AVX vectorization of likelihood derivatives

[ddarriba]

Implement the AVX version of update_sumtable and compute_likelihood_derivatives

[ddarriba]

Sumtable (inner-inner) vectorized in experimental branch

[amkozlov]

Vectorized sumtable (tip-inner) and derivative computation: https://github.com/xflouris/libpll/commit/3035dd1842e6bde3f368691436aa4ce4c8e77484

There is still room for improvement, but even current version together with removal of unneeded log()s (https://github.com/xflouris/libpll/commit/c0f1cb018322028e171cc72a80a7fc482d9337d3) yields > 2x speedup in my tree search tests (DNA data).

[xflouris]

@amkozlov : nice job. A gentle reminder though to follow the project coding rules:

https://github.com/xflouris/libpll/wiki/Contributing-to-libpll

particularly the 80 character long lines. I understand you may not like them, but it's a collaborative project.

[amkozlov]

@xflouris: Fixed.

particularly the 80 character long lines. I understand you may not like them

That's true, especially functions with intrinsics are long&ugly enough as they are :)

[xflouris]

thanks alexey :)

[ddarriba]

Note: Verify for 'odd' number of states (e.g., 5)

[xflouris]

@ddarriba : when you get time, can you extend the odd-states/derivative tests with the following two cases?

• a case where an odd number of states and invariant sites are used together (we had a bug that was not found by the tests)
• derivatives with odd states (the bug you found was not detected by the tests)

[amkozlov]

@ddarriba: thanks, this is fixed now. The new version (my last commit) is also significantly faster.

[ddarriba]

I already have the one with odd states. I created it for checking where did an error in the modules repository come from. I will add both new tests together tomorrow.

On 03.08.2016 18:25, Tomas Flouri wrote:

@ddarriba https://github.com/ddarriba : when you get time, can you extend the odd-states/derivative tests with the following two cases?

• a case where an odd number of states /and/ invariant sites are used together (we had a bug that was not found by the tests)
• derivatives with odd states (the bug you found was not detected by the tests)

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[amkozlov]

Can we close this one or is there something still missing?