1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
|
/*
Copyright 2018, UCAR/Unidata
See COPYRIGHT file for copying and redistribution conditions.
This program tests netcdf-4 performance with some AR-4 3D data.
Ed Hartnett
*/
#include <nc_tests.h>
#include "err_macros.h"
#include <time.h>
#include <sys/time.h>
#include <unistd.h>
/* Prototype from tst_utils.c. */
int nc4_timeval_subtract(struct timeval *result, struct timeval *x,
struct timeval *y);
/* From the data file we are using:
netcdf pr_A1.20C3M_8.CCSM.atmm.1870-01_cat_1999-12 {
dimensions:
lon = 256 ;
lat = 128 ;
bnds = 2 ;
time = UNLIMITED ; // (1560 currently)
variables:
double lon_bnds(lon, bnds) ;
double lat_bnds(lat, bnds) ;
double time_bnds(time, bnds) ;
double time(time) ;
time:calendar = "noleap" ;
time:standard_name = "time" ;
time:axis = "T" ;
time:units = "days since 0000-1-1" ;
time:bounds = "time_bnds" ;
time:long_name = "time" ;
double lat(lat) ;
lat:axis = "Y" ;
lat:standard_name = "latitude" ;
lat:bounds = "lat_bnds" ;
lat:long_name = "latitude" ;
lat:units = "degrees_north" ;
double lon(lon) ;
lon:axis = "X" ;
lon:standard_name = "longitude" ;
lon:bounds = "lon_bnds" ;
lon:long_name = "longitude" ;
lon:units = "degrees_east" ;
float pr(time, lat, lon) ;
pr:comment = "Created using NCL code CCSM_atmm_2cf.ncl on\n",
" machine mineral" ;
pr:missing_value = 1.e+20f ;
pr:_FillValue = 1.e+20f ;
pr:cell_methods = "time: mean (interval: 1 month)" ;
pr:history = "(PRECC+PRECL)*r[h2o]" ;
pr:original_units = "m-1 s-1" ;
pr:original_name = "PRECC, PRECL" ;
pr:standard_name = "precipitation_flux" ;
pr:units = "kg m-2 s-1" ;
pr:long_name = "precipitation_flux" ;
pr:cell_method = "time: mean" ;
*/
#define USAGE "\
[-v] Verbose\n\
[-h] Print output header\n\
[-t] Do a time-series read\n\
[-c CACHE_SIZE] Set the HDF5 chunk cache to this size before read\n\
file Name of netCDF file\n"
static void
usage(void)
{
fprintf(stderr, "tst_ar4 -v -h -t -c CACHE_SIZE file\n%s", USAGE);
}
#define NDIMS3 3
#define DATA_VAR_NAME "pr"
#define NUM_CACHE_TRIES 1
#define LON_DIMID 0
#define LAT_DIMID 1
#define BNDS_DIMID 2
#define TIME_DIMID 3
#define LON_LEN 256
#define LAT_LEN 128
#define BNDS_LEN 2
#define TIME_LEN 1560
#define NUM_TS 1
int
main(int argc, char **argv)
{
extern int optind;
extern int opterr;
extern char *optarg;
int c, header = 0, verbose = 0, timeseries = 0;
int ncid, varid, storage;
char name_in[NC_MAX_NAME + 1];
size_t len;
size_t cs[NDIMS3] = {0, 0, 0};
int cache = MEGABYTE;
int ndims, dimid[NDIMS3];
float hor_data[LAT_LEN * LON_LEN];
int read_1_us, avg_read_us;
float ts_data[TIME_LEN];
size_t start[NDIMS3], count[NDIMS3];
int deflate, shuffle, deflate_level;
struct timeval start_time, end_time, diff_time;
while ((c = getopt(argc, argv, "vhtc:")) != EOF)
switch(c)
{
case 'v':
verbose++;
break;
case 'h':
header++;
break;
case 't':
timeseries++;
break;
case 'c':
sscanf(optarg, "%d", &cache);
break;
case '?':
usage();
return 1;
}
argc -= optind;
argv += optind;
/* If no file arguments left, report and exit */
if (argc < 1)
{
printf("no file specified\n");
return 0;
}
/* Print the header if desired. */
if (header)
{
printf("cs[0]\tcs[1]\tcs[2]\tcache(MB)\tdeflate\tshuffle");
if (timeseries)
printf("\t1st_read_ser(us)\tavg_read_ser(us)\n");
else
