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hdf5internal.c
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/* Copyright 2003-2018, University Corporation for Atmospheric
* Research. See the COPYRIGHT file for copying and redistribution
* conditions.
*/
/**
* @file @internal Internal netcdf-4 functions.
*
* This file contains functions internal to the netcdf4 library. None of
* the functions in this file are exposed in the exetnal API. These
* functions all relate to the manipulation of netcdf-4's in-memory
* buffer of metadata information, i.e. the linked list of NC
* structs.
*
* @author Ed Hartnett
*/
#include "config.h"
#include "nc4internal.h"
#include "nc.h" /* from libsrc */
#include "ncdispatch.h" /* from libdispatch */
#include "ncutf8.h"
#include "H5DSpublic.h"
#undef DEBUGH5
#ifdef DEBUGH5
/**
* @internal Provide a catchable error reporting function
*
* @param ignored Ignored.
*
* @return 0 for success.
*/
static herr_t
h5catch(void* ignored)
{
H5Eprint(NULL);
return 0;
}
#endif
/* These are the default chunk cache sizes for HDF5 files created or
* opened with netCDF-4. */
extern size_t nc4_chunk_cache_size;
extern size_t nc4_chunk_cache_nelems;
extern float nc4_chunk_cache_preemption;
#ifdef LOGGING
/* This is the severity level of messages which will be logged. Use
severity 0 for errors, 1 for important log messages, 2 for less
important, etc. */
extern int nc_log_level;
#endif /* LOGGING */
int nc4_hdf5_initialized = 0; /**< True if initialization has happened. */
/**
* @internal Provide a wrapper for H5Eset_auto
* @param func Pointer to func.
* @param client_data Client data.
*
* @return 0 for success
*/
static herr_t
set_auto(void* func, void *client_data)
{
#ifdef DEBUGH5
return H5Eset_auto2(H5E_DEFAULT,(H5E_auto2_t)h5catch,client_data);
#else
return H5Eset_auto2(H5E_DEFAULT,(H5E_auto2_t)func,client_data);
#endif
}
/**
* @internal Provide a function to do any necessary initialization of
* the HDF5 library.
*/
void
nc4_hdf5_initialize(void)
{
if (set_auto(NULL, NULL) < 0)
LOG((0, "Couldn't turn off HDF5 error messages!"));
LOG((1, "HDF5 error messages have been turned off."));
nc4_hdf5_initialized = 1;
}
/**
* @internal Given a varid, return the maximum length of a dimension
* using dimid.
*
* @param grp Pointer to group info struct.
* @param varid Variable ID.
* @param dimid Dimension ID.
* @param maxlen Pointer that gets the max length.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
static int
find_var_dim_max_length(NC_GRP_INFO_T *grp, int varid, int dimid, size_t *maxlen)
{
hid_t datasetid = 0, spaceid = 0;
NC_VAR_INFO_T *var;
hsize_t *h5dimlen = NULL, *h5dimlenmax = NULL;
int d, dataset_ndims = 0;
int retval = NC_NOERR;
*maxlen = 0;
/* Find this var. */
var = (NC_VAR_INFO_T*)ncindexith(grp->vars,varid);
if (!var) return NC_ENOTVAR;
assert(var->hdr.id == varid);
/* If the var hasn't been created yet, its size is 0. */
if (!var->created)
{
*maxlen = 0;
}
else
{
/* Get the number of records in the dataset. */
if ((retval = nc4_open_var_grp2(grp, var->hdr.id, &datasetid)))
BAIL(retval);
if ((spaceid = H5Dget_space(datasetid)) < 0)
BAIL(NC_EHDFERR);
/* If it's a scalar dataset, it has length one. */
if (H5Sget_simple_extent_type(spaceid) == H5S_SCALAR)
{
*maxlen = (var->dimids && var->dimids[0] == dimid) ? 1 : 0;
