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You should be able to safely run a laptop CPU at 100% with a laptop cooling mat. I've run my laptop cpu at 100% for days on end with a cooling mat.
Yes, that's a good idea
I agree with the rest of your post as well, mine was more of a: "if you don't know what you are doing it might be best way to stick to it" kind of advice.
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If we want to look at OOP vs IP and want to consider blinds just dead money
Well, blinds are not dead money as they count towards subsequent bets so you need to be careful.
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can we set SB and BB at 0 and the actual blinds as dead money in the pot?
Yes but as it is now the same player is going to be OOP both preflop and postflop with this structure.
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I know we can let the program run like that but will it create issues in how PIOpre computes?
Other than inability to change positions preflop it will be fine.
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looking to solve for call OOP vs 3bet, fold, or shove based on EV we have when it folds back to us and it now becomes HU.
So it looks like blinds of other players are included in dead money. In such case this is the correct way to do that. Notice that positions you consider are BTN vs SB for example then there should be 1bb as dead money (from bb) but sb shouldn't be included in dead money (as it counts towards the 3bet).
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What is the recommended flop subset we should be using for PioPre to get accurate results but no overkill to save time for most trees (not referencing just this one)?
It's hard to say as there are a lot of people with a lot of different opinions about it. As it is now we recommend using one of those subsets:
http://pastebin.com/AtyU84qC
(the last column is average error in many metrics).
You can see that 60 is significantly better than 40 and then 80 is siginificantly better.
I personally feel that 74 gives nearly perfect solutions for practical purposes but less than that is needed for very good overview.
If you are just experimenting to see what sizing is better for example then it's likely a good idea to use less to speed-up the calculations.