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Commit 0dd4762a authored by alexgara's avatar alexgara
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seem to fix

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......@@ -2,3 +2,4 @@ align_omp
align_seq
align_mpi
align_cuda
log.txt
align_mpi.c
+ 42
− 108
View file @ 0dd4762a
......@@ -32,7 +32,7 @@
#define END_SIG -2
/* Macro for checking mpi funcs and print if there is a error */
#define MPI_CHEK_FUCKTION( call ) {int ierr = call; int resultlen; if (ierr != MPI_SUCCESS){ char error_msg[MPI_MAX_ERROR_STRING]; MPI_Error_string(ierr, error_msg, &resultlen); fprintf(stderr, "MPI fallo en linea (%d):\n%s\n\n", __LINE__, error_msg); MPI_Abort(MPI_COMM_WORLD, EXIT_FAILURE); fflush(stdout);}}
#define MPI_CHECK_FUNCTION( call ) {int ierr = call; int resultlen; if (ierr != MPI_SUCCESS){ char error_msg[MPI_MAX_ERROR_STRING]; MPI_Error_string(ierr, error_msg, &resultlen); fprintf(stderr, "MPI fallo en linea (%d):\n%s\n\n", __LINE__, error_msg); MPI_Abort(MPI_COMM_WORLD, EXIT_FAILURE); fflush(stdout);}}
/*
* Function: Increment the number of pattern matches on the sequence positions
......@@ -360,7 +360,6 @@ int main(int argc, char *argv[]) {
rng_t random_local = random;
rng_skip(&random_local, my_begin);
generate_rng_sequence( &random_local, prob_G, prob_C, prob_A, sequence, my_size);
//rng_skip(&random, seq_length);
#ifdef DEBUG
/* DEBUG: Print sequence and patterns */
......@@ -397,7 +396,6 @@ int main(int argc, char *argv[]) {
unsigned long pat;
//MPI_Request request;
MPI_Status status;
//int send_to_continue_flag = 0;
// [0]=my_begin+start | [1]= tamaño ya leido del patorn | [2]= numero de patrón
......@@ -413,6 +411,13 @@ int main(int argc, char *argv[]) {
MPI_Abort( MPI_COMM_WORLD, EXIT_FAILURE );
}
/* info for rank and my_size distrib
printf("rank[%d] my_size=%lu, my_begin=%lu\n", rank, my_size, my_begin);
fflush(stdout);
*/
MPI_CHECK_FUNCTION(MPI_Barrier(MPI_COMM_WORLD));
for( pat=0; pat < pat_number; pat++ ) {
/* 5.1. For each posible starting position */
......@@ -429,44 +434,27 @@ int main(int argc, char *argv[]) {
envio_array[2]=pat;
//Envio el parton para que continue el siguente que le toca
MPI_CHEK_FUCKTION(MPI_Send(envio_array, 3, MPI_UNSIGNED_LONG, rank+1, TAG_NO_COMPLETE, MPI_COMM_WORLD));
//printf("\n ENVIA(%d) rank=%d a rank+1=%d pat=%lu\n", (1), rank, rank+1, envio_array[2]);
MPI_CHECK_FUNCTION(MPI_Send(envio_array, 3, MPI_UNSIGNED_LONG, rank+1, TAG_NO_COMPLETE, MPI_COMM_WORLD));
//printf("\n ENVIA(%d) rank=%d a rank+1=%d pat=%lu, START=%lu, LENGHT=%lu\n", (1), rank, rank+1, envio_array[2], envio_array[0], envio_array[1]);
//fflush(stdout);
//send_to_continue_flag = 1;
break;
}
else if ( sequence[start + ind] != pattern[pat][ind] ) break;
}
/* 5.1.2. Check if the loop ended with a match */
//Check if is outside of the loop and the pattern continue in other
/*if(send_to_continue_flag){
send_to_continue_flag = 0;
break;
}*/
if ( ind == pat_length[pat] ) {
pat_found[pat] = my_begin + start;
//printf("RANK(%d) encuentra patrón=%lu\n",rank, pat);
break;
}
}
}
//This will be the las message that rank+1 will recive <= Beacause of MPI politics FIFO(non-overtaking)
//If first finish then send signal that it has no more to do
if(rank == 0){
