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https://github.com/Unidata/netcdf-c.git
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improved program nc_perf/tst_gfs_data_1.c
This commit is contained in:
Edward Hartnett
parent
025fb7b6fe
commit
a71e777c56
@ -13,38 +13,54 @@
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Ed Hartnett, 6/28/20
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*/
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#include <config.h>
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#include <nc_tests.h>
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#include <time.h>
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#include <sys/time.h> /* Extra high precision time info. */
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#include "err_macros.h"
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#include <mpi.h>
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#include <stdio.h>
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#include <string.h>
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#include <math.h>
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#include <netcdf.h>
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#include <netcdf_par.h>
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#include <netcdf_meta.h>
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#define FILE_NAME "tst_gfs_data_1.nc"
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#define TEST_NAME "tst_gfs_data_1"
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#define NUM_META_VARS 7
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#define NUM_META_TRIES 2
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#define NDIM2 2
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#define NDIM4 4
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#define NDIM5 5
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#define NUM_PROC 4
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#define NUM_SHUFFLE_SETTINGS 2
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#ifdef HAVE_H5Z_SZIP
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#define NUM_COMPRESSION_FILTERS 2
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#else
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#define NUM_COMPRESSION_FILTERS 1
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#endif
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#define NUM_SHUFFLE_SETTINGS 1
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/* #define NUM_DEFLATE_LEVELS 3 */
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#define NUM_DEFLATE_LEVELS 3
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#define NUM_UNLIM_TRIES 1
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#define THOUSAND 1000
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#define NUM_DATA_VARS 10
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#define NUM_DATA_VARS 3
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#define ERR_AWFUL 1
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/* #define USE_SMALL 1 */
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#ifdef USE_SMALL
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#define GRID_XT_LEN 8
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#define GRID_YT_LEN 4
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#define PFULL_LEN 4
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#define PHALF_LEN 5
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#else
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#define GRID_XT_LEN 3072
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#define GRID_YT_LEN 1536
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#define PFULL_LEN 127
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#define PHALF_LEN 128
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#endif /* USE_SMALL */
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#define TIME_LEN 1
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#define MAX_COMPRESSION_FILTERS 4
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char compression_filter_name[MAX_COMPRESSION_FILTERS][NC_MAX_NAME + 1];
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int deflate_level[MAX_COMPRESSION_FILTERS][NUM_DEFLATE_LEVELS];
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char dim_name[NDIM5][NC_MAX_NAME + 1] = {"grid_xt", "grid_yt", "pfull",
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"phalf", "time"};
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char var_name[NUM_META_VARS][NC_MAX_NAME + 1] = {"grid_xt", "lon", "grid_yt",
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@ -171,7 +187,6 @@ write_meta(int ncid, int *data_varid, int s, int f, int deflate, int u,
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int varid[NUM_META_VARS];
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double value_time = 2.0;
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int dv;
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int res;
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/* Turn off fill mode. */
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if (nc_set_fill(ncid, NC_NOFILL, NULL)) ERR;
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@ -275,21 +290,15 @@ write_meta(int ncid, int *data_varid, int s, int f, int deflate, int u,
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if (nc_def_var(ncid, data_var_name, NC_FLOAT, NDIM4, dimid_data, &data_varid[dv])) ERR;
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/* Setting any filter only will work for HDF5-1.10.3 and later */
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/* versions. */
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if (!f)
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res = nc_def_var_deflate(ncid, data_varid[dv], s, 1, deflate);
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else
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{
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res = nc_def_var_deflate(ncid, data_varid[dv], s, 0, 0);
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if (!res)
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res = nc_def_var_szip(ncid, data_varid[dv], 32, 32);
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}
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#ifdef HDF5_SUPPORTS_PAR_FILTERS
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if (res) ERR;
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#else
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if (res != NC_EINVAL) ERR;
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#endif
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/* versions. Do nothing for "none". */
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if (!strcmp(compression_filter_name[f], "zlib"))
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if (nc_def_var_deflate(ncid, data_varid[dv], s, 1, deflate)) ERR;
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#if NC_HAS_SZIP_WRITE
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if (!strcmp(compression_filter_name[f], "szip"))
