Komentari na Nacrt pravilnika o uvjetima za izbor u znanstvena zvanja u području tehničkih znanosti

Naslovna slika: Jeff Sheldon | Unsplash (fotografija)

Pred nekoliko tjedana priupitan sam da dam komentare na Nacrt pravilnika o uvjetima pravilnika o uvjetima za izbor u znanstvena zvanja. Svoje komentare na uvjete u području tehničkih znanosti objavljujem i ovdje, kako bih bio siguran da će ostati sačuvani dugoročno.


Za razliku od nekih drugih područja, interdisciplinarno područje znanosti koje uključuje tehničke znanosti ni na koji način nije spomenuto. Konkretno, potrebno je precizirati kako će se bodovati radovi u interdisciplinarnom području tehničkih znanosti i prirodnih znanosti ili biomedicine, za znanstvenika koji se bira u području tehničkih znanosti.

Višeautorski radovi

Brojanje višeautorskih članaka u tehničkim znanostima koje rad do 4 autora boduje svakom autoru sa 100% je korak u pravom smjeru u odnosu na prošli pravilnik. Međutim, problem postoji kod interdisciplinarnih radova u području tehničkih znanosti i području prirodnih znanosti polja fizike, kemije, biologije, geologije, geofizike i interdisciplinarnih prirodnih znanosti.

Znanstveniku koji se bira u području prirodnih znanosti broj autora na radu se ne gleda, što je razumno obzirom da u kolaboracijama teoretiračara i eksperimentalaca često bude i do 10 autora na radu (pa čak i više u nekim poljima). S druge strane, znanstveniku koji se bira u području tehničkih znanosti se gleda broj autora i rad se sukladno boduje. Ovo destimulira kolaboraciju znanstvenika kojemu je cilj izbor u tehničkim znanostima sa znanstvenicima koji rade u području prirodnih znanosti. Potrebno je za znanstvenika koji se bira u području tehničkih znanosti definirati adekvatno bodovanje višeautorskih radova u interdisicplinarnom području tehničkih i prirodnih znanosti.

Razvoj znanstvenih softvera

U polju računarstva prvenstveno, ali i u drugim poljima tehničkih i prirodnih znanosti, znanstvena istraživanja ovise o znanstvenim softverima. Neka od istraživanja vrše razvoj softvera tako da ga vežu uz znanstveni rad koji provode. Razvoj softvera se tada boduje kod izbora u zvanje samo ako su objavljeni članci o novim značajkama u softveru, što nije uvijek moguće. Takav destimulira doprinošenje inkrementalnim promjenama u postojećim softverima; između ostalog, to ograničava suradnju s industrijom koja traži poboljšanja u postojećim softverima sukladno potrebama poslovanja. Potrebno je razviti model bodovanja doprinosa razvoju znanstvenog softvera. Primjer bodovanja koji već postoji i koristi se kod zapošljavanja u industriji su profili na OpenHubu i GitHubu.

The academic and the free software community ideals

Featured image: davide ragusa | Unsplash (photo)

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.

Few searches after, boom, there it is

Google is a powerful tool. The original thread from March 2007 on (now defunct) linux-utf8 mailing list can be found on The Mail Archive. The software website is still up. The patent is out there as well.

Back in 2007 I was in my 3rd year of undergraduate study of mathematics (major) and computer science (minor), used to do Linux workshops in my spare time, and was aiming to do a PhD in mathematics. I disliked the usage and development of proprietary research software which was quite common in much of computer science research I saw back then. Unlike these researchers, I believed that that academia and free software community agreed that knowledge should be free as in freedom, and I wanted to be a part of such a community.

Academic ideals

As a student, you are told continuously that academia is for idealists. People who put freedom before money. People who care about knowledge in and of itself and not how to sell it. And along with these ideas about academia, you are passed one more very important idea: the authority of academia. Whatever the issue, academia (not science, bear in mind) will provide a solution. Teaching? Academia knows how to do it best. Research? You bet. Sure, some professor here and other professor there might disagree on whatever topic, and one of them might be wrong. Regardless, the academia will resolve whatever conflict that arises and produce the right answer. Nothing else but the academia.

The idea, in essence, is that people outside of academia are just outsiders and their work is not relevant because it is not sanctioned by academics. They do not get the right to decide on relevant research. Their criticism of the work of someone from the academia does not matter.

Free software community ideals

Unlike academia, free software community is based on decentralization, lack of imposed hierarchy, individual creativity, and strong opposition to this idea of requiring some sanction from some arbitrary central authority. If you disagree, you are free to create software your way and invite others to do the same. There is no “officially right” and “officially wrong” way.

