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/*********************************************************************
*
* Copyright (C) 2012, Northwestern University and Argonne National Laboratory
* See COPYRIGHT notice in top-level directory.
*
*********************************************************************/
/* This example is similar to collective_write.c but using nonblocking APIs,
* iput or bput (default is iput). 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.
*
* To compile:
* mpicc -O2 nonblocking_write.c -o nonblocking_write -lpnetcdf
*
* To run:
* mpiexec -n num_processes ./nonblocking_write -l len file_name
* where len decides the size of each local array, which is len x len x len.
* Each global 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 -l 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 <string.h> /* strcpy(), strncpy() */
#include <unistd.h> /* getopt() */
#include <mpi.h>
#include <pnetcdf.h>
#define NTIMES 2
#define NDIMS 3
#define SCA_NVARS 5
#define FIX_NVARS 5
#define REC_NVARS 10
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 | -c | -b | -l len] [file_name]\n"
" [-h] Print help\n"
" [-q] Quiet mode (reports when fail)\n"
" [-c] Allocate all write buffers in a contiguous space (default no)\n"
" [-b] Use bput APIs instead of iput APIs (default iput)\n"
" [-l len] size of each dimension of the local array\n"
" [file_name] 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;
}
/*----< 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, "cb_nodes", 64, info_cb_nodes, &flag);
MPI_Info_get(*info_used, "cb_buffer_size", 64, info_cb_buffer_size, &flag);
MPI_Info_get(*info_used, "striping_factor", 64, info_striping_factor, &flag);
MPI_Info_get(*info_used, "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, k, err, nerrs=0, debug=0, use_contig_buf=0, use_bput=0;
int nprocs, len=0, nelems, rank;
int *sca_buf, *fix_buf[FIX_NVARS], *rec_buf[REC_NVARS];
int gsizes[NDIMS], psizes[NDIMS];
double write_timing, max_write_timing, write_bw;
char filename[256], str[512];
int ncid, dimids[NDIMS+1];
int sca_var[SCA_NVARS], fix_var[FIX_NVARS], rec_var[REC_NVARS], *req, *st;
MPI_Offset starts[NDIMS+1], counts[NDIMS+1], write_size, sum_write_size;
MPI_Offset header_size, bbufsize, put_size, sum_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);
verbose = 1;
/* get command-line arguments */
while ((i = getopt(argc, argv, "hqcbl:")) != EOF)
switch(i) {
case 'q': verbose = 0;
break;
case 'c': use_contig_buf = 1;
break;
case 'b': use_bput = 1;
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);
if (rank == 0 && verbose && debug)
printf("Process DIMS psizes=%2d %2d %2d\n",
psizes[0],psizes[1],psizes[2]);
starts[0] = 0;
starts[1] = (rank / (psizes[1] * psizes[2])) % psizes[0];
starts[2] = (rank / psizes[2]) % psizes[1];
starts[3] = rank % psizes[2];
counts[0] = 1;
nelems = 1;
for (i=0; i<NDIMS; i++) {
gsizes[i] = len * psizes[i];
nelems *= len;
starts[i+1] *= len;
counts[i+1] = len;
}
if (verbose && debug)
printf("%2d: starts=%2lld %2lld %2lld %2lld counts=%2lld %2lld %2lld %2lld\n",
rank, starts[0], starts[1], starts[2], starts[3],
