[gmx-developers] rvec x[]

[David van der Spoel]

On Fri, 24 Jun 2005, Nathan Moore wrote:

>Hi All,
>
>Where is the "rvex x[]" class defined?  I assumed that it was a flat array
>in the replacement for move_x below and got compiler errors:
include/types/simple.h

>
>"mvxvf.c", line 196.14: 1506-068 (W) Operation between types "double*" and
>"double" is not allowed.
>"mvxvf.c", line 196.9: 1506-025 (S) Operand must be a modifiable lvalue.
>
call your routine with x[0] as an argument.

>Also,  What does the "where();" fucntion at the bottom of move_f and
>move_x do?
it's for debugging.

>
>My code snippet follows, all suggestions welcome!  I suppose that since X
>isn't flat I'll need to pass it with MPI with a type other that
>MPI_DOUBLE?
are you sure you are using double precision alwyas? It's not a good idea 
to hardcode that, use MPI_REAL rather.

>
>thanks again for all the help!
>
>NTM
>
>    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 tempporary array where x elements are gathered to */
>    double *temp_x = (double *) malloc(array_length * sizeof(double));
make that real 3 times

>
>    /* pass the x array around */
>    NT_status = MPI_Allgatherv(&x[start_element],
>                               num_sent[nsb->nodeid],
>                               MPI_DOUBLE,
>                               &temp_x[0],
>                               &num_sent[0],
>                               &starting_block[0],
>                               MPI_DOUBLE, MPI_COMM_WORLD);
make that MPI_REAL 2 times

>
>    /* update the x array with the gathered temp_x array */
>    for (i = 0; i < array_length; i++) {
>        x[i] = temp_x[i];
>    }
>
>    free(num_sent);
>    free(starting_block);
>    free(temp_x);
try to avoid extra mallocs thay are extremely expensive.

>
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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