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if (nc_def_var_szip(ncid, data_varid[dv], 32, 32)) ERR;
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#endif /* NC_HAS_SZIP_WRITE */
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if (nc_var_par_access(ncid, data_varid[dv], NC_COLLECTIVE)) ERR;
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if (nc_enddef(ncid)) ERR;
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}
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@ -356,9 +365,8 @@ decomp_latlon(int my_rank, int mpi_size, int *dim_len, size_t *latlon_start,
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latlon_start[1] = dim_len[1]/2;
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}
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}
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else if (mpi_size == 36)
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{
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}
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else
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return ERR_AWFUL;
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/* Allocate storage. */
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if (!(*lon = malloc(latlon_count[0] * latlon_count[1] * sizeof(double)))) ERR;
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@ -374,8 +382,8 @@ decomp_latlon(int my_rank, int mpi_size, int *dim_len, size_t *latlon_start,
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}
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}
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printf("%d: latlon_start %ld %ld latlon_count %ld %ld\n", my_rank, latlon_start[0],
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latlon_start[1], latlon_count[0], latlon_count[1]);
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/* printf("%d: latlon_start %ld %ld latlon_count %ld %ld\n", my_rank, latlon_start[0], */
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/* latlon_start[1], latlon_count[0], latlon_count[1]); */
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return 0;
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}
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@ -385,9 +393,11 @@ decomp_latlon(int my_rank, int mpi_size, int *dim_len, size_t *latlon_start,
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int
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decomp_4D(int my_rank, int mpi_size, int *dim_len, size_t *start, size_t *count)
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{
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/* Time dimension. */
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start[0] = 0;
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count[0] = 1;
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/* Vertical dimension (pfull). */
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count[1] = dim_len[2];
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start[1] = 0;
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@ -395,36 +405,28 @@ decomp_4D(int my_rank, int mpi_size, int *dim_len, size_t *start, size_t *count)
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{
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start[2] = 0;
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start[3] = 0;
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count[2] = dim_len[2];
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count[3] = dim_len[3];
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count[2] = dim_len[1];
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count[3] = dim_len[0];
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}
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else if (mpi_size == 4)
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{
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if (my_rank == 0 || my_rank == 1)
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{
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start[2] = 0;
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start[3] = 0;
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}
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else
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{
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start[2] = 768;
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start[3] = 768;
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}
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#ifdef USE_SMALL
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start[2] = (my_rank < 2) ? 0 : 2;
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start[3] = (!my_rank || my_rank == 2) ? 0 : 4;
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count[2] = 2;
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count[3] = 4;
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#else
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start[2] = (my_rank < 2) ? 0 : 768;
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start[3] = (!my_rank || my_rank == 2) ? 0 : 1536;
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count[2] = 768;
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count[3] = 1536;
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}
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else if (mpi_size == 36)
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{
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start[2] = my_rank * 256;
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start[3] = my_rank * 512;
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count[2] = 256;
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count[3] = 512;
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#endif /* USE_SMALL */
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}
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else
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return ERR_AWFUL;
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printf("%d: start %ld %ld %ld %ld count %ld %ld %ld %ld\n", my_rank, start[0],
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start[1], start[2], start[3], count[0], count[1], count[2], count[3]);
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/* printf("%d: start %ld %ld %ld %ld count %ld %ld %ld %ld\n", my_rank, start[0], */
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/* start[1], start[2], start[3], count[0], count[1], count[2], count[3]); */
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return 0;
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}
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@ -495,6 +497,34 @@ decomp_p(int my_rank, int mpi_size, size_t *data_count, int *dim_len,
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return 0;
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}
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/* Determine what compression filters are present. */
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int
