netcdf-c/h5_test/tst_h_files.c

/* This is part of the netCDF package.
   Copyright 2020 University Corporation for Atmospheric Research/Unidata
   See COPYRIGHT file for conditions of use.

   Test HDF5 file code. These are not intended to be exhaustive tests,
   but they use HDF5 the same way that netCDF-4 does, so if these
   tests don't work, than netCDF-4 won't work either.

   Ed Hartnett
*/

#include "h5_err_macros.h"
#include <hdf5.h>
#include <H5DSpublic.h>

#define FILE_NAME "tst_h_files.h5"
#define GRP_NAME "Dectectives"
#define STR_LEN 255

int
main()
{
    printf("\n*** Checking HDF5 file functions.\n");
    printf("*** Checking HDF5 file creates and opens...");
#define OPAQUE_SIZE 20
#define OPAQUE_NAME "type"
#define ATT_NAME "att_name"
#define DIM_LEN 3
    {
        hid_t fileid, access_plist, typeid, spaceid, attid, fapl_id, grpid;
        hsize_t dims[1]; /* netcdf attributes always 1-D. */
        unsigned char data[DIM_LEN][OPAQUE_SIZE];
        hsize_t num_obj, i;
        int obj_class;
        char obj_name[STR_LEN + 1];
        H5T_class_t class;
        int j, k;
        hid_t tmp1;

        H5open();

        /* Initialize some data. */
        for (j = 0; j < DIM_LEN; j++)
            for (k = 0; k < OPAQUE_SIZE; k++)
                data[j][k] = 42;

        /* Set the access list so that closes will fail if something is
         * still open in the file. */
        tmp1 = H5P_FILE_ACCESS;
        if ((access_plist = H5Pcreate(tmp1)) < 0) ERR;
        if (H5Pset_fclose_degree(access_plist, H5F_CLOSE_SEMI)) ERR;

        /* Create file. */
        if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT,
                                access_plist)) < 0) ERR;
        /* Add an opaque type. */
        if ((typeid = H5Tcreate(H5T_OPAQUE, OPAQUE_SIZE)) < 0) ERR;
        if (H5Tcommit1(fileid, OPAQUE_NAME, typeid) < 0) ERR;

        /* Add attribute of this type. */
        dims[0] = 3;
        if ((spaceid = H5Screate_simple(1, dims, NULL)) < 0) ERR;
        if ((attid = H5Acreate1(fileid, ATT_NAME, typeid, spaceid,
                               H5P_DEFAULT)) < 0) ERR;
        if (H5Awrite(attid, typeid, data) < 0) ERR;

        if (H5Aclose(attid) < 0) ERR;
        if (H5Sclose(spaceid) < 0) ERR;
        if (H5Tclose(typeid) < 0) ERR;
        if (H5Fclose(fileid) < 0) ERR;
        if (H5Pclose(access_plist) < 0) ERR;

        if (H5Eset_auto1(NULL, NULL) < 0) ERR;

        /* Reopen the file. */
        if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
        /*if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_SEMI)) ERR;*/
        if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_STRONG)) ERR;
        if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDONLY, fapl_id)) < 0) ERR;
        if ((grpid = H5Gopen1(fileid, "/")) < 0) ERR;

        if (H5Gget_num_objs(grpid, &num_obj) < 0) ERR;
        for (i = 0; i < num_obj; i++)
        {
            if ((obj_class = H5Gget_objtype_by_idx(grpid, i)) < 0) ERR;
            if (H5Gget_objname_by_idx(grpid, i, obj_name,
                                      STR_LEN) < 0) ERR;
            if (obj_class != H5G_TYPE) ERR;
            if ((typeid = H5Topen1(grpid, obj_name)) < 0) ERR;
            if ((class = H5Tget_class(typeid)) < 0) ERR;
            if (class != H5T_OPAQUE) ERR;
            if (!(H5Tget_size(typeid))) ERR;
        }

        /* Close everything. */
        if (H5Pclose(fapl_id)) ERR;
        if (H5Gclose(grpid) < 0) ERR;
        /*if (H5Tclose(typeid) < 0) ERR;*/
        if (H5Fclose(fileid) < 0) ERR;

        if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
        if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_SEMI)) ERR;
        if ((fileid = H5Fopen(FILE_NAME, 0, fapl_id)) < 0) ERR;
        if (H5Fclose(fileid) < 0) ERR;

