norangebit-unisannio-computer-science/KMP-MPI
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Each file read own portion

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This commit is contained in:
Raffaele Mignone 2021-03-27 14:28:35 +01:00
parent 072ad792f1
commit 95cfa8c1e3
Signed by: norangebit
GPG Key ID: F5255658CB220573
3 changed files with 11 additions and 90 deletions
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91
src/parallel.c
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@ -14,12 +14,6 @@
void find_end(int, char *, char *, int **, int *);
void initialize(char *);
void distribute_text();
void distribute_pattern();
void search_for_splitted_pattern(int *residue, int *match_number, int **matches);
void calculate_absolute_indices(int match_number, int *matches);
@ -49,23 +43,16 @@ int main(int argc, char **argv) {
#ifdef TIME
long_long start_time = PAPI_get_real_usec();
#endif
if (rank == MASTER) {
char *text_file_path = get_text_file(argc, argv);
initialize(text_file_path);
}
distribute_text();
if (rank == MASTER)
free(text);
private_text = read_file_portion(text_file_path, size, rank, &private_text_len, &remain);
pattern = read_file("data/pattern.txt", &pattern_len);
#ifdef LOG
printf("%d -> input: %s\n", rank, private_text);
printf("%d -> text len: %d\n", rank, private_text_len);
#endif
distribute_pattern();
// create and build lps array
int lps[pattern_len];
create_lps(pattern, pattern_len, lps);
@ -80,7 +67,7 @@ int main(int argc, char **argv) {
search_for_splitted_pattern(&residue, &match_number, &matches);
free(private_text);
//free(private_text);
calculate_absolute_indices(match_number, matches);
@ -116,7 +103,6 @@ void find_end(int residue, char *pattern, char *text, int **matches, int *match_
int text_len = strlen(text);
int pattern_len = strlen(pattern);
// TODO: match splitted on 3+ node
if (pattern_len - residue > text_len) return;
while (pattern_index < pattern_len && pattern[pattern_index] == text[text_index]) {
@ -131,67 +117,6 @@ void find_end(int residue, char *pattern, char *text, int **matches, int *match_
(*matches)[*match_number - 1] = -residue;
}
void initialize(char *text_file_path) {
text = read_file(text_file_path, &text_len);
pattern = read_file("data/pattern.txt", &pattern_len);
//printf("text: %s\n", text);
//printf("pattern: %s\n", pattern);
private_text_len = text_len / size;
remain = text_len % size;
if (pattern_len > private_text_len)
MPI_Abort(MPI_COMM_WORLD, 1);
text_piece = (int *) malloc(sizeof(int) * size);
displacements = (int *) malloc(sizeof(int) * size);
displacements[0] = 0;
for (int i = 0; i < size - 1; ++i) {
text_piece[i] = private_text_len;
displacements[i + 1] = displacements[i] + private_text_len;
}
text_piece[size - 1] = private_text_len + remain;
}
void distribute_text() {
// distribution of the length of the text portion to each process
MPI_Scatter(text_piece, 1, MPI_INT, &private_text_len, 1, MPI_INT, MASTER, MPI_COMM_WORLD);
// allocation of space for text
private_text = (char *) malloc(sizeof(char) * (private_text_len + 1));
// distribution of the text portion to each process
// scatterv is necessary because the last process receives a larger portion of text in case it is not perfectly divisible.
MPI_Scatterv(
text,
text_piece,
displacements,
MPI_CHAR,
private_text,
private_text_len,
MPI_CHAR, MASTER,
MPI_COMM_WORLD
);
private_text[private_text_len] = '\0';
}
void distribute_pattern() {
// distribution of the length of the pattern to each process
MPI_Bcast(&pattern_len, 1, MPI_INT, MASTER, MPI_COMM_WORLD);
// allocation of space for the pattern
// the master has already done so previously
if (rank != MASTER) {
pattern = (char *) malloc(sizeof(char) * (pattern_len + 1));
}
// distribution of the pattern to each process
MPI_Bcast(pattern, pattern_len + 1, MPI_CHAR, MASTER, MPI_COMM_WORLD);
}
void search_for_splitted_pattern(int *residue, int *match_number, int **matches) {
// send the residue to the next process
if (rank + 1 != size) {
@ -209,13 +134,6 @@ void search_for_splitted_pattern(int *residue, int *match_number, int **matches)
}
void calculate_absolute_indices(int match_number, int *matches) {
// sending the remain to the last process
// this is necessary for the calculation of shift amount
if (rank == MASTER)
MPI_Send(&remain, 1, MPI_INT, size - 1, DEFAULT_TAG, MPI_COMM_WORLD);
else if (rank == size - 1)
MPI_Recv(&remain, 1, MPI_INT, MASTER, DEFAULT_TAG, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
// transformation of match indices from relative to absolute position.
int shift = rank * (private_text_len - remain); // the rest is zero for all but the last process
apply_shift(shift, matches, match_number);
@ -235,6 +153,7 @@ void collect_results(int *match_number, int *matches) {
total_match_number = sum_array(match_numbers, size);
total_matches = (int *) malloc(sizeof(int) * total_match_number);
displacements = (int *) malloc(sizeof(int) * size);
displacements[0] = 0;
for (int i = 0; i < size - 1; ++i) {
displacements[i + 1] = displacements[i] + match_numbers[i];

8
src/util.c
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@ -54,7 +54,7 @@ char *read_file(char *filepath, int *len) {
return content;
}
char *read_file_portion(char *filepath, int size, int rank, int *portion_len) {
char *read_file_portion(char *filepath, int size, int rank, int *portion_len, int *remain) {
FILE *f = fopen(filepath, "r");
fseek(f, 0, SEEK_END);
int total_len = ftell(f) - 1;
@ -63,8 +63,10 @@ char *read_file_portion(char *filepath, int size, int rank, int *portion_len) {
int start_point = rank * len;
int end_point = start_point + len;
if (rank + 1 == size)
end_point += total_len % size;
*remain = total_len % size;
end_point += *remain;
*portion_len = end_point - start_point;
char *content = (char *) malloc(sizeof(char) * (*portion_len));
@ -75,5 +77,5 @@ char *read_file_portion(char *filepath, int size, int rank, int *portion_len) {
content[*portion_len] = '\0';
return NULL;
return content;
}

2
src/util.h
View File

@ -11,6 +11,6 @@ int sum_array(int *, int);
char *get_text_file(int argc, char **argv);
char *read_file_portion(char *filepath, int size, int rank, int *portion_len);
char *read_file_portion(char *filepath, int size, int rank, int *portion_len, int *remain);
#endif //KMP_UTIL_H