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Supercomputers are the fastest of the fast... and they almost all run Linux. When the petaflop-per-second barrier was cracked, it was with a supercomputer running Linux. Check out the top 500 list of supercomputers. Linux currently dominates the scene by running 88.6% of these supercomputers, including the top ten, and is taking over the list a few tenths of a percent at a time.
These supercomputers aren't even necessarily running some sort of specialty distro of Linux. Many supercomputers are just running generic Ubuntu, or Debian, or other distros that are present on everyday computers.
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Parallel Processing Languages
Part of Linux's dominance with making fast computers run fast is because of the abundance of parallel processing languages available for Linux, or even just languages and compilers that support parallelization or have automatic parallelization support built in. These include GCC, PGI and PathScale, available for virtually every distro. Microsoft and Mac just don't have any real equivalents that work as efficiently as those for Linux.
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The Everyday Computer
Just because you don't have a supercomputer of your very own, doesn't mean that Linux still isn't the fastest OS you can run on your system - especially when you look at many of the alternatives.
Simply put, what makes an OS fast is by taking out what might make it slow. Slim the operating system down to only what's necessary. OSs like Windows and OS X tend to create feature-rich displays and programs that may be pretty, but often use messy and inefficient code that just slows up the whole thing. Linux tends to avoid this.
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Where Linux is Slow
There are a few areas where Linux can be beat however - typically while trying to play the other OS's game. Emulators for other systems, such as WINE, tend to slow up the system more than may be desired, however it's really the only way to run the programs of other operating systems on Linux systems.
The other place where Linux can be slowed up is with its drivers. Often, driver information for parts is not made open to the public, meaning that Linux users can't always use the optimum drivers for their systems.
Certain graphical interfaces and distros tend to be faster or slower than others, though they all tend to be fastest than the latest of other operating systems. Running KDE within GNOME to run a program such as Amarok, for instance, might not run at an optimum speed. However, it does depend on your choices as a user. Slower, more feature-rich programs do exist for Linux, but slimmer alternatives that work every bit as well also exist if you really want to go for speed. This isn't so much the case for Microsoft or Macintosh, where you can't cut the slack even when you want to.
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Making it Faster
The biggest reason why Linux is faster than any other OS? You. Users critique, complain about, tweak, mod, alter, and otherwise contribute to the developing process. No stone is left unturned as thousands of users peer deep into the depths of the code and optimize it where possible. Windows and other closed-source proprietary OSs just can't match that kind of process. As time progresses, Linux users will just keep on doing what they've always been doing—making Linux better, stronger, faster.
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For more on Windows vs. Linux read The Great Linux or Windows Debate?