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/*********************************************************************
*
* Copyright (C) 2015, Northwestern University and Argonne National Laboratory
* See COPYRIGHT notice in top-level directory.
*
*********************************************************************/
/* $Id$ */
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* This example shows how to use
* 1. ncmpi_set_fill() to enable fill mode
* 2. ncmpi_def_var_fill() to define the variable's fill value
* 3. ncmpi_inq_var_fill() to inquire the variable's fill mode information
* 4. ncmpi_put_vara_int_all() to write two 2D 4-byte integer array in parallel.
* It first defines a netCDF record variable of size NC_UNLIMITED * global_ny
* where
* global_nx == (NX * number of MPI processes).
* It then defines a netCDF fixed-size variable of size global_nx * global_ny
* where
* global_ny == NY and
* global_nx == (NX * number of MPI processes).
* The data partitioning pattern for both variables are a column-wise
* partitioning across all processes. Each process writes a subarray of size
* ny * nx.
*
* To compile:
* mpicc -O2 fill_mode.c -o fill_mode -lpnetcdf
*
* Example commands for MPI run and outputs from running ncmpidump on the
* NC file produced by this example program:
*
* % mpiexec -n 4 ./fill_mode -q /pvfs2/wkliao/testfile.nc
*
* % ncmpidump /pvfs2/wkliao/testfile.nc
* netcdf testfile {
* // file format: CDF-1
* dimensions:
* REC_DIM = UNLIMITED ; // (2 currently)
* X = 16 ;
* Y = 3 ;
* variables:
* int rec_var(REC_DIM, X) ;
* rec_var:_FillValue = -1 ;
* int fix_var(Y, X) ;
* data:
*
* rec_var =
* 0, 0, 0, _, 1, 1, 1, _, 2, 2, 2, _, 3, 3, 3, _,
* 0, 0, 0, _, 1, 1, 1, _, 2, 2, 2, _, 3, 3, 3, _ ;
*
* fix_var =
* 0, 0, 0, _, 1, 1, 1, _, 2, 2, 2, _, 3, 3, 3, _,
* 0, 0, 0, _, 1, 1, 1, _, 2, 2, 2, _, 3, 3, 3, _,
* 0, 0, 0, _, 1, 1, 1, _, 2, 2, 2, _, 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 3
#define NX 4
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, j, rank, nprocs, err, nerrs=0, rec_varid, fix_varid;
int ncid, cmode, dimid[2], buf[NY][NX], no_fill, fill_value, old_mode;
MPI_Offset global_ny, global_nx;
MPI_Offset start[2], count[2];
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]);
MPI_Bcast(filename, 256, MPI_CHAR, 0, MPI_COMM_WORLD);
/* create a new file for writing ----------------------------------------*/
cmode = NC_CLOBBER;
err = ncmpi_create(MPI_COMM_WORLD, filename, cmode, MPI_INFO_NULL, &ncid);
ERR
/* the global array is NY * (NX * nprocs) */
global_ny = NY;
global_nx = NX * nprocs;
/* define dimensions x and y */
err = ncmpi_def_dim(ncid, "REC_DIM", NC_UNLIMITED, &dimid[0]); ERR
err = ncmpi_def_dim(ncid, "X", global_nx, &dimid[1]); ERR
/* define a 2D variable of integer type */
err = ncmpi_def_var(ncid, "rec_var", NC_INT, 2, dimid, &rec_varid); ERR
err = ncmpi_def_dim(ncid, "Y", global_ny, &dimid[0]); ERR
err = ncmpi_def_var(ncid, "fix_var", NC_INT, 2, dimid, &fix_varid); ERR
/* set the fill mode to NC_FILL for entire file */
err = ncmpi_set_fill(ncid, NC_FILL, &old_mode); ERR
if (verbose) {
if (old_mode == NC_FILL) printf("The old fill mode is NC_FILL\n");
else printf("The old fill mode is NC_NOFILL\n");
}
/* set the fill mode back to NC_NOFILL for entire file */
err = ncmpi_set_fill(ncid, NC_NOFILL, NULL); ERR
/* set the variable's fill mode to NC_FILL with default fill value */
err = ncmpi_def_var_fill(ncid, fix_varid, 0, NULL); ERR
/* set a customized fill value -1 */
fill_value = -1;
err = ncmpi_put_att_int(ncid, rec_varid, "_FillValue", NC_INT, 1, &fill_value);
ERR
/* do not forget to exit define mode */
err = ncmpi_enddef(ncid);
ERR
/* now we are in data mode */
start[0] = 0;
start[1] = NX * rank;
count[0] = NY;
count[1] = NX;
/* initialize user buffer */
for (i=0; i<NY; i++)
for (j=0; j<NX; j++)
buf[i][j] = rank;
/* do not write the variable in full */
count[1]--;
err = ncmpi_put_vara_int_all(ncid, fix_varid, start, count, &buf[0][0]); ERR
err = ncmpi_inq_var_fill(ncid, fix_varid, &no_fill, &fill_value); ERR
if (no_fill != 0)
printf("Error at line %d in %s: expecting no_fill to be 0\n",
__LINE__,__FILE__);
if (fill_value != NC_FILL_INT)
printf("Error at line %d in %s: expecting no_fill to be %d but got %d\n",
__LINE__,__FILE__,NC_FILL_INT,fill_value);
/* fill the 1st record of the record variable */
start[0] = 0;
err = ncmpi_fill_var_rec(ncid, rec_varid, start[0]); ERR
/* write to the 1st record */
count[0] = 1;
err = ncmpi_put_vara_int_all(ncid, rec_varid, start, count, &buf[0][0]); ERR
/* fill the 2nd record of the record variable */
start[0] = 1;
err = ncmpi_fill_var_rec(ncid, rec_varid, start[0]); ERR
/* write to the 2nd record */
err = ncmpi_put_vara_int_all(ncid, rec_varid, start, count, &buf[0][0]); ERR
err = ncmpi_close(ncid);
ERR
nerrs += pnetcdf_check_mem_usage(MPI_COMM_WORLD);
MPI_Finalize();
return (nerrs > 0);
}
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