Re: Implementing distance matrix 2500 X 2500
What exactly does your table contain? Is it as far from a to b as it is from b to a ? If so you need just half the rows. Also you will probably get way less disk io with table designed like that because when select occurs, mysql will have to read just about 3 fields (+some keys) instead of reading 2501 fields (+some keys). Of course you get bigger overhead on the table but i would expect WAY better performance. Also with the 2d table you need indexes on all 2500 fields or mysql will have to read and compare all 2500 values one by one. (there you get overhead too).
If you want to just store the array in mysql you should rather use some function like php's serialize or just binary dump the data into a blob field.
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Re: Implementing distance matrix 2500 X 2500
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