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cuda_main.cu
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cuda_main.cu
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/*
Copyright (c) 2016, Brizzolari Cecilia, Corneo Andrea
We refer as "The Program" to all the files and documentation present
in this repository that reports this declaration.
This file is part of The Program
The Program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
The Program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#include <stdio.h>
#include <stdlib.h>
#include <malloc.h>
//#include <cuda.h>
#include <stdint.h>
//#include <device_functions.h>
//#include <cuda_runtime_api.h>
//#include "cuda_runtime.h"
//#include "device_launch_parameters.h"
#ifdef SILENT
#define printf(...)
#endif
#define PARAM 3 //input (bloom filter), input (reads), output
#define BASES 4
#define BLOCK_DIM 128
#define DATA_PER_THREAD 10
#define READS_LENGTH 35
#define L 10
#define MSEED 7127 //static seed for murmur function
//Spooky utils
#define SSEED 5449 //static seed for spooky function
#define SC_CONST 0xdeadbeefdeadbeefLL
#define SC_NUMVARS 12
#define SC_BLOCKSIZE (8 * SC_NUMVARS)
#define SC_BUFSIZE (2 * SC_BLOCKSIZE)
struct spooky_state
{
uint64_t m_data[2 * SC_NUMVARS];
uint64_t m_state[SC_NUMVARS];
size_t m_length;
unsigned char m_remainder;
};
//City utils
typedef uint8_t uint8;
typedef uint32_t uint32;
typedef uint64_t uint64;
typedef struct _uint128 uint128;
struct _uint128 {
uint64 first;
uint64 second;
};
/************ ERROR HANDLING *****************************/
void HandleError( cudaError_t err,
const char *file,
int line ) {
if (err != cudaSuccess) {
printf( "%s in %s at line %d\n", cudaGetErrorString( err ),
file, line );
exit( EXIT_FAILURE );
}
}
#define HANDLE_ERROR( err ) (HandleError( err, __FILE__, __LINE__ ))
/**************** PROTOTYPES *****************************/
__device__ int CheckBit(uint64_t *, unsigned long, unsigned int);
__device__ int CheckHash(uint64_t *, char *, unsigned int);
__device__ unsigned long djb2_hash(unsigned char *);
__device__ uint64_t MurmurHash64A (const void *, int, unsigned int);
__device__ uint64_t APHash(char *, unsigned int);
__device__ uint64_t fnvhash(char *);
__device__ uint64_t SDBMHash(char *, unsigned int);
__device__ uint64_t RSHash(char *, unsigned int);
//City prototypes
#ifndef CITY_HASH_H_
#define CITY_HASH_H_
__device__ uint64 CityHash64(const char *buf, size_t len);
__device__ static uint64 UNALIGNED_LOAD64(const char *);
__device__ static uint32 UNALIGNED_LOAD32(const char *);
__device__ static uint64 Fetch64(const char *);
__device__ static uint32 Fetch32(const char *);
__device__ uint64 CityHash64(const char *, size_t);
__device__ static uint64 HashLen0to16(const char *, size_t);
__device__ static uint64 HashLen17to32(const char *, size_t);
__device__ static uint64 HashLen33to64(const char *, size_t);
__device__ static uint64 HashLen16(uint64, uint64);
__device__ static inline uint64 Hash128to64(const uint128);
__device__ static uint64 Rotate(uint64, int);
__device__ static uint64 RotateByAtLeast1(uint64, int);
__device__ static uint64 ShiftMix(uint64);
__device__ uint128 WeakHashLen32WithSeeds6(uint64, uint64, uint64, uint64, uint64, uint64);
__device__ uint128 WeakHashLen32WithSeeds(const char *, uint64, uint64);
#endif // CITY_HASH_H_
