/* Copyright 2003-2006, University Corporation for Atmospheric * Research. See COPYRIGHT file for copying and redistribution * conditions.*/ /** * @file * @internal This file handles the HDF5 variable functions. * * @author Ed Hartnett */ #include "config.h" #include #include /** @internal Default size for unlimited dim chunksize */ #define DEFAULT_1D_UNLIM_SIZE (4096) /** * @internal If the HDF5 dataset for this variable is open, then close * it and reopen it, with the perhaps new settings for chunk caching. * * @param grp Pointer to the group info. * @param var Pointer to the var info. * * @returns ::NC_NOERR No error. * @returns ::NC_EHDFERR HDF5 error. * @author Ed Hartnett */ int nc4_reopen_dataset(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var) { hid_t access_pid; if (var->hdf_datasetid) { if ((access_pid = H5Pcreate(H5P_DATASET_ACCESS)) < 0) return NC_EHDFERR; if (H5Pset_chunk_cache(access_pid, var->chunk_cache_nelems, var->chunk_cache_size, var->chunk_cache_preemption) < 0) return NC_EHDFERR; if (H5Dclose(var->hdf_datasetid) < 0) return NC_EHDFERR; if ((var->hdf_datasetid = H5Dopen2(grp->hdf_grpid, var->hdr.name, access_pid)) < 0) return NC_EHDFERR; if (H5Pclose(access_pid) < 0) return NC_EHDFERR; } return NC_NOERR; } /** * @internal Check a set of chunksizes to see if they specify a chunk * that is too big. * * @param grp Pointer to the group info. * @param var Pointer to the var info. * @param chunksizes Array of chunksizes to check. * * @returns ::NC_NOERR No error. * @returns ::NC_EBADID Bad ncid. * @returns ::NC_ENOTVAR Invalid variable ID. * @returns ::NC_EBADCHUNK Bad chunksize. */ static int check_chunksizes(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, const size_t *chunksizes) { double dprod; size_t type_len; int d; int retval; if ((retval = nc4_get_typelen_mem(grp->nc4_info, var->type_info->hdr.id, &type_len))) return retval; if (var->type_info->nc_type_class == NC_VLEN) dprod = (double)sizeof(hvl_t); else dprod = (double)type_len; for (d = 0; d < var->ndims; d++) dprod *= (double)chunksizes[d]; if (dprod > (double) NC_MAX_UINT) return NC_EBADCHUNK; return NC_NOERR; } /** * @internal Determine some default chunksizes for a variable. * * @param grp Pointer to the group info. * @param var Pointer to the var info. * * @returns ::NC_NOERR for success * @returns ::NC_EBADID Bad ncid. * @returns ::NC_ENOTVAR Invalid variable ID. * @author Ed Hartnett */ static int nc4_find_default_chunksizes2(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var) { int d; size_t type_size; float num_values = 1, num_unlim = 0; int retval; size_t suggested_size; #ifdef LOGGING double total_chunk_size; #endif if (var->type_info->nc_type_class == NC_STRING) type_size = sizeof(char *); else type_size = var->type_info->size; #ifdef LOGGING /* Later this will become the total number of bytes in the default * chunk. */ total_chunk_size = (double) type_size; #endif /* How many values in the variable (or one record, if there are * unlimited dimensions). */ for (d = 0; d < var->ndims; d++) { assert(var->dim[d]); if (! var->dim[d]->unlimited) num_values *= (float)var->dim[d]->len; else { num_unlim++; var->chunksizes[d] = 1; /* overwritten below, if all dims are unlimited */ } } /* Special case to avoid 1D vars with unlim dim taking huge amount of space (DEFAULT_CHUNK_SIZE bytes). Instead we limit to about 4KB */ if (var->ndims == 1 && num_unlim == 1) { if (DEFAULT_CHUNK_SIZE / type_size <= 0) suggested_size = 1; else if (DEFAULT_CHUNK_SIZE / type_size > DEFAULT_1D_UNLIM_SIZE) suggested_size = DEFAULT_1D_UNLIM_SIZE; else suggested_size = DEFAULT_CHUNK_SIZE / type_size; var->chunksizes[0] = suggested_size / type_size; LOG((4, "%s: name %s dim %d DEFAULT_CHUNK_SIZE %d num_values %f type_size %d " "chunksize %ld", __func__, var->hdr.name, d, DEFAULT_CHUNK_SIZE, num_values, type_size, var->chunksizes[0])); } if (var->ndims > 1 && var->ndims == num_unlim) { /* all dims unlimited */ suggested_size = pow((double)DEFAULT_CHUNK_SIZE/type_size, 1.0/(double)(var->ndims)); for (d = 0; d < var->ndims; d++) { var->chunksizes[d] = suggested_size ? suggested_size : 1; LOG((4, "%s: name %s dim %d DEFAULT_CHUNK_SIZE %d num_values %f type_size %d " "chunksize %ld", __func__, var->hdr.name, d, DEFAULT_CHUNK_SIZE, num_values, type_size, var->chunksizes[d])); } } /* Pick a chunk length for