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Fix reclamation of the ->format_XXX_info fields

Browse Source 
nc4internal.c contains code to free the format_XXX_info
fields. Since these are format specific, this code
was moved to the dispatch code (libhdf5 and libhdf4
in the current case).

Additionally, there are some fields in nc4internal.h (e.g.
dimscale fields) that are specific to HDF5 and have been moved
to the corresponding HDF5 data structures and code.

Misc. other changes:
1. NC_VAR_INFO_T->hdf5_name renamed to alt_name to avoid
   implying it is necessarily HDF5 specific.
2. prefix NC_FILE_INFO_T with an instance of NC_OBJ for consistency.
   this also requires wrapping move_in_NCList() to keep
   hdr.id consistent.
This commit is contained in:
Dennis Heimbigner 2020-03-29 12:48:59 -06:00
parent be2f7ca7b8
commit b0e0d81aa9
11 changed files with 182 additions and 127 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

5
include/hdf5internal.h
View File

@ -92,6 +92,8 @@ typedef struct NC_HDF5_VAR_INFO
{
hid_t hdf_datasetid;
HDF5_OBJID_T *dimscale_hdf5_objids;
nc_bool_t dimscale; /**< True if var is a dimscale. */
nc_bool_t *dimscale_attached; /**< Array of flags that are true if dimscale is attached for that dim index. */
} NC_HDF5_VAR_INFO_T;
/* Struct to hold HDF5-specific info for a field. */
@ -140,6 +142,7 @@ int nc4_get_hdf_typeid(NC_FILE_INFO_T *h5, nc_type xtype,
int nc4_close_hdf5_file(NC_FILE_INFO_T *h5, int abort, NC_memio *memio);
int nc4_rec_grp_HDF5_del(NC_GRP_INFO_T *grp);
int nc4_enddef_netcdf4_file(NC_FILE_INFO_T *h5);
int nc4_HDF5_close_type(NC_TYPE_INFO_T* type);
/* Break & reform coordinate variables */
int nc4_break_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *coord_var, NC_DIM_INFO_T *dim);
@ -169,6 +172,8 @@ int nc4_hdf5_find_grp_var_att(int ncid, int varid, const char *name, int attnum,
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);
int nc4_HDF5_close_att(NC_ATT_INFO_T *att);
/* Perform lazy read of the rest of the metadata for a var. */
int nc4_get_var_meta(NC_VAR_INFO_T *var);

9
include/nc4internal.h
View File

@ -18,7 +18,6 @@
#include <ctype.h>
#include <string.h>
#include "ncdimscale.h"
#include "nc_logging.h"
#include "ncindex.h"
#include "nc_provenance.h"
@ -45,7 +44,7 @@
/* typedef enum {GET, PUT} NC_PG_T; */
/** These are the different objects that can be in our hash-lists. */
typedef enum {NCNAT, NCVAR, NCDIM, NCATT, NCTYP, NCFLD, NCGRP} NC_SORT;
typedef enum {NCNAT, NCVAR, NCDIM, NCATT, NCTYP, NCFLD, NCGRP, NCFIL} NC_SORT;
/** The netCDF V2 error code. */
#define NC_V2_ERR (-1)
@ -188,7 +187,7 @@ typedef struct NC_ATT_INFO
typedef struct NC_VAR_INFO
{
NC_OBJ hdr; /**< The hdr contains the name and ID. */
char *hdf5_name; /**< Used if name in HDF5 must be different from name. */
char *alt_name; /**< Used if name in dispatcher must be different from hdr.name. */
struct NC_GRP_INFO *container; /**< Pointer to containing group. */
size_t ndims; /**< Number of dims. */
int *dimids; /**< Dim IDs. */
@ -210,8 +209,6 @@ typedef struct NC_VAR_INFO
size_t *chunksizes; /**< For chunked storage, an array (size ndims) of chunksizes. */
int storage; /**< Storage of this var, compact, contiguous, or chunked. */
int parallel_access; /**< Type of parallel access for I/O on variable (collective or independent). */
nc_bool_t dimscale; /**< True if var is a dimscale. */
nc_bool_t *dimscale_attached; /**< Array of flags that are true if dimscale is attached for that dim index. */
nc_bool_t shuffle; /**< True if var has shuffle filter applied. */
nc_bool_t fletcher32; /**< True if var has fletcher32 filter applied. */
size_t chunk_cache_size; /**< Size in bytes of the var chunk chache. */
@ -298,6 +295,7 @@ typedef struct NC_GRP_INFO
* netcdf-4/HDF5 file. */
typedef struct NC_FILE_INFO
{
NC_OBJ hdr;
NC *controller; /**< Pointer to containing NC. */
#ifdef USE_PARALLEL4
MPI_Comm comm; /**< Copy of MPI Communicator used to open the file. */
@ -417,6 +415,7 @@ int nc4_build_root_grp(NC_FILE_INFO_T *h5);
int nc4_rec_grp_del(NC_GRP_INFO_T *grp);
int nc4_enum_member_add(NC_TYPE_INFO_T *type, size_t size, const char *name,
const void *value);
int nc4_att_free(NC_ATT_INFO_T *att);
/* Check and normalize names. */
int NC_check_name(const char *name);

