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代码重构，总共7个kernel

This commit is contained in:
zzh 2023-08-26 00:38:38 +08:00
parent b95e622e7a
commit b53569db63
21 changed files with 1112 additions and 1191 deletions
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4
.vscode/settings.json vendored
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@ -6,6 +6,8 @@
"vector": "c",
"__bit_reference": "c",
"__split_buffer": "c",
"string": "c"
"string": "c",
"cstdint": "c",
"algorithm": "c"
}
}

20
Makefile
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@ -2,13 +2,22 @@ CC= gcc
#CFLAGS= -g -Wall -Wno-unused-function -mavx2
CFLAGS= -Wall -Wno-unused-function -O2 -mavx2
DFLAGS= -DSHOW_PERF
OBJS= ksw_normal.o ksw_avx2.o ksw_cuda.o ksw_avx2_u8.o bsw_avx2.o ksw_avx2_aligned.o thread_mem.o ksw_avx2_u8_aligned.o
PROG= sw_perf
PROG2= sw_perf_discrete
INCLUDES=
LIBS=
SUBDIRS= .
OBJS= ksw_ext_normal.o \
ksw_ext_avx2.o \
ksw_ext_avx2_u8.o \
ksw_ext_cuda.o \
ksw_ext_avx2_heuristics.o \
ksw_ext_avx2_u8_heuristics.o \
ksw_ext_avx2_aligned.o \
ksw_ext_avx2_u8_aligned.o \
thread_mem.o \
utils.o
ifeq ($(shell uname -s),Linux)
LIBS += -lrt
endif
@ -18,16 +27,13 @@ endif
.c.o:
$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $(CPPFLAGS) $< -o $@
all:$(PROG) $(PROG2)
all:$(PROG)
sw_perf:$(OBJS) main.o
$(CC) $(CFLAGS) $(LDFLAGS) $(OBJS) main.o -o $@ -L. $(LIBS)
$(PROG2):$(OBJS) discrete_mem_main.o
$(CC) $(CFLAGS) $(LDFLAGS) $(OBJS) main.o -o $@ -L. $(LIBS)
clean:
rm -f *.o a.out $(PROG) $(PROG2) *~ *.a
rm -f *.o a.out $(PROG) *~ *.a
depend:
( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) $(CPPFLAGS) -- *.c )

243
discrete_mem_main.c
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@ -1,243 +0,0 @@
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <stdint.h>
#include <assert.h>
#include "sys/time.h"
#define SW_NORMAL 0
#define SW_AVX2 1
#define SW_CUDA 2
#define SW_ALL 3
#define BLOCK_BUF_SIZE 1048576
#define READ_BUF_SIZE 2048
#define SEQ_BUF_SIZE (BLOCK_BUF_SIZE + READ_BUF_SIZE)
// 将文件读取到离散的内存里，看一下对sw性能的影响
#ifdef SHOW_PERF
// 用来调试，计算感兴趣部分的运行时间
// 获取当前毫秒数
int64_t get_mseconds()
{
struct timeval tv;
gettimeofday(&tv, NULL);
return (int64_t)1000 * (tv.tv_sec + ((1e-6) * tv.tv_usec));
}
int64_t time_sw_normal = 0,
time_sw_avx2 = 0,
time_sw_avx2_u8 = 0;
#endif
extern int ksw_normal(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int o_del, int e_del, int o_ins, int e_ins, int w, int end_bonus, int zdrop, int h0, int *_qle, int *_tle, int *_gtle, int *_gscore, int *_max_off);
extern int ksw_avx2(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int is_left, int m, const int8_t *mat, int o_del, int e_del,
int o_ins, int e_ins, int a, int b, int w, int end_bonus, int zdrop, int h0, int *_qle, int *_tle, int *_gtle, int *_gscore, int *_max_off);
extern int ksw_avx2_u8(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int is_left, int m, const int8_t *mat, int o_del, int e_del,
int o_ins, int e_ins, int a, int b, int w, int end_bonus, int zdrop, int h0, int *_qle, int *_tle, int *_gtle, int *_gscore, int *_max_off);
/*
* 包含一个参数，用来区分调用那个sw算法
* 参数为 normal/avx2/cuda
*/
// 程序执行入口
int main(int argc, char *argv[])
{
// 初始化一些全局参数
int8_t mat[25] = {1, -4, -4, -4, -1,
-4, 1, -4, -4, -1,
-4, -4, 1, -4, -1,
-4, -4, -4, 1, -1,
-1, -1, -1, -1, -1};
int max_off[2];
int qle, tle, gtle, gscore;
// 读取测试数据
char *query_arr = (char **)malloc(SEQ_BUF_SIZE);
char *target_arr = (char **)malloc(SEQ_BUF_SIZE);
int *info_buf = (int *)malloc(SEQ_BUF_SIZE);
int **info_arr = (int **)malloc(SEQ_BUF_SIZE);
FILE *query_f = 0, *target_f = 0, *info_f = 0;
// const char *qf_path = "/public/home/zzh/data/sw/q_s.fa";
// const char *tf_path = "/public/home/zzh/data/sw/t_s.fa";
// const char *if_path = "/public/home/zzh/data/sw/i_s.txt";
const char *qf_path = "/public/home/zzh/data/sw/q_m.fa";
const char *tf_path = "/public/home/zzh/data/sw/t_m.fa";
const char *if_path = "/public/home/zzh/data/sw/i_m.txt";
// const char *qf_path = "/public/home/zzh/data/sw/q_m.fa";
// const char *tf_path = "/public/home/zzh/data/sw/t_m.fa";
// const char *if_path = "/public/home/zzh/data/sw/i_m.txt";
query_f = fopen(qf_path, "r");
target_f = fopen(tf_path, "r");
info_f = fopen(if_path, "r");
// 每次读取一定量的数据，然后执行，直到处理完所有数据
int total_line_num = 0; // 目前处理的总的数据行数
int block_line_num = 0; // 当前循环包含的数据行数
int i, j;
// const int max_read = READ_BUF_SIZE; // 每次最多读取的字符
char read_buf[READ_BUF_SIZE]; // 读文件缓存
// int ret_code = 0;
// 初始化info_arr数组
i = 0;
j = 0;
while (1)
{
if (j > BLOCK_BUF_SIZE)
break;
info_arr[i] = &info_buf[j];
i += 1;
j += 3;
}
int score_normal = 0, score_avx2 = 0, score_avx2_u8 = 0;
while (!feof(target_f))
{
block_line_num = 0;
// target序列一般占用存储最多，先读取target，看一个buf能读多少行，query和info就按照这个行数来读
int cur_read_size = 0;
while (!feof(target_f) && cur_read_size < BLOCK_BUF_SIZE)
{
if (fgets(read_buf, READ_BUF_SIZE, target_f) == NULL)
break;
const int line_size = strlen(read_buf);
target_arr[block_line_num] = (char *)malloc(line_size);
assert(line_size < READ_BUF_SIZE);
++block_line_num;
++total_line_num;
strncpy(target_arr[block_line_num], read_buf, line_size);
cur_read_size += line_size;
// fprintf(stderr, "%d %d \n", line_size, cur_read_size);
}
// 读query
cur_read_size = 0;
for (i = 0; i < block_line_num; ++i)
{
if (fgets(read_buf, READ_BUF_SIZE, query_f) == NULL)
break;
const int line_size = strlen(read_buf);
assert(line_size < READ_BUF_SIZE);
query_arr[i] = (char *)malloc(line_size);
strncpy(query_arr[i], read_buf, line_size);
cur_read_size += line_size;
}
// 读info
cur_read_size = 0;
for (i = 0; i < block_line_num; ++i)
{
if (fgets(read_buf, READ_BUF_SIZE, info_f) == NULL)
break;
const int line_size = strlen(read_buf);
assert(line_size < READ_BUF_SIZE);
sscanf(read_buf, "%d %d %d\n", &info_arr[i][0], &info_arr[i][1], &info_arr[i][2]);
cur_read_size += line_size;
// fprintf(stderr, "%-8d%-8d%-8d\n", info_arr[i][0], info_arr[i][1], info_arr[i][2]);
// fprintf(stderr, "%s\n", read_buf);
}
// 性能测试
// 普通 sw
int cur_query_pos = 0;
int cur_target_pos = 0;
for (i = 0; i < block_line_num; ++i)
{
#ifdef SHOW_PERF
int64_t start_time = get_mseconds();
#endif
score_normal += ksw_normal(
info_arr[i][0],
(uint8_t *)query_arr[i],
info_arr[i][1],
(uint8_t *)target_arr[i],
5, mat, 6, 1, 6, 1, 100, 5, 100,
info_arr[i][2],
&qle, &tle, &gtle, &gscore, &max_off[0]);
#ifdef SHOW_PERF
time_sw_normal += get_mseconds() - start_time;
#endif
// 更新query和target位置信息
cur_query_pos += info_arr[i][0];
cur_target_pos += info_arr[i][1];
// fprintf(stderr, "%d %d %d %d %d %d %d\n", score_normal, qle, tle, gtle, gscore, max_off[0], max_off[1]);
}
// avx2 sw
cur_query_pos = 0;
cur_target_pos = 0;
for (i = 0; i < block_line_num; ++i)
{
#ifdef SHOW_PERF
int64_t start_time = get_mseconds();
#endif
score_avx2 += ksw_avx2(
info_arr[i][0],
(uint8_t *)query_arr[i],
info_arr[i][1],
(uint8_t *)target_arr[i],
0, 5, mat, 6, 1, 6, 1,
1, 4,
100, 5, 100,
info_arr[i][2],
&qle, &tle, &gtle, &gscore, &max_off[0]);
#ifdef SHOW_PERF
time_sw_avx2 += get_mseconds() - start_time;
#endif
// 更新query和target位置信息
cur_query_pos += info_arr[i][0];
cur_target_pos += info_arr[i][1];
// fprintf(stderr, "%d %d %d %d %d %d %d\n", score_avx2, qle, tle, gtle, gscore, max_off[0], max_off[1]);
}
// avx2 u8 sw
cur_query_pos = 0;
cur_target_pos = 0;
for (i = 0; i < block_line_num; ++i)
{
#ifdef SHOW_PERF
int64_t start_time = get_mseconds();
#endif
score_avx2_u8 += ksw_avx2_u8(
info_arr[i][0],
(uint8_t *)query_arr[i],
info_arr[i][1],
(uint8_t *)target_arr[i],
0, 5, mat, 6, 1, 6, 1,
1, 4,
100, 5, 100,
info_arr[i][2],
&qle, &tle, &gtle, &gscore, &max_off[0]);
#ifdef SHOW_PERF
time_sw_avx2_u8 += get_mseconds() - start_time;
#endif
// 更新query和target位置信息
cur_query_pos += info_arr[i][0];
cur_target_pos += info_arr[i][1];
// fprintf(stderr, "%d %d %d %d %d %d %d\n", score_normal, qle, tle, gtle, gscore, max_off[0], max_off[1]);
}
// fprintf(stderr, "%d %d \n", block_line_num, total_line_num);
}
// fprintf(stderr, "%d \n", score_normal);
#ifdef SHOW_PERF
fprintf(stderr, "time_sw_normal: %f s; score: %d\n", time_sw_normal / 1000.0, score_normal);
fprintf(stderr, "time_sw_avx2: %f s; score: %d\n", time_sw_avx2 / 1000.0, score_avx2);
fprintf(stderr, "time_sw_avx2_u8: %f s; score: %d\n", time_sw_avx2_u8 / 1000.0, score_avx2_u8);
#endif
if (query_f != 0)
fclose(query_f);
if (target_f != 0)
fclose(target_f);
if (info_f != 0)
fclose(info_f);
}