each dimension, if one has not already * been picked above. */ for (d = 0; d < var->ndims; d++) if (!var->chunksizes[d]) { suggested_size = (pow((double)DEFAULT_CHUNK_SIZE/(num_values * type_size), 1.0/(double)(var->ndims - num_unlim)) * var->dim[d]->len - .5); if (suggested_size > var->dim[d]->len) suggested_size = var->dim[d]->len; var->chunksizes[d] = suggested_size ? suggested_size : 1; LOG((4, "%s: name %s dim %d DEFAULT_CHUNK_SIZE %d num_values %f type_size %d " "chunksize %ld", __func__, var->hdr.name, d, DEFAULT_CHUNK_SIZE, num_values, type_size, var->chunksizes[d])); } #ifdef LOGGING /* Find total chunk size. */ for (d = 0; d < var->ndims; d++) total_chunk_size *= (double) var->chunksizes[d]; LOG((4, "total_chunk_size %f", total_chunk_size)); #endif /* But did this result in a chunk that is too big? */ retval = check_chunksizes(grp, var, var->chunksizes); if (retval) { /* Other error? */ if (retval != NC_EBADCHUNK) return retval; /* Chunk is too big! Reduce each dimension by half and try again. */ for ( ; retval == NC_EBADCHUNK; retval = check_chunksizes(grp, var, var->chunksizes)) for (d = 0; d < var->ndims; d++) var->chunksizes[d] = var->chunksizes[d]/2 ? var->chunksizes[d]/2 : 1; } /* Do we have any big data overhangs? They can be dangerous to * babies, the elderly, or confused campers who have had too much * beer. */ for (d = 0; d < var->ndims; d++) { size_t num_chunks; size_t overhang; assert(var->chunksizes[d] > 0); num_chunks = (var->dim[d]->len + var->chunksizes[d] - 1) / var->chunksizes[d]; if(num_chunks > 0) { overhang = (num_chunks * var->chunksizes[d]) - var->dim[d]->len; var->chunksizes[d] -= overhang / num_chunks; } } return NC_NOERR; } /** * @internal This is called when a new netCDF-4 variable is defined * with nc_def_var(). * * @param ncid File ID. * @param name Name. * @param xtype Type. * @param ndims Number of dims. * @param dimidsp Array of dim IDs. * @param varidp Gets the var ID. * * @returns ::NC_NOERR No error. * @returns ::NC_EBADID Bad ncid. * @returns ::NC_ENOTVAR Invalid variable ID. * @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is * not netCDF-4/HDF5. * @returns ::NC_ESTRICTNC3 Attempting netcdf-4 operation on strict nc3 * netcdf-4 file. * @returns ::NC_ELATEDEF Too late to change settings for this variable. * @returns ::NC_ENOTINDEFINE Not in define mode. * @returns ::NC_EPERM File is read only. * @returns ::NC_EMAXDIMS Classic model file exceeds ::NC_MAX_VAR_DIMS. * @returns ::NC_ESTRICTNC3 Attempting to create netCDF-4 type var in * classic model file * @returns ::NC_EBADNAME Bad name. * @returns ::NC_EBADTYPE Bad type. * @returns ::NC_ENOMEM Out of memory. * @returns ::NC_EHDFERR Error returned by HDF5 layer. * @returns ::NC_EINVAL Invalid input * @author Ed Hartnett, Dennis Heimbigner */ int NC4_def_var(int ncid, const char *name, nc_type xtype, int ndims, const int *dimidsp, int *varidp) { NC_GRP_INFO_T *grp; NC_VAR_INFO_T *var; NC_DIM_INFO_T *dim; NC_FILE_INFO_T *h5; NC_TYPE_INFO_T *type_info = NULL; char norm_name[NC_MAX_NAME + 1]; int d; int retval; /* Find info for this file and group, and set pointer to each. */ if ((retval = nc4_find_grp_h5(ncid, &grp, &h5))) BAIL(retval); assert(grp && h5); /* If it's not in define mode, strict nc3 files error out, * otherwise switch to define mode. This will also check that the * file is writable. */ if (!(h5->flags & NC_INDEF)) { if (h5->cmode & NC_CLASSIC_MODEL) BAIL(NC_ENOTINDEFINE); if ((retval = NC4_redef(ncid))) BAIL(retval); } assert(!h5->no_write); /* Check and normalize the name. */ if ((retval = nc4_check_name(name, norm_name))) BAIL(retval); /* Not a Type is, well, not a type.*/ if (xtype == NC_NAT) BAIL(NC_EBADTYPE); /* For classic files, only classic types are allowed. */ if (h5->cmode & NC_CLASSIC_MODEL && xtype > NC_DOUBLE) BAIL(NC_ESTRICTNC3); /* For classic files */ if (h5->cmode & NC_CLASSIC_MODEL && ndims > NC_MAX_VAR_DIMS) BAIL(NC_EMAXDIMS); /* cast needed for braindead systems with signed size_t */ if((unsigned long) ndims > X_INT_MAX) /* Backward compat */ BAIL(NC_EINVAL); /* Check that this name is not in use as a var, grp, or type. */ if ((retval = nc4_check_dup_name(grp, norm_name))) BAIL(retval); /* For non-scalar vars, dim IDs must be provided. */ if (ndims && !dimidsp) BAIL(NC_EINVAL); /* Check all the dimids to make sure they exist. */ for (d = 