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netcdf-c/nc_perf/tst_chunks3.c
Dennis Heimbigner d06938fd1d 1. Fix an additional flaw in fill_value handling where non-atomic default values were not properly being handled. 
2. Rename the NC4_inq_any_type to NC_inq_any_type
3. Fix performance test cases affected by this PR.
2022-01-10 22:26:19 -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.
Runs benchmarks on different chunking sizes.
Russ Rew, Ed Hartnett, Dennis Heimbigner
*/
#include <config.h>
#include <stdio.h>
#include <stdlib.h>
#ifdef HAVE_UNISTD_H
#include <unistd.h> /* for sysconf */
#endif
#ifdef HAVE_SYS_TYPES_H
#include <sys/types.h>
#endif
#ifdef HAVE_SYS_TIMES_H
#include <sys/times.h>
#endif
#ifdef HAVE_SYS_TIME_H
#include <sys/time.h>
#endif
#include <assert.h>
#ifdef HAVE_SYS_RESOURCE_H
#include <sys/resource.h>
#endif
#include "nc_tests.h" /* The ERR macro is here... */
#include "netcdf.h"
#define FILENAME "tst_chunks3.nc"
/*
* The following timing macros can be used by including the necessary
* declarations with
*
* TIMING_DECLS(seconds)
*
* and surrounding sections of code to be timed with the "statements"
*
* TIMING_START
* [code to be timed goes here]
* TIMING_END(seconds)
*
* The macros assume the user has stored a description of what is
* being timed in a 100-char string time_mess, and has included
* <sys/times.h> and <sys/resource.h>. The timing message printed by
* TIMING_END is not terminated by a new-line, to permit appending
* additional text to that line, so user must at least printf("\n")
* after that.
*/
#define TIMING_DECLS(seconds) \
long TMreps; /* counts repetitions of timed code */ \
long TMrepeats; /* repetitions needed to exceed 0.1 second */ \
long emic ; /* elapsed time in microseconds */ \
struct rusage ru; \
long inb, oub; \
char time_mess[100]; \
float seconds;
#define TIMING_START \
TMrepeats = 1; \
do { \
if(getrusage(RUSAGE_SELF, &ru)) { \
printf("getrusage failed, returned %d\n", errno);} \
emic = (1000000*(ru.ru_utime.tv_sec + ru.ru_stime.tv_sec) \
+ ru.ru_utime.tv_usec + ru.ru_stime.tv_usec); \
inb = ru.ru_inblock; \
oub = ru.ru_oublock; \
for(TMreps=0; TMreps < TMrepeats; TMreps++) {
#define TIMING_END(seconds) \
} \
if(getrusage(RUSAGE_SELF, &ru)) { \
printf("getrusage failed, returned %d\n", errno);} \
emic = (1000000*(ru.ru_utime.tv_sec + ru.ru_stime.tv_sec) \
+ ru.ru_utime.tv_usec + ru.ru_stime.tv_usec) - emic; \
inb = ru.ru_inblock - inb; \
oub = ru.ru_oublock - oub; \
TMrepeats *= 2; \
} while (emic < 100000.0 ); \
seconds = emic / (1000000.0 * TMreps); \
printf("%-45.45s %7.2g sec", \
time_mess, seconds);
/* This macro prints an error message with line number and name of
* test program. */
#define ERR1(n) do { \
fflush(stdout); /* Make sure our stdout is synced with stderr. */ \
fprintf(stderr, "Sorry! Unexpected result, %s, line: %d - %s\n", \
__FILE__, __LINE__, nc_strerror(n)); \
return n; \
} while (0)
#define NC_COMPRESSED 1
void
parse_args(int argc, char *argv[], /* from command-line invocation */
int *deflate_levelp, /* returned: 0 uncompressed,
1-9 compression level */
int *shufflep, /* returned: 1 if shuffle, otherwise 0 */
size_t *dims, /* returned: dimension sizes */
