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/*********************************************************************
*
* Copyright (C) 2018, Northwestern University and Argonne National Laboratory
* See COPYRIGHT notice in top-level directory.
*
*********************************************************************/
/* $Id$ */
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* This example shows how to nonblocking IO with burst buffer driver. It is
* same as using without the burst buffer driver with the only exception that
* we may not be able to cancel nonblocking requests
* In this example, every process write its rank to n-th cell in three 1 X N
* variables. N is the number of processes.
* We will try to cancel the write operations on variable A, and C
* While we can cancel the request for variable A, we can not do so for
* variable C because it has already been flushed when we wait on request of
* variable B
*
* To compile:
* mpicc -O2 nonblocking.c -o nonblocking -lpnetcdf
*
* Example commands for MPI run and outputs from running ncmpidump on the
* netCDF file produced by this example program:
*
* % mpiexec -n 4 ./nonblocking -b /scratch testfile.nc
* nonblocking.c: example of nonblocking IO
* Canceling write on variable A, get 0 (No error)
* Waiting on variable B, get 0 (No error)
* Canceling write on variable C, get -306 (Nonblocking requests already flushed.)
*
* % ncmpidump testfile.nc
* netcdf test {
* // file format: CDF-1
* dimensions:
* X = 1 ;
* Y = 4 ;
* variables:
* int A(X, Y) ;
* int B(X, Y) ;
* int C(X, Y) ;
* data:
*
* A =
* _, _, _, _ ;
*
* B =
* 0, 1, 2, 3 ;
*
* C =
* 0, 1, 2, 3 ;
* }
*
* Example batch script for running on Cori at NERSC using SLURM scheduler
*
* #!/bin/bash
* #SBATCH -p debug
* #SBATCH -N 1
* #SBATCH -C haswell
* #SBATCH -t 00:01:00
* #SBATCH -o nonblocking_example.txt
* #SBATCH -L scratch
* #DW jobdw capacity=1289GiB access_mode=private type=scratch pool=sm_pool
* srun -n 4 ./nonblocking -b $DW_JOB_PRIVATE ${SCRATCH}/testfile.nc
*
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include <stdio.h>
#include <stdlib.h>
#include <string.h> /* strcpy(), strncpy(), strdup() */
#include <unistd.h> /* getopt() */
#include <mpi.h>
#include <pnetcdf.h>
#define ERR {if(err!=NC_NOERR){printf("Error at line %d in %s: %s\n", __LINE__,__FILE__, ncmpi_strerror(err));nerrs++;}}
static void
usage(char *argv0)
{
char *help =
"Usage: %s [-h] | [-q] [-b bb_dir] file_name\n"
" [-h] Print help\n"
" [-q] Quiet mode (reports when fail)\n"
" [-b bb_dir] Path to burst buffer\n"
" filename: output netCDF file name\n";
fprintf(stderr, help, argv0);
}
int main(int argc, char** argv)
{
extern int optind;
extern char *optarg;
char filename[256], *bb_dir;
int i, rank, np, verbose=1, err, nerrs=0;
int dimid[2];
int varid[3];
MPI_Offset start[2];
int buffer[3];
int req[3];
int stat;
int ncid, cmode;
MPI_Info info;
MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &np);
/* get command-line arguments */
bb_dir = strdup(".");
while ((i = getopt(argc, argv, "hqb:")) != EOF)
switch(i) {
case 'b': free(bb_dir);
bb_dir = strdup(optarg);
break;
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]);
if (verbose && rank == 0) printf("%s: example of nonblocking IO\n",__FILE__);
/* Set up the hints for burst buffer driver in ncmpi_create
* Note that the remaining part of the code remains unchanged
* PnetCDF will warn if nc_burst_buf_dirname is not set.
*/
MPI_Info_create(&info);
MPI_Info_set(info, "nc_burst_buf", "enable");
MPI_Info_set(info, "nc_burst_buf_dirname", bb_dir);
free(bb_dir);
/* create a new file using clobber mode ----------------------------------*/
cmode = NC_CLOBBER;
err = ncmpi_create(MPI_COMM_WORLD, filename, cmode, info, &ncid);
ERR
/* Info can be freed after file creation */
MPI_Info_free(&info);
/* Fill up the variables with default value */
err = ncmpi_set_fill(ncid, NC_FILL, NULL); ERR
/* Define dimensions */
err = ncmpi_def_dim(ncid, "X", 1, dimid); ERR
err = ncmpi_def_dim(ncid, "Y", np, dimid + 1); ERR
/* Define variables */
err = ncmpi_def_var(ncid, "A", NC_INT, 2, dimid, varid); ERR
err = ncmpi_def_var(ncid, "B", NC_INT, 2, dimid, varid + 1); ERR
err = ncmpi_def_var(ncid, "C", NC_INT, 2, dimid, varid + 2); ERR
/* burst buffer initialize log files on the first time we enters data mode */
err = ncmpi_enddef(ncid);
ERR
/* Preparing the buffer */
buffer[0] = buffer[1] = buffer[2] = rank;
/* Do nonblocking write on variables */
start[0] = 0;
start[1] = rank;
err = ncmpi_iput_var1_int(ncid, varid[0], start, buffer, req); ERR
err = ncmpi_iput_var1_int(ncid, varid[1], start, buffer + 1, req + 1); ERR
err = ncmpi_iput_var1_int(ncid, varid[2], start, buffer + 2, req + 2); ERR
/* Cancel first request */
err = ncmpi_cancel(ncid, 1, req, &stat); ERR
if (verbose && rank == 0)
printf("Canceling write on variable A, get %d (%s)\n", stat, ncmpi_strerror(stat));
/* Wait second request */
err = ncmpi_wait_all(ncid, 1, req + 1, &stat); ERR
if (verbose && rank == 0)
printf("Waiting on variable B, get %d (%s)\n", stat, ncmpi_strerror(stat));
/* Cancel third request */
err = ncmpi_cancel(ncid, 1, req + 2, &stat); ERR
if (verbose && rank == 0)
printf("Canceling write on variable C, get %d (%s)\n", stat, ncmpi_strerror(stat));
/* close file */
err = ncmpi_close(ncid);
ERR
/* check if there is any PnetCDF internal malloc residue */
MPI_Offset malloc_size, sum_size;
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 (nerrs > 0);
}
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