netcdf-c/libhdf5/hdf5internal.c
Dennis Heimbigner 8b9253fef2 Fix various problem around VLEN's
re: https://github.com/Unidata/netcdf-c/issues/541
re: https://github.com/Unidata/netcdf-c/issues/1208
re: https://github.com/Unidata/netcdf-c/issues/2078
re: https://github.com/Unidata/netcdf-c/issues/2041
re: https://github.com/Unidata/netcdf-c/issues/2143

For a long time, there have been known problems with the
management of complex types containing VLENs.  This also
involves the string type because it is stored as a VLEN of
chars.

This PR (mostly) fixes this problem. But note that it adds new
functions to netcdf.h (see below) and this may require bumping
the .so number.  These new functions can be removed, if desired,
in favor of functions in netcdf_aux.h, but netcdf.h seems the
better place for them because they are intended as alternatives
to the nc_free_vlen and nc_free_string functions already in
netcdf.h.

The term complex type refers to any type that directly or
transitively references a VLEN type. So an array of VLENS, a
compound with a VLEN field, and so on.

In order to properly handle instances of these complex types, it
is necessary to have function that can recursively walk
instances of such types to perform various actions on them.  The
term "deep" is also used to mean recursive.

At the moment, the two operations needed by the netcdf library are:
* free'ing an instance of the complex type
* copying an instance of the complex type.

The current library does only shallow free and shallow copy of
complex types. This means that only the top level is properly
free'd or copied, but deep internal blocks in the instance are
not touched.

Note that the term "vector" will be used to mean a contiguous (in
memory) sequence of instances of some type. Given an array with,
say, dimensions 2 X 3 X 4, this will be stored in memory as a
vector of length 2*3*4=24 instances.

The use cases are primarily these.

## nc_get_vars
Suppose one is reading a vector of instances using nc_get_vars
(or nc_get_vara or nc_get_var, etc.).  These functions will
return the vector in the top-level memory provided.  All
interior blocks (form nested VLEN or strings) will have been
dynamically allocated.

After using this vector of instances, it is necessary to free
(aka reclaim) the dynamically allocated memory, otherwise a
memory leak occurs.  So, the recursive reclaim function is used
to walk the returned instance vector and do a deep reclaim of
the data.

Currently functions are defined in netcdf.h that are supposed to
handle this: nc_free_vlen(), nc_free_vlens(), and
nc_free_string().  Unfortunately, these functions only do a
shallow free, so deeply nested instances are not properly
handled by them.

Note that internally, the provided data is immediately written so
there is no need to copy it. But the caller may need to reclaim the
data it passed into the function.

## nc_put_att
Suppose one is writing a vector of instances as the data of an attribute
using, say, nc_put_att.

Internally, the incoming attribute data must be copied and stored
so that changes/reclamation of the input data will not affect
the attribute.

Again, the code inside the netcdf library does only shallow copying
rather than deep copy. As a result, one sees effects such as described
in Github Issue https://github.com/Unidata/netcdf-c/issues/2143.

Also, after defining the attribute, it may be necessary for the user
to free the data that was provided as input to nc_put_att().

## nc_get_att
Suppose one is reading a vector of instances as the data of an attribute
using, say, nc_get_att.

Internally, the existing attribute data must be copied and returned
to the caller, and the caller is responsible for reclaiming
the returned data.

Again, the code inside the netcdf library does only shallow copying
rather than deep copy. So this can lead to memory leaks and errors
because the deep data is shared between the library and the user.

# Solution

The solution is to build properly recursive reclaim and copy
functions and use those as needed.
These recursive functions are defined in libdispatch/dinstance.c
and their signatures are defined in include/netcdf.h.
For back compatibility, corresponding "ncaux_XXX" functions
are defined in include/netcdf_aux.h.
````
int nc_reclaim_data(int ncid, nc_type xtypeid, void* memory, size_t count);
int nc_reclaim_data_all(int ncid, nc_type xtypeid, void* memory, size_t count);
int nc_copy_data(int ncid, nc_type xtypeid, const void* memory, size_t count, void* copy);
int nc_copy_data_all(int ncid, nc_type xtypeid, const void* memory, size_t count, void** copyp);
````
There are two variants. The first two, nc_reclaim_data() and
nc_copy_data(), assume the top-level vector is managed by the
caller. For reclaim, this is so the user can use, for example, a
statically allocated vector. For copy, it assumes the user
provides the space into which the copy is stored.

