/* This file is part of netcdf-4, a netCDF-like interface for HDF5, or a HDF5 backend for netCDF, depending on your point of view. This file handles the nc4 variable functions. Copyright 2003-2006, University Corporation for Atmospheric Research. See COPYRIGHT file for copying and redistribution conditions. */ #include #include "nc4dispatch.h" #include /* Min and max deflate levels tolerated by HDF5. */ #define MIN_DEFLATE_LEVEL 0 #define MAX_DEFLATE_LEVEL 9 /* This is to track opened HDF5 objects to make sure they are * closed. */ #ifdef EXTRA_TESTS extern int num_plists; #endif /* EXTRA_TESTS */ /* One meg is the minimum buffer size. */ #define ONE_MEG 1048576 /* Szip options. */ #define NC_SZIP_EC_OPTION_MASK 4 #define NC_SZIP_NN_OPTION_MASK 32 #define NC_SZIP_MAX_PIXELS_PER_BLOCK 32 extern int nc4_get_default_fill_value(const NC_TYPE_INFO_T *type_info, void *fill_value); /* If the HDF5 dataset for this variable is open, then close it and * reopen it, with the perhaps new settings for chunk caching. */ 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; #ifdef EXTRA_TESTS num_plists++; #endif 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->name, access_pid)) < 0) return NC_EHDFERR; if (H5Pclose(access_pid) < 0) return NC_EHDFERR; #ifdef EXTRA_TESTS num_plists--; #endif } return NC_NOERR; } /* Set chunk cache size for a variable. */ int NC4_set_var_chunk_cache(int ncid, int varid, size_t size, size_t nelems, float preemption) { NC *nc; NC_GRP_INFO_T *grp; NC_HDF5_FILE_INFO_T *h5; NC_VAR_INFO_T *var; int retval; /* Check input for validity. */ if (preemption < 0 || preemption > 1) return NC_EINVAL; /* 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; /* An attempt to do any of these things on a netCDF-3 file is * ignored with no error. */ if (!h5) return NC_NOERR; assert(nc && grp && h5); /* Find the var. */ if (varid < 0 || varid >= grp->vars.nelems) return NC_ENOTVAR; var = grp->vars.value[varid]; if (!var) return NC_ENOTVAR; assert(var->varid == varid); /* Set the values. */ var->chunk_cache_size = size; var->chunk_cache_nelems = nelems; var->chunk_cache_preemption = preemption; if ((retval = nc4_reopen_dataset(grp, var))) return retval; return NC_NOERR; } /* Need this version for fortran. Accept negative numbers to leave * settings as they are. */ int nc_set_var_chunk_cache_ints(int ncid, int varid, int size, int nelems, int preemption) { size_t real_size = H5D_CHUNK_CACHE_NBYTES_DEFAULT; size_t real_nelems = H5D_CHUNK_CACHE_NSLOTS_DEFAULT; float real_preemption = H5D_CHUNK_CACHE_W0_DEFAULT; if (size >= 0) real_size = ((size_t) size) * MEGABYTE; if (nelems >= 0) real_nelems = nelems; if (preemption >= 0) real_preemption = preemption / 100.; return NC4_set_var_chunk_cache(ncid, varid, real_size, real_nelems, real_preemption); } /* Get chunk cache size for a variable. */ int NC4_get_var_chunk_cache(int ncid, int varid, size_t *sizep, size_t *nelemsp, float *preemptionp) { NC *nc; NC_GRP_INFO_T *grp; NC_HDF5_FILE_INFO_T *h5; NC_VAR_INFO_T *var; int retval; /* 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; /* Attempting to do any of these things on a netCDF-3 file produces * an error. */ if (!h5) return NC_ENOTNC4; assert(nc && grp && h5); /* Find the var. */ if (varid < 0 || varid >= grp->vars.nelems) return NC_ENOTVAR; var = grp->vars.value[varid]; if (!var) return NC_ENOTVAR; assert(var->varid == varid); /* Give the user what they want. */ if (sizep) *sizep = var->chunk_cache_size; if (nelemsp) *nelemsp = var->chunk_cache_nelems; if (preemptionp) *preemptionp = var->chunk_cache_preemption; return NC_NOERR; } /* Get chunk cache size for a variable. */ int nc_get_var_chunk_cache_ints(int ncid, int varid, int *sizep, int *nelemsp, int *preemptionp) { size_t