428 lines
17 KiB
C
428 lines
17 KiB
C
#include <stdlib.h>
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#include <stdio.h>
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#include <string.h>
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#include <stdint.h>
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#include <assert.h>
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#include <time.h>
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#include "sys/time.h"
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#include "thread_mem.h"
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#define SW_NORMAL 0
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#define SW_AVX2 1
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#define SW_CUDA 2
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#define SW_ALL 3
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#define BLOCK_BUF_SIZE 1048576
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#define READ_BUF_SIZE 2048
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#define SEQ_BUF_SIZE (BLOCK_BUF_SIZE + READ_BUF_SIZE)
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#define DIVIDE_BY (CLOCKS_PER_SEC * 1.0)
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#ifdef SHOW_PERF
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// 用来调试，计算感兴趣部分的运行时间
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// 获取当前毫秒数
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int64_t get_mseconds()
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{
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// struct timeval tv;
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// gettimeofday(&tv, NULL);
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// return (int64_t)1000 * (tv.tv_sec + ((1e-6) * tv.tv_usec));
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return clock();
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}
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int64_t time_sw_normal = 0,
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time_sw_avx2 = 0,
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time_sw_avx2_u8 = 0,
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time_sw_avx2_u8_aligned = 0,
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time_bsw_avx2 = 0,
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time_bsw_init = 0,
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time_bsw_main_loop = 0,
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time_bsw_find_max = 0,
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time_bsw_adjust_bound = 0,
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time_compare = 0;
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#endif
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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);
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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,
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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);
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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,
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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);
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unsigned char nst_nt4_table[256] = {
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5 /*'-'*/, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4};
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char t_2bit2char[5] = {'A', 'C', 'G', 'T'};
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// 将碱基字符转成2位编码
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void convert_char_to_2bit(char *str)
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{
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int i;
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for (i = 0; i < strlen(str); ++i)
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str[i] = nst_nt4_table[str[i]];
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}
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// 读取测试数据
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int read_data()
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{
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return 0;
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}
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// 程序执行入口
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int main(int argc, char *argv[])
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{
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// 初始化一些全局参数
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int8_t mat[25] = {1, -4, -4, -4, -1,
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-4, 1, -4, -4, -1,
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-4, -4, 1, -4, -1,
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-4, -4, -4, 1, -1,
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-1, -1, -1, -1, -1};
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int max_off[2];
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int qle, tle, gtle, gscore;
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thread_mem_t tmem, tmem_u8;
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init_thread_mem(&tmem);
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init_thread_mem(&tmem_u8);
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// thread_mem_init_alloc(&tmem_u8, 10960);
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// 读取测试数据
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char *query_arr = (char *)malloc(SEQ_BUF_SIZE);
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char *target_arr = (char *)malloc(SEQ_BUF_SIZE);
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int *info_buf = (int *)malloc(SEQ_BUF_SIZE * sizeof(int));
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int **info_arr = (int **)malloc(SEQ_BUF_SIZE * sizeof(int *));
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FILE *query_f = 0, *target_f = 0, *info_f = 0;
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// const char *qf_path = "q.fa";
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// const char *tf_path = "t.fa";
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// const char *if_path = "i.txt";
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// const char *qf_path = "bug_q.fa";
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// const char *tf_path = "bug_t.fa";
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// const char *if_path = "bug_i.txt";
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// const char *qf_path = "/home/zzh/data/sw/q_s.fa";
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// const char *tf_path = "/home/zzh/data/sw/t_s.fa";
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// const char *if_path = "/home/zzh/data/sw/i_s.txt";
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// const char *qf_path = "/home/zzh/data/sw/q_m.fa";
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// const char *tf_path = "/home/zzh/data/sw/t_m.fa";
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// const char *if_path = "/home/zzh/data/sw/i_m.txt";
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const char *qf_path = "/home/zzh/data/sw/q_l.fa";
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const char *tf_path = "/home/zzh/data/sw/t_l.fa";
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const char *if_path = "/home/zzh/data/sw/i_l.txt";
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// const char *qf_path = "/home/zzh/data/sw/query.fa";
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// const char *tf_path = "/home/zzh/data/sw/target.fa";
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// const char *if_path = "/home/zzh/data/sw/info.txt";
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query_f = fopen(qf_path, "r");
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target_f = fopen(tf_path, "r");
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info_f = fopen(if_path, "r");
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// 将每次比对的得分等信息写入文件，进行debug
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FILE *normal_out_f = fopen("normal_out.txt", "w");
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FILE *avx2_out_f = fopen("avx2_out.txt", "w");
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FILE *avx2_u8_out_f = fopen("avx2_u8_out.txt", "w");
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FILE *bsw_avx2_out_f = fopen("bsw_avx2_out.txt", "w");
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// 每次读取一定量的数据，然后执行，直到处理完所有数据
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int total_line_num = 0; // 目前处理的总的数据行数
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int block_line_num = 0; // 当前循环包含的数据行数
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int i, j;
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// const int max_read = READ_BUF_SIZE; // 每次最多读取的字符
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char read_buf[READ_BUF_SIZE]; // 读文件缓存
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// int ret_code = 0;
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// 初始化info_arr数组
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i = 0;