counts[0], counts[1], counts[2], counts[3]);
/* allocate buffers */
if (use_contig_buf) {
/* all write buffers are allocated in a single contiguous space */
size_t total_nelems;
total_nelems = SCA_NVARS + (FIX_NVARS + REC_NVARS) * nelems;
sca_buf = (int*) malloc(sizeof(int) * total_nelems);
for (i=0; i<FIX_NVARS; i++)
fix_buf[i] = sca_buf + SCA_NVARS + nelems * i;
for (i=0; i<REC_NVARS; i++)
rec_buf[i] = sca_buf + SCA_NVARS + FIX_NVARS * nelems + nelems * i;
}
else {
/* allocate individual buffers separately +1 ensure non-contiguity*/
sca_buf = (int*) malloc(sizeof(int) * (SCA_NVARS+1));
for (i=0; i<FIX_NVARS; i++)
fix_buf[i] = (int *) malloc(sizeof(int) * (nelems+1));
for (i=0; i<REC_NVARS; i++)
rec_buf[i] = (int *) malloc(sizeof(int) * (nelems+1));
}
/* initialize buffer contents */
for (j=0; j<SCA_NVARS; j++) sca_buf[j] = rank + j;
for (i=0; i<FIX_NVARS; i++) {
for (j=0; j<nelems; j++) fix_buf[i][j] = rank;
}
for (i=0; i<REC_NVARS; i++) {
for (j=0; j<nelems; j++) rec_buf[i][j] = rank;
}
MPI_Barrier(MPI_COMM_WORLD);
write_timing = MPI_Wtime();
/* 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");
/* disable PnetCDF internal buffering */
MPI_Info_set(info, "nc_ibuf_size", "0");
MPI_Info_set(info, "nc_in_place_swap", "enable");
/* create the file */
err = ncmpi_create(MPI_COMM_WORLD, filename, NC_CLOBBER|NC_64BIT_DATA,
info, &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(MPI_COMM_WORLD, -1);
exit(1);
}
MPI_Info_free(&info);
req = (int*) malloc(sizeof(int) * (SCA_NVARS + FIX_NVARS + REC_NVARS));
st = (int*) malloc(sizeof(int) * (SCA_NVARS + FIX_NVARS + REC_NVARS));
/* define dimensions */
err = ncmpi_def_dim(ncid, "time", NC_UNLIMITED, &dimids[0]);
ERR
for (i=0; i<NDIMS; i++) {
sprintf(str, "%c", 'z'-i);
err = ncmpi_def_dim(ncid, str, gsizes[i], &dimids[i+1]);
ERR
}
/* define scalar variables */
for (i=0; i<SCA_NVARS; i++) {
sprintf(str, "scalar_var_%d", i);
err = ncmpi_def_var(ncid, str, NC_INT, 0, NULL, &sca_var[i]);
ERR
}
/* define fix-sized variables */
for (i=0; i<FIX_NVARS; i++) {
sprintf(str, "fix_var_%d", i);
err = ncmpi_def_var(ncid, str, NC_INT, NDIMS, dimids+1, &fix_var[i]);
ERR
}
/* define record variables */
for (i=0; i<REC_NVARS; i++) {
sprintf(str, "rec_var_%d", i);
err = ncmpi_def_var(ncid, str, NC_INT, NDIMS+1, dimids, &rec_var[i]);
ERR
}
/* exit the define mode */
err = ncmpi_enddef(ncid);
ERR
/* get all the MPI-IO and PnetCDF hints used */
err = ncmpi_inq_file_info(ncid, &info_used);
ERR
if (!use_bput) {
k = 0;
/* only rank 0 writes scalar variables using iput */
if (rank == 0) {
for (i=0; i<SCA_NVARS; i++) {
err = ncmpi_iput_var_int(ncid, sca_var[i], &sca_buf[i], &req[k++]);
ERR
}
}
/* write one fix-sized variable at a time using iput */
for (i=0; i<FIX_NVARS; i++) {
err = ncmpi_iput_vara_int(ncid, fix_var[i], starts+1, counts+1, fix_buf[i], &req[k++]);
ERR
}
/* write one record variable at a time using iput */
for (j=0; j<NTIMES; j++) {
starts[0] = j;
for (i=0; i<REC_NVARS; i++) {
err = ncmpi_iput_vara_int(ncid, rec_var[i], starts, counts, rec_buf[i], &req[k++]);
ERR
}
/* wait for the nonblocking I/O to complete */
err = ncmpi_wait_all(ncid, k, req, st);
ERR
for (i=0; i<k; i++) {