printf("\t1st_read_hor(us)\tavg_read_hor(us)\n");
}
#define PREEMPTION .75
/* Also tried NELEMS of 2500009*/
#define NELEMS 7919
if (nc_set_chunk_cache(cache, NELEMS, PREEMPTION)) ERR;
if (nc_open(argv[0], 0, &ncid)) ERR;
/* Check to make sure that all the dimension information is
* correct. */
if (nc_inq_varid(ncid, DATA_VAR_NAME, &varid)) ERR;
if (nc_inq_dim(ncid, LON_DIMID, name_in, &len)) ERR;
if (strcmp(name_in, "lon") || len != LON_LEN) ERR;
if (nc_inq_dim(ncid, LAT_DIMID, name_in, &len)) ERR;
if (strcmp(name_in, "lat") || len != LAT_LEN) ERR;
if (nc_inq_dim(ncid, BNDS_DIMID, name_in, &len)) ERR;
if (strcmp(name_in, "bnds") || len != BNDS_LEN) ERR;
if (nc_inq_dim(ncid, TIME_DIMID, name_in, &len)) ERR;
if (strcmp(name_in, "time") || len != TIME_LEN) ERR;
if (nc_inq_var(ncid, varid, NULL, NULL, &ndims, dimid, NULL)) ERR;
if (ndims != NDIMS3 || dimid[0] != TIME_DIMID ||
dimid[1] != LAT_DIMID || dimid[2] != LON_DIMID) ERR;
/* Get info about the main data var. */
if (nc_inq_var_chunking(ncid, varid, &storage, cs)) ERR;
if (nc_inq_var_deflate(ncid, varid, &shuffle, &deflate,
&deflate_level)) ERR;
if (timeseries)
{
/* Read the var as a time series. */
start[0] = 0;
start[1] = 0;
start[2] = 0;
count[0] = TIME_LEN;
count[1] = 1;
count[2] = 1;
/* Read the first timeseries. */
if (gettimeofday(&start_time, NULL)) ERR;
if (nc_get_vara_float(ncid, varid, start, count, ts_data)) ERR_RET;
if (gettimeofday(&end_time, NULL)) ERR;
if (nc4_timeval_subtract(&diff_time, &end_time, &start_time)) ERR;
read_1_us = (int)diff_time.tv_sec * MILLION + (int)diff_time.tv_usec;
/* Read all the rest. */
if (gettimeofday(&start_time, NULL)) ERR;
for (start[1] = 0; start[1] < LAT_LEN; start[1]++)
for (start[2] = 1; start[2] < LON_LEN; start[2]++)
if (nc_get_vara_float(ncid, varid, start, count, ts_data)) ERR_RET;
if (gettimeofday(&end_time, NULL)) ERR;
if (nc4_timeval_subtract(&diff_time, &end_time, &start_time)) ERR;
avg_read_us = ((int)diff_time.tv_sec * MILLION + (int)diff_time.tv_usec + read_1_us) /
(LAT_LEN * LON_LEN);
}
else
{
/* Read the data variable in horizontal slices. */
start[0] = 0;
start[1] = 0;
start[2] = 0;
count[0] = 1;
count[1] = LAT_LEN;
count[2] = LON_LEN;
/* Read (and time) the first one. */
if (gettimeofday(&start_time, NULL)) ERR;
if (nc_get_vara_float(ncid, varid, start, count, hor_data)) ERR_RET;
if (gettimeofday(&end_time, NULL)) ERR;
if (nc4_timeval_subtract(&diff_time, &end_time, &start_time)) ERR;
read_1_us = (int)diff_time.tv_sec * MILLION + (int)diff_time.tv_usec;
/* Read (and time) all the rest. */
if (gettimeofday(&start_time, NULL)) ERR;
for (start[0] = 1; start[0] < TIME_LEN; start[0]++)
if (nc_get_vara_float(ncid, varid, start, count, hor_data)) ERR_RET;
if (gettimeofday(&end_time, NULL)) ERR;
if (nc4_timeval_subtract(&diff_time, &end_time, &start_time)) ERR;
avg_read_us = ((int)diff_time.tv_sec * MILLION + (int)diff_time.tv_usec +
read_1_us) / TIME_LEN;
}
/* Close file. */
if (nc_close(ncid)) ERR;
/* Print results. */
printf("%d\t%d\t%d\t%.1f\t\t%d\t%d\t\t",
(int)cs[0], (int)cs[1], (int)cs[2],
(storage == NC_CHUNKED) ? (cache/(float)MEGABYTE) : 0,
deflate, shuffle);
if (timeseries)
printf("%d\t\t%d\n", (int)read_1_us, (int)avg_read_us);
else
printf("%d\t\t%d\n", (int)read_1_us, (int)avg_read_us);
FINAL_RESULTS;
}
|