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find_filters(int *num_compression_filters, char compression_filter_name[][NC_MAX_NAME + 1],
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int deflate_level[][NUM_DEFLATE_LEVELS])
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{
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int nfilters = 0;
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/* Try with no compression. */
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strcpy(compression_filter_name[nfilters], "none");
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nfilters++;
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/* zlib is always present. */
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strcpy(compression_filter_name[nfilters], "zlib");
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deflate_level[nfilters][0] = 1;
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deflate_level[nfilters][1] = 4;
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deflate_level[nfilters][2] = 9;
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nfilters++;
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/* szip is optionally present. */
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#if NC_HAS_SZIP_WRITE
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strcpy(compression_filter_name[nfilters], "szip");
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nfilters++;
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#endif /* NC_HAS_SZIP_WRITE */
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*num_compression_filters = nfilters;
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return 0;
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}
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int
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main(int argc, char **argv)
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{
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@ -524,16 +554,23 @@ main(int argc, char **argv)
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double *lon = NULL;
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double *lat = NULL;
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float *value_data;
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int deflate_level[NUM_DEFLATE_LEVELS] = {1, 4, 9};
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/* Compression filter info. */
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int num_compression_filters;
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int f, s, u;
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int i, j, k, dv, dl;
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int ret;
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/* Initialize MPI. */
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MPI_Init(&argc, &argv);
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MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
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MPI_Comm_rank(MPI_COMM_WORLD, &my_rank);
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/* Determine what compression filters are present. */
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if ((ret = find_filters(&num_compression_filters, compression_filter_name, deflate_level)))
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return ret;
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/* Determine 4D data decomposition to write data vars. */
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if (decomp_4D(my_rank, mpi_size, dim_len, data_start, data_count)) ERR;
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@ -548,42 +585,60 @@ main(int argc, char **argv)
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/* Decompose phalf and pfull. */
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if (decomp_p(my_rank, mpi_size, data_count, dim_len, &phalf_start,
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&phalf_size, &phalf, &pfull_start, &pfull_size, &pfull)) ERR;
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/* printf("%d: data_count[3] %ld data_count[2] %ld data_count[1] %ld\n", my_rank, */
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/* data_count[3], data_count[2], data_count[1]); */
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/* Allocate space to hold the data. */
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if (!(value_data = malloc(data_count[3] * data_count[2] * data_count[1] *
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sizeof(float)))) ERR;
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/* Create some data. */
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size_t cnt = 0;
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for (k = 0; k < data_count[1]; k++)
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{
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for (j = 0; j < data_count[2]; j++)
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{
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for(i = 0; i < data_count[3]; i++)
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value_data[j * data_count[3] + i] = my_rank * 100 + i + j + k;
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{
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value_data[cnt] = my_rank * 1000 + cnt / sqrt(my_rank + cnt + 1);
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/* printf("%d: value_data[%ld] %g\n", my_rank, cnt, value_data[cnt]); */
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cnt++;
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}
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}
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}
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if (my_rank == 0)
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{
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printf("Benchmarking creation of UFS file.\n");
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printf("Benchmarking creation of file similar to one produced by the UFS.\n");
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printf("unlim, comp, level, shuffle, meta wr time (s), data wr rate (MB/s), "
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"file size (MB)\n");
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}
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for (u = 0; u < NUM_UNLIM_TRIES; u++)
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{
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for (f = 0; f < NUM_COMPRESSION_FILTERS; f++)
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for (f = 0; f < num_compression_filters; f++)
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{
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for (s = 0; s < NUM_SHUFFLE_SETTINGS; s++)
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{
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for (dl = 0; dl < NUM_DEFLATE_LEVELS; dl++)
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{
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size_t file_size;