164
ksw_ext.h 100644
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@ -0,0 +1,164 @@
/*********************************************************************************************
Description: Declarations of sw extend functions
Copyright : All right reserved by NCIC.ICT
Author : Zhang Zhonghai
Date : 2023/08/23
***********************************************************************************************/
#ifndef __KSW_EXT_H
#define __KSW_EXT_H
#include <stdint.h>
typedef struct _thread_mem_t thread_mem_t;
// declaration of ksw functions
int ksw_extend_normal(thread_mem_t *tmem, // 内存池
int qlen, // query length 待匹配段碱基的query长度
const uint8_t *query, // read碱基序列
int tlen, // target length reference的长度
const uint8_t *target, // reference序列
int m, // 碱基种类 (5)
const int8_t *mat, // 每个位置的query和target的匹配得分 m*m
int o_del, // deletion 错配开始的惩罚系数
int e_del, // deletion extension的惩罚系数
int o_ins, // insertion 错配开始的惩罚系数
int e_ins, // insertion extension的惩罚系数SIMD_BTYES
int w, // 提前剪枝系数，w =100 匹配位置和beg的最大距离
int end_bonus, // 如果query比对到了最后一个字符，额外奖励分值
int zdrop, // 如果比对过程中，太多mismatch，提前结束比对
int h0, // 该seed的初始得分（完全匹配query的碱基数）
int *_qle, // 匹配得到全局最大得分的碱基在query的位置
int *_tle, // 匹配得到全局最大得分的碱基在reference的位置
int *_gtle, // query全部匹配上的target的长度
int *_gscore, // query的端到端匹配得分
int *_max_off); // 取得最大得分时在query和reference上位置差的 最大值
int ksw_extend_avx2(thread_mem_t *tmem, // 内存池
int qlen, // query length 待匹配段碱基的query长度
const uint8_t *query, // read碱基序列
int tlen, // target length reference的长度
const uint8_t *target, // reference序列
int extend_left, // 是不是向左扩展
int o_del, // deletion 错配开始的惩罚系数
int e_del, // deletion extension的惩罚系数
int o_ins, // insertion 错配开始的惩罚系数
int e_ins, // insertion extension的惩罚系数SIMD_BTYES
int base_match_score, // 碱基match时的分数
int base_mis_score, // 碱基mismatch时的惩罚分数（正数）
int window_size, // 提前剪枝系数，w =100 匹配位置和beg的最大距离
int end_bonus, // 如果query比对到了最后一个字符，额外奖励分值
int init_score, // 该seed的初始得分（完全匹配query的碱基数）
int *_qle, // 匹配得到全局最大得分的碱基在query的位置
int *_tle, // 匹配得到全局最大得分的碱基在reference的位置
int *_gtle, // query全部匹配上的target的长度
int *_gscore, // query的端到端匹配得分
int *_max_off); // 取得最大得分时在query和reference上位置差的 最大值
int ksw_extend_avx2_u8(thread_mem_t *tmem, // 内存池
int qlen, // query length 待匹配段碱基的query长度
const uint8_t *query, // read碱基序列
int tlen, // target length reference的长度
const uint8_t *target, // reference序列
int extend_left, // 是不是向左扩展
int o_del, // deletion 错配开始的惩罚系数
int e_del, // deletion extension的惩罚系数
int o_ins, // insertion 错配开始的惩罚系数
int e_ins, // insertion extension的惩罚系数SIMD_BTYES
int base_match_score, // 碱基match时的分数
int base_mis_score, // 碱基mismatch时的惩罚分数（正数）
int window_size, // 提前剪枝系数，w =100 匹配位置和beg的最大距离
int end_bonus, // 如果query比对到了最后一个字符，额外奖励分值
int init_score, // 该seed的初始得分（完全匹配query的碱基数）
int *_qle, // 匹配得到全局最大得分的碱基在query的位置
int *_tle, // 匹配得到全局最大得分的碱基在reference的位置
int *_gtle, // query全部匹配上的target的长度
int *_gscore, // query的端到端匹配得分
int *_max_off); // 取得最大得分时在query和reference上位置差的 最大值
int ksw_extend_avx2_heuristics(thread_mem_t *tmem, // 内存池
int qlen, // query length 待匹配段碱基的query长度
const uint8_t *query, // read碱基序列
int tlen, // target length reference的长度
const uint8_t *target, // reference序列
int extend_left, // 是不是向左扩展
int o_del, // deletion 错配开始的惩罚系数
int e_del, // deletion extension的惩罚系数
int o_ins, // insertion 错配开始的惩罚系数
int e_ins, // insertion extension的惩罚系数SIMD_BTYES
int base_match_score, // 碱基match时的分数
int base_mis_score, // 碱基mismatch时的惩罚分数（正数）
int window_size, // 提前剪枝系数，w =100 匹配位置和beg的最大距离
int end_bonus, // 如果query比对到了最后一个字符，额外奖励分值
int init_score, // 该seed的初始得分（完全匹配query的碱基数）
int *_qle, // 匹配得到全局最大得分的碱基在query的位置
int *_tle, // 匹配得到全局最大得分的碱基在reference的位置
int *_gtle, // query全部匹配上的target的长度
int *_gscore, // query的端到端匹配得分
int *_max_off); // 取得最大得分时在query和reference上位置差的 最大值
int ksw_extend_avx2_u8_heuristics(thread_mem_t *tmem, // 内存池
int qlen, // query length 待匹配段碱基的query长度
const uint8_t *query, // read碱基序列
int tlen, // target length reference的长度
const uint8_t *target, // reference序列
int extend_left, // 是不是向左扩展
int o_del, // deletion 错配开始的惩罚系数
int e_del, // deletion extension的惩罚系数
int o_ins, // insertion 错配开始的惩罚系数
int e_ins, // insertion extension的惩罚系数SIMD_BTYES
int base_match_score, // 碱基match时的分数
int base_mis_score, // 碱基mismatch时的惩罚分数（正数）
int window_size, // 提前剪枝系数，w =100 匹配位置和beg的最大距离
int end_bonus, // 如果query比对到了最后一个字符，额外奖励分值
int init_score, // 该seed的初始得分（完全匹配query的碱基数）
int *_qle, // 匹配得到全局最大得分的碱基在query的位置
int *_tle, // 匹配得到全局最大得分的碱基在reference的位置
int *_gtle, // query全部匹配上的target的长度
int *_gscore, // query的端到端匹配得分
int *_max_off); // 取得最大得分时在query和reference上位置差的 最大值
int ksw_extend_avx2_aligned(thread_mem_t *tmem, // 内存池
int qlen, // query length 待匹配段碱基的query长度
const uint8_t *query, // read碱基序列
int tlen, // target length reference的长度
const uint8_t *target, // reference序列
int extend_left, // 是不是向左扩展
int o_del, // deletion 错配开始的惩罚系数
int e_del, // deletion extension的惩罚系数
int o_ins, // insertion 错配开始的惩罚系数
int e_ins, // insertion extension的惩罚系数SIMD_BTYES
int base_match_score, // 碱基match时的分数
int base_mis_score, // 碱基mismatch时的惩罚分数（正数）
int window_size, // 提前剪枝系数，w =100 匹配位置和beg的最大距离
int end_bonus, // 如果query比对到了最后一个字符，额外奖励分值
int init_score, // 该seed的初始得分（完全匹配query的碱基数）
int *_qle, // 匹配得到全局最大得分的碱基在query的位置
int *_tle, // 匹配得到全局最大得分的碱基在reference的位置
int *_gtle, // query全部匹配上的target的长度
int *_gscore, // query的端到端匹配得分
int *_max_off); // 取得最大得分时在query和reference上位置差的 最大值
int ksw_extend_avx2_u8_aligned(thread_mem_t *tmem, // 内存池
int qlen, // query length 待匹配段碱基的query长度
const uint8_t *query, // read碱基序列
int tlen, // target length reference的长度
const uint8_t *target, // reference序列
int extend_left, // 是不是向左扩展
int o_del, // deletion 错配开始的惩罚系数
int e_del, // deletion extension的惩罚系数
int o_ins, // insertion 错配开始的惩罚系数
int e_ins, // insertion extension的惩罚系数SIMD_BTYES
int base_match_score, // 碱基match时的分数
int base_mis_score, // 碱基mismatch时的惩罚分数（正数）
int window_size, // 提前剪枝系数，w =100 匹配位置和beg的最大距离
int end_bonus, // 如果query比对到了最后一个字符，额外奖励分值
int init_score, // 该seed的初始得分（完全匹配query的碱基数）
int *_qle, // 匹配得到全局最大得分的碱基在query的位置
int *_tle, // 匹配得到全局最大得分的碱基在reference的位置
int *_gtle, // query全部匹配上的target的长度
int *_gscore, // query的端到端匹配得分
int *_max_off); // 取得最大得分时在query和reference上位置差的 最大值
#endif

331
ksw_avx2.c → ksw_ext_avx2.c
View File

@ -5,6 +5,7 @@
#include <stdio.h>
#include <immintrin.h>
#include <emmintrin.h>
#include "thread_mem.h"
#ifdef __GNUC__
#define LIKELY(x) __builtin_expect((x), 1)
@ -20,9 +21,6 @@
#define MIN(x, y) ((x) < (y) ? (x) : (y))
#define SIMD_WIDTH 16
int ksw_extend2_origin(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int is_left, int m, const int8_t *mat, int o_del, int e_del,
int o_ins, int e_ins, int w, int end_bonus, int zdrop, int h0, int *_qle, int *_tle, int *_gtle, int *_gscore, int *_max_off);
static const uint16_t h_vec_int_mask[SIMD_WIDTH][SIMD_WIDTH] = {
{0xffff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xffff, 0xffff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
@ -41,28 +39,28 @@ static const uint16_t h_vec_int_mask[SIMD_WIDTH][SIMD_WIDTH] = {
{0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0},
{0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff}};
// const int permute_mask = _MM_SHUFFLE(0, 1, 2, 3);
#define permute_mask _MM_SHUFFLE(0, 1, 2, 3)
// #define permute_mask _MM_SHUFFLE(0, 1, 2, 3)
#define permute_mask 27
// 初始化变量
#define SIMD_INIT \
int oe_del = o_del + e_del, oe_ins = o_ins + e_ins; \
__m256i zero_vec; \
__m256i max_vec; \
__m256i oe_del_vec; \
__m256i oe_ins_vec; \
__m256i e_del_vec; \
__m256i e_ins_vec; \
__m256i h_vec_mask[SIMD_WIDTH]; \
zero_vec = _mm256_setzero_si256(); \
oe_del_vec = _mm256_set1_epi16(-oe_del); \
oe_ins_vec = _mm256_set1_epi16(-oe_ins); \
e_del_vec = _mm256_set1_epi16(-e_del); \
e_ins_vec = _mm256_set1_epi16(-e_ins); \
__m256i match_sc_vec = _mm256_set1_epi16(a); \
__m256i mis_sc_vec = _mm256_set1_epi16(-b); \
__m256i amb_sc_vec = _mm256_set1_epi16(-1); \
__m256i amb_vec = _mm256_set1_epi16(4); \
for (i = 0; i < SIMD_WIDTH; ++i) \
#define SIMD_INIT \
int oe_del = o_del + e_del, oe_ins = o_ins + e_ins; \
__m256i zero_vec; \
__m256i max_vec; \
__m256i oe_del_vec; \
__m256i oe_ins_vec; \
__m256i e_del_vec; \
__m256i e_ins_vec; \
__m256i h_vec_mask[SIMD_WIDTH]; \
zero_vec = _mm256_setzero_si256(); \
oe_del_vec = _mm256_set1_epi16(-oe_del); \
oe_ins_vec = _mm256_set1_epi16(-oe_ins); \
e_del_vec = _mm256_set1_epi16(-e_del); \
e_ins_vec = _mm256_set1_epi16(-e_ins); \
__m256i match_sc_vec = _mm256_set1_epi16(base_match_score); \
__m256i mis_sc_vec = _mm256_set1_epi16(-base_mis_score); \
__m256i amb_sc_vec = _mm256_set1_epi16(-1); \
__m256i amb_vec = _mm256_set1_epi16(4); \
for (i = 0; i < SIMD_WIDTH; ++i) \
h_vec_mask[i] = _mm256_loadu_si256((__m256i *)(&h_vec_int_mask[i]));
/*
@ -171,35 +169,33 @@ static const uint16_t h_vec_int_mask[SIMD_WIDTH][SIMD_WIDTH] = {
mA1 = mA2; \
mA2 = tmp;
int ksw_avx2(int qlen, // query length 待匹配段碱基的query长度
const uint8_t *query, // read碱基序列
int tlen, // target length reference的长度
const uint8_t *target, // reference序列
int is_left, // 是不是向左扩展
int m, // 碱基种类 (5)
const int8_t *mat, // 每个位置的query和target的匹配得分 m*m
int o_del, // deletion 错配开始的惩罚系数
int e_del, // deletion extension的惩罚系数
int o_ins, // insertion 错配开始的惩罚系数
int e_ins, // insertion extension的惩罚系数SIMD_BTYES
int a, // 碱基match时的分数
int b, // 碱基mismatch时的惩罚分数（正数）
int w, // 提前剪枝系数，w =100 匹配位置和beg的最大距离
int end_bonus,
int zdrop,
int h0, // 该seed的初始得分（完全匹配query的碱基数）
int *_qle, // 匹配得到全局最大得分的碱基在query的位置
int *_tle, // 匹配得到全局最大得分的碱基在reference的位置
int *_gtle, // query全部匹配上的target的长度
int *_gscore, // query的端到端匹配得分
int *_max_off) // 取得最大得分时在query和reference上位置差的 最大值
int ksw_extend_avx2(thread_mem_t *tmem,
int qlen, // query length 待匹配段碱基的query长度
const uint8_t *query, // read碱基序列
int tlen, // target length reference的长度
const uint8_t *target, // reference序列
int extend_left, // 是不是向左扩展
int o_del, // deletion 错配开始的惩罚系数
int e_del, // deletion extension的惩罚系数
int o_ins, // insertion 错配开始的惩罚系数
int e_ins, // insertion extension的惩罚系数SIMD_BTYES
int base_match_score, // 碱基match时的分数
int base_mis_score, // 碱基mismatch时的惩罚分数（正数）
int window_size, // 提前剪枝系数，w =100 匹配位置和beg的最大距离
int end_bonus, // 如果query比对到了最后一个字符，额外奖励分值
int init_score, // 该seed的初始得分（完全匹配query的碱基数）
int *_qle, // 匹配得到全局最大得分的碱基在query的位置
int *_tle, // 匹配得到全局最大得分的碱基在reference的位置
int *_gtle, // query全部匹配上的target的长度
int *_gscore, // query的端到端匹配得分
int *_max_off) // 取得最大得分时在query和reference上位置差的 最大值
{
int16_t *mA, *hA, *eA, *fA, *mA1, *mA2, *hA0, *hA1, *eA1, *fA1, *hA2, *eA2, *fA2; // hA0保存上上个col的H，其他的保存上个H E F M
int16_t *seq, *ref;
uint8_t *mem;
int16_t *qtmem, *vmem;
int seq_size = qlen + SIMD_WIDTH, ref_size = tlen + SIMD_WIDTH;
int i, iStart, D, j, k, beg, end, max, max_i, max_j, max_ins, max_del, max_ie, gscore, max_off;
int i, iStart, D, j, beg, end, max, max_i, max_j, max_ins, max_del, max_ie, gscore, max_off;
int Dloop = tlen + qlen; // 循环跳出条件
int span, beg1, end1; // 边界条件计算
int col_size = qlen + 2 + SIMD_WIDTH;
@ -208,14 +204,15 @@ int ksw_avx2(int qlen, // query length 待匹配段碱基的query
SIMD_INIT; // 初始化simd用的数据
assert(h0 > 0);
assert(init_score > 0);
// allocate memory
mem = malloc(mem_size);
// mem = malloc(mem_size);
mem = thread_mem_request(tmem, mem_size);
qtmem = (int16_t *)&mem[0];
seq = &qtmem[0];
ref = &qtmem[seq_size];
if (is_left)
if (extend_left)
{
for (i = 0; i < qlen; ++i)
seq[i] = query[qlen - 1 - i];
@ -250,39 +247,37 @@ int ksw_avx2(int qlen, // query length 待匹配段碱基的query
fA1 = &fA[0];
fA2 = &fA[col_size];
// adjust $w if it is too large
k = m * m;
// adjust $window_size if it is too large
// get the max score
for (i = 0, max = 0; i < k; ++i)
max = max > mat[i] ? max : mat[i];
max = base_match_score;
max_ins = (int)((double)(qlen * max + end_bonus - o_ins) / e_ins + 1.);
max_ins = max_ins > 1 ? max_ins : 1;
w = w < max_ins ? w : max_ins;
window_size = window_size < max_ins ? window_size : max_ins;
max_del = (int)((double)(qlen * max + end_bonus - o_del) / e_del + 1.);
max_del = max_del > 1 ? max_del : 1;
w = w < max_del ? w : max_del; // TODO: is this necessary?
window_size = window_size < max_del ? window_size : max_del; // TODO: is this necessary?
if (tlen < qlen)
w = MIN(tlen - 1, w);
window_size = MIN(tlen - 1, window_size);
// DP loop
max = h0, max_i = max_j = -1;
max = init_score, max_i = max_j = -1;
max_ie = -1, gscore = -1;
;
max_off = 0;
beg = 1;
end = qlen;
// init h0
hA0[0] = h0; // 左上角
// init init_score
hA0[0] = init_score; // 左上角
if (qlen == 0 || tlen == 0)
Dloop = 0; // 防止意外情况
if (w >= qlen)
if (window_size >= qlen)
{
max_ie = 0;
gscore = 0;
}
int m_last = 0;
int iend;
for (D = 1; LIKELY(D < Dloop); ++D)
@ -290,13 +285,13 @@ int ksw_avx2(int qlen, // query length 待匹配段碱基的query
// 边界条件一定要注意！ tlen 大于，等于，小于 qlen时的情况
if (D > tlen)
{
span = MIN(Dloop - D, w);
beg1 = MAX(D - tlen + 1, ((D - w) / 2) + 1);
span = MIN(Dloop - D, window_size);
beg1 = MAX(D - tlen + 1, ((D - window_size) / 2) + 1);
}
else
{
span = MIN(D - 1, w);
beg1 = MAX(1, ((D - w) / 2) + 1);
span = MIN(D - 1, window_size);
beg1 = MAX(1, ((D - window_size) / 2) + 1);
}
end1 = MIN(qlen, beg1 + span);
@ -321,12 +316,12 @@ int ksw_avx2(int qlen, // query length 待匹配段碱基的query
// 左边界 处理f (insert)
if (iStart == 0)
{
hA1[end] = MAX(0, h0 - (o_ins + e_ins * end));
hA1[end] = MAX(0, init_score - (o_ins + e_ins * end));
}
// 上边界
if (beg == 1)
{
hA1[0] = MAX(0, h0 - (o_del + e_del * iend));
hA1[0] = MAX(0, init_score - (o_del + e_del * iend));
}
else
{
@ -370,26 +365,12 @@ int ksw_avx2(int qlen, // query length 待匹配段碱基的query
max_ie = gscore > hA2[qlen] ? max_ie : iStart;
gscore = gscore > hA2[qlen] ? gscore : hA2[qlen];
}
// if (m == 0 && m_last == 0)
// break; // 一定要注意，斜对角遍历和按列遍历的不同点
if (m > max)
{
max = m, max_i = mi, max_j = mj;
max_off = max_off > abs(mj - mi) ? max_off : abs(mj - mi);
}
else if (0) //(zdrop > 0)
{
if (mi - max_i > mj - max_j)
{
if (max - m - ((mi - max_i) - (mj - max_j)) * e_del > zdrop)
break;
}
else
{
if (max - m - ((mj - max_j) - (mi - max_i)) * e_ins > zdrop)
break;
}
}
// 调整计算的边界
/*for (j = beg; LIKELY(j <= end); ++j)
@ -411,12 +392,12 @@ int ksw_avx2(int qlen, // query length 待匹配段碱基的query
// beg = 0;
// end = qlen; // uncomment this line for debugging
*/
m_last = m;
// swap m, h, e, f
SWAP_DATA_POINTER;
}
free(mem);
// free(mem);
thread_mem_release(tmem, mem_size);
if (_qle)
*_qle = max_j + 1;
if (_tle)
@ -428,182 +409,4 @@ int ksw_avx2(int qlen, // query length 待匹配段碱基的query
if (_max_off)
*_max_off = max_off;
return max;
}
typedef struct
{
int32_t h, e;
} eh_t;
int ksw_extend2_origin(int qlen, // query length 待匹配段碱基的query长度
const uint8_t *query, // read碱基序列
int tlen, // target length reference的长度
const uint8_t *target, // reference序列
int is_left, // 是不是向左扩展
int m, // 碱基种类 (5)
const int8_t *mat, // 每个位置的query和target的匹配得分 m*m
int o_del, // deletion 错配开始的惩罚系数
int e_del, // deletion extension的惩罚系数
int o_ins, // insertion 错配开始的惩罚系数
int e_ins, // insertion extension的惩罚系数
int w, // 提前剪枝系数，w =100 匹配位置和beg的最大距离
int end_bonus,
int zdrop,
int h0, // 该seed的初始得分（完全匹配query的碱基数）
int *_qle, // 匹配得到全局最大得分的碱基在query的位置
int *_tle, // 匹配得到全局最大得分的碱基在reference的位置
int *_gtle, // query全部匹配上的target的长度
int *_gscore, // query的端到端匹配得分
int *_max_off) // 取得最大得分时在query和reference上位置差的 最大值
{
eh_t *eh; // score array
int8_t *qp; // query profile
int i, j, k, oe_del = o_del + e_del, oe_ins = o_ins + e_ins, beg, end, max, max_i, max_j, max_ins, max_del, max_ie, gscore, max_off;
uint8_t *qmem, *ref, *seq;
assert(h0 > 0);
// allocate memory
qp = malloc(qlen * m);
eh = calloc(qlen + 1, 8);
qmem = malloc(qlen + tlen);
seq = (uint8_t *)&qmem[0];
ref = (uint8_t *)&qmem[qlen];
if (is_left)
{
for (i = 0; i < qlen; ++i)
seq[i] = query[qlen - 1 - i];
for (i = 0; i < tlen; ++i)
ref[i] = target[tlen - 1 - i];
}
else
{
for (i = 0; i < qlen; ++i)
seq[i] = query[i];
for (i = 0; i < tlen; ++i)
ref[i] = target[i];
}
// generate the query profile
for (k = i = 0; k < m; ++k)
{
const int8_t *p = &mat[k * m];
for (j = 0; j < qlen; ++j)
qp[i++] = p[seq[j]];
}
// fill the first row
eh[0].h = h0;
eh[1].h = h0 > oe_ins ? h0 - oe_ins : 0;
for (j = 2; j <= qlen && eh[j - 1].h > e_ins; ++j)
eh[j].h = eh[j - 1].h - e_ins;
// adjust $w if it is too large
k = m * m;
for (i = 0, max = 0; i < k; ++i) // get the max score
max = max > mat[i] ? max : mat[i];
max_ins = (int)((double)(qlen * max + end_bonus - o_ins) / e_ins + 1.);
max_ins = max_ins > 1 ? max_ins : 1;
w = w < max_ins ? w : max_ins;
max_del = (int)((double)(qlen * max + end_bonus - o_del) / e_del + 1.);
max_del = max_del > 1 ? max_del : 1;
w = w < max_del ? w : max_del; // TODO: is this necessary?
// printf("%d\n", w);
// DP loop
max = h0, max_i = max_j = -1;
max_ie = -1, gscore = -1;
max_off = 0;
beg = 0, end = qlen;
for (i = 0; LIKELY(i < tlen); ++i)
{
int t, f = 0, h1, m = 0, mj = -1;
int8_t *q = &qp[ref[i] * qlen];
// apply the band and the constraint (if provided)
if (beg < i - w)
beg = i - w;
if (end > i + w + 1)
end = i + w + 1;
// if (end > qlen) end = qlen; 没用
// compute the first column
if (beg == 0)
{
h1 = h0 - (o_del + e_del * (i + 1));
if (h1 < 0)
h1 = 0;
}
else
h1 = 0;
for (j = beg; LIKELY(j < end); ++j)
{
// At the beginning of the loop: eh[j] = { H(i-1,j-1), E(i,j) }, f = F(i,j) and h1 = H(i,j-1)
// Similar to SSE2-SW, cells are computed in the following order:
// H(i,j) = max{H(i-1,j-1)+S(i,j), E(i,j), F(i,j)}
// E(i+1,j) = max{H(i,j)-gapo, E(i,j)} - gape
// F(i,j+1) = max{H(i,j)-gapo, F(i,j)} - gape
eh_t *p = &eh[j];
int h, M = p->h, e = p->e; // get H(i-1,j-1) and E(i-1,j)
p->h = h1; // set H(i,j-1) for the next row
M = M ? M + q[j] : 0; // separating H and M to disallow a cigar like "100M3I3D20M"
h = M > e ? M : e; // e and f are guaranteed to be non-negative, so h>=0 even if M<0
h = h > f ? h : f;
h1 = h; // save H(i,j) to h1 for the next column
mj = m > h ? mj : j; // record the position where max score is achieved
m = m > h ? m : h; // m is stored at eh[mj+1]
t = M - oe_del;
t = t > 0 ? t : 0;
e -= e_del;
e = e > t ? e : t; // computed E(i+1,j)
p->e = e; // save E(i+1,j) for the next row
t = M - oe_ins;
t = t > 0 ? t : 0;
f -= e_ins;
f = f > t ? f : t; // computed F(i,j+1)
}
eh[end].h = h1;
eh[end].e = 0;
if (j == qlen)
{
max_ie = gscore > h1 ? max_ie : i;
gscore = gscore > h1 ? gscore : h1;
}
if (m == 0)
break;
if (m > max)
{
max = m, max_i = i, max_j = mj;
max_off = max_off > abs(mj - i) ? max_off : abs(mj - i);
}
else if (zdrop > 0)
{
if (i - max_i > mj - max_j)
{
if (max - m - ((i - max_i) - (mj - max_j)) * e_del > zdrop)
break;
}
else
{
if (max - m - ((mj - max_j) - (i - max_i)) * e_ins > zdrop)
break;
}
}
// update beg and end for the next round
for (j = beg; LIKELY(j < end) && eh[j].h == 0 && eh[j].e == 0; ++j)
;
beg = j;
for (j = end; LIKELY(j >= beg) && eh[j].h == 0 && eh[j].e == 0; --j)
;
end = j + 2 < qlen ? j + 2 : qlen;
// beg = 0; end = qlen; // uncomment this line for debugging
}
free(eh);
free(qp);
free(qmem);
if (_qle)
*_qle = max_j + 1;
if (_tle)
*_tle = max_i + 1;
if (_gtle)
*_gtle = max_ie + 1;
if (_gscore)
*_gscore = gscore;
if (_max_off)
*_max_off = max_off;
return max;
}
}