0; d < ndims; d++) if ((retval = nc4_find_dim(grp, dimidsp[d], &dim, NULL))) BAIL(retval); /* These degrubbing messages sure are handy! */ LOG((2, "%s: name %s type %d ndims %d", __func__, norm_name, xtype, ndims)); #ifdef LOGGING { int dd; for (dd = 0; dd < ndims; dd++) LOG((4, "dimid[%d] %d", dd, dimidsp[dd])); } #endif /* If this is a user-defined type, there is a type_info struct with * all the type information. For atomic types, fake up a type_info * struct. */ if (xtype <= NC_STRING) { size_t len; char name[NC_MAX_NAME+1]; char* atomname = nc4_atomic_name[xtype]; size_t namelen = strlen(atomname); memcpy(name,atomname,namelen); name[namelen] = '\0'; nc4_get_typelen_mem(h5,xtype,&len); if((retval = nc4_type_new(grp,len,name,xtype,&type_info))) BAIL(retval); type_info->endianness = NC_ENDIAN_NATIVE; if ((retval = nc4_get_hdf_typeid(h5, xtype, &type_info->hdf_typeid, type_info->endianness))) BAIL(retval); if ((type_info->native_hdf_typeid = H5Tget_native_type(type_info->hdf_typeid, H5T_DIR_DEFAULT)) < 0) BAIL(NC_EHDFERR); if ((retval = nc4_get_typelen_mem(h5, type_info->hdr.id, &type_info->size))) BAIL(retval); /* Set the "class" of the type */ if (xtype == NC_CHAR) type_info->nc_type_class = NC_CHAR; else { H5T_class_t class; if ((class = H5Tget_class(type_info->hdf_typeid)) < 0) BAIL(NC_EHDFERR); switch(class) { case H5T_STRING: type_info->nc_type_class = NC_STRING; break; case H5T_INTEGER: type_info->nc_type_class = NC_INT; break; case H5T_FLOAT: type_info->nc_type_class = NC_FLOAT; break; default: BAIL(NC_EBADTYPID); } } } /* If this is a user defined type, find it. */ else { if (nc4_find_type(grp->nc4_info, xtype, &type_info)) BAIL(NC_EBADTYPE); } /* Create a new var and fill in some HDF5 cache setting values. */ if ((retval = nc4_var_list_add(grp, norm_name, ndims, &var))) BAIL(retval); var->is_new_var = NC_TRUE; /* Point to the type, and increment its ref. count */ var->type_info = type_info; var->type_info->rc++; type_info = NULL; /* Set variables no_fill to match the database default * unless the variable type is variable length (NC_STRING or NC_VLEN) * or is user-defined type. */ if (var->type_info->nc_type_class < NC_STRING) var->no_fill = h5->fill_mode; /* Assign dimensions to the variable */ /* At the same time, check to see if this is a coordinate * variable. If so, it will have the same name as one of its * dimensions. If it is a coordinate var, is it a coordinate var in * the same group as the dim? */ /* Also, check whether we should use contiguous or chunked storage */ var->contiguous = NC_TRUE; for (d = 0; d < ndims; d++) { NC_GRP_INFO_T *dim_grp; /* Look up each dimension */ if ((retval = nc4_find_dim(grp, dimidsp[d], &dim, &dim_grp))) BAIL(retval); /* Check for dim index 0 having the same name, in the same group */ if (d == 0 && dim_grp == grp && strcmp(dim->hdr.name, norm_name) == 0) { var->dimscale = NC_TRUE; dim->coord_var = var; /* Use variable's dataset ID for the dimscale ID. So delete * the HDF5 DIM_WITHOUT_VARIABLE dataset that was created for * this dim. */ if (dim->hdf_dimscaleid) { /* Detach dimscale from any variables using it */ if ((retval = rec_detach_scales(grp, dimidsp[d], dim->hdf_dimscaleid)) < 0) BAIL(retval); /* Close the HDF5 DIM_WITHOUT_VARIABLE dataset. */ if (H5Dclose(dim->hdf_dimscaleid) < 0) BAIL(NC_EHDFERR); dim->hdf_dimscaleid = 0; /* Now delete the DIM_WITHOUT_VARIABLE dataset (it will be * recreated later, if necessary). */ if (H5Gunlink(grp->hdf_grpid, dim->hdr.name) < 0) BAIL(NC_EDIMMETA); } } /* Check for unlimited dimension and turn off contiguous storage. */ if (dim->unlimited) var->contiguous = NC_FALSE; /* Track dimensions for variable */ var->dimids[d] = dimidsp[d]; var->dim[d] = dim; } /* Determine default chunksizes for this variable. (Even for * variables which may be contiguous.) */ LOG((4, "allocating array of %d size_t to hold chunksizes for var %s", var->ndims, var->hdr.name)); if (var->ndims) if (!