    }
    SUMMARIZE_ERR;

    printf("*** Checking HDF5 file creates and opens some more...");
    {
        int objs;
        hid_t fileid, fileid2, grpid, access_plist;

        /* Set the access list so that closes will fail if something is
         * still open in the file. */
        if ((access_plist = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
        if (H5Pset_fclose_degree(access_plist, H5F_CLOSE_SEMI)) ERR;

        /* Create file and create group. */
        if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT,
                                access_plist)) < 0) ERR;
        if ((grpid = H5Gcreate1(fileid, GRP_NAME, 0)) < 0) ERR;

        /* How many open objects are there? */
        if ((objs = H5Fget_obj_count(fileid, H5F_OBJ_ALL)) < 0) ERR;
        if (objs != 2) ERR;
        if ((objs = H5Fget_obj_count(fileid, H5F_OBJ_GROUP)) < 0) ERR;
        if (objs != 1) ERR;

        /* Turn off HDF5 error messages. */
        if (H5Eset_auto1(NULL, NULL) < 0) ERR;

        /* This H5Fclose should fail, because I didn't close the group. */
        if (H5Fclose(fileid) >= 0) ERR;

        /* Now close the group first, and then the file. */
        if (H5Gclose(grpid) < 0 ||
            H5Fclose(fileid) < 0) ERR;

        /* Now create the file again, to make sure that it really is not
         * just nearly dead, but really most sincerely dead. */
        if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT,
                                access_plist)) < 0) ERR;
        if (H5Fclose(fileid) < 0) ERR;

        /* Confirm that the same file can be opened twice at the same time,
         * for read only access. */
        if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0) ERR;
        if ((fileid2 = H5Fopen(FILE_NAME, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0) ERR;
        if (H5Fclose(fileid) < 0) ERR;
        if (H5Fclose(fileid2) < 0) ERR;

        /* Once open for read only access, the file can't be opened again
         * for write access. */
        if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0) ERR;
        if (H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT) >= 0) ERR;
        if (H5Fclose(fileid) < 0) ERR;

        /* But you can open the file for read/write access, and then open
         * it again for read only access. */
        if ((fileid2 = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR;
        if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0) ERR;
        if (H5Fclose(fileid) < 0) ERR;
        if (H5Fclose(fileid2) < 0) ERR;
    }
    SUMMARIZE_ERR;

    printf("*** Creating file...");
    {
#define VAR_NAME "HALs_memory"
#define NDIMS 1
#define DIM1_LEN 40000
#define SC 10000 /* slice count. */
#define MILLION 1000000

        hid_t fileid, write_spaceid, datasetid, mem_spaceid;
        hsize_t start[NDIMS], count[NDIMS];
        hsize_t dims[1];
        int *data;
        int num_steps;
        int i, s;

        /* We will write the same slice of random data over and over to
         * fill the file. */
        if (!(data = malloc(SC * sizeof(int))))
            ERR_RET;
        for (i = 0; i < SC; i++)
            data[i] = rand();

        /* Create file. */
        if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT,
                                H5P_DEFAULT)) < 0) ERR;

        /* Create a space to deal with one slice in memory. */
        dims[0] = SC;
        if ((mem_spaceid = H5Screate_simple(NDIMS, dims, NULL)) < 0) ERR;

        /* Create a space to write all slices. */
        dims[0] = DIM1_LEN;
        if ((write_spaceid = H5Screate_simple(NDIMS, dims, NULL)) < 0) ERR;

        /* Create dataset. */
        if ((datasetid = H5Dcreate1(fileid, VAR_NAME, H5T_NATIVE_INT,
                                    write_spaceid, H5P_DEFAULT)) < 0) ERR;

        /* Write the data in num_step steps. */
        num_steps = DIM1_LEN/SC;
        count[0] = SC;
        for (s = 0; s < num_steps; s++)
        {
            /* Select hyperslab for write of one slice. */
            start[0] = s * SC;
            if (H5Sselect_hyperslab(write_spaceid, H5S_SELECT_SET,
                                    start, NULL, count, NULL) < 0) ERR;

            if (H5Dwrite(datasetid, H5T_NATIVE_INT, mem_spaceid, write_spaceid,
                         H5P_DEFAULT, data) < 0) ERR;
        }

