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/*********************************************************************
*
* Copyright (C) 2013, Northwestern University and Argonne National Laboratory
* See COPYRIGHT notice in top-level directory.
*
*********************************************************************/
/* $Id$ */
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* This example shows how to use a single call of ncmpi_put_varn_float_all()
* to write a sequence of one-element requests with arbitrary array indices.
*
* The compile and run commands are given below, together with an ncmpidump of
* the output file.
*
* % mpicc -O2 -o put_varn_float put_varn_float.c -lpnetcdf
* % mpiexec -n 4 ./put_varn_float /pvfs2/wkliao/testfile.nc
* % ncmpidump /pvfs2/wkliao/testfile.nc
* netcdf testfile {
* // file format: CDF-5 (big variables)
* dimensions:
* Y = 4 ;
* X = 10 ;
* variables:
* int var(Y, X) ;
* data:
*
* var =
* 3, 3, 3, 1, 1, 0, 0, 2, 1, 1,
* 0, 2, 2, 2, 3, 1, 1, 2, 2, 2,
* 1, 1, 2, 3, 3, 3, 0, 0, 1, 1,
* 0, 0, 0, 2, 1, 1, 1, 3, 3, 3 ;
* }
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include <stdio.h>
#include <stdlib.h>
#include <string.h> /* strcpy(), strncpy() */
#include <unistd.h> /* getopt() */
#include <mpi.h>
#include <pnetcdf.h>
#define NY 4
#define NX 10
#define NDIMS 2
static int verbose;
#define ERR {if(err!=NC_NOERR){printf("Error at %s:%d : %s\n", __FILE__,__LINE__, ncmpi_strerror(err));nerrs++;}}
static void
usage(char *argv0)
{
char *help =
"Usage: %s [-h] | [-q] [file_name]\n"
" [-h] Print help\n"
" [-q] Quiet mode (reports when fail)\n"
" [filename] output netCDF file name\n";
fprintf(stderr, help, argv0);
}
/*----< pnetcdf_check_mem_usage() >------------------------------------------*/
/* check PnetCDF library internal memory usage */
static int
pnetcdf_check_mem_usage(MPI_Comm comm)
{
int err, nerrs=0, rank;
MPI_Offset malloc_size, sum_size;
MPI_Comm_rank(comm, &rank);
/* print info about PnetCDF internal malloc usage */
err = ncmpi_inq_malloc_max_size(&malloc_size);
if (err == NC_NOERR) {
MPI_Reduce(&malloc_size, &sum_size, 1, MPI_OFFSET, MPI_SUM, 0, MPI_COMM_WORLD);
if (rank == 0 && verbose)
printf("maximum heap memory allocated by PnetCDF internally is %lld bytes\n",
sum_size);
/* check if there is any PnetCDF internal malloc residue */
err = ncmpi_inq_malloc_size(&malloc_size);
MPI_Reduce(&malloc_size, &sum_size, 1, MPI_OFFSET, MPI_SUM, 0, MPI_COMM_WORLD);
if (rank == 0 && sum_size > 0)
printf("heap memory allocated by PnetCDF internally has %lld bytes yet to be freed\n",
sum_size);
}
else if (err != NC_ENOTENABLED) {
printf("Error at %s:%d: %s\n", __FILE__,__LINE__,ncmpi_strerror(err));
nerrs++;
}
return nerrs;
}
int main(int argc, char** argv)
{
extern int optind;
char filename[256];
int i, rank, nprocs, err, nerrs=0;
int ncid, cmode, varid, dimid[2], num_reqs;
float *buffer;
MPI_Offset **starts=NULL;
MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
verbose = 1;
/* get command-line arguments */
while ((i = getopt(argc, argv, "hq")) != EOF)
switch(i) {
case 'q': verbose = 0;
break;
case 'h':
default: if (rank==0) usage(argv[0]);
MPI_Finalize();
return 1;
}
if (argv[optind] == NULL) strcpy(filename, "testfile.nc");
else snprintf(filename, 256, "%s", argv[optind]);
if (verbose && nprocs != 4 && rank == 0)
printf("Warning: this program is intended to run on 4 processes\n");
/* create a new file for writing ----------------------------------------*/
cmode = NC_CLOBBER;
err = ncmpi_create(MPI_COMM_WORLD, filename, cmode, MPI_INFO_NULL, &ncid);
