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netcdf-c/nc_test4/tst_ar4_4d.c
Dennis Heimbigner 99eef24bc2 - Fix NCF-158 to modify ncgen flag defaults. 
- Fix NCF-157 to modify DAP code to support
  partial variable retrieval.
- Fix of NCF-154 to solve problem of ncgen
  improperly processing data lists for variables
  of size greater than 2**18 bytes.
- Fix ncgen processing of char variables that have
  multiple unlimited dimensions.
- Partly fix Jira issue: NCF-145 (vlen issues).
- Benchmark program nc_test4/tst_ar4_*) requires arguments
  and should only be invoked inside a shell
  script; fixed so that they terminate cleanly
  if invoked with no arguments.
- Fix the Doxygen processing so it will work
  with make distcheck.
- Begin switchover to using an alternative to ncio.
- Begin support for in-memory (diskless) files.
2012-03-14 23:26:48 +00:00

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/*
Copyright 2009, UCAR/Unidata
See COPYRIGHT file for copying and redistribution conditions.
This program tests netcdf-4 performance with some AR-4 3D data.
$Id: tst_ar4_4d.c,v 1.2 2010/01/14 20:25:55 ed Exp $
*/
#include <nc_tests.h>
#include <time.h>
#include <sys/time.h>
#include <unistd.h>
#define MEGABYTE 1048576
#define HALF_MEG (MEGABYTE/2)
#define MILLION 1000000
#define SIXTEEN_MEG 16777216
#define FOUR_MEG (SIXTEEN_MEG/4)
#define THIRTY_TWO_MEG (SIXTEEN_MEG * 2)
#define SIXTY_FOUR_MEG (SIXTEEN_MEG * 4)
#define ONE_TWENTY_EIGHT_MEG (SIXTEEN_MEG * 8)
/* From the data file we are using:
../ncdump/ncdump -h -s thetao_O1.SRESA1B_2.CCSM.ocnm.2000-01_cat_2099-12.nc
netcdf thetao_O1.SRESA1B_2.CCSM.ocnm.2000-01_cat_2099-12 {
dimensions:
lon = 320 ;
lat = 395 ;
depth = 40 ;
bnds = 2 ;
time = UNLIMITED ; // (1200 currently)
variables:
double lon_bnds(lon, bnds) ;
double lat_bnds(lat, bnds) ;
double depth_bnds(depth, bnds) ;
double time_bnds(time, bnds) ;
double lon(lon) ;
lon:axis = "X" ;
lon:standard_name = "longitude" ;
lon:bounds = "lon_bnds" ;
lon:long_name = "Longitude" ;
lon:units = "degrees_east" ;
double lat(lat) ;
lat:axis = "Y" ;
lat:standard_name = "latitude" ;
lat:bounds = "lat_bnds" ;
lat:long_name = "Latitude" ;
lat:units = "degrees_north" ;
double depth(depth) ;
depth:axis = "Z" ;
depth:standard_name = "depth" ;
depth:positive = "down" ;
depth:units = "m" ;
depth:bounds = "depth_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" ;
float thetao(time, depth, lat, lon) ;
thetao:comment = "Created using NCL code CCSM_ocnm_2cf.ncl on\n",
" machine mineral" ;
thetao:missing_value = 1.e+20f ;
thetao:long_name = "sea_water_potential_temperature" ;
thetao:cell_methods = "time: mean (interval: 1 month)" ;
thetao:history = "Interpolated to regular grid from dipole grid,\n",
"TEMP+273.15" ;
thetao:units = "K" ;
thetao:original_units = "C" ;
thetao:original_name = "TEMP" ;
thetao:standard_name = "sea_water_potential_temperature" ;
thetao:_FillValue = 1.e+20f ;
// global attributes:
:table_id = "Table O1" ;
:title = "model output prepared for IPCC AR4" ;
:institution = "NCAR (National Center for Atmospheric \n",
"Research, Boulder, CO, USA)" ;
:source = "CCSM3.0, version beta19 (2004): \n",
"atmosphere: CAM3.0, T85L26;\n",
"ocean : POP1.4.3 (modified), gx1v3\n",
"sea ice : CSIM5.0, gx1v3;\n",