2
libhdf4/hdf4file.c
View File

@ -69,6 +69,8 @@ hdf4_rec_grp_del(NC_GRP_INFO_T *grp)
* scale. */
if (hdf4_var->sdsid && SDendaccess(hdf4_var->sdsid) < 0)
return NC_EHDFERR;
nullfree(hdf4_var);
}
return NC_NOERR;

20
libhdf5/hdf5attr.c
View File

@ -325,6 +325,7 @@ NC4_HDF5_del_att(int ncid, int varid, const char *name)
deletedid = att->hdr.id;
/* Remove this attribute in this list */
if((retval=nc4_HDF5_close_att(att))) return retval;
if ((retval = nc4_att_list_del(attlist, att)))
return retval;
@ -523,7 +524,6 @@ nc4_put_att(NC_GRP_INFO_T* grp, int varid, const char *name, nc_type file_type,
if (!(att->format_att_info = calloc(1, sizeof(NC_HDF5_ATT_INFO_T))))
BAIL(NC_ENOMEM);
}
/* Now fill in the metadata. */
att->dirty = NC_TRUE;
att->nc_typeid = file_type;
@ -559,16 +559,16 @@ nc4_put_att(NC_GRP_INFO_T* grp, int varid, const char *name, nc_type file_type,
if (att->nc_typeid != var->type_info->hdr.id)
return NC_EBADTYPE;
if (att->len != 1)
return NC_EINVAL;
BAIL(NC_EINVAL);
/* If we already wrote to the dataset, then return an error. */
if (var->written_to)
return NC_ELATEFILL;
BAIL(NC_ELATEFILL);
/* Get the length of the veriable data type. */
if ((retval = nc4_get_typelen_mem(grp->nc4_info, var->type_info->hdr.id,
&type_size)))
return retval;
BAIL(retval);
/* Already set a fill value? Now I'll have to free the old
* one. Make up your damn mind, would you? */
@ -577,7 +577,7 @@ nc4_put_att(NC_GRP_INFO_T* grp, int varid, const char *name, nc_type file_type,
if (var->type_info->nc_type_class == NC_VLEN)
{
if ((retval = nc_free_vlen(var->fill_value)))
return retval;
BAIL(retval);
}
else if (var->type_info->nc_type_class == NC_STRING)
{
@ -597,7 +597,7 @@ nc4_put_att(NC_GRP_INFO_T* grp, int varid, const char *name, nc_type file_type,
/* Allocate space for the fill value. */
if (!(var->fill_value = calloc(1, size)))
return NC_ENOMEM;
BAIL(NC_ENOMEM);
/* Copy the fill_value. */
LOG((4, "Copying fill value into metadata for variable %s", var->hdr.name));
@ -610,11 +610,11 @@ nc4_put_att(NC_GRP_INFO_T* grp, int varid, const char *name, nc_type file_type,
/* get the basetype and its size */
basetype = var->type_info;
if ((retval = nc4_get_typelen_mem(grp->nc4_info, basetype->hdr.id, &basetypesize)))
return retval;
BAIL(retval);
/* shallow clone the content of the vlen; shallow because it has only a temporary existence */
fv_vlen->len = in_vlen->len;
if (!(fv_vlen->p = malloc(basetypesize * in_vlen->len)))
return NC_ENOMEM;
BAIL(NC_ENOMEM);
memcpy(fv_vlen->p, in_vlen->p, in_vlen->len * basetypesize);
}
else if (var->type_info->nc_type_class == NC_STRING)
@ -622,7 +622,7 @@ nc4_put_att(NC_GRP_INFO_T* grp, int varid, const char *name, nc_type file_type,
if (*(char **)data)
{
if (!(*(char **)(var->fill_value) = malloc(strlen(*(char **)data) + 1)))
return NC_ENOMEM;
BAIL(NC_ENOMEM);
strcpy(*(char **)var->fill_value, *(char **)data);
}
else
@ -645,7 +645,7 @@ nc4_put_att(NC_GRP_INFO_T* grp, int varid, const char *name, nc_type file_type,
/* Get class for this type. */
if ((retval = nc4_get_typeclass(h5, file_type, &type_class)))
return retval;
BAIL(retval);
assert(data);
if (type_class == NC_VLEN)

2
libhdf5/hdf5debug.c
View File

@ -15,7 +15,9 @@
#define STSIZE 1000
#if !defined _WIN32 && !defined __CYGWIN__
static void* stacktrace[STSIZE];
#endif
int
nch5breakpoint(int err)