real_size, real_nelems; float real_preemption; int ret; if ((ret = NC4_get_var_chunk_cache(ncid, varid, &real_size, &real_nelems, &real_preemption))) return ret; if (sizep) *sizep = real_size / MEGABYTE; if (nelemsp) *nelemsp = (int)real_nelems; if(preemptionp) *preemptionp = (int)(real_preemption * 100); return NC_NOERR; } /* Check a set of chunksizes to see if they specify a chunk that is too big. */ 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->nc_typeid, 0, &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++) { if (chunksizes[d] < 1) return NC_EINVAL; dprod *= (double) chunksizes[d]; } if (dprod > (double) NC_MAX_UINT) return NC_EBADCHUNK; return NC_NOERR; } /* Find the default chunk nelems (i.e. length of chunk along each * dimension). */ 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 */ #define DEFAULT_1D_UNLIM_SIZE (4096) /* TODO: make build-time parameter? */ 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->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->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->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; } #define NC_ARRAY_GROWBY 4 int nc4_vararray_add(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var) { NC_VAR_INFO_T **vp = NULL; if (grp->vars.nalloc == 0) { assert(grp->vars.nelems == 0); vp = (NC_VAR_INFO_T **) malloc(NC_ARRAY_GROWBY * sizeof(NC_VAR_INFO_T *)); if(vp == NULL) return NC_ENOMEM; grp->vars.value = vp; grp->vars.nalloc = NC_ARRAY_GROWBY; } else if(grp->vars.nelems +1 > grp->vars.nalloc) { vp = (NC_VAR_INFO_T **) realloc(grp->vars.value, (grp->vars.nalloc + NC_ARRAY_GROWBY) * sizeof(NC_VAR_INFO_T *)); if(vp == NULL) return NC_ENOMEM; grp->vars.value = vp; grp->vars.nalloc += NC_ARRAY_GROWBY; } if(var != NULL) { assert(var->varid == grp->vars.nelems); grp->vars.value[grp->vars.nelems] = var; grp->vars.nelems++; } return NC_NOERR; } /* This is called when a new netCDF-4 variable is defined. Break it * down! */ static int nc_def_var_nc4(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_HDF5_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. */ if (!(h5->flags & NC_INDEF)) { if (h5->cmode & NC_CLASSIC_MODEL) BAIL(NC_ENOTINDEFINE); if ((retval = NC4_redef(ncid))) BAIL(retval); } /* 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); /* cast needed for braindead systems with signed size_t */ if((unsigned long) ndims > X_INT_MAX) /* Backward compat */ BAIL(NC_EINVAL); /* Classic model files have a limit on number of vars. */ if(h5->cmode & NC_CLASSIC_MODEL && h5->nvars >= NC_MAX_VARS) BAIL(NC_EMAXVARS); /* 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); /* If the file is read-only, return an error. */ if (h5->no_write) BAIL(NC_EPERM); /* 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((3, "%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 /* Add a new var. */ if ((retval = nc4_var_add(&var))) BAIL(retval); /* Now fill in the values in the var info structure. */ if (!(var->name = malloc((strlen(norm_name) + 1) * sizeof(char)))) BAIL(NC_ENOMEM); strcpy(var->name, norm_name); var->hash = hash_fast(norm_name, strlen(norm_name)); var->varid = grp->nvars++; var->ndims = ndims; var->is_new_var = NC_TRUE; nc4_vararray_add(grp, var); /* 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) { if (!(type_info = calloc(1, sizeof(NC_TYPE_INFO_T)))) BAIL(NC_ENOMEM); type_info->nc_typeid = xtype; 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->nc_typeid, 0, &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); } /* Point to the type, and increment its ref. count */ var->type_info = type_info; var->type_info->rc++; type_info = NULL; /* Allocate space for dimension information. */ if (ndims) { if (!(var->dim = calloc(ndims, sizeof(NC_DIM_INFO_T *)))) BAIL(NC_ENOMEM); if (!