The second two, nc_reclaim_data_all() and
nc_copy_data_all(), allows the functions to manage the
top-level.  So for nc_reclaim_data_all, the top level is
assumed to be dynamically allocated and will be free'd by
nc_reclaim_data_all().  The nc_copy_data_all() function
will allocate the top level and return a pointer to it to the
user. The user can later pass that pointer to
nc_reclaim_data_all() to reclaim the instance(s).

# Internal Changes
The netcdf-c library internals are changed to use the proper
reclaim and copy functions.  It turns out that the places where
these functions are needed is quite pervasive in the netcdf-c
library code.  Using these functions also allows some
simplification of the code since the stdata and vldata fields of
NC_ATT_INFO are no longer needed.  Currently this is commented
out using the SEPDATA \#define macro.  When any bugs are largely
fixed, all this code will be removed.

# Known Bugs

1. There is still one known failure that has not been solved.
   All the failures revolve around some variant of this .cdl file.
   The proximate cause of failure is the use of a VLEN FillValue.
````
        netcdf x {
        types:
          float(*) row_of_floats ;
        dimensions:
          m = 5 ;
        variables:
          row_of_floats ragged_array(m) ;
              row_of_floats ragged_array:_FillValue = {-999} ;
        data:
          ragged_array = {10, 11, 12, 13, 14}, {20, 21, 22, 23}, {30, 31, 32},
                         {40, 41}, _ ;
        }
````
When a solution is found, I will either add it to this PR or post a new PR.

# Related Changes

* Mark nc_free_vlen(s) as deprecated in favor of ncaux_reclaim_data.
* Remove the --enable-unfixed-memory-leaks option.
* Remove the NC_VLENS_NOTEST code that suppresses some vlen tests.
* Document this change in docs/internal.md
* Disable the tst_vlen_data test in ncdump/tst_nccopy4.sh.
* Mark types as fixed size or not (transitively) to optimize the reclaim
  and copy functions.

# Misc. Changes

* Make Doxygen process libdispatch/daux.c
* Make sure the NC_ATT_INFO_T.container field is set.
2022-01-08 18:30:00 -07:00

