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torognes / vsearch

Versatile open-source tool for microbiome analysis
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Port VSEARCH to Linux on the ARM architecture #285

Closed torognes closed 5 years ago

torognes commented 6 years ago

ARM cpus seems to become a cost-effective platform for bioinformatics. I have access to such a system at UiO.

Porting VSEARCH to this platform requires rewriting of the SIMD code using ARM's Advanced SIMD (NEON) technology. There is an intrinsics reference manual.

Otherwise it appears to be rather easy.

colinbrislawn commented 6 years ago

Wow! I didn't know ARM servers were commercially available. But they totally are, and you can rent them for cheap.

I appreciate your commitment to porting vsearch to many architectures, even underdogs like ARM and POWER8.

GenomicaMicrob commented 5 years ago

I was wondering if you have already ported vsearch for ARM; I have just bought a 96 core server.

torognes commented 5 years ago

No, we haven't started porting it to ARM yet. No definite plans yet, but increasingly interesting.

torognes commented 5 years ago

ARM Neon Programmer's guide:

https://static.docs.arm.com/den0018/a/DEN0018A_neon_programmers_guide_en.pdf

GenomicaMicrob commented 5 years ago

Eagerly waiting for the ARM version of vsearch!

torognes commented 5 years ago

I am working on porting it to ARM now.

torognes commented 5 years ago

64-bit ARMv8 support is ready! Available in vsearch 2.10.3 just released. Enjoy!

frederic-mahe commented 5 years ago

Awesome work! @GenomicaMicrob could you please confirm that this port works on your new server?

torognes commented 5 years ago

There is something wrong with version 2.10.3. It produces wrong alignments. Do not use. I discovered this today despite a lot of testing before the release after changing the alignment code.

GenomicaMicrob commented 5 years ago

Sorry I haven’t been able to test it since the server is down because of the holidays, next Monday I’ll test it, can’t wait to do it.

Bruno Gomez-Gil CIAD, Mazatlán Unit AP 711 Mazatlán, Sinaloa México 82000 +(52)669 9898700 ext 245 https://www.researchgate.net/profile/Bruno_Gomez-Gil El 20 de dic de 2018 2:21 -0600, Frédéric Mahé notifications@github.com, escribió:

Awesome work! @GenomicaMicrob could you please confirm that this port works on your new server? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

GenomicaMicrob commented 5 years ago

So far I have tested --cluster_fast, --usearch_global, --uchime_ref without any problems! Great work, thanks. I'll keep testing it. Our ARM (2 ThunderX_CP 64-bit ARMv8 48 cores ea.) server has more or least the same benchmarking as our Dell PowerEdge R810 (4 AMD Opteron Processor 6272 x 16 cores ea.), but this is just a preliminary appreciation.

torognes commented 5 years ago

It seems to be working fine, so I am closing this issue.