Permanent Brain refers to a chess engine's ability to keep calculating during the opponent's thinking time. All important chess engines use this technique. The chess engine continues its calculations in the background during the opponent's thinking time. If the opponent plays the expected move, the program accesses the results it has already determined and will play its response immediately or at least very quickly. With a high hit rate this saves a great deal of thinking time and leads to a significant increase in practical playing strength.
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If you like to run position tests or solution comparisons with your chess engines, you should switch Permanent Brain off. Otherwise it could happen that the chess engine accesses already-calculated values in the hash tables. This makes concrete comparisons of measured solution times considerably more difficult.