294 lines
9.6 KiB
C
294 lines
9.6 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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#include "ksw_ext.h"
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#include "utils.h"
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#include "common.h"
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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 INIT_ALLOC_SIZE 4096
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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[KERNEL_NUM] = {0};
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#endif
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#ifdef DEBUG_RETURN_VALUE
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#define OUTPUT_RETVAL(kernel_num) \
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fprintf(retval_f_arr[kernel_num], "%d\t%d\t%d\t%d\t%d\t%d\n", score[kernel_num], qle, tle, gtle, gscore, max_off[0])
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#else
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#define OUTPUT_RETVAL(out_f)
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#endif
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#define _PERFORMANCE_TEST_NORMAL(kernel_num, func) \
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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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score[kernel_num] = func( \
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&tmem[kernel_num], \
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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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score_total[kernel_num] += score[kernel_num]; \
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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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OUTPUT_RETVAL(0); \
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}
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#define _PERFORMANCE_TEST_AVX2(kernel_num, func) \
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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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score[kernel_num] = func( \
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&tmem[kernel_num], \
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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_total[kernel_num] += score[kernel_num]; \
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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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OUTPUT_RETVAL(kernel_num); \
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}
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#ifdef SHOW_PERF
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#define PERFORMANCE_TEST_NORMAL(kernel_num, func) \
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start_time = get_mseconds(); \
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_PERFORMANCE_TEST_NORMAL(kernel_num, func); \
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time_sw[kernel_num] += get_mseconds() - start_time
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#define PERFORMANCE_TEST_AVX2(kernel_num, func) \
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start_time = get_mseconds(); \
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_PERFORMANCE_TEST_AVX2(kernel_num, func); \
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time_sw[kernel_num] += get_mseconds() - start_time
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#else
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#define PERFORMANCE_TEST_NORMAL(kernel_num, func) _PERFORMANCE_TEST_NORMAL(kernel_num, func)
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#define PERFORMANCE_TEST_AVX2(kernel_num, func) _PERFORMANCE_TEST_AVX2(kernel_num, func)
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#endif
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// 读取一行序列数据
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int read_seq_line(char *read_buf, FILE *f_ptr, char *out_arr)
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{
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if (fgets(read_buf, READ_BUF_SIZE, f_ptr) == NULL)
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return 0;
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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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memcpy(out_arr, read_buf, line_size);
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return line_size;
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}
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// 全局变量
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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 *ins_ext_f_arr[KERNEL_NUM] = {0},
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*del_ext_f_arr[KERNEL_NUM] = {0},
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*score_f_arr[KERNEL_NUM] = {0},
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*retval_f_arr[KERNEL_NUM] = {0};
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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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const char *qf_path = argv[1];
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const char *tf_path = argv[2];
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const char *if_path = argv[3];
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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[KERNEL_NUM];
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int i, j;
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for (i = 0; i < KERNEL_NUM; ++i)
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{
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thread_mem_init_alloc(tmem + i, INIT_ALLOC_SIZE);
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}
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// 记录计算出的分数
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int score[KERNEL_NUM] = {0};
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int64_t score_total[KERNEL_NUM] = {0};
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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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// 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 cur_query_pos, cur_target_pos;
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int64_t start_time;
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char read_buf[READ_BUF_SIZE]; // 读文件缓存
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#ifdef DEBUG_OUT
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for (i = 0; i < KERNEL_NUM; ++i)
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{
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char out_path[64];
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sprintf(out_path, "/home/zzh/work/sw_perf/output/ins_%d.txt", i);
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ins_ext_f_arr[i] = fopen(out_path, "w");
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sprintf(out_path, "/home/zzh/work/sw_perf/output/del_%d.txt", i);
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del_ext_f_arr[i] = fopen(out_path, "w");
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sprintf(out_path, "/home/zzh/work/sw_perf/output/score_%d.txt", i);
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score_f_arr[i] = fopen(out_path, "w");
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}
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#endif
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#ifdef DEBUG_RETURN_VALUE
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for (i = 0; i < KERNEL_NUM; ++i)
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{
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char out_path[64];
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sprintf(out_path, "/home/zzh/work/sw_perf/output/retval_%d.txt", i);
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retval_f_arr[i] = fopen(out_path, "w");
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}
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#endif
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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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// 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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while (!feof(target_f))
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{
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block_line_num = 0; // 记录每次读取的行数
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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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int line_size = read_seq_line(read_buf, target_f, target_arr + cur_read_size);
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// fprintf(stderr, "line: %d\n", line_size);
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if (line_size == 0)
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break;
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cur_read_size += line_size;
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++block_line_num;
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++total_line_num;
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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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int line_size = read_seq_line(read_buf, query_f, query_arr + cur_read_size);
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if (line_size == 0)
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break;
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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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// normal sw
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PERFORMANCE_TEST_NORMAL(0, ksw_extend_normal);
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// avx2
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PERFORMANCE_TEST_AVX2(1, ksw_extend_avx2);
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// avx2 heuristics
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PERFORMANCE_TEST_AVX2(2, ksw_extend_avx2_heuristics);
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// avx2 mem aligned
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PERFORMANCE_TEST_AVX2(3, ksw_extend_avx2_aligned);
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// avx2 u8
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PERFORMANCE_TEST_AVX2(4, ksw_extend_avx2_u8);
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// avx2 u8 heuristics
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PERFORMANCE_TEST_AVX2(5, ksw_extend_avx2_u8_heuristics);
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// avx2 u8 mem aligned
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PERFORMANCE_TEST_AVX2(6, ksw_extend_avx2_u8_aligned);
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}
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#ifdef SHOW_PERF
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char *kernel_names[7] = {
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"normal",
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"avx2",
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"avx2_heuristics",
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"avx2_aligned",
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"avx2_u8",
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"avx2_u8_heuristics",
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"avx2_u8_aligned"};
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for (i = 0; i < KERNEL_NUM; ++i)
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{
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fprintf(stderr, "[%18s] time: %9.6f s; score: %ld\n", kernel_names[i], time_sw[i] / DIVIDE_BY, score_total[i]);
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}
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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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for (i = 0; i < KERNEL_NUM; ++i)
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{
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if (ins_ext_f_arr[i] != 0)
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fclose(ins_ext_f_arr[i]);
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if (del_ext_f_arr[i] != 0)
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fclose(del_ext_f_arr[i]);
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if (score_f_arr[i] != 0)
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fclose(score_f_arr[i]);
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if (retval_f_arr[i] != 0)
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fclose(retval_f_arr[i]);
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}
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}
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