norangebit-unisannio-computer-science/KMP-MPI
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Raffaele Mignone 2021-05-03 12:05:50 +02:00
parent d68792ae1c
commit 51b2770b8f
Signed by: norangebit
GPG Key ID: F5255658CB220573
2 changed files with 0 additions and 242 deletions
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6
CMakeLists.txt
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cmake_minimum_required(VERSION 3.17)
project(kmp C)
set(CMAKE_C_STANDARD 99)
add_executable(kmp main.c kmp.c kmp.h util.h util.c)

236
main.c
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#include <stdio.h>
#include <string.h>
#include "kmp.h"
#include "util.h"
#include <mpi.h>
#include <malloc.h>
#include <papi.h>
#define MASTER 0
#define DEFAULT_TAG 17
void find_end(int, char *, char *, int **, int *);
void initialize();
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);
void collect_results(int *match_number, int *matches);
int rank, size;
int text_len; // length of all text
int private_text_len; // length of private text
int pattern_len; //length of the pattern
char *text;
char *pattern;
int remain = 0;
int *text_piece;
int *displacements;
char *private_text;
int *match_numbers;
int *total_matches;
int total_match_number;
int main() {
MPI_Init(NULL, NULL);
MPI_Comm_size(MPI_COMM_WORLD, &size);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
long_long start_time = PAPI_get_real_usec();
if (rank == MASTER)
initialize();
distribute_text();
if (rank == MASTER)
free(text);
//printf("%d -> input: %s\n", rank, private_text);
//printf("%d -> text len: %d\n", rank, private_text_len);
distribute_pattern();
// create and build lps array
int lps[pattern_len];
create_lps(pattern, pattern_len, lps);
// search for matches
int match_number = 0;
int residue;
long_long start_search = PAPI_get_real_usec();
int *matches = search_pattern(private_text, pattern, lps, &match_number, &residue);
search_for_splitted_pattern(&residue, &match_number, &matches);
free(private_text);
calculate_absolute_indices(match_number, matches);
//printf("%d -> result number: %d\n", rank, match_number);
collect_results(&match_number, matches);
long_long end_time = PAPI_get_real_usec();
MPI_Finalize();
if (rank == MASTER) {
printf("total matches: %d\n", total_match_number);
printf("matches index: ");
print_array(total_matches, total_match_number);
printf("total elapsed: %d\n", end_time - start_time);
printf("search elapsed: %d\n", end_time - start_search);
}
}
void find_end(int residue, char *pattern, char *text, int **matches, int *match_number) {
int pattern_index = residue;
int text_index = 0;
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]) {
pattern_index++;
text_index++;
}
if (pattern_index != pattern_len) return;
*match_number = *match_number + 1;
*matches = (int *) realloc(*matches, *match_number * sizeof(int));
(*matches)[*match_number - 1] = -residue;
}
void initialize() {
text = read_file("data/dante.txt", &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) {
MPI_Send(residue, 1, MPI_INT, rank + 1, DEFAULT_TAG, MPI_COMM_WORLD);
}
// receiving the residue from the previous process
if (rank != 0) {
MPI_Recv(residue, 1, MPI_INT, rank - 1, DEFAULT_TAG, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
if (*residue != 0)
// search for a split match
find_end(*residue, pattern, private_text, matches, match_number);
}
}
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);
}
void collect_results(int *match_number, int *matches) {
if (rank == MASTER) {
// allocation for the array containing the number of matches of each process
match_numbers = (int *) malloc(sizeof(int) * size);
}
// collection of the number of matches from each process
MPI_Gather(match_number, 1, MPI_INT, match_numbers, 1, MPI_INT, MASTER, MPI_COMM_WORLD);
if (rank == MASTER) {
// preparation of the data structures needed to receive match indices from all processes
total_match_number = sum_array(match_numbers, size);
total_matches = (int *) malloc(sizeof(int) * total_match_number);
displacements[0] = 0;
for (int i = 0; i < size - 1; ++i) {
displacements[i + 1] = displacements[i] + match_numbers[i];
}
}
// collection of match indices from each process
// gatherv is necessary because each process will have a different number of matches
MPI_Gatherv(
matches,
*match_number,
MPI_INT,
total_matches,
match_numbers,
displacements,
MPI_INT, MASTER,
MPI_COMM_WORLD
);
}