86
ksw_avx2_aligned.c → ksw_ext_avx2_aligned.c
View File

@ -198,28 +198,26 @@ static const uint16_t h_vec_int_mask[SIMD_WIDTH][SIMD_WIDTH] = {
cur_match_arr = next_match_arr; \
next_match_arr = tmp;
// uint8_t mem_addr[102400];
int ksw_avx2_aligned(thread_mem_t *tmem,
int qlen, // query length 待匹配段碱基的query长度
const uint8_t *query, // read碱基序列
int tlen, // target length reference的长度
const uint8_t *target, // reference序列
int extend_left, // 是不是向左扩展
int o_del, // deletion 错配开始的惩罚系数
int e_del, // deletion extension的惩罚系数
int o_ins, // insertion 错配开始的惩罚系数
int e_ins, // insertion extension的惩罚系数SIMD_BTYES
int base_match_score, // 碱基match时的分数
int base_mis_score, // 碱基mismatch时的惩罚分数（正数）
int window_size, // 提前剪枝系数，w =100 匹配位置和beg的最大距离
int end_bonus, // 如果query比对到了最后一个字符，额外奖励分值
int init_score, // 该seed的初始得分（完全匹配query的碱基数）
int *_qle, // 匹配得到全局最大得分的碱基在query的位置
int *_tle, // 匹配得到全局最大得分的碱基在reference的位置
int *_gtle, // query全部匹配上的target的长度
int *_gscore, // query的端到端匹配得分
int *_max_off) // 取得最大得分时在query和reference上位置差的 最大值
int ksw_extend_avx2_aligned(thread_mem_t *tmem,
int qlen, // query length 待匹配段碱基的query长度
const uint8_t *query, // read碱基序列
int tlen, // target length reference的长度
const uint8_t *target, // reference序列
int extend_left, // 是不是向左扩展
int o_del, // deletion 错配开始的惩罚系数
int e_del, // deletion extension的惩罚系数
int o_ins, // insertion 错配开始的惩罚系数
int e_ins, // insertion extension的惩罚系数SIMD_BTYES
int base_match_score, // 碱基match时的分数
int base_mis_score, // 碱基mismatch时的惩罚分数（正数）
int window_size, // 提前剪枝系数，w =100 匹配位置和beg的最大距离
int end_bonus, // 如果query比对到了最后一个字符，额外奖励分值
int init_score, // 该seed的初始得分（完全匹配query的碱基数）
int *_qle, // 匹配得到全局最大得分的碱基在query的位置
int *_tle, // 匹配得到全局最大得分的碱基在reference的位置
int *_gtle, // query全部匹配上的target的长度
int *_gscore, // query的端到端匹配得分
int *_max_off) // 取得最大得分时在query和reference上位置差的 最大值
{
int16_t *cur_match_arr, *next_match_arr,
*last_max_arr, *cur_max_arr, *next_max_arr,
@ -333,8 +331,8 @@ int ksw_avx2_aligned(thread_mem_t *tmem,
if (read_start_pos > read_end_pos)
break; // 不用计算了，直接跳出，否则hA2没有被赋值，里边是上一轮hA0的值，会出bug
// read_start_pos = 1;
// read_end_pos = qlen;
read_start_pos = 1;
read_end_pos = qlen;
ref_end_pos = di - (read_start_pos - 1); // ref开始计算的位置，倒序
span = read_end_pos - read_start_pos;
ref_start_pos = ref_end_pos - span - 1; // 0开始的ref索引位置
@ -411,26 +409,26 @@ int ksw_avx2_aligned(thread_mem_t *tmem,
}
// 调整计算的边界
for (j = read_start_pos; LIKELY(j <= read_end_pos); ++j)
{
int has_val = cur_max_arr[j - 1] | next_max_arr[j];
if (has_val)
{
break;
}
}
read_start_pos = j;
next_max_arr[read_end_pos + 1] = 0;
for (j = read_end_pos + 1; LIKELY(j >= read_start_pos); --j)
{
int has_val = cur_max_arr[j - 1] | next_max_arr[j];
if (has_val)
{
break;
}
}
read_end_pos = j + 1 <= qlen ? j + 1 : qlen;
// for (j = read_start_pos; LIKELY(j <= read_end_pos); ++j)
//{
// int has_val = cur_max_arr[j - 1] | next_max_arr[j];
// if (has_val)
// {
// break;
// }
//}
// read_start_pos = j;
//
// next_max_arr[read_end_pos + 1] = 0;
// for (j = read_end_pos + 1; LIKELY(j >= read_start_pos); --j)
//{
// int has_val = cur_max_arr[j - 1] | next_max_arr[j];
// if (has_val)
// {
// break;
// }
//}
// read_end_pos = j + 1 <= qlen ? j + 1 : qlen;
// swap m, h, e, f
SWAP_DATA_POINTER;
}

