mirror of
https://github.com/Unidata/netcdf-c.git
synced 2024-11-27 07:30:33 +08:00
getting tst_gfs_data_1 ready to merge
This commit is contained in:
Edward Hartnett
parent
94c285afed
commit
98088adb46
@ -34,6 +34,7 @@
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#define NUM_COMPRESSION_FILTERS 1
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#endif
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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 ERR_AWFUL 1
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@ -72,10 +73,10 @@ get_file_size(char *filename, size_t *file_size)
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/* Check all the metadata, including coordinate variable data. */
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int
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check_meta(int ncid, int *data_varid, int s, int f, int deflate,
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check_meta(int ncid, int *data_varid, int s, int f, int deflate, int u,
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size_t phalf_size, size_t phalf_start, float *phalf, size_t *data_start,
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size_t *data_count, float *pfull, size_t grid_xt_start,
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size_t grid_xt_size, double *grid_xt, size_t grid_yt_start,
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size_t *data_count, size_t pfull_start, size_t pfull_size, float *pfull,
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size_t grid_xt_start, size_t grid_xt_size, double *grid_xt, size_t grid_yt_start,
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size_t grid_yt_size, double *grid_yt, size_t *latlon_start,
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size_t *latlon_count, double *lat, double *lon, int my_rank)
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{
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@ -93,7 +94,8 @@ check_meta(int ncid, int *data_varid, int s, int f, int deflate,
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/* Check number of dims, vars, atts. */
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if (nc_inq(ncid, &ndims, &nvars, &natts, &unlimdimid)) ERR;
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if (ndims != NDIM5 || nvars != NUM_META_VARS + NUM_DATA_VARS ||
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natts != 0 || unlimdimid != 4) ERR;
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natts != 0) ERR;
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if (unlimdimid != (u ? 4 : -1)) ERR;
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/* Check the dimensions. */
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for (d = 0; d < NDIM5; d++)
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@ -139,9 +141,9 @@ check_meta(int ncid, int *data_varid, int s, int f, int deflate,
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free(lat_in);
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/* Check the values for pfull. */
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if (!(pfull_in = malloc(data_count[1] * sizeof(float)))) ERR;
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if (nc_get_vara_float(ncid, 4, &data_start[1], &data_count[1], pfull_in)) ERR;
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for (i = 0; i < data_count[1]; i++)
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if (!(pfull_in = malloc(pfull_size * sizeof(float)))) ERR;
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if (nc_get_vara_float(ncid, 4, &pfull_start, &pfull_size, pfull_in)) ERR;
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for (i = 0; i < pfull_size; i++)
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if (pfull_in[i] != pfull[i]) ERR;
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free(pfull_in);
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@ -157,10 +159,10 @@ check_meta(int ncid, int *data_varid, int s, int f, int deflate,
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/* Write all the metadata, including coordinate variable data. */
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int
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write_meta(int ncid, int *data_varid, int s, int f, int deflate,
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write_meta(int ncid, int *data_varid, int s, int f, int deflate, int u,
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size_t phalf_size, size_t phalf_start, float *phalf, size_t *data_start,
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size_t *data_count, float *pfull, size_t grid_xt_start,
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size_t grid_xt_size, double *grid_xt, size_t grid_yt_start,
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size_t *data_count, size_t pfull_start, size_t pfull_size, float *pfull,
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size_t grid_xt_start, size_t grid_xt_size, double *grid_xt, size_t grid_yt_start,
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size_t grid_yt_size, double *grid_yt, size_t *latlon_start,
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size_t *latlon_count, double *lat, double *lon, int my_rank)
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{
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@ -211,7 +213,7 @@ write_meta(int ncid, int *data_varid, int s, int f, int deflate,
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if (nc_def_var(ncid, var_name[4], var_type[4], 1, &dimid[2], &varid[4])) ERR;
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if (nc_var_par_access(ncid, varid[4], NC_INDEPENDENT)) ERR;
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if (nc_enddef(ncid)) ERR;
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if (nc_put_vara_float(ncid, varid[4], &data_start[1], &data_count[1], pfull)) ERR;