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char file_name[NC_MAX_NAME * 3 + 1];
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/* No deflate levels for szip. */
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if (f && dl) continue;
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/* No deflate levels for szip or none. */
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if (!strcmp(compression_filter_name[f], "szip") && dl) continue;
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if (!strcmp(compression_filter_name[f], "none") && dl) continue;
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/* Use the same filename every time, so we don't
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* create many large files, just one. ;-) */
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sprintf(file_name, "%s.nc", TEST_NAME);
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/* nc_set_log_level(3); */
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/* Create a parallel netcdf-4 file. */
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meta_start_time = MPI_Wtime();
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if (nc_create_par(FILE_NAME, NC_NETCDF4, comm, info,
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if (nc_create_par(file_name, NC_NETCDF4, comm, info,
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&ncid)) ERR;
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if (write_meta(ncid, data_varid, s, f, deflate_level[dl], u,
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if (write_meta(ncid, data_varid, s, f, deflate_level[f][dl], u,
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phalf_size, phalf_start, phalf,
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data_start, data_count, pfull_start, pfull_size, pfull, grid_xt_start,
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grid_xt_size, grid_xt, grid_yt_start,
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@ -598,8 +653,11 @@ main(int argc, char **argv)
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/* Write one record each of the data variables. */
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for (dv = 0; dv < NUM_DATA_VARS; dv++)
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{
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if (nc_put_vara_float(ncid, data_varid[dv], data_start,
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data_count, value_data)) ERR;
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/* printf("%d: data_start %ld %ld %ld %ld data_count %ld %ld %ld %ld\n", my_rank, data_start[0], data_start[1], */
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/* data_start[2], data_start[3], data_count[0], data_count[1], data_count[2], data_count[3]); */
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/* MPI_Barrier(MPI_COMM_WORLD); */
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if (nc_put_vara_float(ncid, data_varid[dv], data_start, data_count,
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value_data)) ERR;
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if (nc_redef(ncid)) ERR;
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}
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@ -611,28 +669,29 @@ main(int argc, char **argv)
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data_stop_time = MPI_Wtime();
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/* Get the file size. */
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if (get_file_size(FILE_NAME, &file_size)) ERR;
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if (get_file_size(file_name, &file_size)) ERR;
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/* Check the file metadata for correctness. */
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if (nc_open_par(FILE_NAME, NC_NOWRITE, comm, info, &ncid)) ERR;
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if (check_meta(ncid, data_varid, s, f, deflate_level[dl], u,
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phalf_size, phalf_start, phalf,
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data_start, data_count, pfull_start, pfull_size,
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pfull, grid_xt_start, grid_xt_size, grid_xt,
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grid_yt_start, grid_yt_size, grid_yt, latlon_start,
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latlon_count, lat, lon, my_rank)) ERR;
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if (nc_open_par(file_name, NC_NOWRITE, comm, info, &ncid)) ERR;
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if (check_meta(ncid, data_varid, s, f, deflate_level[f][dl], u,
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phalf_size, phalf_start, phalf,
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data_start, data_count, pfull_start, pfull_size,
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pfull, grid_xt_start, grid_xt_size, grid_xt,
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grid_yt_start, grid_yt_size, grid_yt, latlon_start,
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latlon_count, lat, lon, my_rank)) ERR;
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if (nc_close(ncid)) ERR;
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/* Print out results. */
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if (my_rank == 0)
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{
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float data_size, data_rate;
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data_size = NUM_DATA_VARS * dim_len[0] * dim_len[1] *
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dim_len[3] * sizeof(float)/1000000;
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data_size = (NUM_DATA_VARS * dim_len[0] * dim_len[1] * dim_len[2] *
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dim_len[4] * sizeof(float))/MILLION;
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/* printf("data_size %f (data_stop_time - data_start_time) %g\n", data_size, (data_stop_time - data_start_time)); */
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data_rate = data_size / (data_stop_time - data_start_time);
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printf("%d %s, %d, %d, %g, %g, %g\n", u, (f ? "szip" : "zlib"),
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deflate_level[dl], s, meta_stop_time - meta_start_time,
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data_rate, (float)file_size/1000000);
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printf("%d, %s, %d, %d, %g, %g, %g\n", u, compression_filter_name[f],
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deflate_level[f][dl], s, meta_stop_time - meta_start_time,
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data_rate, (float)file_size/MILLION);
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}
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MPI_Barrier(MPI_COMM_WORLD);
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} /* next deflate level */
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