(var->chunksizes = calloc(var->ndims, sizeof(size_t)))) BAIL(NC_ENOMEM); if ((retval = nc4_find_default_chunksizes2(grp, var))) BAIL(retval); /* Is this a variable with a chunksize greater than the current * cache size? */ if ((retval = nc4_adjust_var_cache(grp, var))) BAIL(retval); /* If the user names this variable the same as a dimension, but * doesn't use that dimension first in its list of dimension ids, * is not a coordinate variable. I need to change its HDF5 name, * because the dimension will cause a HDF5 dataset to be created, * and this var has the same name. */ dim = (NC_DIM_INFO_T*)ncindexlookup(grp->dim,norm_name); if (dim && (!var->ndims || dimidsp[0] != dim->hdr.id)) { /* Set a different hdf5 name for this variable to avoid name * clash. */ if (strlen(norm_name) + strlen(NON_COORD_PREPEND) > NC_MAX_NAME) BAIL(NC_EMAXNAME); if (!(var->hdf5_name = malloc((strlen(NON_COORD_PREPEND) + strlen(norm_name) + 1) * sizeof(char)))) BAIL(NC_ENOMEM); sprintf(var->hdf5_name, "%s%s", NON_COORD_PREPEND, norm_name); } /* If this is a coordinate var, it is marked as a HDF5 dimension * scale. (We found dim above.) Otherwise, allocate space to * remember whether dimension scales have been attached to each * dimension. */ if (!var->dimscale && ndims) if (!(var->dimscale_attached = calloc(ndims, sizeof(nc_bool_t)))) BAIL(NC_ENOMEM); /* Return the varid. */ if (varidp) *varidp = var->hdr.id; LOG((4, "new varid %d", var->hdr.id)); exit: if (type_info) if ((retval = nc4_type_free(type_info))) BAIL2(retval); return retval; } /** * @internal This functions sets extra stuff about a netCDF-4 variable which * must be set before the enddef but after the def_var. * * @note All pointer parameters may be NULL, in which case they are ignored. * @param ncid File ID. * @param varid Variable ID. * @param shuffle Pointer to shuffle setting. * @param deflate Pointer to deflate setting. * @param deflate_level Pointer to deflate level. * @param fletcher32 Pointer to fletcher32 setting. * @param contiguous Pointer to contiguous setting. * @param chunksizes Array of chunksizes. * @param no_fill Pointer to no_fill setting. * @param fill_value Pointer to fill value. * @param endianness Pointer to endianness setting. * * @returns ::NC_NOERR for success * @returns ::NC_EBADID Bad ncid. * @returns ::NC_ENOTVAR Invalid variable ID. * @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is * not netCDF-4/HDF5. * @returns ::NC_ESTRICTNC3 Attempting netcdf-4 operation on strict nc3 * netcdf-4 file. * @returns ::NC_ELATEDEF Too late to change settings for this variable. * @returns ::NC_ENOTINDEFINE Not in define mode. * @returns ::NC_EPERM File is read only. * @returns ::NC_EINVAL Invalid input * @returns ::NC_EBADCHUNK Bad chunksize. * @author Ed Hartnett */ static int nc_def_var_extra(int ncid, int varid, int *shuffle, int *deflate, int *deflate_level, int *fletcher32, int *contiguous, const size_t *chunksizes, int *no_fill, const void *fill_value, int *endianness) { NC *nc; NC_GRP_INFO_T *grp; NC_FILE_INFO_T *h5; NC_VAR_INFO_T *var; int d; int retval; /* All or none of these will be provided. */ assert((deflate && deflate_level && shuffle) || (!deflate && !deflate_level && !shuffle)); LOG((2, "%s: ncid 0x%x varid %d", __func__, ncid, varid)); /* Find info for this file and group, and set pointer to each. */ if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5))) return retval; assert(nc && grp && h5); /* Trying to write to a read-only file? No way, Jose! */ if (h5->no_write) return NC_EPERM; /* Find the var. */ var = (NC_VAR_INFO_T*)ncindexith(grp->vars,varid); if(!var) return NC_ENOTVAR; assert(var && var->hdr.id == varid); /* Can't turn on parallel and deflate/fletcher32/szip/shuffle. */ if (nc->mode & (NC_MPIIO | NC_MPIPOSIX)) { if (deflate || fletcher32 || shuffle) return NC_EINVAL; } /* If the HDF5 dataset has already been created, then it is too * late to set all the extra stuff. */ if (var->created) return NC_ELATEDEF; /* Check compression options. */ if (deflate && !deflate_level) return NC_EINVAL; /* Valid deflate level? */ if (deflate) { if (*deflate) if (*deflate_level < NC_MIN_DEFLATE_LEVEL || *deflate_level > NC_MAX_DEFLATE_LEVEL) return NC_EINVAL; /* For scalars, just ignore attempt to deflate. */ if (!var->ndims) return NC_NOERR; /* Well, if we couldn't find any errors, I guess we have to take * the users settings. Darn! */ var->contiguous = NC_FALSE; var->deflate = *deflate; if (*deflate) var->deflate_level = *deflate_level; LOG((3, "%s: *deflate_level %d", __func__, *deflate_level)); } /* Shuffle filter? */ if (shuffle) { var->shuffle = *shuffle; var->contiguous = NC_FALSE; } /* Fletcher32 checksum error protection? */ if (fletcher32) { var->fletcher32 = *fletcher32; var->contiguous = NC_FALSE; } /* Does the user want a contiguous dataset? Not so fast! Make sure * that there are no unlimited dimensions, and no filters in use * for this data. */ if (contiguous && *contiguous) { if (var->deflate || var->fletcher32 || var->shuffle) return NC_EINVAL; for (d = 0; d < var->ndims; d++) if (var->dim[d]->unlimited) return NC_EINVAL; var->contiguous = NC_TRUE; } /* Chunksizes anyone? */ if (contiguous && *contiguous == NC_CHUNKED) { var->contiguous = NC_FALSE; /* If the user provided chunksizes, check that they are not too * big, and that their total size of chunk is less than 4 GB. */ if (chunksizes) { if ((retval = check_chunksizes(grp, var, chunksizes))) return retval; /* Ensure chunksize is smaller than dimension size */ for (d = 0; d < var->ndims; d++) if(!var->dim[d]->unlimited && var->dim[d]->len > 0 && chunksizes[d] > var->dim[d]->len) return NC_EBADCHUNK; /* Set the chunksizes for this variable. */ for (d = 0; d < var->ndims; d++) var->chunksizes[d] = chunksizes[d]; } } /* Is this a variable with a chunksize greater than the current * cache size? */ if (!var->contiguous && (deflate || contiguous)) { /* Determine default chunksizes for this variable (do nothing * for scalar vars). */ if (var->chunksizes && !var->chunksizes[0]) if ((retval = nc4_find_default_chunksizes2(grp, var))) return retval; /* Adjust the cache. */ if ((retval = nc4_adjust_var_cache(grp, var))) return retval; } /* Are we setting a fill modes? */ if (no_fill) { if (*no_fill) { /* NC_STRING types may not turn off fill mode. It's disallowed * by HDF5 and will cause a HDF5 error later. */ if (*no_fill) if (var->type_info->hdr.id == NC_STRING) return NC_EINVAL; /* Set the no-fill mode. */ var->no_fill = NC_TRUE; } else var->no_fill = NC_FALSE; } /* Are we setting a fill value? */ if (fill_value && !var->no_fill) { /* Copy the fill_value. */ LOG((4, "Copying fill value into metadata for variable %s", var->hdr.name)); /* If there's a _FillValue attribute, delete it. */ retval = NC4_del_att(ncid, varid, _FillValue); if (retval && retval != NC_ENOTATT) return retval; /* Create a _FillValue attribute. */ if ((retval = nc_put_att(ncid, varid, _FillValue, var->type_info->hdr.id, 1, fill_value))) return retval; } /* Is the user setting the endianness? */ if (endianness) var->type_info->endianness = *endianness; return NC_NOERR; } /** * @internal Set compression settings on a variable. This is called by * nc_def_var_deflate(). * * @param ncid File ID. * @param varid Variable ID. * @param shuffle True to turn on the shuffle filter. * @param deflate True to turn on deflation. * @param deflate_level A number between 0 (no compression) and 9 * (maximum compression). * * @returns ::NC_NOERR No error. * @returns ::NC_EBADID Bad ncid. * @returns ::NC_ENOTVAR Invalid variable ID. * @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is * not netCDF-4/HDF5. * @returns ::NC_ELATEDEF Too late to change settings for this variable. * @returns ::NC_ENOTINDEFINE Not in define mode. * @returns ::NC_EINVAL Invalid input * @author Ed Hartnett, Dennis Heimbigner */ int NC4_def_var_deflate(int ncid, int varid, int shuffle, int deflate, int deflate_level) { return nc_def_var_extra(ncid, varid, &shuffle, &deflate, &deflate_level, NULL, NULL, NULL, NULL, NULL, NULL); } /** * @internal Set checksum on a variable. This is called by * nc_def_var_fletcher32(). * * @param ncid File ID. * @param varid Variable ID. * @param fletcher32 Pointer to fletcher32 setting. * * @returns ::NC_NOERR No error. * @returns ::NC_EBADID Bad ncid. * @returns ::NC_ENOTVAR Invalid variable ID. * @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is * not netCDF-4/HDF5. * @returns ::NC_ELATEDEF Too late to change settings for this variable. * @returns ::NC_ENOTINDEFINE Not in define mode. * @returns ::NC_EINVAL Invalid input * @author Ed Hartnett, Dennis Heimbigner */ int NC4_def_var_fletcher32(int ncid, int varid, int fletcher32) { return nc_def_var_extra(ncid, varid, NULL, NULL, NULL, &fletcher32, NULL, NULL, NULL, NULL, NULL); } /** * @internal Define chunking stuff for a var. This is called by * nc_def_var_chunking(). Chunking is required in any dataset with one * or more unlimited dimensions in HDF5, or any dataset using a * filter. * * @param ncid File ID. * @param varid Variable ID. * @param contiguous Pointer to contiguous setting. * @param