON -DUSE_SOUP2=ON.

webkitgtk-6.0 contains a bunch of API changes, and all deprecated APIs were removed. If you’re upgrading to webkitgtk-6.0, then you’re also upgrading your application from GTK 3 to GTK 4, and have to adapt to much bigger GTK API changes anyway, so this seemed like a good opportunity to break compatibility and fix old mistakes for the first time in a very long time.

webkit2gtk-4.1 is exactly the same as webkit2gtk-4.0, except for the libsoup API version that it links against.

webkit2gtk-4.0 is — remarkably — mostly API stable since it was released in September 2014. Some particular C APIs have been deprecated and don’t work properly anymore, but no stable C APIs have been removed during this time, and library ABI is maintained. (Caveat: WebKitGTK used to have unstable DOM APIs, some of which were removed before the DOM API was eventually stabilized. Nowadays, the DOM APIs are all stable but deprecated in webkit2gtk-4.1 and webkit2gtk-4.0, and removed in webkitgtk-6.0.)

If you are interested in history, here are the older API versions that do not matter anymore:

  • webkit2gtk-5.0: This was an unstable API version used during development of the GTK 4 API, intended for WebKit developers rather than application developers. It was obsoleted by webkitgtk-6.0.
  • webkit2gtk-3.0: original API version of WebKitGTK for GTK 3 and libsoup 2, obsoleted by webkit2gtk-4.0. This was the original “WebKit 2” API version, which was only used by a few applications before it was removed one decade ago (history).
  • webkitgtk-3.0: note the missing “2”, this is “WebKit 1” (predating the modern multiprocess architecture) for GTK 3. This API version was widely-used on Linux, and its removal one decade ago precipitated a security crisis which I called The Great API Break. (This crisis was worth it. Modern WebKit’s multiprocess architecture is far more secure than the old single-process architecture.)
  • webkitgtk-1.0: the original WebKitGTK API version, this is “WebKit 1” for GTK 2. This API version was also widely-used on Linux before it was removed in The Great API Break.

Fedora and RHEL users, are you confused by all the different confusing downstream package names? Here is your map:

  • webkitgtk6.0, webkit2gtk4.1, and webkit2gtk4.0: This is the current binary package naming in Fedora, corresponding precisely to the WebKitGTK API version to reduce confusion.
  • webkit2gtk3: old name for webkit2gtk4.0, still used in RHEL 9 and RHEL 8
  • webkitgtk4: even older name for webkit2gtk4.0, still used in RHEL 7
  • webkitgtk3: this is the webkitgtk-3.0 API version, still used in RHEL 7
  • webkitgtk: this is webkitgtk-1.0, used in RHEL 6

Notably, webkit2gtk4.0, webkit2gtk3, and webkitgtk4 are all the same thing.

Nouvelle version du container Docker PHP-FPM pour Nextcloud avec s6-overlay

Posted by Guillaume Kulakowski on 2025-04-27 12:29:37 UTC

La nouvelle version de mon container Docker pour Nextcloud remplace s6-overlay par supervisor, offrant ainsi une personnalisation plus avancée. Vous pouvez désormais ajouter des configurations pour PHP et PHP-FPM ou exécuter des scripts à l’initialisation (comme l’ajout de drivers Intel). Le PUID et PGID restent également personnalisables. Cette mise à jour s’inscrit dans la lignée […]

Cet article Nouvelle version du container Docker PHP-FPM pour Nextcloud avec s6-overlay est apparu en premier sur Guillaume Kulakowski's blog.

Démarrer un Raspberry Pi 4 sur un disque SSD

Posted by Didier Fabert on 2025-04-27 00:00:00 UTC

Remplacer la carte SD par un disque dur SSD sur un raspberry pi 4

Mise à jour du système

Pas de mystère ici, c'est des commandes debian tout ce qui a de plus standard.

sudo apt update
sudo apt full-upgrade

Mise à jour du firmware

Un peu plus trekky, on met à jour le firmware

sudo rpi-update
 *** Raspberry Pi firmware updater by Hexxeh, enhanced by AndrewS and Dom
 *** Performing self-update
 *** Relaunching after update
 *** Raspberry Pi firmware updater by Hexxeh, enhanced by AndrewS and Dom
 *** We're running for the first time
 *** Backing up files (this will take a few minutes)
 *** Backing up firmware
 *** Backing up modules 5.10.103-v8+
#############################################################
WARNING: This update bumps to rpi-5.15.y linux tree
See: https://forums.raspberrypi.com/viewtopic.php?t=322879

'rpi-update' should only be used if there is a specific
reason to do so - for example, a request by a Raspberry Pi
engineer or if you want to help the testing effort
and are comfortable with restoring if there are regressions.

DO NOT use 'rpi-update' as part of a regular update process.
##############################################################
Would you like to proceed? (y/N)
 *** Downloading specific firmware revision (this will take a few minutes)
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   173  100   173    0     0   1184      0 --:--:-- --:--:-- --:--:--  1184
100  111M  100  111M    0     0  1051k      0  0:01:48  0:01:48 --:--:-- 1023k
 *** Updating firmware
 *** Updating kernel modules
 *** depmod 5.15.35-v8+
 *** depmod 5.15.35+
 *** depmod 5.15.35-v7+
 *** depmod 5.15.35-v7l+
 *** Updating VideoCore libraries
 *** Using SoftFP libraries
 *** Updating SDK
 *** Running ldconfig
 *** Storing current firmware revision
 *** Deleting downloaded files
 *** Syncing changes to disk
 *** If no errors appeared, your firmware was successfully updated to 6db8c1cdd3da2f070866d2149c956ce86a4ccdd5
 *** A reboot is needed to activate the new firmware

On redémarre pour activer le nouveau firmware

sudo reboot

Mise à jour du bootloader

S'assurer que dans le fichier /etc/default/rpi-eeprom-update, la variable FIRMWARE_RELEASE_STATUS soit à stable ou latest. Avec la valeur default, ce n'est pas toujours le dernier firmware qui est installé.

FIRMWARE_RELEASE_STATUS="stable"
sudo rpi-eeprom-update -d -a
*** INSTALLING EEPROM UPDATES ***

BOOTLOADER: update available
   CURRENT: jeudi 3 septembre 2020, 12:11:43 (UTC+0000) (1599135103)
    LATEST: mardi 25 janvier 2022, 14:30:41 (UTC+0000) (1643121041)
   RELEASE: default (/lib/firmware/raspberrypi/bootloader/default)
            Use raspi-config to change the release.

  VL805_FW: Using bootloader EEPROM
     VL805: up to date
   CURRENT: 000138a1
    LATEST: 000138a1
   CURRENT: jeudi 3 septembre 2020, 12:11:43 (UTC+0000) (1599135103)
    UPDATE: mardi 25 janvier 2022, 14:30:41 (UTC+0000) (1643121041)
    BOOTFS: /boot

EEPROM updates pending. Please reboot to apply the update.
To cancel a pending update run "sudo rpi-eeprom-update -r".

On redémarre pour activer le nouveau bootloader

sudo reboot

Si on relance la commande précédente, la version CURRENT doit être identique à LATEST. Dans le cas contraire, il faut une nouvelle fois redémarrer.

Modification des options du bootloader

sudo raspi-config
  1. On sélectionne le menu des options avancées

    Advanced Options

  2. Puis le menu de la version du bootloader

    Bootloader Version

  3. On sélectionne Utiliser le bootloader avec...