Segmentation fault when declaring arrays
I have the following code:
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <mpi.h>
void pgmsize (char *filename, int *nx, int *ny);
void pgmread (char *filename, void *vx, int nx, int ny);
void pgmwrite(char *filename, void *vx, int nx, int ny);
#define FILENAME "edge768x768.pgm"
#define M 768
#define N 768
#define P 2
#define DEL 1
#define CHECKFREQ 500
#define MAXITER 5000
int main(int argc, char **argv){
MPI_Init(&argc, &argv);
int rank,size;
MPI_Comm_size(MPI_COMM_WORLD, &size);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
FILE *fp;
char outname[64];
sprintf(outname,"out_%d.dat",P);
fp = fopen( outname, "w" );
fprintf(fp,"del,iter,avg\n");
MPI_Status status;
MPI_Request req;
MPI_Comm cart_comm;
int dims[2] = {0,0};
int periods[2] = {0,0};
int coords[2];
MPI_Dims_create(P, 2, dims);
MPI_Cart_create(MPI_COMM_WORLD,2,dims,periods,1, &cart_comm);
MPI_Cart_coords(cart_comm, rank, 2, coords);
int Px = dims[0];
int Py = dims[1];
int i,j,locali,localj,iter;
printf("%d,%d,%d\n",rank,M/Px,N/Py);
double masterarray[M][N];
double outarray[M][N];
double local_array[M/Px][N/Py];
double local_padded_array[M/Px+2][N/Py+2];
double old[M/Px+2][N/Py+2];
printf("%d,%d,%d\n",rank,Px,Py);
fclose(fp);
MPI_Finalize();
}
The following error appears when compiling and running:
mpiexec noticed that rank 0 with PID 28696 on node My-MacBook-Air exited signal 11 (Segmentation fault: 11).
However, if I change the declaration of the main array to:
float masterarray[M][N]
it compiles and works fine. Can anyone please help? Also works great if all arrays are declared as floats
. Perhaps a better understanding of the difference between the two types can help me understand what's going on.
Continuing to write my code using all floating point arrays, I have now come up with another problem related to arrays. Now my code is:
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <mpi.h>
void pgmsize (char *filename, int *nx, int *ny);
void pgmread (char *filename, void *vx, int nx, int ny);
void pgmwrite(char *filename, void *vx, int nx, int ny);
#define FILENAME "edge768x768.pgm"
#define M 768
#define N 768
#define P 2
#define DEL 1
#define CHECKFREQ 500
#define MAXITER 5000
int main(int argc, char **argv){
MPI_Init(&argc, &argv);
int rank,size;
MPI_Comm_size(MPI_COMM_WORLD, &size);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
FILE *fp;
char outname[64];
sprintf(outname,"out_%d.dat",P);
fp = fopen( outname, "w" );
fprintf(fp,"del,iter,avg\n");
MPI_Status status;
MPI_Request req;
MPI_Comm cart_comm;
int dims[2] = {0,0};
int periods[2] = {0,0};
int coords[2];
MPI_Dims_create(P, 2, dims);
MPI_Cart_create(MPI_COMM_WORLD,2,dims,periods,1, &cart_comm);
MPI_Cart_coords(cart_comm, rank, 2, coords);
int Px = dims[0];
int Py = dims[1];
int i,j,locali,localj,iter;
float masterarray[M][N];
float outarray[M][N];
float local_array[M/Px][N/Py];
float local_padded_array[M/Px+2][N/Py+2];
float old[M/Px+2][N/Py+2];
float new[M/Px+2][N/Py+2];
if (rank == 0){
pgmread(FILENAME, masterarray, M, N);
}
MPI_Bcast(masterarray,M*N,MPI_FLOAT,0,MPI_COMM_WORLD);
for(i=0;i<M/Px;i++){
for(j=0;j<N/Py;j++){
locali = i + coords[0] * M/Px;
localj = j + coords[1] * N/Py;
local_array[i][j] = masterarray[locali][localj];
}
}
for (i = 0;i<M/Px +2;i++){
for (j = 0;j<N/Py +2;j++){
local_padded_array[i][j] = 255.0;
}
}
for (i = 1;i<M/Px +1;i++){
for (j = 1;j<N/Py +1;j++){
local_padded_array[i][j] = local_array[i-1][j-1];
}
}
for (i = 0;i<M/Px +2;i++){
for (j = 0;j<N/Py +2;j++){
old[i][j] = 255.0;