envio_array[0] = (unsigned long) END_SIG;
envio_array[1] = (unsigned long) END_SIG;
envio_array[2] = (unsigned long) END_SIG;
MPI_CHEK_FUCKTION(MPI_Send(envio_array, 3, MPI_UNSIGNED_LONG, rank+1, TAG_NO_COMPLETE, MPI_COMM_WORLD));
//printf("\n ENVIA FIN rank=%d a rank+1=%d \n", rank, rank+1);
fflush(stdout);
}
/* Until this part all fine
MPI_CHEK_FUCKTION(MPI_Barrier(MPI_COMM_WORLD));
/**
MPI_CHECK_FUNCTION(MPI_Barrier(MPI_COMM_WORLD));
printf("==================\n rank=%d LLEGA pat=%lu, sig=%d\n", rank, pat, rank+1);
fflush(stdout);
MPI_CHEK_FUCKTION(MPI_Barrier(MPI_COMM_WORLD));
MPI_CHECK_FUNCTION(MPI_Barrier(MPI_COMM_WORLD));
*/
//NOW PROCESS CHECK FOR THE REAMAING PATTERN THAT ITS PREVIOUS DOSENT HAVE FOUND
......@@ -474,41 +462,27 @@ int main(int argc, char *argv[]) {
while(1 && (rank != 0)){
//First check if the previous process has finished & have nothing more to do
MPI_CHEK_FUCKTION(MPI_Recv(recibo_array, 3, MPI_UNSIGNED_LONG, rank-1, MPI_ANY_TAG, MPI_COMM_WORLD, &status));
MPI_CHECK_FUNCTION(MPI_Recv(recibo_array, 3, MPI_UNSIGNED_LONG, rank-1, TAG_NO_COMPLETE, MPI_COMM_WORLD, &status));
//else continue because the rank-1 send work to do
start_r = recibo_array[0]; //Were the patter was start to be detected
length_r = recibo_array[1]; //Lenght already checked
pat_r = recibo_array[2]; //Pattern searching
//THEN its end sigal the first so no more thing to do
if(pat_r == (unsigned long) END_SIG){
/*
printf("\n GET FIN rank=%d desde rank-1=%d \n", rank, status.MPI_SOURCE);
fflush(stdout);
*/
if(rank != nprocs-1){
envio_array[0] = END_SIG;
envio_array[1] = END_SIG;
envio_array[2] = END_SIG;
MPI_CHEK_FUCKTION(MPI_Send(envio_array, 3, MPI_UNSIGNED_LONG, rank+1, TAG_NO_COMPLETE, MPI_COMM_WORLD));
/*
printf("\n ENVIA FIN rank=%d a rank+1=%d \n", rank, rank+1);
fflush(stdout);
*/
}
break;
}
//else {
/*
printf("\n RECIBE rank=%d desde rank-1=%d pat=%lu con TAG=%d\n" ,rank, status.MPI_SOURCE, recibo_array[2], status.MPI_TAG);
else {
printf("\n RECIBE rank=%d desde rank-1=%d pat=%lu con TAG=%d, START=%lu, LENGHT=%lu\n" ,rank, status.MPI_SOURCE, pat_r, status.MPI_TAG, start_r, length_r);
fflush(stdout);
}
*/
//}
//search for the pattern in my space
......@@ -521,34 +495,38 @@ int main(int argc, char *argv[]) {
envio_array[2]=pat_r;
//Send to the next rank
MPI_CHEK_FUCKTION(MPI_Send(envio_array, 3, MPI_UNSIGNED_LONG, rank+1, TAG_NO_COMPLETE, MPI_COMM_WORLD));
MPI_CHECK_FUNCTION(MPI_Send(envio_array, 3, MPI_UNSIGNED_LONG, rank+1, TAG_NO_COMPLETE, MPI_COMM_WORLD));
/*
printf("\n ENVIA(%d) rank=%d a rank+1=%d pat=%lu\n", (1), rank, rank+1, envio_array[2]);
printf("\n ENVIA(%d) rank=%d a rank+1=%d pat=%lu, START=%lu, LENGHT=%lu\n", (2), rank, rank+1, envio_array[2], envio_array[0], envio_array[1]);
fflush(stdout);
*/
//send_to_continue_flag = 1;
break;
}
else if ( sequence[ind] != pattern[pat_r][ind+length_r] ) break;
}
//Check if is outside of the loop and the pattern continue in other
/*if(send_to_continue_flag){
send_to_continue_flag = 0;
break;
}*/
// else we have a match
if ( ind+length_r == pat_length[pat_r] ) {
pat_found[pat_r] = start_r;
//printf("RANK(%d) encuentra patrón=%lu\n",rank, pat_r);
break;
}
}
//Wait until all the process finish
//MPI_CHEK_FUCKTION(MPI_Barrier(MPI_COMM_WORLD));
if(rank != nprocs-1){