197
bsw_avx2.c → ksw_ext_avx2_heuristics.c
View File

@ -5,6 +5,7 @@
#include <stdio.h>
#include <immintrin.h>
#include <emmintrin.h>
#include "thread_mem.h"
#ifdef __GNUC__
#define LIKELY(x) __builtin_expect((x), 1)
@ -119,16 +120,6 @@ static const uint16_t h_vec_int_mask[SIMD_WIDTH][SIMD_WIDTH] = {
hn_vec = _mm256_max_epi16(hn_vec, zero_vec);
// 存储向量化结果
// #define SIMD_STORE
// __m256i cur_max_vec = _mm256_max_epu8(max_vec, hn_vec); \
// __m256i vcmp = _mm256_cmpgt_epi8(cur_max_vec, max_vec); \
// uint32_t mask = _mm256_movemask_epi8(vcmp); \
// if (mask > 0) \
// { \
// simd_i = i; \
// simd_j = j; \
// }
#define SIMD_STORE \
max_vec = _mm256_max_epu8(max_vec, hn_vec); \
_mm256_storeu_si256((__m256i *)&next_del_arr[j], en_vec); \
@ -199,45 +190,45 @@ static const uint16_t h_vec_int_mask[SIMD_WIDTH][SIMD_WIDTH] = {
cur_match_arr = next_match_arr; \
next_match_arr = tmp;
uint8_t mem[102400];
// uint8_t mem[102400];
int bsw_avx2(int qlen, // query length 待匹配段碱基的query长度
const uint8_t *query, // read碱基序列
int tlen, // target length reference的长度
const uint8_t *target, // reference序列
int extend_left, // 是不是向左扩展
int o_del, // deletion 错配开始的惩罚系数
int e_del, // deletion extension的惩罚系数
int o_ins, // insertion 错配开始的惩罚系数
int e_ins, // insertion extension的惩罚系数SIMD_BTYES
int base_match_score, // 碱基match时的分数
int base_mis_score, // 碱基mismatch时的惩罚分数（正数）
int window_size, // 提前剪枝系数，w =100 匹配位置和beg的最大距离
int end_bonus, // 如果query比对到了最后一个字符，额外奖励分值
int init_score, // 该seed的初始得分（完全匹配query的碱基数）
int *_qle, // 匹配得到全局最大得分的碱基在query的位置
int *_tle, // 匹配得到全局最大得分的碱基在reference的位置
int *_gtle, // query全部匹配上的target的长度
int *_gscore, // query的端到端匹配得分
int *_max_off) // 取得最大得分时在query和reference上位置差的 最大值
int ksw_extend_avx2_heuristics(thread_mem_t *tmem,
int qlen, // query length 待匹配段碱基的query长度
const uint8_t *query, // read碱基序列
int tlen, // target length reference的长度
const uint8_t *target, // reference序列
int extend_left, // 是不是向左扩展
int o_del, // deletion 错配开始的惩罚系数
int e_del, // deletion extension的惩罚系数
int o_ins, // insertion 错配开始的惩罚系数
int e_ins, // insertion extension的惩罚系数SIMD_BTYES
int base_match_score, // 碱基match时的分数
int base_mis_score, // 碱基mismatch时的惩罚分数（正数）
int window_size, // 提前剪枝系数，w =100 匹配位置和beg的最大距离
int end_bonus, // 如果query比对到了最后一个字符，额外奖励分值
int init_score, // 该seed的初始得分（完全匹配query的碱基数）
int *_qle, // 匹配得到全局最大得分的碱基在query的位置
int *_tle, // 匹配得到全局最大得分的碱基在reference的位置
int *_gtle, // query全部匹配上的target的长度
int *_gscore, // query的端到端匹配得分
int *_max_off) // 取得最大得分时在query和reference上位置差的 最大值
{
return 0;
// return 0;
int16_t *mA, *eA, *hA, *fA,
*cur_match_arr, *next_match_arr,
*last_max_arr, *cur_max_arr, *next_max_arr,
*cur_del_arr, *next_del_arr,
*cur_ins_arr, *next_ins_arr; // hA0保存上上个col的H，其他的保存上个H E F M
int16_t *seq, *ref;
// uint8_t *mem;
uint8_t *mem;
int16_t *qtmem, *vmem;
int seq_size = qlen + SIMD_WIDTH, ref_size = tlen + SIMD_WIDTH;
int i, iStart, D, j, k, beg, end, max, max_i, max_j, max_ins, max_del, max_ie, gscore, max_off;
int i, iStart, D, j, beg, end, max, max_i, max_j, max_ins, max_del, max_ie, gscore, max_off;
int Dloop = tlen + qlen; // 循环跳出条件 D从1开始遍历
int span, beg1, end1; // 边界条件计算
int col_size = qlen + 2 + SIMD_WIDTH;
int val_mem_size = (col_size * 9 * 2 + 31) >> 5 << 5; // 32字节的整数倍
int mem_size = (seq_size + ref_size) * 2 + val_mem_size;
int simd_i = -1, simd_j = -1;
SIMD_INIT; // 初始化simd用的数据
@ -245,6 +236,7 @@ int bsw_avx2(int qlen, // query length 待匹配段碱基的query
// allocate memory
// mem = malloc(mem_size);
mem = thread_mem_request(tmem, mem_size);
qtmem = (int16_t *)&mem[0];
seq = &qtmem[0];
ref = &qtmem[seq_size];
@ -313,7 +305,6 @@ int bsw_avx2(int qlen, // query length 待匹配段碱基的query
gscore = 0;
}
int m_last = 0;
int iend;
for (D = 1; LIKELY(D < Dloop); ++D)
@ -331,8 +322,8 @@ int bsw_avx2(int qlen, // query length 待匹配段碱基的query
}
end1 = MIN(qlen, beg1 + span);
// beg = 1;
// end = qlen;
beg = 1;
end = qlen;
if (beg < beg1)
beg = beg1;
@ -402,134 +393,38 @@ int bsw_avx2(int qlen, // query length 待匹配段碱基的query
max_ie = gscore > next_max_arr[qlen] ? max_ie : iStart;
gscore = gscore > next_max_arr[qlen] ? gscore : next_max_arr[qlen];
}
// if (m == 0 && m_last == 0)
// break; // 一定要注意，斜对角遍历和按列遍历的不同点
if (m > max)
{
max = m, max_i = mi, max_j = mj;
max_off = max_off > abs(mj - mi) ? max_off : abs(mj - mi);
}
// 调整计算的边界
// fprintf(stderr, "beg: %d, end: %d ", beg, end);
/* for (j = beg; j <= end; j += SIMD_WIDTH)
{
__m256i h1 = _mm256_loadu_si256((__m256i *)(&cur_max_arr[j - 1]));
__m256i h2 = _mm256_loadu_si256((__m256i *)(&next_max_arr[j]));
__m256i orvec = _mm256_or_si256(h1, h2);
__m256i vcmp = _mm256_cmpgt_epi16(orvec, zero_vec);
uint32_t mask = _mm256_movemask_epi8(vcmp);
if (mask > 0)
{
// vcmp = _mm256_permute4x64_epi64(vcmp, permute_mask);
// vcmp = _mm256_shufflelo_epi16(vcmp, permute_mask);
// vcmp = _mm256_shufflehi_epi16(vcmp, permute_mask);
// mask = _mm256_movemask_epi8(vcmp);
//// int pos = SIMD_WIDTH - 1 - ((__builtin_clz(mask)) >> 1);
// int pos = ((__builtin_clz(mask)) >> 1);
// beg = j + pos;
int pos = __builtin_ctz(mask) >> 1;
beg = j + pos;
// if (beg > end)
// beg = end;
// beg = j + pos;
// beg = 0;
break;
}
}
*/
// beg = 0;
// fprintf(stderr, "new beg: %d\n", beg);
// int pos = 0;
// for (j = beg; j <= end; j += SIMD_WIDTH)
// for (j = beg; LIKELY(j <= end); ++j)
//{
// __m256i h1 = _mm256_loadu_si256((__m256i *)(&cur_max_arr[j - 1]));
// __m256i h2 = _mm256_loadu_si256((__m256i *)(&next_max_arr[j]));
// __m256i orvec = _mm256_or_si256(h1, h2);
// int *val = (int *)&orvec;
// for (i = 0; i < SIMD_WIDTH; ++i)
// if (val[i])
// {
// pos = SIMD_WIDTH - 1 - i;
// break;
// }
//}
// int has_val = cur_max_arr[j - 1] | next_max_arr[j];
// if (has_val)
// {
// break;
// }
// }
// beg = j;
for (j = beg; LIKELY(j <= end); ++j)
{
int has_val = cur_max_arr[j - 1] | next_max_arr[j];
if (has_val)
{
break;
}
}
beg = j;
// next_max_arr[end + 1] = 0;
// for (j = end + 1; LIKELY(j >= beg); --j)
//{
// int has_val = cur_max_arr[j - 1] | next_max_arr[j];
// if (has_val)
// {
// break;
// }
// }
// end = j + 1 <= qlen ? j + 1 : qlen;
next_max_arr[end + 1] = 0;
for (j = end + 1; LIKELY(j >= beg); --j)
{
int has_val = cur_max_arr[j - 1] | next_max_arr[j];
if (has_val)
{
break;
}
// else
// last_max_arr[j - 1] = 0;
}
end = j + 1 <= qlen ? j + 1 : qlen;
/* for (j = end + 1; j >= beg; j -= SIMD_WIDTH) // 没有考虑beg附近，且长度小于SIMD_WIDTH的数据
{
__m256i h1 = _mm256_loadu_si256((__m256i *)(&cur_max_arr[j - 1]));
__m256i h2 = _mm256_loadu_si256((__m256i *)(&next_max_arr[j]));
__m256i orvec = _mm256_or_si256(h1, h2);
__m256i vcmp = _mm256_cmpgt_epi16(orvec, zero_vec);
uint32_t mask = _mm256_movemask_epi8(vcmp);
if (mask > 0)
{
int pos = __builtin_clz(mask) >> 1;
const int new_end = j + SIMD_WIDTH - pos;
end = new_end <= qlen ? new_end : qlen;
break;
}
else
{
_mm256_storeu_si256((__m256i *)&last_max_arr[j - 1], zero_vec);
}
}
*/
// beg = 0;
// end = qlen; // uncomment this line for debugging
m_last = m;
// swap m, h, e, f
SWAP_DATA_POINTER;
}
// __m256i origin_max_vec = max_vec;
// max_vec = _mm256_max_epu16(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 2));
// max_vec = _mm256_max_epu16(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 4));
// max_vec = _mm256_max_epu16(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 6));
// max_vec = _mm256_max_epu16(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 8));
// max_vec = _mm256_max_epu16(max_vec, _mm256_permute2x128_si256(max_vec, max_vec, 0x01));
// int16_t *maxVal = (int16_t *)&max_vec;
// max = maxVal[0];
// if (max > 0)
// {
// __m256i vcmp = _mm256_cmpeq_epi16(origin_max_vec, max_vec);
// uint32_t mask = _mm256_movemask_epi8(vcmp);
// if (mask > 0)
// {
// int pos = SIMD_WIDTH - 1 - ((__builtin_clz(mask)) >> 1);
// int mj = simd_j - 1 + pos;
// int mi = simd_i - 1 - pos;
// max_i = mi, max_j = mj;
// max_off = max_off > abs(mj - mi) ? max_off : abs(mj - mi);
// }
// }
// free(mem);
thread_mem_release(tmem, mem_size);
if (_qle)
*_qle = max_j + 1;
if (_tle)