(var->dimids = calloc(ndims, sizeof(int)))) BAIL(NC_ENOMEM); } /* 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 && dim->hash == var->hash && strcmp(dim->name, norm_name) == 0) { var->dimscale = NC_TRUE; dim->coord_var = var; /* Use variable's dataset ID for the dimscale ID */ 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); if (H5Dclose(dim->hdf_dimscaleid) < 0) BAIL(NC_EHDFERR); dim->hdf_dimscaleid = 0; /* Now delete the dataset (it will be recreated later, if necessary) */ if (H5Gunlink(grp->hdf_grpid, dim->name) < 0) BAIL(NC_EDIMMETA); } } /* Check for unlimited dimension and turn off contiguous storage */ /* (unless HDF4 file) */ #ifdef USE_HDF4 if (dim->unlimited && !h5->hdf4) #else if (dim->unlimited) #endif 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->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. */ for (dim = grp->dim; dim; dim = dim->l.next) if (dim->hash == var->hash && !strcmp(dim->name, norm_name) && (!var->ndims || dimidsp[0] != dim->dimid)) { /* 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 (ndims && !(var->dimscale_attached = calloc(ndims, sizeof(nc_bool_t)))) BAIL(NC_ENOMEM); /* Return the varid. */ if (varidp) *varidp = var->varid; LOG((4, "new varid %d", var->varid)); exit: if (type_info) if ((retval = nc4_type_free(type_info))) BAIL2(retval); return retval; } /* Create a new variable to hold user data. This is what it's all * about baby! */ int NC4_def_var(int ncid, const char *name, nc_type xtype, int ndims, const int *dimidsp, int *varidp) { NC *nc; NC_HDF5_FILE_INFO_T *h5; LOG((2, "%s: ncid 0x%x name %s xtype %d ndims %d", __func__, ncid, name, xtype, ndims)); /* If there are dimensions, I need their ids. */ if (ndims && !dimidsp) return NC_EINVAL; /* Find metadata for this file. */ if (!(nc = nc4_find_nc_file(ncid,&h5))) return NC_EBADID; /* Handle netcdf-4 cases. */ return nc_def_var_nc4(ncid, name, xtype, ndims, dimidsp, varidp); } /* Get all the information about a variable. Pass NULL for whatever * you don't care about. This is an internal function, not exposed to * the user. */ int NC4_inq_var_all(int ncid, int varid, char *name, nc_type *xtypep, int *ndimsp, int *dimidsp, int *nattsp, int *shufflep, int *deflatep, int *deflate_levelp, int *fletcher32p, int *contiguousp, size_t *chunksizesp, int *no_fill, void *fill_valuep, int *endiannessp, int *options_maskp, int *pixels_per_blockp) { NC *nc; NC_GRP_INFO_T *grp; NC_HDF5_FILE_INFO_T *h5; NC_VAR_INFO_T *var; NC_ATT_INFO_T *att; int natts=0; int d; int retval; 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); assert(grp && h5); /* Walk through the list of vars, and return the info about the one with a matching varid. If the varid is -1, find the global atts and call it a day. */ if (varid == NC_GLOBAL) { if (nattsp) { for (att = grp->att; att; att = att->l.next) natts++; *nattsp = natts; } return NC_NOERR; } /* Find the var. */ if (varid < 0 || varid >= grp->vars.nelems) return NC_ENOTVAR; var = grp->vars.value[varid]; if (!var) return NC_ENOTVAR; assert(var->varid == varid); /* Copy the data to the user's data buffers. */ if (name) strcpy(name, var->name); if (xtypep) *xtypep = var->type_info->nc_typeid; if (ndimsp) *ndimsp = var->ndims; if (dimidsp) for (d = 0; d < var->ndims; d++) dimidsp[d] = var->dimids[d]; if (nattsp) { for (att = var->att; att; att = att->l.next) natts++; *nattsp = natts; } /* Chunking stuff. */ if (!var->contiguous && chunksizesp) for (d = 0; d < var->ndims; d++) { chunksizesp[d] = var->chunksizes[d]; LOG((4, "chunksizesp[%d]=%d", d, chunksizesp[d])); } if (contiguousp) *contiguousp = var->contiguous ? NC_CONTIGUOUS : NC_CHUNKED; /* Filter stuff. */ if (deflatep) *deflatep = (int)var->deflate; if (deflate_levelp) *deflate_levelp = var->deflate_level; if (shufflep) *shufflep = (int)var->shuffle; if (fletcher32p) *fletcher32p = (int)var->fletcher32; /* NOTE: No interface for returning szip flag currently (but it should never * be set). */ if (options_maskp) *options_maskp = var->options_mask; if (pixels_per_blockp) *pixels_per_blockp = var->pixels_per_block; /* Fill value stuff. */ if (no_fill) *no_fill = (int)var->no_fill; /* Don't do a thing with fill_valuep if no_fill mode is set for * this var, or if fill_valuep is NULL. */ if (!var->no_fill && fill_valuep) { /* Do we have a fill value for this var? */ if (var->fill_value) { if (var->type_info->nc_type_class == NC_STRING) { if (*(char **)var->fill_value) { if (!(fill_valuep = calloc(1, sizeof(char *)))) return NC_ENOMEM; if (!(*(char **)fill_valuep = strdup(*(char **)var->fill_value))) { free(fill_valuep); return NC_ENOMEM; } } } else { assert(var->type_info->size); memcpy(fill_valuep, var->fill_value, var->type_info->size); } } else { if (var->type_info->nc_type_class == NC_STRING) { if (!(fill_valuep = calloc(1, sizeof(char *)))) return NC_ENOMEM; if ((retval = nc4_get_default_fill_value(var->type_info, (char **)fill_valuep))) { free(fill_valuep); return retval; } else { free(fill_valuep); } } else { if ((retval = nc4_get_default_fill_value(var->type_info, fill_valuep))) return retval; } } } /* Does the user want the endianness of this variable? */ if (endiannessp) *endiannessp = var->type_info->endianness; return NC_NOERR; } /* This functions sets extra stuff about a netCDF-4 variable which must be set before the enddef but after the def_var. This is an internal function, deliberately hidden from the user so that we can change the prototype of this functions without changing the API. */ 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_HDF5_FILE_INFO_T *h5; NC_VAR_INFO_T *var; NC_DIM_INFO_T *dim; int d; int retval; nc_bool_t ishdf4 = NC_FALSE; /* Use this to avoid so many ifdefs */ 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; #ifdef USE_HDF4 ishdf4 = h5->hdf4; #endif /* Attempting to do any of these things on a netCDF-3 file produces * an error. */ if (!h5) return NC_ENOTNC4; assert(nc && grp && h5); /* Find the var. */ if (varid < 0 || varid >= grp->vars.nelems) return NC_ENOTVAR; var = grp->vars.value[varid]; if (!var) return NC_ENOTVAR; assert(var->varid == varid); /* Can't turn on contiguous and deflate/fletcher32/szip. */ if (contiguous) if ((*contiguous != NC_CHUNKED && deflate) || (*contiguous != NC_CHUNKED && fletcher32)) return NC_EINVAL; /* 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 && deflate_level) { if (*deflate) if (*deflate_level < MIN_DEFLATE_LEVEL || *deflate_level > 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; if (!ishdf4) { for (d = 0; d < var->ndims; d++) { dim = var->dim[d]; if (dim->unlimited) return NC_EINVAL; } var->contiguous = NC_TRUE; } } /* Chunksizes anyone? */ if (!ishdf4 && 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; for (d = 0; d < var->ndims; d++) { if(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 && (chunksizes || deflate || contiguous)) { /* Determine default chunksizes for this variable. */ if (!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) 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->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->nc_typeid, 1, fill_value))) return retval; } /* Is the user setting the endianness? */ if (endianness) var->type_info->endianness = *endianness; return NC_NOERR; } /* Set the deflate level for a var, lower is faster, higher is * better. Must be called after nc_def_var and before nc_enddef or any * functions which writes data to the file. */ 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); } /* Set checksum for a var. This