xtn_inner.cu File Reference

The core algorithm on the high-level abstraction concerning data manupulation operations in all 4 stream. More...

#include "generate_combination.cu"
#include "cub.cu"
#include "kernel.cu"
#include "codec.cu"
#include "stream.cu"
#include <limits.h>

Functions
int	NUM_BLOCK (int len)
	private function. More...
int	cal_offsets (Int3 *inputKeys, int *&inputOffsets, int *&outputLengths, int n, int *buffer)
	private function. More...
int	cal_offsets_lowerbound (Int3 *inputKeys, int *inputValues, int *&inputOffsets, int *&outputLengths, int lowerbound, int n, int *buffer)
	private function. More...
int	gen_pairs (int *input, int *inputOffsets, int *outputLengths, Int2 *&output, int *&lesserIndex, int lowerbound, int carry, int n, int seqLen)
	private function. More...
int	gen_smaller_index (int *input, int *inputOffsets, int *outputLengths, int *&output, int carry, int n)
	private function. More...
int	deduplicate (Int2 *input, Int2 *output, int n, int *buffer)
	private function. More...
int	postprocessing (char *allStr, unsigned int *allStrOffsets, Int2 *uniquePairs, int distance, char measure, Int2 *&pairOutput, char *&distanceOutput, int uniqueLen, int *buffer, int seqLen)
	private function. More...
void	make_output (Int2 *pairOut, char *distanceOut, int len, XTNOutput &output)
	private function. More...
void	gen_next_chunk (Chunk< Int3 > &keyInOut, Chunk< int > &valueInOut, int *valueOffsets, int offsetLen, int lowerbound, int *buffer)
	private function. More...
int	solve_next_bin (int *chunksizes, int start, int maxSize, int n)
	solve bin packing on spot when precalculation is impossible. More...
int	solve_bin_packing_lowerbounds (int *histograms, int *&lowerboundsOutput, int n, int seqLen, int *buffer, MemoryContext ctx)
	solve bin packing for lower bound calculation. More...
int	solve_bin_packing_offsets (int *histograms, int **&offsetOutput, int n, int *buffer, MemoryContext ctx)
	solve bin packing for 2 dimensional buffer. More...
void	stream_handler1 (Chunk< Int3 > input, Int3 *&deletionsOutput, int *&indexOutput, std::vector< int *> &histogramOutput, int &outputLen, int distance, int &carry, MemoryContext ctx)
	handle all GPU operations in stream 1. More...
void	stream_handler2 (Chunk< Int3 > &keyInOut, Chunk< int > &valueInOut, std::vector< int *> &histogramOutput, size_t &throughput2B, int distance, int seqLen, int *buffer, MemoryContext ctx)
	handle all GPU operations in stream 2. More...
void	stream_handler3 (Chunk< Int3 > &keyInOut, Chunk< int > &valueInOut, void callback(Int2 *, int), std::vector< int *> &histogramOutput, int lowerbound, int seqLen, int *buffer, MemoryContext ctx)
	handle all GPU operations in stream 3. More...
void	stream_handler4_nn (Chunk< Int2 > pairInput, XTNOutput &output, char *allStr, unsigned int *allStrOffsets, int seqLen, int distance, char measure, int *buffer)
	handle all GPU operations in stream 4 nn mode. More...
void	convertString (char *allStr, unsigned int *allStrOffsets, Int3 *output, int seqLen)
	convert all sequences to int3 form More...

Variables
const int	NUM_THREADS = 256
const unsigned int	UINT_MIN = 0

Detailed Description

The core algorithm on the high-level abstraction concerning data manupulation operations in all 4 stream.

Function Documentation

cal_offsets()

int cal_offsets	(	Int3 *	inputKeys,
		int *&	inputOffsets,
		int *&	outputLengths,
		int	n,
		int *	buffer
	)

private function.

cal_offsets_lowerbound()

int cal_offsets_lowerbound	(	Int3 *	inputKeys,
		int *	inputValues,
		int *&	inputOffsets,
		int *&	outputLengths,
		int	lowerbound,
		int	n,
		int *	buffer
	)

private function.

convertString()

void convertString	(	char *	allStr,
		unsigned int *	allStrOffsets,
		Int3 *	output,
		int	seqLen
	)

convert all sequences to int3 form

Parameters

allStr	all CDR3 sequences
allStrOffsets	offset of CDR3 sequences
output	sequence outputs
seqLen	number of input CDR3 sequences

deduplicate()

int deduplicate	(	Int2 *	input,
		Int2 *	output,
		int	n,
		int *	buffer
	)

private function.

gen_next_chunk()

void gen_next_chunk	(	Chunk< Int3 > &	keyInOut,
		Chunk< int > &	valueInOut,
		int *	valueOffsets,
		int	offsetLen,
		int	lowerbound,
		int *	buffer
	)

private function.

gen_pairs()

int gen_pairs	(	int *	input,
		int *	inputOffsets,
		int *	outputLengths,
		Int2 *&	output,
		int *&	lesserIndex,
		int	lowerbound,
		int	carry,
		int	n,
		int	seqLen
	)

private function.

gen_smaller_index()

int gen_smaller_index	(	int *	input,
		int *	inputOffsets,
		int *	outputLengths,
		int *&	output,
		int	carry,
		int	n
	)

private function.

make_output()

void make_output	(	Int2 *	pairOut,
		char *	distanceOut,
		int	len,
		XTNOutput &	output
	)

private function.