envio_array[0] =(unsigned long) END_SIG;
envio_array[1] =(unsigned long) END_SIG;
envio_array[2] = (unsigned long)END_SIG;
MPI_CHECK_FUNCTION(MPI_Send(envio_array, 3, MPI_UNSIGNED_LONG, rank+1, TAG_NO_COMPLETE, MPI_COMM_WORLD));
//printf("\n ENVIA FIN rank=%d a rank+1=%d \n", rank, rank+1);
//fflush(stdout);
}
//Wait until all the process finish
//MPI_CHECK_FUNCTION(MPI_Barrier(MPI_COMM_WORLD));
/*
MPI_CHEK_FUCKTION(MPI_Barrier(MPI_COMM_WORLD));
MPI_CHECK_FUNCTION(MPI_Barrier(MPI_COMM_WORLD));
printf("==================\n rank=%d LLEGA pat=%lu, sig=%d\n", rank, pat, rank+1);
fflush(stdout);
*/
......@@ -556,7 +534,7 @@ int main(int argc, char *argv[]) {
unsigned long *recive_pat_found;
//Define a recv buffer for for the master
if( rank == 0 || rank == 1 || rank == 2){
if(rank==0){
recive_pat_found = (unsigned long *)malloc( sizeof(unsigned long) * pat_number );
if ( recive_pat_found == NULL ) {
fprintf(stderr,"\n-- Error allocating aux pattern structure for size: %d\n", pat_number );
......@@ -564,29 +542,7 @@ int main(int argc, char *argv[]) {
}
}
//Wait to all process, so we get all the patterns
//MPI_CHEK_FUCKTION(MPI_Barrier(MPI_COMM_WORLD));
// rank 0 will be the master
/*if(rank == 0){
//Get the min pat_found)
MPI_CHEK_FUCKTION(MPI_Reduce(pat_found, recive_pat_found, pat_number, MPI_UNSIGNED_LONG, MPI_MIN, 0, MPI_COMM_WORLD));
//Send the pat_found to the other rank that will perform checksums
MPI_CHEK_FUCKTION(MPI_Isend(recive_pat_found, pat_number, MPI_UNSIGNED_LONG, 1,TAG_SEND_PAT_FOUND,MPI_COMM_WORLD, &request ));
MPI_CHEK_FUCKTION(MPI_Isend(recive_pat_found, pat_number, MPI_UNSIGNED_LONG, 2,TAG_SEND_PAT_FOUND,MPI_COMM_WORLD, &request ));
}
else {
//The other ranks send to the master
MPI_CHEK_FUCKTION(MPI_Reduce(pat_found, NULL, pat_number, MPI_UNSIGNED_LONG, MPI_MIN, 0, MPI_COMM_WORLD));
if(rank == 1 || rank == 2){
MPI_CHEK_FUCKTION(MPI_Recv(recive_pat_found, pat_number, MPI_UNSIGNED_LONG, 0, TAG_SEND_PAT_FOUND, MPI_COMM_WORLD, &status));
}
}*/
MPI_CHEK_FUCKTION(MPI_Reduce(pat_found, recive_pat_found, pat_number, MPI_UNSIGNED_LONG, MPI_MIN, 0, MPI_COMM_WORLD));
MPI_CHECK_FUNCTION(MPI_Reduce(pat_found, recive_pat_found, pat_number, MPI_UNSIGNED_LONG, MPI_MIN, 0, MPI_COMM_WORLD));
/*printf("recive_pat_found:");
for( debug_pat=0; debug_pat<pat_number; debug_pat++ ) {
......@@ -610,28 +566,6 @@ int main(int argc, char *argv[]) {
}
}
//rank 1 calculate checksum_found
/*if(rank == 1){
for(ind=0;ind<pat_number;ind++)
if(pat_found[ind] != (unsigned long) NOT_FOUND)
checksum_found = (checksum_found + pat_found[ind]) % CHECKSUM_MAX;
// Send to rank == 0 the checksum
MPI_CHEK_FUCKTION(MPI_Isend(&checksum_found, 1, MPI_UNSIGNED_LONG, 0, TAG_SEND_CHECKSUM, MPI_COMM_WORLD, &request));
}*/
//Recv the calculated checksum from rank 1
/*if( rank == 0) {
MPI_CHEK_FUCKTION(MPI_Recv(&checksum_found, 1, MPI_UNSIGNED_LONG, 1, TAG_SEND_CHECKSUM, MPI_COMM_WORLD, &status));
}*/
// rank 2 TODO calculate checksum_matches
/** Esta parte de momento la consideramos opcional
for( ind=0; ind < seq_length; ind++) {
if ( seq_matches[ind] != (unsigned long)NOT_FOUND )
checksum_matches = ( checksum_matches + seq_matches[ind] ) % CHECKSUM_MAX;
}
**/
#ifdef DEBUG
/* DEBUG: Write results */
......
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