must be called after the nc_def_var * but before the nc_enddef. */ 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); } /* Define chunking stuff for a var. This must be done after nc_def_var and before nc_enddef. Chunking is required in any dataset with one or more unlimited dimensions in HDF5, or any dataset using a filter. Where chunksize is a pointer to an array of size ndims, with the chunksize in each dimension. */ 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); } /* Inquire about chunking stuff for a var. This is a private, * undocumented function, used by the f77 API to avoid size_t * problems. */ int nc_inq_var_chunking_ints(int ncid, int varid, int *contiguousp, int *chunksizesp) { NC *nc; NC_GRP_INFO_T *grp; NC_VAR_INFO_T *var; NC_HDF5_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; retval = NC4_inq_var_all(ncid, varid, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, contiguousp, cs, NULL, NULL, NULL, NULL, NULL); /* Copy from size_t array. */ if (*contiguousp == NC_CHUNKED) for (i = 0; i < var->ndims; i++) { chunksizesp[i] = (int)cs[i]; if (cs[i] > NC_MAX_INT) retval = NC_ERANGE; } if (var->ndims) free(cs); return retval; } /* This function defines the chunking with ints, which works better * with F77 portability. It is a secret function, which has been * rendered unmappable, and it is impossible to apparate anywhere in * this function. */ 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_HDF5_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); #ifdef USE_HDF4 if(h5->hdf4) return NC_NOERR; #endif /* 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; } /* Define fill value behavior for a variable. This must be done after nc_def_var and before nc_enddef. */ 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); } /* Define the endianness of a variable. */ 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); } /* Get var id from name. */ int NC4_inq_varid(int ncid, const char *name, int *varidp) { NC *nc; NC_GRP_INFO_T *grp; NC_VAR_INFO_T *var; char norm_name[NC_MAX_NAME + 1]; int retval; uint32_t nn_hash; int i; if (!name) return NC_EINVAL; if (!varidp) return NC_NOERR; LOG((2, "%s: ncid 0x%x name %s", __func__, ncid, name)); /* Find info for this file and group, and set pointer to each. */ if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, NULL))) return retval; /* Normalize name. */ if ((retval = nc4_normalize_name(name, norm_name))) return retval; nn_hash = hash_fast(norm_name, strlen(norm_name)); /* Find var of this name. */ for (i=0; i < grp->vars.nelems; i++) { var = grp->vars.value[i]; if (!var) continue; if (nn_hash == var->hash && !(strcmp(var->name, norm_name))) { *varidp = var->varid; return NC_NOERR; } } return NC_ENOTVAR; } /* Rename a var to "bubba," for example. According to the netcdf-3.5 docs: If the new name is longer than the old name, the netCDF dataset must be in define mode. */ int NC4_rename_var(int ncid, int varid, const char *name) { NC *nc; NC_GRP_INFO_T *grp; NC_HDF5_FILE_INFO_T *h5; NC_VAR_INFO_T *var, *tmp_var; uint32_t nn_hash; int retval = NC_NOERR; int i; 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); /* 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; /* Check if name is in use, and retain a pointer to the correct variable */ nn_hash = hash_fast(name, strlen(name)); tmp_var = NULL; for (i=0; i < grp->vars.nelems; i++) { var = grp->vars.value[i]; if (!var) continue; if (nn_hash == var->hash && !strncmp(var->name, name, NC_MAX_NAME)) return NC_ENAMEINUSE; if (var->varid == varid) tmp_var = var; } if (!tmp_var) return NC_ENOTVAR; var = tmp_var; /* 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->name) && (h5->cmode & NC_CLASSIC_MODEL)) return NC_ENOTINDEFINE; /* Change the HDF5 file, if this var has already been created there. */ if (var->created) { if (H5Gmove(grp->hdf_grpid, var->name, name) < 0) BAIL(NC_EHDFERR); } /* Now change the name in our metadata. */ free(var->name); if (!