"land : CLM3.0, T85" ;
:contact = "ccsm@ucar.edu" ;
:project_id = "IPCC Fourth Assessment" ;
:Conventions = "CF-1.0" ;
:references = "Collins, W.D., et al., 2005:\n",
" The Community Climate System Model, Version 3\n",
" Journal of Climate\n",
" \n",
" Main website: http://www.ccsm.ucar.edu" ;
:acknowledgment = " Any use of CCSM data should acknowledge the contribution\n",
" of the CCSM project and CCSM sponsor agencies with the \n",
" following citation:\n",
" \'This research uses data provided by the Community Climate\n",
" System Model project (www.ccsm.ucar.edu), supported by the\n",
" Directorate for Geosciences of the National Science Foundation\n",
" and the Office of Biological and Environmental Research of\n",
" the U.S. Department of Energy.\'\n",
"In addition, the words \'Community Climate System Model\' and\n",
" \'CCSM\' should be included as metadata for webpages referencing\n",
" work using CCSM data or as keywords provided to journal or book\n",
"publishers of your manuscripts.\n",
"Users of CCSM data accept the responsibility of emailing\n",
" citations of publications of research using CCSM data to\n",
" ccsm@ucar.edu.\n",
"Any redistribution of CCSM data must include this data\n",
" acknowledgement statement." ;
:realization = 2 ;
:experiment_id = "720 ppm stabilization experiment (SRES A1B)" ;
:history = "Created from CCSM3 case b30.040b\n",
" by strandwg@ucar.edu\n",
" on Sun Apr 24 22:35:53 MDT 2005\n",
" \n",
" For all data, added IPCC requested metadata" ;
:comment = "This simulation was initiated from year 2000 of \n",
" CCSM3 model run b30.030b and executed on \n",
" hardware bluesky.ucar.edu. The input external forcings are\n",
"ozone forcing : A1B.ozone.128x64_L18_1991-2100_c040528.nc\n",
"aerosol optics : AerosolOptics_c040105.nc\n",
"aerosol MMR : AerosolMass_V_128x256_clim_c031022.nc\n",
"carbon scaling : carbonscaling_A1B_1990-2100_c040609.nc\n",
"solar forcing : Fixed at 1366.5 W m-2\n",
"GHGs : ghg_ipcc_A1B_1870-2100_c040521.nc\n",
"GHG loss rates : noaamisc.r8.nc\n",
"volcanic forcing : none\n",
"DMS emissions : DMS_emissions_128x256_clim_c040122.nc\n",
"oxidants : oxid_128x256_L26_clim_c040112.nc\n",
"SOx emissions : SOx_emissions_A1B_128x256_L2_1990-2100_c040608.nc\n",
" Physical constants used for derived data:\n",
" Lv (latent heat of evaporation): 2.501e6 J kg-1\n",
" Lf (latent heat of fusion ): 3.337e5 J kg-1\n",
" r[h2o] (density of water ): 1000 kg m-3\n",
" g2kg (grams to kilograms ): 1000 g kg-1\n",
" \n",
" Integrations were performed by NCAR and CRIEPI with support\n",
" and facilities provided by NSF, DOE, MEXT and ESC/JAMSTEC." ;
:_Format = "classic" ;
}
*/
/* Subtract the `struct timeval' values X and Y, storing the result in
RESULT. Return 1 if the difference is negative, otherwise 0. This
function from the GNU documentation. */
static int
timeval_subtract (result, x, y)
struct timeval *result, *x, *y;
{
/* Perform the carry for the later subtraction by updating Y. */
if (x->tv_usec < y->tv_usec) {
int nsec = (y->tv_usec - x->tv_usec) / MILLION + 1;
y->tv_usec -= MILLION * nsec;
y->tv_sec += nsec;
}
if (x->tv_usec - y->tv_usec > MILLION) {
int nsec = (x->tv_usec - y->tv_usec) / MILLION;
y->tv_usec += MILLION * nsec;
y->tv_sec -= nsec;
}
/* Compute the time remaining to wait.
