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netcdf-c/nc_perf/tst_files3.c
wkliao 52198b3f12 count argument in H5Sselect_hyperslab 
Argument 'count' in NetCDF is not exactly the same as the 'count' in
H5Sselect_hyperslabs(space_id, op, start, stride, count, block).
When the argument 'stride' is NULL, NetCDF's 'count' should be used in
argument 'block', for example,
   H5Sselect_hyperslabs(space_id, op, start, NULL, ones, count);
where 'one' is an array of all 1s. Although using NULL 'block' below
   H5Sselect_hyperslabs(space_id, op, start, NULL, count, NULL);
has the same effect, HDF5 internally stores the space of a subarray as a
list of single elements, instead of a "block", which can affect the
performance.
2023-12-12 16:45:19 -07:00

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/* This is part of the netCDF package. Copyright 2005-2018 University
Corporation for Atmospheric Research/Unidata See COPYRIGHT file for
conditions of use.
This is a benchmark program which tests file writes with compressed
data.
Ed Hartnett
*/
#include <nc_tests.h>
#include "err_macros.h"
#include <hdf5.h>
#include <unistd.h>
#include <time.h>
#include <sys/time.h> /* Extra high precision time info. */
#define NDIMS1 1
#define NDIMS 3
#define FILE_NAME "tst_files3.nc"
#define X_LEN 120
#define Y_LEN 64
#define Z_LEN 128
#define NUM_TRIES 200
/* Prototype from tst_utils.c. */
int nc4_timeval_subtract(struct timeval *result, struct timeval *x,
struct timeval *y);
int dump_file2(const float *data, int docompression, int usedefdim)
{
int ncid, dimids[NDIMS], var;
size_t start[NDIMS] = {0, 0, 0};
size_t count[NDIMS] = {1, 1, Z_LEN};
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR_RET;
if (nc_def_dim(ncid, "time", X_LEN, &dimids[0])) ERR_RET;
if (nc_def_dim(ncid, "lat", Y_LEN, &dimids[1])) ERR_RET;
if (nc_def_dim(ncid, "lon", Z_LEN, &dimids[2])) ERR_RET;
if (nc_def_var(ncid, "test", NC_FLOAT, NDIMS, dimids, &var)) ERR_RET;
if (docompression)
if (nc_def_var_deflate(ncid, var, 1, 1, 1)) ERR_RET;
if (nc_enddef(ncid)) ERR_RET;
for (start[0] = 0; start[0] < X_LEN; start[0]++)
for (start[1] = 0; start[1] < Y_LEN; start[1]++)
if (nc_put_vara_float(ncid, var, start, count, data)) ERR_RET;
if (nc_close(ncid)) ERR_RET;
return 0;
}
int dump_file(const float *data, int docompression, int usedefdim)
{
int ncmode, ncid, dimids[NDIMS], var;
size_t start[NDIMS] = {0, 0, 0}, count[NDIMS] = {X_LEN, Y_LEN, Z_LEN};
ptrdiff_t stride[NDIMS] = {1, 1, 1};
ncmode = NC_CLOBBER|NC_NETCDF4;
if (nc_create(FILE_NAME, ncmode, &ncid)) ERR_RET;
if (nc_def_dim(ncid, "time", X_LEN, &dimids[0])) ERR_RET;
if (nc_def_dim(ncid, "lat", Y_LEN, &dimids[1])) ERR_RET;
if (nc_def_dim(ncid, "lon", Z_LEN, &dimids[2])) ERR_RET;
if (nc_def_var(ncid, "test", NC_FLOAT, NDIMS, dimids, &var)) ERR_RET;
if (docompression)
if (nc_def_var_deflate(ncid, var, 1, 1, 1)) ERR_RET;
if (nc_enddef(ncid)) ERR_RET;
if (nc_put_vars_float(ncid, var, start, count, stride, data)) ERR_RET;
if (nc_close(ncid)) ERR_RET;
return 0;
}
int dump_file3(const float *data, int docompression, int usedefdim)
{
int ncmode, ncid, dimids[NDIMS], var;
size_t start[NDIMS] = {0, 0, 0}, count[NDIMS] = {X_LEN, Y_LEN, Z_LEN};
ptrdiff_t stride[NDIMS] = {1, 1, 1};
ncmode = NC_CLOBBER|NC_NETCDF4;
if (nc_create(FILE_NAME, ncmode, &ncid)) ERR_RET;
if (nc_def_dim(ncid, "time", X_LEN, &dimids[0])) ERR_RET;
if (nc_def_dim(ncid, "lat", Y_LEN, &dimids[1])) ERR_RET;
if (nc_def_dim(ncid, "lon", Z_LEN, &dimids[2])) ERR_RET;
if (nc_def_var(ncid, "test", NC_FLOAT, NDIMS, dimids, &var)) ERR_RET;
if (docompression)
if (nc_def_var_deflate(ncid, var, 1, 1, 1)) ERR_RET;
if (nc_enddef(ncid)) ERR_RET;
if (nc_put_vars_float(ncid, var, start, count, stride, data)) ERR_RET;
if (nc_close(ncid)) ERR_RET;
return 0;
}
int dump_hdf_file(const float *data, int docompression)
{