434
ksw_ext_avx2_u8.c 100644
View File

@ -0,0 +1,434 @@
#include <stdlib.h>
#include <stdint.h>
#include <assert.h>
#include <emmintrin.h>
#include <stdio.h>
#include <immintrin.h>
#include <emmintrin.h>
#include "thread_mem.h"
#ifdef __GNUC__
#define LIKELY(x) __builtin_expect((x), 1)
#define UNLIKELY(x) __builtin_expect((x), 0)
#else
#define LIKELY(x) (x)
#define UNLIKELY(x) (x)
#endif
#undef MAX
#undef MIN
#define MAX(x, y) ((x) > (y) ? (x) : (y))
#define MIN(x, y) ((x) < (y) ? (x) : (y))
#define SIMD_WIDTH 32
static const uint8_t h_vec_int_mask[SIMD_WIDTH][SIMD_WIDTH] = {
{0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff}};
// static const uint8_t reverse_mask[SIMD_WIDTH] = {1, 0, 3, 2, 5, 4, 7, 6, 9, 8, 11, 10, 13, 12, 15, 14, 1, 0, 3, 2, 5, 4, 7, 6, 9, 8, 11, 10, 13, 12, 15, 14};
static const uint8_t reverse_mask[SIMD_WIDTH] = {7, 6, 5, 4, 3, 2, 1, 0, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 0, 15, 14, 13, 12, 11, 10, 9, 8};
// const int permute_mask = _MM_SHUFFLE(0, 1, 2, 3);
#define permute_mask _MM_SHUFFLE(0, 1, 2, 3)
// 初始化变量
#define SIMD_INIT \
int oe_del = o_del + e_del, oe_ins = o_ins + e_ins; \
__m256i zero_vec; \
__m256i max_vec; \
__m256i oe_del_vec; \
__m256i oe_ins_vec; \
__m256i e_del_vec; \
__m256i e_ins_vec; \
__m256i h_vec_mask[SIMD_WIDTH]; \
__m256i reverse_mask_vec; \
zero_vec = _mm256_setzero_si256(); \
oe_del_vec = _mm256_set1_epi8(oe_del); \
oe_ins_vec = _mm256_set1_epi8(oe_ins); \
e_del_vec = _mm256_set1_epi8(e_del); \
e_ins_vec = _mm256_set1_epi8(e_ins); \
__m256i match_sc_vec = _mm256_set1_epi8(base_match_score); \
__m256i mis_sc_vec = _mm256_set1_epi8(base_mis_score); \
__m256i amb_sc_vec = _mm256_set1_epi8(1); \
__m256i amb_vec = _mm256_set1_epi8(4); \
reverse_mask_vec = _mm256_loadu_si256((__m256i *)(reverse_mask)); \
for (i = 0; i < SIMD_WIDTH; ++i) \
h_vec_mask[i] = _mm256_loadu_si256((__m256i *)(&h_vec_int_mask[i]));
/*
* e 表示当前ref的碱基被删除
* f 表示当前seq的碱基插入
* m 表示当前碱基匹配（可以相等，也可以不想等）
* h 表示最大值
*/
// load向量化数据
#define SIMD_LOAD \
__m256i m1 = _mm256_loadu_si256((__m256i *)(&mA1[j])); \
__m256i e1 = _mm256_loadu_si256((__m256i *)(&eA1[j])); \
__m256i m1j1 = _mm256_loadu_si256((__m256i *)(&mA1[j - 1])); \
__m256i f1j1 = _mm256_loadu_si256((__m256i *)(&fA1[j - 1])); \
__m256i h0j1 = _mm256_loadu_si256((__m256i *)(&hA0[j - 1])); \
__m256i qs_vec = _mm256_loadu_si256((__m256i *)(&seq[j - 1])); \
__m256i ts_vec = _mm256_loadu_si256((__m256i *)(&ref[i]));
// 比对ref和seq的序列，计算罚分
#define SIMD_CMP_SEQ \
ts_vec = _mm256_permute4x64_epi64(ts_vec, permute_mask); \
ts_vec = _mm256_shuffle_epi8(ts_vec, reverse_mask_vec); \
__m256i match_mask_vec = _mm256_cmpeq_epi8(qs_vec, ts_vec); \
__m256i mis_score_vec = _mm256_andnot_si256(match_mask_vec, mis_sc_vec); \
__m256i match_score_vec = _mm256_and_si256(match_sc_vec, match_mask_vec); \
__m256i q_amb_mask_vec = _mm256_cmpeq_epi8(qs_vec, amb_vec); \
__m256i t_amb_mask_vec = _mm256_cmpeq_epi8(ts_vec, amb_vec); \
__m256i amb_mask_vec = _mm256_or_si256(q_amb_mask_vec, t_amb_mask_vec); \
__m256i amb_score_vec = _mm256_and_si256(amb_mask_vec, amb_sc_vec); \
mis_score_vec = _mm256_andnot_si256(amb_mask_vec, mis_score_vec); \
mis_score_vec = _mm256_or_si256(amb_score_vec, mis_score_vec); \
match_score_vec = _mm256_andnot_si256(amb_mask_vec, match_score_vec);
// 向量化计算h, e, f, m
#define SIMD_COMPUTE \
__m256i en_vec0 = _mm256_max_epu8(m1, oe_del_vec); \
en_vec0 = _mm256_subs_epu8(en_vec0, oe_del_vec); \
__m256i en_vec1 = _mm256_max_epu8(e1, e_del_vec); \
en_vec1 = _mm256_subs_epu8(en_vec1, e_del_vec); \
__m256i en_vec = _mm256_max_epu8(en_vec0, en_vec1); \
__m256i fn_vec0 = _mm256_max_epu8(m1j1, oe_ins_vec); \
fn_vec0 = _mm256_subs_epu8(fn_vec0, oe_ins_vec); \
__m256i fn_vec1 = _mm256_max_epu8(f1j1, e_ins_vec); \
fn_vec1 = _mm256_subs_epu8(fn_vec1, e_ins_vec); \
__m256i fn_vec = _mm256_max_epu8(fn_vec0, fn_vec1); \
__m256i mn_vec0 = _mm256_adds_epu8(h0j1, match_score_vec); \
mn_vec0 = _mm256_max_epu8(mn_vec0, mis_score_vec); \
mn_vec0 = _mm256_subs_epu8(mn_vec0, mis_score_vec); \
__m256i mn_mask = _mm256_cmpeq_epi8(h0j1, zero_vec); \
__m256i mn_vec = _mm256_andnot_si256(mn_mask, mn_vec0); \
__m256i hn_vec0 = _mm256_max_epu8(en_vec, fn_vec); \
__m256i hn_vec = _mm256_max_epu8(hn_vec0, mn_vec);
// 存储向量化结果
#define SIMD_STORE \
max_vec = _mm256_max_epu8(max_vec, hn_vec); \
_mm256_storeu_si256((__m256i *)&eA2[j], en_vec); \
_mm256_storeu_si256((__m256i *)&fA2[j], fn_vec); \
_mm256_storeu_si256((__m256i *)&mA2[j], mn_vec); \
_mm256_storeu_si256((__m256i *)&hA2[j], hn_vec);
// 去除多余的部分
#define SIMD_REMOVE_EXTRA \
en_vec = _mm256_and_si256(en_vec, h_vec_mask[end - j]); \
fn_vec = _mm256_and_si256(fn_vec, h_vec_mask[end - j]); \
mn_vec = _mm256_and_si256(mn_vec, h_vec_mask[end - j]); \
hn_vec = _mm256_and_si256(hn_vec, h_vec_mask[end - j]);
// 找最大值和位置
#define SIMD_FIND_MAX \
uint8_t *maxVal = (uint8_t *)&max_vec; \
max_vec = _mm256_max_epu8(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 1)); \
max_vec = _mm256_max_epu8(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 2)); \
max_vec = _mm256_max_epu8(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 3)); \
max_vec = _mm256_max_epu8(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 4)); \
max_vec = _mm256_max_epu8(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 5)); \
max_vec = _mm256_max_epu8(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 6)); \
max_vec = _mm256_max_epu8(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 7)); \
max_vec = _mm256_max_epu8(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 8)); \
max_vec = _mm256_max_epu8(max_vec, _mm256_permute2x128_si256(max_vec, max_vec, 0x01)); \
m = maxVal[0]; \
if (m > 0) \
{ \
for (j = beg, i = iend; j <= end; j += SIMD_WIDTH, i -= SIMD_WIDTH) \
{ \
__m256i h2_vec = _mm256_loadu_si256((__m256i *)(&hA2[j])); \
__m256i vcmp = _mm256_cmpeq_epi8(h2_vec, max_vec); \
uint32_t mask = _mm256_movemask_epi8(vcmp); \
if (mask > 0) \
{ \
int pos = SIMD_WIDTH - 1 - __builtin_clz(mask); \
mj = j - 1 + pos; \
mi = i - 1 - pos; \
} \
} \
}
// 每轮迭代后，交换数组
#define SWAP_DATA_POINTER \
uint8_t *tmp = hA0; \
hA0 = hA1; \
hA1 = hA2; \
hA2 = tmp; \
tmp = eA1; \
eA1 = eA2; \
eA2 = tmp; \
tmp = fA1; \
fA1 = fA2; \
fA2 = tmp; \
tmp = mA1; \
mA1 = mA2; \
mA2 = tmp;
int ksw_extend_avx2_u8(thread_mem_t *tmem,
int qlen, // query length 待匹配段碱基的query长度
const uint8_t *query, // read碱基序列
int tlen, // target length reference的长度
const uint8_t *target, // reference序列
int extend_left, // 是不是向左扩展
int o_del, // deletion 错配开始的惩罚系数
int e_del, // deletion extension的惩罚系数
int o_ins, // insertion 错配开始的惩罚系数
int e_ins, // insertion extension的惩罚系数SIMD_BTYES
int base_match_score, // 碱基match时的分数
int base_mis_score, // 碱基mismatch时的惩罚分数（正数）
int window_size, // 提前剪枝系数，w =100 匹配位置和beg的最大距离
int end_bonus, // 如果query比对到了最后一个字符，额外奖励分值
int init_score, // 该seed的初始得分（完全匹配query的碱基数）
int *_qle, // 匹配得到全局最大得分的碱基在query的位置
int *_tle, // 匹配得到全局最大得分的碱基在reference的位置
int *_gtle, // query全部匹配上的target的长度
int *_gscore, // query的端到端匹配得分
int *_max_off) // 取得最大得分时在query和reference上位置差的 最大值
{
uint8_t *mA, *hA, *eA, *fA, *mA1, *mA2, *hA0, *hA1, *eA1, *fA1, *hA2, *eA2, *fA2; // hA0保存上上个col的H，其他的保存上个H E F M
uint8_t *seq, *ref;
uint8_t *mem, *qtmem, *vmem;
int seq_size = qlen + SIMD_WIDTH, ref_size = tlen + SIMD_WIDTH;
int i, iStart, D, j, beg, end, max, max_i, max_j, max_ins, max_del, max_ie, gscore, max_off;
int Dloop = tlen + qlen; // 循环跳出条件
int span, beg1, end1; // 边界条件计算
int col_size = qlen + 2 + SIMD_WIDTH;
int val_mem_size = (col_size * 9 + 31) >> 5 << 5; // 32字节的整数倍
int mem_size = seq_size + ref_size + val_mem_size;
SIMD_INIT; // 初始化simd用的数据
assert(init_score > 0);
// allocate memory
// mem = malloc(mem_size);
mem = thread_mem_request(tmem, mem_size);
qtmem = &mem[0];
seq = (uint8_t *)&qtmem[0];
ref = (uint8_t *)&qtmem[seq_size];
if (extend_left)
{
for (i = 0; i < qlen; ++i)
seq[i] = query[qlen - 1 - i];
for (i = 0; i < tlen; ++i)
ref[i + SIMD_WIDTH] = target[tlen - 1 - i];
}
else
{
for (i = 0; i < qlen; ++i)
seq[i] = query[i];
for (i = 0; i < tlen; ++i)
ref[i + SIMD_WIDTH] = target[i];
}
vmem = &ref[ref_size];
for (i = 0; i < val_mem_size; i += SIMD_WIDTH)
{
_mm256_storeu_si256((__m256i *)&vmem[i], zero_vec);
}
hA = &vmem[0];
mA = &vmem[col_size * 3];
eA = &vmem[col_size * 5];
fA = &vmem[col_size * 7];
hA0 = &hA[0];
hA1 = &hA[col_size];
hA2 = &hA1[col_size];
mA1 = &mA[0];
mA2 = &mA[col_size];
eA1 = &eA[0];
eA2 = &eA[col_size];
fA1 = &fA[0];
fA2 = &fA[col_size];
// adjust $window_size if it is too large
// get the max score
max = base_match_score;
max_ins = (int)((double)(qlen * max + end_bonus - o_ins) / e_ins + 1.);
max_ins = max_ins > 1 ? max_ins : 1;
window_size = window_size < max_ins ? window_size : max_ins;
max_del = (int)((double)(qlen * max + end_bonus - o_del) / e_del + 1.);
max_del = max_del > 1 ? max_del : 1;
window_size = window_size < max_del ? window_size : max_del; // TODO: is this necessary?
if (tlen < qlen)
window_size = MIN(tlen - 1, window_size);
// DP loop
max = init_score, max_i = max_j = -1;
max_ie = -1, gscore = -1;
;
max_off = 0;
beg = 1;
end = qlen;
// init init_score
hA0[0] = init_score; // 左上角
if (qlen == 0 || tlen == 0)
Dloop = 0; // 防止意外情况
if (window_size >= qlen)
{
max_ie = 0;
gscore = 0;
}
int iend;
for (D = 1; LIKELY(D < Dloop); ++D)
{
// 边界条件一定要注意！ tlen 大于，等于，小于 qlen时的情况
if (D > tlen)
{
span = MIN(Dloop - D, window_size);
beg1 = MAX(D - tlen + 1, ((D - window_size) / 2) + 1);
}
else
{
span = MIN(D - 1, window_size);
beg1 = MAX(1, ((D - window_size) / 2) + 1);
}
end1 = MIN(qlen, beg1 + span);
if (beg < beg1)
beg = beg1;
if (end > end1)
end = end1;
if (beg > end)
break; // 不用计算了，直接跳出，否则hA2没有被赋值，里边是上一轮hA0的值，会出bug
beg = 1;
end = qlen;
iend = D - (beg - 1); // ref开始计算的位置，倒序
span = end - beg;
iStart = iend - span - 1; // 0开始的ref索引位置
// 每一轮需要记录的数据
int m = 0, mj = -1, mi = -1;
max_vec = zero_vec;
// 要处理边界
// 左边界 处理f (insert)
if (iStart == 0)
{
hA1[end] = MAX(0, init_score - (o_ins + e_ins * end));
}
// 上边界
if (beg == 1)
{
hA1[0] = MAX(0, init_score - (o_del + e_del * iend));
}
else
{
hA1[beg - 1] = 0;
eA1[beg - 1] = 0;
}
for (j = beg, i = iend; j <= end + 1 - SIMD_WIDTH; j += SIMD_WIDTH, i -= SIMD_WIDTH)
{
// 取数据
SIMD_LOAD;
// 比对seq，计算罚分
SIMD_CMP_SEQ;
// 计算
SIMD_COMPUTE;
// 存储结果
SIMD_STORE;
}
// 剩下的计算单元
if (j <= end)
{
// 取数据
SIMD_LOAD;
// 比对seq，计算罚分
SIMD_CMP_SEQ;
// 计算
SIMD_COMPUTE;
// 去除多余计算的部分
SIMD_REMOVE_EXTRA;
// 存储结果
SIMD_STORE;
}
SIMD_FIND_MAX;
// 注意最后跳出循环j的值
j = end + 1;
if (j == qlen + 1)
{
max_ie = gscore > hA2[qlen] ? max_ie : iStart;
gscore = gscore > hA2[qlen] ? gscore : hA2[qlen];
}
if (m > max)
{
max = m, max_i = mi, max_j = mj;
max_off = max_off > abs(mj - mi) ? max_off : abs(mj - mi);
}
// 调整计算的边界
// for (j = beg; LIKELY(j <= end); ++j)
//{
// int has_val = hA1[j - 1] | hA2[j];
// if (has_val)
// break;
//}
// beg = j;
// for (j = end + 1; LIKELY(j >= beg); --j)
//{
// int has_val = hA1[j - 1] | hA2[j];
// if (has_val)
// break;
// else
// hA0[j - 1] = 0;
//}
// end = j + 1 <= qlen ? j + 1 : qlen;
// swap m, h, e, f
SWAP_DATA_POINTER;
}
// free(mem);
thread_mem_release(tmem, mem_size);
if (_qle)
*_qle = max_j + 1;
if (_tle)
*_tle = max_i + 1;
if (_gtle)
*_gtle = max_ie + 1;
if (_gscore)
*_gscore = gscore;
if (_max_off)
*_max_off = max_off;
return max;
}

