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

[Nathan 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);

}