size_t *chunks, /* returned: chunk sizes */
size_t *cache_sizep, /* returned: cache size (bytes) */
size_t *cache_nelemsp, /* returned: cache capacity (chunks) */
float *cache_prep) /* returned: cache preemption policy (0-1) */
{
if(argc > 1) {
*deflate_levelp = atol(argv[1]);
if (*deflate_levelp < 0) {
*deflate_levelp = -*deflate_levelp;
*shufflep = NC_SHUFFLE;
}
}
if(argc > 2)
dims[0] = atol(argv[2]);
if(argc > 3)
chunks[0] = atol(argv[3]);
else
chunks[0] = (dims[0]+7)/8;
if(argc > 4)
dims[1] = atol(argv[4]);
else
dims[1] = dims[0];
if(argc > 5)
chunks[1] = atol(argv[5]);
else
chunks[1] = chunks[0];
if(argc > 6)
dims[2] = atol(argv[6]);
else
dims[2] = dims[1];
if(argc > 7)
chunks[2] = atol(argv[7]);
else
chunks[2] = chunks[1];
if(argc > 8)
*cache_sizep = atol(argv[8]);
if(argc > 9)
*cache_nelemsp = atol(argv[9]);
if(argc > 10)
*cache_prep = atof(argv[10]);
if(argc > 11) {
printf("Usage: %s [def_level] [dim1] [chunk1] [dim2] [chunk2] [dim3] [chunk3] [cache_size] [cache_nelems] [cache_pre]\n",
argv[0]);
exit(1);
}
return;
}
void *
emalloc(size_t bytes) {
size_t *memory;
memory = malloc(bytes);
if(memory == 0) {
printf("malloc failed\n");
exit(2);
}
return memory;
}
/* compare contiguous, chunked, and compressed performance */
int
main(int argc, char *argv[]) {
int stat; /* return status */
int ncid; /* netCDF id */
int i, j, k;
int dim1id, dim2id, dim3id;
int varid_g; /* varid for contiguous */
int varid_k; /* varid for chunked */
int varid_x; /* varid for compressed */
float *varxy, *varxz, *varyz; /* 2D memory slabs used for I/O */
int mm;
size_t dims[] = {256, 256, 256}; /* default dim lengths */
size_t chunks[] = {32, 32, 32}; /* default chunk sizes */
size_t start[3], count[3];
float contig_time, chunked_time, compressed_time, ratio;
int deflate_level = 1; /* default compression level, 9 is
* better and slower. If negative,
* turn on shuffle filter also. */
int shuffle = NC_NOSHUFFLE;
size_t cache_size_def;
size_t cache_hash_def;
float cache_pre_def;
size_t cache_size = 0; /* use library default */
size_t cache_hash = 0; /* use library default */
float cache_pre = -1.0f; /* use library default */
/* rank (number of dimensions) for each variable */
# define RANK_var1 3
/* variable shapes */
int var_dims[RANK_var1];
TIMING_DECLS(TMsec) ;
/* From args, get parameters for timing, including variable and
chunk sizes. Negative deflate level means also use shuffle
filter. */
parse_args(argc, argv, &deflate_level, &shuffle, dims,
chunks, &cache_size, &cache_hash, &cache_pre);
/* get cache defaults, then set cache parameters that are not default */
if((stat = nc_get_chunk_cache(&cache_size_def, &cache_hash_def,
&cache_pre_def)))
ERR1(stat);
if(cache_size == 0)
cache_size = cache_size_def;
if(cache_hash == 0)
cache_hash = cache_hash_def;
if(cache_pre == -1.0f)
cache_pre = cache_pre_def;
if((stat = nc_set_chunk_cache(cache_size, cache_hash, cache_pre)))
ERR1(stat);
printf("cache: %3.2f MBytes %ld objs %3.2f preempt, ",
cache_size/1.e6, cache_hash, cache_pre);
if(deflate_level == 0) {
printf("uncompressed ");
} else {
printf("compression level %d", deflate_level);
}
if(shuffle == 1) {
printf(", shuffled");
}
printf("\n\n");
