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/*********************************************************************
*
* Copyright (C) 2014, Northwestern University and Argonne National Laboratory
* See COPYRIGHT notice in top-level directory.
*
*********************************************************************/
/* $Id$ */
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* This example is the read counterpart of example put_vara.cpp. It shows how to
* use NcmpiVar::getVar_all() to read a 2D 4-byte integer array in parallel.
* It also reads a global attribute and two attribute of variable named "var".
* The data partitioning pattern is a column-wise partitioning across all
* processes. Each process reads a subarray of size local_ny * local_nx.
*
* To compile:
* mpicxx -O2 get_vara.cpp -o get_vara -lpnetcdf
*
* Input file is the output file produced by put_vara.cpp. Here is the CDL
* dumped from running ncmpidump.
*
* % ncmpidump /pvfs2/wkliao/testfile.nc
* netcdf testfile {
* // file format: CDF-1
* 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 ;
* }
*
* Example command for MPI run:
*
* % mpiexec -n 4 ./get_vara /pvfs2/wkliao/testfile.nc
*
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include <stdio.h>
#include <stdlib.h>
#include <iostream>
using namespace std;
#include <string.h> /* strcpy(), strncpy() */
#include <unistd.h> /* getopt() */
#include <pnetcdf>
using namespace PnetCDF;
using namespace PnetCDF::exceptions;
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] input netCDF file name\n"
<< argv0;
}
int main(int argc, char** argv)
{
extern int optind;
char filename[256], str_att[NC_MAX_NAME];
int i, rank, nprocs, err, verbose=1;
MPI_Offset len, global_ny, global_nx, local_ny, local_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 {
/* open an existing file for reading --------------------------------*/
NcmpiFile ncFile(MPI_COMM_WORLD, filename, NcmpiFile::read);
// Check the format.
if (ncFile.getFormat() != NcmpiFile::classic5) {
cout << "unexpected file format"<<endl;
throw NcmpiException("read Error ",__FILE__,__LINE__);
}
/* get global attribute named "history" */
NcmpiGroupAtt att = ncFile.getAtt("history");
att.getValues(str_att);
len = att.getAttLength();
str_att[len] = '\0'; /* add a NULL char at the end */
if (rank == 0 && verbose)
printf("global attribute \"history\" of text: %s\n",str_att);
/* get dimension IDs for dimensions Y and X */
NcmpiDim yDim = ncFile.getDim("Y");
NcmpiDim xDim = ncFile.getDim("X");
/* get dimension lengths for dimensions Y and X */
global_ny = yDim.getSize();
global_nx = xDim.getSize();
/* get the variable ID of a 2D variable of integer type */
NcmpiVar var = ncFile.getVar("var");
/* get variable's attribute named "str_att_name" */
NcmpiVarAtt vatt = var.getAtt("str_att_name");
vatt.getValues(str_att);
len = vatt.getAttLength();
str_att[len] = '\0'; /* add a NULL char at the end */
if (rank == 0 && verbose)
printf("variable attribute \"str_att_name\" of type text = \"%s\"\n",
str_att);
/* get the length of variable's attribute named "float_att_name" */
NcmpiVarAtt flt_vatt = var.getAtt("float_att_name");
len = flt_vatt.getAttLength();
/* get attribute contents */
float *float_att = (float*) malloc(sizeof(float) * len);
flt_vatt.getValues(float_att);
/* the local array size */
local_ny = global_ny;
local_nx = global_nx / nprocs;
int *buf = (int*) malloc(sizeof(int) * local_nx * local_ny);
/* prepare reading subarray */
vector<MPI_Offset> start(2), count(2);
start[0] = 0;
start[1] = local_nx * rank;
count[0] = local_ny;
count[1] = local_nx;
/* read a subarray in collective mode */
// var.getVar_all(start, count, &buf[0][0]);
var.getVar_all(start, count, buf);
free(buf);
free(float_att);
/* 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;
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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