14
libhdf5/hdf5file.c
View File

@ -103,10 +103,12 @@ detect_preserve_dimids(NC_GRP_INFO_T *grp, nc_bool_t *bad_coord_orderp)
/* Iterate over variables in this group */
for (i=0; i < ncindexsize(grp->vars); i++)
{
NC_HDF5_VAR_INFO_T *hdf5_var;
var = (NC_VAR_INFO_T*)ncindexith(grp->vars,i);
if (var == NULL) continue;
hdf5_var = (NC_HDF5_VAR_INFO_T*)var->format_var_info;
/* Only matters for dimension scale variables, with non-scalar dimensionality */
if (var->dimscale && var->ndims)
if (hdf5_var->dimscale && var->ndims)
{
/* If the user writes coord vars in a different order then he
* defined their dimensions, then, when the file is reopened, the
@ -301,9 +303,11 @@ nc4_close_netcdf4_file(NC_FILE_INFO_T *h5, int abort, NC_memio *memio)
}
/* Free the HDF5-specific info. */
if (h5->format_file_info)
free(h5->format_file_info);
if (h5->format_file_info) {
NC_HDF5_FILE_INFO_T* hdf5_file = (NC_HDF5_FILE_INFO_T*)h5->format_file_info;
free(hdf5_file);
}
/* Free the NC_FILE_INFO_T struct. */
if ((retval = nc4_nc4f_list_del(h5)))
return retval;
@ -346,7 +350,7 @@ nc4_close_hdf5_file(NC_FILE_INFO_T *h5, int abort, NC_memio *memio)
if ((retval = nc4_rec_grp_HDF5_del(h5->root_grp)))
return retval;
/* Release all intarnal lists and metadata associated with this
/* Release all internal lists and metadata associated with this
* file. All HDF5 objects have already been released. */
if ((retval = nc4_close_netcdf4_file(h5, abort, memio)))
return retval;

103
libhdf5/hdf5internal.c
View File

@ -285,6 +285,7 @@ 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 &&
@ -305,16 +306,16 @@ nc4_break_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *coord_var,
if (coord_var->ndims)
{
/* Coordinate variables shouldn't have dimscales attached. */
assert(!coord_var->dimscale_attached);
assert(!coord_h5var->dimscale_attached);
/* Allocate space for tracking them */
if (!(coord_var->dimscale_attached = calloc(coord_var->ndims,
if (!(coord_h5var->dimscale_attached = calloc(coord_var->ndims,
sizeof(nc_bool_t))))
return NC_ENOMEM;
}
/* Detach dimension from variable */
coord_var->dimscale = NC_FALSE;
coord_h5var->dimscale = NC_FALSE;
dim->coord_var = NULL;
/* Set state transition indicators */
@ -407,7 +408,7 @@ nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, NC_DIM_INFO_T *dim)
hdf5_var = (NC_HDF5_VAR_INFO_T *)var->format_var_info;
/* Detach dimscales from the [new] coordinate variable. */
if (var->dimscale_attached)
if (hdf5_var->dimscale_attached)
{
int dims_detached = 0;
int finished = 0;
@ -417,7 +418,7 @@ nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, NC_DIM_INFO_T *dim)
for (d = 0; d < var->ndims && !finished; d++)
{
/* Is there a dimscale attached to this axis? */
if (var->dimscale_attached[d])
if (hdf5_var->dimscale_attached[d])
{
NC_GRP_INFO_T *g;
int k;
@ -455,7 +456,7 @@ nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, NC_DIM_INFO_T *dim)
dim_datasetid, d) < 0)
BAIL(NC_EHDFERR);
}
