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Optimization in alignment. #21

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merged 1 commit into from
Jul 17, 2023

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andrewdavidsmith
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This should fix a bug affecting certain reads on macOS Ventura, intel and gcc-13 with O3 optimization.

I added directives for compiler to do less aggressive vector optimization around the tight loops that iterate in parallel while doing alignment in a band. Specifically, the from_diag, from_above and from_left, both those with and without traceback. I was able to alter only a subset of those 6 functions and make certain test cases work, but the only way the entire regression test file in dnmtools would pass is with all 6 functions allowing at not more than the very-cheap option for dynamic vectorization. It seems like a second directive can turn the optimization back on for functions below in the file.

…on around the tight loops that iterate in parallel while doing alignment in a band.
@andrewdavidsmith andrewdavidsmith merged commit 1dd5a16 into master Jul 17, 2023
@andrewdavidsmith andrewdavidsmith deleted the alignment_strange_optimization branch July 17, 2023 19:50
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2 participants