-
Notifications
You must be signed in to change notification settings - Fork 36
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
GPU implementation of hamming distance #541
base: main
Are you sure you want to change the base?
Conversation
for more information, see https://pre-commit.ci
… into numba_hamming
for more information, see https://pre-commit.ci
… into numba_hamming
for more information, see https://pre-commit.ci
…tcrdist distance metrics
… into numba_hamming
for more information, see https://pre-commit.ci
… into numba_hamming
for more information, see https://pre-commit.ci
… into numba_hamming
…curing in all sequences
for more information, see https://pre-commit.ci
…into gpu_hamming
for more information, see https://pre-commit.ci
…into gpu_hamming
for more information, see https://pre-commit.ci
…ceCalculator` in documentation
…into gpu_hamming
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
…into gpu_hamming
for more information, see https://pre-commit.ci
For a large Matrix in the Hamming-Kernel have you checked that int is enough to cover the indexing of data? |
…into gpu_hamming
for more information, see https://pre-commit.ci
That's a good point, but I think for our purposes int should be enough for the kernels. I think the most problematic part is the indptr array of the CSR matrices, therefore I added some int32 overflow checks. If such an overflow occures, the user can try it with a smaller cutoff to get less result values that need to be stored in the CSR matrix. |
Hamming distance implementation with numba.cuda for GPU support.
This is built on top of the changes in Hamming distance implementation with Numba #512
@grst:
Close #479