}
else
{
/* Check to make sure ndims is right, then get the len of each
dim in the space. */
if ((dataset_ndims = H5Sget_simple_extent_ndims(spaceid)) < 0)
BAIL(NC_EHDFERR);
if (dataset_ndims != var->ndims)
BAIL(NC_EHDFERR);
if (!(h5dimlen = malloc(dataset_ndims * sizeof(hsize_t))))
BAIL(NC_ENOMEM);
if (!(h5dimlenmax = malloc(dataset_ndims * sizeof(hsize_t))))
BAIL(NC_ENOMEM);
if ((dataset_ndims = H5Sget_simple_extent_dims(spaceid,
h5dimlen, h5dimlenmax)) < 0)
BAIL(NC_EHDFERR);
LOG((5, "find_var_dim_max_length: varid %d len %d max: %d",
varid, (int)h5dimlen[0], (int)h5dimlenmax[0]));
for (d=0; d<dataset_ndims; d++) {
if (var->dimids[d] == dimid) {
*maxlen = *maxlen > h5dimlen[d] ? *maxlen : h5dimlen[d];
}
}
}
}
exit:
if (spaceid > 0 && H5Sclose(spaceid) < 0)
BAIL2(NC_EHDFERR);
if (h5dimlen) free(h5dimlen);
if (h5dimlenmax) free(h5dimlenmax);
return retval;
}
/**
* @internal Search for type with a given HDF type id.
*
* @param h5 File
* @param target_hdf_typeid HDF5 type ID to find.
*
* @return Pointer to type info struct, or NULL if not found.
* @author Ed Hartnett
*/
NC_TYPE_INFO_T *
nc4_rec_find_hdf_type(NC_HDF5_FILE_INFO_T* h5, hid_t target_hdf_typeid)
{
NC_TYPE_INFO_T *type;
htri_t equal;
int i;
assert(h5);
for(i=0;i<nclistlength(h5->alltypes);i++) {
type = (NC_TYPE_INFO_T*)nclistget(h5->alltypes,i);
if(type == NULL) continue;
/* Is this the type we are searching for? */
if ((equal = H5Tequal(type->native_hdf_typeid ? type->native_hdf_typeid : type->hdf_typeid, target_hdf_typeid)) < 0)
return NULL;
if (equal)
return type;
}
/* Can't find it. Fate, why do you mock me? */
return NULL;
}
/**
* @internal Find the actual length of a dim by checking the length of
* that dim in all variables that use it, in grp or children. **len
* must be initialized to zero before this function is called.
*
* @param grp Pointer to group info struct.
* @param dimid Dimension ID.
* @param len Pointer to pointer that gets length.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
int
nc4_find_dim_len(NC_GRP_INFO_T *grp, int dimid, size_t **len)
{
NC_GRP_INFO_T *g;
NC_VAR_INFO_T *var;
int retval;
int i;
assert(grp && len);
LOG((3, "nc4_find_dim_len: grp->name %s dimid %d", grp->hdr.name, dimid));
/* If there are any groups, call this function recursively on
* them. */
for(i=0;i<ncindexsize(grp->children);i++) {
g = (NC_GRP_INFO_T*)ncindexith(grp->children,i);
if(g == NULL) continue;
if ((retval = nc4_find_dim_len(g, dimid, len)))
return retval;
}
/* For all variables in this group, find the ones that use this
* dimension, and remember the max length. */
for (i=0; i < ncindexsize(grp->vars); i++)
{
size_t mylen;
var = (NC_VAR_INFO_T*)ncindexith(grp->vars,i);
if (var == NULL) continue;
/* Find max length of dim in this variable... */
if ((retval = find_var_dim_max_length(grp, var->hdr.id, dimid, &mylen)))
return retval;
**len = **len > mylen ? **len : mylen;
}
return NC_NOERR;
}
/**
* @internal Break a coordinate variable to separate the dimension and
* the variable.
*
* This is called from nc_rename_dim() and nc_rename_var(). In some
* renames, the coord variable must stay, but it is no longer a coord
* variable. This function changes a coord var into an ordinary
* variable.
*
* @param grp Pointer to group info struct.
* @param coord_var Pointer to variable info struct.
