Separate the closing of HDF5 objects from freeing of internal metadata

include/hdf5internal.h

@@ -60,7 +60,7 @@ typedef struct  NC_HDF5_FILE_INFO
 int rec_detach_scales(NC_GRP_INFO_T *grp, int dimid, hid_t dimscaleid);
 int rec_reattach_scales(NC_GRP_INFO_T *grp, int dimid, hid_t dimscaleid);
 void reportopenobjects(int log, hid_t);
-
+int nc4_rec_grp_HDF5_del(NC_GRP_INFO_T *grp);
 
 /* Used by NC4_set_provenance */
 int nc4_put_att(NC_GRP_INFO_T* grp, int varid, const char *name, nc_type file_type,

include/nc4internal.h

@@ -376,10 +376,8 @@ int nc4_var_list_add(NC_GRP_INFO_T* grp, const char* name, int ndims, NC_VAR_INF
 int nc4_var_list_add2(NC_GRP_INFO_T* grp, const char* name, NC_VAR_INFO_T **var);
 int nc4_var_set_ndims(NC_VAR_INFO_T *var, int ndims);
 int nc4_var_list_del(NC_GRP_INFO_T* grp, NC_VAR_INFO_T *var);
-int nc4_var_free(NC_VAR_INFO_T *var);
 int nc4_dim_list_add(NC_GRP_INFO_T* grp, const char* name, size_t len, int assignedid, NC_DIM_INFO_T **dim);
 int nc4_dim_list_del(NC_GRP_INFO_T* grp, NC_DIM_INFO_T *dim);
-int nc4_dim_free(NC_DIM_INFO_T *dim);
 int nc4_type_new(NC_GRP_INFO_T *grp, size_t size, const char *name, int assignedid, NC_TYPE_INFO_T **type);
 int nc4_type_list_add(NC_GRP_INFO_T *grp, size_t size, const char *name, NC_TYPE_INFO_T **type);
 int nc4_type_list_del(NC_GRP_INFO_T* grp, NC_TYPE_INFO_T *type);
@@ -389,7 +387,6 @@ int nc4_field_list_add(NC_TYPE_INFO_T* parent, const char *name,
 		       nc_type xtype, int ndims, const int *dim_sizesp);
 int nc4_att_list_add(NCindex* list, const char* name, NC_ATT_INFO_T **att);
 int nc4_att_list_del(NCindex* list, NC_ATT_INFO_T *att);
-int nc4_att_free(NC_ATT_INFO_T *att);
 int nc4_grp_list_add(NC_FILE_INFO_T *h5, NC_GRP_INFO_T *parent, char *name, NC_GRP_INFO_T **grp);
 int nc4_build_root_grp(NC_FILE_INFO_T* h5);
 int nc4_rec_grp_del(NC_GRP_INFO_T *grp);
@@ -410,7 +407,8 @@ int nc4_check_dup_name(NC_GRP_INFO_T *grp, char *norm_name);
 int nc4_get_default_fill_value(const NC_TYPE_INFO_T *type_info, void *fill_value);
 
 /* Close the file. */
-int nc4_close_netcdf4_file(NC_FILE_INFO_T *h5, int abort, NC_memio*);
+int nc4_close_hdf5_file(NC_FILE_INFO_T *h5, int abort, NC_memio *memio);
+int nc4_close_netcdf4_file(NC_FILE_INFO_T *h5, int abort, NC_memio *memio);
 
 /* HDF5 initialization/finalization */
 extern int nc4_hdf5_initialized;

libhdf5/hdf5create.c

@@ -240,7 +240,7 @@ nc4_create_file(const char *path, int cmode, size_t initialsz,
 #endif
    if (fapl_id != H5P_DEFAULT) H5Pclose(fapl_id);
    if(!nc4_info) return retval;
-   nc4_close_netcdf4_file(nc4_info,1,NULL); /* treat like abort */
+   nc4_close_hdf5_file(nc4_info, 1, NULL); /* treat like abort */
    return retval;
 }
 

libhdf5/hdf5file.c

@@ -163,7 +163,7 @@ sync_netcdf4_file(NC_FILE_INFO_T *h5)
  * @author Ed Hartnett, Dennis Heimbigner
  */
 int
-nc4_close_netcdf4_file(NC_FILE_INFO_T *h5, int abort, NC_memio* memio)
+nc4_close_netcdf4_file(NC_FILE_INFO_T *h5, int abort, NC_memio *memio)
 {
    NC_HDF5_FILE_INFO_T *hdf5_info;
    int retval;
@@ -174,16 +174,6 @@ nc4_close_netcdf4_file(NC_FILE_INFO_T *h5, int abort, NC_memio* memio)
    /* Get HDF5 specific info. */
    hdf5_info = (NC_HDF5_FILE_INFO_T *)h5->format_file_info;
 