ERR
/* create a global array of size NY * NX */
err = ncmpi_def_dim(ncid, "Y", NY, &dimid[0]);
ERR
err = ncmpi_def_dim(ncid, "X", NX, &dimid[1]);
ERR
err = ncmpi_def_var(ncid, "var", NC_FLOAT, NDIMS, dimid, &varid);
ERR
if (nprocs < 4) { /* need 4 processes to fill the variables */
err = ncmpi_set_fill(ncid, NC_FILL, NULL);
ERR
}
err = ncmpi_enddef(ncid);
ERR
/* pick arbitrary numbers of requests for 4 processes */
num_reqs = 0;
if (rank == 0) num_reqs = 8;
else if (rank == 1) num_reqs = 13;
else if (rank == 2) num_reqs = 9;
else if (rank == 3) num_reqs = 10;
if (num_reqs > 0) {
starts = (MPI_Offset**) malloc(sizeof(MPI_Offset*) * num_reqs);
starts[0] = (MPI_Offset*) calloc(num_reqs*NDIMS, sizeof(MPI_Offset));
for (i=1; i<num_reqs; i++)
starts[i] = starts[i-1] + NDIMS;
}
/* assign arbitrary starts */
const int y=0, x=1;
if (rank == 0) {
starts[0][y] = 0; starts[0][x] = 5;
starts[1][y] = 1; starts[1][x] = 0;
starts[2][y] = 2; starts[2][x] = 6;
starts[3][y] = 3; starts[3][x] = 0;
starts[4][y] = 0; starts[4][x] = 6;
starts[5][y] = 2; starts[5][x] = 7;
starts[6][y] = 3; starts[6][x] = 1;
starts[7][y] = 3; starts[7][x] = 2;
/* rank 0 is writing the following locations: ("-" means skip)
- - - - - 0 0 - - -
0 - - - - - - - - -
- - - - - - 0 0 - -
0 0 0 - - - - - - -
*/
} else if (rank ==1) {
starts[ 0][y] = 0; starts[ 0][x] = 3;
starts[ 1][y] = 0; starts[ 1][x] = 8;
starts[ 2][y] = 1; starts[ 2][x] = 5;
starts[ 3][y] = 2; starts[ 3][x] = 0;
starts[ 4][y] = 2; starts[ 4][x] = 8;
starts[ 5][y] = 3; starts[ 5][x] = 4;
starts[ 6][y] = 0; starts[ 6][x] = 4;
starts[ 7][y] = 0; starts[ 7][x] = 9;
starts[ 8][y] = 1; starts[ 8][x] = 6;
starts[ 9][y] = 2; starts[ 9][x] = 1;
starts[10][y] = 2; starts[10][x] = 9;
starts[11][y] = 3; starts[11][x] = 5;
starts[12][y] = 3; starts[12][x] = 6;
/* rank 1 is writing the following locations: ("-" means skip)
- - - 1 1 - - - 1 1
- - - - - 1 1 - - -
1 1 - - - - - - 1 1
- - - - 1 1 1 - - -
*/
} else if (rank ==2) {
starts[0][y] = 0; starts[0][x] = 7;
starts[1][y] = 1; starts[1][x] = 1;
starts[2][y] = 1; starts[2][x] = 7;
starts[3][y] = 2; starts[3][x] = 2;
starts[4][y] = 3; starts[4][x] = 3;
starts[5][y] = 1; starts[5][x] = 2;
starts[6][y] = 1; starts[6][x] = 8;
starts[7][y] = 1; starts[7][x] = 3;
starts[8][y] = 1; starts[8][x] = 9;
/* rank 2 is writing the following locations: ("-" means skip)
- - - - - - - 2 - -
- 2 2 2 - - - 2 2 2
- - 2 - - - - - - -
- - - 2 - - - - - -
*/
} else if (rank ==3) {
starts[0][y] = 0; starts[0][x] = 0;
starts[1][y] = 1; starts[1][x] = 4;
starts[2][y] = 2; starts[2][x] = 3;
starts[3][y] = 3; starts[3][x] = 7;
starts[4][y] = 0; starts[4][x] = 1;
starts[5][y] = 2; starts[5][x] = 4;
starts[6][y] = 3; starts[6][x] = 8;
starts[7][y] = 0; starts[7][x] = 2;
starts[8][y] = 2; starts[8][x] = 5;
starts[9][y] = 3; starts[9][x] = 9;
/* rank 3 is writing the following locations: ("-" means skip)
3 3 3 - - - - - - -
- - - - 3 - - - - -
- - - 3 3 3 - - - -
- - - - - - - 3 3 3
*/
}
/* allocate I/O buffer and initialize its contents */
buffer = (float*) malloc(sizeof(float) * num_reqs);
for (i=0; i<num_reqs; i++) buffer[i] = (float)rank;
/* set the buffer pointers to different offsets to the I/O buffer */
err = ncmpi_put_varn_float_all(ncid, varid, num_reqs, starts, NULL, buffer);
ERR
err = ncmpi_close(ncid);
ERR
free(buffer);
if (num_reqs > 0) {
free(starts[0]);
free(starts);
}
nerrs += pnetcdf_check_mem_usage(MPI_COMM_WORLD);
MPI_Finalize();
return (nerrs > 0);
}
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