* @param dim Pointer to dimension info struct.
*
* @return ::NC_NOERR No error.
* @return ::NC_ENOMEM Out of memory.
* @author Quincey Koziol, Ed Hartnett
*/
int
nc4_break_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *coord_var, NC_DIM_INFO_T *dim)
{
int retval = NC_NOERR;
/* Sanity checks */
assert(grp && coord_var && dim && dim->coord_var == coord_var &&
coord_var->dim[0] == dim && coord_var->dimids[0] == dim->hdr.id &&
!dim->hdf_dimscaleid);
LOG((3, "%s dim %s was associated with var %s, but now has different name",
__func__, dim->hdr.name, coord_var->hdr.name));
/* If we're replacing an existing dimscale dataset, go to
* every var in the file and detach this dimension scale. */
if ((retval = rec_detach_scales(grp->nc4_info->root_grp,
dim->hdr.id, coord_var->hdf_datasetid)))
return retval;
/* Allow attached dimscales to be tracked on the [former]
* coordinate variable */
if (coord_var->ndims)
{
/* Coordinate variables shouldn't have dimscales attached. */
assert(!coord_var->dimscale_attached);
/* Allocate space for tracking them */
if (!(coord_var->dimscale_attached = calloc(coord_var->ndims,
sizeof(nc_bool_t))))
return NC_ENOMEM;
}
/* Remove the atts that go with being a coordinate var. */
/* if ((retval = remove_coord_atts(coord_var->hdf_datasetid))) */
/* return retval; */
/* Detach dimension from variable */
coord_var->dimscale = NC_FALSE;
dim->coord_var = NULL;
/* Set state transition indicators */
coord_var->was_coord_var = NC_TRUE;
coord_var->became_coord_var = NC_FALSE;
return NC_NOERR;
}
/**
* @internal Delete an existing dimscale-only dataset.
*
* A dimscale-only HDF5 dataset is created when a dim is defined
* without an accompanying coordinate variable.
*
* Sometimes, during renames, or late creation of variables, an
* existing, dimscale-only dataset must be removed. This means
* detaching all variables that use the dataset, then closing and
* unlinking it.
*
* @param grp The grp of the dimscale-only dataset to be deleted, or a
* higher group in the hierarchy (ex. root group).
* @param dimid id of the dimension
* @param dim Pointer to the dim with the dimscale-only dataset to be
* deleted.
*
* @return ::NC_NOERR No error.
* @return ::NC_EHDFERR HDF5 error.
* @author Ed Hartnett
*/
int
delete_existing_dimscale_dataset(NC_GRP_INFO_T *grp, int dimid, NC_DIM_INFO_T *dim)
{
int retval;
assert(grp && dim);
LOG((2, "%s: deleting dimscale dataset %s dimid %d", __func__, dim->hdr.name,
dimid));
/* Detach dimscale from any variables using it */
if ((retval = rec_detach_scales(grp, dimid, dim->hdf_dimscaleid)) < 0)
return retval;
/* Close the HDF5 dataset */
if (H5Dclose(dim->hdf_dimscaleid) < 0)
return NC_EHDFERR;
dim->hdf_dimscaleid = 0;
/* Now delete the dataset. */
if (H5Gunlink(grp->hdf_grpid, dim->hdr.name) < 0)
return NC_EHDFERR;
return NC_NOERR;
}
/**
* @internal Reform a coordinate variable from a dimension and a
* variable.
*
* @param grp Pointer to group info struct.
* @param var Pointer to variable info struct.
* @param dim Pointer to dimension info struct.
*
* @return ::NC_NOERR No error.