//Spooky prototypes
__device__ static inline uint64_t rot64(uint64_t x, int k);
__device__ static inline void mix(const uint64_t *, uint64_t *, uint64_t *, uint64_t *, uint64_t *, uint64_t *, uint64_t *, uint64_t *, uint64_t *, uint64_t *, uint64_t *, uint64_t *, uint64_t *);
__device__ static inline void endPartial(uint64_t *, uint64_t *, uint64_t *, uint64_t *, uint64_t *, uint64_t *, uint64_t *, uint64_t *, uint64_t *, uint64_t *, uint64_t *, uint64_t *);
__device__ static inline void end(uint64_t *, uint64_t *, uint64_t *, uint64_t *, uint64_t *, uint64_t *, uint64_t *, uint64_t *, uint64_t *, uint64_t *, uint64_t *, uint64_t *);
__device__ static inline void short_mix(uint64_t *, uint64_t *, uint64_t *, uint64_t *);
__device__ static inline void short_end(uint64_t *, uint64_t *, uint64_t *, uint64_t *);
__device__ void spooky_shorthash(const void *, size_t , uint64_t *, uint64_t *);
__device__ void spooky_init(struct spooky_state *, uint64_t, uint64_t);
__device__ void spooky_update(struct spooky_state *, const void *, size_t);
__device__ void spooky_final(struct spooky_state *, uint64_t *, uint64_t *);
__device__ uint64_t spooky_hash64(const void *, size_t, uint64_t);
__device__ void spooky_hash128(const void *, size_t, uint64_t *, uint64_t *);
/**************** GLOBAL VARIABLE ************************/
/* Allocate vector of bases on device memory,
* used to substitute character in the attempt of correcting reads
* In order to reduce acces latency it will be stored on shared memory
*/
__shared__ char bases[BASES];
/**************** DEVICE FUNCTIONS *********************/
/* @requires v poining to actual matrix
*
*/
__device__ ushort2 matrix_maximum(unsigned short int * v) {
unsigned short int i, j, maximum=0;
ushort2 couple;
couple.x=0;
couple.y=0;
for(i=0; i<READS_LENGTH; i++) {
for(j=0;j<BASES;j++) {
if(*(v + i*BASES + j) >= maximum) {
maximum = *(v + i*BASES + j);
couple.x=i;
couple.y=j;
}
}
}
return couple;
}
/* @requires v poining to actual string
*
*/
__device__ void gpu_strcpy(char * a, char * b) {
unsigned short int i=0;
do {
*(a+i) = *(b+i);
i++;
} while (*(b+i-1) != '\0' && i<READS_LENGTH);
}
__device__ void gpu_strncpy(char * a, char* b, unsigned short int l){
unsigned short int i=0;
do{
*(a+i) = *(b+i);
i++;
}
while(i<l && *(b+i-1) != '\0');
}
/************************* KERNEL ****************************************************/
/***************** VOTING KERNEL ***************************/
__global__ void voting(char * reads, unsigned short int * voting_matrix_array, unsigned int inputDim, uint64_t * gpu_hashed_spectrum, unsigned int spectrum_size){
char * read;
char subseq[L+1], subcpy[L+1]; //substring of dimension L, copy with substituted character
unsigned short int * voting_matrix;
int j, c;
unsigned short h;
int idx = blockDim.x * blockIdx.x + threadIdx.x;
if( threadIdx.x == 0){
bases[0] = 'A';
bases[1] = 'C';
bases[2] = 'G';
bases[3] = 'T';
}
__syncthreads();
for(h=0; h<DATA_PER_THREAD; h++){
if(inputDim/DATA_PER_THREAD*h + idx >= inputDim)
return;
/* Get data
*
*/
