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I recently installed Dota 2 on Ubuntu 13.10 and it has been running well. The only problem is that suddenly the game loses frame rate. The movements loses the smoothness. After sometime it just returns to normal.

Does anyone know how to fix this issue?

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Braiam gave a good answer as to what might be happening with your computer, but are you sure it is framerate? packet loss or packet choke will cause a "rubber-banding" affect(your view pops back a few frames) if packet loss is only minimal, you will not notice the return to the prior frame but it will seem slightly jerky... – TrailRider Nov 11 '13 at 1:33

There could be several reasons why it happens:

  1. An application start running in background.
  2. Your system runs out of memory and start swapping.
  3. Your system disk is heavily fragmented.
  4. Your graphic card has problem rendering an specific artifact
  5. Gremlins in your PC.

You should run heuristics diagnosis on your system, make sure everything is optimized for playing, that nothing could slow it down.

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