var->dimscale_attached[d] = NC_FALSE;
hdf5_var->dimscale_attached[d] = NC_FALSE;
if (dims_detached++ == var->ndims)
finished++;
}
@ -465,8 +466,8 @@ nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, NC_DIM_INFO_T *dim)
} /* next variable dimension */
/* Release & reset the array tracking attached dimscales. */
free(var->dimscale_attached);
var->dimscale_attached = NULL;
free(hdf5_var->dimscale_attached);
hdf5_var->dimscale_attached = NULL;
need_to_reattach_scales++;
}
@ -485,7 +486,7 @@ nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, NC_DIM_INFO_T *dim)
}
/* Attach variable to dimension. */
var->dimscale = NC_TRUE;
hdf5_var->dimscale = NC_TRUE;
dim->coord_var = var;
/* Check if this variable used to be a coord. var */
@ -526,9 +527,27 @@ close_gatts(NC_GRP_INFO_T *grp)
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;
att = (NC_ATT_INFO_T *)ncindexith(grp->att, a);
assert(att && att->format_att_info);
hdf5_att = (NC_HDF5_ATT_INFO_T *)att->format_att_info;
@ -536,7 +555,9 @@ close_gatts(NC_GRP_INFO_T *grp)
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;
}
@ -585,30 +606,25 @@ close_vars(NC_GRP_INFO_T *grp)
/* Free the HDF5 typeids. */
if (var->type_info->rc == 1)
{
if (((NC_HDF5_TYPE_INFO_T *)(var->type_info->format_type_info))->hdf_typeid &&
H5Tclose(((NC_HDF5_TYPE_INFO_T *)(var->type_info->format_type_info))->hdf_typeid) < 0)
return NC_EHDFERR;
if (((NC_HDF5_TYPE_INFO_T *)(var->type_info->format_type_info))->native_hdf_typeid &&
H5Tclose(((NC_HDF5_TYPE_INFO_T *)(var->type_info->format_type_info))->native_hdf_typeid) < 0)
return NC_EHDFERR;
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);
for (a = 0; a < ncindexsize(var->att); a++)
{
NC_HDF5_ATT_INFO_T *hdf5_att;
att = (NC_ATT_INFO_T *)ncindexith(var->att, a);
assert(att && att->format_att_info);
hdf5_att = (NC_HDF5_ATT_INFO_T *)att->format_att_info;
/* Close the HDF5 typeid if one is open. */
if (hdf5_att->native_hdf_typeid &&
H5Tclose(hdf5_att->native_hdf_typeid) < 0)
return NC_EHDFERR;
}
/* Delete information about the attachment status of dimscales. */
if (hdf5_var->dimscale_attached)
free(hdf5_var->dimscale_attached);
nullfree(hdf5_var);
}
return NC_NOERR;
@ -642,6 +658,7 @@ close_dims(NC_GRP_INFO_T *grp)
* dim. */
if (hdf5_dim->hdf_dimscaleid && H5Dclose(hdf5_dim->hdf_dimscaleid) < 0)
return NC_EHDFERR;
nullfree(hdf5_dim);
}
return NC_NOERR;
@ -666,9 +683,29 @@ close_types(NC_GRP_INFO_T *grp)
for (i = 0; i < ncindexsize(grp->type); i++)
{
NC_TYPE_INFO_T *type;
NC_HDF5_TYPE_INFO_T *hdf5_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. */
@ -682,7 +719,7 @@ close_types(NC_GRP_INFO_T *grp)
H5Tclose(hdf5_type->native_hdf_typeid) < 0)
return NC_EHDFERR;
hdf5_type->native_hdf_typeid = 0;
}
nullfree(hdf5_type);
return NC_NOERR;
}
@ -737,6 +774,8 @@ nc4_rec_grp_HDF5_del(NC_GRP_INFO_T *grp)
if (hdf5_grp->hdf_grpid && H5Gclose(hdf5_grp->hdf_grpid) < 0)
return NC_EHDFERR;
nullfree(hdf5_grp);
return NC_NOERR;
}