-   /* According to the docs, always end define mode on close. */
-   if (h5->flags & NC_INDEF)
-      h5->flags ^= NC_INDEF;
-
-   /* Sync the file, unless we're aborting, or this is a read-only
-    * file. */
-   if (!h5->no_write && !abort)
-      if ((retval = sync_netcdf4_file(h5)))
-         return retval;
-
    /* Delete all the list contents for vars, dims, and atts, in each
     * group. */
    if ((retval = nc4_rec_grp_del(h5->root_grp)))
@@ -252,6 +242,53 @@ nc4_close_netcdf4_file(NC_FILE_INFO_T *h5, int abort, NC_memio* memio)
    return NC_NOERR;
 }
 
+/**
+ * @internal This function will recurse through an open HDF5 file and
+ * release resources. All open HDF5 objects in the file will be
+ * closed.
+ *
+ * @param h5 Pointer to HDF5 file info struct.
+ * @param abort True if this is an abort.
+ * @param memio the place to return a core image if not NULL
+ *
+ * @return ::NC_NOERR No error.
+ * @return ::NC_EHDFERR HDF5 could not close the file.
+ * @author Ed Hartnett
+ */
+int
+nc4_close_hdf5_file(NC_FILE_INFO_T *h5, int abort,  NC_memio *memio)
+{
+   NC_HDF5_FILE_INFO_T *hdf5_info;
+   int retval;
+
+   assert(h5 && h5->root_grp && h5->format_file_info);
+   LOG((3, "%s: h5->path %s abort %d", __func__, h5->controller->path, abort));
+
+   /* Get HDF5 specific info. */
+   hdf5_info = (NC_HDF5_FILE_INFO_T *)h5->format_file_info;
+
+   /* According to the docs, always end define mode on close. */
+   if (h5->flags & NC_INDEF)
+      h5->flags ^= NC_INDEF;
+
+   /* Sync the file, unless we're aborting, or this is a read-only
+    * file. */
+   if (!h5->no_write && !abort)
+      if ((retval = sync_netcdf4_file(h5)))
+         return retval;
+
+   /* Close all open HDF5 objects within the file. */
+   if ((retval = nc4_rec_grp_HDF5_del(h5->root_grp)))
+      return retval;
+
+   /* Release all intarnal 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;
+
+   return NC_NOERR;
+}
+
 /**
  * @internal Output a list of still-open objects in the HDF5
  * file. This is only called if the file fails to close cleanly.
@@ -515,7 +552,7 @@ NC4_abort(int ncid)
 
    /* Free any resources the netcdf-4 library has for this file's
     * metadata. */
-   if ((retval = nc4_close_netcdf4_file(nc4_info, 1, NULL)))
+   if ((retval = nc4_close_hdf5_file(nc4_info, 1, NULL)))
       return retval;
 
    /* Delete the file, if we should. */
@@ -564,7 +601,7 @@ NC4_close(int ncid, void* params)
    }
 
    /* Call the nc4 close. */
-   if ((retval = nc4_close_netcdf4_file(grp->nc4_info, 0, memio)))
+   if ((retval = nc4_close_hdf5_file(grp->nc4_info, 0, memio)))
       return retval;
 
    return NC_NOERR;

libhdf5/hdf5internal.c

@@ -478,6 +478,129 @@ nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, NC_DIM_INFO_T *dim)
    return retval;
 }
 