1129 lines
32 KiB
C

/* 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 "hdf5internal.h"
#include "hdf5err.h" /* For BAIL2 */
#ifdef _WIN32
#include <windows.h>
#endif
#undef DEBUGH5
#ifdef DEBUGH5
/**
* @internal Provide a catchable error reporting function
*
* @param ignored Ignored.
*
* @return 0 for success.
*/
static herr_t
h5catch(void* ignored)
{
H5Eprint1(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_filter_initialize();
nc4_hdf5_initialized = 1;
}
/**
* @internal Provide a function to do any necessary finalization of
* the HDF5 library.
*/
void
nc4_hdf5_finalize(void)
{
/* Reclaim global resources */
NC4_provenance_finalize();
NC4_hdf5_filter_finalize();
nc4_hdf5_initialized = 0;
}
/**
* @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_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++)
{
NC_HDF5_TYPE_INFO_T *hdf5_type;
hid_t hdf_typeid;
type = (NC_TYPE_INFO_T*)nclistget(h5->alltypes, i);
if(type == NULL) continue;
/* Get HDF5-specific type info. */
hdf5_type = (NC_HDF5_TYPE_INFO_T *)type->format_type_info;
/* Select the HDF5 typeid to use. */
hdf_typeid = hdf5_type->native_hdf_typeid ?
hdf5_type->native_hdf_typeid : hdf5_type->hdf_typeid;
/* Is this the type we are searching for? */
if ((equal = H5Tequal(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_VAR_INFO_T *var;
int retval;
int i;
assert(grp && len);
LOG((3, "%s: grp->name %s dimid %d", __func__, grp->hdr.name, dimid));
/* If there are any groups, call this function recursively on
* them. */
for (i = 0; i < ncindexsize(grp->children); i++)
if ((retval = nc4_find_dim_len((NC_GRP_INFO_T*)ncindexith(grp->children, i),
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);
assert(var);
/* 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_HDF5_VAR_INFO_T* coord_h5var = (NC_HDF5_VAR_INFO_T*)coord_var->format_var_info;
/* Sanity checks */
assert(grp && coord_var && dim && dim->coord_var == coord_var &&
coord_var->dim[0] == dim && coord_var->dimids[0] == dim->hdr.id &&
!((NC_HDF5_DIM_INFO_T *)(dim->format_dim_info))->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,
((NC_HDF5_VAR_INFO_T *)(coord_var->format_var_info))->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_h5var->dimscale_attached);
/* Allocate space for tracking them */
if (!(coord_h5var->dimscale_attached = calloc(coord_var->ndims,
sizeof(nc_bool_t))))
return NC_ENOMEM;
}
/* Detach dimension from variable */
coord_h5var->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_dimscale_dataset(NC_GRP_INFO_T *grp, int dimid, NC_DIM_INFO_T *dim)
{
NC_HDF5_DIM_INFO_T *hdf5_dim;
NC_HDF5_GRP_INFO_T *hdf5_grp;
int retval;
assert(grp && grp->format_grp_info && dim && dim->format_dim_info);
LOG((2, "%s: deleting dimscale dataset %s dimid %d", __func__, dim->hdr.name,
dimid));
/* Get HDF5 specific grp and dim info. */
hdf5_dim = (NC_HDF5_DIM_INFO_T *)dim->format_dim_info;
hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->format_grp_info;
/* Detach dimscale from any variables using it */
if ((retval = rec_detach_scales(grp, dimid, hdf5_dim->hdf_dimscaleid)) < 0)
return retval;
/* Close the HDF5 dataset */
if (H5Dclose(hdf5_dim->hdf_dimscaleid) < 0)
return NC_EHDFERR;
hdf5_dim->hdf_dimscaleid = 0;
/* Now delete the dataset. */
if (H5Gunlink(hdf5_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, Ed Hartnett
*/
int
nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, NC_DIM_INFO_T *dim)
{
NC_HDF5_DIM_INFO_T *hdf5_dim;
NC_HDF5_GRP_INFO_T *hdf5_grp;
NC_HDF5_VAR_INFO_T *hdf5_var;
int need_to_reattach_scales = 0;
int retval = NC_NOERR;
assert(grp && grp->format_grp_info && var && var->format_var_info &&
dim && dim->format_dim_info);
LOG((3, "%s: dim->hdr.name %s var->hdr.name %s", __func__, dim->hdr.name,
var->hdr.name));
/* Get HDF5-specific dim, group, and var info. */
hdf5_dim = (NC_HDF5_DIM_INFO_T *)dim->format_dim_info;
hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->format_grp_info;
hdf5_var = (NC_HDF5_VAR_INFO_T *)var->format_var_info;
/* Detach dimscales from the [new] coordinate variable. */
if (hdf5_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 (hdf5_var->dimscale_attached[d])
{
NC_GRP_INFO_T *g;
int k;
for (g = grp; g && !finished; g = g->parent)
{
NC_DIM_INFO_T *dim1;
NC_HDF5_DIM_INFO_T *hdf5_dim1;
for (k = 0; k < ncindexsize(g->dim); k++)
{
dim1 = (NC_DIM_INFO_T *)ncindexith(g->dim, k);
assert(dim1 && dim1->format_dim_info);
hdf5_dim1 = (NC_HDF5_DIM_INFO_T *)dim1->format_dim_info;
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 = ((NC_HDF5_VAR_INFO_T *)
(dim1->coord_var->format_var_info))->hdf_datasetid;
else
dim_datasetid = hdf5_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(hdf5_var->hdf_datasetid,
dim_datasetid, d) < 0)
BAIL(NC_EHDFERR);
}
hdf5_var->dimscale_attached[d] = NC_FALSE;
if (dims_detached++ == var->ndims)
finished++;
}
}
}
}
} /* next variable dimension */
/* Release & reset the array tracking attached dimscales. */
free(hdf5_var->dimscale_attached);
hdf5_var->dimscale_attached = NULL;
need_to_reattach_scales++;
}
/* Use variable's dataset ID for the dimscale ID. */
if (hdf5_dim->hdf_dimscaleid && grp != NULL)
{
LOG((3, "closing and unlinking dimscale dataset %s", dim->hdr.name));
if (H5Dclose(hdf5_dim->hdf_dimscaleid) < 0)
BAIL(NC_EHDFERR);
hdf5_dim->hdf_dimscaleid = 0;
/* Now delete the dimscale's dataset (it will be recreated
later, if necessary). */
if (H5Gunlink(hdf5_grp->hdf_grpid, dim->hdr.name) < 0)
return NC_EDIMMETA;
}
/* Attach variable to dimension. */
hdf5_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], hdf5_var->hdf_datasetid)))
return retval;
/* Set state transition indicator (cancels earlier
* transition). */
var->was_coord_var = NC_FALSE;
}
/* Set state transition indicator */
var->became_coord_var = NC_TRUE;
exit:
return retval;
}
/**
* @internal Close HDF5 resources for global atts in a group.
*
* @param grp Pointer to group info struct.
*
* @return ::NC_NOERR No error.
* @return ::NC_EHDFERR HDF5 error.
* @author Ed Hartnett
*/
static int
close_gatts(NC_GRP_INFO_T *grp)
{
NC_ATT_INFO_T *att;
int a;
for (a = 0; a < ncindexsize(grp->att); a++)
{
att = (NC_ATT_INFO_T *)ncindexith(grp->att, a);
assert(att && att->format_att_info);
nc4_HDF5_close_att(att);
}
return NC_NOERR;
}
/**
* @internal Close HDF5 resources for a single attribute
*
* @param att Pointer to att info struct.
*
* @return ::NC_NOERR No error.
* @return ::NC_EHDFERR HDF5 error.
* @author Dennis Heimbigner, Ed Hartnett
*/
int
nc4_HDF5_close_att(NC_ATT_INFO_T *att)
{
NC_HDF5_ATT_INFO_T *hdf5_att;
assert(att && att->format_att_info);
hdf5_att = (NC_HDF5_ATT_INFO_T *)att->format_att_info;
/* Close the HDF5 typeid. */
if (hdf5_att->native_hdf_typeid &&
