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/*********************************************************************
*
* Copyright (C) 2024, Northwestern University and Argonne National Laboratory
* See COPYRIGHT notice in top-level directory.
*
*********************************************************************/
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
*
* This example shows how to use PnetCDF blocking and nonblocking flexible APIs
* by supplying an MPI derived datatype and MPI_BOTTOM in the buffer argument.
* The MPI derived datatype is constructed through MPI_Type_create_hindexed(),
* which defines a noncontiguous memory space consisting of two separate blocks.
*
* A 2D global variable of size NY * NX * nprocs of type float is defined in
* the file. Each process allocates two write buffers and constructs an MPI
* derived datatype for the two buffers.
*
* The compile and run commands are given below.
*
* % mpicc -O2 -o flexible_bottom flexible_bottom.c -lpnetcdf
*
* % mpiexec -l -n 4 ./flexible_bottom ./testfile.nc
*
* % ncmpidump ./testfile.nc
* netcdf testfile {
* // file format: CDF-5 (big variables)
* dimensions:
* Y = 4 ;
* X = 16 ;
* variables:
* float var(Y, X) ;
* data:
*
* var =
* 10, 10, 10, 10, 11, 11, 11, 11, 12, 12, 12, 12, 13, 13, 13, 13,
* 10, 10, 10, 10, 11, 11, 11, 11, 12, 12, 12, 12, 13, 13, 13, 13,
* 50, 50, 50, 50, 51, 51, 51, 51, 52, 52, 52, 52, 53, 53, 53, 53,
* 50, 50, 50, 50, 51, 51, 51, 51, 52, 52, 52, 52, 53, 53, 53, 53 ;
* }
*
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include <stdio.h>
#include <stdlib.h>
#include <string.h> /* strcpy(), strncpy() */
#include <unistd.h> /* getopt() */
#include <mpi.h>
#include <pnetcdf.h>
#define NY 4
#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++;}}
#define CHECK_MPI_ERR \
if (err != MPI_SUCCESS) { \
int errorStringLen; \
char errorString[MPI_MAX_ERROR_STRING]; \
MPI_Error_string(err, errorString, &errorStringLen); \
printf("Error at line %d: %s\n",__LINE__, errorString); \
}
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, rank, nprocs, err, nerrs=0, req, status;
int ncid, cmode, varid, dimid[2];
float *buf[2];
MPI_Offset start[2], count[2];
MPI_Datatype btype;
int array_of_blocklengths[2];
MPI_Aint array_of_displacements[2];
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]);
if (verbose && rank == 0) printf("%s: example of using MPI_BOTTOM in flexible APIs\n",__FILE__);
/* create a new file for writing ----------------------------------------*/
cmode = NC_CLOBBER | NC_64BIT_DATA;
err = ncmpi_create(MPI_COMM_WORLD, filename, cmode, MPI_INFO_NULL, &ncid);
ERR
/* define dimensions */
err = ncmpi_def_dim(ncid, "Y", NY, &dimid[0]); ERR
err = ncmpi_def_dim(ncid, "X", NX*nprocs, &dimid[1]); ERR
/* define a variable of size NY * (NX * nprocs) */
err = ncmpi_def_var(ncid, "var", NC_FLOAT, 2, dimid, &varid); ERR
/* exit define mode */
err = ncmpi_enddef(ncid); ERR
/* allocate two buffers */
buf[0] = (float*) malloc(sizeof(float) * NY * NX / 2);
buf[1] = (float*) malloc(sizeof(float) * NY * NX / 2);
for (i=0; i<NY*NX/2; i++) {
buf[0][i] = rank + 10;
buf[1][i] = rank + 50;
}
/* create a noncontiguous buffer datatype consisting 2 blocks */
MPI_Get_address(buf[0], &array_of_displacements[0]);
MPI_Get_address(buf[1], &array_of_displacements[1]);
array_of_blocklengths[0] = NY * NX / 2;
array_of_blocklengths[1] = NY * NX / 2;
err = MPI_Type_create_hindexed(2, array_of_blocklengths,
array_of_displacements,
MPI_FLOAT, &btype);
CHECK_MPI_ERR
err = MPI_Type_commit(&btype);
CHECK_MPI_ERR
start[0] = 0;
start[1] = NX * rank;
count[0] = NY;
count[1] = NX;
/* calling a blocking flexible API */
err = ncmpi_put_vara_all(ncid, varid, start, count, MPI_BOTTOM, 1, btype);
ERR
/* calling a blocking flexible API */
err = ncmpi_get_vara_all(ncid, varid, start, count, MPI_BOTTOM, 1, btype);
ERR
/* calling a nonblocking flexible API */
err = ncmpi_iput_vara(ncid, varid, start, count, MPI_BOTTOM, 1, btype, &req);
ERR
err = ncmpi_wait_all(ncid, 1, &req, &status); ERR
/* calling a nonblocking flexible API */
err = ncmpi_iget_vara(ncid, varid, start, count, MPI_BOTTOM, 1, btype, &req);
ERR
err = ncmpi_wait_all(ncid, 1, &req, &status); ERR
free(buf[0]);
free(buf[1]);
MPI_Type_free(&btype);
err = ncmpi_close(ncid); ERR
nerrs += pnetcdf_check_mem_usage(MPI_COMM_WORLD);
MPI_Finalize();
return (nerrs > 0);
}
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