voting_matrix = voting_matrix_array + (inputDim/DATA_PER_THREAD*h + idx)*BASES*(READS_LENGTH);
read = reads + (inputDim/DATA_PER_THREAD*h + idx)*(READS_LENGTH+1);
/* Initialize voting matrix to zeroes
*
*/
for(j=0; j<READS_LENGTH; j++)
for(c=0; c<BASES; c++)
*(voting_matrix + j*BASES + c) = 0;
/* Voting procedure
*
*/
for(j=0; j<(READS_LENGTH-L+1); j++){
gpu_strncpy(subseq, read+j, L); //take substring of length L
subseq[L] = '\0';
if(!(CheckHash(gpu_hashed_spectrum, subseq, spectrum_size))){ //begin voting procedure for non-solid tuples
for(int p=0; p<L; p++){
for(c=0; c<BASES; c++){
if(subseq[p] != bases[c]){
gpu_strcpy(subcpy, subseq);
subcpy[p]=bases[c]; //substitute current base with any other one
if(CheckHash(gpu_hashed_spectrum, subcpy, spectrum_size))
*(voting_matrix + (j+p)*BASES + c) = *(voting_matrix + (j+p)*BASES + c) + 1; //increment number of solid tuples with that correction
}
}
}
}
}
}
}
/***************** FIXING KERNEL ***************************/
__global__ void fixing(char * reads, unsigned short int * voting_matrix_array, unsigned int inputDim, uint64_t * gpu_hashed_spectrum, unsigned int spectrum_size) {
unsigned short int i,h,k;
int idx = blockIdx.x * blockDim.x + threadIdx.x;
/* If first thread in the block should copy in shared memory
* the variables from the global memory
*
*/
if(threadIdx.x == 0) {
bases[0] = 'A';
bases[1] = 'C';
bases[2] = 'G';
bases[3] = 'T';
}
__syncthreads();
char * read_ptr;
char read[READS_LENGTH+1];
unsigned short int * voting_matrix;
char rc[READS_LENGTH+1];
unsigned short int j;
char tuple[L+1];
bool corrected_flag, trimmed_flag;
ushort2 couple;
for(h=0; h<DATA_PER_THREAD; h++) {
if(idx + inputDim/DATA_PER_THREAD * h >= inputDim)
return;
read_ptr = reads + (idx + inputDim/DATA_PER_THREAD * h) * (READS_LENGTH+1);
gpu_strcpy(read, read_ptr);
voting_matrix = voting_matrix_array + (idx + inputDim/DATA_PER_THREAD * h) * READS_LENGTH * BASES;
couple = matrix_maximum(voting_matrix);
if(*(voting_matrix + couple.x * BASES + couple.y) == 0) {
continue; //read is already correct
}
gpu_strcpy(rc, read);
rc[READS_LENGTH] = '\0';
rc[couple.x] = bases[couple.y];
corrected_flag=1;
trimmed_flag=0;
for(j=0;j < (READS_LENGTH-L+1); j++) {
//Create tuple
gpu_strncpy(tuple, rc+j, L);
tuple[L] = '\0';
if( !(CheckHash(gpu_hashed_spectrum, tuple, spectrum_size)) ) { /* Query bloom filter for tuple */
corrected_flag = 0;
}
else {
trimmed_flag = 1;
}
}
if(corrected_flag) {
gpu_strcpy(read_ptr, rc); //Return corrected read
continue;
}
bool flag=0;
int max_length=0;
if(trimmed_flag) {
//Trim read
for(k=0; k < READS_LENGTH-L+1; k++) {
for(j=READS_LENGTH-k; j>L+1 && !flag; j--) {
gpu_strncpy(rc, read+k, j);
rc[j] = '\0';
//Check each tuple of shorter string
flag=1;
for(i=0; i<j-L+1; i++) {
gpu_strncpy(tuple, read+i, L);
tuple[L] = '\0';
flag = flag && (CheckHash(gpu_hashed_spectrum, tuple, spectrum_size));
}
//Copy trimmered read
if(flag) {
if(j-k > max_length) {
gpu_strncpy(read_ptr, rc, j);
*(read_ptr+j-k+1) = '\0';
max_length = j-k;
}
}
}
flag=0;
}
continue;
}
//Uncorrect read, return empty string
*(read_ptr) = '\0';
}
}
/******************** MAIN ***********************************************************/