if (st[i] != NC_NOERR)
printf("Error at line %d in %s: nonblocking write fails on request %d (%s)\n",
__LINE__,__FILE__,i, ncmpi_strerror(st[i]));
}
k = 0;
}
}
else { /* write using bput */
/* bbufsize must be max of data type converted before and after */
bbufsize = (SCA_NVARS + nelems * (FIX_NVARS + REC_NVARS)) * sizeof(int);
err = ncmpi_buffer_attach(ncid, bbufsize);
ERR
k = 0;
/* only rank 0 writes scalar variables time using bput */
if (rank == 0) {
for (i=0; i<SCA_NVARS; i++) {
err = ncmpi_bput_var_int(ncid, sca_var[i], &sca_buf[i], &req[k++]);
ERR
}
}
/* write one fix_sized variable at a time using bput */
for (i=0; i<FIX_NVARS; i++) {
err = ncmpi_bput_vara_int(ncid, fix_var[i], starts+1, counts+1, fix_buf[i], &req[k++]);
ERR
/* can safely change contents of fix_buf[i] here */
}
/* write one record variable at a time using bput */
for (j=0; j<NTIMES; j++) {
starts[0] = j;
for (i=0; i<REC_NVARS; i++) {
err = ncmpi_bput_vara_int(ncid, rec_var[i], starts, counts, rec_buf[i], &req[k++]);
ERR
}
/* wait for the nonblocking I/O to complete */
err = ncmpi_wait_all(ncid, k, req, st);
ERR
for (i=0; i<k; i++) {
if (st[i] != NC_NOERR)
printf("Error at line %d in %s: nonblocking write fails on request %d (%s)\n",
__LINE__,__FILE__,i, ncmpi_strerror(st[i]));
}
k = 0;
}
/* detach the temporary buffer */
err = ncmpi_buffer_detach(ncid);
ERR
}
ncmpi_inq_put_size(ncid, &put_size);
ncmpi_inq_header_size(ncid, &header_size);
/* close the file */
err = ncmpi_close(ncid);
ERR
if (use_contig_buf)
free(sca_buf);
else {
free(sca_buf);
for (i=0; i<FIX_NVARS; i++) free(fix_buf[i]);
for (i=0; i<REC_NVARS; i++) free(rec_buf[i]);
}
free(req);
free(st);
write_timing = MPI_Wtime() - write_timing;
write_size = nelems * (FIX_NVARS + NTIMES * REC_NVARS) + SCA_NVARS;
write_size *= sizeof(int);
MPI_Reduce(&write_size, &sum_write_size, 1, MPI_OFFSET, MPI_SUM, 0, MPI_COMM_WORLD);
MPI_Reduce(&put_size, &sum_put_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);
/* rank 0 also writes header and updates the record number to the file
* header NTIME times
*/
if (rank == 0 && verbose) {
sum_write_size += header_size + NTIMES * 8;
printf("\n");
if (use_bput)
printf("Using PnetCDF nonblocking APIs: bput\n");
else
printf("Using PnetCDF nonblocking APIs: iput\n");
if (use_contig_buf)
printf("All write buffers are in a contiguous space\n");
else
printf("All write buffers are allocated separately\n");
printf("Total amount writes (include header) = %lld bytes\n", sum_write_size);
printf("Total amount writes reported by pnetcdf (include header) = %lld bytes\n", sum_put_size);
printf("\n");
float subarray_size = (float)nelems*sizeof(int)/1048576.0;
print_info(&info_used);
printf("Local array size %d x %d x %d integers, size = %.2f MB\n",len,len,len,subarray_size);
sum_write_size /= 1048576.0;
printf("Global array size %d x %d x %d integers, write size = %.2f GB\n",
gsizes[0], gsizes[1], gsizes[2], sum_write_size/1024.0);
write_bw = sum_write_size/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);
nerrs += pnetcdf_check_mem_usage(MPI_COMM_WORLD);
MPI_Finalize();
return (nerrs > 0);
}
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