* @author Quincey Koziol
*/
int
nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, NC_DIM_INFO_T *dim)
{
int need_to_reattach_scales = 0;
int retval = NC_NOERR;
assert(grp && var && dim);
LOG((3, "%s: dim->hdr.name %s var->hdr.name %s", __func__, dim->hdr.name, var->hdr.name));
/* Detach dimscales from the [new] coordinate variable */
if(var->dimscale_attached)
{
int dims_detached = 0;
int finished = 0;
int d;
/* Loop over all dimensions for variable */
for (d = 0; d < var->ndims && !finished; d++)
{
/* Is there a dimscale attached to this axis? */
if(var->dimscale_attached[d])
{
NC_GRP_INFO_T *g;
int k;
for (g = grp; g && !finished; g = g->parent)
{
NC_DIM_INFO_T *dim1;
for(k=0;k<ncindexsize(g->dim);k++)
{
if((dim1 = (NC_DIM_INFO_T*)ncindexith(g->dim,k)) == NULL) continue;
if (var->dimids[d] == dim1->hdr.id)
{
hid_t dim_datasetid; /* Dataset ID for dimension */
/* Find dataset ID for dimension */
if (dim1->coord_var)
dim_datasetid = dim1->coord_var->hdf_datasetid;
else
dim_datasetid = dim1->hdf_dimscaleid;
/* dim_datasetid may be 0 in some cases when
* renames of dims and vars are happening. In
* this case, the scale has already been
* detached. */
if (dim_datasetid > 0)
{
LOG((3, "detaching scale from %s", var->hdr.name));
if (H5DSdetach_scale(var->hdf_datasetid, dim_datasetid, d) < 0)
BAIL(NC_EHDFERR);
}
var->dimscale_attached[d] = NC_FALSE;
if (dims_detached++ == var->ndims)
finished++;
}
}
}
}
} /* next variable dimension */
/* Release & reset the array tracking attached dimscales */
free(var->dimscale_attached);
var->dimscale_attached = NULL;
need_to_reattach_scales++;
}
/* Use variable's dataset ID for the dimscale ID. */
if (dim->hdf_dimscaleid && grp != NULL)
{
LOG((3, "closing and unlinking dimscale dataset %s", dim->hdr.name));
if (H5Dclose(dim->hdf_dimscaleid) < 0)
BAIL(NC_EHDFERR);
dim->hdf_dimscaleid = 0;
/* Now delete the dimscale's dataset
(it will be recreated later, if necessary) */
if (H5Gunlink(grp->hdf_grpid, dim->hdr.name) < 0)
return NC_EDIMMETA;
}
/* Attach variable to dimension */
var->dimscale = NC_TRUE;
dim->coord_var = var;
/* Check if this variable used to be a coord. var */
if (need_to_reattach_scales || (var->was_coord_var && grp != NULL))
{
/* Reattach the scale everywhere it is used. */
/* (Recall that netCDF dimscales are always 1-D) */
if ((retval = rec_reattach_scales(grp->nc4_info->root_grp,
var->dimids[0], var->hdf_datasetid)))
return retval;
/* Set state transition indicator (cancels earlier transition) */
var->was_coord_var = NC_FALSE;
}
else
/* Set state transition indicator */
var->became_coord_var = NC_TRUE;
exit:
return retval;
}
#ifdef LOGGING
/**
* This is the same as nc_set_log_level(), but will also turn on HDF5
* internal logging, in addition to netCDF logging.
*
* @param new_level The new logging level.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
int
hdf5_set_log_level(int new_level)
{
if (!nc4_hdf5_initialized)
nc4_hdf5_initialize();
/* If the user wants to completely turn off logging, turn off HDF5
logging too. Now I truely can't think of what to do if this
fails, so just ignore the return code. */
if (new_level == NC_TURN_OFF_LOGGING)
{
set_auto(NULL, NULL);
LOG((1, "HDF5 error messages turned off!"));
}
/* Do we need to turn HDF5 logging back on? */
if (new_level > NC_TURN_OFF_LOGGING &&
nc_log_level <= NC_TURN_OFF_LOGGING)
{
if (set_auto((H5E_auto_t)&H5Eprint, stderr) < 0)
LOG((0, "H5Eset_auto failed!"));
LOG((1, "HDF5 error messages turned on."));
}
/* Now remember the new level. */
nc_set_log_level(new_level);
return NC_NOERR;
}
#endif /* LOGGING */