int main (int argc, char * argv[]) {
int i, j;
if(argc < PARAM+1) {
fprintf(stdout, "Error: parameters\n");
exit(1);
}
/************** INITIALIZATION **************/
/* Allocate and store the spectrum on the host,
* reading it from the input file
*
*/
uint64_t * hashed_spectrum;
unsigned int spectrum_size;
FILE * spectrumFP = fopen(argv[1], "r");
fscanf(spectrumFP, "%u\n", &spectrum_size);
if(!(hashed_spectrum = (uint64_t *)malloc(sizeof(uint64_t) * spectrum_size))) {
fprintf(stdout, "Error: allocation\n");
exit(1);
}
for(i=0; i<spectrum_size; i++) {
fscanf(spectrumFP, "%lu", &hashed_spectrum[i]);
//printf("%lu\n", hashed_spectrum[i]);
}
fclose(spectrumFP);
unsigned int inputDim;
FILE * readsFP = fopen(argv[2], "r");
fscanf(readsFP, "%u\n", &inputDim);
/* Allocate and read from input file the sequence reads,
* on host memory
*
*/
char * reads;
if(!(reads = (char *)malloc(sizeof(char) * (READS_LENGTH+1) * inputDim))) {
fprintf(stdout, "Error: allocation\n");
exit(1);
}
char cons;
for(i=0; i<inputDim; i++) {
for(j=0; j<READS_LENGTH; j++) {
fscanf(readsFP, "%c", reads + (READS_LENGTH+1) * i + j);
}
*(reads + (READS_LENGTH+1) * i + j) = '\0';
//printf("%s\n", reads + (READS_LENGTH+1)*i);
fscanf(readsFP, "%c", &cons);
}
fclose(readsFP);
/************* CUDA ALLOCATION ***************/
/* Allocate spectrum on texture memory
* Inlcude memcopy of the spectrum data
*
*
*/
uint64_t * gpu_hashed_spectrum;
HANDLE_ERROR(cudaMalloc(&gpu_hashed_spectrum, sizeof(uint64_t) * spectrum_size));
HANDLE_ERROR(cudaMemcpy(gpu_hashed_spectrum, hashed_spectrum, sizeof(uint64_t) * spectrum_size, cudaMemcpyHostToDevice));
/* Allocate reads on device memory as gpu_reads
* Include memcopy of already filled data
*
*/
char * gpu_reads;
HANDLE_ERROR(cudaMalloc(&gpu_reads, sizeof(char) * inputDim * (READS_LENGTH+1)));
HANDLE_ERROR(cudaMemcpy(gpu_reads, reads, sizeof(char) * inputDim * (READS_LENGTH+1), cudaMemcpyHostToDevice));
/* Allocate space gpu_voting_matrix
*
*/
unsigned short int * gpu_voting_matrix;
HANDLE_ERROR(cudaMalloc(&gpu_voting_matrix, sizeof(unsigned short int) * inputDim * READS_LENGTH * BASES));
/************ KERNEL **************************/
/************* VOTING ***************/
/* Already allocated and initializated voting_matrix and gpu_voting_matrix;
* reads and gpu_reads allocated and filled with data;
* inputDim is defined as gpu_inputDim;
*/
//Execute kernel
voting <<< inputDim/BLOCK_DIM/DATA_PER_THREAD, BLOCK_DIM >>> (gpu_reads, gpu_voting_matrix, inputDim, gpu_hashed_spectrum, spectrum_size);
/*
//DEBUG
unsigned short int * v;
v = (unsigned short int *)malloc(sizeof(unsigned short int) * inputDim * READS_LENGTH * BASES);
HANDLE_ERROR(cudaMemcpy(v, gpu_voting_matrix, sizeof(unsigned short int) * inputDim * READS_LENGTH * BASES, cudaMemcpyDeviceToHost));
for(int k=0; k<inputDim; k++) {
for(i=0; i<BASES; i++) {
for(j=0; j<READS_LENGTH; j++) {
printf("%3d", *(v + j*BASES + i));
//if (*(v + j*BASES + i)) printf("%3d", *(v + j*BASES + i));
}
printf("\n");
}
printf("\n\n\n");
}
//END DEBUG
*/
/************* FIXING ***************/
/* Assume gpu_voting_matrix already computed and stored in device memory,
* as gpu_reads. Do not remove from the device memory
*
*/
