Just off the top of my head: package management, live-cd functionality, architecture support, command-line interfaces, GUI variety, kernel customization, scaling to low-powered harware, licencing.

GUI "variety"? Are you joking? The very reason there exists so much "variety" is that they all suck. Windows has one GUI system and it's worked darn well for quite a long time, and will continue to do so. Linux might be able to let you make your windows do somersaults so you can show off to your friends, but it still hasn't been able to get the basics right, like focus-stealing prevention. Windows is miles ahead of Linux on GUI -- if there's one thing I can tell you for sure, it's that.

And Linux is "miles ahead of Windows for research because of its command-line interfaces"? Really? Since when are 25-year-old command-line shells research products? Not to mention stuff like http://mywiki.wooledge.org/BashPitfalls

As for package management, when it works it works, but sometimes I wish it could burn in hell. I can't tell you how many times I've run into problems getting packages to work because their dependencies were either (1) no longer available ("sorry! our servers changed, your version of Linux is outdated"), (2) only available in source code form (but good luck compiling it!), or (3) not available for my version ("sorry, this version is too new for your OS"), among other things. Distributing your dependencies along with your application might not be sound engineering practice, but it sure as hell can make things actually work out of the box so you can focus on what you actually want to do.

"miles ahead of Windows for research" For example, only 2 of the currently fastest 500 super computers run Windows and 1 of them is owned by Microsoft. All of the others run Linux or Unix.

"Since when are 25-year-old command-line shells research products?" The shell is a researcher's best friend as they have always been (and will be for the foreseeable future) the direct interface between data and the user. I honestly can't think of a faster and easier way to parse a nasty 10GB log file from a simulation than bash. The fact that its old and still in use is a testament to its usefulness.

You have heard of powershell?

REPL are way superior as shown in any Xerox PARC OS.

And shells are indeed REPLs (in the sense that they run a loop in which they read, evaluate, and print things).

Though to be fair, REPLs for languages like MATLAB or Julia are likely far more useful from a scientific standpoint than a typical shell (which is more useful for system administration).

Compared with what I know from Xerox PARC documentation and what I self experienced in Oberon and Visual Works Smalltalk, shells are like REPLs yes, but not quite.

It is a very different experience when the shell (e.g. Transcript in Smalltalk) is capable of interacting with the whole OS.

For example in Cedar, which Oberon copied, any public function/procedure exported by dynamic libraries can be used in the shell via modulename.function.

Depending on their signature they act on REPL text input, the active selected graphical element or some other OS element.

While this can kind of be emulated on an UNIX shell, it breaks down that there isn't an OS wide standard API to bring everything together.

I don't know... Ubuntu's UI is pretty consistant and I think simpler to use than Windows. I wouldn't say it sucks... at all.

After using Ubuntu Desktop recently for the first time in a few years, I completely agree. I'm really surprised it's not more popular yet.

>like focus-stealing prevention

Example? I could show you thousands of issues on windows where a window has stolen focus and it wasn't prevented[0]

[0]: http://www.eightforums.com/

Could you link me to 2-3 of the actual posts instead of linking me to the entire forum?

In the meantime, it seems to me you've already conceded that Linux can't get it right, so I'm glad we agree there.

As a current Ubuntu user, I think you are just spreading old, outdated FUD.

The GUI works and it is in fact just as good as Win8 (which I dualboot). When using virtual desktops, it's far better, and makes me more productive.

The package management is amazing. Chocolatey sucks in comparison.

What I fail to see, is what these basic computer functions have to do with research.

Visual Studio has a lot to do with research, and it is a fantastic tool in its own right. The GDB debugger is a piece of ancient garbage in comparison to VS debugger.

You could have focused on the real issues instead of your uninformed outdated FUD.

What is the latest version of Ubuntu that you consider "outdated"?

Also, Windows has package management in the form of Chocolatey/OneGet: http://blogs.technet.com/b/windowsserver/archive/2014/04/03/.... It just isn't used by most end-users so awareness is limited.

Ehhh....that's "installer downloading and executing", which is a far cry from "package management". Notably, it doesn't provide dependency resolution (which is 90% of a package manager's job, IMO), and Windows' software packaging conventions don't really work well for an apt-like system, since they are intended to be mostly self-contained outside of shared frameworks.

I use chocolatey, but it's not anywhere near the level of apt-get. That's more Windows and Windows developers' fault than chocolatey's though. They've done a great job given what they have to work with.

Package management covers this, but is too understated: many of the applications that researchers use are downright hard to get working on Windows--particularly if you require any customization. I've run into this in a maddening way when working with geospatial tools. Need custom OGR/GDAL support? Prepare to spend hours figuring out how to make it work with Windows. Some deal to a lesser extent with R. Amount of time spent on edge cases is Windows > Mac > Linux. I use a Mac, but every time I build up an R environment with lots of library dependencies on Linux, I find myself saying, "well, that was easier than I expected." Conversely, when I use Windows, I'm right back to fighting library dependencies.

Windows makes simple things easy, but complex things nearly intractable.