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j = 0;
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while (1)
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{
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if (j > BLOCK_BUF_SIZE)
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break;
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info_arr[i] = &info_buf[j];
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i += 1;
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j += 3;
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// fprintf(stderr, "%d\t%d\n", i, j);
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}
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int score_normal = 0, score_avx2 = 0, score_avx2_u8 = 0, score_bsw_avx2 = 0;
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int score_normal_total = 0, score_avx2_total = 0, score_avx2_u8_total = 0, score_bsw_avx2_total = 0;
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int score_avx2_u8_aligned = 0, score_avx2_u8_aligned_total = 0;
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while (!feof(target_f))
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{
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// fprintf(stderr, "debug\n");
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block_line_num = 0;
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// 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
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int cur_read_size = 0;
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while (!feof(target_f) && cur_read_size < BLOCK_BUF_SIZE)
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{
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if (fgets(read_buf, READ_BUF_SIZE, target_f) == NULL)
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break;
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int line_size = strlen(read_buf);
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assert(line_size < READ_BUF_SIZE);
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if (read_buf[line_size - 1] == '\n')
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{
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read_buf[line_size - 1] = '\0';
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line_size--;
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}
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convert_char_to_2bit(read_buf);
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++block_line_num;
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++total_line_num;
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strncpy(target_arr + cur_read_size, read_buf, line_size);
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cur_read_size += line_size;
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// fprintf(stderr, "%d %d \n", line_size, cur_read_size);
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// fprintf(stderr, "%d %d \n", block_line_num, total_line_num);
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}
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// fprintf(stderr, "here\n");
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// 读query
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cur_read_size = 0;
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for (i = 0; i < block_line_num; ++i)
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{
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if (fgets(read_buf, READ_BUF_SIZE, query_f) == NULL)
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break;
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int line_size = strlen(read_buf);
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assert(line_size < READ_BUF_SIZE);
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if (read_buf[line_size - 1] == '\n')
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{
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read_buf[line_size - 1] = '\0';
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line_size--;
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}
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convert_char_to_2bit(read_buf);
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strncpy(query_arr + cur_read_size, read_buf, line_size);
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cur_read_size += line_size;
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}
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// 读info
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cur_read_size = 0;
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for (i = 0; i < block_line_num; ++i)
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{
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if (fgets(read_buf, READ_BUF_SIZE, info_f) == NULL)
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break;
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const int line_size = strlen(read_buf);
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assert(line_size < READ_BUF_SIZE);
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sscanf(read_buf, "%d %d %d\n", &info_arr[i][0], &info_arr[i][1], &info_arr[i][2]);
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cur_read_size += line_size;
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// fprintf(stderr, "%-8d%-8d%-8d\n", info_arr[i][0], info_arr[i][1], info_arr[i][2]);
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// fprintf(stderr, "%s\n", read_buf);
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}
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// 性能测试
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int cur_query_pos = 0;
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int cur_target_pos = 0;
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for (i = 0; i < block_line_num; ++i)
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{
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#ifdef SHOW_PERF
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int64_t start_time = get_mseconds();
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#endif
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// 普通 sw
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score_normal = ksw_normal(
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info_arr[i][0],
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(uint8_t *)query_arr + cur_query_pos,
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info_arr[i][1],
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(uint8_t *)target_arr + cur_target_pos,
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5, mat, 6, 1, 6, 1, 100, 5, 100,
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info_arr[i][2],
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&qle, &tle, >le, &gscore, &max_off[0]);
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#ifdef SHOW_PERF
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time_sw_normal += get_mseconds() - start_time;
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#endif
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score_normal_total += score_normal;
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// fprintf(normal_out_f, "%d %d\n", info_arr[i][2], score_normal);
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// fprintf(stderr, "%d %d %d %d %d %d %d\n", info_arr[i][2], score_normal, qle, tle, gtle, gscore, max_off[0]);
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// #ifdef SHOW_PERF
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// start_time = get_mseconds();
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// #endif
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// score_bsw_avx2 = ksw_avx2_aligned(
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// &tmem,
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// info_arr[i][0],
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// (uint8_t *)query_arr + cur_query_pos,
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// info_arr[i][1],
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// (uint8_t *)target_arr + cur_target_pos,
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// 0, 6, 1, 6, 1,
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// 1, 4,
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// 100, 5,
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// info_arr[i][2],
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// &qle, &tle, >le, &gscore, &max_off[0]);
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// #ifdef SHOW_PERF
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// time_bsw_avx2 += get_mseconds() - start_time;
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// #endif
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// score_bsw_avx2_total += score_bsw_avx2;
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// fprintf(avx2_out_f, "%d %d\n", info_arr[i][2], score_avx2);
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// 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]);
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/**/
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#ifdef SHOW_PERF
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start_time = get_mseconds();
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#endif