/* initialize 2D slabs for writing along each axis with phony data */
varyz = (float *) emalloc(sizeof(float) * 1 * dims[1] * dims[2]);
varxz = (float *) emalloc(sizeof(float) * dims[0] * 1 * dims[2]);
varxy = (float *) emalloc(sizeof(float) * dims[0] * dims[1] * 1);
mm = 0;
for(j = 0; j < dims[1]; j++) {
for(k = 0; k < dims[2]; k++) {
varyz[mm++] = k + dims[2]*j;
}
}
mm = 0;
for(i = 0; i < dims[0]; i++) {
for(k = 0; k < dims[2]; k++) {
varxz[mm++] = k + dims[2]*i;
}
}
mm = 0;
for(i = 0; i < dims[0]; i++) {
for(j = 0; j < dims[1]; j++) {
varxy[mm++] = j + dims[1]*i;
}
}
if((stat = nc_create(FILENAME, NC_NETCDF4 | NC_CLASSIC_MODEL, &ncid)))
ERR1(stat);
/* define dimensions */
if((stat = nc_def_dim(ncid, "dim1", dims[0], &dim1id)))
ERR1(stat);
if((stat = nc_def_dim(ncid, "dim2", dims[1], &dim2id)))
ERR1(stat);
if((stat = nc_def_dim(ncid, "dim3", dims[2], &dim3id)))
ERR1(stat);
/* define variables */
var_dims[0] = dim1id;
var_dims[1] = dim2id;
var_dims[2] = dim3id;
if((stat = nc_def_var(ncid, "var_contiguous", NC_FLOAT, RANK_var1,
var_dims, &varid_g)))
ERR1(stat);
if((stat = nc_def_var(ncid, "var_chunked", NC_FLOAT, RANK_var1,
var_dims, &varid_k)))
ERR1(stat);
if((stat = nc_def_var(ncid, "var_compressed", NC_FLOAT, RANK_var1,
var_dims, &varid_x)))
ERR1(stat);
if((stat = nc_def_var_chunking(ncid, varid_g, NC_CONTIGUOUS, 0)))
ERR1(stat);
if((stat = nc_def_var_chunking(ncid, varid_k, NC_CHUNKED, chunks)))
ERR1(stat);
if((stat = nc_def_var_chunking(ncid, varid_x, NC_CHUNKED, chunks)))
ERR1(stat);
if (deflate_level != 0) {
if((stat = nc_def_var_deflate(ncid, varid_x, shuffle,
NC_COMPRESSED, deflate_level)))
ERR1(stat);
}
/* leave define mode */
if((stat = nc_enddef (ncid)))
ERR1(stat);
/* write each variable one yz slab at a time */
start[0] = 0;
start[1] = 0;
start[2] = 0;
count[0] = 1;
count[1] = dims[1];
count[2] = dims[2];
sprintf(time_mess," contiguous write %3d %3ld %3ld",
1, dims[1], dims[2]);
TIMING_START ;
for(i = 0; i < dims[0]; i++) {
start[0] = i;
if((stat = nc_put_vara(ncid, varid_g, start, count, &varyz[0])))
ERR1(stat);
}
TIMING_END(TMsec) ;
printf("\n");
contig_time = TMsec;
sprintf(time_mess," chunked write %3d %3ld %3ld %3ld %3ld %3ld",
1, dims[1], dims[2], chunks[0], chunks[1], chunks[2]);
TIMING_START ;
for(i = 0; i < dims[0]; i++) {
start[0] = i;
if((stat = nc_put_vara(ncid, varid_k, start, count, &varyz[0])))
ERR1(stat);
}
TIMING_END(TMsec) ;
chunked_time = TMsec;
ratio = contig_time/chunked_time;
if(ratio >= 1.0)
printf(" %5.2g x faster\n", ratio);
else
printf(" %5.2g x slower\n", 1.0/ratio);
sprintf(time_mess," compressed write %3d %3ld %3ld %3ld %3ld %3ld",
1, dims[1], dims[2], chunks[0], chunks[1], chunks[2]);
TIMING_START ;
for(i = 0; i < dims[0]; i++) {
start[0] = i;
if((stat = nc_put_vara(ncid, varid_x, start, count, &varyz[0])))
ERR1(stat);
}
TIMING_END(TMsec) ;
compressed_time = TMsec;
ratio = contig_time/compressed_time;
if(ratio >= 1.0)
printf(" %5.2g x faster\n", ratio);
else
printf(" %5.2g x slower\n", 1.0/ratio);
printf("\n");
/* write each variable one xz slab at a time */
start[0] = 0;
start[1] = 0;
start[2] = 0;
count[0] = dims[0];
count[1] = 1;
count[2] = dims[2];
sprintf(time_mess," contiguous write %3ld %3d %3ld",
dims[0], 1, dims[2]);