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if (nc_put_vara_float(ncid, varid[4], &pfull_start, &pfull_size, pfull)) ERR;
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if (nc_redef(ncid)) ERR;
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/* Define dimension phalf. This dim is only used by the phalf coord var. */
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@ -224,173 +226,9 @@ write_meta(int ncid, int *data_varid, int s, int f, int deflate,
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if (nc_put_vara_float(ncid, varid[5], &phalf_start, &phalf_size, phalf)) ERR;
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if (nc_redef(ncid)) ERR;
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/* Define dimension time, the unlimited dimension. */
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if (nc_def_dim(ncid, dim_name[4], NC_UNLIMITED, &dimid[4])) ERR;
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/* if (nc_def_dim(ncid, dim_name[4], 1, &dimid[4])) ERR; */
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/* Define variable time and write data. */
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if (nc_def_var(ncid, var_name[6], var_type[6], 1, &dimid[4], &varid[6])) ERR;
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if (nc_var_par_access(ncid, varid[6], NC_INDEPENDENT)) ERR;
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if (nc_enddef(ncid)) ERR;
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/* In NOAA code, do all processors write the single time value? */
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if (my_rank == 0)
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if (nc_put_var_double(ncid, varid[6], &value_time)) ERR;;
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if (nc_redef(ncid)) ERR;
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/* Write variable grid_xt data. */
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if (nc_enddef(ncid)) ERR;
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if (nc_put_vara_double(ncid, varid[0], &grid_xt_start, &grid_xt_size, grid_xt)) ERR;
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if (nc_redef(ncid)) ERR;
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/* Write lon data. */
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if (nc_enddef(ncid)) ERR;
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if (nc_put_vara_double(ncid, varid[1], latlon_start, latlon_count, lon)) ERR;
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if (nc_redef(ncid)) ERR;
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/* Write grid_yt data. */
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if (nc_enddef(ncid)) ERR;
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if (nc_put_vara_double(ncid, varid[2], &grid_yt_start, &grid_yt_size, grid_yt)) ERR;
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if (nc_redef(ncid)) ERR;
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/* Write lat data. */
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if (nc_enddef(ncid)) ERR;
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if (nc_put_vara_double(ncid, varid[3], latlon_start, latlon_count, lat)) ERR;
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/* Specify dimensions for our data vars. */
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dimid_data[0] = dimid[4];
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dimid_data[1] = dimid[2];
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dimid_data[2] = dimid[1];
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dimid_data[3] = dimid[0];
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/* Define data variables. */
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for (dv = 0; dv < NUM_DATA_VARS; dv++)
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{
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char data_var_name[NC_MAX_NAME + 1];
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sprintf(data_var_name, "var_%d", dv);
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if (nc_redef(ncid)) ERR;
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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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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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if (nc_redef(ncid)) ERR;
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if (nc_put_att_text(ncid, varid[0], "long_name", strlen("T-cell longitude"), "T-cell longitude")) ERR;
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if (nc_put_att_text(ncid, varid[0], "units", strlen("degrees_E"), "degrees_E")) ERR;
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if (nc_put_att_text(ncid, varid[2], "long_name", strlen("T-cell latiitude"), "T-cell latiitude")) ERR;
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if (nc_put_att_text(ncid, varid[2], "units", strlen("degrees_N"), "degrees_N")) ERR;
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if (nc_enddef(ncid)) ERR;
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if (nc_redef(ncid)) ERR;
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for (dv = 0; dv < NUM_DATA_VARS; dv++)
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{
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float compress_err = 42.22;
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int nbits = 5;
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if (nc_put_att_float(ncid, data_varid[dv], "max_abs_compression_error", NC_FLOAT, 1, &compress_err)) ERR;
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if (nc_put_att_int(ncid, data_varid[dv], "nbits", NC_INT, 1, &nbits)) ERR;
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}