//Execute kernel
fixing <<< inputDim/BLOCK_DIM/DATA_PER_THREAD, BLOCK_DIM >>> (gpu_reads, gpu_voting_matrix, inputDim, gpu_hashed_spectrum, spectrum_size);
/*********** READ BACK ************************/
HANDLE_ERROR(cudaMemcpy(reads, gpu_reads, sizeof(char) * inputDim * (READS_LENGTH+1), cudaMemcpyDeviceToHost));
/*
//DEBUG hashed_spectrum
HANDLE_ERROR(cudaMemcpy(hashed_spectrum, gpu_hashed_spectrum, sizeof(uint64_t) * spectrum_size, cudaMemcpyDeviceToHost));
for(i=0; i<spectrum_size;i++)
printf("%lu\n", *(hashed_spectrum + i));
*/
/*********** WRITE OUT ************************/
FILE * outFP = fopen(argv[3], "w+");
for(i=0; i<inputDim; i++) {
if( 1/* *(reads + (READS_LENGTH+1) * i) != '\0' */) { //If not discarded
for(j=0; j<READS_LENGTH && *(reads + (READS_LENGTH+1) * i + j) != '\0'; j++) {
fprintf(outFP, "%c", *(reads + (READS_LENGTH+1) * i + j));
}
fprintf(outFP, "\n");
}
}
fclose(outFP);
free(reads);
free(hashed_spectrum);
cudaFree(gpu_reads);
cudaFree(gpu_hashed_spectrum);
cudaFree(gpu_voting_matrix);
return 0;
}
/***************************** UTILITY FUNCTION **************************************************/
//Check that the bit is in the filter
__device__ int CheckBit(uint64_t* filter, unsigned long i, unsigned int n) {
unsigned long k = i % n;
unsigned long pos = i % 64;
uint64_t bit = 1, res;
bit = bit << pos;
res = filter[k] & bit;
if(res !=0)
return 1;
else
return 0;
}
//Hashes the read and checks
__device__ int CheckHash(uint64_t* filter, char* read, unsigned int n) {
int flag = 1;
unsigned long i;
for(int k=1; k<=8 && flag; k++){
switch (k){
case 1:
i = djb2_hash((unsigned char*)read);
break;
case 2:
i = MurmurHash64A(read, L, MSEED);
break;
case 3:
i = APHash(read, L);
break;
case 4:
i = CityHash64(read, L);
break;
case 5:
i = spooky_hash64(read, L, SSEED);
break;
case 6:
i = fnvhash(read);
break;
case 7:
i = SDBMHash(read, L);
break;
case 8:
i = RSHash(read, L);
break;
default: break;
}
flag = CheckBit(filter, i, n);
}
return flag;
}
/****************** HASHES *******************/
const uint64_t FNV_PRIME = 1099511628211;
const uint64_t OFFSET_BASIS = 14695981039346656037UL;
//djb2 hash
__device__ unsigned long djb2_hash(unsigned char *str){
unsigned long hash = 5381;
int c;
while (c = *str++)
hash = ((hash << 5) + hash) + c; /* hash * 33 + c */
return hash;
}
// MurmurHash
// For the license and copyright, refer to BloomFilter/hashes.c
//
__device__ uint64_t MurmurHash64A ( const void * key, int len, unsigned int seed )
{
const uint64_t m = 0xc6a4a7935bd1e995;
const int r = 47;
uint64_t h = seed ^ (len * m);
const uint64_t * data = (const uint64_t *)key;
const uint64_t * end = data + (len/8);
while(data != end)
{
uint64_t k = *data++;
k *= m;
k ^= k >> r;
k *= m;
h ^= k;
h *= m;
}
const unsigned char * data2 = (const unsigned char*)data;
switch(len & 7)
{
case 7: h ^= (uint64_t)data2[6] << 48;
case 6: h ^= (uint64_t)data2[5] << 40;
case 5: h ^= (uint64_t)data2[4] << 32;
case 4: h ^= (uint64_t)data2[3] << 24;
case 3: h ^= (uint64_t)data2[2] << 16;
case 2: h ^= (uint64_t)data2[1] << 8;
case 1: h ^= (uint64_t)data2[0];
h *= m;
};
h ^= h >> r;
h *= m;
h ^= h >> r;
return h;
}
//AP hash
__device__ uint64_t APHash(char* str, unsigned int length) {
uint64_t hash = 0xAAAAAAAA;
