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/*********************************************************************
*
* Copyright (C) 2015, Northwestern University and Argonne National Laboratory
* See COPYRIGHT notice in top-level directory.
*
*********************************************************************/
/* $Id$ */
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* This example is mostly the same as column_wise.c but shows how to use
* NC_REQ_ALL to commit all pending nonblocking I/O without checking the status
* of individual requests. In this case, the first encountered error will be
* returned in ncmpi_wait_all().
*
* The compile and run commands are given below, together with an ncmpidump of
* the output file.
*
* % mpicc -O2 -o req_all req_all.c -lpnetcdf
* % mpiexec -l -n 4 ./column_wise /pvfs2/wkliao/testfile.nc
* 0: 0: myOff= 0 myNX= 4
* 1: 1: myOff= 4 myNX= 4
* 2: 2: myOff= 8 myNX= 4
* 3: 3: myOff= 12 myNX= 4
* 0: 0: start= 0 0 count= 10 1
* 1: 1: start= 0 1 count= 10 1
* 2: 2: start= 0 2 count= 10 1
* 3: 3: start= 0 3 count= 10 1
*
* % ncmpidump /pvfs2/wkliao/testfile.nc
* netcdf testfile {
* // file format: CDF-1
* dimensions:
* Y = 10 ;
* X = 16 ;
* variables:
* int var(Y, X) ;
* data:
*
* var =
* 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3,
* 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3,
* 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3,
* 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3,
* 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3,
* 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3,
* 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3,
* 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3,
* 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3,
* 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3 ;
* }
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include <stdio.h>
#include <stdlib.h>
#include <string.h> /* strcpy(), strncpy() */
#include <unistd.h> /* getopt() */
#include <mpi.h>
#include <pnetcdf.h>
#define NY 10
#define NX 4
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;
}
int main(int argc, char** argv)
{
extern int optind;
char filename[256];
int i, j, rank, nprocs, err, nerrs=0, myNX, G_NX, myOff;
int ncid, varid, dimid[2], **buf;
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]);
/* set an MPI-IO hint to disable file offset alignment for fixed-size
* variables */
MPI_Info_create(&info);
MPI_Info_set(info, "nc_var_align_size", "1");
err = ncmpi_create(MPI_COMM_WORLD, filename, NC_CLOBBER, info, &ncid); ERR
MPI_Info_free(&info);
/* the global array is NY * (NX * nprocs) */
G_NX = NX * nprocs;
myOff = NX * rank;
myNX = NX;
if (verbose) printf("%2d: myOff=%3d myNX=%3d\n",rank,myOff,myNX);
err = ncmpi_def_dim(ncid, "Y", NY, &dimid[0]); ERR
err = ncmpi_def_dim(ncid, "X", G_NX, &dimid[1]); ERR
err = ncmpi_def_var(ncid, "var", NC_INT, 2, dimid, &varid); ERR
err = ncmpi_enddef(ncid); ERR
/* initialize the buffer with rank ID */
buf = (int**) malloc(sizeof(int*) * myNX);
for (i=0; i<myNX; i++) {
buf[i] = (int*) malloc(sizeof(int) * NY);
for (j=0; j<NY; j++) buf[i][j] = rank;
}
/* each proc writes myNX single columns of the 2D array */
start[0] = 0; start[1] = rank;
count[0] = NY; count[1] = 1;
if (verbose)
printf("%2d: start=%3lld %3lld count=%3lld %3lld\n",
rank, start[0],start[1], count[0],count[1]);
for (i=0; i<myNX; i++) {
err = ncmpi_iput_vara_int(ncid, varid, start, count, buf[i], NULL);
ERR
start[1] += nprocs;
}
err = ncmpi_wait_all(ncid, NC_REQ_ALL, NULL, NULL); ERR
err = ncmpi_close(ncid); ERR
/* read back using the same access pattern */
err = ncmpi_open(MPI_COMM_WORLD, filename, NC_NOWRITE, info, &ncid); ERR
err = ncmpi_inq_varid(ncid, "var", &varid); ERR
for (i=0; i<myNX; i++)
for (j=0; j<NY; j++) buf[i][j] = -1;
/* each proc reads myNX single columns of the 2D array */
start[0] = 0; start[1] = rank;
count[0] = NY; count[1] = 1;
for (i=0; i<myNX; i++) {
err = ncmpi_iget_vara_int(ncid, varid, start, count, buf[i], NULL);
ERR
start[1] += nprocs;
}
err = ncmpi_wait_all(ncid, NC_REQ_ALL, NULL, NULL); ERR
/* check contents of read data of all requests */
for (i=0; i<myNX; i++) {
for (j=0; j<NY; j++)
if (buf[i][j] != rank)
printf("Error at line %d in %s: expect buf[%d][%d]=%d but got %d\n",
__LINE__,__FILE__,i,j,rank,buf[i][j]);
}
err = ncmpi_close(ncid); ERR
for (i=0; i<myNX; i++) free(buf[i]);
free(buf);
nerrs += pnetcdf_check_mem_usage(MPI_COMM_WORLD);
MPI_Finalize();
return (nerrs > 0);
}
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