add CUDA distance implementation #123
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
lkeegan
force-pushed
the
cuda
branch
3 times, most recently
from
08f0f26 to
bb33c84
Compare
- python interface changes
- add `from_fasta_to_lower_triangular`
- this constructs lower triangular matrix file directly from fasta file
- for now only works on GPU
- faster & requires less RAM than doing `from_fasta` followed by `dump_lower_triangular`
- requires 1.5GB RAM per 100k genomes on gpu + 1GB buffer to store partial distances matrix
- add `use_gpu` option to `from_fasta`
- if True and include_x is False then the GPU is used to calcuate distances matrix
- add `cuda_gpu_available()` utility function
- CUDA implementation
- each block of threads calculates a single element of the distances matrix
- a kernel is launched running on a grid of these blocks to calculate a subset of the distances matrix
- I/O is interleaved with computation: the CPU writes the previous kernel results as the next kernel is running
- print basic timing info to cout
- add libfmt library
- migrate to using v3 of catch2
- build wheels using manylinux2014 image with CUDA 11.8 pre-installed from https://github.com/ameli/manylinux-cuda
- add a couple of performance plots
- bump version to 1.0.0
- resolves #111
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
from_fasta_to_lower_triangular- this constructs lower triangular matrix file directly from fasta file - for now only works on GPU - faster & requires less RAM than doingfrom_fastafollowed bydump_lower_triangularuse_gpuoption tofrom_fastacuda_gpu_available()utility function