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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 a single call of NcmpiVar::putVarn_all() to
* write a sequence of requests with arbitrary array indices and lengths.
* Using ncmpi_put_varn_int_all() can achieve the same effect of HDF5 writing
* a sequence of selected file locations through the following 2 APIs.
*
* H5Sselect_elements(fid, H5S_SELECT_SET, NUMP, (const hssize_t **)coord);
* H5Dwrite(dataset, H5T_NATIVE_INT, mid, fid, H5P_DEFAULT, val);
*
* Note that in NcmpiVar::putVarn_all(), users can write more than one
* element starting at each selected location.
*
* The compile and run commands are given below, together with an ncmpidump of
* the output file.
*
* % mpicc -O2 -o put_varn_int put_varn_int.cpp -lpnetcdf
* % mpiexec -n 4 ./put_varn_int /pvfs2/wkliao/testfile.nc
* % ncmpidump /pvfs2/wkliao/testfile.nc
* netcdf testfile {
* // file format: CDF-5 (big variables)
* dimensions:
* Y = 4 ;
* X = 10 ;
* variables:
* int var(Y, X) ;
* data:
*
* var =
* 3, 3, 3, 1, 1, 0, 0, 2, 1, 1,
* 0, 2, 2, 2, 3, 1, 1, 2, 2, 2,
* 1, 1, 2, 3, 3, 3, 0, 0, 1, 1,
* 0, 0, 0, 2, 1, 1, 1, 3, 3, 3 ;
* }
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#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 4
#define NX 10
#define NDIMS 2
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, rank, nprocs, verbose=1;
int num_reqs, *buffer;
MPI_Offset w_len, **starts=NULL, **counts=NULL;
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]);
if (nprocs != 4 && rank == 0 && verbose)
printf("Warning: this program is intended to run on 4 processes\n");
try {
/* create a new file for writing ------------------------------------*/
NcmpiFile nc(MPI_COMM_WORLD, filename, NcmpiFile::replace,
NcmpiFile::classic5);
/* define dimensions Y and X */
vector<NcmpiDim> dimid(2);
dimid[0] = nc.addDim("Y", NY);
dimid[1] = nc.addDim("X", NX);
/* define a 2D variable of integer type */
NcmpiVar var = nc.addVar("var", ncmpiInt, dimid);
if (nprocs < 4) /* need 4 processes to fill the variables */
nc.set_fill(NcmpiFile::Fill, NULL);
/* pick arbitrary numbers of requests for 4 processes */
num_reqs = 0;
if (rank == 0) num_reqs = 4;
else if (rank == 1) num_reqs = 6;
else if (rank == 2) num_reqs = 5;
else if (rank == 3) num_reqs = 4;
if (num_reqs > 0) {
starts = (MPI_Offset**) malloc(sizeof(MPI_Offset*) * num_reqs);
counts = (MPI_Offset**) malloc(sizeof(MPI_Offset*) * num_reqs);
starts[0] = (MPI_Offset*) calloc(num_reqs * NDIMS, sizeof(MPI_Offset));
counts[0] = (MPI_Offset*) calloc(num_reqs * NDIMS, sizeof(MPI_Offset));
for (i=1; i<num_reqs; i++) {
starts[i] = starts[i-1] + NDIMS;
counts[i] = counts[i-1] + NDIMS;
}
}
/* assign arbitrary starts and counts */
const int y=0, x=1;
if (rank == 0) {
starts[0][y] = 0; starts[0][x] = 5; counts[0][y] = 1; counts[0][x] = 2;
starts[1][y] = 1; starts[1][x] = 0; counts[1][y] = 1; counts[1][x] = 1;
starts[2][y] = 2; starts[2][x] = 6; counts[2][y] = 1; counts[2][x] = 2;
starts[3][y] = 3; starts[3][x] = 0; counts[3][y] = 1; counts[3][x] = 3;
/* rank 0 is writing the followings: ("-" means skip)
- - - - - 0 0 - - -
0 - - - - - - - - -
- - - - - - 0 0 - -
0 0 0 - - - - - - -
*/
} else if (rank ==1) {
starts[0][y] = 0; starts[0][x] = 3; counts[0][y] = 1; counts[0][x] = 2;
starts[1][y] = 0; starts[1][x] = 8; counts[1][y] = 1; counts[1][x] = 2;
starts[2][y] = 1; starts[2][x] = 5; counts[2][y] = 1; counts[2][x] = 2;
starts[3][y] = 2; starts[3][x] = 0; counts[3][y] = 1; counts[3][x] = 2;
starts[4][y] = 2; starts[4][x] = 8; counts[4][y] = 1; counts[4][x] = 2;
starts[5][y] = 3; starts[5][x] = 4; counts[5][y] = 1; counts[5][x] = 3;
/* rank 1 is writing the followings: ("-" means skip)
- - - 1 1 - - - 1 1
- - - - - 1 1 - - -
1 1 - - - - - - 1 1
- - - - 1 1 1 - - -
*/
} else if (rank ==2) {
starts[0][y] = 0; starts[0][x] = 7; counts[0][y] = 1; counts[0][x] = 1;
starts[1][y] = 1; starts[1][x] = 1; counts[1][y] = 1; counts[1][x] = 3;
starts[2][y] = 1; starts[2][x] = 7; counts[2][y] = 1; counts[2][x] = 3;
starts[3][y] = 2; starts[3][x] = 2; counts[3][y] = 1; counts[3][x] = 1;
starts[4][y] = 3; starts[4][x] = 3; counts[4][y] = 1; counts[4][x] = 1;
/* rank 2 is writing the followings: ("-" means skip)
- - - - - - - 2 - -
- 2 2 2 - - - 2 2 2
- - 2 - - - - - - -
- - - 2 - - - - - -
*/
} else if (rank ==3) {
starts[0][y] = 0; starts[0][x] = 0; counts[0][y] = 1; counts[0][x] = 3;
starts[1][y] = 1; starts[1][x] = 4; counts[1][y] = 1; counts[1][x] = 1;
starts[2][y] = 2; starts[2][x] = 3; counts[2][y] = 1; counts[2][x] = 3;
starts[3][y] = 3; starts[3][x] = 7; counts[3][y] = 1; counts[3][x] = 3;
/* rank 3 is writing the followings: ("-" means skip)
3 3 3 - - - - - - -
- - - - 3 - - - - -
- - - 3 3 3 - - - -
- - - - - - - 3 3 3
*/
}
w_len = 0; /* total write length for this process */
for (i=0; i<num_reqs; i++) {
MPI_Offset w_req_len=1;
for (j=0; j<NDIMS; j++)
w_req_len *= counts[i][j];
w_len += w_req_len;
}
/* allocate I/O buffer and initialize its contents */
buffer = (int*) malloc(sizeof(int) * w_len);
for (i=0; i<w_len; i++) buffer[i] = rank;
/* set the buffer pointers to different offsets to the I/O buffer */
var.putVarn_all(num_reqs, starts, counts, buffer);
free(buffer);
if (num_reqs > 0) {
free(starts[0]);
free(counts[0]);
free(starts);
free(counts);
}
/* 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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