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/*********************************************************************
*
* Copyright (C) 2015, Northwestern University and Argonne National Laboratory
* See COPYRIGHT notice in top-level directory.
*
*********************************************************************/
/* $Id$ */
/*
* This example shows how to use varm API to write a 2D array buffer with ghost
* cells to a variables. The size of ghost cells is nghosts and the ghost cells
* cells appear on both ends of each dimension. The contents of ghost cells are
* -8s and non-ghost cells are the process rank IDs.
*
* To compile:
* mpicc -O2 ghost_cell.c -o ghost_cell -lpnetcdf
* To run:
* mpiexec -n num_processes ./ghost_cell [filename] [len]
* where len decides the size of local array, which is len x len+1.
* So, the variable is of size len*(len+1) * nprocs * sizeof(int)
*
* The screen outputs from running ncmpidump on the output file produced by
* command:
* % mpiexec -n 4 ./ghost_cell -q /pvfs2/wkliao/testfile.nc 4
*
* % ncmpidump /pvfs2/wkliao/testfile.nc
* netcdf testfile {
* // file format: CDF-5 (big variables)
* dimensions:
* Y = 8 ;
* X = 10 ;
* variables:
* int var(Y, X) ;
* data:
*
* var =
* 0, 0, 0, 0, 0, 1, 1, 1, 1, 1,
* 0, 0, 0, 0, 0, 1, 1, 1, 1, 1,
* 0, 0, 0, 0, 0, 1, 1, 1, 1, 1,
* 0, 0, 0, 0, 0, 1, 1, 1, 1, 1,
* 2, 2, 2, 2, 2, 3, 3, 3, 3, 3,
* 2, 2, 2, 2, 2, 3, 3, 3, 3, 3,
* 2, 2, 2, 2, 2, 3, 3, 3, 3, 3,
* 2, 2, 2, 2, 2, 3, 3, 3, 3, 3 ;
* }
*
* In this case, the contents of local buffers are shown below.
*
* rank 0: rank 1:
* -8, -8, -8, -8, -8, -8, -8, -8, -8 -8, -8, -8, -8, -8, -8, -8, -8, -8
* -8, -8, -8, -8, -8, -8, -8, -8, -8 -8, -8, -8, -8, -8, -8, -8, -8, -8
* -8, -8, 0, 0, 0, 0, 0, -8, -8 -8, -8, 1, 1, 1, 1, 1, -8, -8
* -8, -8, 0, 0, 0, 0, 0, -8, -8 -8, -8, 1, 1, 1, 1, 1, -8, -8
* -8, -8, 0, 0, 0, 0, 0, -8, -8 -8, -8, 1, 1, 1, 1, 1, -8, -8
* -8, -8, 0, 0, 0, 0, 0, -8, -8 -8, -8, 1, 1, 1, 1, 1, -8, -8
* -8, -8, -8, -8, -8, -8, -8, -8, -8 -8, -8, -8, -8, -8, -8, -8, -8, -8
* -8, -8, -8, -8, -8, -8, -8, -8, -8 -8, -8, -8, -8, -8, -8, -8, -8, -8
*
* rank 2: rank 3:
* -8, -8, -8, -8, -8, -8, -8, -8, -8 -8, -8, -8, -8, -8, -8, -8, -8, -8
* -8, -8, -8, -8, -8, -8, -8, -8, -8 -8, -8, -8, -8, -8, -8, -8, -8, -8
* -8, -8, 2, 2, 2, 2, 2, -8, -8 -8, -8, 3, 3, 3, 3, 3, -8, -8
* -8, -8, 2, 2, 2, 2, 2, -8, -8 -8, -8, 3, 3, 3, 3, 3, -8, -8
* -8, -8, 2, 2, 2, 2, 2, -8, -8 -8, -8, 3, 3, 3, 3, 3, -8, -8
* -8, -8, 2, 2, 2, 2, 2, -8, -8 -8, -8, 3, 3, 3, 3, 3, -8, -8
* -8, -8, -8, -8, -8, -8, -8, -8, -8 -8, -8, -8, -8, -8, -8, -8, -8, -8
* -8, -8, -8, -8, -8, -8, -8, -8, -8 -8, -8, -8, -8, -8, -8, -8, -8, -8
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h> /* strcpy(), strncpy() */
#include <unistd.h> /* getopt() */
#include <mpi.h>
#include <pnetcdf.h>
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] [-k format] [-l len] [file_name]\n"
" [-h] Print this help\n"
" [-q] quiet mode\n"
" [-k format] file format: 1 for CDF-1, 2 for CDF-2, 3 for NetCDF4,\n"
" 4 for NetCDF4 classic model, 5 for CDF-5\n"
" [-l len] size of each dimension of the local array\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;
}
/*----< pnetcdf_io() >-------------------------------------------------------*/
static int
pnetcdf_io(MPI_Comm comm, char *filename, int cmode, int len)
{
int i, j, rank, nprocs, ncid, err, nerrs=0;
int psizes[2], local_rank[2], dimids[2], varid, nghosts;
int *buf, *buf_ptr;
size_t bufsize;