`tv_usec' is certainly positive. */
result->tv_sec = x->tv_sec - y->tv_sec;
result->tv_usec = x->tv_usec - y->tv_usec;
/* Return 1 if result is negative. */
return x->tv_sec < y->tv_sec;
}
#define USAGE "\
[-h] Print output header\n\
[-t] Do a time-series read\n\
[-v] Vertical profile 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 -h -t -v -c CACHE_SIZE file\n%s", USAGE);
}
#define NDIMS4 4
#define DATA_VAR_NAME "thetao"
#define NUM_CACHE_TRIES 1
#define LON_DIMID 0
#define LAT_DIMID 1
#define DEPTH_DIMID 2
#define BNDS_DIMID 3
#define TIME_DIMID 4
#define LON_LEN 320
#define LAT_LEN 395
#define BNDS_LEN 2
#define DEPTH_LEN 40
#define TIME_LEN 1200
#define NUM_TS 1
#define MAX_READ_COUNT 100
int
main(int argc, char **argv)
{
extern int optind;
extern int opterr;
extern char *optarg;
int c, header = 0, vertical_profile = 0, timeseries = 0;
int ncid, varid, storage;
char name_in[NC_MAX_NAME + 1];
size_t len;
size_t cs[NDIMS4] = {0, 0, 0, 0};
int cache = MEGABYTE;
int ndims, dimid[NDIMS4];
float hor_data[LAT_LEN * LON_LEN];
float vert_data[DEPTH_LEN];
int read_1_us, avg_read_us;
float ts_data[TIME_LEN];
size_t start[NDIMS4], count[NDIMS4];
int deflate, shuffle, deflate_level;
struct timeval start_time, end_time, diff_time;
int read_count = 0, num_reads;
while ((c = getopt(argc, argv, "vhtc:")) != EOF)
switch(c)
{
case 'v':
vertical_profile++;
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 if (vertical_profile)
printf("\t1st_read_vert(us)\tavg_read_vert(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, DEPTH_DIMID, name_in, &len)) ERR;
if (strcmp(name_in, "depth") || len != DEPTH_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 != NDIMS4 || dimid[0] != TIME_DIMID ||
dimid[1] != DEPTH_DIMID || dimid[2] != LAT_DIMID ||
dimid[3] != 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;
start[3] = 0;
count[0] = TIME_LEN;
count[1] = 1;
count[2] = 1;
count[3] = 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 (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; read_count < MAX_READ_COUNT && start[1] < LAT_LEN; start[1]++)
for (start[2] = 1; read_count < MAX_READ_COUNT && start[2] < LON_LEN; start[2]++)
for (start[3] = 1; read_count < MAX_READ_COUNT && start[3] < DEPTH_LEN; start[3]++)
{
if (nc_get_vara_float(ncid, varid, start, count, ts_data)) ERR_RET;
read_count++;
}
if (gettimeofday(&end_time, NULL)) ERR;
if (timeval_subtract(&diff_time, &end_time, &start_time)) ERR;
num_reads = (read_count == MAX_READ_COUNT) ? MAX_READ_COUNT : (LAT_LEN * LON_LEN * DEPTH_LEN);
avg_read_us = ((int)diff_time.tv_sec * MILLION + (int)diff_time.tv_usec + read_1_us) /
num_reads;
}
else if (vertical_profile)
{
/* Read the var as a vertical profile. */
start[0] = 0;
start[1] = 0;
start[2] = 0;
start[3] = 0;
count[0] = 1;
count[1] = DEPTH_LEN;
count[2] = 1;
count[3] = 1;
/* Read the first vertical profile. */
if (gettimeofday(&start_time, NULL)) ERR;
if (nc_get_vara_float(ncid, varid, start, count, vert_data)) ERR_RET;
if (gettimeofday(&end_time, NULL)) ERR;
if (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[0] = 0; read_count < MAX_READ_COUNT && start[1] < LAT_LEN; start[1]++) */
/* for (start[1] = 0; read_count < MAX_READ_COUNT && start[1] < LAT_LEN; start[1]++) */
/* for (start[2] = 1; read_count < MAX_READ_COUNT && start[2] < LON_LEN; start[2]++) */
/* for (start[] = 1; read_count < MAX_READ_COUNT && start[3] < DEPTH_LEN; start[3]++) */
/* { */
/* if (nc_get_vara_float(ncid, varid, start, count, vert_data)) ERR_RET; */
/* read_count++; */
/* } */
if (gettimeofday(&end_time, NULL)) ERR;
if (timeval_subtract(&diff_time, &end_time, &start_time)) ERR;
num_reads = (read_count == MAX_READ_COUNT) ? MAX_READ_COUNT : (LAT_LEN * LON_LEN * DEPTH_LEN);
avg_read_us = ((int)diff_time.tv_sec * MILLION + (int)diff_time.tv_usec + read_1_us) /
num_reads;
}
else
{
/* Read the data variable in horizontal slices. */
start[0] = 0;
start[1] = 0;
start[2] = 0;
start[3] = 0;
count[0] = 1;
count[1] = 1;
count[2] = LAT_LEN;
count[3] = 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 (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] = 0; read_count < MAX_READ_COUNT && start[0] < TIME_LEN; start[0]++)
for (start[1] = 1; read_count < MAX_READ_COUNT && start[1] < DEPTH_LEN; start[1]++)
{
if (nc_get_vara_float(ncid, varid, start, count, hor_data)) ERR_RET;
read_count++;
}
if (gettimeofday(&end_time, NULL)) ERR;
if (timeval_subtract(&diff_time, &end_time, &start_time)) ERR;
num_reads = (read_count == MAX_READ_COUNT) ? MAX_READ_COUNT : TIME_LEN;
avg_read_us = ((int)diff_time.tv_sec * MILLION + (int)diff_time.tv_usec +
read_1_us) / num_reads;
}
/* 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);
return 0;
}
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