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.

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

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.?

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

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

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

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

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

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

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

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

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

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

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

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

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?

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

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

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

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

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).