unsigned int i = 0;
for (i = 0; i < length; str++, i++)
{
hash ^= ((i & 1) == 0) ? ((hash << 7) ^ (*str) * (hash >> 3)) :
(~((hash << 11) + ((*str) ^ (hash >> 5))));
}
return hash;
}
//FNV hash
__device__ uint64_t fnvhash(char * string){
uint64_t hash = OFFSET_BASIS;
for(uint8_t * c = (uint8_t*)string; *c != 0; ++c){
hash ^= *c;
hash *= FNV_PRIME;
}
return hash;
}
//SDBM hash
__device__ uint64_t SDBMHash(char* str, unsigned int length) {
uint64_t hash = 0;
unsigned int i = 0;
for (i = 0; i < length; str++, i++)
{
hash = (*str) + (hash << 6) + (hash << 16) - hash;
}
return hash;
}
//RS hash
__device__ uint64_t RSHash(char* str, unsigned int length) {
unsigned int b = 378551;
unsigned int a = 63689;
uint64_t hash = 0;
unsigned int i = 0;
for (i = 0; i < length; str++, i++)
{
hash = hash * a + (*str);
a = a * b;
}
return hash;
}
/*************** CITY HASH **********************/
// CityHash, by Geoff Pike and Jyrki Alakuijala
// For the license and copyright, refer to BloomFilter/city.c
//
#define Uint128Low64(x) (x).first
#define Uint128High64(x) (x).second
#if !defined(WORDS_BIGENDIAN)
#define uint32_in_expected_order(x) (x)
#define uint64_in_expected_order(x) (x)
#else
#ifdef _MSC_VER
#include <stdlib.h>
#define bswap_32(x) _byteswap_ulong(x)
#define bswap_64(x) _byteswap_uint64(x)
#elif defined(__APPLE__)
// Mac OS X / Darwin features
#include <libkern/OSByteOrder.h>
#define bswap_32(x) OSSwapInt32(x)
#define bswap_64(x) OSSwapInt64(x)
#else
#include <byteswap.h>
#endif
#define uint32_in_expected_order(x) (bswap_32(x))
#define uint64_in_expected_order(x) (bswap_64(x))
#endif // WORDS_BIGENDIAN
#if !defined(LIKELY)
#if HAVE_BUILTIN_EXPECT
#define LIKELY(x) (__builtin_expect(!!(x), 1))
#else
#define LIKELY(x) (x)
#endif
#endif
static const uint64 k0 = 0xc3a5c85c97cb3127ULL;
static const uint64 k1 = 0xb492b66fbe98f273ULL;
static const uint64 k2 = 0x9ae16a3b2f90404fULL;
static const uint64 k3 = 0xc949d7c7509e6557ULL;
__device__ static uint64 UNALIGNED_LOAD64(const char *p) {
uint64 result;
memcpy(&result, p, sizeof(result));
return result;
}
__device__ static uint32 UNALIGNED_LOAD32(const char *p) {
uint32 result;
memcpy(&result, p, sizeof(result));
return result;
}
__device__ static uint64 Fetch64(const char *p) {
return uint64_in_expected_order(UNALIGNED_LOAD64(p));
}
__device__ static uint32 Fetch32(const char *p) {
return uint32_in_expected_order(UNALIGNED_LOAD32(p));
}
__device__ uint64 CityHash64(const char *s, size_t len) {
if (len <= 32) {
if (len <= 16) {
return HashLen0to16(s, len);
} else {
return HashLen17to32(s, len);
}
} else if (len <= 64) {
return HashLen33to64(s, len);
}
// For strings over 64 bytes we hash the end first, and then as we
// loop we keep 56 bytes of state: v, w, x, y, and z.
uint64 x = Fetch64(s + len - 40);
uint64 y = Fetch64(s + len - 16) + Fetch64(s + len - 56);
uint64 z = HashLen16(Fetch64(s + len - 48) + len, Fetch64(s + len - 24));
uint64 temp;
uint128 v = WeakHashLen32WithSeeds(s + len - 64, len, z);
uint128 w = WeakHashLen32WithSeeds(s + len - 32, y + k1, x);
x = x * k1 + Fetch64(s);
// Decrease len to the nearest multiple of 64, and operate on 64-byte chunks.
