#include "pch.h"
#include <cuda_runtime_api.h>
#include <cusparse.h>
#include <stdio.h>
#include <stdlib.h>
#include <iostream>
#include <numeric>
#include <algorithm>
#include <vector>

Macros
#define	METHOD_EXPORTS

#define	EXPORT __declspec(dllexport)

#define	CHECK_CUDA(status) { checkCuda(status, __LINE__); }

#define	CHECK_CUSPARSE(status) { checkCusparse(status, __LINE__); }

Functions
EXPORT int *	findTopCandidatesCuda (int csrRowoffsets, int csrColIdx, int spectraValues, int spectraIdx, int csrRowoffsetsLength, int csrNNZ, int sVLength, int sILength, int n, float tolerance, bool normalize, bool gaussianTol, int verbose)
	A function that calculates the top n candidates for each spectrum (SpM*V) using f32 operations.

EXPORT int *	findTopCandidatesCudaInt (int csrRowoffsets, int csrColIdx, int spectraValues, int spectraIdx, int csrRowoffsetsLength, int csrNNZ, int sVLength, int sILength, int n, float tolerance, bool normalize, bool gaussianTol, int verbose)
	A function that calculates the top n candidates for each spectrum (SpM*V) using i8 and 32 operations.

EXPORT int *	findTopCandidatesCudaBatched (int csrRowoffsets, int csrColIdx, int spectraValues, int spectraIdx, int csrRowoffsetsLength, int csrNNZ, int sVLength, int sILength, int n, float tolerance, bool normalize, bool gaussianTol, int batchSize, int verbose)
	A function that calculates the top n candidates for each spectrum. Uses cusparseSpGEMM to calculate matrix product.

EXPORT int *	findTopCandidatesCudaBatched2 (int csrRowoffsets, int csrColIdx, int spectraValues, int spectraIdx, int csrRowoffsetsLength, int csrNNZ, int sVLength, int sILength, int n, float tolerance, bool normalize, bool gaussianTol, int batchSize, int verbose)
	A function that calculates the top n candidates for each spectrum. Uses cusparseSpMM to calculate matrix product.

EXPORT int	releaseMemoryCuda (int *result)
	Free memory after result has been marshalled.

float	squared (float x)
	Returns the square for a given value x.

float	normpdf (float x, float mu, float sigma)
	Returns the PDF for a given x for the normal distribution given by mu and sigma.

int	getRowIdx (int *csrRowoffsets, int csrRowoffsetsLength, int colIdxPos)
	Gets the row index of a specific position in the csr_column_indices array.

int	checkCuda (cudaError_t, int line)

int	checkCusparse (cusparseStatus_t, int line)

BOOL APIENTRY	DllMain (HMODULE hModule, DWORD ul_reason_for_call, LPVOID lpReserved)

Variables
const int	versionMajor = 1

const int	versionMinor = 5

const int	versionFix = 1

const int	MASS_RANGE = 5000

const int	MASS_MULTIPLIER = 100

const int	ENCODING_SIZE = MASS_RANGE * MASS_MULTIPLIER

const float	ROUNDING_ACCURACY = (float) INT8_MAX / 7.0f

const double	ONE_OVER_SQRT_PI = 0.39894228040143267793994605993438

Macro Definition Documentation

◆ CHECK_CUDA

#define CHECK_CUDA ( status ) { checkCuda(status, __LINE__); }

Definition at line 23 of file findTopCandidatesCudaInt.cpp.

◆ CHECK_CUSPARSE

#define CHECK_CUSPARSE ( status ) { checkCusparse(status, __LINE__); }

Definition at line 24 of file findTopCandidatesCudaInt.cpp.

◆ EXPORT

#define EXPORT __declspec(dllexport)

Definition at line 18 of file findTopCandidatesCudaInt.cpp.

◆ METHOD_EXPORTS

#define METHOD_EXPORTS

Definition at line 16 of file findTopCandidatesCudaInt.cpp.

Function Documentation

◆ checkCuda()

int checkCuda	(	cudaError_t	status,
		int	line
	)

Definition at line 77 of file findTopCandidatesCudaInt.cpp.

◆ checkCusparse()

int checkCusparse	(	cusparseStatus_t	status,
		int	line
	)

Definition at line 87 of file findTopCandidatesCudaInt.cpp.

◆ DllMain()

BOOL APIENTRY DllMain	(	HMODULE	hModule,
		DWORD	ul_reason_for_call,
		LPVOID	lpReserved
	)

Definition at line 946 of file findTopCandidatesCudaInt.cpp.

◆ findTopCandidatesCuda()

int * findTopCandidatesCuda	(	int *	csrRowoffsets,
		int *	csrColIdx,
		int *	spectraValues,
		int *	spectraIdx,
		int	csrRowoffsetsLength,
		int	csrNNZ,
		int	sVLength,
		int	sILength,
		int	n,
		float	tolerance,
		bool	normalize,
		bool	gaussianTol,
		int	verbose
	)

A function that calculates the top n candidates for each spectrum (SpM*V) using f32 operations.