18
libhdf5/hdf5open.c
View File

@ -529,7 +529,7 @@ rec_match_dimscales(NC_GRP_INFO_T *grp)
}
/* Skip dimension scale variables */
if (var->dimscale)
if (hdf5_var->dimscale)
continue;
/* If we have already read hidden coordinates att, then we don't
@ -538,7 +538,7 @@ rec_match_dimscales(NC_GRP_INFO_T *grp)
continue;
/* Skip dimension scale variables */
if (!var->dimscale)
if (!hdf5_var->dimscale)
{
int d;
int j;
@ -1151,13 +1151,13 @@ get_attached_info(NC_VAR_INFO_T *var, NC_HDF5_VAR_INFO_T *hdf5_var, int ndims,
/* If an enddef has already been called, the dimscales will already
* be taken care of. */
if (num_scales && ndims && !var->dimscale_attached)
if (num_scales && ndims && !hdf5_var->dimscale_attached)
{
/* Allocate space to remember whether the dimscale has been
* attached for each dimension, and the HDF5 object IDs of the
* scale(s). */
assert(!hdf5_var->dimscale_hdf5_objids);
if (!(var->dimscale_attached = calloc(ndims, sizeof(nc_bool_t))))
if (!(hdf5_var->dimscale_attached = calloc(ndims, sizeof(nc_bool_t))))
return NC_ENOMEM;
if (!(hdf5_var->dimscale_hdf5_objids = malloc(ndims *
sizeof(struct hdf5_objid))))
@ -1171,7 +1171,7 @@ get_attached_info(NC_VAR_INFO_T *var, NC_HDF5_VAR_INFO_T *hdf5_var, int ndims,
if (H5DSiterate_scales(hdf5_var->hdf_datasetid, d, NULL, dimscale_visitor,
&(hdf5_var->dimscale_hdf5_objids[d])) < 0)
return NC_EHDFERR;
var->dimscale_attached[d] = NC_TRUE;
hdf5_var->dimscale_attached[d] = NC_TRUE;
LOG((4, "dimscale attached"));
}
}
@ -1208,7 +1208,7 @@ get_scale_info(NC_GRP_INFO_T *grp, NC_DIM_INFO_T *dim, NC_VAR_INFO_T *var,
if (dim)
{
assert(ndims);
var->dimscale = NC_TRUE;
hdf5_var->dimscale = NC_TRUE;
/* If this is a multi-dimensional coordinate var, then the
* dimids must be stored in the hidden coordinates attribute. */
@ -1298,7 +1298,7 @@ nc4_get_var_meta(NC_VAR_INFO_T *var)
if ((retval = nc4_adjust_var_cache(var->container, var)))
BAIL(retval);
if (var->coords_read && !var->dimscale)
if (var->coords_read && !hdf5_var->dimscale)
if ((retval = get_attached_info(var, hdf5_var, var->ndims, hdf5_var->hdf_datasetid)))
return retval;
@ -1408,6 +1408,8 @@ exit:
* delete the var info struct we just created. */
if (incr_id_rc && H5Idec_ref(datasetid) < 0)
BAIL2(NC_EHDFERR);
if(var && var->format_var_info)
free(var->format_var_info);
if (var)
nc4_var_list_del(grp, var);
}
@ -2130,6 +2132,8 @@ exit:
{
/* NC_EBADTYPID will be normally converted to NC_NOERR so that
the parent iterator does not fail. */
/* Free up the format_att_info */
if((retval=nc4_HDF5_close_att(att))) return retval;
retval = nc4_att_list_del(list, att);
att = NULL;
}

