mirror of
https://github.com/Unidata/netcdf-c.git
synced 2024-12-09 08:11:38 +08:00
3db4f013bf
Specific changes:
1. Add dap4 code: libdap4 and dap4_test.
Note that until the d4ts server problem is solved, dap4 is turned off.
2. Modify various files to support dap4 flags:
configure.ac, Makefile.am, CMakeLists.txt, etc.
3. Add nc_test/test_common.sh. This centralizes
the handling of the locations of various
things in the build tree: e.g. where is
ncgen.exe located. See nc_test/test_common.sh
for details.
4. Modify .sh files to use test_common.sh
5. Obsolete separate oc2 by moving it to be part of
netcdf-c. This means replacing code with netcdf-c
equivalents.
5. Add --with-testserver to configure.ac to allow
override of the servers to be used for --enable-dap-remote-tests.
6. There were multiple versions of nctypealignment code. Try to
centralize in libdispatch/doffset.c and include/ncoffsets.h
7. Add a unit test for the ncuri code because of its complexity.
8. Move the findserver code out of libdispatch and into
a separate, self contained program in ncdap_test and dap4_test.
9. Move the dispatch header files (nc{3,4}dispatch.h) to
.../include because they are now shared by modules.
10. Revamp the handling of TOPSRCDIR and TOPBUILDDIR for shell scripts.
11. Make use of MREMAP if available
12. Misc. minor changes e.g.
- #include <config.h> -> #include "config.h"
- Add some no-install headers to /include
- extern -> EXTERNL and vice versa as needed
- misc header cleanup
- clean up checking for misc. unix vs microsoft functions
13. Change copyright decls in some files to point to LICENSE file.
14. Add notes to RELEASENOTES.md
615 lines
17 KiB
C
615 lines
17 KiB
C
#include <config.h>
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#include <stdio.h>
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#include <stdlib.h>
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#ifdef HAVE_UNISTD_H
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#include <unistd.h> /* for sysconf */
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#endif
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#ifdef HAVE_SYS_TYPES_H
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#include <sys/types.h>
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#endif
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#ifdef HAVE_SYS_TIMES_H
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# include <sys/times.h>
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#endif
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#ifdef HAVE_SYS_TIME_H
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#include <sys/time.h>
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#endif
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#include <assert.h>
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#ifdef HAVE_SYS_RESOURCE_H
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# include <sys/resource.h>
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#endif
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#include "nc_tests.h" /* The ERR macro is here... */
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#include "netcdf.h"
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#define FILENAME "tst_chunks3.nc"
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/*
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* The following timing macros can be used by including the necessary
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* declarations with
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*
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* TIMING_DECLS(seconds)
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*
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* and surrounding sections of code to be timed with the "statements"
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*
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* TIMING_START
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* [code to be timed goes here]
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* TIMING_END(seconds)
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*
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* The macros assume the user has stored a description of what is
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* being timed in a 100-char string time_mess, and has included
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* <sys/times.h> and <sys/resource.h>. The timing message printed by
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* TIMING_END is not terminated by a new-line, to permit appending
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* additional text to that line, so user must at least printf("\n")
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* after that.
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*/
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#define TIMING_DECLS(seconds) \
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long TMreps; /* counts repetitions of timed code */ \
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long TMrepeats; /* repetitions needed to exceed 0.1 second */ \
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long emic ; /* elapsed time in microseconds */ \
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struct rusage ru; \
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long inb, oub; \
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char time_mess[100]; \
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float seconds;
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#define TIMING_START \
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TMrepeats = 1; \
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do { \
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if(getrusage(RUSAGE_SELF, &ru)) { \
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printf("getrusage failed, returned %d\n", errno);} \
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emic = (1000000*(ru.ru_utime.tv_sec + ru.ru_stime.tv_sec) \
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+ ru.ru_utime.tv_usec + ru.ru_stime.tv_usec); \
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inb = ru.ru_inblock; \
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oub = ru.ru_oublock; \
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for(TMreps=0; TMreps < TMrepeats; TMreps++) {
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#define TIMING_END(seconds) \
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} \
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if(getrusage(RUSAGE_SELF, &ru)) { \
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printf("getrusage failed, returned %d\n", errno);} \
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emic = (1000000*(ru.ru_utime.tv_sec + ru.ru_stime.tv_sec) \
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+ ru.ru_utime.tv_usec + ru.ru_stime.tv_usec) - emic; \
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inb = ru.ru_inblock - inb; \
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oub = ru.ru_oublock - oub; \
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TMrepeats *= 2; \
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} while (emic < 100000.0 ); \
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seconds = emic / (1000000.0 * TMreps); \
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printf("%-45.45s %7.2g sec", \
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time_mess, seconds);
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/* This macro prints an error message with line number and name of
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* test program. */
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#define ERR1(n) do { \
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fflush(stdout); /* Make sure our stdout is synced with stderr. */ \
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fprintf(stderr, "Sorry! Unexpected result, %s, line: %d - %s\n", \
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__FILE__, __LINE__, nc_strerror(n)); \
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return n; \
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} while (0)
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#define NC_COMPRESSED 1
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void
