发现并解决开辟内存的bug（开辟指针时候没有考虑每个指针占用的字节数），用clock试试计算运行时间
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53332e34e1
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12
ksw_normal.c
12
ksw_normal.c
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@ -127,12 +127,12 @@ int ksw_normal(int qlen, const uint8_t *query, int tlen, const uint8_t *target,
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}
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}
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// update beg and end for the next round
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for (j = beg; LIKELY(j < end) && eh[j].h == 0 && eh[j].e == 0; ++j)
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;
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beg = j;
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for (j = end; LIKELY(j >= beg) && eh[j].h == 0 && eh[j].e == 0; --j)
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;
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end = j + 2 < qlen ? j + 2 : qlen; // 剪枝没考虑f，即insert
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// for (j = beg; LIKELY(j < end) && eh[j].h == 0 && eh[j].e == 0; ++j)
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// ;
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// beg = j;
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// for (j = end; LIKELY(j >= beg) && eh[j].h == 0 && eh[j].e == 0; --j)
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// ;
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// end = j + 2 < qlen ? j + 2 : qlen; // 剪枝没考虑f，即insert
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beg = 0, end = qlen; // uncomment this line for debugging
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// fprintf(stderr, "\n");
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// fprintf(stderr, "%d\n", end);
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66
main.c
66
main.c
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@ -3,6 +3,7 @@
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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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#define SW_NORMAL 0
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@ -14,14 +15,17 @@
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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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// 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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@ -111,8 +115,8 @@ int main(int argc, char *argv[])
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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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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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@ -120,18 +124,18 @@ int main(int argc, char *argv[])
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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 = "/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_l.fa";
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const char *tf_path = "/public/home/zzh/data/sw/t_l.fa";
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const char *if_path = "/public/home/zzh/data/sw/i_l.txt";
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// const char *qf_path = "/public/home/zzh/data/sw/query.fa";
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// const char *tf_path = "/public/home/zzh/data/sw/target.fa";
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// const char *if_path = "/public/home/zzh/data/sw/info.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 = "/public/home/zzh/data/sw/query.fa";
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// const char *tf_path = "/public/home/zzh/data/sw/target.fa";
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// const char *if_path = "/public/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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@ -149,7 +153,6 @@ int main(int argc, char *argv[])
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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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@ -160,6 +163,7 @@ int main(int argc, char *argv[])
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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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@ -167,6 +171,7 @@ int main(int argc, char *argv[])
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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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@ -187,8 +192,10 @@ int main(int argc, char *argv[])
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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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@ -223,7 +230,6 @@ int main(int argc, char *argv[])
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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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@ -231,6 +237,7 @@ int main(int argc, char *argv[])
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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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@ -370,16 +377,19 @@ int main(int argc, char *argv[])
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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_total);
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fprintf(stderr, "time_bsw_avx2: %f s; score: %d\n", time_bsw_avx2 / 1000.0, score_bsw_avx2_total);
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// fprintf(stderr, "time_sw_avx2: %f s; score: %d\n", time_sw_avx2 / 1000.0, score_avx2_total);
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fprintf(stderr, "time_sw_avx2_u8: %f s; score: %d\n", time_sw_avx2_u8 / 1000.0, score_avx2_u8_total);
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fprintf(stderr, "time_sw_normal: %f s; score: %d\n", time_sw_normal / DIVIDE_BY, score_normal_total);
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fprintf(stderr, "time_bsw_avx2: %f s; score: %d\n", time_bsw_avx2 / DIVIDE_BY, score_bsw_avx2_total);
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// fprintf(stderr, "time_sw_avx2: %f s; score: %d\n", time_sw_avx2 / DIVIDE_BY, score_avx2_total);
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fprintf(stderr, "time_sw_avx2_u8: %f s; score: %d\n", time_sw_avx2_u8 / DIVIDE_BY, score_avx2_u8_total);
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fprintf(stderr, "time_bsw_init: %f s\n", time_bsw_init / 1000.0);
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fprintf(stderr, "time_bsw_main_loop: %f s\n", (time_bsw_main_loop - time_compare) / 1000.0);
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fprintf(stderr, "time_bsw_find_max: %f s\n", (time_bsw_find_max - time_compare) / 1000.0);
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fprintf(stderr, "time_bsw_adjust_bound: %f s\n", (time_bsw_adjust_bound - time_compare) / 1000.0);
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fprintf(stderr, "time_compare: %f s\n", time_compare / 1000.0);
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fprintf(stderr, "time_bsw_init: %f s\n", time_bsw_init / DIVIDE_BY);
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// fprintf(stderr, "time_bsw_main_loop: %f s\n", (time_bsw_main_loop) / DIVIDE_BY);
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// fprintf(stderr, "time_bsw_find_max: %f s\n", (time_bsw_find_max) / DIVIDE_BY);
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// fprintf(stderr, "time_bsw_adjust_bound: %f s\n", (time_bsw_adjust_bound) / DIVIDE_BY);
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fprintf(stderr, "time_bsw_main_loop: %f s\n", (time_bsw_main_loop - time_compare) / DIVIDE_BY);
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fprintf(stderr, "time_bsw_find_max: %f s\n", (time_bsw_find_max - time_compare) / DIVIDE_BY);
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fprintf(stderr, "time_bsw_adjust_bound: %f s\n", (time_bsw_adjust_bound - time_compare) / DIVIDE_BY);
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fprintf(stderr, "time_compare: %f s\n", time_compare / DIVIDE_BY);
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#endif
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if (query_f != 0)
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