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9983b9d911
re pull request https://github.com/Unidata/netcdf-c/pull/405 re pull request https://github.com/Unidata/netcdf-c/pull/446 Notes: 1. This branch is a cleanup of the magic.dmh branch. 2. magic.dmh was originally merged, but caused problems with parallel IO. It was re-issued as pull request https://github.com/Unidata/netcdf-c/pull/446. 3. This branch + pull request replace any previous pull requests and magic.dmh branch. Given an otherwise valid netCDF file that has a corrupted header, the netcdf library currently crashes. Instead, it should return NC_ENOTNC. Additionally, the NC_check_file_type code does not do the forward search required by hdf5 files. It currently only looks at file position 0 instead of 512, 1024, 2048,... Also, it turns out that the HDF4 magic number is assumed to always be at the beginning of the file (unlike HDF5). The change is localized to libdispatch/dfile.c See https://support.hdfgroup.org/release4/doc/DSpec_html/DS.pdf Also, it turns out that the code in NC_check_file_type is duplicated (mostly) in the function libsrc4/nc4file.c#nc_check_for_hdf. This branch does the following. 1. Make NC_check_file_type return NC_ENOTNC instead of crashing. 2. Remove nc_check_for_hdf and centralize all file format checking NC_check_file_type. 3. Add proper forward search for HDF5 files (but not HDF4 files) to look for the magic number at offsets of 0, 512, 1024... 4. Add test tst_hdf5_offset.sh. This tests that hdf5 files with an offset are properly recognized. It does so by prefixing a legal file with some number of zero bytes: 512, 1024, etc. 5. Off-topic: Added -N flag to ncdump to force a specific output dataset name.
305 lines
9.4 KiB
C
305 lines
9.4 KiB
C
/*
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Copyright 2007, UCAR/Unidata
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See COPYRIGHT file for copying and redistribution conditions.
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This program creates a test file.
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$Id: tst_create_files.c,v 1.11 2008/01/09 16:30:23 ed Exp $
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*/
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#include <config.h>
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#include <nc_tests.h>
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#include "err_macros.h"
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#include <netcdf.h>
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#include <stdio.h>
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#include <string.h>
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#include "ncdispatch.h"
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#include <math.h>
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/* We will create this file. */
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#define FILE_NAME "tst_floats_1D.nc"
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int
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main(int argc, char **argv)
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{
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int nc_argc = argc;
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int nc_argv = argv;
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printf("\n*** Create some files for testing benchmarks.\n");
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#ifdef LARGE_FILE_TESTS
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printf("*** Creating very large 3D file...");
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{
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#define LARGE_VAR_NAME "Really_Large_Variable"
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#define LARGE_FILE "tst_large.nc"
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#define NDIMS3 3
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#define D0 400
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#define D1 2000
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#define D2 2000
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int ncid, dimids[NDIMS3], varid;
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size_t start[NDIMS3], count[NDIMS3];
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size_t dim_len[NDIMS3] = {D0, D1, D2};
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size_t chunk_sizes[NDIMS3] = {1, D1, D2};
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float *data;
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char file_name[NC_MAX_NAME * 2 + 1];
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int d, i;
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/* Initialize the data to random floats. */
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if (!(data = (float *)malloc(D1 * D2 * sizeof(float)))) ERR;
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for (i = 0; i < D1 * D2; i++)
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data[i] = (float)rand();
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/* User TEMP_LARGE as the directory. */
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if (strlen(TEMP_LARGE) + strlen(LARGE_FILE) > NC_MAX_NAME * 2) ERR;
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sprintf(file_name, "%s/%s", TEMP_LARGE, LARGE_FILE);
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/* Create file with 3 dims, one variable. */
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if (nc_create(file_name, NC_NETCDF4|NC_CLASSIC_MODEL, &ncid)) ERR;
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if (nc_def_dim(ncid, "d0", D0, &dimids[0])) ERR;
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if (nc_def_dim(ncid, "d1", D1, &dimids[1])) ERR;
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if (nc_def_dim(ncid, "d2", D2, &dimids[2])) ERR;
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if (nc_def_var(ncid, LARGE_VAR_NAME, NC_FLOAT, NDIMS3, dimids, &varid)) ERR;
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#ifndef NOBUG
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{int status;
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status = nc_def_var_chunking(ncid, varid, NC_CHUNKED, chunk_sizes);
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if(status)
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printf("nc_def_var_chunking fail: %d: %s\n",status,nc_strerror(status));
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}
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#else
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if (nc_def_var_chunking(ncid, varid, NC_CHUNKED, chunk_sizes)) ERR;
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#endif
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if (nc_enddef(ncid)) ERR;
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/* Write the data one slice at a time. */
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start[0] = 0;
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count[0] = 1;
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for (d = 1; d < NDIMS3; d++)
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{
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start[d] = 0;
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count[d] = dim_len[d];
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}
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for ( ; start[0] < D0; (start[0])++)
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if (nc_put_vara_float(ncid, varid, start, count, (const float *) data))
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ERR_RET;
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/* Close up shop. */
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if (nc_close(ncid)) ERR;
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free(data);
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}
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SUMMARIZE_ERR;
