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/*********************************************************************
*
* Copyright (C) 2014, Northwestern University and Argonne National Laboratory
* See COPYRIGHT notice in top-level directory.
*
*********************************************************************/
/* $Id$ */
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* This example sets PnetCDF hint:
* nc_var_align_size
* and prints the hint values as well as the header size, header extent, and
* two variables' starting file offsets.
*
* The compile and run commands are given below.
*
* % mpicxx -O2 -o hints hints.c -lpnetcdf
*
* % mpiexec -l -n 4 ./hints /pvfs2/wkliao/testfile.nc
*
* nc_var_align_size set to = 512
* nc_header_read_chunk_size set to = 256
* header size = 252
* header extent = 1024
* var_zy start file offset = 1024
* var_yx start file offset = 3072
*
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#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;
}
static
void print_hints(NcmpiFile &ncFile,
NcmpiVar &var0,
NcmpiVar &var1)
{
char value[MPI_MAX_INFO_VAL];
int len, flag;
MPI_Offset header_size, header_extent, var_zy_start, var_yx_start;
MPI_Offset v_align=-1, h_chunk=-1;
MPI_Info info_used;
ncFile.Inq_header_size(&header_size);
ncFile.Inq_header_extent(&header_extent);
var0.Inq_file_offset(&var_zy_start);
var1.Inq_file_offset(&var_yx_start);
/* get all the hints used */
ncFile.Inq_file_info(&info_used);
MPI_Info_get_valuelen(info_used, (char*)"nc_var_align_size", &len, &flag);
if (flag) {
MPI_Info_get(info_used, (char*)"nc_var_align_size", len+1, value, &flag);
v_align = strtoll(value,NULL,10);
}
MPI_Info_get_valuelen(info_used, (char*)"nc_header_read_chunk_size", &len, &flag);
if (flag) {
MPI_Info_get(info_used, (char*)"nc_header_read_chunk_size", len+1, value,&flag);
h_chunk = strtoll(value,NULL,10);
}
MPI_Info_free(&info_used);
if (v_align == -1)
printf("nc_var_align_size is NOT set\n");
else
printf("nc_var_align_size set to = %lld\n", v_align);
if (h_chunk == -1)
printf("nc_header_read_chunk_size is NOT set\n");
else
printf("nc_header_read_chunk_size set to = %lld\n", h_chunk);
printf("header size = %lld\n", header_size);
printf("header extent = %lld\n", header_extent);
printf("var_zy start file offset = %lld\n", var_zy_start);
printf("var_yx start file offset = %lld\n", var_yx_start);
}
int main(int argc, char** argv)
{
extern int optind;
char filename[256];
int i, rank, nprocs, verbose=1, *buf_zy;
float *buf_yx;
vector<MPI_Offset> start(2), count(2);
MPI_Info info;
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 {
MPI_Info_create(&info);
MPI_Info_set(info, (char*)"nc_var_align_size", (char*)"512");
MPI_Info_set(info, (char*)"nc_header_read_chunk_size", (char*)"256");
/* note that set the above values to 1 to disable the alignment */
/* create a new file for writing -------------------------------------*/
NcmpiFile ncFile(MPI_COMM_WORLD, filename, NcmpiFile::replace,
NcmpiFile::classic5, info);
MPI_Info_free(&info);
/* define 3 dimensions */
vector<NcmpiDim> dimid(3);
dimid[0] = ncFile.addDim("Z", NZ*nprocs);
dimid[1] = ncFile.addDim("Y", NY*nprocs);
dimid[2] = ncFile.addDim("X", NX*nprocs);
/* define a variable of size (NZ * nprocs) * (NY * nprocs) */
vector<NcmpiDim> dimid_zy(2);
dimid_zy[0] = dimid[0];
dimid_zy[1] = dimid[1];
NcmpiVar var0 = ncFile.addVar("var_zy", ncmpiInt, dimid_zy);
/* define a variable of size (NY * nprocs) * (NX * nprocs) */
vector<NcmpiDim> dimid_yx(2);
dimid_yx[0] = dimid[1];
dimid_yx[1] = dimid[2];
NcmpiVar var1 = ncFile.addVar("var_yx", ncmpiFloat, dimid_yx);
/* var_zy is partitioned along Z dimension */
buf_zy = (int*) malloc(sizeof(int) * NZ * (NY * nprocs));
for (i=0; i<NZ*(NY*nprocs); i++) buf_zy[i] = i;
start[0] = NZ * rank; start[1] = 0;
count[0] = NZ; count[1] = NY * nprocs;
var0.putVar_all(start, count, buf_zy);
/* var_yx is partitioned along X dimension */
buf_yx = (float*) malloc(sizeof(float) * (NY * nprocs) * NX);
for (i=0; i<(NY*nprocs)*NX; i++) buf_yx[i] = i;
start[0] = 0; start[1] = NX * rank;
count[0] = NY * nprocs; count[1] = NX;
var1.putVar_all(start, count, buf_yx);
if (rank == 0 && verbose) print_hints(ncFile, var0, var1);
free(buf_zy);
free(buf_yx);
}
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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