Scatter a Matrix - MPI

I tried scattering a matrix by row to all the processors but it resulted in a segmentation fault.. I don't know what i am doing wrong.. Here is my code

      if(rank == 0) {
                    A_row = 10;
                    A_col = 10;
                    /* calculate the strip size */
                    strip_size = A_row / size;

                    /* genarate Matrix A */
                    A = (double **)malloc(sizeof(double*) * 10);
                    int k = 0;
                    for(i = 0; i < 10; i++) {
                            A[i] = (double*)malloc(sizeof(double) * 10);
                            for(j = 0; j < 10; j++) {
                                    A[i][j] = k;
                                    k++;
                                    printf("%lf  ", A[i][j]);
                            }
                            printf("\n");
                    }
            }

            /* Broadcasting the row, column size of Matrix A as well as strip size and Matrix B*/
            MPI_Bcast(&A_row, 1, MPI_INT, 0, MPI_COMM_WORLD);
            MPI_Bcast(&A_col, 1, MPI_INT, 0, MPI_COMM_WORLD);
            MPI_Bcast(&strip_size, 1, MPI_INT, 0, MPI_COMM_WORLD);

            /* defining a datatype for sub-matrix */
            MPI_Type_vector(strip_size, A_col, A_col, MPI_DOUBLE, &strip);
            MPI_Type_commit(&strip);

            strip_A = (double **)malloc(sizeof(double*)*strip_size);
            for(i= 0; i< strip_size; i++) {
                    strip_A[i] = (double*)malloc(sizeof(double)*A_col);
            }

            MPI_Scatter(&A[0][0], 1, strip, &strip_A[0][0], 1, strip, 0, MPI_COMM_WORLD);

            for(i = 0; i < strip_size; i++) {
                    if(i == 0) {
                            printf("rank = %d\n", rank);
                    }
                    for(j = 0; j < A_col; j++) {
                            printf("%lf  ", strip_A[i][j]);
                    }
                    printf("\n");
            }

Can anyone tell me what is wrong...

here is my error when I run

mpirun -np 2 ./a.out



 0.000000  1.000000  2.000000  3.000000  4.000000  5.000000  6.000000  7.000000  8.000000  9.000000
 10.000000  11.000000  12.000000  13.000000  14.000000  15.000000  16.000000  17.000000  18.000000  19.000000
 20.000000  21.000000  22.000000  23.000000  24.000000  25.000000  26.000000  27.000000  28.000000  29.000000
 30.000000  31.000000  32.000000  33.000000  34.000000  35.000000  36.000000  37.000000  38.000000  39.000000
 40.000000  41.000000  42.000000  43.000000  44.000000  45.000000  46.000000  47.000000  48.000000  49.000000
 50.000000  51.000000  52.000000  53.000000  54.000000  55.000000  56.000000  57.000000  58.000000  59.000000
 60.000000  61.000000  62.000000  63.000000  64.000000  65.000000  66.000000  67.000000  68.000000  69.000000
 70.000000  71.000000  72.000000  73.000000  74.000000  75.000000  76.000000  77.000000  78.000000  79.000000
 80.000000  81.000000  82.000000  83.000000  84.000000  85.000000  86.000000  87.000000  88.000000  89.000000
 90.000000  91.000000  92.000000  93.000000  94.000000  95.000000  96.000000  97.000000  98.000000  99.000000 

 rank = 1
 42.000000  43.000000  44.000000  45.000000  46.000000  47.000000  48.000000  49.000000  0.000000  0.000000
 52.000000  53.000000  54.000000  55.000000  56.000000  57.000000  58.000000  59.000000  0.000000  0.000000
 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000
 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.00000开发者_如何学运维0  0.000000  0.000000
 0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000 
[seismicmstm:07338] *** Process received signal *** [seismicmstm:07338] Signal:
 Segmentation fault (11)
 [seismicmstm:07338] Signal code: 
 (128) [seismicmstm:07338] Failing at
 address: (nil)
 -------------------------------------------------------------------------- mpirun noticed that process rank 1 with PID 7338 on node seismicmstm.cluster exited on signal 11 (Segmentation fault).
 --------------------------------------------------------------------------

There's a couple things going on here. The good news is that the hardest stuff -- getting the mpi data type created, and the basic structure of the MPI_Scatter call -- are correct.