        /* Close. */
        free(data);
        if (H5Dclose(datasetid) < 0 ||
            H5Sclose(write_spaceid) < 0 ||
            H5Sclose(mem_spaceid) < 0 ||
            H5Fclose(fileid) < 0)
            ERR;
    }
    SUMMARIZE_ERR;
#ifdef LARGE_FILE_TESTS

#define NDIMS2 2
#define DIM1 2048
#define DIM2 2097153            /* DIM1*DIM2*sizeof(char)   > 2**32 */
#define DIM_WITHOUT_VARIABLE "This is a netCDF dimension but not a netCDF variable."
#define VAR_NAME2 "var"
#define MAX_DIMS 255

    printf("*** large file test for HDF5...");
    {
        hid_t fapl_id, fcpl_id, fileid, grpid, spaceid, datasetid;
        hid_t dim1_dimscaleid, dim2_dimscaleid, plistid, file_spaceid;
        hid_t mem_spaceid, xfer_plistid, native_typeid;
        hsize_t *chunksize, dims[1], maxdims[1], *dimsize, *maxdimsize;
        hsize_t fdims[MAX_DIMS], fmaxdims[MAX_DIMS];
        hsize_t start[MAX_DIMS],  count[MAX_DIMS];
        char file_name[STR_LEN + 1];
        char dimscale_wo_var[STR_LEN];
        void *bufr;
        void *fillp = NULL;

        sprintf(file_name, "%s/%s", TEMP_LARGE, FILE_NAME);

        /* Create file access and create property lists. */
        if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
        if ((fcpl_id = H5Pcreate(H5P_FILE_CREATE)) < 0) ERR;

        /* Set latest_format in access propertly list. This ensures that
         * the latest, greatest, HDF5 versions are used in the file. */
        if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) ERR;

        /* Set H5P_CRT_ORDER_TRACKED in the creation property list. This
         * turns on HDF5 creation ordering in the file. */
        if (H5Pset_link_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
                                                 H5P_CRT_ORDER_INDEXED)) < 0) ERR;
        if (H5Pset_attr_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
                                                 H5P_CRT_ORDER_INDEXED)) < 0) ERR;

        /* Create the file. */
        if ((fileid = H5Fcreate(file_name, H5F_ACC_TRUNC, fcpl_id, fapl_id)) < 0) ERR;

        /* Open the root group. */
        if ((grpid = H5Gopen2(fileid, "/", H5P_DEFAULT)) < 0) ERR;

        /* Set up the dataset creation property list for the two dimensions. */
/*      if (H5Pset_chunk(plistid, 1, chunksize) < 0) ERR;*/

        /* Create the dim1 dimscale. */
        if ((plistid = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
        dims[0] = DIM1;
        maxdims[0] = DIM1;
        if ((spaceid = H5Screate_simple(1, dims, maxdims)) < 0) ERR;
        if (H5Pset_attr_creation_order(plistid, H5P_CRT_ORDER_TRACKED|
                                       H5P_CRT_ORDER_INDEXED) < 0) ERR;
        if ((dim1_dimscaleid = H5Dcreate1(grpid, "dim1", H5T_IEEE_F32BE,
                                         spaceid, plistid)) < 0) ERR;
        if (H5Sclose(spaceid) < 0) ERR;
        if (H5Pclose(plistid) < 0) ERR;
        sprintf(dimscale_wo_var, "%s%10d", DIM_WITHOUT_VARIABLE, DIM1);
        if (H5DSset_scale(dim1_dimscaleid, dimscale_wo_var) < 0) ERR;

        /* Create the dim2 dimscale. */
        if ((plistid = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
        dims[0] = DIM2;
        maxdims[0] = DIM2;
        if ((spaceid = H5Screate_simple(1, dims, maxdims)) < 0) ERR;
        if (H5Pset_attr_creation_order(plistid, H5P_CRT_ORDER_TRACKED|
                                       H5P_CRT_ORDER_INDEXED) < 0) ERR;
        if ((dim2_dimscaleid = H5Dcreate1(grpid, "dim2", H5T_IEEE_F32BE,
                                         spaceid, plistid)) < 0) ERR;
        if (H5Sclose(spaceid) < 0) ERR;
        if (H5Pclose(plistid) < 0) ERR;
        sprintf(dimscale_wo_var, "%s%10d", DIM_WITHOUT_VARIABLE, DIM2);
        if (H5DSset_scale(dim2_dimscaleid, dimscale_wo_var) < 0) ERR;