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#endif /* LARGE_FILE_TESTS */
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printf("*** Creating a file with floats...");
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{
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#define DIM_NAME "stupidity"
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#define NUMDIMS 1
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#define DIMLEN 10000
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int ncid, dimids[NUMDIMS], varid;
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char var_name[NC_MAX_NAME + 1] = {"Billy-Bob"};
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int ndims, nvars, natts, unlimdimid;
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nc_type xtype;
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char name_in[NC_MAX_NAME + 1];
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size_t len;
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float data[DIMLEN], data_in[DIMLEN];
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int i;
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for (i = 0; i < DIMLEN; i++)
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data[i] = ((float)rand() / (float)(RAND_MAX));
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/* Create a netCDF netCDF-4/HDF5 format file, with 1 var. */
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/* if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;*/
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if (nc_create(FILE_NAME, 0, &ncid)) ERR;
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if (nc_def_dim(ncid, DIM_NAME, DIMLEN, dimids)) ERR;
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if (nc_def_var(ncid, var_name, NC_FLOAT, NUMDIMS, dimids, &varid)) ERR;
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if (nc_enddef(ncid)) ERR;
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if (nc_put_var_float(ncid, varid, data)) ERR;
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if (nc_close(ncid)) ERR;
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/* Reopen and check the file. */
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if (nc_open(FILE_NAME, 0, &ncid)) ERR;
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if (nc_inq(ncid, &ndims, &nvars, &natts, &unlimdimid)) ERR;
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if (ndims != NUMDIMS || nvars != 1 || natts != 0 || unlimdimid != -1) ERR;
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if (nc_inq_dimids(ncid, &ndims, dimids, 1)) ERR;
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if (ndims != 1 || dimids[0] != 0) ERR;
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if (nc_inq_dim(ncid, 0, name_in, &len)) ERR;
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if (strcmp(name_in, DIM_NAME) || len != DIMLEN) ERR;
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if (nc_inq_var(ncid, 0, name_in, &xtype, &ndims, dimids, &natts)) ERR;
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if (strcmp(name_in, var_name) || xtype != NC_FLOAT || ndims != 1 ||
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dimids[0] != 0 || natts != 0) ERR;
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if (nc_get_var_float(ncid, 0, data_in)) ERR;
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for (i = 0; i < DIMLEN; i++)
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if (data_in[i] != data[i]) ERR;
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if (nc_close(ncid)) ERR;
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}
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SUMMARIZE_ERR;
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printf("*** Creating files of various dimensions with various types...");
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{
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#define TOTAL_SIZE 100000
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#define MAX_DIMS 6
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#define VAR_NAME "Unimaginatively_Named_Variable"
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#define MAX_TYPES 3
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int ncid, dimids[MAX_DIMS], varid;
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char dim_name[NC_MAX_NAME + 1], file_name[NC_MAX_NAME + 1];
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char type_name[MAX_TYPES][NC_MAX_NAME + 1] = {"floats", "ints", "shorts"};
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int typeid[MAX_TYPES] = {NC_FLOAT, NC_INT, NC_SHORT};
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size_t len;
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float fdata[TOTAL_SIZE];
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int idata[TOTAL_SIZE];
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short sdata[TOTAL_SIZE];
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void *data[MAX_TYPES];
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int ndims;
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int i, d, t;
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/* Initialize the data to random floats. */
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for (i = 0; i < TOTAL_SIZE; i++)
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{
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fdata[i] = (float)rand();
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idata[i] = rand();
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sdata[i] = (short)rand();
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}
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data[0] = fdata;
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data[1] = idata;
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data[2] = sdata;
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/* Do the file creation process below for each type. */
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for (t = 0; t < MAX_TYPES; t++)
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{
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/* Create MAX_DIMS files, each with different number of
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* dimensions. */
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for (ndims = 1; ndims <= MAX_DIMS; ndims++)
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{
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sprintf(file_name, "tst_%s2_%dD.nc", type_name[t], ndims);
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if (nc_create(file_name, 0, &ncid)) ERR;
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for (len = pow(TOTAL_SIZE, (float)1/ndims), d = 0; d < ndims; d++)
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{
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sprintf(dim_name, "dim_%d", d);
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if (nc_def_dim(ncid, dim_name, len, &dimids[d])) ERR;
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}
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if (nc_def_var(ncid, VAR_NAME, typeid[t], ndims, dimids, &varid)) ERR;
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if (nc_enddef(ncid)) ERR;
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if (nc_put_var(ncid, varid, data[t])) ERR;
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if (nc_close(ncid)) ERR;
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} /* next ndims. */
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} /* next type */
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}
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SUMMARIZE_ERR;
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printf("*** Creating file like in http://hdfeos.org/workshops/ws06/presentations/Pourmal/HDF5_IO_Perf.pdf...");
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{
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#define XLEN 256
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#define YLEN 256