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score_avx2 = bsw_avx2(
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info_arr[i][0],
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(uint8_t *)query_arr + cur_query_pos,
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info_arr[i][1],
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(uint8_t *)target_arr + cur_target_pos,
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0, 6, 1, 6, 1,
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1, 4,
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100, 5,
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info_arr[i][2],
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&qle, &tle, >le, &gscore, &max_off[0]);
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// score_avx2 = ksw_avx2(
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// info_arr[i][0],
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// (uint8_t *)query_arr + cur_query_pos,
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// info_arr[i][1],
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// (uint8_t *)target_arr + cur_target_pos,
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// 0, 5, mat, 6, 1, 6, 1,
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// 1, 4,
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// 100, 5, 100,
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// info_arr[i][2],
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// &qle, &tle, >le, &gscore, &max_off[0]);
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#ifdef SHOW_PERF
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time_sw_avx2 += get_mseconds() - start_time;
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#endif
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score_avx2_total += score_avx2;
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// fprintf(avx2_out_f, "%d %d\n", info_arr[i][2], score_avx2);
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// fprintf(stderr, "%d %d %d %d %d %d %d\n", info_arr[i][2], score_avx2, qle, tle, gtle, gscore, max_off[0]);
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#ifdef SHOW_PERF
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start_time = get_mseconds();
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#endif
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score_avx2_u8 = ksw_avx2_u8(
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info_arr[i][0],
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(uint8_t *)query_arr + cur_query_pos,
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info_arr[i][1],
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(uint8_t *)target_arr + cur_target_pos,
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0, 5, mat, 6, 1, 6, 1,
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1, 4,
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100, 5, 100,
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info_arr[i][2],
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&qle, &tle, >le, &gscore, &max_off[0]);
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#ifdef SHOW_PERF
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time_sw_avx2_u8 += get_mseconds() - start_time;
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#endif
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score_avx2_u8_total += score_avx2_u8;
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// fprintf(avx2_u8_out_f, "%d %d %d %d %d %d\n", score_avx2_u8, qle, tle, gtle, gscore, max_off[0]);
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#ifdef SHOW_PERF
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start_time = get_mseconds();
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#endif
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score_avx2_u8_aligned = ksw_avx2_u8_aligned(
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&tmem_u8,
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info_arr[i][0],
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(uint8_t *)query_arr + cur_query_pos,
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info_arr[i][1],
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(uint8_t *)target_arr + cur_target_pos,
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0, 5, mat, 6, 1, 6, 1,
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1, 4,
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100, 5, 100,
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info_arr[i][2],
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&qle, &tle, >le, &gscore, &max_off[0]);
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#ifdef SHOW_PERF
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time_sw_avx2_u8_aligned += get_mseconds() - start_time;
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#endif
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score_avx2_u8_aligned_total += score_avx2_u8_aligned;
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// fprintf(avx2_u8_out_f, "%d %d %d %d %d %d\n", score_avx2_u8, qle, tle, gtle, gscore, max_off[0]);
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// 更新query和target位置信息
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cur_query_pos += info_arr[i][0];
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cur_target_pos += info_arr[i][1];
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// fprintf(stderr, "%d %d %d %d %d %d %d\n", score_normal, qle, tle, gtle, gscore, max_off[0], max_off[1]);
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}
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/*
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// avx2 sw
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cur_query_pos = 0;
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cur_target_pos = 0;
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for (i = 0; i < block_line_num; ++i)
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{
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#ifdef SHOW_PERF
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int64_t start_time = get_mseconds();
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#endif
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score_avx2 += ksw_avx2(
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info_arr[i][0],
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(uint8_t *)query_arr + cur_query_pos,
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info_arr[i][1],
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(uint8_t *)target_arr + cur_target_pos,
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0, 5, mat, 6, 1, 6, 1,
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1, 4,
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100, 5, 100,
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info_arr[i][2],
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&qle, &tle, >le, &gscore, &max_off[0]);
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#ifdef SHOW_PERF
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time_sw_avx2 += get_mseconds() - start_time;
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#endif
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// 更新query和target位置信息
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cur_query_pos += info_arr[i][0];
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cur_target_pos += info_arr[i][1];
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// fprintf(stderr, "%d %d %d %d %d %d %d\n", score_avx2, qle, tle, gtle, gscore, max_off[0], max_off[1]);
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}
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// avx2 u8 sw
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cur_query_pos = 0;
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cur_target_pos = 0;
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for (i = 0; i < block_line_num; ++i)
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{
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#ifdef SHOW_PERF
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int64_t start_time = get_mseconds();
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#endif
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score_avx2_u8 += ksw_avx2_u8(
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info_arr[i][0],
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(uint8_t *)query_arr + cur_query_pos,
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info_arr[i][1],
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(uint8_t *)target_arr + cur_target_pos,
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0, 5, mat, 6, 1, 6, 1,
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1, 4,
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100, 5, 100,
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info_arr[i][2],
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&qle, &tle, >le, &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 / 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);
|
||
#endif
|
||
|
||
if (query_f != 0)
|
||
fclose(query_f);
|
||
if (target_f != 0)
|
||
fclose(target_f);
|
||
if (info_f != 0)
|
||
fclose(info_f);
|
||
if (avx2_out_f != 0)
|
||
fclose(avx2_out_f);
|
||
if (avx2_u8_out_f != 0)
|
||
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);
|
||
}
|