        /* Now create the 2D dataset. */
        if ((plistid = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
        if (!(fillp = malloc(1))) ERR;
#define FILL_BYTE 255
        *(signed char *)fillp = FILL_BYTE;
        if(H5Pset_fill_value(plistid, H5T_NATIVE_SCHAR, fillp) < 0) ERR;
        if (!(chunksize = malloc(NDIMS2 * sizeof(hsize_t)))) ERR;
        chunksize[0] = 1024;
        chunksize[1] = 1048576;
        if (H5Pset_chunk(plistid, NDIMS2, chunksize) < 0) ERR;
        if (!(dimsize = malloc(NDIMS2 * sizeof(hsize_t)))) ERR;
        if (!(maxdimsize = malloc(NDIMS2 * sizeof(hsize_t)))) ERR;
        dimsize[0] = 2048;
        dimsize[1] = 2097153;
        maxdimsize[0] = 2048;
        maxdimsize[1] = 2097153;
        if ((spaceid = H5Screate_simple(NDIMS2, dimsize, maxdimsize)) < 0) ERR;
        if (H5Pset_attr_creation_order(plistid, H5P_CRT_ORDER_TRACKED|
                                       H5P_CRT_ORDER_INDEXED) < 0) ERR;
        if ((datasetid = H5Dcreate1(grpid, VAR_NAME2, H5T_NATIVE_SCHAR, spaceid, plistid)) < 0) ERR;

        free(fillp);
        free(chunksize);
        free(dimsize);
        free(maxdimsize);
        if (H5Pclose(plistid) < 0) ERR;
        if (H5Sclose(spaceid) < 0) ERR;

        if (H5DSattach_scale(datasetid, dim1_dimscaleid, 0) < 0) ERR;
        if (H5DSattach_scale(datasetid, dim2_dimscaleid, 1) < 0) ERR;
        H5Fflush(fileid, H5F_SCOPE_GLOBAL);

        /* Read a slice of data. */
        if ((file_spaceid = H5Dget_space(datasetid)) < 0) ERR;
        if (H5Sget_simple_extent_dims(file_spaceid, fdims, fmaxdims) < 0) ERR;
        if (H5Sget_simple_extent_type(file_spaceid) == H5S_SCALAR) ERR;
        start[0] = 0;
        start[1] = 0;
        count[0] = 1;
        count[1] = 2097153;
        if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET, start, NULL, count, NULL) < 0) ERR;
        if ((mem_spaceid = H5Screate_simple(NDIMS2, count, NULL)) < 0) ERR;
        if ((xfer_plistid = H5Pcreate(H5P_DATASET_XFER)) < 0) ERR;
        if ((native_typeid = H5Tget_native_type(H5T_NATIVE_SCHAR, H5T_DIR_DEFAULT)) < 0) ERR;
        if (!(bufr = malloc(DIM2))) ERR;
        if (H5Dwrite(datasetid, native_typeid, mem_spaceid, file_spaceid, xfer_plistid, bufr) < 0) ERR;
        free(bufr);
        if (H5Tclose(native_typeid) < 0) ERR;

        /* Close down the show. */
        if (H5Pclose(fapl_id) < 0) ERR;
        if (H5Pclose(fcpl_id) < 0) ERR;
        if (H5Dclose(dim1_dimscaleid) < 0) ERR;
        if (H5Dclose(dim2_dimscaleid) < 0) ERR;
        if (H5Dclose(datasetid) < 0) ERR;
        if (H5Gclose(grpid) < 0) ERR;
        if (H5Fclose(fileid) < 0) ERR;

        /* Delete the huge data file we created. */
        (void) remove(file_name);
    }
    SUMMARIZE_ERR;
#endif /* LARGE_FILE_TESTS */

    FINAL_RESULTS;
}