27
libhdf5/hdf5var.c
View File

@ -9,9 +9,7 @@
*/
#include "config.h"
#ifdef USE_HDF5
#include <hdf5internal.h>
#endif
#include <math.h> /* For pow() used below. */
#include "netcdf.h"
@ -291,11 +289,11 @@ give_var_secret_name(NC_VAR_INFO_T *var, const char *name)
* clash. */
if (strlen(name) + strlen(NON_COORD_PREPEND) > NC_MAX_NAME)
return NC_EMAXNAME;
if (!(var->hdf5_name = malloc((strlen(NON_COORD_PREPEND) +
if (!(var->alt_name = malloc((strlen(NON_COORD_PREPEND) +
strlen(name) + 1) * sizeof(char))))
return NC_ENOMEM;
sprintf(var->hdf5_name, "%s%s", NON_COORD_PREPEND, name);
sprintf(var->alt_name, "%s%s", NON_COORD_PREPEND, name);
return NC_NOERR;
}
@ -342,6 +340,7 @@ NC4_def_var(int ncid, const char *name, nc_type xtype, int ndims,
NC_TYPE_INFO_T *type = NULL;
NC_HDF5_TYPE_INFO_T *hdf5_type;
NC_HDF5_GRP_INFO_T *hdf5_grp;
NC_HDF5_VAR_INFO_T* hdf5_var;
char norm_name[NC_MAX_NAME + 1];
int d;
int retval;
@ -488,6 +487,8 @@ NC4_def_var(int ncid, const char *name, nc_type xtype, int ndims,
if (!(var->format_var_info = calloc(1, sizeof(NC_HDF5_VAR_INFO_T))))
BAIL(NC_ENOMEM);
hdf5_var = (NC_HDF5_VAR_INFO_T*)var->format_var_info;
/* Set these state flags for the var. */
var->is_new_var = NC_TRUE;
var->meta_read = NC_TRUE;
@ -524,7 +525,7 @@ NC4_def_var(int ncid, const char *name, nc_type xtype, int ndims,
/* 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;
hdf5_var->dimscale = NC_TRUE;
dim->coord_var = var;
/* Use variable's dataset ID for the dimscale ID. So delete
@ -590,8 +591,8 @@ NC4_def_var(int ncid, const char *name, nc_type xtype, int ndims,
* 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))))
if (!hdf5_var->dimscale && ndims)
if (!(hdf5_var->dimscale_attached = calloc(ndims, sizeof(nc_bool_t))))
BAIL(NC_ENOMEM);
/* Return the varid. */
@ -1126,6 +1127,7 @@ NC4_rename_var(int ncid, int varid, const char *name)
NC_HDF5_GRP_INFO_T *hdf5_grp;
NC_FILE_INFO_T *h5;
NC_VAR_INFO_T *var;
NC_HDF5_VAR_INFO_T *hdf5_var;
NC_DIM_INFO_T *other_dim;
int use_secret_name = 0;
int retval = NC_NOERR;
@ -1190,13 +1192,16 @@ NC4_rename_var(int ncid, int varid, const char *name)
use_secret_name++;
}
hdf5_var = (NC_HDF5_VAR_INFO_T*)var->format_var_info;
assert(hdf5_var != NULL);
/* Change the HDF5 file, if this var has already been created
there. */
if (var->created)
{
int v;
char *hdf5_name; /* Dataset will be renamed to this. */
hdf5_name = use_secret_name ? var->hdf5_name: (char *)name;
hdf5_name = use_secret_name ? var->alt_name: (char *)name;
/* Do we need to read var metadata? */
if (!var->meta_read)
@ -1261,7 +1266,7 @@ NC4_rename_var(int ncid, int varid, const char *name)
/* 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))
if (hdf5_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])))
@ -1269,7 +1274,7 @@ NC4_rename_var(int ncid, int varid, const char *name)
}
/* Check if this should become a coordinate variable. */
if (!var->dimscale)
if (!hdf5_var->dimscale)
{
/* Only variables with >0 dimensions can become coordinate
* variables. */
@ -2290,7 +2295,7 @@ nc_set_var_chunk_cache_ints(int ncid, int varid, int size, int nelems,
float real_preemption = CHUNK_CACHE_PREEMPTION;
LOG((1, "%s: ncid 0x%x varid %d size %d nelems %d preemption %d",
__func__, ncid, varid, size, nelems, preemptions));
__func__, ncid, varid, size, nelems, preemption));
if (size >= 0)
real_size = ((size_t) size) * MEGABYTE;

