2011/3/23 brunetto <brunetto.zi...@gmail.com>
> Hi All!!
>
> I'm quite new to pytables and this mailing list so I'm sorry if my
> question is a bit stupid!:)
>
> I'm using pytables to buil a persistent binary tree containing from
> 10^3 to 10^8 (may be in future 10^10) integer numbers. The structure
> reflects a previus binary tree entirely built in memory.
> For now traversing the tree in the hdf5 file it's 10 time slower than
> traversing the tree in memory...
>
How many data are you putting into the leaves? Also, how many leaves do you
have in your binary tree?
>
> It's possible to load the entire tree in memory before traversing the
> nodes instead of use the read/caching method so the traversing can be
> faster?
>
Without knowing more about the number of nodes you have, I'd say that a
factor 10x slower than memory is expected. But you can play with the
internal cache and try to load everything in memory. You may want to
experiment with a large negative value for the
``NODE_CACHE_SLOTS``parameter of PyTables. See appendix C of User's
Guide for how to change
this setting:
http://www.pytables.org/docs/manual/apc.html
Hope this helps,
--
Francesc Alted
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