[gmx-developers] using arrays of rvec[] (ie x, v, f, etc)

[Nathan Moore]

I've figured out a possible fix.  I've defined temp_x in the following way,

    rvec *temp_x = (rvec *) malloc(array_length * sizeof(rvec));

and then copied the array contents with,

for (i = 0; i < array_length; i++) {
        x[i][0] = temp_x[i][0];
        x[i][1] = temp_x[i][1];
        x[i][2] = temp_x[i][2];
    }

Comments?

NT Moore


> I'm working to rewrite the move_x/move_f functions to allow for the use of
> an MPI_AllgatherV on an IBM BlueGene system.  I'm struggling at present
> with the definition of the x and f arrays as "rvec[]" or "real variables.
> The code below fails on compile with errors:
>
> "mvxvf.c", line 196.25: 1506-019 (S) Expecting an array or a pointer to
> object type.
> "mvxvf.c", line 197.25: 1506-019 (S) Expecting an array or a pointer to
> object type.
> "mvxvf.c", line 198.25: 1506-019 (S) Expecting an array or a pointer to
> object type.
>
> I assume that the compiler doesn't like how I'm copying the temp_x array
> back to the x array after the MPI_Allgatherv.  Any suggestions as to how
> this section should be written?
>
> Also, I'd like to lose the malloc definition of temp_x, but I'm not sure
> if there's a #define'd size for that array.  ie, I'd like to say
> statically at the beginning of this function,
>      real temp_x[N_ATOMS]
> Is the problem size (NUM_ATOMS or similar) defined outside of the
> (nsb->natoms)?
>
> thanks,
>
> NT Moore
>
>
> void move_x(FILE * log,
>        int left, int right, rvec x[], t_nsborder * nsb, t_nrnb * nrnb)
> {
> int i;
>
>     int NT_status;              /* Did the send work? */
>
>     int array_length;           /* length of the whole x array */
>     array_length = DIM * (nsb->natoms);
>
>     int start_element;          /* index of where this node's array
> begins*/
>     start_element = nsb->index[nsb->nodeid];
>
>     /* The number of elements each node sends */
>     int *num_sent = (int *) malloc((nsb->nnodes) * sizeof(int));
>     for (i = 0; i < (nsb->nnodes); i++) {
>         num_sent[i] = nsb->homenr[i];
>     }
>
>     /* The starting index of each node's block of elements */
>     /* note the obvious redundancy that
> start_element==starting_block[nsb->nodeid] */
>     int *starting_block = (int *) malloc((nsb->nnodes) * sizeof(int));
>     for (i = 0; i < (nsb->nnodes); i++) {
>         starting_block[i] = nsb->index[i];
>     }
>
>     /* The temporary array where x elements are gathered to */
>     real *temp_x = (real *) malloc(array_length * sizeof(real));
>
>     /* pass the x array around */
>     NT_status = MPI_Allgatherv(&x[start_element],
>                                num_sent[nsb->nodeid],
>                                MPI_REAL,
>                                &temp_x[0],
>                                &num_sent[0],
>                                &starting_block[0],
>                                MPI_REAL, MPI_COMM_WORLD);
>
>     /* update the x array with the gathered temp_x array */
>     for (i = 0; i < array_length; i++) {
>         x[i][0] = temp_x[i][0];
>         x[i][1] = temp_x[i][1];
>         x[i][2] = temp_x[i][2];
>     }
>
>     free(num_sent);
>     free(starting_block);
>     free(temp_x);
>
> }
>
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