39
libhdf5/nc4hdf.c
View File

@ -19,6 +19,7 @@
#include "nc4internal.h"
#include "ncdispatch.h"
#include "hdf5internal.h"
#include "hdf5debug.h"
#include <math.h>
#ifdef HAVE_INTTYPES_H
@ -100,9 +101,11 @@ rec_reattach_scales(NC_GRP_INFO_T *grp, int dimid, hid_t dimscaleid)
assert(var && var->format_var_info);
hdf5_var = (NC_HDF5_VAR_INFO_T *)var->format_var_info;
hdf5_var = (NC_HDF5_VAR_INFO_T*)var->format_var_info;
assert(hdf5_var != NULL);
for (d = 0; d < var->ndims; d++)
{
if (var->dimids[d] == dimid && !var->dimscale)
if (var->dimids[d] == dimid && !hdf5_var->dimscale)
{
LOG((2, "%s: attaching scale for dimid %d to var %s",
__func__, var->dimids[d], var->hdr.name));
@ -111,7 +114,7 @@ rec_reattach_scales(NC_GRP_INFO_T *grp, int dimid, hid_t dimscaleid)
if (H5DSattach_scale(hdf5_var->hdf_datasetid,
dimscaleid, d) < 0)
return NC_EHDFERR;
var->dimscale_attached[d] = NC_TRUE;
hdf5_var->dimscale_attached[d] = NC_TRUE;
}
}
}
@ -164,18 +167,18 @@ rec_detach_scales(NC_GRP_INFO_T *grp, int dimid, hid_t dimscaleid)
for (d = 0; d < var->ndims; d++)
{
if (var->dimids[d] == dimid && !var->dimscale)
if (var->dimids[d] == dimid && !hdf5_var->dimscale)
{
LOG((2, "%s: detaching scale for dimid %d to var %s",
__func__, var->dimids[d], var->hdr.name));
if (var->created)
{
if (var->dimscale_attached && var->dimscale_attached[d])
if (hdf5_var->dimscale_attached && hdf5_var->dimscale_attached[d])
{
if (H5DSdetach_scale(hdf5_var->hdf_datasetid,
dimscaleid, d) < 0)
return NC_EHDFERR;
var->dimscale_attached[d] = NC_FALSE;
hdf5_var->dimscale_attached[d] = NC_FALSE;
}
}
}
@ -1051,7 +1054,7 @@ var_create_dataset(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, nc_bool_t write_dimid
BAIL(NC_EHDFERR);
/* At long last, create the dataset. */
name_to_use = var->hdf5_name ? var->hdf5_name : var->hdr.name;
name_to_use = var->alt_name ? var->alt_name : var->hdr.name;
LOG((4, "%s: about to H5Dcreate2 dataset %s of type 0x%x", __func__,
name_to_use, typeid));
if ((hdf5_var->hdf_datasetid = H5Dcreate2(hdf5_grp->hdf_grpid, name_to_use, typeid,
@ -1070,7 +1073,7 @@ var_create_dataset(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, nc_bool_t write_dimid
/* If this is a dimscale, mark it as such in the HDF5 file. Also
* find the dimension info and store the dataset id of the dimscale
* dataset. */
if (var->dimscale)
if (hdf5_var->dimscale)
{
if (H5DSset_scale(hdf5_var->hdf_datasetid, var->hdr.name) < 0)
BAIL(NC_EHDFERR);
@ -1442,16 +1445,16 @@ attach_dimscales(NC_GRP_INFO_T *grp)
/* Scales themselves do not attach. But I really wish they
* would. */
if (var->dimscale)
if (hdf5_var->dimscale)
continue;
/* Find the scale for each dimension, if any, and attach it. */
for (d = 0; d < var->ndims; d++)
{
/* Is there a dimscale for this dimension? */
if (var->dimscale_attached)
if (hdf5_var->dimscale_attached)
{
if (!var->dimscale_attached[d])
if (!hdf5_var->dimscale_attached[d])
{
hid_t dsid; /* Dataset ID for dimension */
assert(var->dim[d] && var->dim[d]->hdr.id == var->dimids[d] &&
@ -1470,7 +1473,7 @@ attach_dimscales(NC_GRP_INFO_T *grp)
/* Attach the scale. */
if (H5DSattach_scale(hdf5_var->hdf_datasetid, dsid, d) < 0)
return NC_EHDFERR;
var->dimscale_attached[d] = NC_TRUE;
hdf5_var->dimscale_attached[d] = NC_TRUE;
}
}
}
@ -1668,7 +1671,7 @@ write_var(NC_VAR_INFO_T *var, NC_GRP_INFO_T *grp, nc_bool_t write_dimid)
/* If this is not a dimension scale, remove any attached scales,
* and delete dimscale attributes from the var. */
if (var->was_coord_var && var->dimscale_attached)
if (var->was_coord_var && hdf5_var->dimscale_attached)
{
int d;
@ -1681,7 +1684,7 @@ write_var(NC_VAR_INFO_T *var, NC_GRP_INFO_T *grp, nc_bool_t write_dimid)
/* If this is a regular var, detach all its dim scales. */
for (d = 0; d < var->ndims; d++)
{
if (var->dimscale_attached[d])
if (hdf5_var->dimscale_attached[d])
{
hid_t dsid; /* Dataset ID for dimension */
assert(var->dim[d] && var->dim[d]->hdr.id == var->dimids[d] &&
@ -1697,7 +1700,7 @@ write_var(NC_VAR_INFO_T *var, NC_GRP_INFO_T *grp, nc_bool_t write_dimid)
/* Detach this dim scale. */
if (H5DSdetach_scale(hdf5_var->hdf_datasetid, dsid, d) < 0)
return NC_EHDFERR;
var->dimscale_attached[d] = NC_FALSE;
hdf5_var->dimscale_attached[d] = NC_FALSE;
}
}
}
@ -1733,7 +1736,7 @@ write_var(NC_VAR_INFO_T *var, NC_GRP_INFO_T *grp, nc_bool_t write_dimid)
{
/* If this is a dimension scale, reattach the scale everywhere it
* is used. (Recall that netCDF dimscales are always 1-D). */
if(var->dimscale)
if(hdf5_var->dimscale)
{
if ((retval = rec_reattach_scales(grp->nc4_info->root_grp,
var->dimids[0], hdf5_var->hdf_datasetid)))
@ -1743,8 +1746,8 @@ write_var(NC_VAR_INFO_T *var, NC_GRP_INFO_T *grp, nc_bool_t write_dimid)
* so the dimensions are re-attached. */
else
{
if (var->dimscale_attached)
memset(var->dimscale_attached, 0, sizeof(nc_bool_t) * var->ndims);
if (hdf5_var->dimscale_attached)
memset(hdf5_var->dimscale_attached, 0, sizeof(nc_bool_t) * var->ndims);
}
}
@ -2146,7 +2149,7 @@ nc4_rec_match_dimscales(NC_GRP_INFO_T *grp)
}
/* Skip dimension scale variables */
if (!var->dimscale)
if (!hdf5_var->dimscale)
{
int d;
int j;