len = (len - 1) & ~(size_t)(63);
do {
x = Rotate(x + y + v.first + Fetch64(s + 8), 37) * k1;
y = Rotate(y + v.second + Fetch64(s + 48), 42) * k1;
x ^= w.second;
y += v.first + Fetch64(s + 40);
z = Rotate(z + w.first, 33) * k1;
v = WeakHashLen32WithSeeds(s, v.second * k1, x + w.first);
w = WeakHashLen32WithSeeds(s + 32, z + w.second, y + Fetch64(s + 16));
temp = z;
z = x;
x = temp;
s += 64;
len -= 64;
} while (len != 0);
return HashLen16(HashLen16(v.first, w.first) + ShiftMix(y) * k1 + z,
HashLen16(v.second, w.second) + x);
}
__device__ static uint64 HashLen0to16(const char *s, size_t len) {
if (len > 8) {
uint64 a = Fetch64(s);
uint64 b = Fetch64(s + len - 8);
return HashLen16(a, RotateByAtLeast1(b + len, len)) ^ b;
}
if (len >= 4) {
uint64 a = Fetch32(s);
return HashLen16(len + (a << 3), Fetch32(s + len - 4));
}
if (len > 0) {
uint8 a = s[0];
uint8 b = s[len >> 1];
uint8 c = s[len - 1];
uint32 y = (uint32)(a) + ((uint32)(b) << 8);
uint32 z = len + ((uint32)(c) << 2);
return ShiftMix(y * k2 ^ z * k3) * k2;
}
return k2;
}
__device__ static uint64 HashLen17to32(const char *s, size_t len) {
uint64 a = Fetch64(s) * k1;
uint64 b = Fetch64(s + 8);
uint64 c = Fetch64(s + len - 8) * k2;
uint64 d = Fetch64(s + len - 16) * k0;
return HashLen16(Rotate(a - b, 43) + Rotate(c, 30) + d,
a + Rotate(b ^ k3, 20) - c + len);
}
__device__ static uint64 HashLen33to64(const char *s, size_t len) {
uint64 z = Fetch64(s + 24);
uint64 a = Fetch64(s) + (len + Fetch64(s + len - 16)) * k0;
uint64 b = Rotate(a + z, 52);
uint64 c = Rotate(a, 37);
a += Fetch64(s + 8);
c += Rotate(a, 7);
a += Fetch64(s + 16);
uint64 vf = a + z;
uint64 vs = b + Rotate(a, 31) + c;
a = Fetch64(s + 16) + Fetch64(s + len - 32);
z = Fetch64(s + len - 8);
b = Rotate(a + z, 52);
c = Rotate(a, 37);
a += Fetch64(s + len - 24);
c += Rotate(a, 7);
a += Fetch64(s + len - 16);
uint64 wf = a + z;
uint64 ws = b + Rotate(a, 31) + c;
uint64 r = ShiftMix((vf + ws) * k2 + (wf + vs) * k0);
return ShiftMix(r * k0 + vs) * k2;
}
__device__ static uint64 HashLen16(uint64 u, uint64 v) {
uint128 result;
result.first = u;
result.second = v;
return Hash128to64(result);
}
__device__ static inline uint64 Hash128to64(const uint128 x) {
// Murmur-inspired hashing.
const uint64 kMul = 0x9ddfea08eb382d69ULL;
uint64 a = (Uint128Low64(x) ^ Uint128High64(x)) * kMul;
a ^= (a >> 47);
uint64 b = (Uint128High64(x) ^ a) * kMul;
b ^= (b >> 47);
b *= kMul;
return b;
}
__device__ static uint64 Rotate(uint64 val, int shift) {
// Avoid shifting by 64: doing so yields an undefined result.
return shift == 0 ? val : ((val >> shift) | (val << (64 - shift)));
}
__device__ static uint64 RotateByAtLeast1(uint64 val, int shift) {
return (val >> shift) | (val << (64 - shift));
}
__device__ static uint64 ShiftMix(uint64 val) {
return val ^ (val >> 47);
}
__device__ uint128 WeakHashLen32WithSeeds6(
uint64 w, uint64 x, uint64 y, uint64 z, uint64 a, uint64 b) {
a += w;
b = Rotate(b + a + z, 21);
uint64 c = a;
a += x;
a += y;
b += Rotate(a, 44);
uint128 result;
result.first = (uint64) (a + z);
result.second = (uint64) (b + c);
return result;
}
__device__ uint128 WeakHashLen32WithSeeds(
const char* s, uint64 a, uint64 b) {
