NVIDIA-Genomics-Research / GenomeWorks

SDK for GPU accelerated genome assembly and analysis
https://clara-parabricks.github.io/GenomeWorks/
Apache License 2.0
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[sdk] Update CUB submodule to new URL and version 1.11.0 #569

Closed ahehn-nv closed 3 years ago

mimaric commented 3 years ago

Should we still download CUB when using CUDA 11? I guess one cannot know CUDA version upfront, but in that case we probably should not have downloaded CUB in the include path

ahehn-nv commented 3 years ago

Some logic in CMake to use the submodule only for CUDA <11.0 makes sense. However, for CUDA 11 it shouldn't make much difference, since I updated the submodule to the version shipped with CUDA 11.

mimaric commented 3 years ago

I agree. I would suggest linking this PR to issue #570, but not closing it until that is done in a separate PR

tijyojwad commented 3 years ago

@ahehn-nv - the CUDA 9.0 test seems to have failed. Can you have a look? perhaps we should make this change once we remove CUDA 9.0 support?

ahehn-nv commented 3 years ago

Yes, let's postpone this. CUDA 9 compilation fails due to a bug in CUB - see https://github.com/NVIDIA/cub/pull/207. Since there's also a ticket for this task, I'll close this PR.

mimaric commented 3 years ago

PR https://github.com/NVIDIA/cub/pull/207 has been merged into CUB. The bug it solved was preventing us from using latest CUB version with CUDA 9. Reopening this PR. CUB 1.11.0 (RC available) bring big improvement to radix sort which in turn improves the performance of cudamapper.

mimaric commented 3 years ago

The tests pass now. I suggest waiting for non-rc version of CUB 1.11.0 and merging then

tijyojwad commented 3 years ago

@mimaric @ahehn-nv - CUDA 9 has been removed from our CI now.

mimaric commented 3 years ago

@ahehn-nv CUB 1.11.0 has been released (https://github.com/NVIDIA/cub/releases/tag/1.11.0). Can you update this PR?

ahehn-nv commented 3 years ago

The PR is already up-to-date. CUB's 1.11.0-rc1 and 1.11.0 tags point to the same commit.