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#define ZLEN 1024
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#define NDIMS 3
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#define E_VAR_NAME "Like_Elenas_Benchmark"
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#define ELENA_FILE_NAME "tst_elena_int_3D.nc"
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#define E_TYPE_SIZE 4
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int ncid, dimids[NDIMS], varid;
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int *idata;
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int i;
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/* Initialize data to random int between 0 and 255. */
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if (!(idata = malloc(XLEN * YLEN * ZLEN * E_TYPE_SIZE)))
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return NC_ENOMEM;
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for (i = 0; i < XLEN * YLEN * ZLEN; i++)
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idata[i] = rand() % 255;
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/* Create a 3D file with one var. */
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if (nc_create(ELENA_FILE_NAME, NC_CLOBBER, &ncid)) ERR;
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if (nc_def_dim(ncid, "z", ZLEN, &dimids[0])) ERR;
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if (nc_def_dim(ncid, "y", YLEN, &dimids[1])) ERR;
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if (nc_def_dim(ncid, "x", XLEN, &dimids[2])) ERR;
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if (nc_def_var(ncid, E_VAR_NAME, NC_INT, NDIMS, dimids, &varid)) ERR;
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if (nc_enddef(ncid)) ERR;
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/* Write the data. */
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if (nc_put_var(ncid, varid, idata)) ERR;
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if (nc_close(ncid)) ERR;
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}
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SUMMARIZE_ERR;
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printf("*** Creating super simple file to test non-sequential reads...");
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{
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#define DIM_LEN 10
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#define NDIMS1 1
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#define S_VAR_NAME "My_Favorite_Numbers_in_order"
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#define S_FILE_NAME "tst_simple.nc"
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int ncid, dimids[NDIMS1], varid;
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int data[DIM_LEN];
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int i;
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/* Initialize data to my favorite numbers. */
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for (i = 0; i < DIM_LEN; i++)
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data[i] = i;
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/* Create a file with one var. */
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if (nc_create(S_FILE_NAME, NC_CLOBBER, &ncid)) ERR;
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if (nc_def_dim(ncid, "a", DIM_LEN, &dimids[0])) ERR;
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if (nc_def_var(ncid, S_VAR_NAME, NC_INT, NDIMS1, dimids, &varid)) ERR;
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if (nc_enddef(ncid)) ERR;
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/* Write the data. */
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if (nc_put_var(ncid, varid, data)) ERR;
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if (nc_close(ncid)) ERR;
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}
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SUMMARIZE_ERR;
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printf("*** Creating very simple 3D file...");
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{
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#define SIMPLE_VAR_NAME "Paul_Mau_Dib"
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#define MAX_TYPES 3
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int ncid, dimids[MAX_DIMS], varid;
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char dim_name[NC_MAX_NAME + 1], file_name[NC_MAX_NAME + 1];
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char type_name[MAX_TYPES][NC_MAX_NAME + 1] = {"floats", "ints", "shorts"};
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int typeid[MAX_TYPES] = {NC_FLOAT, NC_INT, NC_SHORT};
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size_t len;
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float fdata[TOTAL_SIZE];
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int idata[TOTAL_SIZE];
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short sdata[TOTAL_SIZE];
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void *data[MAX_TYPES];
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int ndims;
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int i, d, t;
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/* Initialize the data to random floats. */
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for (i = 0; i < TOTAL_SIZE; i++)
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{
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fdata[i] = (float)rand();
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idata[i] = rand();
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sdata[i] = (short)rand();
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}
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data[0] = fdata;
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data[1] = idata;
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data[2] = sdata;
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/* Do the file creation process below for each type. */
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for (t = 0; t < MAX_TYPES; t++)
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{
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/* Create MAX_DIMS files, each with different number of
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* dimensions. */
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for (ndims = 1; ndims <= MAX_DIMS; ndims++)
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{
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sprintf(file_name, "tst_%s2_%dD.nc", type_name[t], ndims);
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if (nc_create(file_name, 0, &ncid)) ERR;
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for (len = pow(TOTAL_SIZE, (float)1/ndims), d = 0; d < ndims; d++)
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{
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sprintf(dim_name, "dim_%d", d);
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if (nc_def_dim(ncid, dim_name, len, &dimids[d])) ERR;
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}
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if (nc_def_var(ncid, SIMPLE_VAR_NAME, typeid[t], ndims, dimids, &varid)) ERR;
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if (nc_enddef(ncid)) ERR;
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if (nc_put_var(ncid, varid, data[t])) ERR;
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if (nc_close(ncid)) ERR;
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} /* next ndims. */
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} /* next type */
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}
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SUMMARIZE_ERR;
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FINAL_RESULTS;
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}
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