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/*********************************************************************
*
* Copyright (C) 2014, Northwestern University and Argonne National Laboratory
* See COPYRIGHT notice in top-level directory.
*
*********************************************************************/
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* This example shows how to use nc_put_vara_int() to write a 2D 4-byte integer
* array in parallel and read it back using the same array partitioning pattern.
* It first defines a netCDF variable of size global_nx * global_ny where
* global_ny == NY and
* global_nx == (NX * number of MPI processes).
* The data partitioning pattern is a column-wise partitioning across all
* processes. Each process writes a subarray of size ny * nx.
*
* To compile:
* mpicc -O2 parallel_vara.c -o parallel_vara -lnetcdf -lpnetcdf
*
* Example commands for MPI run and outputs from running ncdump on the
* NC file produced by this example program:
*
* % mpiexec -n 4 ./parallel_vara /pvfs2/wkliao/testfile.nc
*
* % ncdump /pvfs2/wkliao/testfile.nc
* netcdf testfile {
* dimensions:
* y = 10 ;
* x = 16 ;
* variables:
* int var(y, x) ;
* var:str_att_name = "example attribute of type text." ;
* var:float_att_name = 0.f, 1.f, 2.f, 3.f, 4.f, 5.f, 6.f, 7.f ;
* // global attributes:
* :history = "Wed Apr 30 11:18:58 2014\n",
* "" ;
* data:
*
* var =
* 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3,
* 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3,
* 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3,
* 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3,
* 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3,
* 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3,
* 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3,
* 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3,
* 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3,
* 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3 ;
* }
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include <stdio.h>
#include <stdlib.h>
#include <string.h> /* strcpy() */
#include <unistd.h> /* getopt() */
#include <time.h> /* time() localtime(), asctime() */
#include <assert.h>
#include <mpi.h>
#include <netcdf.h>
#include <netcdf_par.h>
#define NY 10
#define NX 4
#define FATAL_ERR {if(err!=NC_NOERR) {printf("Error at line=%d: %s Aborting ...\n", __LINE__, nc_strerror(err)); goto fn_exit;}}
#define ERR {if(err!=NC_NOERR)printf("Error at line=%d: %s\n", __LINE__, nc_strerror(err));}
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);
}
int main(int argc, char** argv)
{
extern int optind;
char filename[128];
int i, j, rank, nprocs, verbose=1, err;
int ncid, cmode, omode, varid, dimid[2], buf[NY][NX];
char str_att[128];
float float_att[100];
size_t global_ny, global_nx, start[2], count[2];
MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
/* 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 0;
}
argc -= optind;
argv += optind;
if (argc == 1) strcpy(filename, argv[0]); /* optional argument */
else strcpy(filename, "testfile.nc");
MPI_Bcast(filename, 128, MPI_CHAR, 0, MPI_COMM_WORLD);
/* create a new file for writing ----------------------------------------*/
cmode = NC_CLOBBER;
err = nc_create_par(filename, cmode, MPI_COMM_WORLD, MPI_INFO_NULL, &ncid); FATAL_ERR
/* the global array is NY * (NX * nprocs) */
global_ny = NY;
global_nx = NX * nprocs;
for (i=0; i<NY; i++)
for (j=0; j<NX; j++)
buf[i][j] = rank;
/* add a global attribute: a time stamp at rank 0 */
time_t ltime = time(NULL); /* get the current calendar time */
asctime_r(localtime(<ime), str_att);
/* make sure the time string are consistent among all processes */
MPI_Bcast(str_att, strlen(str_att), MPI_CHAR, 0, MPI_COMM_WORLD);
err = nc_put_att_text(ncid, NC_GLOBAL, "history", strlen(str_att),
&str_att[0]); ERR
/* define dimensions x and y */
err = nc_def_dim(ncid, "Y", global_ny, &dimid[0]); ERR
err = nc_def_dim(ncid, "X", global_nx, &dimid[1]); ERR
/* define a 2D variable of integer type */
err = nc_def_var(ncid, "var", NC_INT, 2, dimid, &varid); ERR
/* add attributes to the variable */
strcpy(str_att, "example attribute of type text.");
err = nc_put_att_text(ncid, varid, "str_att_name", strlen(str_att),
&str_att[0]); ERR
for (i=0; i<8; i++) float_att[i] = i;
err = nc_put_att_float(ncid, varid, "float_att_name", NC_FLOAT, 8,
&float_att[0]); ERR
/* do not forget to exit define mode */
err = nc_enddef(ncid); ERR
/* set to use MPI collective I/O */
err = nc_var_par_access(ncid, NC_GLOBAL, NC_COLLECTIVE); ERR
/* now we are in data mode */
start[0] = 0;
start[1] = NX * rank;
count[0] = NY;
count[1] = NX;
err = nc_put_vara_int(ncid, varid, start, count, &buf[0][0]); ERR
err = nc_close(ncid); ERR
omode = NC_NOWRITE;
err = nc_open_par(filename, omode, MPI_COMM_WORLD, MPI_INFO_NULL, &ncid); FATAL_ERR
/* inquire dimension IDs and lengths */
err = nc_inq_dimid(ncid, "Y", &dimid[0]); ERR
err = nc_inq_dimid(ncid, "X", &dimid[1]); ERR
err = nc_inq_dimlen(ncid, dimid[0], &global_ny); ERR
err = nc_inq_dimlen(ncid, dimid[1], &global_nx); ERR
/* obtain variable ID */
err = nc_inq_varid(ncid, "var", &varid); ERR
/* set to use MPI collective I/O */
err = nc_var_par_access(ncid, NC_GLOBAL, NC_COLLECTIVE); ERR
/* each process reads its subarray from the file */
err = nc_get_vara_int(ncid, varid, start, count, &buf[0][0]); ERR
/* close the file */
err = nc_close(ncid); ERR
fn_exit:
MPI_Finalize();
return 0;
}
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