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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 PnetCDF flexible APIs, NcmpiVar::putVar_all()
* to write two 2D array variables (one is of 4-byte integer byte and the
* other float type) in parallel. It first defines 2 netCDF variables of sizes
* var_zy: NZ*nprocs x NY
* var_yx: NY x NX*nprocs
*
* The data partitioning patterns on the 2 variables are row-wise and
* column-wise, respectively. Each process writes a subarray of size
* NZ x NY and NY x NX to var_zy and var_yx, respectively.
* Both local buffers have a ghost cell of length 3 surrounded along each
* dimension.
*
* The compile and run commands are given below.
*
* % mpicxx -O2 -o flexible_api flexible_api.cpp -lpnetcdf
*
* % mpiexec -l -n 4 ./flexible_api /pvfs2/wkliao/testfile.nc
*
* % ncmpidump /pvfs2/wkliao/testfile.nc
* netcdf testfile {
* // file format: CDF-5 (big variables)
* dimensions:
* Z = 20 ;
* Y = 5 ;
* X = 20 ;
* variables:
* int var_zy(Z, Y) ;
* float var_yx(Y, X) ;
* data:
*
* var_zy =
* 0, 0, 0, 0, 0,
* 0, 0, 0, 0, 0,
* 0, 0, 0, 0, 0,
* 0, 0, 0, 0, 0,
* 0, 0, 0, 0, 0,
* 1, 1, 1, 1, 1,
* 1, 1, 1, 1, 1,
* 1, 1, 1, 1, 1,
* 1, 1, 1, 1, 1,
* 1, 1, 1, 1, 1,
* 2, 2, 2, 2, 2,
* 2, 2, 2, 2, 2,
* 2, 2, 2, 2, 2,
* 2, 2, 2, 2, 2,
* 2, 2, 2, 2, 2,
* 3, 3, 3, 3, 3,
* 3, 3, 3, 3, 3,
* 3, 3, 3, 3, 3,
* 3, 3, 3, 3, 3,
* 3, 3, 3, 3, 3 ;
*
* var_yx =
* 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3,
* 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3,
* 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3,
* 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3,
* 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 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 <pnetcdf>
using namespace PnetCDF;
using namespace PnetCDF::exceptions;
#define NZ 5
#define NY 5
#define NX 5
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, rank, nprocs, verbose=1, ghost_len=3;
int *buf_zy;
float *buf_yx;
MPI_Datatype subarray;
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 nc(MPI_COMM_WORLD, filename, NcmpiFile::replace,
NcmpiFile::classic5);
/* define 3 dimensions */
vector<NcmpiDim> dimid(3);
dimid[0] = nc.addDim("Z", NZ*nprocs);
dimid[1] = nc.addDim("Y", NY);
dimid[2] = nc.addDim("X", NX*nprocs);
vector<NcmpiDim> dimid0(2), dimid1(2);
dimid0[0] = dimid[0];
dimid0[1] = dimid1[0] = dimid[1];
dimid1[1] = dimid[2];
/* define a variable of size (NZ * nprocs) * NY */
NcmpiVar var0 = nc.addVar("var_zy", ncmpiInt, dimid0);
/* define a variable of size NY * (NX * nprocs) */
NcmpiVar var1 = nc.addVar("var_yx", ncmpiFloat, dimid1);
/* var_zy is partitioned along Z dimension */
int array_of_sizes[2], array_of_subsizes[2], array_of_starts[2];
array_of_sizes[0] = NZ + 2*ghost_len;
array_of_sizes[1] = NY + 2*ghost_len;
array_of_subsizes[0] = NZ;
array_of_subsizes[1] = NY;
array_of_starts[0] = ghost_len;
array_of_starts[1] = ghost_len;
MPI_Type_create_subarray(2, array_of_sizes, array_of_subsizes,
array_of_starts, MPI_ORDER_C, MPI_INT,
&subarray);
MPI_Type_commit(&subarray);
/* allocate buffer buf_zy and initialize its contents */
int buffer_len = (NZ+2*ghost_len) * (NY+2*ghost_len);
buf_zy = (int*) malloc(sizeof(int) * buffer_len);
for (i=0; i<buffer_len; i++) buf_zy[i] = rank;
vector <MPI_Offset> start(2), count(2);
start[0] = NZ * rank; start[1] = 0;
count[0] = NZ; count[1] = NY;
if (verbose)
printf("%d: start=%lld %lld count=%lld %lld\n",rank,
start[0],start[1],count[0],count[1]);
/* calling a blocking flexible API */
var0.putVar_all(start, count, &buf_zy[0], 1, subarray);
free(buf_zy);
MPI_Type_free(&subarray);
/* var_yx is partitioned along X dimension */
array_of_sizes[0] = NY + 2*ghost_len;
array_of_sizes[1] = NX + 2*ghost_len;
array_of_subsizes[0] = NY;
array_of_subsizes[1] = NX;
array_of_starts[0] = ghost_len;
array_of_starts[1] = ghost_len;
MPI_Type_create_subarray(2, array_of_sizes, array_of_subsizes,
array_of_starts, MPI_ORDER_C, MPI_FLOAT,
&subarray);
MPI_Type_commit(&subarray);
/* allocate buffer buf_yx and initialize its contents */
buffer_len = (NY+2*ghost_len) * (NX+2*ghost_len);
buf_yx = (float*) malloc(sizeof(float) * buffer_len);
for (i=0; i<buffer_len; i++) buf_yx[i] = rank;
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]);
/* calling a non-blocking flexible API */
var1.putVar_all(start, count, buf_yx, 1, subarray);
free(buf_yx);
MPI_Type_free(&subarray);
/* 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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