Parameters

csrRowoffsets	Rowoffsets (int array) of the CSR sparse matrix (L: rows + 1).
csrColIdx	Column indices (int array) of the CSR sparse matrix (L: NNZ).
spectraValues	An integer array of peaks from experimental spectra flattened.
spectraIdx	An integer array that contains indices of where each spectrum starts in spectraValues.
csrRowoffsetsLength	Length (int) of csrRowoffsets (rows + 1).
csrNNZ	Number of non-zero entries (int) in the CSR sparse matrix.
sVLength	Length (int) of spectraValues.
sILength	Length (int) of spectraIdx.
n	How many of the best hits should be returned (int).
tolerance	Tolerance for peak matching (float).
normalize	If candidate vectors should be normalized to sum(elements) = 1 (bool).
gaussianTol	If spectrum peaks should be modelled as normal distributions or not (bool).
verbose	Print info every (int) processed spectra.

Returns: An integer array of length sILength * n containing the indexes of the top n candidates for each spectrum.

Parameters

csrRowoffsets	Rowoffsets (int array) of the CSR sparse matrix (L: rows + 1).
csrColIdx	Column indices (int array) of the CSR sparse matrix (L: NNZ).
spectraValues	An integer array of peaks from experimental spectra flattened.
spectraIdx	An integer array that contains indices of where each spectrum starts in spectraValues.
csrRowoffsetsLength	Length (int) of csrRowoffsets (rows + 1).
csrNNZ	Number of non-zero entries (int) in the CSR sparse matrix.
sVLength	Length (int) of spectraValues.
sILength	Length (int) of spectraIdx.
n	How many of the best hits should be returned (int).
tolerance	Tolerance for peak matching (float).
normalize	If candidate vectors should be normalized to sum(elements) = 1 (bool).
gaussianTol	If spectrum peaks should be modelled as normal distributions or not (bool).
verbose	Print info every (int) processed spectra.

Returns: An integer array of length sILength * n containing the indexes of the top n candidates for each spectrum.

Exceptions

std::invalid_argument Thrown if n is greater than cILength, cannot return more hits than number of candidates.

Definition at line 114 of file findTopCandidatesCudaInt.cpp.

◆ findTopCandidatesCudaBatched()

int * findTopCandidatesCudaBatched	(	int *	csrRowoffsets,
		int *	csrColIdx,
		int *	spectraValues,
		int *	spectraIdx,
		int	csrRowoffsetsLength,
		int	csrNNZ,
		int	sVLength,
		int	sILength,
		int	n,
		float	tolerance,
		bool	normalize,
		bool	gaussianTol,
		int	batchSize,
		int	verbose
	)

A function that calculates the top n candidates for each spectrum. Uses cusparseSpGEMM to calculate matrix product.

Parameters

csrRowoffsets	Rowoffsets (int array) of the CSR sparse matrix (L: rows + 1).
csrColIdx	Column indices (int array) of the CSR sparse matrix (L: NNZ).
spectraValues	An integer array of peaks from experimental spectra flattened.
spectraIdx	An integer array that contains indices of where each spectrum starts in spectraValues.
csrRowoffsetsLength	Length (int) of csrRowoffsets (rows + 1).
csrNNZ	Number of non-zero entries (int) in the CSR sparse matrix.
sVLength	Length (int) of spectraValues.
sILength	Length (int) of spectraIdx.
n	How many of the best hits should be returned (int).
tolerance	Tolerance for peak matching (float).
normalize	If candidate vectors should be normalized to sum(elements) = 1 (bool).
gaussianTol	If spectrum peaks should be modelled as normal distributions or not (bool).
batchSize	How many spectra (int) should be searched at once.
verbose	Print info every (int) processed spectra.

Returns: An integer array of length sILength * n containing the indexes of the top n candidates for each spectrum.

Parameters

csrRowoffsets	Rowoffsets (int array) of the CSR sparse matrix (L: rows + 1).
csrColIdx	Column indices (int array) of the CSR sparse matrix (L: NNZ).
spectraValues	An integer array of peaks from experimental spectra flattened.
spectraIdx	An integer array that contains indices of where each spectrum starts in spectraValues.
csrRowoffsetsLength	Length (int) of csrRowoffsets (rows + 1).
csrNNZ	Number of non-zero entries (int) in the CSR sparse matrix.
sVLength	Length (int) of spectraValues.
sILength	Length (int) of spectraIdx.
n	How many of the best hits should be returned (int).
tolerance	Tolerance for peak matching (float).
normalize	If candidate vectors should be normalized to sum(elements) = 1 (bool).
gaussianTol	If spectrum peaks should be modelled as normal distributions or not (bool).
batchSize	How many spectra (int) should be searched at once.
verbose	Print info every (int) processed spectra.

Returns: An integer array of length sILength * n containing the indexes of the top n candidates for each spectrum.

Exceptions

std::invalid_argument Thrown if n is greater than cILength, cannot return more hits than number of candidates.

Definition at line 435 of file findTopCandidatesCudaInt.cpp.