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if (nc_enddef(ncid)) ERR;
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return 0;
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}
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/* Write all the metadata, including coordinate variable data. */
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int
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write_meta2(int ncid, int *data_varid, int s, int f, int deflate, size_t phalf_size, size_t phalf_start,
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float *phalf, size_t *data_start, size_t *data_count, float *pfull,
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size_t grid_xt_start, size_t grid_xt_size, double *grid_xt, size_t grid_yt_start,
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size_t grid_yt_size, double *grid_yt, size_t *latlon_start, size_t *latlon_count,
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double *lat, double *lon, int my_rank)
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{
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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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int dimid[NDIM5];
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int dimid_data[NDIM4];
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char var_name[NUM_META_VARS][NC_MAX_NAME + 1] = {"grid_xt", "lon", "grid_yt",
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"lat", "pfull", "phalf", "time"};
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int var_type[NUM_META_VARS] = {NC_DOUBLE, NC_DOUBLE, NC_DOUBLE, NC_DOUBLE,
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NC_FLOAT, NC_FLOAT, NC_DOUBLE};
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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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/* Define dimension grid_xt. */
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if (nc_def_dim(ncid, dim_name[0], dim_len[0], &dimid[0])) ERR;
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/* Define dimension grid_yt. */
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if (nc_def_dim(ncid, dim_name[1], dim_len[1], &dimid[1])) ERR;
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/* Define variable grid_xt. */
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if (nc_def_var(ncid, var_name[0], var_type[0], 1, &dimid[0], &varid[0])) ERR;
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if (nc_var_par_access(ncid, varid[0], NC_INDEPENDENT)) ERR;
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/* Define variable lon. */
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if (nc_def_var(ncid, var_name[1], var_type[1], 2, dimid, &varid[1])) ERR;
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if (nc_var_par_access(ncid, varid[1], NC_INDEPENDENT));
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if (nc_put_att_text(ncid, varid[1], "long_name", strlen("T-cell longitude"), "T-cell longitude")) ERR;
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if (nc_put_att_text(ncid, varid[1], "units", strlen("degrees_E"), "degrees_E")) ERR;
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if (nc_put_att_text(ncid, varid[0], "cartesian_axis", strlen("X"), "X")) ERR;
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/* Define variable grid_yt. */
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if (nc_def_var(ncid, var_name[2], var_type[2], 1, &dimid[1], &varid[2])) ERR;
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if (nc_var_par_access(ncid, varid[2], NC_INDEPENDENT)) ERR;
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/* Define variable lat. */
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if (nc_def_var(ncid, var_name[3], var_type[3], 2, dimid, &varid[3])) ERR;
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if (nc_var_par_access(ncid, varid[3], NC_INDEPENDENT)) ERR;
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if (nc_put_att_text(ncid, varid[3], "long_name", strlen("T-cell latitude"), "T-cell latitude")) ERR;
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if (nc_put_att_text(ncid, varid[3], "units", strlen("degrees_N"), "degrees_N")) ERR;
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if (nc_put_att_text(ncid, varid[2], "cartesian_axis", strlen("Y"), "Y")) ERR;
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/* Define dimension pfull. */
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if (nc_def_dim(ncid, dim_name[2], dim_len[2], &dimid[2])) ERR;
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/* Define variable pfull and write data. */
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if (nc_def_var(ncid, var_name[4], var_type[4], 1, &dimid[2], &varid[4])) ERR;
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if (nc_var_par_access(ncid, varid[4], NC_INDEPENDENT)) ERR;
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if (nc_enddef(ncid)) ERR;
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if (nc_put_vara_float(ncid, varid[4], &data_start[1], &data_count[1], pfull)) ERR;
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if (nc_redef(ncid)) ERR;
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/* Define dimension phalf. This dim is only used by the phalf coord var. */
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if (nc_def_dim(ncid, dim_name[3], dim_len[3], &dimid[3])) ERR;
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/* Define coord variable phalf and write data. */
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if (nc_def_var(ncid, var_name[5], var_type[5], 1, &dimid[3], &varid[5])) ERR;
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if (nc_var_par_access(ncid, varid[5], NC_INDEPENDENT)) ERR;
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if (nc_enddef(ncid)) ERR;