+/**
+ * @internal Recursively free HDF5 objects for a group (and everything
+ * it contains).
+ *
+ * @param grp Pointer to group info struct.
+ *
+ * @return ::NC_NOERR No error.
+ * @author Ed Hartnett
+ */
+int
+nc4_rec_grp_HDF5_del(NC_GRP_INFO_T *grp)
+{
+   NC_VAR_INFO_T *var;
+   NC_DIM_INFO_T *dim;
+   NC_ATT_INFO_T *att;
+   int a;
+   int i;
+   int retval;
+
+   assert(grp);
+   LOG((3, "%s: grp->name %s", __func__, grp->hdr.name));
+
+   /* 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 attributes. */
+   for (a = 0; a < ncindexsize(grp->att); a++)
+   {
+      att = (NC_ATT_INFO_T *)ncindexith(grp->att, a);
+      assert(att);
+
+      /* Close the HDF5 typeid. */
+      if (att->native_hdf_typeid && H5Tclose(att->native_hdf_typeid) < 0)
+         return NC_EHDFERR;
+   }
+
+   /* Close HDF5 resources associated with vars. */
+   for (i = 0; i < ncindexsize(grp->vars); i++)
+   {
+      var = (NC_VAR_INFO_T *)ncindexith(grp->vars, i);
+      assert(var);
+
+      /* Close the HDF5 dataset associated with this var. */
+      if (var->hdf_datasetid)
+      {
+         LOG((3, "closing HDF5 dataset %lld", var->hdf_datasetid));
+         if (H5Dclose(var->hdf_datasetid) < 0)
+            return NC_EHDFERR;
+      }
+
+      for (a = 0; a < ncindexsize(var->att); a++)
+      {
+         att = (NC_ATT_INFO_T *)ncindexith(var->att, a);
+         assert(att);
+
+         /* Close the HDF5 typeid if one is open. */
+         if (att->native_hdf_typeid && H5Tclose(att->native_hdf_typeid) < 0)
+            return NC_EHDFERR;
+      }
+   }
+
+   /* Close HDF5 resources associated with dims. */
+   for (i = 0; i < ncindexsize(grp->dim); i++)
+   {
+      dim = (NC_DIM_INFO_T *)ncindexith(grp->dim, i);
+      assert(dim);
+
+      /* If this is a dim without a coordinate variable, then close
+       * the HDF5 DIM_WITHOUT_VARIABLE dataset associated with this
+       * dim. */
+      if (dim->hdf_dimscaleid && H5Dclose(dim->hdf_dimscaleid) < 0)
+         return NC_EHDFERR;
+   }
+
+   /* Close HDF5 resources associated with types. Set values to 0
+    * after closing types. Because of type reference counters, these
+    * closes can be called multiple times. */
+   for (i = 0; i < ncindexsize(grp->type); i++)
+   {
+      NC_TYPE_INFO_T *type = (NC_TYPE_INFO_T *)ncindexith(grp->type, i);
+      assert(type);
+
+      /* Close any open user-defined HDF5 typeids. */
+      if (type->hdf_typeid && H5Tclose(type->hdf_typeid) < 0)
+         return NC_EHDFERR;
+      type->hdf_typeid = 0;
+      if (type->native_hdf_typeid && H5Tclose(type->native_hdf_typeid) < 0)
+         return NC_EHDFERR;
+      type->native_hdf_typeid = 0;
+
+      /* Class-specific cleanup. Only enums and vlens have HDF5
+       * resources to close. */
+      switch (type->nc_type_class)
+      {
+      case NC_ENUM:
+         if (type->u.e.base_hdf_typeid && H5Tclose(type->u.e.base_hdf_typeid) < 0)
+            return NC_EHDFERR;
+         type->u.e.base_hdf_typeid = 0;
+         break;
+
+      case NC_VLEN:
+         if (type->u.v.base_hdf_typeid && H5Tclose(type->u.v.base_hdf_typeid) < 0)
+            return NC_EHDFERR;
+         type->u.v.base_hdf_typeid = 0;
+         break;
+
+      default: /* Do nothing. */
+         break;
+      }
+   }
+
+   /* Close the HDF5 group. */
+   LOG((4, "%s: closing group %s", __func__, grp->hdr.name));
+   if (grp->hdf_grpid && H5Gclose(grp->hdf_grpid) < 0)
+      return NC_EHDFERR;
+
+   return NC_NOERR;
+}
+
 #ifdef LOGGING
 /* We will need to check against nc log level from nc4internal.c. */
 extern int nc_log_level;

libhdf5/hdf5open.c

@@ -552,7 +552,7 @@ nc4_open_file(const char *path, int mode, void* parameters, NC *nc)
    if (fapl_id > 0 && fapl_id != H5P_DEFAULT)
       H5Pclose(fapl_id);
    if (nc4_info)
-      nc4_close_netcdf4_file(nc4_info, 1, 0); /*  treat like abort*/
+      nc4_close_hdf5_file(nc4_info, 1, 0); /*  treat like abort*/
    return retval;
 }