Pfthb

I have to use MPI to compute value of concentration from a 3D matrix.

I divide my matrix in slices depending on the value of the number of proc I will use.

I get smaller 3D matrix which work independently but I want that the values of concentration they compute to be writen in the same file such as the 0 to n-1 lines are writen by proc 0, n to 2n-1 by proc 1,..

I know that i can use an offset in the mpi_file_write_at function to perform such a thing but i don't know how to implement it.

I know that an easy solution would be to ask proc 0 to open the file, write and close it then proc 1 opens.

Don't mind the code in itself as it is not finished

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

int main(int argc, char *argv)

 char *name = argv[1];

 double h, m, L, T_max, v_x, v_y, v_z, D, r_thresh;
 unsigned int S;

 FILE *file = fopen(name, "rb");


 if(!file)
 
 fprintf(stderr, "Not able to open the file %sn", name);
 
 else
 printf("Able to open the file %sn", name);

 fscanf(file, "%lf", &h);
 fscanf(file, "%lf", &m);
 fscanf(file, "%lf", &L);
 fscanf(file, "%lf", &T_max);
 fscanf(file, "%lf", &v_x);
 fscanf(file, "%lf", &v_y);
 fscanf(file, "%lf", &v_z);
 fscanf(file, "%lf", &D);
 fscanf(file, "%u", &S);
 fscanf(file, "%lf", &r_thresh);

 fclose(file);

 if(((L/h) % 2) != 0)
 printf("Uncorrect parameters L and h ! n");
 return -1;
 
 else
 unsigned int edge = (L/h);
 unsigned int middle = edge/2;
 unsigned int N = edge+1;
 
 if(((T_max/m) % 1) != 0)
 printf("Uncorrect parameters T_max and m ! n");
 return -1;
 
 else
 unsigned int t_end = T_max/m;
 

 unsigned int myrank, nbproc;
 MPI_Init(&argc, &argv) ;
 MPI_Comm_rank( MPI_COMM_WORLD , &myrank );
 MPI_Comm_size( MPI_COMM_WORLD , &nbproc );

 double w = N/nbproc;
 unsigned int width = round(w);
 unsigned int k_min, k_max;
 k_min = myrank*width;
 k_max = (myrank+1)*width-1;
 width = width+2; 
 if(nbproc==1)
 width = N;
 
 else if(myrank==(nbproc-1))
 k_max = N-1; 
 width = k_max-k_min+1; 
 width = width+1; 
 
 else if(myrank==0)
 width = width-1; 
 



 double ***C ;
 C = malloc(width * sizeof(*C)); 
 for(k=0 ; k < width ; k++)
 C[k] = malloc(N * sizeof(**C));
 
 for(k=0 ; k < width ; k++)
 for(j=0 ; j < N ; j++)
 C[k][j] = malloc(N * sizeof(***C));
 
 


 unsigned int i,j,k,n;
 for(k=0 ; k<width ; k++)
 for(j=0 ; j<N ; j++)
 for(i=0 ; i<N ; i++)
 C[k][j][i]=0;
 
 
 
 if(middle>=k_min && middle=<k_max)
 C[middle-k_min][middle][middle] = 1;
 


 if(myrank==0 

Each process in an MPI program has a local address space. File I/O changes that: a file is a globally accessible linear stream of bytes. You need to think about where in the global space each process is writing. A couple ways to do this:

• sometimes you can just have each process write to a corresponding chunk of the file. rank zero writes to the first megabyte, rank 1 to the 2nd, and so on. Might be too simplistic for your 3d array.




• For more sophisticated decomposition, you set a "file view": you construct an MPI datatype describing the layout of data on disk. in your case, MPI_TYPE_CREATE_SUBARRAY is probably what you want: a 3d global matrix and each process contributes some subaray to the global picture.