cuSBF: cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ > Struct Template Reference

cuSBF

Loading...

Searching...

No Matches

Compile-time configuration for a cusbf::filter. More...

Public Types
using	Alphabet = Alphabet_

Static Public Attributes
static constexpr uint16_t	k = K_
	K-mer length in symbols.

static constexpr uint16_t	m = M_
	Minimizer width in symbols.

static constexpr uint16_t	s = S_
	S-mer width (Bloom hash seed) in symbols.

static constexpr uint64_t	hashCount = HashCount_
	Independent Bloom hash functions.

static constexpr uint64_t	alphabetSize = Alphabet::symbolCount
	Number of symbols in the alphabet.

static constexpr uint64_t	symbolWidth = Alphabet::symbolWidth
	Input bytes per symbol.

static constexpr uint64_t	symbolBits = cuda::std::bit_width(alphabetSize - 1)
	Bits per packed symbol in a uint64_t k-mer.

static constexpr uint64_t	symbolMask = (uint64_t{1} << symbolBits) - 1
	Low symbolBits mask for one encoded symbol.

static constexpr uint64_t	filterBlockBits = 256
	Bits per shard (filter block).

static constexpr uint64_t	cudaBlockSize = CudaBlockSize_
	CUDA threads per kernel block.

static constexpr uint64_t	wordBits = 64
	Bits per shard word.

static constexpr uint64_t	blockWordCount = filterBlockBits / wordBits
	64-bit words per 256-bit shard.

static constexpr uint64_t	minimizerSpan = k - m + 1
	M-mers evaluated per k-mer window.

static constexpr uint64_t	findereSpan = k - s + 1
	S-mers hashed per k-mer (findere).

static constexpr uint64_t	insertGroupSize = blockWordCount
	Threads cooperating on insert.

static constexpr uint64_t	queryGroupSize = 1
	Threads cooperating on query (fused path).

static constexpr uint64_t	maxRunKmers = cudaBlockSize
	Max consecutive k-mers per warp run.

Detailed Description

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>
struct cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >

Compile-time configuration for a cusbf::filter.

All filter behaviour (k-mer length, minimizer width, s-mer width, hash count, CUDA block size, and alphabet) is encoded in this struct so that separate configurations produce completely independent Filter types with zero run-time overhead.

Template Parameters

K_	k-mer length (1-32).
S_	s-mer width used as the Bloom hash seed (1-k).
M_	minimizer width used for shard selection (1-k).
HashCount_	number of independent Bloom hash functions (1-16, default 4).
CudaBlockSize_	CUDA threads per block (multiple of 32, default 256).
Alphabet_	byte-to-symbol alphabet encoding.

Definition at line 35 of file config.cuh.

Member Typedef Documentation

◆ Alphabet

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

using cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::Alphabet = Alphabet_

Definition at line 36 of file config.cuh.

Member Data Documentation

◆ alphabetSize

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::alphabetSize = Alphabet::symbolCount

staticconstexpr

Number of symbols in the alphabet.

Definition at line 47 of file config.cuh.

◆ blockWordCount

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::blockWordCount = filterBlockBits / wordBits

staticconstexpr

64-bit words per 256-bit shard.

Definition at line 62 of file config.cuh.

◆ cudaBlockSize

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::cudaBlockSize = CudaBlockSize_

staticconstexpr

CUDA threads per kernel block.

Definition at line 57 of file config.cuh.

◆ filterBlockBits

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::filterBlockBits = 256

staticconstexpr

Bits per shard (filter block).

Definition at line 55 of file config.cuh.

◆ findereSpan

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::findereSpan = k - s + 1

staticconstexpr

S-mers hashed per k-mer (findere).

Definition at line 66 of file config.cuh.

◆ hashCount

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::hashCount = HashCount_

staticconstexpr

Independent Bloom hash functions.

Definition at line 45 of file config.cuh.

◆ insertGroupSize

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::insertGroupSize = blockWordCount

staticconstexpr

Threads cooperating on insert.

Definition at line 68 of file config.cuh.

◆ k

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint16_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::k = K_

staticconstexpr

K-mer length in symbols.

Definition at line 39 of file config.cuh.

◆ m

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint16_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::m = M_

staticconstexpr

Minimizer width in symbols.

Definition at line 41 of file config.cuh.

◆ maxRunKmers

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::maxRunKmers = cudaBlockSize

staticconstexpr

Max consecutive k-mers per warp run.

Definition at line 72 of file config.cuh.

◆ minimizerSpan

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::minimizerSpan = k - m + 1

staticconstexpr

M-mers evaluated per k-mer window.

Definition at line 64 of file config.cuh.

◆ queryGroupSize

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::queryGroupSize = 1

staticconstexpr

Threads cooperating on query (fused path).

Definition at line 70 of file config.cuh.

◆ s

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint16_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::s = S_

staticconstexpr

S-mer width (Bloom hash seed) in symbols.

Definition at line 43 of file config.cuh.

◆ symbolBits

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::symbolBits = cuda::std::bit_width(alphabetSize - 1)

staticconstexpr

Bits per packed symbol in a uint64_t k-mer.

Definition at line 51 of file config.cuh.

◆ symbolMask

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::symbolMask = (uint64_t{1} << symbolBits) - 1

staticconstexpr

Low symbolBits mask for one encoded symbol.

Definition at line 53 of file config.cuh.

◆ symbolWidth

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::symbolWidth = Alphabet::symbolWidth

staticconstexpr

Input bytes per symbol.

Definition at line 49 of file config.cuh.

◆ wordBits

template<uint16_t K_, uint16_t S_, uint16_t M_, uint64_t HashCount_ = 4, uint64_t CudaBlockSize_ = 256, Alphabet Alphabet_ = DnaAlphabet>

constexpr uint64_t cusbf::Config< K_, S_, M_, HashCount_, CudaBlockSize_, Alphabet_ >::wordBits = 64

staticconstexpr

Bits per shard word.

Definition at line 60 of file config.cuh.

The documentation for this struct was generated from the following file:

config.cuh