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parse_args(int argc, char *argv[], /* from command-line invocation */
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int *deflate_levelp, /* returned: 0 uncompressed,
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1-9 compression level */
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int *shufflep, /* returned: 1 if shuffle, otherwise 0 */
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size_t *dims, /* returned: dimension sizes */
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size_t *chunks, /* returned: chunk sizes */
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size_t *cache_sizep, /* returned: cache size (bytes) */
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size_t *cache_nelemsp, /* returned: cache capacity (chunks) */
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float *cache_prep) /* returned: cache preemption policy (0-1) */
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{
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if(argc > 1) {
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*deflate_levelp = atol(argv[1]);
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if (*deflate_levelp < 0) {
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*deflate_levelp = -*deflate_levelp;
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*shufflep = NC_SHUFFLE;
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}
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}
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if(argc > 2)
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dims[0] = atol(argv[2]);
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if(argc > 3)
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chunks[0] = atol(argv[3]);
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else
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chunks[0] = (dims[0]+7)/8;
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if(argc > 4)
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dims[1] = atol(argv[4]);
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else
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dims[1] = dims[0];
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if(argc > 5)
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chunks[1] = atol(argv[5]);
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else
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chunks[1] = chunks[0];
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if(argc > 6)
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dims[2] = atol(argv[6]);
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else
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dims[2] = dims[1];
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if(argc > 7)
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chunks[2] = atol(argv[7]);
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else
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chunks[2] = chunks[1];
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if(argc > 8)
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*cache_sizep = atol(argv[8]);
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if(argc > 9)
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*cache_nelemsp = atol(argv[9]);
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if(argc > 10)
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*cache_prep = atof(argv[10]);
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if(argc > 11) {
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printf("Usage: %s [def_level] [dim1] [chunk1] [dim2] [chunk2] [dim3] [chunk3] [cache_size] [cache_nelems] [cache_pre]\n",
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argv[0]);
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exit(1);
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}
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return;
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}
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void *
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emalloc(size_t bytes) {
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size_t *memory;
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memory = malloc(bytes);
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if(memory == 0) {
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printf("malloc failed\n");
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exit(2);
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}
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return memory;
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}
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/* compare contiguous, chunked, and compressed performance */
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int
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main(int argc, char *argv[]) {
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int stat; /* return status */
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int ncid; /* netCDF id */
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int i, j, k;
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int dim1id, dim2id, dim3id;
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int varid_g; /* varid for contiguous */
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int varid_k; /* varid for chunked */
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int varid_x; /* varid for compressed */
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float *varxy, *varxz, *varyz; /* 2D memory slabs used for I/O */
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int mm;
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size_t dims[] = {256, 256, 256}; /* default dim lengths */
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size_t chunks[] = {32, 32, 32}; /* default chunk sizes */
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size_t start[3], count[3];
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float contig_time, chunked_time, compressed_time, ratio;
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int deflate_level = 1; /* default compression level, 9 is
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* better and slower. If negative,
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* turn on shuffle filter also. */
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int shuffle = NC_NOSHUFFLE;
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size_t cache_size_def;
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size_t cache_hash_def;
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float cache_pre_def;
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size_t cache_size = 0; /* use library default */
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size_t cache_hash = 0; /* use library default */
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float cache_pre = -1.0f; /* use library default */
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/* rank (number of dimensions) for each variable */
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# define RANK_var1 3
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/* variable shapes */
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int var_dims[RANK_var1];
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TIMING_DECLS(TMsec) ;
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/* From args, get parameters for timing, including variable and
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chunk sizes. Negative deflate level means also use shuffle
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filter. */
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parse_args(argc, argv, &deflate_level, &shuffle, dims,
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chunks, &cache_size, &cache_hash, &cache_pre);
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/* get cache defaults, then set cache parameters that are not default */
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if((stat = nc_get_chunk_cache(&cache_size_def, &cache_hash_def,
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&cache_pre_def)))
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ERR1(stat);
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if(cache_size == 0)
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cache_size = cache_size_def;