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if (nc_put_vara_float(ncid, varid[5], &phalf_start, &phalf_size, phalf)) ERR;
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if (nc_redef(ncid)) ERR;
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/* Define dimension time, the unlimited dimension. */
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if (nc_def_dim(ncid, dim_name[4], NC_UNLIMITED, &dimid[4])) ERR;
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/* if (nc_def_dim(ncid, dim_name[4], 1, &dimid[4])) ERR; */
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/* Define dimension time, sometimes the unlimited dimension,
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* sometimes a fixed dim of 1. */
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if (nc_def_dim(ncid, dim_name[4], (u ? NC_UNLIMITED : 1), &dimid[4])) ERR;
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/* Define variable time and write data. */
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if (nc_def_var(ncid, var_name[6], var_type[6], 1, &dimid[4], &varid[6])) ERR;
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@ -550,12 +388,9 @@ decomp_4D(int my_rank, int mpi_size, int *dim_len, size_t *start, size_t *count)
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start[0] = 0;
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count[0] = 1;
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count[1] = dim_len[2]/mpi_size;
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start[1] = my_rank * count[1];
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/* Add any extra to the end. */
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if (my_rank == mpi_size - 1)
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count[1] = count[1] + dim_len[2] % mpi_size;
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count[1] = dim_len[2];
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start[1] = 0;
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if (mpi_size == 1)
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{
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start[2] = 0;
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@ -628,9 +463,11 @@ decomp_grid(int my_rank, int mpi_size, int *dim_len, size_t *grid_xt_start, size
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return 0;
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}
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/* Decompose the pfull and phalf coordinate vars. */
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int
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decomp_p(int my_rank, int mpi_size, size_t *data_count, int *dim_len,
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size_t *phalf_start, size_t *phalf_size, float **phalf, float **pfull)
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size_t *phalf_start, size_t *phalf_size, float **phalf,
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size_t *pfull_start, size_t *pfull_size, float **pfull)
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{
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int i;
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@ -640,6 +477,11 @@ decomp_p(int my_rank, int mpi_size, size_t *data_count, int *dim_len,
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if (my_rank == mpi_size - 1)
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*phalf_size = *phalf_size + dim_len[3] % mpi_size;
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*pfull_size = dim_len[2]/mpi_size;
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*pfull_start = my_rank * *pfull_size;
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if (my_rank == mpi_size - 1)
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*pfull_size = *pfull_size + dim_len[2] % mpi_size;
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/* Allocate space on this pe to hold the coordinate var data for this pe. */
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if (!(*pfull = malloc(data_count[1] * sizeof(float)))) ERR;
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if (!(*phalf = malloc(*phalf_size * sizeof(float)))) ERR;
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@ -653,7 +495,6 @@ 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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int
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main(int argc, char **argv)
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{
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@ -672,6 +513,7 @@ main(int argc, char **argv)
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/* Variables. */
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int data_varid[NUM_DATA_VARS];
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size_t pfull_size, pfull_start;
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float *pfull = NULL;
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size_t phalf_size, phalf_start;
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float *phalf = NULL;
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@ -684,7 +526,7 @@ main(int argc, char **argv)
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float *value_data;
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int deflate_level[NUM_DEFLATE_LEVELS] = {1, 4, 9};
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int f, s, meta;
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int f, s, u;
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int i, j, k, dv, dl;
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/* Initialize MPI. */
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@ -705,7 +547,7 @@ 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)) ERR;
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&phalf_size, &phalf, &pfull_start, &pfull_size, &pfull)) ERR;