TIMING_START ;
for(i = 0; i < dims[1]; i++) {
start[1] = i;
if((stat = nc_put_vara(ncid, varid_g, start, count, &varxz[0])))
ERR1(stat);
}
TIMING_END(TMsec) ;
printf("\n");
contig_time = TMsec;
sprintf(time_mess," chunked write %3ld %3d %3ld %3ld %3ld %3ld",
dims[0], 1, dims[2], chunks[0], chunks[1], chunks[2]);
TIMING_START ;
for(i = 0; i < dims[1]; i++) {
start[1] = i;
if((stat = nc_put_vara(ncid, varid_k, start, count, &varxz[0])))
ERR1(stat);
}
TIMING_END(TMsec) ;
chunked_time = TMsec;
ratio = contig_time/chunked_time;
if(ratio >= 1.0)
printf(" %5.2g x faster\n", ratio);
else
printf(" %5.2g x slower\n", 1.0/ratio);
sprintf(time_mess," compressed write %3ld %3d %3ld %3ld %3ld %3ld",
dims[0], 1, dims[2], chunks[0], chunks[1], chunks[2]);
TIMING_START ;
for(i = 0; i < dims[1]; i++) {
start[1] = i;
if((stat = nc_put_vara(ncid, varid_x, start, count, &varxz[0])))
ERR1(stat);
}
TIMING_END(TMsec) ;
compressed_time = TMsec;
ratio = contig_time/compressed_time;
if(ratio >= 1.0)
printf(" %5.2g x faster\n", ratio);
else
printf(" %5.2g x slower\n", 1.0/ratio);
printf("\n");
/* write each variable one xy slab at a time */
start[0] = 0;
start[1] = 0;
start[2] = 0;
count[0] = dims[0];
count[1] = dims[1];
count[2] = 1;
sprintf(time_mess," contiguous write %3ld %3ld %3d",
dims[0], dims[1], 1);
TIMING_START ;
for(i = 0; i < dims[2]; i++) {
start[2] = i;
if((stat = nc_put_vara(ncid, varid_g, start, count, &varxy[0])))
ERR1(stat);
}
TIMING_END(TMsec) ;
printf("\n");
contig_time = TMsec;
sprintf(time_mess," chunked write %3ld %3ld %3d %3ld %3ld %3ld",
dims[0], dims[1], 1, chunks[0], chunks[1], chunks[2]);
TIMING_START ;
for(i = 0; i < dims[2]; i++) {
start[2] = i;
if((stat = nc_put_vara(ncid, varid_k, start, count, &varxy[0])))
ERR1(stat);
}
TIMING_END(TMsec) ;
chunked_time = TMsec;
ratio = contig_time/chunked_time;
if(ratio >= 1.0)
printf(" %5.2g x faster\n", ratio);
else
printf(" %5.2g x slower\n", 1.0/ratio);
sprintf(time_mess," compressed write %3ld %3ld %3d %3ld %3ld %3ld",
dims[0], dims[1], 1, chunks[0], chunks[1], chunks[2]);
TIMING_START ;
for(i = 0; i < dims[2]; i++) {
start[2] = i;
if((stat = nc_put_vara(ncid, varid_x, start, count, &varxy[0])))
ERR1(stat);
}
TIMING_END(TMsec) ;
compressed_time = TMsec;
ratio = contig_time/compressed_time;
if(ratio >= 1.0)
printf(" %5.2g x faster\n", ratio);
else
printf(" %5.2g x slower\n", 1.0/ratio);
printf("\n");
/* read each variable one yz slab at a time */
start[0] = 0;
start[1] = 0;
start[2] = 0;
count[0] = 1;
count[1] = dims[1];
count[2] = dims[2];
sprintf(time_mess," contiguous read %3d %3ld %3ld",
1, dims[1], dims[2]);
TIMING_START ;
for(i = 0; i < dims[0]; i++) {
start[0] = i;
if((stat = nc_get_vara(ncid, varid_g, start, count, &varyz[0])))
ERR1(stat);
}
TIMING_END(TMsec) ;
printf("\n");
contig_time = TMsec;
sprintf(time_mess," chunked read %3d %3ld %3ld %3ld %3ld %3ld",
1, dims[1], dims[2] , chunks[0], chunks[1], chunks[2]);
TIMING_START ;
for(i = 0; i < dims[0]; i++) {
start[0] = i;
if((stat = nc_get_vara(ncid, varid_k, start, count, &varyz[0])))
ERR1(stat);
}
TIMING_END(TMsec) ;
chunked_time = TMsec;
ratio = contig_time/chunked_time;
if(ratio >= 1.0)
printf(" %5.2g x faster\n", ratio);
else
