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alexdobin / STAR

RNA-seq aligner
MIT License
1.84k stars 505 forks source link

Intel intrinsics and SIMDe #1160

Open smoe opened 3 years ago

smoe commented 3 years ago

Dear Alex,

I was a bit too quick when I uploaded 2.7.8a to Debian - the Intel-specific instructions prohibited a smooth build on other platforms. Now, a contribution from Debian Med had prepared a patch to use https://github.com/simd-everywhere/simde which is https://salsa.debian.org/med-team/rna-star/-/blob/master/debian/patches/simde.patch .

Since Debian is about to freeze, and conda and guix already ship 2.7.8a, is why I was so quick and this is also why we are now just a bit nervous that we are doing the right thing. With that patch, the package locally builds (and autotests) on all platforms, so we would be good to go, this is unless you are objecting to the idea to use simde. In the contrary, if you happen to like this, you may then want to adopt that patch to keep ARM in particular in the loop.

Many thanks and regards, Steffen

alexdobin commented 3 years ago

Hi Steffen,

thanks - It's a great idea to start taking care of ARMs. I will look into simde more closely. It seems that SIMDE_ENABLE_NATIVE_ALIASES is not a generally recommended solution, but since it works we can go with it for now. The simd instructions are used in the OPAL package, so changing the APIs to simde will take some work.

Cheers Alex

mr-c commented 3 years ago

It seems that SIMDE_ENABLE_NATIVE_ALIASES is not a generally recommended solution

Hello @alexdobin ; I'm a co-maintainer for SIMDe. We say that out of an abundance of caution; for this codebase it should be fine. Would you like a PR to add SIMDe?

smoe commented 3 years ago

@mr-c is another developer for Debian ... did not know about your upstream work on SIMDe. Great! :o)