◆ findTopCandidatesCudaBatched2()

int * findTopCandidatesCudaBatched2	(	int *	csrRowoffsets,
		int *	csrColIdx,
		int *	spectraValues,
		int *	spectraIdx,
		int	csrRowoffsetsLength,
		int	csrNNZ,
		int	sVLength,
		int	sILength,
		int	n,
		float	tolerance,
		bool	normalize,
		bool	gaussianTol,
		int	batchSize,
		int	verbose
	)

A function that calculates the top n candidates for each spectrum. Uses cusparseSpMM to calculate matrix product.

Parameters

csrRowoffsets	Rowoffsets (int array) of the CSR sparse matrix (L: rows + 1).
csrColIdx	Column indices (int array) of the CSR sparse matrix (L: NNZ).
spectraValues	An integer array of peaks from experimental spectra flattened.
spectraIdx	An integer array that contains indices of where each spectrum starts in spectraValues.
csrRowoffsetsLength	Length (int) of csrRowoffsets (rows + 1).
csrNNZ	Number of non-zero entries (int) in the CSR sparse matrix.
sVLength	Length (int) of spectraValues.
sILength	Length (int) of spectraIdx.
n	How many of the best hits should be returned (int).
tolerance	Tolerance for peak matching (float).
normalize	If candidate vectors should be normalized to sum(elements) = 1 (bool).
gaussianTol	If spectrum peaks should be modelled as normal distributions or not (bool).
batchSize	How many spectra (int) should be searched at once.
verbose	Print info every (int) processed spectra.

Returns: An integer array of length sILength * n containing the indexes of the top n candidates for each spectrum.

Parameters

csrRowoffsets	Rowoffsets (int array) of the CSR sparse matrix (L: rows + 1).
csrColIdx	Column indices (int array) of the CSR sparse matrix (L: NNZ).
spectraValues	An integer array of peaks from experimental spectra flattened.
spectraIdx	An integer array that contains indices of where each spectrum starts in spectraValues.
csrRowoffsetsLength	Length (int) of csrRowoffsets (rows + 1).
csrNNZ	Number of non-zero entries (int) in the CSR sparse matrix.
sVLength	Length (int) of spectraValues.
sILength	Length (int) of spectraIdx.
n	How many of the best hits should be returned (int).
tolerance	Tolerance for peak matching (float).
normalize	If candidate vectors should be normalized to sum(elements) = 1 (bool).
gaussianTol	If spectrum peaks should be modelled as normal distributions or not (bool).
batchSize	How many spectra (int) should be searched at once.
verbose	Print info every (int) processed spectra.

Returns: An integer array of length sILength * n containing the indexes of the top n candidates for each spectrum.

Exceptions

std::invalid_argument Thrown if n is greater than cILength, cannot return more hits than number of candidates.

Definition at line 710 of file findTopCandidatesCudaInt.cpp.

◆ findTopCandidatesCudaInt()

int * findTopCandidatesCudaInt	(	int *	csrRowoffsets,
		int *	csrColIdx,
		int *	spectraValues,
		int *	spectraIdx,
		int	csrRowoffsetsLength,
		int	csrNNZ,
		int	sVLength,
		int	sILength,
		int	n,
		float	tolerance,
		bool	normalize,
		bool	gaussianTol,
		int	verbose
	)

A function that calculates the top n candidates for each spectrum (SpM*V) using i8 and 32 operations.

Parameters

csrRowoffsets	Rowoffsets (int array) of the CSR sparse matrix (L: rows + 1).
csrColIdx	Column indices (int array) of the CSR sparse matrix (L: NNZ).
spectraValues	An integer array of peaks from experimental spectra flattened.
spectraIdx	An integer array that contains indices of where each spectrum starts in spectraValues.
csrRowoffsetsLength	Length (int) of csrRowoffsets (rows + 1).
csrNNZ	Number of non-zero entries (int) in the CSR sparse matrix.
sVLength	Length (int) of spectraValues.
sILength	Length (int) of spectraIdx.
n	How many of the best hits should be returned (int).
tolerance	Tolerance for peak matching (float).
normalize	If candidate vectors should be normalized to sum(elements) = 1 (bool).
gaussianTol	If spectrum peaks should be modelled as normal distributions or not (bool).
verbose	Print info every (int) processed spectra.

Returns: An integer array of length sILength * n containing the indexes of the top n candidates for each spectrum.

Definition at line 272 of file findTopCandidatesCudaInt.cpp.

◆ getRowIdx()

int getRowIdx	(	int *	csrRowoffsets,
		int	csrRowoffsetsLength,
		int	colIdxPos
	)

Gets the row index of a specific position in the csr_column_indices array.

Parameters

csrRowoffsets	The csr_row_offsets array.
csrRowoffsetsLength	Length (int) of the csr_row_offsets array.
colIdxPos	The position (int) of the element in question of the csr_column_indices array.

Returns: Associated row index (int) or throws an error if the row index could not be found.

Parameters

csrRowoffsets	The csr_row_offsets array.
csrRowoffsetsLength	Length (int) of the csr_row_offsets array.
colIdxPos	The position (int) of the element in question of the csr_column_indices array.