H5Tclose(hdf5_att->native_hdf_typeid) < 0)
return NC_EHDFERR;
nullfree(hdf5_att);
att->format_att_info = NULL;
return NC_NOERR;
}
/**
* @internal Close HDF5 resources for vars in a group.
*
* @param grp Pointer to group info struct.
*
* @return ::NC_NOERR No error.
* @return ::NC_EHDFERR HDF5 error.
* @author Ed Hartnett
*/
static int
close_vars(NC_GRP_INFO_T *grp)
{
NC_VAR_INFO_T *var;
NC_HDF5_VAR_INFO_T *hdf5_var;
NC_ATT_INFO_T *att;
int a, i;
for (i = 0; i < ncindexsize(grp->vars); i++)
{
var = (NC_VAR_INFO_T *)ncindexith(grp->vars, i);
assert(var && var->format_var_info);
hdf5_var = (NC_HDF5_VAR_INFO_T *)var->format_var_info;
/* Close the HDF5 dataset associated with this var. */
if (hdf5_var->hdf_datasetid)
{
LOG((3, "closing HDF5 dataset %lld", hdf5_var->hdf_datasetid));
if (H5Dclose(hdf5_var->hdf_datasetid) < 0)
return NC_EHDFERR;
if (var->fill_value)
{
if (var->type_info)
{
#ifdef SEPDATA
if (var->type_info->nc_type_class == NC_VLEN)
nc_free_vlen((nc_vlen_t *)var->fill_value);
else if (var->type_info->nc_type_class == NC_STRING && *(char **)var->fill_value)
free(*(char **)var->fill_value);
#else
int stat = NC_NOERR;
if((stat = nc_reclaim_data(grp->nc4_info->controller->ext_ncid,var->type_info->hdr.id,var->fill_value,1)))
return stat;
nullfree(var->fill_value);
}
#endif
var->fill_value = NULL;
}
}
/* Free the HDF5 typeids. */
if (var->type_info->rc == 1)
{
if(var->type_info->hdr.id <= NC_STRING)
/* This was a constructed atomic type; free its info */
nc4_HDF5_close_type(var->type_info);
}
for (a = 0; a < ncindexsize(var->att); a++)
{
att = (NC_ATT_INFO_T *)ncindexith(var->att, a);
assert(att && att->format_att_info);
nc4_HDF5_close_att(att);
}
/* Delete any HDF5 dimscale objid information. */
if (hdf5_var->dimscale_hdf5_objids)
free(hdf5_var->dimscale_hdf5_objids);
/* Delete information about the attachment status of dimscales. */
if (hdf5_var->dimscale_attached)
free(hdf5_var->dimscale_attached);
nullfree(hdf5_var);
/* Reclaim filters */
if(var->filters != NULL) {
(void)NC4_hdf5_filter_freelist(var);
}
var->filters = NULL;
}
return NC_NOERR;
}
/**
* @internal Close HDF5 resources for dims in a group.
*
* @param grp Pointer to group info struct.
*
* @return ::NC_NOERR No error.
* @return ::NC_EHDFERR HDF5 error.
* @author Ed Hartnett
*/
static int
close_dims(NC_GRP_INFO_T *grp)
{
NC_DIM_INFO_T *dim;
int i;
for (i = 0; i < ncindexsize(grp->dim); i++)
{
NC_HDF5_DIM_INFO_T *hdf5_dim;
dim = (NC_DIM_INFO_T *)ncindexith(grp->dim, i);
assert(dim && dim->format_dim_info);
hdf5_dim = (NC_HDF5_DIM_INFO_T *)dim->format_dim_info;
/* If this is a dim without a coordinate variable, then close
* the HDF5 DIM_WITHOUT_VARIABLE dataset associated with this
* dim. */
if (hdf5_dim->hdf_dimscaleid && H5Dclose(hdf5_dim->hdf_dimscaleid) < 0)
return NC_EHDFERR;
nullfree(hdf5_dim);
}
return NC_NOERR;
}
/**
* @internal Close HDF5 resources for types in a group. Set values to
* 0 after closing types. Because of type reference counters, these
* closes can be called multiple times.
*
* @param grp Pointer to group info struct.
*
* @return ::NC_NOERR No error.
* @return ::NC_EHDFERR HDF5 error.
* @author Ed Hartnett, Dennis Heimbigner
*/
static int
close_types(NC_GRP_INFO_T *grp)
{
int i;
for (i = 0; i < ncindexsize(grp->type); i++)
{
NC_TYPE_INFO_T *type;
type = (NC_TYPE_INFO_T *)ncindexith(grp->type, i);