137
ksw_avx2_u8_aligned.c → ksw_ext_avx2_u8_aligned.c
View File

@ -69,17 +69,15 @@ static const uint8_t h_vec_int_mask[SIMD_WIDTH][SIMD_WIDTH] = {
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0},
{0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff}};
// static const uint8_t reverse_mask[SIMD_WIDTH] = {1, 0, 3, 2, 5, 4, 7, 6, 9, 8, 11, 10, 13, 12, 15, 14, 1, 0, 3, 2, 5, 4, 7, 6, 9, 8, 11, 10, 13, 12, 15, 14};
static const uint8_t reverse_mask[SIMD_WIDTH] = {7, 6, 5, 4, 3, 2, 1, 0, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 0, 15, 14, 13, 12, 11, 10, 9, 8};
// const int permute_mask = _MM_SHUFFLE(0, 1, 2, 3);
// #define permute_mask _MM_SHUFFLE(0, 1, 2, 3)
#define permute_mask 27
// 初始化变量
#define SIMD_INIT \
int oe_del = o_del + e_del, oe_ins = o_ins + e_ins; \
__m256i zero_vec; \
__m256i max_vec, last_max_vec = _mm256_set1_epi8(h0); \
__m256i max_vec, last_max_vec = _mm256_set1_epi8(init_score); \
__m256i oe_del_vec; \
__m256i oe_ins_vec; \
__m256i e_del_vec; \
@ -91,8 +89,8 @@ static const uint8_t reverse_mask[SIMD_WIDTH] = {7, 6, 5, 4, 3, 2, 1, 0, 15, 14,
oe_ins_vec = _mm256_set1_epi8(oe_ins); \
e_del_vec = _mm256_set1_epi8(e_del); \
e_ins_vec = _mm256_set1_epi8(e_ins); \
__m256i match_sc_vec = _mm256_set1_epi8(a); \
__m256i mis_sc_vec = _mm256_set1_epi8(b); \
__m256i match_sc_vec = _mm256_set1_epi8(base_match_score); \
__m256i mis_sc_vec = _mm256_set1_epi8(base_mis_score); \
__m256i amb_sc_vec = _mm256_set1_epi8(1); \
__m256i amb_vec = _mm256_set1_epi8(4); \
reverse_mask_vec = _mm256_loadu_si256((__m256i *)(reverse_mask)); \
@ -200,7 +198,7 @@ static const uint8_t reverse_mask[SIMD_WIDTH] = {7, 6, 5, 4, 3, 2, 1, 0, 15, 14,
{ \
if (read_seq[mj + 2] == ref_seq[mi + 1 + SIMD_WIDTH]) \
{ \
m += a; \
m += base_match_score; \
} \
else \
{ \
@ -228,37 +226,31 @@ static const uint8_t reverse_mask[SIMD_WIDTH] = {7, 6, 5, 4, 3, 2, 1, 0, 15, 14,
mA1 = mA2; \
mA2 = tmp;
int ksw_avx2_u8_aligned(thread_mem_t *tmem,
int qlen, // query length 待匹配段碱基的query长度
const uint8_t *query, // read碱基序列
int tlen, // target length reference的长度
const uint8_t *target, // reference序列
int is_left, // 是不是向左扩展
int m, // 碱基种类 (5)
const int8_t *mat, // 每个位置的query和target的匹配得分 m*m
int o_del, // deletion 错配开始的惩罚系数
int e_del, // deletion extension的惩罚系数
int o_ins, // insertion 错配开始的惩罚系数
int e_ins, // insertion extension的惩罚系数
int a, // 碱基match时的分数
int b, // 碱基mismatch时的惩罚分数（正数）
int w, // 提前剪枝系数，w =100 匹配位置和beg的最大距离
int end_bonus,
int zdrop,
int h0, // 该seed的初始得分（完全匹配query的碱基数）
int *_qle, // 匹配得到全局最大得分的碱基在query的位置
int *_tle, // 匹配得到全局最大得分的碱基在reference的位置
int *_gtle, // query全部匹配上的target的长度
int *_gscore, // query的端到端匹配得分
int *_max_off) // 取得最大得分时在query和reference上位置差的 最大值
int ksw_extend_avx2_u8_aligned(thread_mem_t *tmem,
int qlen, // query length 待匹配段碱基的query长度
const uint8_t *query, // read碱基序列
int tlen, // target length reference的长度
const uint8_t *target, // reference序列
int extend_left, // 是不是向左扩展
int o_del, // deletion 错配开始的惩罚系数
int e_del, // deletion extension的惩罚系数
int o_ins, // insertion 错配开始的惩罚系数
int e_ins, // insertion extension的惩罚系数SIMD_BTYES
int base_match_score, // 碱基match时的分数
int base_mis_score, // 碱基mismatch时的惩罚分数（正数）
int window_size, // 提前剪枝系数，w =100 匹配位置和beg的最大距离
int end_bonus, // 如果query比对到了最后一个字符，额外奖励分值
int init_score, // 该seed的初始得分（完全匹配query的碱基数）
int *_qle, // 匹配得到全局最大得分的碱基在query的位置
int *_tle, // 匹配得到全局最大得分的碱基在reference的位置
int *_gtle, // query全部匹配上的target的长度
int *_gscore, // query的端到端匹配得分
int *_max_off) // 取得最大得分时在query和reference上位置差的 最大值
{
uint8_t *mA, *hA, *eA, *fA, *mA1, *mA2, *hA0, *hA1, *eA1, *fA1, *hA2, *eA2, *fA2; // hA0保存上上个col的H，其他的保存上个H E F M
uint8_t *mA1, *mA2, *hA0, *hA1, *eA1, *fA1, *hA2, *eA2, *fA2; // hA0保存上上个col的H，其他的保存上个H E F M
uint8_t *read_seq, *ref_seq;
int i, iStart, D, j, k, beg, end, max, max_i, max_j, max_ins, max_del, max_ie, gscore, max_off;
int i, iStart, D, j, beg, end, max, max_i, max_j, max_ins, max_del, max_ie, gscore, max_off;
int span, beg1, end1; // 边界条件计算
int col_size = qlen + 2 + SIMD_WIDTH;
int val_mem_size = (col_size * 9 + 31) >> 5 << 5; // 32字节的整数倍
// int mem_size = seq_size + ref_size + val_mem_size;
uint8_t *mem_addr;
int read_size = align_number(qlen * BASE_BYTES + MEM_ALIGN_BYTES);
@ -271,14 +263,14 @@ int ksw_avx2_u8_aligned(thread_mem_t *tmem,
SIMD_INIT; // 初始化simd用的数据
assert(h0 > 0);
assert(init_score > 0);
mem_addr = thread_mem_request(tmem, request_mem_size);
mem_addr = (void *)align_mem((uint64_t)mem_addr);
ref_seq = (uint8_t *)&mem_addr[0];
read_seq = (uint8_t *)(mem_addr + ref_size + SIMD_BYTES - BASE_BYTES);
if (is_left)
if (extend_left)
{
for (i = 0; i < qlen; ++i)
read_seq[i + 1] = query[qlen - 1 - i];
@ -310,39 +302,36 @@ int ksw_avx2_u8_aligned(thread_mem_t *tmem,
fA1 = &eA2[score_element_num];
fA2 = &fA1[score_element_num];
// adjust $w if it is too large
k = m * m;
// get the max score
for (i = 0, max = 0; i < k; ++i)
max = max > mat[i] ? max : mat[i];
// adjust $window_size if it is too large
max = base_match_score;
max_ins = (int)((double)(qlen * max + end_bonus - o_ins) / e_ins + 1.);
max_ins = max_ins > 1 ? max_ins : 1;
w = w < max_ins ? w : max_ins;
window_size = window_size < max_ins ? window_size : max_ins;
max_del = (int)((double)(qlen * max + end_bonus - o_del) / e_del + 1.);
max_del = max_del > 1 ? max_del : 1;
w = w < max_del ? w : max_del; // TODO: is this necessary?
window_size = window_size < max_del ? window_size : max_del; // TODO: is this necessary?
if (tlen < qlen)
w = MIN(tlen - 1, w);
window_size = MIN(tlen - 1, window_size);
// DP loop
max = h0, max_i = max_j = -1;
max = init_score, max_i = max_j = -1;
max_ie = -1, gscore = -1;
;
max_off = 0;
beg = 1;
end = qlen;
// init h0
hA0[0] = h0; // 左上角
// init init_score
hA0[0] = init_score; // 左上角
if (qlen == 0 || tlen == 0)
back_diagnal_num = 0; // 防止意外情况
if (w >= qlen)
if (window_size >= qlen)
{
max_ie = 0;
gscore = 0;
}
int m_last = 0;
int iend;
for (D = 1; LIKELY(D < back_diagnal_num); ++D)
@ -350,13 +339,13 @@ int ksw_avx2_u8_aligned(thread_mem_t *tmem,
// 边界条件一定要注意！ tlen 大于，等于，小于 qlen时的情况
if (D > tlen)
{
span = MIN(back_diagnal_num - D, w);
beg1 = MAX(D - tlen + 1, ((D - w) / 2) + 1);
span = MIN(back_diagnal_num - D, window_size);
beg1 = MAX(D - tlen + 1, ((D - window_size) / 2) + 1);
}
else
{
span = MIN(D - 1, w);
beg1 = MAX(1, ((D - w) / 2) + 1);
span = MIN(D - 1, window_size);
beg1 = MAX(1, ((D - window_size) / 2) + 1);
}
end1 = MIN(qlen, beg1 + span);
@ -367,8 +356,8 @@ int ksw_avx2_u8_aligned(thread_mem_t *tmem,
if (beg > end)
break; // 不用计算了，直接跳出，否则hA2没有被赋值，里边是上一轮hA0的值，会出bug
// beg = 1;
// end = qlen;
beg = 1;
end = qlen;
iend = D - (beg - 1); // ref开始计算的位置，倒序
span = end - beg;
iStart = iend - span - 1; // 0开始的ref索引位置
@ -381,12 +370,12 @@ int ksw_avx2_u8_aligned(thread_mem_t *tmem,
// 左边界 处理f (insert)
if (iStart == 0)
{
hA1[end] = MAX(0, h0 - (o_ins + e_ins * end));
hA1[end] = MAX(0, init_score - (o_ins + e_ins * end));
}
// 上边界
if (beg == 1)
{
hA1[0] = MAX(0, h0 - (o_del + e_del * iend));
hA1[0] = MAX(0, init_score - (o_del + e_del * iend));
}
else
{
@ -438,26 +427,22 @@ int ksw_avx2_u8_aligned(thread_mem_t *tmem,
}
// 调整计算的边界
for (j = beg; LIKELY(j <= end); ++j)
{
int has_val = hA1[j - 1] | hA2[j];
if (has_val)
break;
}
beg = j;
hA2[end + 1] = 0;
for (j = end + 1; LIKELY(j >= beg); --j)
{
int has_val = hA1[j - 1] | hA2[j];
if (has_val)
break;
}
end = j + 1 <= qlen ? j + 1 : qlen;
// for (j = beg; LIKELY(j <= end); ++j)
//{
// int has_val = hA1[j - 1] | hA2[j];
// if (has_val)
// break;
//}
// beg = j;
// hA2[end + 1] = 0;
// for (j = end + 1; LIKELY(j >= beg); --j)
//{
// int has_val = hA1[j - 1] | hA2[j];
// if (has_val)
// break;
//}
// end = j + 1 <= qlen ? j + 1 : qlen;
// beg = 0;
// end = qlen;
m_last = m;
// swap m, h, e, f
SWAP_DATA_POINTER;
}

176
ksw_avx2_u8.c → ksw_ext_avx2_u8_heuristics.c
View File

@ -5,6 +5,7 @@
#include <stdio.h>
#include <immintrin.h>
#include <emmintrin.h>
#include "thread_mem.h"
#ifdef __GNUC__
#define LIKELY(x) __builtin_expect((x), 1)
@ -64,7 +65,7 @@ static const uint8_t reverse_mask[SIMD_WIDTH] = {7, 6, 5, 4, 3, 2, 1, 0, 15, 14,
#define SIMD_INIT \
int oe_del = o_del + e_del, oe_ins = o_ins + e_ins; \
__m256i zero_vec; \
__m256i max_vec, last_max_vec = _mm256_set1_epi8(h0); \
__m256i max_vec, last_max_vec = _mm256_set1_epi8(init_score); \
__m256i oe_del_vec; \
__m256i oe_ins_vec; \
__m256i e_del_vec; \
@ -76,8 +77,8 @@ static const uint8_t reverse_mask[SIMD_WIDTH] = {7, 6, 5, 4, 3, 2, 1, 0, 15, 14,
oe_ins_vec = _mm256_set1_epi8(oe_ins); \
e_del_vec = _mm256_set1_epi8(e_del); \
e_ins_vec = _mm256_set1_epi8(e_ins); \
__m256i match_sc_vec = _mm256_set1_epi8(a); \
__m256i mis_sc_vec = _mm256_set1_epi8(b); \
__m256i match_sc_vec = _mm256_set1_epi8(base_match_score); \
__m256i mis_sc_vec = _mm256_set1_epi8(base_mis_score); \
__m256i amb_sc_vec = _mm256_set1_epi8(1); \
__m256i amb_vec = _mm256_set1_epi8(4); \
reverse_mask_vec = _mm256_loadu_si256((__m256i *)(reverse_mask)); \
@ -185,7 +186,7 @@ static const uint8_t reverse_mask[SIMD_WIDTH] = {7, 6, 5, 4, 3, 2, 1, 0, 15, 14,
{ \
if (seq[mj + 1] == ref[mi + 1 + SIMD_WIDTH]) \
{ \
m += a; \
m += base_match_score; \
} \
else \
{ \
@ -213,45 +214,35 @@ static const uint8_t reverse_mask[SIMD_WIDTH] = {7, 6, 5, 4, 3, 2, 1, 0, 15, 14,
mA1 = mA2; \
mA2 = tmp;
uint8_t mem1[102400];
// uint8_t mem1[102400];
int ksw_avx2_u8(int qlen, // query length 待匹配段碱基的query长度
const uint8_t *query, // read碱基序列
int tlen, // target length reference的长度
const uint8_t *target, // reference序列
int is_left, // 是不是向左扩展
int m, // 碱基种类 (5)
const int8_t *mat, // 每个位置的query和target的匹配得分 m*m
int o_del, // deletion 错配开始的惩罚系数
int e_del, // deletion extension的惩罚系数
int o_ins, // insertion 错配开始的惩罚系数
int e_ins, // insertion extension的惩罚系数
int a, // 碱基match时的分数
int b, // 碱基mismatch时的惩罚分数（正数）
int w, // 提前剪枝系数，w =100 匹配位置和beg的最大距离
int end_bonus,
int zdrop,
int h0, // 该seed的初始得分（完全匹配query的碱基数）
int *_qle, // 匹配得到全局最大得分的碱基在query的位置
int *_tle, // 匹配得到全局最大得分的碱基在reference的位置
int *_gtle, // query全部匹配上的target的长度
int *_gscore, // query的端到端匹配得分
int *_max_off) // 取得最大得分时在query和reference上位置差的 最大值
int ksw_extend_avx2_u8_heuristics(thread_mem_t *tmem,
int qlen, // query length 待匹配段碱基的query长度
const uint8_t *query, // read碱基序列
int tlen, // target length reference的长度
const uint8_t *target, // reference序列
int extend_left, // 是不是向左扩展
int o_del, // deletion 错配开始的惩罚系数
int e_del, // deletion extension的惩罚系数
int o_ins, // insertion 错配开始的惩罚系数
int e_ins, // insertion extension的惩罚系数SIMD_BTYES
int base_match_score, // 碱基match时的分数
int base_mis_score, // 碱基mismatch时的惩罚分数（正数）
int window_size, // 提前剪枝系数，w =100 匹配位置和beg的最大距离
int end_bonus, // 如果query比对到了最后一个字符，额外奖励分值
int init_score, // 该seed的初始得分（完全匹配query的碱基数）
int *_qle, // 匹配得到全局最大得分的碱基在query的位置
int *_tle, // 匹配得到全局最大得分的碱基在reference的位置
int *_gtle, // query全部匹配上的target的长度
int *_gscore, // query的端到端匹配得分
int *_max_off) // 取得最大得分时在query和reference上位置差的 最大值
{
// return h0;
#ifdef SHOW_PERF
// extern int64_t time_bsw_init;
// extern int64_t time_bsw_main_loop;
// extern int64_t time_bsw_find_max;
// extern int64_t time_bsw_adjust_bound;
// extern int64_t time_compare;
// int64_t start_time = get_mseconds();
#endif
// return init_score;
uint8_t *mA, *hA, *eA, *fA, *mA1, *mA2, *hA0, *hA1, *eA1, *fA1, *hA2, *eA2, *fA2; // hA0保存上上个col的H，其他的保存上个H E F M
uint8_t *seq, *ref;
uint8_t *mem = &mem1[0], *qtmem, *vmem;
uint8_t *mem, *qtmem, *vmem;
int seq_size = qlen + SIMD_WIDTH, ref_size = tlen + SIMD_WIDTH;
int i, iStart, D, j, k, beg, end, max, max_i, max_j, max_ins, max_del, max_ie, gscore, max_off;
int i, iStart, D, j, beg, end, max, max_i, max_j, max_ins, max_del, max_ie, gscore, max_off;
int Dloop = tlen + qlen; // 循环跳出条件
int span, beg1, end1; // 边界条件计算
int col_size = qlen + 2 + SIMD_WIDTH;
@ -260,14 +251,15 @@ int ksw_avx2_u8(int qlen, // query length 待匹配段碱基的que
SIMD_INIT; // 初始化simd用的数据
assert(h0 > 0);
assert(init_score > 0);
// allocate memory
// mem = malloc(mem_size);
mem = thread_mem_request(tmem, mem_size);
qtmem = &mem[0];
seq = (uint8_t *)&qtmem[0];
ref = (uint8_t *)&qtmem[seq_size];
if (is_left)
if (extend_left)
{
for (i = 0; i < qlen; ++i)
seq[i] = query[qlen - 1 - i];
@ -303,39 +295,36 @@ int ksw_avx2_u8(int qlen, // query length 待匹配段碱基的que
fA1 = &fA[0];
fA2 = &fA[col_size];
// adjust $w if it is too large
k = m * m;
// adjust $window_size if it is too large
// get the max score
for (i = 0, max = 0; i < k; ++i)
max = max > mat[i] ? max : mat[i];
max = base_match_score;
max_ins = (int)((double)(qlen * max + end_bonus - o_ins) / e_ins + 1.);
max_ins = max_ins > 1 ? max_ins : 1;
w = w < max_ins ? w : max_ins;
window_size = window_size < max_ins ? window_size : max_ins;
max_del = (int)((double)(qlen * max + end_bonus - o_del) / e_del + 1.);
max_del = max_del > 1 ? max_del : 1;
w = w < max_del ? w : max_del; // TODO: is this necessary?
window_size = window_size < max_del ? window_size : max_del; // TODO: is this necessary?
if (tlen < qlen)
w = MIN(tlen - 1, w);
window_size = MIN(tlen - 1, window_size);
// DP loop
max = h0, max_i = max_j = -1;
max = init_score, max_i = max_j = -1;
max_ie = -1, gscore = -1;
;
max_off = 0;
beg = 1;
end = qlen;
// init h0
hA0[0] = h0; // 左上角
// init init_score
hA0[0] = init_score; // 左上角
if (qlen == 0 || tlen == 0)
Dloop = 0; // 防止意外情况
if (w >= qlen)
if (window_size >= qlen)
{
max_ie = 0;
gscore = 0;
}
int m_last = 0;
int iend;
#ifdef SHOW_PERF
// time_bsw_init += get_mseconds() - start_time;
@ -349,13 +338,13 @@ int ksw_avx2_u8(int qlen, // query length 待匹配段碱基的que
// 边界条件一定要注意！ tlen 大于，等于，小于 qlen时的情况
if (D > tlen)
{
span = MIN(Dloop - D, w);
beg1 = MAX(D - tlen + 1, ((D - w) / 2) + 1);
span = MIN(Dloop - D, window_size);
beg1 = MAX(D - tlen + 1, ((D - window_size) / 2) + 1);
}
else
{
span = MIN(D - 1, w);
beg1 = MAX(1, ((D - w) / 2) + 1);
span = MIN(D - 1, window_size);
beg1 = MAX(1, ((D - window_size) / 2) + 1);
}
end1 = MIN(qlen, beg1 + span);
@ -366,8 +355,8 @@ int ksw_avx2_u8(int qlen, // query length 待匹配段碱基的que
if (beg > end)
break; // 不用计算了，直接跳出，否则hA2没有被赋值，里边是上一轮hA0的值，会出bug
// beg = 1;
// end = qlen;
beg = 1;
end = qlen;
iend = D - (beg - 1); // ref开始计算的位置，倒序
span = end - beg;
iStart = iend - span - 1; // 0开始的ref索引位置
@ -380,12 +369,12 @@ int ksw_avx2_u8(int qlen, // query length 待匹配段碱基的que
// 左边界 处理f (insert)
if (iStart == 0)
{
hA1[end] = MAX(0, h0 - (o_ins + e_ins * end));
hA1[end] = MAX(0, init_score - (o_ins + e_ins * end));
}
// 上边界
if (beg == 1)
{
hA1[0] = MAX(0, h0 - (o_del + e_del * iend));
hA1[0] = MAX(0, init_score - (o_del + e_del * iend));
}
else
{
@ -418,19 +407,9 @@ int ksw_avx2_u8(int qlen, // query length 待匹配段碱基的que
// 存储结果
SIMD_STORE;
}
#ifdef SHOW_PERF
// time_bsw_main_loop += get_mseconds() - start_time;
#endif
#ifdef SHOW_PERF
// start_time = get_mseconds();
#endif
SIMD_FIND_MAX;
#ifdef SHOW_PERF
// time_bsw_find_max += get_mseconds() - start_time;
#endif
#ifdef SHOW_PERF
// start_time = get_mseconds();
#endif
// 注意最后跳出循环j的值
j = end + 1;
@ -439,50 +418,30 @@ int ksw_avx2_u8(int qlen, // query length 待匹配段碱基的que
max_ie = gscore > hA2[qlen] ? max_ie : iStart;
gscore = gscore > hA2[qlen] ? gscore : hA2[qlen];
}
// if (m == 0 && m_last == 0)
// break; // 一定要注意，斜对角遍历和按列遍历的不同点
if (m > max)
{
max = m, max_i = mi, max_j = mj;
max_off = max_off > abs(mj - mi) ? max_off : abs(mj - mi);
}
else if (0) // (zdrop > 0)
{
if (mi - max_i > mj - max_j)
{
if (max - m - ((mi - max_i) - (mj - max_j)) * e_del > zdrop)
break;
}
else
{
if (max - m - ((mj - max_j) - (mi - max_i)) * e_ins > zdrop)
break;
}
}
// 调整计算的边界
for (j = beg; LIKELY(j <= end); ++j)
{
int has_val = hA1[j - 1] | hA2[j];
if (has_val)
break;
}
beg = j;
hA2[end + 1] = 0;
for (j = end + 1; LIKELY(j >= beg); --j)
{
int has_val = hA1[j - 1] | hA2[j];
if (has_val)
break;
// else
// hA0[j - 1] = 0;
}
end = j + 1 <= qlen ? j + 1 : qlen;
// for (j = beg; LIKELY(j <= end); ++j)
//{
// int has_val = hA1[j - 1] | hA2[j];
// if (has_val)
// break;
//}
// beg = j;
// hA2[end + 1] = 0;
// for (j = end + 1; LIKELY(j >= beg); --j)
//{
// int has_val = hA1[j - 1] | hA2[j];
// if (has_val)
// break;
//}
// end = j + 1 <= qlen ? j + 1 : qlen;
// beg = 0;
// end = qlen;
m_last = m;
// swap m, h, e, f
SWAP_DATA_POINTER;
#ifdef SHOW_PERF
@ -493,6 +452,7 @@ int ksw_avx2_u8(int qlen, // query length 待匹配段碱基的que
}
// free(mem);
thread_mem_release(tmem, mem_size);
if (_qle)
*_qle = max_j + 1;
if (_tle)