chunksizesp Array of chunksizes. * * @returns ::NC_NOERR No error. * @returns ::NC_EBADID Bad ncid. * @returns ::NC_ENOTVAR Invalid variable ID. * @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is * not netCDF-4/HDF5. * @returns ::NC_ELATEDEF Too late to change settings for this variable. * @returns ::NC_ENOTINDEFINE Not in define mode. * @returns ::NC_EINVAL Invalid input * @returns ::NC_EBADCHUNK Bad chunksize. * @author Ed Hartnett, Dennis Heimbigner */ int NC4_def_var_chunking(int ncid, int varid, int contiguous, const size_t *chunksizesp) { return nc_def_var_extra(ncid, varid, NULL, NULL, NULL, NULL, &contiguous, chunksizesp, NULL, NULL, NULL); } /** * @internal Define chunking stuff for a var. This is called by * the fortran API. * * @param ncid File ID. * @param varid Variable ID. * @param contiguous Pointer to contiguous setting. * @param chunksizesp Array of chunksizes. * * @returns ::NC_NOERR No error. * @returns ::NC_EBADID Bad ncid. * @returns ::NC_ENOTVAR Invalid variable ID. * @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is * not netCDF-4/HDF5. * @returns ::NC_ELATEDEF Too late to change settings for this variable. * @returns ::NC_ENOTINDEFINE Not in define mode. * @returns ::NC_EINVAL Invalid input * @returns ::NC_EBADCHUNK Bad chunksize. * @author Ed Hartnett */ int nc_def_var_chunking_ints(int ncid, int varid, int contiguous, int *chunksizesp) { NC *nc; NC_GRP_INFO_T *grp; NC_VAR_INFO_T *var; NC_FILE_INFO_T *h5; size_t *cs = NULL; int i, retval; /* Find this ncid's file info. */ if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5))) return retval; assert(nc); /* Find var cause I need the number of dims. */ if ((retval = nc4_find_g_var_nc(nc, ncid, varid, &grp, &var))) return retval; /* Allocate space for the size_t copy of the chunksizes array. */ if (var->ndims) if (!(cs = malloc(var->ndims * sizeof(size_t)))) return NC_ENOMEM; /* Copy to size_t array. */ for (i = 0; i < var->ndims; i++) cs[i] = chunksizesp[i]; retval = nc_def_var_extra(ncid, varid, NULL, NULL, NULL, NULL, &contiguous, cs, NULL, NULL, NULL); if (var->ndims) free(cs); return retval; } /** * @internal This functions sets fill value and no_fill mode for a * netCDF-4 variable. It is called by nc_def_var_fill(). * * @note All pointer parameters may be NULL, in which case they are ignored. * @param ncid File ID. * @param varid Variable ID. * @param no_fill No_fill setting. * @param fill_value Pointer to fill value. * * @returns ::NC_NOERR for success * @returns ::NC_EBADID Bad ncid. * @returns ::NC_ENOTVAR Invalid variable ID. * @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is * not netCDF-4/HDF5. * @returns ::NC_ESTRICTNC3 Attempting netcdf-4 operation on strict nc3 * netcdf-4 file. * @returns ::NC_ELATEDEF Too late to change settings for this variable. * @returns ::NC_ENOTINDEFINE Not in define mode. * @returns ::NC_EPERM File is read only. * @returns ::NC_EINVAL Invalid input * @author Ed Hartnett */ int NC4_def_var_fill(int ncid, int varid, int no_fill, const void *fill_value) { return nc_def_var_extra(ncid, varid, NULL, NULL, NULL, NULL, NULL, NULL, &no_fill, fill_value, NULL); } /** * @internal This functions sets endianness for a netCDF-4 * variable. Called by nc_def_var_endian(). * * @note All pointer parameters may be NULL, in which case they are ignored. * @param ncid File ID. * @param varid Variable ID. * @param endianness Endianness setting. * * @returns ::NC_NOERR for success * @returns ::NC_EBADID Bad ncid. * @returns ::NC_ENOTVAR Invalid variable ID. * @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is * not netCDF-4/HDF5. * @returns ::NC_ESTRICTNC3 Attempting netcdf-4 operation on strict nc3 * netcdf-4 file. * @returns ::NC_ELATEDEF Too late to change settings for this variable. * @returns ::NC_ENOTINDEFINE Not in define mode. * @returns ::NC_EPERM File is read only. * @returns ::NC_EINVAL Invalid input * @author Ed Hartnett */ int NC4_def_var_endian(int ncid, int varid, int endianness) { return nc_def_var_extra(ncid, varid, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, &endianness); } /** * @internal Define filter settings. Called by nc_def_var_filter(). * * @param ncid File ID. * @param varid Variable ID. * @param id Filter ID * @param nparams Number of parameters for filter. * @param parms Filter parameters. * * @returns ::NC_NOERR