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/*********************************************************************
*
* Copyright (C) 2014, Northwestern University and Argonne National Laboratory
* See COPYRIGHT notice in top-level directory.
*
*********************************************************************/
/* $Id$ */
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* This example shows how to use NcmpiVar::putVar_all() to write a 2D
* 4-byte integer array in parallel. 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:
* mpicxx -O2 put_vara.cpp -o put_vara -lpnetcdf
*
* Example commands for MPI run and outputs from running ncmpidump on the
* NC file produced by this example program:
*
* % mpiexec -n 4 ./put_vara /pvfs2/wkliao/testfile.nc
*
* % ncmpidump /pvfs2/wkliao/testfile.nc
* netcdf testfile {
* // file format: CDF-5 (big variables)
* 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 = "Mon Aug 13 21:27:48 2018" ;
* "" ;
* 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 <iostream>
using namespace std;
#include <string.h> /* strcpy(), strncpy() */
#include <unistd.h> /* getopt() */
#include <time.h> /* time() localtime(), asctime() */
#include <pnetcdf>
using namespace PnetCDF;
using namespace PnetCDF::exceptions;
#define NY 10
#define NX 4
static void
usage(char *argv0)
{
cerr <<
"Usage: %s [-h] | [-q] [file_name]\n"
" [-h] Print help\n"
" [-q] Quiet mode (reports when fail)\n"
" [filename] output netCDF file name\n"
<< argv0;
}
int main(int argc, char** argv)
{
extern int optind;
char filename[256], str_att[256];
int i, j, verbose=1, rank, nprocs, buf[NY][NX];
float float_att[100];
MPI_Offset global_ny, global_nx;
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 1;
}
if (argv[optind] == NULL) strcpy(filename, "testfile.nc");
else snprintf(filename, 256, "%s", argv[optind]);
try {
/* create a new file for writing ------------------------------------*/
NcmpiFile ncFile(MPI_COMM_WORLD, filename, NcmpiFile::replace,
NcmpiFile::classic5);
/* 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);
strcpy(str_att, "Mon Aug 13 21:27:48 2018");
/* make sure the time string are consistent among all processes */
MPI_Bcast(str_att, 256, MPI_CHAR, 0, MPI_COMM_WORLD);
ncFile.putAtt(string("history"), string(str_att));
/* define dimensions Y and X */
vector<NcmpiDim> dimid(2);
dimid[0] = ncFile.addDim("Y", global_ny);
dimid[1] = ncFile.addDim("X", global_nx);
/* define a 2D variable of integer type */
NcmpiVar var = ncFile.addVar("var", ncmpiInt, dimid);
/* add attributes to the variable */
var.putAtt(string("str_att_name"),
string("example attribute of type text."));
for (i=0; i<8; i++) float_att[i] = i;
var.putAtt(string("float_att_name"), ncmpiFloat, 8, float_att);
/* now we are in data mode */
vector<MPI_Offset> start(2), count(2);
start[0] = 0;
start[1] = NX * rank;
count[0] = NY;
count[1] = NX;
if (verbose)
printf("%d: start=%lld %lld count=%lld %lld\n",rank,
start[0],start[1],count[0],count[1]);
var.putVar_all(start, count, &buf[0][0]);
/* file is close implicitly */
}
catch(NcmpiException& e) {
cout << e.what() << " error code=" << e.errorCode() << " Error!\n";
return 1;
}
/* check if there is any PnetCDF internal malloc residue */
MPI_Offset malloc_size, sum_size;
int err = ncmpi_inq_malloc_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 && sum_size > 0)
printf("heap memory allocated by PnetCDF internally has %lld bytes yet to be freed\n",
sum_size);
}
MPI_Finalize();
return 0;
}
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