remove unsed files
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F5255658CB220573
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cmake_minimum_required(VERSION 3.17)
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project(kmp C)
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set(CMAKE_C_STANDARD 99)
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add_executable(kmp main.c kmp.c kmp.h util.h util.c)
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236
main.c
236
main.c
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#include <stdio.h>
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#include <string.h>
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#include "kmp.h"
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#include "util.h"
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#include <mpi.h>
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#include <malloc.h>
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#include <papi.h>
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#define MASTER 0
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#define DEFAULT_TAG 17
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void find_end(int, char *, char *, int **, int *);
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void initialize();
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void distribute_text();
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void distribute_pattern();
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void search_for_splitted_pattern(int *residue, int *match_number, int **matches);
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void calculate_absolute_indices(int match_number, int *matches);
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void collect_results(int *match_number, int *matches);
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int rank, size;
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int text_len; // length of all text
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int private_text_len; // length of private text
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int pattern_len; //length of the pattern
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char *text;
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char *pattern;
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int remain = 0;
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int *text_piece;
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int *displacements;
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char *private_text;
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int *match_numbers;
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int *total_matches;
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int total_match_number;
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int main() {
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MPI_Init(NULL, NULL);
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MPI_Comm_size(MPI_COMM_WORLD, &size);
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MPI_Comm_rank(MPI_COMM_WORLD, &rank);
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long_long start_time = PAPI_get_real_usec();
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if (rank == MASTER)
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initialize();
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distribute_text();
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if (rank == MASTER)
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free(text);
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//printf("%d -> input: %s\n", rank, private_text);
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//printf("%d -> text len: %d\n", rank, private_text_len);
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distribute_pattern();
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// create and build lps array
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int lps[pattern_len];
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create_lps(pattern, pattern_len, lps);
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// search for matches
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int match_number = 0;
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int residue;
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long_long start_search = PAPI_get_real_usec();
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int *matches = search_pattern(private_text, pattern, lps, &match_number, &residue);
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search_for_splitted_pattern(&residue, &match_number, &matches);
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free(private_text);
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calculate_absolute_indices(match_number, matches);
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//printf("%d -> result number: %d\n", rank, match_number);
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collect_results(&match_number, matches);
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long_long end_time = PAPI_get_real_usec();
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MPI_Finalize();
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if (rank == MASTER) {
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printf("total matches: %d\n", total_match_number);
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printf("matches index: ");
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print_array(total_matches, total_match_number);
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printf("total elapsed: %d\n", end_time - start_time);
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printf("search elapsed: %d\n", end_time - start_search);
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}
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}
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void find_end(int residue, char *pattern, char *text, int **matches, int *match_number) {
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int pattern_index = residue;
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int text_index = 0;
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int text_len = strlen(text);
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int pattern_len = strlen(pattern);
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// TODO: match splitted on 3+ node
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if (pattern_len - residue > text_len) return;
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while (pattern_index < pattern_len && pattern[pattern_index] == text[text_index]) {
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pattern_index++;
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text_index++;
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}
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if (pattern_index != pattern_len) return;
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*match_number = *match_number + 1;
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*matches = (int *) realloc(*matches, *match_number * sizeof(int));
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(*matches)[*match_number - 1] = -residue;
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}
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void initialize() {
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text = read_file("data/dante.txt", &text_len);
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pattern = read_file("data/pattern.txt", &pattern_len);
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//printf("text: %s\n", text);
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//printf("pattern: %s\n", pattern);
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private_text_len = text_len / size;
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remain = text_len % size;
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if (pattern_len > private_text_len)
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MPI_Abort(MPI_COMM_WORLD, 1);
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text_piece = (int *) malloc(sizeof(int) * size);
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displacements = (int *) malloc(sizeof(int) * size);
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displacements[0] = 0;
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for (int i = 0; i < size - 1; ++i) {
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text_piece[i] = private_text_len;
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displacements[i + 1] = displacements[i] + private_text_len;
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}
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text_piece[size - 1] = private_text_len + remain;
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}
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void distribute_text() {
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// distribution of the length of the text portion to each process
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MPI_Scatter(text_piece, 1, MPI_INT, &private_text_len, 1, MPI_INT, MASTER, MPI_COMM_WORLD);
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// allocation of space for text
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private_text = (char *) malloc(sizeof(char) * (private_text_len + 1));
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// distribution of the text portion to each process
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// scatterv is necessary because the last process receives a larger portion of text in case it is not perfectly divisible.
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MPI_Scatterv(
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text,
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text_piece,
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displacements,
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MPI_CHAR,
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private_text,
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private_text_len,
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MPI_CHAR, MASTER,
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MPI_COMM_WORLD
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);
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private_text[private_text_len] = '\0';
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}
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void distribute_pattern() {
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// distribution of the length of the pattern to each process
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MPI_Bcast(&pattern_len, 1, MPI_INT, MASTER, MPI_COMM_WORLD);
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// allocation of space for the pattern
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// the master has already done so previously
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if (rank != MASTER) {
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pattern = (char *) malloc(sizeof(char) * (pattern_len + 1));
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}
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// distribution of the pattern to each process
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MPI_Bcast(pattern, pattern_len + 1, MPI_CHAR, MASTER, MPI_COMM_WORLD);
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}
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void search_for_splitted_pattern(int *residue, int *match_number, int **matches) {
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// send the residue to the next process
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if (rank + 1 != size) {
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MPI_Send(residue, 1, MPI_INT, rank + 1, DEFAULT_TAG, MPI_COMM_WORLD);
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}
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// receiving the residue from the previous process
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if (rank != 0) {
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MPI_Recv(residue, 1, MPI_INT, rank - 1, DEFAULT_TAG, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
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if (*residue != 0)
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// search for a split match
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find_end(*residue, pattern, private_text, matches, match_number);
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}
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}
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void calculate_absolute_indices(int match_number, int *matches) {
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// sending the remain to the last process
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// this is necessary for the calculation of shift amount
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if (rank == MASTER)
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MPI_Send(&remain, 1, MPI_INT, size - 1, DEFAULT_TAG, MPI_COMM_WORLD);
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else if (rank == size - 1)
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MPI_Recv(&remain, 1, MPI_INT, MASTER, DEFAULT_TAG, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
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// transformation of match indices from relative to absolute position.
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int shift = rank * (private_text_len - remain); // the rest is zero for all but the last process
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apply_shift(shift, matches, match_number);
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}
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void collect_results(int *match_number, int *matches) {
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if (rank == MASTER) {
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// allocation for the array containing the number of matches of each process
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match_numbers = (int *) malloc(sizeof(int) * size);
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}
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// collection of the number of matches from each process
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MPI_Gather(match_number, 1, MPI_INT, match_numbers, 1, MPI_INT, MASTER, MPI_COMM_WORLD);
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if (rank == MASTER) {
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// preparation of the data structures needed to receive match indices from all processes
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total_match_number = sum_array(match_numbers, size);
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total_matches = (int *) malloc(sizeof(int) * total_match_number);
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displacements[0] = 0;
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for (int i = 0; i < size - 1; ++i) {
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displacements[i + 1] = displacements[i] + match_numbers[i];
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}
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}
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// collection of match indices from each process
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// gatherv is necessary because each process will have a different number of matches
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MPI_Gatherv(
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matches,
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*match_number,
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MPI_INT,
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total_matches,
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match_numbers,
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displacements,
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MPI_INT, MASTER,
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MPI_COMM_WORLD
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);
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}
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