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tseemann / snp-dists

Pairwise SNP distance matrix from a FASTA sequence alignment
GNU General Public License v3.0
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Add multithreading #44

Closed terhorst closed 3 years ago

terhorst commented 3 years ago

If you are interested, it is very easy to parallelize this program using OpenMP. This PR passes all tests, and I have also used it on one (large) example, where the computation time went from >3 hours to 15 minutes.

tseemann commented 3 years ago

@terhorst i had always wanted to add OpenMP to snp-dists, and i treied to write with that in mind for the future! This is amazing and i will check it out soona nd hopefully merge it.

If/when we write a paper (maybe for JOSS) you will be included as an author.

rpetit3 commented 3 years ago

Hi @terhorst, I updated the bioconda recipe to include openmp.

Do you think you could test to make sure it works fine?

terhorst commented 3 years ago

Sorry for the late reply. I don't actually use bioconda, so I may not be the best person to test this, but I was able to install the package using conda and it appears to work.

On Mon, Jul 26, 2021 at 6:54 PM Robert A. Petit III < @.***> wrote:

Hi @terhorst https://github.com/terhorst, I updated the bioconda recipe to include openmp.

Do you think you could test to make sure it works fine?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/tseemann/snp-dists/pull/44#issuecomment-887080351, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAEOHG4FWNIJUJR4GJ6DVDTZXRS7ANCNFSM46XJK6XA .

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rpetit3 commented 3 years ago

Great thanks!