Needleman-Wunsch算法是一种常用于比对两个字符串的算法。该算法的串行实现效率较低,因此可以通过使用OpenMP进行并行化来提高效率。
以下是基于OpenMP的Needleman-Wunsch算法的示例代码:
#include
#include
#include
#include
int max(int a, int b, int c) {
int m = a;
if (b > m) m = b;
if (c > m) m = c;
return m;
}
int main() {
char *s1 = "AGTACGCA";
char *s2 = "TATGC";
int n = strlen(s1);
int m = strlen(s2);
int **score = (int**) calloc(n+1, sizeof(int*));
for (int i = 0; i <= n; i++) {
score[i] = (int*) calloc(m+1, sizeof(int));
}
int gap_penalty = -2;
int match_score = 2;
int mismatch_score = -1;
double start_time = omp_get_wtime();
// Initialize the score matrix
for (int i = 1; i <= n; i++) {
score[i][0] = i * gap_penalty;
}
for (int j = 1; j <= m; j++) {
score[0][j] = j * gap_penalty;
}
// Compute the score matrix
#pragma omp parallel for
for (int i = 1; i <= n; i++) {
for (int j = 1; j <= m; j++) {
int match = score[i-1][j-1] + (s1[i-1] == s2[j-1] ? match_score : mismatch_score);
int delete = score[i-1][j] + gap_penalty;
int insert = score[i][j-1] + gap_penalty;
score[i][j] = max(match, delete, insert);
}
}
double end_time = omp_get_wtime();
printf("Time: %f\n", end_time - start_time);
// Print the score matrix
for (int i = 0; i <= n; i++) {
for (int j = 0; j <= m; j++) {
printf("%d ", score[i][j]);
}
printf("\n");
}
// Free memory
for (int i = 0; i <= n; i++) {
free(score[i]);
}
free(score);
return 0;
}
在此示例中,我们使用OpenMP的“parallel for”指令并行化了计算得分矩阵的循环。因此,对于每个i,j的组合,都会生成一个线程来计算它们的得分。
值得注意的是,并行化Needleman-Wunsch算法并不能总是
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