}
}
int down_rank,up_rank,right_rank,left_rank;
MPI_Cart_shift(cart_comm,0,1,&right_rank,&left_rank);
MPI_Cart_shift(cart_comm,1,1,&down_rank,&up_rank);
MPI_Datatype col;
MPI_Type_vector(M/Px,1,N/Py+2,MPI_FLOAT,&col);
MPI_Type_commit(&col);
float globaldel = 1000.0;
float globalsum = 0.0;
double time1 = MPI_Wtime();
for(iter = 0;iter < MAXITER;iter++){
MPI_Issend(&old[1][N/Py], 1,col,up_rank, 0,cart_comm, &req);
MPI_Recv(&old[1][0], 1,col, down_rank, 0,cart_comm, &status);
MPI_Issend(&old[1][1], 1,col ,down_rank, 0,cart_comm, &req);
MPI_Recv(&old[1][N/Py+1], 1,col ,up_rank, 0,cart_comm, &status);
MPI_Issend(&old[M/Px][1], N/Py,MPI_FLOAT,left_rank, 0,cart_comm, &req);
MPI_Recv(&old[0][1], N/Py,MPI_FLOAT, right_rank, 0,cart_comm, &status);
MPI_Issend(&old[1][1], N/Py,MPI_FLOAT,right_rank, 0,cart_comm, &req);
MPI_Recv(&old[M/Px+1][1], N/Py,MPI_FLOAT, left_rank, 0,cart_comm, &status);
for (i = 1;i<M/Px +1;i++){
for (j = 1;j<N/Py +1;j++){
new[i][j] = 0.25*(old[i][j-1]+old[i][j+1]+old[i-1][j]+old[i+1][j] - local_padded_array[i][j]);
}
}
}
printf("%d,%d,%d\n",rank,M/Px,N/Py);
fclose(fp);
MPI_Finalize();
}
which on startup gives another segmentation fault which seems to be fixed if in the last loop I don't set the elements in the new array. So it seems like there are some serious problems in creating my arrays! The code also looks ok if used #define P 3
instead of#define P 2
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There is probably not enough memory on the stack. If you are not familiar with the difference between stack and heap, check: What and where are the stack and the heap? ... If I change to using heap everything works out fine.
To allocate memory from the heap for your arrays use:
double *masterarray = malloc(sizeof(double) * M * N);
double *outarray = malloc(sizeof(double) * M * N);
double *local_array = malloc(sizeof(double) * M/Px * N/Py);
double *local_padded_array = malloc(sizeof(double) * (M/Px+2) * (N/Py+2));
double *old = malloc(sizeof(double) * (M/Px+2) * (N/Py+2));
Here's my version of your original code, which works fine (some extra junk removed to avoid creating files and whatnot):
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <mpi.h>
#define M 768
#define N 768
#define P 2
#define DEL 1
#define CHECKFREQ 500
#define MAXITER 5000
int main(int argc, char **argv)
{
MPI_Init(&argc, &argv);
int rank,size;
MPI_Comm_size(MPI_COMM_WORLD, &size);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Status status;
MPI_Request req;
MPI_Comm cart_comm;
int dims[2] = {0,0};
int periods[2] = {0,0};
int coords[2];
MPI_Dims_create(P, 2, dims);
MPI_Cart_create(MPI_COMM_WORLD,2,dims,periods,1, &cart_comm);
MPI_Cart_coords(cart_comm, rank, 2, coords);
int Px = dims[0];
int Py = dims[1];
int i,j,locali,localj,iter;
printf("%d,%d,%d\n",rank,M/Px,N/Py);
double *masterarray = malloc(sizeof(double) * M * N);
double *outarray = malloc(sizeof(double) * M * N);
double *local_array = malloc(sizeof(double) * M/Px * N/Py);
double *local_padded_array = malloc(sizeof(double) * (M/Px+2) * (N/Py+2));
double *old = malloc(sizeof(double) * (M/Px+2) * (N/Py+2));
if (masterarray == NULL) fprintf(stderr, "MASTERARRAY == NULL");
if (outarray == NULL) fprintf(stderr, "OUTARRAY == NULL");
if (local_array == NULL) fprintf(stderr, "LOCAL_ARRAY == NULL");
if (local_padded_array == NULL) fprintf(stderr, "LOCAL_PADDED_ARRAY == NULL");
if (old == NULL) fprintf(stderr, "OLD == NULL");
printf("%d,%d,%d\n",rank,Px,Py);
MPI_Finalize();
return 0;
}
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