262 lines
9.0 KiB
C
262 lines
9.0 KiB
C
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#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 "sys/time.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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#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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}
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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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#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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/*
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* 包含一个参数，用来区分调用那个sw算法
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* 参数为 normal/avx2/cuda
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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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/*
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int sw_algo = SW_NORMAL;
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// 判断执行的sw的实现类型
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if (argc > 1)
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{
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if (strcmp(argv[1], "normal") == 0)
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{
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sw_algo = SW_NORMAL;
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}
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else if (strcmp(argv[1], "avx2") == 0)
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{
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sw_algo = SW_AVX2;
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}
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else if (strcmp(argv[1], "cuda") == 0)
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{
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sw_algo = SW_CUDA;
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}
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else
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{
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sw_algo = SW_ALL;
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}
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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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// 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);
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int **info_arr = (int **)malloc(SEQ_BUF_SIZE);
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FILE *query_f = 0, *target_f = 0, *info_f = 0;
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// const char *qf_path = "/public/home/zzh/data/sw/q_s.fa";
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// const char *tf_path = "/public/home/zzh/data/sw/t_s.fa";
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// const char *if_path = "/public/home/zzh/data/sw/i_s.txt";
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const char *qf_path = "/public/home/zzh/data/sw/q_m.fa";
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const char *tf_path = "/public/home/zzh/data/sw/t_m.fa";
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const char *if_path = "/public/home/zzh/data/sw/i_m.txt";
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// const char *qf_path = "/public/home/zzh/data/sw/q_m.fa";
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// const char *tf_path = "/public/home/zzh/data/sw/t_m.fa";
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// const char *if_path = "/public/home/zzh/data/sw/i_m.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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// 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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}
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int score_normal = 0, score_avx2 = 0, score_avx2_u8 = 0;
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while (!feof(target_f))
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{
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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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const int line_size = strlen(read_buf);
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assert(line_size < READ_BUF_SIZE);
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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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}
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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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const int line_size = strlen(read_buf);
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assert(line_size < READ_BUF_SIZE);
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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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// 普通 sw
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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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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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// 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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// 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]);
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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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// 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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// fprintf(stderr, "%d %d \n", block_line_num, total_line_num);
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}
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// fprintf(stderr, "%d \n", score_normal);
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#ifdef SHOW_PERF
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fprintf(stderr, "time_sw_normal: %f s; score: %d\n", time_sw_normal / 1000.0, score_normal);
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fprintf(stderr, "time_sw_avx2: %f s; score: %d\n", time_sw_avx2 / 1000.0, score_avx2);
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fprintf(stderr, "time_sw_avx2_u8: %f s; score: %d\n", time_sw_avx2_u8 / 1000.0, score_avx2_u8);
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#endif
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if (query_f != 0)
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fclose(query_f);
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if (target_f != 0)
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fclose(target_f);
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if (info_f != 0)
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fclose(info_f);
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}
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