The first issue is that the MPI_Scatter line uses &(A[0][0]) -- but in all but rank zero, you haven't set A to point to anything! So you dereference a random pointer twice, and there's your segfault.

A more subtle issue, as suggested by suszterpatt, is that there's no guarantee that your rows of allocated memory are contiguous, so your scatter operation may not work even if you fix the above. You are trying to send strip_size * A_col doubles from somewhere in A to strip_A, but strip_A may not consist of that many doubles contiguously - it could be A_col doubles, and then some padding, then A_col doubles -- or indeed, the various rows could be scattered all over memory. The three ways of fixing that are, in order of ease (IMHO): (a) make the data contiguous in memory by creating the entire array and then creating the two-d C arrays to point to the right places; (b) to just send one row at a time; or (c) to create an MPI data type that actually reflects how your data is mapped (perhaps randomly) in memory.

An approach using (a) that seems to work (for A_row evenly divided by size, anyway) looks like below:

#include <stdio.h>
#include <mpi.h>
#include <stdlib.h>

int main(int argc, char** argv) {
  int rank, size;
  int strip_size, A_row, A_col;
  double **A, **strip_A, *Adata, *stripdata;
  MPI_Datatype strip;
  int i,j;

  MPI_Init(&argc,&argv) ;

  MPI_Comm_rank(MPI_COMM_WORLD,&rank) ;
  MPI_Comm_size(MPI_COMM_WORLD,&size) ;

      if(rank == 0) {
                    A_row = 10;
                    A_col = 10;
                    /* calculate the strip size */
                    strip_size = A_row / size;

                    /* genarate Matrix A */
                    Adata = (double *)malloc(sizeof(double)*A_row*A_col);
                    A = (double **)malloc(sizeof(double*) * A_row);
                    for(i = 0; i < A_row; i++) {
                            A[i] = &(Adata[i*A_col]);
                    }
                    int k = 0;
                    for(i = 0; i < A_row; i++) {
                            for(j = 0; j < A_col; j++) {
                                    A[i][j] = k;
                                    k++;
                            }
                    }
            }

            /* Broadcasting the row, column size of Matrix A as well as strip size and Matrix B*/
            MPI_Bcast(&A_row, 1, MPI_INT, 0, MPI_COMM_WORLD);
            MPI_Bcast(&A_col, 1, MPI_INT, 0, MPI_COMM_WORLD);
            MPI_Bcast(&strip_size, 1, MPI_INT, 0, MPI_COMM_WORLD);

            /* defining a datatype for sub-matrix */
            MPI_Type_vector(strip_size, A_col, A_col, MPI_DOUBLE, &strip);
            MPI_Type_commit(&strip);

            stripdata = (double *)malloc(sizeof(double)*strip_size*A_col);
            strip_A = (double **)malloc(sizeof(double*)*strip_size);
            for(i= 0; i< strip_size; i++) {
                    strip_A[i] = &(stripdata[i*A_col]);
            }

            MPI_Scatter(Adata, 1, strip, &(strip_A[0][0]), 1, strip, 0, MPI_COMM_WORLD);
            //MPI_Scatter(Adata, A_col*strip_size, MPI_DOUBLE, &(strip_A[0][0]), A_col*strip_size, MPI_DOUBLE, 0, MPI_COMM_WORLD);

            for(i = 0; i < strip_size; i++) {
                    if(i == 0) {
                            printf("rank = %d\n", rank);
                    }
                    for(j = 0; j < A_col; j++) {
                            printf("%lf  ", strip_A[i][j]);
                    }
                    printf("\n");
            }

    MPI_Type_free(&strip);
    free(strip_A);
    free(stripdata);
    free(Adata);
    free(A);
    return 0;
}

I think that ultimately, what you're doing wrong is storing your matrix as an array of arrays. I think you'll find that if you were to store it in a single array (in row-major or column-major order, whichever suits your fancy), things will become much easier.