(var->name = malloc((strlen(name) + 1) * sizeof(char)))) return NC_ENOMEM; strcpy(var->name, name); var->hash = nn_hash; /* Check if this was a coordinate variable previously, but names are different now */ if (var->dimscale && strcmp(var->name, var->dim[0]->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->name, name) == 0 && dim_grp == grp) { /* Reform the coordinate variable */ if ((retval = nc4_reform_coord_var(grp, var, dim))) return retval; } } } exit: return retval; } int NC4_var_par_access(int ncid, int varid, int par_access) { #ifndef USE_PARALLEL4 return NC_ENOPAR; #else NC *nc; NC_GRP_INFO_T *grp; NC_HDF5_FILE_INFO_T *h5; NC_VAR_INFO_T *var; int retval; LOG((1, "%s: ncid 0x%x varid %d par_access %d", __func__, ncid, varid, par_access)); if (par_access != NC_INDEPENDENT && par_access != NC_COLLECTIVE) return NC_EINVAL; /* 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; /* This function only for files opened with nc_open_par or nc_create_par. */ if (!h5->parallel) return NC_ENOPAR; /* Find the var, and set its preference. */ if (varid < 0 || varid >= grp->vars.nelems) return NC_ENOTVAR; var = grp->vars.value[varid]; if (!var) return NC_ENOTVAR; assert(var->varid == varid); if (par_access) var->parallel_access = NC_COLLECTIVE; else var->parallel_access = NC_INDEPENDENT; return NC_NOERR; #endif /* USE_PARALLEL4 */ } static int nc4_put_vara_tc(int ncid, int varid, nc_type mem_type, int mem_type_is_long, const size_t *startp, const size_t *countp, const void *op) { NC *nc; LOG((2, "%s: ncid 0x%x varid %d mem_type %d mem_type_is_long %d", __func__, ncid, varid, mem_type, mem_type_is_long)); if (!(nc = nc4_find_nc_file(ncid,NULL))) return NC_EBADID; return nc4_put_vara(nc, ncid, varid, startp, countp, mem_type, mem_type_is_long, (void *)op); } #ifdef USE_HDF4 static int nc4_get_hdf4_vara(NC *nc, int ncid, int varid, const size_t *startp, const size_t *countp, nc_type mem_nc_type, int is_long, void *data) { NC_GRP_INFO_T *grp; NC_HDF5_FILE_INFO_T *h5; NC_VAR_INFO_T *var; int32 start32[NC_MAX_VAR_DIMS], edge32[NC_MAX_VAR_DIMS]; int retval, d; /* Find our metadata for this file, group, and var. */ assert(nc); if ((retval = nc4_find_g_var_nc(nc, ncid, varid, &grp, &var))) return retval; h5 = NC4_DATA(nc); assert(grp && h5 && var && var->name); for (d = 0; d < var->ndims; d++) { start32[d] = startp[d]; edge32[d] = countp[d]; } if (SDreaddata(var->sdsid, start32, NULL, edge32, data)) return NC_EHDFERR; return NC_NOERR; } #endif /* USE_HDF4 */ /* Get an array. */ static int nc4_get_vara_tc(int ncid, int varid, nc_type mem_type, int mem_type_is_long, const size_t *startp, const size_t *countp, void *ip) { NC *nc; NC_HDF5_FILE_INFO_T* h5; LOG((2, "%s: ncid 0x%x varid %d mem_type %d mem_type_is_long %d", __func__, ncid, varid, mem_type, mem_type_is_long)); if (!(nc = nc4_find_nc_file(ncid,&h5))) return NC_EBADID; #ifdef USE_HDF4 /* Handle HDF4 cases. */ if (h5->hdf4) return nc4_get_hdf4_vara(nc, ncid, varid, startp, countp, mem_type, mem_type_is_long, (void *)ip); #endif /* USE_HDF4 */ /* Handle HDF5 cases. */ return nc4_get_vara(nc, ncid, varid, startp, countp, mem_type, mem_type_is_long, (void *)ip); } int NC4_put_vara(int ncid, int varid, const size_t *startp, const size_t *countp, const void *op, int memtype) { return nc4_put_vara_tc(ncid, varid, memtype, 0, startp, countp, op); } /* Read an array of values. */ int NC4_get_vara(int ncid, int varid, const size_t *startp, const size_t *countp, void *ip, int memtype) { return nc4_get_vara_tc(ncid, varid, memtype, 0, startp, countp, ip); }