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[WIP] Faster SequentialEnsemble - #204
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jhprinz merged 20 commits intoApr 22, 2015
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Committing because I need to merge in the ensemble name changes in master before continuing.
This was referenced Apr 5, 2015
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Still need to actually USE this cache.
Also skeletons for test of seq ens cache
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This was a bit more complicated than I thought (I should have known -- anything dealing with I suggest we merge the progress so far, although we should make more improvements along these lines later. |
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Looks good. Looking forward to faster Ensembles!!! Yes |
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[WIP] Faster SequentialEnsemble
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The current version of$O(N^2)$ scaling with the number of frames in a trajectory.
SequentialEnsemblechecks the entire trajectory every time can-append is called. This is redundant, since the earlier frames were already assigned to an ensemble in the sequence the previous time can-append was called. The current implementation hasFor normal TIS trajectories (length ~100 frames), that doesn't hurt too much. However, this can be a serious problem for minus interface trajectories (length >1000 frames).
Looks like it should be pretty easy to fix: either I was thinking about doing something like this when I initially implemented
SequentialEnsemble, or I'm really lucky. The code even pretty much points out how to start with the cached values; just need to figure out when to cache the values and when to reset the cache.Tasks
can_appendcan_prepend