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if(cache_hash == 0)
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cache_hash = cache_hash_def;
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if(cache_pre == -1.0f)
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cache_pre = cache_pre_def;
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if((stat = nc_set_chunk_cache(cache_size, cache_hash, cache_pre)))
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ERR1(stat);
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printf("cache: %3.2f MBytes %ld objs %3.2f preempt, ",
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cache_size/1.e6, cache_hash, cache_pre);
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if(deflate_level == 0) {
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printf("uncompressed ");
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} else {
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printf("compression level %d", deflate_level);
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}
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if(shuffle == 1) {
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printf(", shuffled");
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}
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printf("\n\n");
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/* initialize 2D slabs for writing along each axis with phony data */
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varyz = (float *) emalloc(sizeof(float) * 1 * dims[1] * dims[2]);
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varxz = (float *) emalloc(sizeof(float) * dims[0] * 1 * dims[2]);
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varxy = (float *) emalloc(sizeof(float) * dims[0] * dims[1] * 1);
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mm = 0;
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for(j = 0; j < dims[1]; j++) {
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for(k = 0; k < dims[2]; k++) {
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varyz[mm++] = k + dims[2]*j;
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}
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}
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mm = 0;
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for(i = 0; i < dims[0]; i++) {
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for(k = 0; k < dims[2]; k++) {
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varxz[mm++] = k + dims[2]*i;
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}
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}
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mm = 0;
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for(i = 0; i < dims[0]; i++) {
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for(j = 0; j < dims[1]; j++) {
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varxy[mm++] = j + dims[1]*i;
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}
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}
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if((stat = nc_create(FILENAME, NC_NETCDF4 | NC_CLASSIC_MODEL, &ncid)))
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ERR1(stat);
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/* define dimensions */
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if((stat = nc_def_dim(ncid, "dim1", dims[0], &dim1id)))
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ERR1(stat);
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if((stat = nc_def_dim(ncid, "dim2", dims[1], &dim2id)))
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ERR1(stat);
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if((stat = nc_def_dim(ncid, "dim3", dims[2], &dim3id)))
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ERR1(stat);
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/* define variables */
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var_dims[0] = dim1id;
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var_dims[1] = dim2id;
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var_dims[2] = dim3id;
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if((stat = nc_def_var(ncid, "var_contiguous", NC_FLOAT, RANK_var1,
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var_dims, &varid_g)))
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ERR1(stat);
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if((stat = nc_def_var(ncid, "var_chunked", NC_FLOAT, RANK_var1,
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var_dims, &varid_k)))
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ERR1(stat);
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if((stat = nc_def_var(ncid, "var_compressed", NC_FLOAT, RANK_var1,
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var_dims, &varid_x)))
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ERR1(stat);
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if((stat = nc_def_var_chunking(ncid, varid_g, NC_CONTIGUOUS, 0)))
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ERR1(stat);
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if((stat = nc_def_var_chunking(ncid, varid_k, NC_CHUNKED, chunks)))
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ERR1(stat);
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if((stat = nc_def_var_chunking(ncid, varid_x, NC_CHUNKED, chunks)))
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ERR1(stat);
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if (deflate_level != 0) {
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if((stat = nc_def_var_deflate(ncid, varid_x, shuffle,
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NC_COMPRESSED, deflate_level)))
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ERR1(stat);
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}
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/* leave define mode */
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if((stat = nc_enddef (ncid)))
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ERR1(stat);
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/* write each variable one yz slab at a time */
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start[0] = 0;
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start[1] = 0;
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start[2] = 0;
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count[0] = 1;
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count[1] = dims[1];
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count[2] = dims[2];
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sprintf(time_mess," contiguous write %3ld %3ld %3ld",
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1, dims[1], dims[2]);
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TIMING_START ;
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for(i = 0; i < dims[0]; i++) {
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start[0] = i;
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if((stat = nc_put_vara(ncid, varid_g, start, count, &varyz[0])))
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ERR1(stat);
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}
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TIMING_END(TMsec) ;
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printf("\n");
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contig_time = TMsec;
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sprintf(time_mess," chunked write %3ld %3ld %3ld %3ld %3ld %3ld",
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1, dims[1], dims[2], chunks[0], chunks[1], chunks[2]);
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TIMING_START ;
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for(i = 0; i < dims[0]; i++) {
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start[0] = i;
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if((stat = nc_put_vara(ncid, varid_k, start, count, &varyz[0])))
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ERR1(stat);
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}
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TIMING_END(TMsec) ;
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chunked_time = TMsec;
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ratio = contig_time/chunked_time;