hid_t file_id, dataset_id, propid;
hid_t file_spaceid, mem_spaceid, access_plistid, xfer_plistid;
hsize_t dims[NDIMS] = {X_LEN, Y_LEN, Z_LEN};
hsize_t start[NDIMS] = {0, 0, 0};
hsize_t count[NDIMS] = {1, 1, Z_LEN};
hsize_t ones[NDIMS] = {1, 1, 1};
/* create file */
file_id = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC,
H5P_DEFAULT, H5P_DEFAULT);
/* create property for dataset */
propid = H5Pcreate(H5P_DATASET_CREATE);
if (docompression)
{
if (H5Pset_layout(propid, H5D_CHUNKED) < 0) ERR;
if (H5Pset_chunk(propid, NDIMS, dims) < 0) ERR;
/* values[0]=9; */
/* status = H5Pset_filter(propid, H5Z_FILTER_DEFLATE,0,1,&values[0]); */
/* printf("deflat estatus is: %i\n",status); */
/* sets defalte level */
if (H5Pset_deflate(propid, 1)) ERR;
}
if ((file_spaceid = H5Screate_simple(NDIMS, dims, dims)) < 0) ERR;
/* Set up the cache. */
if ((access_plistid = H5Pcreate(H5P_DATASET_ACCESS)) < 0) ERR;
if (H5Pset_chunk_cache(access_plistid, CHUNK_CACHE_NELEMS,
CHUNK_CACHE_SIZE, CHUNK_CACHE_PREEMPTION) < 0) ERR;
/* Create the dataset. */
if ((dataset_id = H5Dcreate2(file_id, "dset", H5T_NATIVE_FLOAT, file_spaceid,
H5P_DEFAULT, propid, access_plistid)) < 0) ERR;
/* if ((file_spaceid = H5Dget_space(dataset_id)) < 0) ERR;*/
if ((mem_spaceid = H5Screate_simple(NDIMS, count, NULL)) < 0) ERR;
if ((xfer_plistid = H5Pcreate(H5P_DATASET_XFER)) < 0) ERR;
/* Write the dataset. */
for (start[0] = 0; start[0] < X_LEN; start[0]++)
for (start[1] = 0; start[1] < Y_LEN; start[1]++)
{
if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET, start, NULL,
ones, count) < 0) ERR_RET;
if (H5Dwrite(dataset_id, H5T_NATIVE_FLOAT, mem_spaceid, file_spaceid,
xfer_plistid, data) < 0) ERR_RET;
}
/* Close property lists. */
if (H5Pclose(propid) < 0) ERR;
if (H5Pclose(access_plistid) < 0) ERR;
if (H5Pclose(xfer_plistid) < 0) ERR;
/* Close spaces. */
if (H5Sclose(file_spaceid) < 0) ERR;
if (H5Sclose(mem_spaceid) < 0) ERR;
/* End access to the dataset and release resources used by it. */
if (H5Dclose(dataset_id) < 0) ERR;
/* close file */
if (H5Fclose(file_id) < 0) ERR;
return 0;
}
void
get_mem_used2(int *mem_used)
{
char buf[30];
FILE *pf;
snprintf(buf, 30, "/proc/%u/statm", (unsigned)getpid());
pf = NCfopen(buf, "r");
if (pf) {
unsigned size; /* total program size */
unsigned resident;/* resident set size */
unsigned share;/* shared pages */
unsigned text;/* text (code) */
unsigned lib;/* library */
unsigned data;/* data/stack */
/*unsigned dt; dirty pages (unused in Linux 2.6)*/
fscanf(pf, "%u %u %u %u %u %u", &size, &resident, &share,
&text, &lib, &data);
*mem_used = data;
}
else
*mem_used = -1;
fclose(pf);
}
int main(void)
{
float data[X_LEN * Y_LEN * Z_LEN];
int i;
printf("\n*** Testing netcdf-4 file functions with caching.\n");
/* Initialize data. */
for (i = 0; i < (X_LEN * Y_LEN * Z_LEN); i++)
data[i] = i;
printf("*** testing a bunch of file writes with compressed data...\n");
{
int mem_used, mem_used1;
printf("*** testing netcdf-4 writes...\n");
for (i = 0; i < NUM_TRIES; i++)
{
get_mem_used2(&mem_used);
if (dump_file3(data, 1, 0)) ERR_RET;
get_mem_used2(&mem_used1);
if (mem_used1 - mem_used)
printf("delta %d bytes of memory for try %d\n", mem_used1 - mem_used, i);
}
printf("*** testing HDF5 writes...\n");
for (i = 0; i < NUM_TRIES; i++)
{
get_mem_used2(&mem_used);
if (dump_hdf_file(data, 1)) ERR_RET;
get_mem_used2(&mem_used1);
if (mem_used1 - mem_used)
printf("delta %d bytes of memory for try %d\n", mem_used1 - mem_used, i);
}
printf("*** testing netcdf-4 writes again...\n");
for (i = 0; i < NUM_TRIES; i++)
{
get_mem_used2(&mem_used);
if (dump_file2(data, 1, 0)) ERR_RET;
get_mem_used2(&mem_used1);
if (mem_used1 - mem_used)
printf("delta %d bytes of memory for try %d\n", mem_used1 - mem_used, i);
}
}
SUMMARIZE_ERR;
FINAL_RESULTS;
}
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