In my experience a lot of this isn't becuase it can't work on windows, but because the developer didn't take the time to make it work on Windows. I also had my fair share on build and dependency problems on Linux when wanting something custom.

I think this is much more a ecosystem thing than a systems thing. Which do count of course.

I use linux for research for several reasons. The most important reason is that I own several high performance computing resources that need to run code with as little interference from the OS as possible. Furthermore I need these machines to share a file system and I need to be able to set it up myself with little IT experience.

For my purposes Linux is dead simple to use, well documented (most of the time), and does exactly what I need it to do which is to stay the hell out of the way while I burn cycles on real work.

This.

Basically, Windows for scientific software is as bad as Linux was for 3D FPS gaming fifteen years ago. Just ask anyone who has tried compiling anything scientific under Cygwin.

And don't get me started on MS's own compilers. They STILL don't support C99, a sixteen year old standard for one of the most important programming languages!

I thought most of the scientific computation is written in Fortran. Anyways, I have used a big closed source scientific computation package several jobs ago to conduct experiments. The entire stack was running on windows at the time, but the operating system really did not (and does not) matter. I agree with you that MS compilers should support C99 but it has very little to do with how useful windows is for scientific computing. (Worst case scenario you can use an opensource compiler).

I think the reason why the top 500 HPC clusters are using linux is the price of the operating system and not the functionality.

What do you mean by scientific? There's a lot of Windows only software for research. Mostly for applied things. But also things like data collection. There's even more if you look at development in things like engineering. Even industrial is surisingly much Windows only.

Well, yes, I'll give you that "scientific software" is indeed too broad. If I restrict it to "software developed by teams of scientists working at universities and research labs" it's better.

And yes, lots of data aquisition stuff is Windows only, particularly the stuff that gets sold along instruments. But then, in that category, the trend seems to be requiring a (preferrably air-gapped) PC running XP. I've even seen stuff running only on Win98 still in use, and I've seen software for rheometers that is STILL distributed on 3.5" floppies. And don't get me started on the "needs-crypto-usb-dongle-to-function" stuff - someone should really tell them that the $300k instrument is a sufficient protection against software piracy.

Makes sense. My concern really is if Linux gets any better for these use cases. I think a lot of Linux development is to much software and to little real world "science". You hear a lot how powerful Linux is, but in a lot of cases powerful things are run by XP as you say.

I kind of gave on Linux a couple of years ago when at the same time when Apple had totally neglected the Mac Pro all you could find from the Linux community was how cool the latest 3D effects on the desktop where and chromium was much better than Firefox. Trying instead finding something like say a 2D library more modern than Cairo and there's a deafening silence.

Yes, I'm exaggerating a bit and there is some good developments. Like CERN making waves in electronics by hacking on KiCad. Though I'm sure they would be happier if they could replace Wx with something more modern, which I'm not sure the current alternatives are.

From what I gather, Qt has "won" the war, if there was ever such a thing, but GTK and Cairo will not be going away. What are your gripes with Cairo, anyways?

Also, when you start getting into scientific software, very few projects explicitly state "Runs best on Linux" even though that may be the case. If you are looking for examples though, I will give some: PETSc/Elemental/Trilinos/etc Clawpack/PyClaw/OpenFOAM/etc Gromacs/NAMD/HOOMD/Quantum Espresso/etc Julia/Nimrod/etc Paraview/VisIt/VMD/etc OpenMPI/MPICH/MVAPICH/etc ImageJ/Fiji/etc GNU Radio/RTL-SDR/etc

There's tons of it out there!

You seem to use Linux for applications. It appears you have nothing to do with research about the Linux source code and design.

So? The Linux ecosystem is the best there is for science. Period. Even OSX lags behind, just look at all the work people put into MacPorts and Homebrew just to get it almost on par with Linux. To this day, none of those systems properly handle the case of multiple packages providing implementations of a library that other packages depend on (e.g. OpenMPI vs. MPICH). Not to talk down on the guys working on that, they are very talented, and the amount of effort they put in is of huge value to the community. (Hello Sean, hello Geoff.)

In the kernel:

1. Access to hardware performance counters and energy counters

2. Easily loadable custom drivers

3. File system that is not slow as hell ("Getting the modification time of a file ... seems to be about 100 times slower on Windows than it is on Linux"[1])

4. Practical mechanism to allocate large pages

5. Futex

In the ecosystem:

1. Package manager

2. C99 compiler

3. POSIX environment (a lot of scientific libraries and tools depend on it)

[1] http://www.aosabook.org/en/posa/ninja.html

Being Unix-like.

SMP is probably one of the reasons Linux is so beloved in research, Windows may have caught up there somewhat, but it wasn't too long ago when you had to pay extra for a version of Windows that would allow you to use a second processor. Windows isn't even an also-ran in supercomputers, which is a shame really. Also being able to have farms of Linux boxes without fussing about with Windows licenses.

Networking is another. Windows at least used to have a bunch of different crippleware SKUs with differing networking abilities

Filesystems, Linux supports tons of them out of the box.