70
libsrc4/nc4internal.c
View File

@ -28,6 +28,7 @@ size_t nc4_chunk_cache_size = CHUNK_CACHE_SIZE; /**< Default chunk ca
size_t nc4_chunk_cache_nelems = CHUNK_CACHE_NELEMS; /**< Default chunk cache number of elements. */
float nc4_chunk_cache_preemption = CHUNK_CACHE_PREEMPTION; /**< Default chunk cache preemption. */
static int NC4_move_in_NCList(NC* nc, int new_id);
static void freefilterlist(NClist* filters);
#ifdef LOGGING
@ -158,7 +159,7 @@ nc4_file_change_ncid(int ncid, unsigned short new_ncid_index)
* occupied. */
LOG((3, "moving nc->ext_ncid %d nc->ext_ncid >> ID_SHIFT %d",
nc->ext_ncid, nc->ext_ncid >> ID_SHIFT));
if (move_in_NCList(nc, new_ncid_index))
if (NC4_move_in_NCList(nc, new_ncid_index))
return NC_EIO;
LOG((3, "moved to new_ncid_index %d new nc->ext_ncid %d", new_ncid_index,
nc->ext_ncid));
@ -239,6 +240,10 @@ nc4_nc4f_list_add(NC *nc, const char *path, int mode)
nc->dispatchdata = h5;
h5->controller = nc;
h5->hdr.sort = NCFIL;
h5->hdr.name = strdup(path);
h5->hdr.id = nc->ext_ncid;
/* Hang on to cmode, and note that we're in define mode. */
h5->cmode = mode | NC_INDEF;
@ -972,17 +977,16 @@ nc4_type_new(size_t size, const char *name, int assignedid,
if (!(new_type = calloc(1, sizeof(NC_TYPE_INFO_T))))
return NC_ENOMEM;
new_type->hdr.sort = NCTYP;
new_type->hdr.hashkey = NC_hashmapkey(name, strlen(name));
new_type->hdr.id = assignedid;
/* Remember info about this type. */
new_type->hdr.id = assignedid;
new_type->size = size;
if (!(new_type->hdr.name = strdup(name))) {
free(new_type);
return NC_ENOMEM;
}
new_type->hdr.hashkey = NC_hashmapkey(name, strlen(name));
/* Return a pointer to the new type. */
*type = new_type;
@ -1219,10 +1223,6 @@ nc4_type_free(NC_TYPE_INFO_T *type)
break;
}
/* Release any HDF5-specific type info. */
if (type->format_type_info)
free(type->format_type_info);
/* Release the memory. */
free(type);
}
@ -1238,8 +1238,8 @@ nc4_type_free(NC_TYPE_INFO_T *type)
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
static int
att_free(NC_ATT_INFO_T *att)
int
nc4_att_free(NC_ATT_INFO_T *att)
{
int i;
@ -1277,11 +1277,6 @@ att_free(NC_ATT_INFO_T *att)
free(att->vldata);
}
/* Free any format-sepecific info. Some formats use this (ex. HDF5)
* and some don't (ex. HDF4). So it may be NULL. */
if (att->format_att_info)
free(att->format_att_info);
free(att);
return NC_NOERR;
}
@ -1306,7 +1301,7 @@ var_free(NC_VAR_INFO_T *var)
/* First delete all the attributes attached to this var. */
for (i = 0; i < ncindexsize(var->att); i++)
if ((retval = att_free((NC_ATT_INFO_T *)ncindexith(var->att, i))))
if ((retval = nc4_att_free((NC_ATT_INFO_T *)ncindexith(var->att, i))))
return retval;
ncindexfree(var->att);
@ -1314,8 +1309,8 @@ var_free(NC_VAR_INFO_T *var)
if (var->chunksizes)
free(var->chunksizes);
if (var->hdf5_name)
free(var->hdf5_name);
if (var->alt_name)
free(var->alt_name);
if (var->hdr.name)
free(var->hdr.name);
@ -1335,17 +1330,9 @@ var_free(NC_VAR_INFO_T *var)
if ((retval = nc4_type_free(var->type_info)))
return retval;
/* Delete information about the attachment status of dimscales. */
if (var->dimscale_attached)
free(var->dimscale_attached);
/* Release filter information. */
freefilterlist(var->filters);
/* Delete any format-specific info. */
if (var->format_var_info)
free(var->format_var_info);
/* Delete the var. */
free(var);
@ -1394,10 +1381,6 @@ dim_free(NC_DIM_INFO_T *dim)
if (dim->hdr.name)
free(dim->hdr.name);
/* Release any format-specific information. */
if (dim->format_dim_info)
free(dim->format_dim_info);
free(dim);
return NC_NOERR;
}
@ -1450,9 +1433,9 @@ nc4_rec_grp_del(NC_GRP_INFO_T *grp)
return retval;
ncindexfree(grp->children);
/* Free attributes, but leave in parent list */
/* Free attributes */
for (i = 0; i < ncindexsize(grp->att); i++)
if ((retval = att_free((NC_ATT_INFO_T *)ncindexith(grp->att, i))))
if ((retval = nc4_att_free((NC_ATT_INFO_T *)ncindexith(grp->att, i))))
return retval;
ncindexfree(grp->att);
@ -1479,10 +1462,6 @@ nc4_rec_grp_del(NC_GRP_INFO_T *grp)
/* Free the name. */
free(grp->hdr.name);
/* Release any format-specific information about this group. */
if (grp->format_grp_info)
free(grp->format_grp_info);
/* Free up this group */
free(grp);
@ -1504,7 +1483,7 @@ nc4_att_list_del(NCindex *list, NC_ATT_INFO_T *att)
{
assert(att && list);
ncindexidel(list, ((NC_OBJ *)att)->id);
return att_free(att);
return nc4_att_free(att);
}
/**
@ -1565,6 +1544,7 @@ nc4_nc4f_list_del(NC_FILE_INFO_T *h5)
nclistfree(h5->alltypes);
/* Free the NC_FILE_INFO_T struct. */
nullfree(h5->hdr.name);
free(h5);
return NC_NOERR;
@ -1702,9 +1682,9 @@ rec_print_metadata(NC_GRP_INFO_T *grp, int tab_count)
strcat(storage_str, "compact");
else
strcat(storage_str, "chunked");
LOG((2, "%s VARIABLE - varid: %d name: %s ndims: %d dimscale: %d "
LOG((2, "%s VARIABLE - varid: %d name: %s ndims: %d "
"dimids:%s storage: %s", tabs, var->hdr.id, var->hdr.name,
var->ndims, (int)var->dimscale,
var->ndims,
(dims_string ? dims_string : " -"), storage_str));
for (j = 0; j < ncindexsize(var->att); j++)
{
@ -1837,3 +1817,15 @@ freefilterlist(NClist* filters)
}
nclistfree(filters);
}
static int
NC4_move_in_NCList(NC* nc, int new_id)
{
int stat = move_in_NCList(nc,new_id);
if(stat == NC_NOERR) {
/* Synchronize header */
if(nc->dispatchdata)
((NC_OBJ*)nc->dispatchdata)->id = nc->ext_ncid;
}
return stat;
}