for success * @returns ::NC_EBADID Bad ncid. * @returns ::NC_ENOTVAR Invalid variable ID. * @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is * not netCDF-4/HDF5. * @returns ::NC_ELATEDEF Too late to change settings for this variable. * @returns ::NC_EFILTER Filter error. * @returns ::NC_EINVAL Invalid input * @author Dennis Heimbigner */ int NC4_def_var_filter(int ncid, int varid, unsigned int id, size_t nparams, const unsigned int* parms) { int retval = NC_NOERR; NC *nc; NC_GRP_INFO_T *grp; NC_FILE_INFO_T *h5; NC_VAR_INFO_T *var; LOG((2, "%s: ncid 0x%x varid %d", __func__, ncid, varid)); /* Find info for this file and group, and set pointer to each. */ if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5))) return retval; assert(nc && grp && h5); /* Find the var. */ var = (NC_VAR_INFO_T*)ncindexith(grp->vars,varid); if(!var) return NC_ENOTVAR; assert(var->hdr.id == varid); /* Can't turn on parallel and filters */ if (nc->mode & (NC_MPIIO | NC_MPIPOSIX)) { return NC_EINVAL; } /* If the HDF5 dataset has already been created, then it is too * late to set all the extra stuff. */ if (var->created) return NC_ELATEDEF; #ifdef HAVE_H5Z_SZIP if(id == H5Z_FILTER_SZIP) { if(nparams != 2) return NC_EFILTER; /* incorrect no. of parameters */ } #else /*!HAVE_H5Z_SZIP*/ if(id == H5Z_FILTER_SZIP) return NC_EFILTER; /* Not allowed */ #endif #if 0 { unsigned int fcfg = 0; herr_t herr = H5Zget_filter_info(id,&fcfg); if(herr < 0) return NC_EFILTER; if((H5Z_FILTER_CONFIG_ENCODE_ENABLED & fcfg) == 0 || (H5Z_FILTER_CONFIG_DECODE_ENABLED & fcfg) == 0) return NC_EFILTER; } #endif /*0*/ var->filterid = id; var->nparams = nparams; var->params = NULL; if(parms != NULL) { var->params = (unsigned int*)calloc(nparams,sizeof(unsigned int)); if(var->params == NULL) return NC_ENOMEM; memcpy(var->params,parms,sizeof(unsigned int)*var->nparams); } return NC_NOERR; } /** * @internal Rename a var to "bubba," for example. This is called by * nc_rename_var() for netCDF-4 files. * * @param ncid File ID. * @param varid Variable ID * @param name New name of the variable. * * @returns ::NC_NOERR No error. * @returns ::NC_EBADID Bad ncid. * @returns ::NC_ENOTVAR Invalid variable ID. * @returns ::NC_EBADNAME Bad name. * @returns ::NC_EMAXNAME Name is too long. * @returns ::NC_ENAMEINUSE Name in use. * @returns ::NC_ENOMEM Out of memory. * @author Ed Hartnett */ int NC4_rename_var(int ncid, int varid, const char *name) { NC *nc; NC_GRP_INFO_T *grp; NC_FILE_INFO_T *h5; NC_VAR_INFO_T *var, *tmpvar; int retval = NC_NOERR; if (!name) return NC_EINVAL; LOG((2, "%s: ncid 0x%x varid %d name %s", __func__, ncid, varid, name)); /* Find info for this file and group, and set pointer to each. */ if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5))) return retval; assert(h5 && grp && h5); /* Is the new name too long? */ if (strlen(name) > NC_MAX_NAME) return NC_EMAXNAME; /* Trying to write to a read-only file? No way, Jose! */ if (h5->no_write) return NC_EPERM; /* Check name validity, if strict nc3 rules are in effect for this * file. */ if ((retval = NC_check_name(name))) return retval; /* Get the variable wrt varid */ var = (NC_VAR_INFO_T*)ncindexith(grp->vars,varid); if (!var) return NC_ENOTVAR; /* Check if new name is in use; note that renaming to same name is still an error according to the nc_test/test_write.c code. Why?*/ tmpvar = (NC_VAR_INFO_T*)ncindexlookup(grp->vars,name); if(tmpvar != NULL) return NC_ENAMEINUSE; /* If we're not in define mode, new name must be of equal or less size, if strict nc3 rules are in effect for this . */ if (!(h5->flags & NC_INDEF) && strlen(name) > strlen(var->hdr.name) && (h5->cmode & NC_CLASSIC_MODEL)) return NC_ENOTINDEFINE; /* Change the HDF5 file, if this var has already been created there. Should we check here to ensure there is not already a dimscale dataset of name name??? */ if (var->created) { /* Is there an existing dimscale-only dataset of this name? If * so, it must be deleted. */ if (var->ndims && var->dim[0]->hdf_dimscaleid) { if ((retval = delete_existing_dimscale_dataset(grp, var->dim[0]->hdr.id, var->dim[0]))) return retval; } LOG((3, "Moving dataset %s to %s", var->hdr.name, name)); if (H5Gmove(grp->hdf_grpid, var->hdr.name, name) < 0) BAIL(NC_EHDFERR); } /* Now change the name in our metadata. */ free(var->hdr.name); if (!