NUM_BLOCK()

int NUM_BLOCK

(

int

len

)

private function.

postprocessing()

int postprocessing	(	char *	allStr,
		unsigned int *	allStrOffsets,
		Int2 *	uniquePairs,
		int	distance,
		char	measure,
		Int2 *&	pairOutput,
		char *&	distanceOutput,
		int	uniqueLen,
		int *	buffer,
		int	seqLen
	)

private function.

solve_bin_packing_lowerbounds()

int solve_bin_packing_lowerbounds	(	int *	histograms,
		int *&	lowerboundsOutput,
		int	n,
		int	seqLen,
		int *	buffer,
		MemoryContext	ctx
	)

solve bin packing for lower bound calculation.

Parameters

histograms	flatten histogram matrix
lowerboundsOutput	output assignment
n	row count of histograms
seqLen	array length of sequences
buffer	reusable 4-byte buffer
ctx	memory constraints and info

Returns

the length of lowerboundsOutput array

solve_bin_packing_offsets()

int solve_bin_packing_offsets	(	int *	histograms,
		int **&	offsetOutput,
		int	n,
		int *	buffer,
		MemoryContext	ctx
	)

solve bin packing for 2 dimensional buffer.

Parameters

histograms	flatten histogram matrix
offsetOutput	output assignment
n	row count of histograms
buffer	reusable 4-byte buffer
ctx	memory constraints and info

Returns

the second dimension of offsetOutput matrix

solve_next_bin()

int solve_next_bin	(	int *	chunksizes,
		int	start,
		int	maxSize,
		int	n
	)

solve bin packing on spot when precalculation is impossible.

Parameters

chunksizes	array of chunk sizes
start	offset of the latest processed chunk
maxSize	bin size
n	array length of chunkSizes

Returns

the number of chunks to process

stream_handler1()

void stream_handler1	(	Chunk< Int3 >	input,
		Int3 *&	deletionsOutput,
		int *&	indexOutput,
		std::vector< int *> &	histogramOutput,
		int &	outputLen,
		int	distance,
		int &	carry,
		MemoryContext	ctx
	)

handle all GPU operations in stream 1.

Parameters

input	input CDR3 sequences
deletionsOutput	generated deletion forms of CDR3 sequence
indexOutput	original index of each deletion forms
histogramOutput	histogram of deletion forms
outputLen	number of output deletion forms
distance	distance threshold
carry	index offset of the chunk
ctx	memory context

stream_handler2()

void stream_handler2	(	Chunk< Int3 > &	keyInOut,
		Chunk< int > &	valueInOut,
		std::vector< int *> &	histogramOutput,
		size_t &	throughput2B,
		int	distance,
		int	seqLen,
		int *	buffer,
		MemoryContext	ctx
	)

handle all GPU operations in stream 2.

Parameters

keyInOut	deletion forms of CDR3 sequence
valueInOut	index of each deletion forms
histogramOutput	histogram of indexes
throughput2B	throughput counting variable
distance	distance threshold
seqLen	number of input CDR3 sequences
buffer	integer buffer
ctx	memory context

stream_handler3()

void stream_handler3	(	Chunk< Int3 > &	keyInOut,
		Chunk< int > &	valueInOut,
		void	callbackInt2 *, int,
		std::vector< int *> &	histogramOutput,
		int	lowerbound,
		int	seqLen,
		int *	buffer,
		MemoryContext	ctx
	)

handle all GPU operations in stream 3.

Parameters

keyInOut	deletion forms of CDR3 sequence
valueInOut	index of each deletion forms
callback	pair outputs
histogramOutput	histogram of generating pairs
lowerbound	bound of generating pairs
seqLen	number of input CDR3 sequences
buffer	integer buffer
ctx	memory context

stream_handler4_nn()

void stream_handler4_nn	(	Chunk< Int2 >	pairInput,
		XTNOutput &	output,
		char *	allStr,
		unsigned int *	allStrOffsets,
		int	seqLen,
		int	distance,
		char	measure,
		int *	buffer
	)

handle all GPU operations in stream 4 nn mode.

Parameters

pairInput	nearest neighbor pairs
output	returning output
allStr	all CDR3 sequences
allStrOffsets	offset of CDR3 sequences
seqLen	number of input CDR3 sequences
distance	distance threshold
measure	type of measurement (levenshtein/hamming)
buffer	integer buffer

Variable Documentation

NUM_THREADS

const int NUM_THREADS = 256

UINT_MIN

const unsigned int UINT_MIN = 0