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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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@ -720,97 +562,83 @@ main(int argc, char **argv)
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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("meta, comp, level, shuffle, meta wr time (s), data wr rate (MB/s), "
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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 (meta = 0; meta < NUM_META_TRIES; meta++)
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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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{
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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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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++)
|
||||
{
|
||||
size_t file_size;
|
||||
|
||||
/* No deflate levels for szip. */
|
||||
if (f && dl) continue;
|
||||
/* No deflate levels for szip. */
|
||||
if (f && dl) continue;
|
||||
|
||||
/* nc_set_log_level(3); */
|
||||
/* Create a parallel netcdf-4 file. */
|
||||
meta_start_time = MPI_Wtime();
|
||||
if (nc_create_par(FILE_NAME, NC_NETCDF4, comm, info,
|
||||
/* nc_set_log_level(3); */
|
||||
/* Create a parallel netcdf-4 file. */
|
||||
meta_start_time = MPI_Wtime();
|
||||
if (nc_create_par(FILE_NAME, NC_NETCDF4, comm, info,
|
||||
&ncid)) ERR;
|
||||
|
||||
if (meta)
|
||||
{
|
||||
if (write_meta2(ncid, data_varid, s, f, deflate_level[dl],
|
||||
phalf_size, phalf_start, phalf,
|
||||
data_start, data_count, pfull, grid_xt_start,
|
||||
grid_xt_size, grid_xt, grid_yt_start,
|
||||
grid_yt_size, grid_yt, latlon_start,
|
||||
latlon_count, lat, lon, my_rank)) ERR;
|
||||
}
|
||||
else
|
||||
{
|
||||
if (write_meta(ncid, data_varid, s, f, deflate_level[dl],
|
||||
phalf_size, phalf_start, phalf,
|
||||
data_start, data_count, pfull, grid_xt_start,
|
||||
grid_xt_size, grid_xt, grid_yt_start,
|
||||
grid_yt_size, grid_yt, latlon_start,
|
||||
latlon_count, lat, lon, my_rank)) ERR;
|
||||
}
|
||||
|
||||
/* Stop the timer for metadata writes. */
|
||||
MPI_Barrier(MPI_COMM_WORLD);
|
||||
meta_stop_time = MPI_Wtime();
|
||||
data_start_time = MPI_Wtime();
|
||||
|
||||
/* Write one record each of the data variables. */
|
||||
for (dv = 0; dv < NUM_DATA_VARS; dv++)
|
||||
{
|
||||
if (nc_put_vara_float(ncid, data_varid[dv], data_start,
|
||||
data_count, value_data)) ERR;
|
||||
if (nc_redef(ncid)) ERR;
|
||||
}
|
||||
|
||||
/* Close the file. */
|
||||
if (nc_close(ncid)) ERR;
|
||||
|
||||
/* Stop the data timer. */
|
||||
MPI_Barrier(MPI_COMM_WORLD);
|
||||
data_stop_time = MPI_Wtime();
|
||||
|
||||
/* Get the file size. */
|
||||
if (get_file_size(FILE_NAME, &file_size)) ERR;
|
||||
|
||||
/* Check the file metadata for correctness. */
|
||||
if (nc_open_par(FILE_NAME, NC_NOWRITE, comm, info, &ncid)) ERR;
|
||||
if (check_meta(ncid, data_varid, s, f, deflate_level[dl],
|
||||
if (write_meta(ncid, data_varid, s, f, deflate_level[dl], u,
|
||||
phalf_size, phalf_start, phalf,
|
||||
data_start, data_count, pfull, grid_xt_start,
|
||||
data_start, data_count, pfull_start, pfull_size, pfull, grid_xt_start,
|
||||
grid_xt_size, grid_xt, grid_yt_start,
|
||||
grid_yt_size, grid_yt, latlon_start,
|
||||
latlon_count, lat, lon, my_rank)) ERR;
|
||||
if (nc_close(ncid)) ERR;
|
||||
|
||||
/* Print out results. */
|
||||
if (my_rank == 0)
|
||||
/* Stop the timer for metadata writes. */
|
||||
MPI_Barrier(MPI_COMM_WORLD);
|
||||
meta_stop_time = MPI_Wtime();
|
||||
data_start_time = MPI_Wtime();
|
||||
|
||||
/* Write one record each of the data variables. */
|
||||
for (dv = 0; dv < NUM_DATA_VARS; dv++)
|
||||
{
|
||||
if (nc_put_vara_float(ncid, data_varid[dv], data_start,
|
||||
data_count, value_data)) ERR;
|
||||
if (nc_redef(ncid)) ERR;
|
||||
}
|
||||
|
||||
/* Close the file. */
|
||||
if (nc_close(ncid)) ERR;
|
||||
|
||||
/* Stop the data timer. */
|
||||
MPI_Barrier(MPI_COMM_WORLD);
|
||||
data_stop_time = MPI_Wtime();
|
||||
|
||||
/* Get the file size. */
|
||||
if (get_file_size(FILE_NAME, &file_size)) ERR;
|
||||
|
||||
/* Check the file metadata for correctness. */
|
||||
if (nc_open_par(FILE_NAME, NC_NOWRITE, comm, info, &ncid)) ERR;
|
||||
if (check_meta(ncid, data_varid, s, f, deflate_level[dl], u,
|
||||
phalf_size, phalf_start, phalf,
|
||||
data_start, data_count, pfull_start, pfull_size,
|
||||
pfull, grid_xt_start, grid_xt_size, grid_xt,
|
||||
grid_yt_start, grid_yt_size, grid_yt, latlon_start,
|
||||
latlon_count, lat, lon, my_rank)) ERR;
|
||||
if (nc_close(ncid)) ERR;
|
||||
|
||||
/* Print out results. */
|
||||
if (my_rank == 0)
|
||||
{
|
||||
float data_size, data_rate;
|
||||
data_size = NUM_DATA_VARS * dim_len[0] * dim_len[1] *
|
||||
dim_len[3] * sizeof(float)/1000000;
|
||||
data_rate = data_size / (data_stop_time - data_start_time);
|
||||
printf("%d, %s, %d, %d, %g, %g, %g\n", meta,
|
||||
(f ? "szip" : "zlib"), deflate_level[dl], s,
|
||||
meta_stop_time - meta_start_time, data_rate,
|
||||
(float)file_size/1000000);
|
||||
printf("%d %s, %d, %d, %g, %g, %g\n", u, (f ? "szip" : "zlib"),
|
||||
deflate_level[dl], s, meta_stop_time - meta_start_time,
|
||||
data_rate, (float)file_size/1000000);
|
||||
}
|
||||
MPI_Barrier(MPI_COMM_WORLD);
|
||||
} /* next deflate level */
|
||||
} /* next shuffle filter test */
|
||||
} /* next compression filter (zlib and szip) */
|
||||
} /* next ed */
|
||||
MPI_Barrier(MPI_COMM_WORLD);
|
||||
} /* next deflate level */
|
||||
} /* next shuffle filter test */
|
||||
} /* next compression filter (zlib and szip) */
|
||||
} /* next unlim_try */
|
||||
|
||||
/* Free resources. */
|
||||
if (grid_xt)
|
||||
|
||||
Loading…
Reference in New Issue
Block a user