return WeakHashLen32WithSeeds6(Fetch64(s),
Fetch64(s + 8),
Fetch64(s + 16),
Fetch64(s + 24),
a,
b);
}
/**************** SPOOKY HASH *******************/
// A C version of Bob Jenkins' spooky hash
// Spooky Hash
// For license and copyright, refer to BloomFilter/spooky.c
//
#include <stddef.h>
#ifdef HAVE_CONFIG_H
# include <config.h>
# ifndef HAVE_ALIGNED_ACCESS_REQUIRED
# define ALLOW_UNALIGNED_READS 1
# else
# define ALLOW_UNALIGNED_READS 0
# endif
#else
# if defined(__i386__) || defined(__x86_64__) // add more architectures here
# define ALLOW_UNALIGNED_READS 1
# else
# define ALLOW_UNALIGNED_READS 0
# endif
#endif /* HAVE_CONFIG_H */
#include <memory.h>
__device__ static inline uint64_t rot64(uint64_t x, int k)
{
return (x << k) | (x >> (64 - k));
}
__device__ static inline void mix
(
const uint64_t *data,
uint64_t *s0, uint64_t *s1, uint64_t *s2, uint64_t *s3,
uint64_t *s4, uint64_t *s5, uint64_t *s6, uint64_t *s7,
uint64_t *s8, uint64_t *s9, uint64_t *s10, uint64_t *s11
)
{
*s0 += data[0]; *s2 ^= *s10; *s11 ^= *s0; *s0 = rot64(*s0, 11); *s11 += *s1;
*s1 += data[1]; *s3 ^= *s11; *s0 ^= *s1; *s1 = rot64(*s1, 32); *s0 += *s2;
*s2 += data[2]; *s4 ^= *s0; *s1 ^= *s2; *s2 = rot64(*s2, 43); *s1 += *s3;
*s3 += data[3]; *s5 ^= *s1; *s2 ^= *s3; *s3 = rot64(*s3, 31); *s2 += *s4;
*s4 += data[4]; *s6 ^= *s2; *s3 ^= *s4; *s4 = rot64(*s4, 17); *s3 += *s5;
*s5 += data[5]; *s7 ^= *s3; *s4 ^= *s5; *s5 = rot64(*s5, 28); *s4 += *s6;
*s6 += data[6]; *s8 ^= *s4; *s5 ^= *s6; *s6 = rot64(*s6, 39); *s5 += *s7;
*s7 += data[7]; *s9 ^= *s5; *s6 ^= *s7; *s7 = rot64(*s7, 57); *s6 += *s8;
*s8 += data[8]; *s10 ^= *s6; *s7 ^= *s8; *s8 = rot64(*s8, 55); *s7 += *s9;
*s9 += data[9]; *s11 ^= *s7; *s8 ^= *s9; *s9 = rot64(*s9, 54); *s8 += *s10;
*s10 += data[10]; *s0 ^= *s8; *s9 ^= *s10; *s10 = rot64(*s10, 22); *s9 += *s11;
*s11 += data[11]; *s1 ^= *s9; *s10 ^= *s11; *s11 = rot64(*s11, 46); *s10 += *s0;
}
__device__ static inline void endPartial
(
uint64_t *h0, uint64_t *h1, uint64_t *h2, uint64_t *h3,
uint64_t *h4, uint64_t *h5, uint64_t *h6, uint64_t *h7,
uint64_t *h8, uint64_t *h9, uint64_t *h10, uint64_t *h11
)
{
*h11+= *h1; *h2 ^= *h11; *h1 = rot64(*h1, 44);
*h0 += *h2; *h3 ^= *h0; *h2 = rot64(*h2, 15);
*h1 += *h3; *h4 ^= *h1; *h3 = rot64(*h3, 34);
*h2 += *h4; *h5 ^= *h2; *h4 = rot64(*h4, 21);
*h3 += *h5; *h6 ^= *h3; *h5 = rot64(*h5, 38);
*h4 += *h6; *h7 ^= *h4; *h6 = rot64(*h6, 33);
*h5 += *h7; *h8 ^= *h5; *h7 = rot64(*h7, 10);
*h6 += *h8; *h9 ^= *h6; *h8 = rot64(*h8, 13);
*h7 += *h9; *h10^= *h7; *h9 = rot64(*h9, 38);
*h8 += *h10; *h11^= *h8; *h10= rot64(*h10, 53);
*h9 += *h11; *h0 ^= *h9; *h11= rot64(*h11, 42);
*h10+= *h0; *h1 ^= *h10; *h0 = rot64(*h0, 54);
}
__device__ static inline void end
(
uint64_t *h0, uint64_t *h1, uint64_t *h2, uint64_t *h3,
uint64_t *h4, uint64_t *h5, uint64_t *h6, uint64_t *h7,
uint64_t *h8, uint64_t *h9, uint64_t *h10, uint64_t *h11
)
{
endPartial(h0, h1, h2, h3, h4, h5, h6, h7, h8, h9, h10, h11);
endPartial(h0, h1, h2, h3, h4, h5, h6, h7, h8, h9, h10, h11);
endPartial(h0, h1, h2, h3, h4, h5, h6, h7, h8, h9, h10, h11);
}
__device__ static inline void short_mix
(
uint64_t *h0,
uint64_t *h1,