Patent pending open source code

“Some guy from the academia” in the case I mentioned above was Robert D. Cameron from Simon Fraser University, asking free software community to look at his code:

u8u16-0.9  is available as open source software under an OSL 3.0 license at http://u8u16.costar.sfu.ca/

Rich Felker was enthusiastic at first, but quickly saw the software in question was patent pending:

On second thought, I will not offer any further advice on this. The website refers to “patent-pending technology”. Software patents are fundamentally wrong and unless you withdraw this nonsense you are an enemy of Free Software, of programmers, and users in general, and deserve to be ostracized by the community. Even if you intend to license the patents obtained freely for use in Free Software, it’s still wrong to obtain them because it furthers a precedent that software patents are valid, particularly stupid patents like “applying vectorization in the obvious way to existing problem X”.

There were also doubts presented regarding relevance of this research at all, along with suggestions for better methods. While interesting, they are outside the scope of this blog post.

A patent is a state-granted monopoly designed to stimulate research, yet frequently used to stop competition and delay access to new knowledge. Both Mises Institute and Electronic Frontier Foundation have written many articles on patents which I highly recommend for more information. In addition, as an excellent overview of the issues regarding the patent system, I can recommend the Patent Absurdity: How software patents broke the system movie.

So, there was a guy from the idealistic academia, who from my perspective seemed to take the wrong stance. And there was a guy outside of the idealistic academia, and was seemingly taking the right stance. It made absolutely no sense at first that the academia was working against freedom and an outsider was standing for freedom. Then it finally hit me: the academia and the free software community do not hold the same ideals and do not pursue the same goals. And this was also the moment I chose my side: the free software community first and the academia second.

However, academics tend to be very creative in proving they care about freedom of knowledge. Section 9 of the paper (the only part of the paper I read) goes:

A Simon Fraser University spin-off company, International Characters, has been formed to commercialize the results of the ongoing parallel bit stream research using an open source model. Several patent applications have been filed on various aspects of parallel bit stream technology and inductive doubling architecture.

Whoa, open source and patents. What’s going on here?

However, any issued patents are being dedicated to free use in research, teaching, experimentation and open-source software. This includes commercial use of open-source software provided that the software is actually publically available. However, commercial licenses are required for proprietary software applications as well as combinations of hardware and software.

Were it not for the patents, but for the licenses, I would completely agree with this approach. “If you are open sourcing your stuff, you are free to use my open source stuff. If you are not open source, you are required to get a different license from me.” That is how copyleft licenses work.

The problem is, as Rich says above, every filling of a patent enforces the validity of the patent system itself. The patent in question is just a normal patent and this is precisely the problem. Furthermore:

From an industry perspective, the growth of software patents and open-source software are both undeniable phenomena. However, these industry trends are often seen to be in conflict, even though both are based in principle on disclosure and publication of technology details.

Unlike patents, free and open source software is based on the principle of free unrestricted usage, modification, and distribution. These industry trends are seen in conflict, and that is the right way to see them.

It is hoped that the patentleft model advanced by this commercialization effort will be seen as at least one constructive approach to resolving the conflict. A fine result would ultimately be legislative reform that publication of open source software is a form of knowledge dissemination that is considered fair use of any patented technology.

While it would certainly be nice if open source was protected from patent lawsuits, this tries to shift the focus from the real issue, which is the patent itself and restrictions it imposes.

Opening the patents

First possible solution is not to patent at all.

Second possible solution is to license the patent differently. Instead of being picky about the applications of the patent to decide whether royalties ought to be paid, which is the classical academic approach and also used above, one can simply license it royalty-free to everyone. This way, one prevents innovations from being patented and licensed in a classical way. This is what Tesla Motors does.

Third possible solution is to use the copyleft-style patent license, which allows royalty-free use of knowledge given that you license your developments under the same terms. The approach uses the existing patent system in a reverse way, just like the copyleft licenses use the copyright system in a reverse way. This can be seen as an evolution of what Open Invention Network and BiOS already do.

This approach still relies on giving validity to the patent system, but unlike the classical academic approach it also forces anyone to either go copyleft with their derivative patents or not use your technology. Effectively, this approach uses the patent system to expand the technology commons accessible to everyone, which is an interesting reverse of its originally intended usage.

I am still not buying the “new open source-friendly Microsoft” bullshit

Featured image: Georgi Petrov | Unsplash (photo)

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.

Despite the fact that 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.

Really, 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.

1. Fully support OpenDocument and make it the default format in Office applications

Microsoft has accepted the web standards defined by W3C. Making OpenDocument the default format in Office would be the equivalent of accepting independently standardized HTML and CSS. Even after accepting the format, Microsoft could still compete with free and open source office suites. They could offer more features, more beautiful user interface, better performance, or better quality support. They would, however, lose the vendor lock-in ability.