MPI_Offset gsizes[2], starts[2], counts[2], imap[2];
MPI_Comm_rank(comm, &rank);
MPI_Comm_size(comm, &nprocs);
/* calculate number of processes along each dimension */
psizes[0] = psizes[1] = 0;
MPI_Dims_create(nprocs, 2, psizes);
if (verbose && rank == 0)
printf("psizes=%d %d\n", psizes[0], psizes[1]);
gsizes[0] = (MPI_Offset)len * psizes[0]; /* global array size */
gsizes[1] = (MPI_Offset)(len+1) * psizes[1];
if (verbose && rank == 0)
printf("global variable shape: %lld %lld\n", gsizes[0],gsizes[1]);
/* find its local rank IDs along each dimension */
local_rank[0] = rank / psizes[1];
local_rank[1] = rank % psizes[1];
if (verbose)
printf("rank %d: dim rank=%d %d\n", rank,local_rank[0],local_rank[1]);
counts[0] = len;
counts[1] = len+1;
starts[0] = local_rank[0] * counts[0];
starts[1] = local_rank[1] * counts[1];
if (verbose)
printf("starts=%lld %lld counts=%lld %lld\n",starts[0],starts[1],counts[0],counts[1]);
/* allocate and initialize buffer with ghost cells on both ends of each dim */
nghosts = 2;
bufsize = (counts[0] + 2 * nghosts) * (counts[1] + 2 * nghosts);
buf = (int *) malloc(sizeof(int) * bufsize);
for (i=0; i<counts[0]+2*nghosts; i++)
for (j=0; j<counts[1]+2*nghosts; j++) {
if (nghosts <= i && i < counts[0]+nghosts &&
nghosts <= j && j < counts[1]+nghosts)
buf[i*(counts[1]+2*nghosts) + j] = rank;
else
buf[i*(counts[1]+2*nghosts) + j] = -8; /* all ghost cells have value -8 */
}
/* create the file */
cmode |= NC_CLOBBER;
err = ncmpi_create(comm, filename, cmode, MPI_INFO_NULL, &ncid);
if (err != NC_NOERR) {
printf("Error at line %d in %s: ncmpi_create() file %s (%s)\n",
__LINE__,__FILE__,filename,ncmpi_strerror(err));
MPI_Abort(comm, -1);
exit(1);
}
/* define dimensions */
err = ncmpi_def_dim(ncid, "Y", gsizes[0], &dimids[0]); ERR
err = ncmpi_def_dim(ncid, "X", gsizes[1], &dimids[1]); ERR
/* define variable */
err = ncmpi_def_var(ncid, "var", NC_INT, 2, dimids, &varid); ERR
/* exit the define mode */
err = ncmpi_enddef(ncid); ERR
/* set up imap[] for excluding ghost cells */
imap[1] = 1;
imap[0] = counts[1] + 2 * nghosts;
/* find the first non-ghost cell of the user buf */
buf_ptr = buf + nghosts * (counts[1]+2*nghosts + 1);
/* write the whole variable in file */
err = ncmpi_put_varm_int_all(ncid, varid, starts, counts, NULL, imap, buf_ptr); ERR
/* close the file */
err = ncmpi_close(ncid); ERR
free(buf);
return nerrs;
}
/*----< main() >------------------------------------------------------------*/
int main(int argc, char **argv)
{
extern int optind;
extern char *optarg;
char filename[256];
int i, rank, cmode, kind=0, len=0, nerrs=0;
MPI_Init(&argc,&argv);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
verbose = 1;
/* get command-line arguments */
while ((i = getopt(argc, argv, "hqk:l:")) != EOF)
switch(i) {
case 'q': verbose = 0;
break;
case 'k': kind = atoi(optarg);
break;
case 'l': len = atoi(optarg);
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]);
len = (len <= 0) ? 4 : len;
switch (kind) {
case(2): cmode = NC_64BIT_OFFSET; break;
case(3): cmode = NC_NETCDF4; break;
case(4): cmode = NC_NETCDF4|NC_CLASSIC_MODEL; break;
case(5): cmode = NC_64BIT_DATA; break;
default: cmode = 0;
}
#ifndef PNETCDF_DRIVER_NETCDF4
/* netcdf4 driver is not enabled, skip */
if (kind == 3 || kind == 4) {
MPI_Finalize();
return 0;
}
#endif
nerrs += pnetcdf_io(MPI_COMM_WORLD, filename, cmode, len);
nerrs += pnetcdf_check_mem_usage(MPI_COMM_WORLD);
MPI_Finalize();
return (nerrs > 0);
}
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