assert(type && type->format_type_info);
nc4_HDF5_close_type(type);
}
return NC_NOERR;
}
/**
* @internal Close a single type instance
*
* @param type Pointer to type info struct.
*
* @return ::NC_NOERR No error.
* @return ::NC_EHDFERR HDF5 error.
* @author Dennis Heimbigner, Ed Hartnett
*/
int
nc4_HDF5_close_type(NC_TYPE_INFO_T* type)
{
NC_HDF5_TYPE_INFO_T *hdf5_type;
assert(type && type->format_type_info);
/* Get HDF5-specific type info. */
hdf5_type = (NC_HDF5_TYPE_INFO_T *)type->format_type_info;
/* Close any open user-defined HDF5 typeids. */
if (hdf5_type->hdf_typeid && H5Tclose(hdf5_type->hdf_typeid) < 0)
return NC_EHDFERR;
hdf5_type->hdf_typeid = 0;
if (hdf5_type->native_hdf_typeid &&
H5Tclose(hdf5_type->native_hdf_typeid) < 0)
return NC_EHDFERR;
hdf5_type->native_hdf_typeid = 0;
nullfree(hdf5_type);
return NC_NOERR;
}
/**
* @internal Recursively free HDF5 objects for a group (and everything
* it contains).
*
* @param grp Pointer to group info struct.
*
* @return ::NC_NOERR No error.
* @return ::NC_EHDFERR HDF5 error.
* @author Ed Hartnett
*/
int
nc4_rec_grp_HDF5_del(NC_GRP_INFO_T *grp)
{
NC_HDF5_GRP_INFO_T *hdf5_grp;
int i;
int retval;
assert(grp && grp->format_grp_info);
LOG((3, "%s: grp->name %s", __func__, grp->hdr.name));
hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->format_grp_info;
/* Recursively call this function for each child, if any, stopping
* if there is an error. */
for (i = 0; i < ncindexsize(grp->children); i++)
if ((retval = nc4_rec_grp_HDF5_del((NC_GRP_INFO_T *)ncindexith(grp->children,
i))))
return retval;
/* Close HDF5 resources associated with global attributes. */
if ((retval = close_gatts(grp)))
return retval;
/* Close HDF5 resources associated with vars. */
if ((retval = close_vars(grp)))
return retval;
/* Close HDF5 resources associated with dims. */
if ((retval = close_dims(grp)))
return retval;
/* Close HDF5 resources associated with types. */
if ((retval = close_types(grp)))
return retval;
/* Close the HDF5 group. */
LOG((4, "%s: closing group %s", __func__, grp->hdr.name));
if (hdf5_grp->hdf_grpid && H5Gclose(hdf5_grp->hdf_grpid) < 0)
return NC_EHDFERR;
nullfree(hdf5_grp);
return NC_NOERR;
}
/**
* @internal Given an ncid and varid, get pointers to the group and var
* metadata. Lazy var metadata reads are done as needed.
*
* @param ncid File ID.
* @param varid Variable ID.
* @param h5 Pointer that gets pointer to the NC_FILE_INFO_T struct
* for this file. Ignored if NULL.
* @param grp Pointer that gets pointer to group info. Ignored if
* NULL.
* @param var Pointer that gets pointer to var info. Ignored if NULL.
*
* @return ::NC_NOERR No error.
* @return ::NC_ENOTVAR Variable not found.
* @author Ed Hartnett
*/
int
nc4_hdf5_find_grp_h5_var(int ncid, int varid, NC_FILE_INFO_T **h5,
NC_GRP_INFO_T **grp, NC_VAR_INFO_T **var)
{
NC_VAR_INFO_T *my_var;
int retval;
/* Delegate to libsrc4 */
if((retval = nc4_find_grp_h5_var(ncid,varid,h5,grp,&my_var))) return retval;
/* Do we need to read var metadata? (hdf5 specific) */
if (!my_var->meta_read && my_var->created)
if ((retval = nc4_get_var_meta(my_var)))
return retval;
if (var) *var = my_var;
return NC_NOERR;
}
/**
* @internal Given an ncid, varid, and attribute name, return
* normalized name and pointers to the file, group, var, and att info
* structs. Lazy reads of attributes and variable metadata are done as
