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/*********************************************************************
*
* Copyright (C) 2014, Northwestern University and Argonne National Laboratory
* See COPYRIGHT notice in top-level directory.
*
*********************************************************************/
/* $Id$ */
/* This example is similar to collective_write.c but using nonblocking APIs.
* It creates a netcdf file in CD-5 format and writes a number of
* 3D integer non-record variables. The measured write bandwidth is reported
* at the end. Usage: (for example)
* To compile:
* mpicxx -O2 nonblocking_write.cpp -o nonblocking_write -lpnetcdf
* To run:
* mpiexec -n num_processes ./nonblocking_write [filename] [len]
* where len decides the size of each local array, which is len x len x len.
* So, each non-record variable is of size len*len*len * nprocs * sizeof(int)
* All variables are partitioned among all processes in a 3D
* block-block-block fashion. Below is an example standard output from
* command:
* mpiexec -n 32 ./nonblocking_write /pvfs2/wkliao/testfile.nc 100
*
* MPI hint: cb_nodes = 2
* MPI hint: cb_buffer_size = 16777216
* MPI hint: striping_factor = 32
* MPI hint: striping_unit = 1048576
* Local array size 100 x 100 x 100 integers, size = 3.81 MB
* Global array size 400 x 400 x 200 integers, write size = 0.30 GB
* procs Global array size exec(sec) write(MB/s)
* ------- ------------------ --------- -----------
* 32 400 x 400 x 200 6.67 45.72
*/
#include <stdio.h>
#include <stdlib.h>
#include <iostream>
#include <sstream> // for ostringstream
using namespace std;
#include <string.h> /* strcpy(), strncpy() */
#include <unistd.h> /* getopt() */
#include <pnetcdf>
using namespace PnetCDF;
using namespace PnetCDF::exceptions;
#define NDIMS 3
#define NUM_VARS 10
static void
usage(char *argv0)
{
cerr <<
"Usage: %s [-h] | [-q] [-l len] [file_name]\n"
" [-h] Print help\n"
" [-q] Quiet mode (reports when fail)\n"
" [-l len] size of each dimension of the local array\n"
" [filename] output netCDF file name\n"
<< argv0;
}
/*----< print_info() >------------------------------------------------------*/
static
void print_info(MPI_Info *info_used)
{
int flag;
char info_cb_nodes[64], info_cb_buffer_size[64];
char info_striping_factor[64], info_striping_unit[64];
strcpy(info_cb_nodes, "undefined");
strcpy(info_cb_buffer_size, "undefined");
strcpy(info_striping_factor, "undefined");
strcpy(info_striping_unit, "undefined");
MPI_Info_get(*info_used, (char*)"cb_nodes", 64, info_cb_nodes, &flag);
MPI_Info_get(*info_used, (char*)"cb_buffer_size", 64, info_cb_buffer_size, &flag);
MPI_Info_get(*info_used, (char*)"striping_factor", 64, info_striping_factor, &flag);
MPI_Info_get(*info_used, (char*)"striping_unit", 64, info_striping_unit, &flag);
printf("MPI hint: cb_nodes = %s\n", info_cb_nodes);
printf("MPI hint: cb_buffer_size = %s\n", info_cb_buffer_size);
printf("MPI hint: striping_factor = %s\n", info_striping_factor);
printf("MPI hint: striping_unit = %s\n", info_striping_unit);
}
/*----< main() >------------------------------------------------------------*/
int main(int argc, char **argv)
{
extern int optind;
extern char *optarg;
int i, j, verbose=1;
int nprocs, len=0, *buf[NUM_VARS], bufsize, rank;
int gsizes[NDIMS], psizes[NDIMS];
double write_timing, max_write_timing, write_bw;
char filename[256];
int req[NUM_VARS], st[NUM_VARS];
MPI_Offset write_size, sum_write_size;
vector<MPI_Offset> starts(NDIMS), counts(NDIMS);
MPI_Offset bbufsize, put_size;
MPI_Info info, info_used;
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, "hql:")) != EOF)
switch(i) {
case 'q': verbose = 0;
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) ? 10 : len;