2. Open source large parts of Windows and the tools required to build custom versions

Apple has been open sourcing large parts of OS X (but not all of it, one should say) since the version 10.0. With significant effort, it is possible to build something like PureDarwin, an open source operating system based on the source released by Apple. Note that, for example, PureDarwin does not use OS X GUI, since Apple has not open sourced it.

Microsoft could do the same with Windows as Apple did with OS X: open source large parts of the code, and allow people to combine it with other software to build custom versions. Even if some parts of the code remain proprietary, it is still a big improvement over what Microsoft is doing now.

3. Spin off the department for Secure Boot bootloader signing into an independent non-profit entity

Since 2012, the machines with UEFI Secure Boot have started to appear on the market. To get your laptop or desktop PC certified for Windows 8, a manufacturer had to support Secure Boot, include Microsoft keys, turn Secure Boot on by default, and allow the user to turn it off. Microsoft agreed to sign binaries for vendors of other operating systems, and vendors like Fedora and Canonical got the signatures.

With Windows 10, the requirement to allow the user to turn Secure Boot off vanished, which prevents booting of unsigned operating systems. Furthermore, Microsoft can at any time revoke the key used for signing operating systems other than Windows and render all of them unbootable. Finally, since the key used to sign other operating systems is a separate key from the one used to sign Windows, the revoking would not affect Windows in any way.

The situation gives Microsoft an enormous amount of power and control over desktops and laptops. It would be much better if the signing process and management of keys was done by an independent non-profit entity, governed by a consortium of companies.


I am sure there are people, even among those who work for Microsoft right now, who would agree with these ideas. However, the support for these ideas itself does not matter much unless and until Microsoft starts taking action in that direction.

And, unless and until that happens, I am not buying the “new open source-friendly Microsoft” bullshit.

AMD and the open source community are writing history

Featured image: Maya Karmon | Unsplash (photo)

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 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 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 well written reminiscence on Phoronix.

Intel and NVIDIA

AMD’s only competitors are Intel and NVIDIA. More then a decade ago, these three had other other companies competing with them. However, all the companies that used to produce graphics processors either ceased to exist due to bankruptcy/acquisition or changed their focus to other markets.

Intel has very good open source drivers and this has been the case for almost a decade now. However, they only produce integrated GPU which are not very interesting for gaming and heterogeneous computing. Sadly, their open source support does not include Xeon Phi, which is a sort of interesting device for heterogeneous computing.

NVIDIA, on the other hand, has very good proprietary drivers, and this has been true for more then a decade. Aside from Linux, these drivers also support FreeBSD and Solaris (however, CUDA, the compute stack, is Linux-only).

To put it simply, if using a proprietary driver for graphics and computing is acceptable, NVIDIA simply does better job with proprietary drivers than AMD. You buy the hardware, you install the proprietary driver on Linux, and you play your games or run the computations. From a consumer’s perspective, this is how hardware should work: stable and on the release day. From the perspective of an activist fighting for software freedom, this is unacceptable.

Yes, if AMD tries to compete with proprietary drivers against NVIDIA’s proprietary drivers, NVIDA wins. When both companies do not really care about free and open source software, I (and probably others) will just pick the one that works better at this moment, and not think much about it.

To give a real-world example, back in 2012 we started a new course on GPU computing at University of Rijeka Department of Informatics. If AMD had the open source heterogeneous computing stack ready, we would gladly pick their technology, even if hardware had slightly lower performance (you do not really care for teaching anyway). However, since it came down to proprietary vs. proprietary, NVIDIA offered more stable and mature solution and we went with them.

Even with the arguments that NVIDIA is anti-competitive because G-Sync works only on their hardware, that AMD’s hardware is not so bad and you can still play games on it, and that if AMD crashes NVIDIA will have a monopoly, I personally could not care less. It is completely useless to buy AMD’s hardware just so that they don’t crash as a company; AMD is not a charity and I require value in return when I give money to them.

To summarize, AMD with (usually more buggy and less stable) proprietary drivers just did not really have an attractive value proposition.

GPUOpen changing the game

However, AMD having the open source driver as their main one gives a reason to ignore their slight disadvantage in terms of the performance per watt and the performance per dollar. Now that AMD is developing a part of the open source graphics ecosystem and improving it for them as well as the rest of the community, they are a very valuable graphics hardware vendor.

This change empowers the community to disagree with AMD about what should be developed first and take the lead. As a user, you can fix the bug that annoys you when you decide and do not need to wait for AMD to fix it when they care to do it. Even if you don’t have sufficient knowledge to do it yourself, you can pay someone to fix it for you. And this freedom is what is very valuable with open source driver.

Critics might say, this is easy to promise, AMD has said many things many times. And this is true; however, the commits by AMD developers in the Kernel, LLVM, and Mesa repositories shows that AMD is walking the walk. Doing a quick grep for e-mail addresses that contain amd.com shows a nice and steady increase in both the number of developers and the number of commits since 2011.