* needed.
*
* @param ncid File/group ID.
* @param varid Variable ID.
* @param name Name to of attribute.
* @param attnum Number of attribute.
* @param use_name If true, use the name to get the
* attribute. Otherwise use the attnum.
* @param norm_name Pointer to storage of size NC_MAX_NAME + 1,
* which will get the normalized name, if use_name is true. Ignored if
* NULL.
* @param h5 Pointer to pointer that gets file info struct. Ignored if
* NULL.
* @param grp Pointer to pointer that gets group info struct. Ignored
* if NULL.
* @param h5 Pointer to pointer that gets variable info
* struct. Ignored if NULL.
* @param att Pointer to pointer that gets attribute info
* struct. Ignored if NULL.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_ENOTVAR Variable not found.
* @return ::NC_ENOTATT Attribute not found.
* @author Ed Hartnett
*/
int
nc4_hdf5_find_grp_var_att(int ncid, int varid, const char *name, int attnum,
int use_name, char *norm_name, NC_FILE_INFO_T **h5,
NC_GRP_INFO_T **grp, NC_VAR_INFO_T **var,
NC_ATT_INFO_T **att)
{
NC_FILE_INFO_T *my_h5;
NC_GRP_INFO_T *my_grp;
NC_VAR_INFO_T *my_var = NULL;
NC_ATT_INFO_T *my_att;
char my_norm_name[NC_MAX_NAME + 1] = "";
NCindex *attlist = NULL;
int retval;
LOG((4, "%s: ncid %d varid %d attnum %d use_name %d", __func__, ncid, varid,
attnum, use_name));
/* Don't need to provide name unless getting att pointer and using
* use_name. */
assert(!att || ((use_name && name) || !use_name));
/* Find info for this file, group, and h5 info. */
if ((retval = nc4_find_nc_grp_h5(ncid, NULL, &my_grp, &my_h5)))
return retval;
assert(my_grp && my_h5);
/* Get either the global or a variable attribute list. */
if (varid == NC_GLOBAL)
{
/* Do we need to read the atts? */
if (!my_grp->atts_read)
if ((retval = nc4_read_atts(my_grp, NULL)))
return retval;
attlist = my_grp->att;
}
else
{
if (!(my_var = (NC_VAR_INFO_T *)ncindexith(my_grp->vars, varid)))
return NC_ENOTVAR;
/* Do we need to read the var attributes? */
if (!my_var->atts_read)
if ((retval = nc4_read_atts(my_grp, my_var)))
return retval;
/* Do we need to read var metadata? */
if (!my_var->meta_read && my_var->created)
if ((retval = nc4_get_var_meta(my_var)))
return retval;
attlist = my_var->att;
}
assert(attlist);
/* Need a name if use_name is true. */
if (use_name && !name)
return NC_EBADNAME;
/* Normalize the name. */
if (use_name)
if ((retval = nc4_normalize_name(name, my_norm_name)))
return retval;
/* Now find the attribute by name or number. */
if (att)
{
my_att = use_name ? (NC_ATT_INFO_T *)ncindexlookup(attlist, my_norm_name) :
(NC_ATT_INFO_T *)ncindexith(attlist, attnum);
if (!my_att)
return NC_ENOTATT;
}
/* Give the people what they want. */
if (norm_name)
{
strncpy(norm_name, my_norm_name, NC_MAX_NAME);
norm_name[NC_MAX_NAME] = 0;
}
if (h5)
*h5 = my_h5;
if (grp)
*grp = my_grp;
if (var)
*var = my_var;
if (att)
*att = my_att;
return NC_NOERR;
}
/**
* @internal Get the file chunk cache settings from HDF5.
*
* @param ncid File ID of a NetCDF/HDF5 file.
* @param sizep Pointer that gets size in bytes to set cache. Ignored
* if NULL.
* @param nelemsp Pointer that gets number of elements to hold in
* cache. Ignored if NULL.
* @param preemptionp Pointer that gets preemption stragety (between 0
* and 1). Ignored if NULL.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
int