0
ksw_cuda.c → ksw_ext_cuda.c
View File

16
ksw_normal.c → ksw_ext_normal.c
View File

@ -2,6 +2,7 @@
#include <stdlib.h>
#include <assert.h>
#include <stdio.h>
#include "thread_mem.h"
#ifdef __GNUC__
#define LIKELY(x) __builtin_expect((x), 1)
@ -16,15 +17,17 @@ typedef struct
int32_t h, e;
} eh_t;
int ksw_normal(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int o_del, int e_del, int o_ins, int e_ins, int w, int end_bonus, int zdrop, int h0, int *_qle, int *_tle, int *_gtle, int *_gscore, int *_max_off)
int ksw_extend_normal(thread_mem_t *tmem, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int o_del, int e_del, int o_ins, int e_ins, int w, int end_bonus, int zdrop, int h0, int *_qle, int *_tle, int *_gtle, int *_gscore, int *_max_off)
{
return h0;
// return h0;
eh_t *eh; // score array
int8_t *qp; // query profile
int i, j, k, oe_del = o_del + e_del, oe_ins = o_ins + e_ins, beg, end, max, max_i, max_j, max_ins, max_del, max_ie, gscore, max_off;
assert(h0 > 0);
qp = malloc(qlen * m);
eh = calloc(qlen + 1, 8);
// qp = malloc(qlen * m);
// eh = calloc(qlen + 1, 8);
qp = thread_mem_request(tmem, qlen * m);
eh = thread_mem_request_and_clean(tmem, (qlen + 1) * 8);
// generate the query profile
for (k = i = 0; k < m; ++k)
{
@ -140,8 +143,9 @@ int ksw_normal(int qlen, const uint8_t *query, int tlen, const uint8_t *target,
// fprintf(stderr, "\n");
// fprintf(stderr, "%d\n", end);
}
free(eh);
free(qp);
// free(eh);
// free(qp);
thread_mem_release(tmem, qlen * m + (qlen + 1) * 8);
if (_qle)
*_qle = max_j + 1;
if (_tle)