Critics might also say that AMD is just getting free work from the community and giving ‘nothing’ in return. Well, I wish more companies sourced free work from the community in this way and gave their code as free and open source software (the ‘nothing’). Specifically, I really wish NVIDIA follows AMD’s lead. Anyhow, this is precisely the way Netscape started what we know today as Firefox, and Sun Microsystems started what we know today as LibreOffice.

To summarize, AMD with open source drivers as the main lineup is very attractive. Free and open source software enthusiasts do not (nor they should) care if AMD is ‘slightly less evil’, ‘more pro-free market’, ‘cares more about the teddy bear from your childhood’ than NVIDIA (other types of activists might or might not care about some of these issues). For the open source community, including Linux users, AMD either has the open source drivers and works to improve open source graphics ecosystem or they do not. If AMD wants Linux users on their side, they have to remain committed to developing open source drivers. It’s that simple, open or irrelevant.

Non-free Radeon firmware

Free Software Foundation calls for reverse engineering of the Radeon firmware. While I do believe we should aim for the free firmware and hardware, I have a two problems with this. First, I disagree with a part of Stallman’s position (which is basically mirrored by FSF):

I wish ATI would free this microcode, or put it in ROM, so that we could endorse its products and stop preferring the products of a company that is no friend of ours.

I can not agree with the idea that the non-free firmware, when included in a ROM on the card, is somehow better than the same non-free firmware uploaded by the driver. The reasoning behind this argument makes exactly zero sense to me. Finally, the same reasoning has been applied elsewhere: in 2011 LWN covered the story of GTA04, which used the ‘include firmware in hardware’ trick to be compliant with FSF’s goals.

Second, AMD, for whatever reason, does not want to release firmware as free and open source, but their firmware is freely redistributable. (They have the freedom not to open it and even disagree with us that they should, of course.) While not ideal, for me this is a reasonable compromise that works in practice. I can install latest Fedora or Debian and small firmware blob is packaged with the distro, despite being non-free. It doesn’t depend on kernel version, it doesn’t even depend on whether I run Linux or FreeBSD kernel.

To summarize, I would like to see AMD release free firmware as much as anyone supporting FSF’s ideas. And I do not hide that from AMD nor do I think anyone else should. However, I do not consider this issue of non-free firmware to be anywhere as important as having a supported free and open source driver, which they finally have. Since NVIDIA is no better regarding free firmware, I do not believe that right now we have the leverage required to convince AMD to change their position.

AMD and the open source community

Just like Netscape and Sun Microsystems before them, AMD right now needs the community as much as the community needs them. I sincerely hope AMD is aware of this, and I know that the community is. Together, we have the chance of the decade to free another part of the industry that has been locked down with proprietary software dominating it for so long. Together, we have the chance to start a new chapter in graphics and computing history.

Having leverage and using it for pushing open source adoption

Featured image: JD Weiher | Unsplash (photo)

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 a how she used a proprietary quantum chemistry software during her PhD; 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.

She is now a postdoc in Van Voorhis Group at MIT. Interestingly enough, Professor Troy Van Voorhis happens to be one of the scientist behind Q-Chem, a proprietary quantum chemistry software. I am sure most of us in academia, knowing MIT’s reputation and having utmost respect for achievements of MIT’s scientists, don’t imagine having an interview for a position at MIT and acting like “I would like to continue using software I choose and this is my condicio sine qua non“. I am also sure that we are even less likely to imagine interview going like this if the software in the question was a direct competitor (in conventional economic terms) to the software your group leader is developing.

Yet, this is precisely how the interview went in Valérie’s situation. Furthermore, standing up in this way for more openness in existing academic institutions is how the world of science moves towards open source software. This is precisely how you get to use your work time to support the things you believe in.

I am sure there are skeptics. They may say: “Yeah, that might be the right thing to do in the ideal world, but you know, it does not work that way in the real world. Just give up trying, you will never pull it off.” Or maybe: “Do you really want to risk your career for promotion of your ideals?” I heard the former too many times to count, and the latter on a Marie Curie fellowship workshop. For me, there was no question about it: “Yes, of course.” Academia should be about freedom and openness first.

Surely, it can work in practice. There is no either/or relationship here, you really can demand both: excellent science in a highly respected institution and science done using open source software. There is, however, something you need to be in position to set the terms: leverage. If you have done your work, you know your stuff, and someone knows what you can do and finds your skills useful, they might be willing to bend on the software choices in your favor. After all, the group leaders want to hire excellent scientists and want them to be motivated.

For me, standing up in this way is the open source scientific software activism at its finest and I hope to see it being done more and more.