nc4_hdf5_get_chunk_cache(int ncid, size_t *sizep, size_t *nelemsp,
float *preemptionp)
{
NC_FILE_INFO_T *h5;
NC_HDF5_FILE_INFO_T *hdf5_info;
hid_t plistid;
double dpreemption;
int retval;
/* Find info for this file, group, and h5 info. */
if ((retval = nc4_find_nc_grp_h5(ncid, NULL, NULL, &h5)))
return retval;
assert(h5 && h5->format_file_info);
hdf5_info = (NC_HDF5_FILE_INFO_T *)h5->format_file_info;
/* Get the file access property list. */
if ((plistid = H5Fget_access_plist(hdf5_info->hdfid)) < 0)
return NC_EHDFERR;
/* Get the chunk cache values from HDF5 for this property list. */
if (H5Pget_cache(plistid, NULL, nelemsp, sizep, &dpreemption) < 0)
return NC_EHDFERR;
if (preemptionp)
*preemptionp = dpreemption;
return NC_NOERR;
}
#ifdef LOGGING
/* We will need to check against nc log level from nc4internal.c. */
extern int nc_log_level;
/**
* @internal This is like nc_set_log_level(), but will also turn on
* HDF5 internal logging, in addition to netCDF logging. This should
* never be called by the user. It is called in open/create when the
* nc logging level has changed.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
int
hdf5_set_log_level()
{
/* If the user wants to completely turn off logging, turn off HDF5
logging too. Now I truly can't think of what to do if this
fails, so just ignore the return code. */
if (nc_log_level == NC_TURN_OFF_LOGGING)
{
set_auto(NULL, NULL);
LOG((1, "HDF5 error messages turned off!"));
}
else
{
if (set_auto((H5E_auto_t)&H5Eprint1, stderr) < 0)
LOG((0, "H5Eset_auto failed!"));
LOG((1, "HDF5 error messages turned on."));
}
return NC_NOERR;
}
void
nc_log_hdf5(void)
{
#ifdef USE_HDF5
H5Eprint1(NULL);
#endif /* USE_HDF5 */
}
#endif /* LOGGING */
#if 0
#ifdef _WIN32
/**
* Converts the filename from ANSI to UTF-8 if HDF5 >= 1.10.6.
* nc4_hdf5_free_pathbuf must be called to free pb.
*
* @param pb Pointer that conversion information is stored.
* @param path The filename to be converted.
*
* @return The converted filename if succeeded. NULL if failed.
*/
const char *
nc4_ndf5_ansi_to_utf8(pathbuf_t *pb, const char *path)
{
const uint UTF8_MAJNUM = 1;
const uint UTF8_MINNUM = 10;
const uint UTF8_RELNUM = 6;
static enum {UNDEF, ANSI, UTF8} hdf5_encoding = UNDEF;
wchar_t wbuf[MAX_PATH];
wchar_t *ws = NULL;
char *ns = NULL;
int n;
if (hdf5_encoding == UNDEF) {
#ifdef HDF5_UTF8_PATHS
hdf5_encoding = UTF8;
#else
hdf5_encoding = ANSI;
#endif
}
if (hdf5_encoding == ANSI) {
pb->ptr = NULL;
return path;
}
n = MultiByteToWideChar(CP_ACP, 0, path, -1, NULL, 0);
if (!n) {
errno = EILSEQ;
goto done;
}
ws = n <= _countof(wbuf) ? wbuf : malloc(sizeof *ws * n);
if (!ws)
goto done;
if (!MultiByteToWideChar(CP_ACP, 0, path, -1, ws, n)) {
errno = EILSEQ;
goto done;
}
n = WideCharToMultiByte(CP_UTF8, 0, ws, -1, NULL, 0, NULL, NULL);
if (!n) {
errno = EILSEQ;
goto done;
}
ns = n <= sizeof pb->buffer ? pb->buffer : malloc(n);
if (!ns)
goto done;
if (!WideCharToMultiByte(CP_UTF8, 0, ws, -1, ns, n, NULL, NULL)) {
if (ns != pb->buffer)
free(ns);
ns = NULL;
errno = EILSEQ;
goto done;
}
done:
if (ws != wbuf)
free (ws);
pb->ptr = ns;
return ns;
}
/**
* Free the conversion information used by nc4_ndf5_ansi_to_utf8.
*
* @param pb Pointer that hold conversion information to be freed.
*/
void
nc4_hdf5_free_pathbuf(pathbuf_t *pb)
{
if (pb->ptr && pb->ptr != pb->buffer)
free(pb->ptr);
}
#endif /* _WIN32 */
#endif /*0*/