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psathyrella / partis

B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference, and affinity prediction
GNU General Public License v3.0
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Minimize number of states in each loop #168

Closed psathyrella closed 8 years ago

psathyrella commented 8 years ago

i.e. in trellis::Viterbi/Forward see if we can reduce the number of times we go through the loops.

This may or may not be equivalent to the pre-alignment they talk about in the repgenhmm paper (i.e. assuming each position in the sequence can only be a certain state in the V or J)

matsen commented 8 years ago

All of our time is spent calculating the DP table. Main gain has been avoiding calculating it.

This issue concerns speeding calculation of DP table.

E says: loop unrolling?

psathyrella commented 8 years ago

Looks like the gcc option -Ofast is, among many other things, unrolling loops that it deems useful.

matsen commented 8 years ago

Yes, though it can only fully unroll loops if the number of iterations is fixed at compile time.

psathyrella commented 8 years ago

huh, this is still open... well I spent a bunch of time optimizing/caching for the loops a month or so ago. There's always more to do, but I don't need this open any more.