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if(ratio >= 1.0)
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printf(" %5.2g x faster\n", ratio);
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else
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printf(" %5.2g x slower\n", 1.0/ratio);
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sprintf(time_mess," compressed write %3ld %3ld %3ld %3ld %3ld %3ld",
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1, dims[1], dims[2], chunks[0], chunks[1], chunks[2]);
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TIMING_START ;
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for(i = 0; i < dims[0]; i++) {
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start[0] = i;
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if((stat = nc_put_vara(ncid, varid_x, start, count, &varyz[0])))
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ERR1(stat);
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}
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TIMING_END(TMsec) ;
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compressed_time = TMsec;
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ratio = contig_time/compressed_time;
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if(ratio >= 1.0)
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printf(" %5.2g x faster\n", ratio);
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else
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printf(" %5.2g x slower\n", 1.0/ratio);
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printf("\n");
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/* write each variable one xz slab at a time */
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start[0] = 0;
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start[1] = 0;
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start[2] = 0;
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count[0] = dims[0];
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count[1] = 1;
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count[2] = dims[2];
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sprintf(time_mess," contiguous write %3ld %3ld %3ld",
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dims[0], 1, dims[2]);
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TIMING_START ;
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for(i = 0; i < dims[1]; i++) {
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start[1] = i;
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if((stat = nc_put_vara(ncid, varid_g, start, count, &varxz[0])))
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ERR1(stat);
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}
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TIMING_END(TMsec) ;
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printf("\n");
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contig_time = TMsec;
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sprintf(time_mess," chunked write %3ld %3ld %3ld %3ld %3ld %3ld",
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dims[0], 1, dims[2], chunks[0], chunks[1], chunks[2]);
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TIMING_START ;
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for(i = 0; i < dims[1]; i++) {
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start[1] = i;
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if((stat = nc_put_vara(ncid, varid_k, start, count, &varxz[0])))
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ERR1(stat);
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}
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TIMING_END(TMsec) ;
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chunked_time = TMsec;
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ratio = contig_time/chunked_time;
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if(ratio >= 1.0)
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printf(" %5.2g x faster\n", ratio);
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else
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printf(" %5.2g x slower\n", 1.0/ratio);
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sprintf(time_mess," compressed write %3ld %3ld %3ld %3ld %3ld %3ld",
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dims[0], 1, dims[2], chunks[0], chunks[1], chunks[2]);
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TIMING_START ;
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for(i = 0; i < dims[1]; i++) {
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start[1] = i;
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if((stat = nc_put_vara(ncid, varid_x, start, count, &varxz[0])))
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ERR1(stat);
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}
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TIMING_END(TMsec) ;
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compressed_time = TMsec;
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ratio = contig_time/compressed_time;
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if(ratio >= 1.0)
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printf(" %5.2g x faster\n", ratio);
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else
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printf(" %5.2g x slower\n", 1.0/ratio);
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printf("\n");
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/* write each variable one xy slab at a time */
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start[0] = 0;
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start[1] = 0;
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start[2] = 0;
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count[0] = dims[0];
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count[1] = dims[1];
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count[2] = 1;
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sprintf(time_mess," contiguous write %3ld %3ld %3ld",
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dims[0], dims[1], 1);
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TIMING_START ;
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for(i = 0; i < dims[2]; i++) {
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start[2] = i;
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if((stat = nc_put_vara(ncid, varid_g, start, count, &varxy[0])))
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ERR1(stat);
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}
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TIMING_END(TMsec) ;
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printf("\n");
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contig_time = TMsec;
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sprintf(time_mess," chunked write %3ld %3ld %3ld %3ld %3ld %3ld",
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dims[0], dims[1], 1, chunks[0], chunks[1], chunks[2]);
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TIMING_START ;
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for(i = 0; i < dims[2]; i++) {
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start[2] = i;
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if((stat = nc_put_vara(ncid, varid_k, start, count, &varxy[0])))
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ERR1(stat);
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}
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TIMING_END(TMsec) ;
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chunked_time = TMsec;
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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 %3ld %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 %3ld %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 %3ld %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 %3ld %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 %3ld %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 %3ld %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 %3ld %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 %3ld",
|
|
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 %3ld %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 %3ld %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);
|
|
|
|
return 0;
|
|
}
|