Simply add MPI_Finalize(); to your command. ;) See the code below and output. The output is right but it is not printing correctly because of barrier. either you can use MPI_Barrier() or use MPI_Isend() and MPI_Irecv(). Enjoy

#include <stdio.h>
#include <mpi.h>
#include <stdlib.h>

int main(int argc, char** argv) {
int rank, size;
int strip_size, A_row, A_col;
double **A, **strip_A, *Adata, *stripdata;
MPI_Datatype strip;
int i,j;

MPI_Init(&argc,&argv) ;

MPI_Comm_rank(MPI_COMM_WORLD,&rank) ;
MPI_Comm_size(MPI_COMM_WORLD,&size) ;

  if(rank == 0) {
                A_row = 10;
                A_col = 10;
                /* calculate the strip size */
                strip_size = A_row / size;

                /* genarate Matrix A */
                Adata = (double *)malloc(sizeof(double)*A_row*A_col);
                A = (double **)malloc(sizeof(double*) * A_row);
                for(i = 0; i < A_row; i++) {
                        A[i] = &(Adata[i*A_col]);
                }
                int k = 0;
                for(i = 0; i < A_row; i++) {
                        for(j = 0; j < A_col; j++) {
                                A[i][j] = k;
                                k++;
                        }
                }
        }

        /* Broadcasting the row, column size of Matrix A as well as strip size and Matrix B*/
        MPI_Bcast(&A_row, 1, MPI_INT, 0, MPI_COMM_WORLD);
        MPI_Bcast(&A_col, 1, MPI_INT, 0, MPI_COMM_WORLD);
        MPI_Bcast(&strip_size, 1, MPI_INT, 0, MPI_COMM_WORLD);

        /* defining a datatype for sub-matrix */
        MPI_Type_vector(strip_size, A_col, A_col, MPI_DOUBLE, &strip);
        MPI_Type_commit(&strip);

        stripdata = (double *)malloc(sizeof(double)*strip_size*A_col);
        strip_A = (double **)malloc(sizeof(double*)*strip_size);
        for(i= 0; i< strip_size; i++) {
                strip_A[i] = &(stripdata[i*A_col]);
        }

        MPI_Scatter(Adata, 1, strip, &(strip_A[0][0]), 1, strip, 0, MPI_COMM_WORLD);
        //MPI_Scatter(Adata, A_col*strip_size, MPI_DOUBLE, &(strip_A[0][0]), A_col*strip_size, MPI_DOUBLE, 0, MPI_COMM_WORLD);

        for(i = 0; i < strip_size; i++) {
                if(i == 0) {
                        printf("rank = %d\n", rank);
                }
                for(j = 0; j < A_col; j++) {
                        printf("%lf  ", strip_A[i][j]);
                }
                printf("\n");
        }
if(rank == 0){
MPI_Type_free(&strip);
free(strip_A);
free(stripdata);
free(Adata);
free(A);}

 MPI_Finalize();

 return 0;
}

output

rank = 0
0.000000  1.000000  2.000000  3.000000  4.000000  5.000000  6.000000  7.000000  8.000000  9.000000
rank = 2
 20.000000  21.000000  22.000000  23.000000  24.000000  25.000000  26.000000  27.000000  28.000000  29.000000  
rank = 6
60.000000  61.000000  62.000000  63.000000  64.000000  65.000000  66.000000  67.000000  68.000000  69.000000  
rank = 1
 10.000000  11.000000  12.000000  13.000000  14.000000  15.000000  16.000000  17.000000  18.000000  19.000000  
rank = 3
30.000000  31.000000  32.000000  33.000000  34.000000  35.000000  36.000000  37.000000  38.000000  39.000000  
rank = 5
50.000000  51.000000  52.000000  53.000000  54.000000  55.000000  56.000000  57.000000  58.000000  59.000000  
rank = 8
80.000000  81.000000  82.000000  83.000000  84.000000  85.000000  86.000000  87.000000  88.000000  89.000000  
rank = 7
70.000000  71.000000  72.000000  73.000000  74.000000  75.000000  76.000000  77.000000  78.000000  79.000000  
rank = 9
90.000000  91.000000  92.000000  93.000000  94.000000  95.000000  96.000000  97.000000  98.000000  99.000000  
rank = 4
40.000000  41.000000  42.000000  43.000000  44.000000  45.000000  46.000000  47.000000  48.000000  49.000000