printf(" %5.2g x slower\n", 1.0/ratio);
sprintf(time_mess," compressed read %3d %3ld %3ld %3ld %3ld %3ld",
1, dims[1], dims[2] , chunks[0], chunks[1], chunks[2]);
TIMING_START ;
for(i = 0; i < dims[0]; i++) {
start[0] = i;
if((stat = nc_get_vara(ncid, varid_x, start, count, &varyz[0])))
ERR1(stat);
}
TIMING_END(TMsec) ;
compressed_time = TMsec;
ratio = contig_time/compressed_time;
if(ratio >= 1.0)
printf(" %5.2g x faster\n", ratio);
else
printf(" %5.2g x slower\n", 1.0/ratio);
printf("\n");
/* read each variable one xz slab at a time */
start[0] = 0;
start[1] = 0;
start[2] = 0;
count[0] = dims[0];
count[1] = 1;
count[2] = dims[2];
sprintf(time_mess," contiguous read %3ld %3d %3ld",
dims[0], 1, dims[2]);
TIMING_START ;
for(i = 0; i < dims[1]; i++) {
start[1] = i;
if((stat = nc_get_vara(ncid, varid_g, start, count, &varxz[0])))
ERR1(stat);
}
TIMING_END(TMsec) ;
printf("\n");
contig_time = TMsec;
sprintf(time_mess," chunked read %3ld %3d %3ld %3ld %3ld %3ld",
dims[0], 1, dims[2], chunks[0], chunks[1], chunks[2]);
TIMING_START ;
for(i = 0; i < dims[1]; i++) {
start[1] = i;
if((stat = nc_get_vara(ncid, varid_k, start, count, &varxz[0])))
ERR1(stat);
}
TIMING_END(TMsec) ;
chunked_time = TMsec;
ratio = contig_time/chunked_time;
if(ratio >= 1.0)
printf(" %5.2g x faster\n", ratio);
else
printf(" %5.2g x slower\n", 1.0/ratio);
sprintf(time_mess," compressed read %3ld %3d %3ld %3ld %3ld %3ld",
dims[0], 1, dims[2], chunks[0], chunks[1], chunks[2]);
TIMING_START ;
for(i = 0; i < dims[1]; i++) {
start[1] = i;
if((stat = nc_get_vara(ncid, varid_x, start, count, &varxz[0])))
ERR1(stat);
}
TIMING_END(TMsec) ;
compressed_time = TMsec;
ratio = contig_time/compressed_time;
if(ratio >= 1.0)
printf(" %5.2g x faster\n", ratio);
else
printf(" %5.2g x slower\n", 1.0/ratio);
printf("\n");
/* read variable one xy slab at a time */
start[0] = 0;
start[1] = 0;
start[2] = 0;
count[0] = dims[0];
count[1] = dims[1];
count[2] = 1;
sprintf(time_mess," contiguous read %3ld %3ld %3d",
dims[0], dims[1], 1);
TIMING_START ;
for(i = 0; i < dims[2]; i++) {
start[2] = i;
if((stat = nc_get_vara(ncid, varid_g, start, count, &varxy[0])))
ERR1(stat);
}
TIMING_END(TMsec) ;
printf("\n");
contig_time = TMsec;
sprintf(time_mess," chunked read %3ld %3ld %3d %3ld %3ld %3ld",
dims[0], dims[1], 1, chunks[0], chunks[1], chunks[2]);
TIMING_START ;
for(i = 0; i < dims[2]; i++) {
start[2] = i;
if((stat = nc_get_vara(ncid, varid_k, start, count, &varxy[0])))
ERR1(stat);
}
TIMING_END(TMsec) ;
chunked_time = TMsec;
ratio = contig_time/chunked_time;
if(ratio >= 1.0)
printf(" %5.2g x faster\n", ratio);
else
printf(" %5.2g x slower\n", 1.0/ratio);
sprintf(time_mess," compressed read %3ld %3ld %3d %3ld %3ld %3ld",
dims[0], dims[1], 1, chunks[0], chunks[1], chunks[2]);
TIMING_START ;
for(i = 0; i < dims[2]; i++) {
start[2] = i;
if((stat = nc_get_vara(ncid, varid_x, start, count, &varxy[0])))
ERR1(stat);
}
TIMING_END(TMsec) ;
compressed_time = TMsec;
ratio = contig_time/compressed_time;
if(ratio >= 1.0)
printf(" %5.2g x faster\n", ratio);
else
printf(" %5.2g x slower\n", 1.0/ratio);
if((stat = nc_close(ncid)))
ERR1(stat);
free(varyz);
free(varxz);
free(varxy);
return 0;
}
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