(var->hdr.name = strdup(name))) return NC_ENOMEM; LOG((3, "var is now %s", var->hdr.name)); var->hdr.hashkey = NC_hashmapkey(var->hdr.name,strlen(var->hdr.name)); /* Fix hash key */ if(!ncindexrebuild(grp->vars)) return NC_EINTERNAL; /* Check if this was a coordinate variable previously, but names are different now */ if (var->dimscale && strcmp(var->hdr.name, var->dim[0]->hdr.name)) { /* Break up the coordinate variable */ if ((retval = nc4_break_coord_var(grp, var, var->dim[0]))) return retval; } /* Check if this should become a coordinate variable */ if (!var->dimscale) { /* Only variables with >0 dimensions can become coordinate variables */ if (var->ndims) { NC_GRP_INFO_T *dim_grp; NC_DIM_INFO_T *dim; /* Check to see if this is became a coordinate variable. If so, it * will have the same name as dimension index 0. If it is a * coordinate var, is it a coordinate var in the same group as the dim? */ if ((retval = nc4_find_dim(grp, var->dimids[0], &dim, &dim_grp))) return retval; if (!strcmp(dim->hdr.name, name) && dim_grp == grp) { /* Reform the coordinate variable */ if ((retval = nc4_reform_coord_var(grp, var, dim))) return retval; var->became_coord_var = NC_TRUE; } } } exit: return retval; } /** * @internal Write an array of data to a variable. This is called by * nc_put_vara() and other nc_put_vara_* functions, for netCDF-4 * files. * * @param ncid File ID. * @param varid Variable ID. * @param startp Array of start indices. * @param countp Array of counts. * @param op pointer that gets the data. * @param memtype The type of these data in memory. * * @returns ::NC_NOERR for success * @author Ed Hartnett, Dennis Heimbigner */ int NC4_put_vara(int ncid, int varid, const size_t *startp, const size_t *countp, const void *op, int memtype) { NC *nc; if (!(nc = nc4_find_nc_file(ncid, NULL))) return NC_EBADID; return nc4_put_vars(nc, ncid, varid, startp, countp, NULL, memtype, (void *)op); } /** * Read an array of values. This is called by nc_get_vara() for * netCDF-4 files, as well as all the other nc_get_vara_* * functions. * * @param ncid File ID. * @param varid Variable ID. * @param startp Array of start indices. * @param countp Array of counts. * @param ip pointer that gets the data. * @param memtype The type of these data after it is read into memory. * @returns ::NC_NOERR for success * @author Ed Hartnett, Dennis Heimbigner */ int NC4_get_vara(int ncid, int varid, const size_t *startp, const size_t *countp, void *ip, int memtype) { NC *nc; NC_FILE_INFO_T* h5; LOG((2, "%s: ncid 0x%x varid %d memtype %d", __func__, ncid, varid, memtype)); if (!(nc = nc4_find_nc_file(ncid, &h5))) return NC_EBADID; /* Get the data. */ return nc4_get_vars(nc, ncid, varid, startp, countp, NULL, memtype, (void *)ip); } /** * @internal Write an array of data to a variable. This is called by * nc_put_vars() and other nc_put_vars_* functions, for netCDF-4 * files. * * @param ncid File ID. * @param varid Variable ID. * @param startp Array of start indices. * @param countp Array of counts. * @param stridep Array of strides. * @param op pointer that gets the data. * @param memtype The type of these data in memory. * * @returns ::NC_NOERR for success * @author Dennis Heimbigner */ int NC4_put_vars(int ncid, int varid, const size_t *startp, const size_t *countp, const ptrdiff_t* stridep, const void *op, int memtype) { NC *nc; if (!(nc = nc4_find_nc_file(ncid, NULL))) return NC_EBADID; return nc4_put_vars(nc, ncid, varid, startp, countp, stridep, memtype, (void *)op); } /** * Read an array of values. This is called by nc_get_vars() for * netCDF-4 files, as well as all the other nc_get_vars_* * functions. * * @param ncid File ID. * @param varid Variable ID. * @param startp Array of start indices. * @param countp Array of counts. * @param stridep Array of strides. * @param ip pointer that gets the data. * @param memtype The type of these data after it is read into memory. * @returns ::NC_NOERR for success * @author Dennis Heimbigner */ int NC4_get_vars(int ncid, int varid, const size_t *startp, const size_t *countp, const ptrdiff_t *stridep, void *ip, int memtype) { NC *nc; NC_FILE_INFO_T *h5; LOG((2, "%s: ncid 0x%x varid %d memtype %d", __func__, ncid, varid, memtype)); if (!(nc = nc4_find_nc_file(ncid, &h5))) return NC_EBADID; /* Get the data. */ return nc4_get_vars(nc, ncid, varid, startp, countp, stridep, memtype, (void *)ip); }