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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 the vard API ncmpi_put_vard() and
* ncmpi_get_vard() to write and read 2D record and fixed-size variables.
*
* To compile:
* mpicxx -O2 vard_int.cpp -o vard_int -lpnetcdf
*
* Example commands for MPI run and outputs from running ncmpidump on the
* NC file produced by this example program:
*
* % mpiexec -n 4 ./vard_int /pvfs2/wkliao/testfile.nc
*
* The expected results from the output file contents are:
*
* % ncmpidump /pvfs2/wkliao/testfile.nc
* netcdf testfile {
* // file format: CDF-1
* dimensions:
* REC_DIM = UNLIMITED ; // (2 currently)
* X = 12 ;
* FIX_DIM = 2 ;
* variables:
* int rec_var(REC_DIM, X) ;
* int fix_var(FIX_DIM, X) ;
* data:
*
* rec_var =
* 0, 1, 2, 100, 101, 102, 200, 201, 202, 300, 301, 302,
* 10, 11, 12, 110, 111, 112, 210, 211, 212, 310, 311, 312 ;
*
* fix_var =
* 0, 1, 2, 100, 101, 102, 200, 201, 202, 300, 301, 302,
* 10, 11, 12, 110, 111, 112, 210, 211, 212, 310, 311, 312 ;
* }
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#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;
#define NY 2
#define NX 3
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];
int i, j, verbose=1;
int rank, nprocs, array_of_blocklengths[2], buf[NY][NX];
int array_of_sizes[2], array_of_subsizes[2], array_of_starts[2];
MPI_Offset recsize, bufcount, len;
MPI_Aint array_of_displacements[2];
MPI_Datatype buftype, rec_filetype, fix_filetype;
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]);
vector <int> start(2), count(2);
start[0] = 0; start[1] = NX*rank;
count[0] = 2; count[1] = NX;
if (verbose)
printf("%d: start=%d %d count=%d %d\n",rank,
start[0],start[1],count[0],count[1]);
/* create a file type for the fixed-size variable */
array_of_sizes[0] = 2;
array_of_sizes[1] = NX*nprocs;
array_of_subsizes[0] = count[0];
array_of_subsizes[1] = count[1];
array_of_starts[0] = start[0];
array_of_starts[1] = start[1];
MPI_Type_create_subarray(2, array_of_sizes, array_of_subsizes,
array_of_starts, MPI_ORDER_C,
MPI_INT, &fix_filetype);
MPI_Type_commit(&fix_filetype);
buftype = MPI_INT;
bufcount = count[0] * count[1];
try {
/* create a new file for writing ------------------------------------*/
NcmpiFile nc(MPI_COMM_WORLD, filename, NcmpiFile::replace);
/* define 3 dimensions */
vector<NcmpiDim> recdimid(2);
recdimid[0] = nc.addDim("REC_DIM", NC_UNLIMITED);
recdimid[1] = nc.addDim("X", NX*nprocs);
vector<NcmpiDim> fixdimid(2);
fixdimid[0] = nc.addDim("FIX_DIM", 2);
fixdimid[1] = recdimid[1];
/* define a variable of size (NZ * nprocs) * NY */
NcmpiVar var0 = nc.addVar("rec_var", ncmpiInt, recdimid);
/* define a variable of size NY * (NX * nprocs) */
NcmpiVar var1 = nc.addVar("fix_var", ncmpiInt, fixdimid);
nc.enddef();
/* create a file type for the record variable */
recsize = nc.getRecSize();
for (i=0; i<count[0]; i++) {
array_of_blocklengths[i] = count[1];
array_of_displacements[i] = start[1]*sizeof(int) + recsize * i;
}
MPI_Type_create_hindexed(2, array_of_blocklengths,
array_of_displacements, MPI_INT, &rec_filetype);
MPI_Type_commit(&rec_filetype);
/* initialize the contents of the array */
for (j=0; j<NY; j++) for (i=0; i<NX; i++)
buf[j][i] = rank*100 + j*10 + i;
/* write the record variable */
var0.putVard_all(rec_filetype, buf, bufcount, buftype);
/* check if the number of records changed to 2 */
len = recdimid[0].getSize();
if (len != 2)
cout << "Error: number of records should be 2 but got " << len << "\n";
/* write the fixed-size variable */
var1.putVard_all(fix_filetype, buf, bufcount, buftype);
/* file is close implicitly */
}
catch(NcmpiException& e) {
cout << e.what() << " error code=" << e.errorCode() << " Error!\n";
return 1;
}
try {
/* open file for reading -----------------------------------------*/
NcmpiFile nc(MPI_COMM_WORLD, filename, NcmpiFile::read);
NcmpiVar var0 = nc.getVar("rec_var");
NcmpiVar var1 = nc.getVar("fix_var");
/* read the record variable */
var0.getVard_all(rec_filetype, buf, bufcount, buftype);
/* read the fixed-size variable */
var1.getVard_all(fix_filetype, buf, bufcount, buftype);
MPI_Type_free(&rec_filetype);
MPI_Type_free(&fix_filetype);
}
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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