for (i=0; i<NDIMS; i++) psizes[i] = 0;
MPI_Dims_create(nprocs, NDIMS, psizes);
starts[0] = rank % psizes[0];
starts[1] = (rank / psizes[1]) % psizes[1];
starts[2] = (rank / (psizes[0] * psizes[1])) % psizes[2];
bufsize = 1;
for (i=0; i<NDIMS; i++) {
gsizes[i] = len * psizes[i];
starts[i] *= len;
counts[i] = len;
bufsize *= len;
}
/* allocate buffer and initialize with some non-zero numbers */
for (i=0; i<NUM_VARS; i++) {
buf[i] = (int *) malloc(sizeof(int) * bufsize);
for (j=0; j<bufsize; j++) buf[i][j] = rank * i + 123 + j;
}
MPI_Barrier(MPI_COMM_WORLD);
write_timing = MPI_Wtime();
try {
MPI_Info_create(&info);
MPI_Info_set(info, (char*)"nc_var_align_size", (char*)"1");
/* create the file */
NcmpiFile nc(MPI_COMM_WORLD, filename, NcmpiFile::replace,
NcmpiFile::classic5, info);
MPI_Info_free(&info);
/* define dimensions */
vector<NcmpiDim> dimids(NDIMS);
for (i=0; i<NDIMS; i++) {
char name[2];
name[0] = 'x'+i;
name[1] = '\0';
dimids[i] = nc.addDim(name, gsizes[i]);
}
/* define variables */
vector<NcmpiVar> vars(NUM_VARS);
for (i=0; i<NUM_VARS; i++) {
std::ostringstream name;
name << "var" << i;
vars[i] = nc.addVar(name.str(), ncmpiInt, dimids);
}
/* get all the hints used */
nc.Inq_file_info(&info_used);
/* write one variable at a time using iput */
for (i=0; i<NUM_VARS; i++)
vars[i].iputVar(starts, counts, &buf[i][0], &req[i]);
/* wait for the nonblocking I/O to complete */
nc.Wait_all(NUM_VARS, req, st);
for (i=0; i<NUM_VARS; i++) {
if (st[i] != NC_NOERR)
printf("Error: nonblocking write fails on request %d (%s)\n",
i, ncmpi_strerror(st[i]));
}
/* write one variable at a time using bput */
/* bbufsize must be max of data type converted before and after */
bbufsize = bufsize * NUM_VARS * sizeof(int);
nc.Buffer_attach(bbufsize);
for (i=0; i<NUM_VARS; i++) {
vars[i].bputVar(starts, counts, buf[i], &req[i]);
/* can safely change contents or free up the buf[i] here */
}
/* wait for the nonblocking I/O to complete */
nc.Wait_all(NUM_VARS, req, st);
for (i=0; i<NUM_VARS; i++) {
if (st[i] != NC_NOERR)
printf("Error: nonblocking write fails on request %d (%s)\n",
i, ncmpi_strerror(st[i]));
}
/* detach the temporary buffer */
nc.Buffer_detach();
nc.Inq_put_size(&put_size);
MPI_Allreduce(MPI_IN_PLACE, &put_size, 1, MPI_OFFSET, MPI_SUM, MPI_COMM_WORLD);
}
catch(NcmpiException& e) {
cout << e.what() << " error code=" << e.errorCode() << " Error!\n";
return 1;
}
write_timing = MPI_Wtime() - write_timing;
write_size = bufsize * NUM_VARS * sizeof(int);
for (i=0; i<NUM_VARS; i++) free(buf[i]);
MPI_Reduce(&write_size, &sum_write_size, 1, MPI_OFFSET, MPI_SUM, 0, MPI_COMM_WORLD);
MPI_Reduce(&write_timing, &max_write_timing, 1, MPI_DOUBLE, MPI_MAX, 0, MPI_COMM_WORLD);
if (rank == 0 && verbose) {
double write_amount = sum_write_size;
float subarray_size = (float)bufsize*sizeof(int)/1048576.0;
printf("\n");
printf("Total amount writes to variables only (exclude header) = %lld bytes\n", sum_write_size);
printf("Total amount writes reported by pnetcdf (include header) = %lld bytes\n", put_size);
printf("\n");
print_info(&info_used);
printf("Local array size %d x %d x %d integers, size = %.2f MB\n",len,len,len,subarray_size);
write_amount /= 1048576.0;
printf("Global array size %d x %d x %d integers, write size = %.2f GB\n",
gsizes[0], gsizes[1], gsizes[2], write_amount/1024.0);
write_bw = write_amount/max_write_timing;
printf(" procs Global array size exec(sec) write(MB/s)\n");
printf("------- ------------------ --------- -----------\n");
printf(" %4d %4d x %4d x %4d %8.2f %10.2f\n", nprocs,
gsizes[0], gsizes[1], gsizes[2], max_write_timing, write_bw);
}
MPI_Info_free(&info_used);
/* 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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