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/*********************************************************************
*
* Copyright (C) 2013, 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.
*
* % mpicc -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 <string.h> /* strcpy(), strncpy() */
#include <unistd.h> /* getopt() */
#include <mpi.h>
#include <pnetcdf.h>
#define NZ 5
#define NY 5
#define NX 5
static int verbose;
#define ERR {if(err!=NC_NOERR){printf("Error at %s:%d : %s\n", __FILE__,__LINE__, ncmpi_strerror(err));nerrs++;}}
static void
usage(char *argv0)
{
char *help =
"Usage: %s [-h] | [-q] [file_name]\n"
" [-h] Print help\n"
" [-q] Quiet mode (reports when fail)\n"
" [filename] output netCDF file name\n";
fprintf(stderr, help, argv0);
}
/*----< pnetcdf_check_mem_usage() >------------------------------------------*/
/* check PnetCDF library internal memory usage */
static int
pnetcdf_check_mem_usage(MPI_Comm comm)
{
int err, nerrs=0, rank;
MPI_Offset malloc_size, sum_size;
MPI_Comm_rank(comm, &rank);
/* print info about PnetCDF internal malloc usage */
err = ncmpi_inq_malloc_max_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 && verbose)
printf("maximum heap memory allocated by PnetCDF internally is %lld bytes\n",
sum_size);
/* check if there is any PnetCDF internal malloc residue */
err = ncmpi_inq_malloc_size(&malloc_size);
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);
}
else if (err != NC_ENOTENABLED) {
printf("Error at %s:%d: %s\n", __FILE__,__LINE__,ncmpi_strerror(err));
nerrs++;
}
return nerrs;
}
static
int print_hints(int ncid,
int varid0,
int varid1)
{
char value[MPI_MAX_INFO_VAL];
int err, len, flag, nerrs=0;
MPI_Offset header_size, header_extent, var_zy_start, var_yx_start;
MPI_Offset v_align=-1, h_chunk=-1;
MPI_Info info_used;
err = ncmpi_inq_header_size (ncid, &header_size); ERR
err = ncmpi_inq_header_extent(ncid, &header_extent); ERR
err = ncmpi_inq_varoffset(ncid, varid0, &var_zy_start); ERR
err = ncmpi_inq_varoffset(ncid, varid1, &var_yx_start); ERR
err = ncmpi_inq_file_info(ncid, &info_used); ERR
MPI_Info_get_valuelen(info_used, "nc_var_align_size", &len, &flag);
if (flag) {
MPI_Info_get(info_used, "nc_var_align_size", len+1, value, &flag);
v_align = strtoll(value,NULL,10);
}
MPI_Info_get_valuelen(info_used, "nc_header_read_chunk_size", &len, &flag);
if (flag) {
MPI_Info_get(info_used, "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);
return nerrs;
}
int main(int argc, char** argv)
{
extern int optind;
char filename[256];
int i, rank, nprocs, err, nerrs=0;
int ncid, cmode, varid0, varid1, dimid[3], *buf_zy;
float *buf_yx;
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);
verbose = 1;
/* 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]);
MPI_Info_create(&info);
MPI_Info_set(info, "nc_var_align_size", "512"); /* size in bytes */
MPI_Info_set(info, "nc_header_read_chunk_size", "256"); /* size in bytes */
/* note that set the above values to 1 to disable the alignment */
/* create a new file for writing ----------------------------------------*/
cmode = NC_CLOBBER | NC_64BIT_DATA;
err = ncmpi_create(MPI_COMM_WORLD, filename, cmode, info, &ncid); ERR
MPI_Info_free(&info);
/* define 3 dimensions */
err = ncmpi_def_dim(ncid, "Z", NZ*nprocs, &dimid[0]); ERR
err = ncmpi_def_dim(ncid, "Y", NY*nprocs, &dimid[1]); ERR
err = ncmpi_def_dim(ncid, "X", NX*nprocs, &dimid[2]); ERR
/* define a variable of size (NZ * nprocs) * (NY * nprocs) */
err = ncmpi_def_var(ncid, "var_zy", NC_INT, 2, &dimid[0], &varid0); ERR
/* define a variable of size (NY * nprocs) * (NX * nprocs) */
err = ncmpi_def_var(ncid, "var_yx", NC_FLOAT, 2, &dimid[1], &varid1); ERR
err = ncmpi_enddef(ncid); ERR
/* 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;
err = ncmpi_put_vara_int_all(ncid, varid0, start, count, buf_zy); ERR
/* 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;
err = ncmpi_put_vara_float_all(ncid, varid1, start, count, buf_yx); ERR
if (rank == 0 && verbose) nerrs += print_hints(ncid, varid0, varid1);
err = ncmpi_close(ncid); ERR
free(buf_zy);
free(buf_yx);
nerrs += pnetcdf_check_mem_usage(MPI_COMM_WORLD);
MPI_Finalize();
return (nerrs > 0);
}
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