419
main.c
View File

@ -6,6 +6,8 @@
#include <time.h>
#include "sys/time.h"
#include "thread_mem.h"
#include "ksw_ext.h"
#include "utils.h"
#define SW_NORMAL 0
#define SW_AVX2 1
@ -15,9 +17,12 @@
#define BLOCK_BUF_SIZE 1048576
#define READ_BUF_SIZE 2048
#define SEQ_BUF_SIZE (BLOCK_BUF_SIZE + READ_BUF_SIZE)
#define INIT_ALLOC_SIZE 4096
#define DIVIDE_BY (CLOCKS_PER_SEC * 1.0)
#define KERNEL_NUM 7
#ifdef SHOW_PERF
// 用来调试，计算感兴趣部分的运行时间
// 获取当前毫秒数
@ -29,60 +34,89 @@ int64_t get_mseconds()
return clock();
}
int64_t time_sw_normal = 0,
time_sw_avx2 = 0,
time_sw_avx2_u8 = 0,
time_sw_avx2_u8_aligned = 0,
time_bsw_avx2 = 0,
time_bsw_init = 0,
time_bsw_main_loop = 0,
time_bsw_find_max = 0,
time_bsw_adjust_bound = 0,
time_compare = 0;
int64_t time_sw[KERNEL_NUM] = {0};
#endif
extern int ksw_normal(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int o_del, int e_del, int o_ins, int e_ins, int w, int end_bonus, int zdrop, int h0, int *_qle, int *_tle, int *_gtle, int *_gscore, int *_max_off);
extern int ksw_avx2(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int is_left, int m, const int8_t *mat, int o_del, int e_del,
int o_ins, int e_ins, int a, int b, int w, int end_bonus, int zdrop, int h0, int *_qle, int *_tle, int *_gtle, int *_gscore, int *_max_off);
extern int ksw_avx2_u8(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int is_left, int m, const int8_t *mat, int o_del, int e_del,
int o_ins, int e_ins, int a, int b, int w, int end_bonus, int zdrop, int h0, int *_qle, int *_tle, int *_gtle, int *_gscore, int *_max_off);
#define _PERFORMANCE_TEST_NORMAL(kernel_num, func) \
cur_query_pos = 0; \
cur_target_pos = 0; \
for (i = 0; i < block_line_num; ++i) \
{ \
score[kernel_num] = func( \
&tmem[kernel_num], \
info_arr[i][0], \
(uint8_t *)query_arr + cur_query_pos, \
info_arr[i][1], \
(uint8_t *)target_arr + cur_target_pos, \
5, mat, 6, 1, 6, 1, 100, 5, 100, \
info_arr[i][2], \
&qle, &tle, &gtle, &gscore, &max_off[0]); \
score_total[kernel_num] += score[kernel_num]; \
cur_query_pos += info_arr[i][0]; \
cur_target_pos += info_arr[i][1]; \
}
unsigned char nst_nt4_table[256] = {
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5 /*'-'*/, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4};
char t_2bit2char[5] = {'A', 'C', 'G', 'T'};
// 将碱基字符转成2位编码
void convert_char_to_2bit(char *str)
{
int i;
for (i = 0; i < strlen(str); ++i)
str[i] = nst_nt4_table[str[i]];
}
#define _PERFORMANCE_TEST_AVX2(kernel_num, func) \
cur_query_pos = 0; \
cur_target_pos = 0; \
for (i = 0; i < block_line_num; ++i) \
{ \
score[kernel_num] = func( \
&tmem[kernel_num], \
info_arr[i][0], \
(uint8_t *)query_arr + cur_query_pos, \
info_arr[i][1], \
(uint8_t *)target_arr + cur_target_pos, \
0, 6, 1, 6, 1, \
1, 4, \
100, 5, \
info_arr[i][2], \
&qle, &tle, &gtle, &gscore, &max_off[0]); \
score_total[kernel_num] += score[kernel_num]; \
cur_query_pos += info_arr[i][0]; \
cur_target_pos += info_arr[i][1]; \
}
// 读取测试数据
int read_data()
#ifdef SHOW_PERF
#define PERFORMANCE_TEST_NORMAL(kernel_num, func) \
start_time = get_mseconds(); \
_PERFORMANCE_TEST_NORMAL(kernel_num, func); \
time_sw[kernel_num] += get_mseconds() - start_time
#define PERFORMANCE_TEST_AVX2(kernel_num, func) \
start_time = get_mseconds(); \
_PERFORMANCE_TEST_AVX2(kernel_num, func); \
time_sw[kernel_num] += get_mseconds() - start_time
#else
#define PERFORMANCE_TEST_NORMAL(kernel_num, func) _PERFORMANCE_TEST_NORMAL(kernel_num, func)
#define PERFORMANCE_TEST_AVX2(kernel_num, func) _PERFORMANCE_TEST_AVX2(kernel_num, func)
#endif
// 读取一行序列数据
int read_seq_line(char *read_buf, FILE *f_ptr, char *out_arr)
{
return 0;
if (fgets(read_buf, READ_BUF_SIZE, f_ptr) == NULL)
return 0;
int line_size = strlen(read_buf);
assert(line_size < READ_BUF_SIZE);
if (read_buf[line_size - 1] == '\n')
{
read_buf[line_size - 1] = '\0';
line_size--;
}
convert_char_to_2bit(read_buf);
strncpy(out_arr, read_buf, line_size);
return line_size;
}
// 程序执行入口
int main(int argc, char *argv[])
{
const char *qf_path = argv[1];
const char *tf_path = argv[2];
const char *if_path = argv[3];
// 初始化一些全局参数
int8_t mat[25] = {1, -4, -4, -4, -1,
-4, 1, -4, -4, -1,
@ -91,52 +125,41 @@ int main(int argc, char *argv[])
-1, -1, -1, -1, -1};
int max_off[2];
int qle, tle, gtle, gscore;
thread_mem_t tmem, tmem_u8;
init_thread_mem(&tmem);
init_thread_mem(&tmem_u8);
// thread_mem_init_alloc(&tmem_u8, 10960);
thread_mem_t tmem[KERNEL_NUM];
int i, j;
for (i = 0; i < KERNEL_NUM; ++i)
{
thread_mem_init_alloc(tmem + i, INIT_ALLOC_SIZE);
}
// 记录计算出的分数
int score[KERNEL_NUM] = {0};
int score_total[KERNEL_NUM] = {0};
// 读取测试数据
char *query_arr = (char *)malloc(SEQ_BUF_SIZE);
char *target_arr = (char *)malloc(SEQ_BUF_SIZE);
int *info_buf = (int *)malloc(SEQ_BUF_SIZE * sizeof(int));
int **info_arr = (int **)malloc(SEQ_BUF_SIZE * sizeof(int *));
FILE *query_f = 0, *target_f = 0, *info_f = 0;
// const char *qf_path = "q.fa";
// const char *tf_path = "t.fa";
// const char *if_path = "i.txt";
// const char *qf_path = "bug_q.fa";
// const char *tf_path = "bug_t.fa";
// const char *if_path = "bug_i.txt";
// const char *qf_path = "/home/zzh/data/sw/q_s.fa";
// const char *tf_path = "/home/zzh/data/sw/t_s.fa";
// const char *if_path = "/home/zzh/data/sw/i_s.txt";
// const char *qf_path = "/home/zzh/data/sw/q_m.fa";
// const char *tf_path = "/home/zzh/data/sw/t_m.fa";
// const char *if_path = "/home/zzh/data/sw/i_m.txt";
const char *qf_path = "/home/zzh/data/sw/q_l.fa";
const char *tf_path = "/home/zzh/data/sw/t_l.fa";
const char *if_path = "/home/zzh/data/sw/i_l.txt";
// const char *qf_path = "/home/zzh/data/sw/query.fa";
// const char *tf_path = "/home/zzh/data/sw/target.fa";
// const char *if_path = "/home/zzh/data/sw/info.txt";
FILE *normal_out_f = 0, *avx2_out_f = 0, *avx2_u8_out_f = 0;
query_f = fopen(qf_path, "r");
target_f = fopen(tf_path, "r");
info_f = fopen(if_path, "r");
// 将每次比对的得分等信息写入文件，进行debug
FILE *normal_out_f = fopen("normal_out.txt", "w");
FILE *avx2_out_f = fopen("avx2_out.txt", "w");
FILE *avx2_u8_out_f = fopen("avx2_u8_out.txt", "w");
FILE *bsw_avx2_out_f = fopen("bsw_avx2_out.txt", "w");
// normal_out_f = fopen("normal_out.txt", "w");
// avx2_out_f = fopen("avx2_out.txt", "w");
// avx2_u8_out_f = fopen("avx2_u8_out.txt", "w");
// 每次读取一定量的数据，然后执行，直到处理完所有数据
int total_line_num = 0; // 目前处理的总的数据行数
int block_line_num = 0; // 当前循环包含的数据行数
int i, j;
// const int max_read = READ_BUF_SIZE; // 每次最多读取的字符
int cur_query_pos, cur_target_pos;
int64_t start_time;
char read_buf[READ_BUF_SIZE]; // 读文件缓存
// int ret_code = 0;
// 初始化info_arr数组
i = 0;
j = 0;
@ -147,55 +170,30 @@ int main(int argc, char *argv[])
info_arr[i] = &info_buf[j];
i += 1;
j += 3;
// fprintf(stderr, "%d\t%d\n", i, j);
}
int score_normal = 0, score_avx2 = 0, score_avx2_u8 = 0, score_bsw_avx2 = 0;
int score_normal_total = 0, score_avx2_total = 0, score_avx2_u8_total = 0, score_bsw_avx2_total = 0;
int score_avx2_u8_aligned = 0, score_avx2_u8_aligned_total = 0;
while (!feof(target_f))
{
// fprintf(stderr, "debug\n");
block_line_num = 0;
block_line_num = 0; // 记录每次读取的行数
// target序列一般占用存储最多，先读取target，看一个buf能读多少行，query和info就按照这个行数来读
int cur_read_size = 0;
while (!feof(target_f) && cur_read_size < BLOCK_BUF_SIZE)
{
if (fgets(read_buf, READ_BUF_SIZE, target_f) == NULL)
int line_size = read_seq_line(read_buf, target_f, target_arr + cur_read_size);
if (line_size == 0)
break;
int line_size = strlen(read_buf);
assert(line_size < READ_BUF_SIZE);
if (read_buf[line_size - 1] == '\n')
{
read_buf[line_size - 1] = '\0';
line_size--;
}
convert_char_to_2bit(read_buf);
cur_read_size += line_size;
++block_line_num;
++total_line_num;
strncpy(target_arr + cur_read_size, read_buf, line_size);
cur_read_size += line_size;
// fprintf(stderr, "%d %d \n", line_size, cur_read_size);
// fprintf(stderr, "%d %d \n", block_line_num, total_line_num);
}
// fprintf(stderr, "here\n");
// 读query
cur_read_size = 0;
for (i = 0; i < block_line_num; ++i)
{
if (fgets(read_buf, READ_BUF_SIZE, query_f) == NULL)
int line_size = read_seq_line(read_buf, query_f, query_arr + cur_read_size);
if (line_size == 0)
break;
int line_size = strlen(read_buf);
assert(line_size < READ_BUF_SIZE);
if (read_buf[line_size - 1] == '\n')
{
read_buf[line_size - 1] = '\0';
line_size--;
}
convert_char_to_2bit(read_buf);
strncpy(query_arr + cur_read_size, read_buf, line_size);
cur_read_size += line_size;
}
@ -215,199 +213,42 @@ int main(int argc, char *argv[])
// 性能测试
int cur_query_pos = 0;
int cur_target_pos = 0;
for (i = 0; i < block_line_num; ++i)
{
#ifdef SHOW_PERF
int64_t start_time = get_mseconds();
#endif
// 普通 sw
score_normal = ksw_normal(
info_arr[i][0],
(uint8_t *)query_arr + cur_query_pos,
info_arr[i][1],
(uint8_t *)target_arr + cur_target_pos,
5, mat, 6, 1, 6, 1, 100, 5, 100,
info_arr[i][2],
&qle, &tle, &gtle, &gscore, &max_off[0]);
#ifdef SHOW_PERF
time_sw_normal += get_mseconds() - start_time;
#endif
score_normal_total += score_normal;
// fprintf(normal_out_f, "%d %d\n", info_arr[i][2], score_normal);
// fprintf(stderr, "%d %d %d %d %d %d %d\n", info_arr[i][2], score_normal, qle, tle, gtle, gscore, max_off[0]);
// normal sw
PERFORMANCE_TEST_NORMAL(0, ksw_extend_normal);
// #ifdef SHOW_PERF
// start_time = get_mseconds();
// #endif
// score_bsw_avx2 = ksw_avx2_aligned(
// &tmem,
// info_arr[i][0],
// (uint8_t *)query_arr + cur_query_pos,
// info_arr[i][1],
// (uint8_t *)target_arr + cur_target_pos,
// 0, 6, 1, 6, 1,
// 1, 4,
// 100, 5,
// info_arr[i][2],
// &qle, &tle, &gtle, &gscore, &max_off[0]);
// #ifdef SHOW_PERF
// time_bsw_avx2 += get_mseconds() - start_time;
// #endif
// score_bsw_avx2_total += score_bsw_avx2;
// fprintf(avx2_out_f, "%d %d\n", info_arr[i][2], score_avx2);
// fprintf(stderr, "%d %d %d %d %d %d %d\n", info_arr[i][2], score_bsw_avx2_total, qle, tle, gtle, gscore, max_off[0]);
/**/
#ifdef SHOW_PERF
start_time = get_mseconds();
#endif
score_avx2 = bsw_avx2(
info_arr[i][0],
(uint8_t *)query_arr + cur_query_pos,
info_arr[i][1],
(uint8_t *)target_arr + cur_target_pos,
0, 6, 1, 6, 1,
1, 4,
100, 5,
info_arr[i][2],
&qle, &tle, &gtle, &gscore, &max_off[0]);
// score_avx2 = ksw_avx2(
// info_arr[i][0],
// (uint8_t *)query_arr + cur_query_pos,
// info_arr[i][1],
// (uint8_t *)target_arr + cur_target_pos,
// 0, 5, mat, 6, 1, 6, 1,
// 1, 4,
// 100, 5, 100,
// info_arr[i][2],
// &qle, &tle, &gtle, &gscore, &max_off[0]);
#ifdef SHOW_PERF
time_sw_avx2 += get_mseconds() - start_time;
#endif
score_avx2_total += score_avx2;
// fprintf(avx2_out_f, "%d %d\n", info_arr[i][2], score_avx2);
// fprintf(stderr, "%d %d %d %d %d %d %d\n", info_arr[i][2], score_avx2, qle, tle, gtle, gscore, max_off[0]);
// avx2
PERFORMANCE_TEST_AVX2(1, ksw_extend_avx2);
#ifdef SHOW_PERF
start_time = get_mseconds();
#endif
score_avx2_u8 = ksw_avx2_u8(
info_arr[i][0],
(uint8_t *)query_arr + cur_query_pos,
info_arr[i][1],
(uint8_t *)target_arr + cur_target_pos,
0, 5, mat, 6, 1, 6, 1,
1, 4,
100, 5, 100,
info_arr[i][2],
&qle, &tle, &gtle, &gscore, &max_off[0]);
#ifdef SHOW_PERF
time_sw_avx2_u8 += get_mseconds() - start_time;
#endif
score_avx2_u8_total += score_avx2_u8;
// fprintf(avx2_u8_out_f, "%d %d %d %d %d %d\n", score_avx2_u8, qle, tle, gtle, gscore, max_off[0]);
// avx2 u8
PERFORMANCE_TEST_AVX2(2, ksw_extend_avx2_u8);
#ifdef SHOW_PERF
start_time = get_mseconds();
#endif
score_avx2_u8_aligned = ksw_avx2_u8_aligned(
&tmem_u8,
info_arr[i][0],
(uint8_t *)query_arr + cur_query_pos,
info_arr[i][1],
(uint8_t *)target_arr + cur_target_pos,
0, 5, mat, 6, 1, 6, 1,
1, 4,
100, 5, 100,
info_arr[i][2],
&qle, &tle, &gtle, &gscore, &max_off[0]);
#ifdef SHOW_PERF
time_sw_avx2_u8_aligned += get_mseconds() - start_time;
#endif
score_avx2_u8_aligned_total += score_avx2_u8_aligned;
// fprintf(avx2_u8_out_f, "%d %d %d %d %d %d\n", score_avx2_u8, qle, tle, gtle, gscore, max_off[0]);
// avx2 heuristics
PERFORMANCE_TEST_AVX2(3, ksw_extend_avx2_heuristics);
// 更新query和target位置信息
cur_query_pos += info_arr[i][0];
cur_target_pos += info_arr[i][1];
// fprintf(stderr, "%d %d %d %d %d %d %d\n", score_normal, qle, tle, gtle, gscore, max_off[0], max_off[1]);
}
/*
// avx2 sw
cur_query_pos = 0;
cur_target_pos = 0;
for (i = 0; i < block_line_num; ++i)
{
#ifdef SHOW_PERF
int64_t start_time = get_mseconds();
#endif
score_avx2 += ksw_avx2(
info_arr[i][0],
(uint8_t *)query_arr + cur_query_pos,
info_arr[i][1],
(uint8_t *)target_arr + cur_target_pos,
0, 5, mat, 6, 1, 6, 1,
1, 4,
100, 5, 100,
info_arr[i][2],
&qle, &tle, &gtle, &gscore, &max_off[0]);
#ifdef SHOW_PERF
time_sw_avx2 += get_mseconds() - start_time;
#endif
// 更新query和target位置信息
cur_query_pos += info_arr[i][0];
cur_target_pos += info_arr[i][1];
// fprintf(stderr, "%d %d %d %d %d %d %d\n", score_avx2, qle, tle, gtle, gscore, max_off[0], max_off[1]);
}
// avx2 u8 heuristics
PERFORMANCE_TEST_AVX2(4, ksw_extend_avx2_u8_heuristics);
// avx2 u8 sw
cur_query_pos = 0;
cur_target_pos = 0;
for (i = 0; i < block_line_num; ++i)
{
#ifdef SHOW_PERF
int64_t start_time = get_mseconds();
#endif
score_avx2_u8 += ksw_avx2_u8(
info_arr[i][0],
(uint8_t *)query_arr + cur_query_pos,
info_arr[i][1],
(uint8_t *)target_arr + cur_target_pos,
0, 5, mat, 6, 1, 6, 1,
1, 4,
100, 5, 100,
info_arr[i][2],
&qle, &tle, &gtle, &gscore, &max_off[0]);
#ifdef SHOW_PERF
time_sw_avx2_u8 += get_mseconds() - start_time;
#endif
// 更新query和target位置信息
cur_query_pos += info_arr[i][0];
cur_target_pos += info_arr[i][1];
// fprintf(stderr, "%d %d %d %d %d %d %d\n", score_normal, qle, tle, gtle, gscore, max_off[0], max_off[1]);
}
*/
// fprintf(stderr, "%d %d \n", block_line_num, total_line_num);
// avx2 mem aligned
PERFORMANCE_TEST_AVX2(5, ksw_extend_avx2_aligned);
// avx2 u8 mem aligned
PERFORMANCE_TEST_AVX2(6, ksw_extend_avx2_u8_aligned);
}
// fprintf(stderr, "%d \n", score_normal);
#ifdef SHOW_PERF
fprintf(stderr, "time_sw_normal: %f s; score: %d\n", time_sw_normal / DIVIDE_BY, score_normal_total);
fprintf(stderr, "time_bsw_avx2: %f s; score: %d\n", time_bsw_avx2 / DIVIDE_BY, score_bsw_avx2_total);
fprintf(stderr, "time_sw_avx2: %f s; score: %d\n", time_sw_avx2 / DIVIDE_BY, score_avx2_total);
fprintf(stderr, "time_sw_avx2_u8: %f s; score: %d\n", time_sw_avx2_u8 / DIVIDE_BY, score_avx2_u8_total);
fprintf(stderr, "time_sw_avx2_u8_aligned: %f s; score: %d\n", time_sw_avx2_u8_aligned / DIVIDE_BY, score_avx2_u8_aligned_total);
fprintf(stderr, "thread mem capacity: %d\t%d\n", tmem.capacity, tmem_u8.capacity);
fprintf(stderr, "time_bsw_init: %f s\n", time_bsw_init / DIVIDE_BY);
// fprintf(stderr, "time_bsw_main_loop: %f s\n", (time_bsw_main_loop) / DIVIDE_BY);
// fprintf(stderr, "time_bsw_find_max: %f s\n", (time_bsw_find_max) / DIVIDE_BY);
// fprintf(stderr, "time_bsw_adjust_bound: %f s\n", (time_bsw_adjust_bound) / DIVIDE_BY);
// fprintf(stderr, "time_bsw_main_loop: %f s\n", (time_bsw_main_loop - time_compare) / DIVIDE_BY);
// fprintf(stderr, "time_bsw_find_max: %f s\n", (time_bsw_find_max - time_compare) / DIVIDE_BY);
// fprintf(stderr, "time_bsw_adjust_bound: %f s\n", (time_bsw_adjust_bound - time_compare) / DIVIDE_BY);
// fprintf(stderr, "time_compare: %f s\n", time_compare / DIVIDE_BY);
char *kernel_names[7] = {
"normal",
"avx2",
"avx2_u8",
"avx2_heuristics",
"avx2_u8_heuristics",
"avx2_aligned",
"avx2_u8_aligned"};
for (i = 0; i < KERNEL_NUM; ++i)
{
fprintf(stderr, "[%18s] time: %9.6f s; score: %d\n", kernel_names[i], time_sw[i] / DIVIDE_BY, score_total[i]);
}
#endif
if (query_f != 0)
@ -422,6 +263,4 @@ int main(int argc, char *argv[])
fclose(avx2_u8_out_f);
if (normal_out_f != 0)
fclose(normal_out_f);
if (bsw_avx2_out_f != 0)
fclose(bsw_avx2_out_f);
}

2
run_all.sh 100755
View File

@ -0,0 +1,2 @@
#!/bin/bash
/home/zzh/work/sw_perf/sw_perf /home/zzh/data/sw/query.fa /home/zzh/data/sw/target.fa /home/zzh/data/sw/info.txt

2
run_l.sh 100755
View File

@ -0,0 +1,2 @@
#!/bin/bash
/home/zzh/work/sw_perf/sw_perf /home/zzh/data/sw/q_l.fa /home/zzh/data/sw/t_l.fa /home/zzh/data/sw/i_l.txt

2
run_m.sh 100755
View File

@ -0,0 +1,2 @@
#!/bin/bash
/home/zzh/work/sw_perf/sw_perf /home/zzh/data/sw/q_m.fa /home/zzh/data/sw/t_m.fa /home/zzh/data/sw/i_m.txt

2
run_s.sh 100755
View File

@ -0,0 +1,2 @@
#!/bin/bash
/home/zzh/work/sw_perf/sw_perf /home/zzh/data/sw/q_s.fa /home/zzh/data/sw/t_s.fa /home/zzh/data/sw/i_s.txt

8
thread_mem.c
View File

@ -9,6 +9,7 @@
#include "thread_mem.h"
#include <stdio.h>
#include <string.h>
// 创建
thread_mem_t *create_thread_mem()
@ -64,6 +65,13 @@ void *thread_mem_request(thread_mem_t *tmem, size_t byte_cnt)
return ret_mem;
}
void *thread_mem_request_and_clean(thread_mem_t *tmem, size_t byte_cnt)
{
void *mem = thread_mem_request(tmem, byte_cnt);
memset(mem, 0, byte_cnt);
return mem;
}
// 将不用的内存归还给thread mem
void thread_mem_release(thread_mem_t *tmem, size_t byte_cnt)
{

6
thread_mem.h
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@ -16,7 +16,7 @@
#define MEM_ALIGN_BYTE 8
#define MEM_MOVE_BIT 3
typedef struct
typedef struct _thread_mem_t
{
size_t occupied; // 已经占用的容量（字节数） 对齐的
size_t capacity; // 总容量（字节数）
@ -29,9 +29,13 @@ thread_mem_t *create_thread_mem();
void init_thread_mem(thread_mem_t *tmem);
// 初始化并开辟一定量的内存
void thread_mem_init_alloc(thread_mem_t *tmem, size_t byte_cnt);
// 请求内存
void *thread_mem_request(thread_mem_t *tmem, size_t byte_cnt);
// 请求内存并初始化为零
void *thread_mem_request_and_clean(thread_mem_t *tmem, size_t byte_cnt);
// 将不用的内存归还给thread mem
void thread_mem_release(thread_mem_t *tmem, size_t byte_cnt);

39
utils.c 100644
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@ -0,0 +1,39 @@
/*********************************************************************************************
Description: Some useful functions
Copyright : All right reserved by NCIC.ICT
Author : Zhang Zhonghai
Date : 2023/08/25
***********************************************************************************************/
#include "utils.h"
#include <string.h>
#include <stdint.h>
unsigned char nst_nt4_table[256] = {
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5 /*'-'*/, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4};
char t_2bit2char[5] = {'A', 'C', 'G', 'T', 'N'};
// 将碱基字符转成2位编码
void convert_char_to_2bit(char *str)
{
int i;
for (i = 0; i < strlen(str); ++i)
str[i] = nst_nt4_table[(uint8_t)str[i]];
}

15
utils.h 100644
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@ -0,0 +1,15 @@
/*********************************************************************************************
Description: Some useful functions
Copyright : All right reserved by NCIC.ICT
Author : Zhang Zhonghai
Date : 2023/08/25
***********************************************************************************************/
#ifndef __UTILS_H
#define __UTILS_H
// 将碱基字符转成2位编码
void convert_char_to_2bit(char *str);
#endif