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cleanup

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This commit is contained in:
Ed Hartnett 2018-07-17 09:03:19 -06:00
parent b0f9f965b7
commit 752e76df22
2 changed files with 60 additions and 46 deletions
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14
libhdf5/hdf5create.c
View File

@ -39,7 +39,8 @@ extern int NC4_create_image_file(NC_FILE_INFO_T* h5, size_t);
* @author Ed Hartnett, Dennis Heimbigner
*/
static int
nc4_create_file(const char *path, int cmode, size_t initialsz, void* parameters, NC *nc)
nc4_create_file(const char *path, int cmode, size_t initialsz,
void* parameters, NC *nc)
{
hid_t fcpl_id, fapl_id = -1;
unsigned flags;
@ -51,8 +52,8 @@ nc4_create_file(const char *path, int cmode, size_t initialsz, void* parameters,
NC_MPI_INFO* mpiinfo = NULL;
MPI_Comm comm;
MPI_Info info;
int comm_duped = 0; /* Whether the MPI Communicator was duplicated */
int info_duped = 0; /* Whether the MPI Info object was duplicated */
int comm_duped = 0; /* Whether the MPI Communicator was duplicated */
int info_duped = 0; /* Whether the MPI Info object was duplicated */
#endif /* !USE_PARALLEL4 */
assert(nc && path);
@ -165,7 +166,8 @@ nc4_create_file(const char *path, int cmode, size_t initialsz, void* parameters,
#if H5_VERSION_GE(1,10,2)
if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_EARLIEST, H5F_LIBVER_V18) < 0)
#else
if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_EARLIEST, H5F_LIBVER_LATEST) < 0)
if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_EARLIEST,
H5F_LIBVER_LATEST) < 0)
#endif
BAIL(NC_EHDFERR);
#endif
@ -256,8 +258,8 @@ exit: /*failure exit*/
* @param basepe Ignored by this function.
* @param chunksizehintp Ignored by this function.
* @param use_parallel 0 for sequential, non-zero for parallel I/O.
* @param parameters pointer to struct holding extra data (e.g. for parallel I/O)
* layer. Ignored if NULL.
* @param parameters pointer to struct holding extra data (e.g. for
* parallel I/O) layer. Ignored if NULL.
* @param dispatch Pointer to the dispatch table for this file.
* @param nc_file Pointer to an instance of NC.
*

92
libhdf5/hdf5open.c
View File

@ -61,7 +61,7 @@ typedef struct NC4_rec_read_metadata_obj_info
hid_t oid; /* HDF5 object ID */
char oname[NC_MAX_NAME + 1]; /* Name of object */
H5G_stat_t statbuf; /* Information about the object */
struct NC4_rec_read_metadata_obj_info *next; /* Pointer to next node in list */
struct NC4_rec_read_metadata_obj_info *next; /* Pointer to next node in list */
} NC4_rec_read_metadata_obj_info_t;
/**
@ -82,9 +82,9 @@ typedef struct {
} att_iter_info;
/**
* @internal Given an HDF5 type, set a pointer to netcdf type_info struct,
* either an existing one (for user-defined types) or a newly created
* one.
* @internal Given an HDF5 type, set a pointer to netcdf type_info
* struct, either an existing one (for user-defined types) or a newly
* created one.
*
* @param h5 Pointer to HDF5 file info struct.
* @param datasetid HDF5 dataset ID.
@ -154,7 +154,8 @@ get_type_info2(NC_FILE_INFO_T *h5, hid_t datasetid,
{
if ((is_str = H5Tis_variable_str(native_typeid)) < 0)
return NC_EHDFERR;
/* Make sure fixed-len strings will work like variable-len strings */
/* Make sure fixed-len strings will work like variable-len
* strings */
if (is_str || H5Tget_size(hdf_typeid) > 1)
{
/* Set a class for the type */
@ -172,18 +173,16 @@ get_type_info2(NC_FILE_INFO_T *h5, hid_t datasetid,
{
for (t = 1; t < NUM_TYPES - 1; t++)
{
if ((equal = H5Tequal(native_typeid, h5_native_type_constant_g[t])) < 0)
if ((equal = H5Tequal(native_typeid,
h5_native_type_constant_g[t])) < 0)
return NC_EHDFERR;
if (equal)
break;
}
/* Find out about endianness.
* As of HDF 1.8.6, this works with all data types
* Not just H5T_INTEGER.
*
* See https://www.hdfgroup.org/HDF5/doc/RM/RM_H5T.html#Datatype-GetOrder
*/
/* Find out about endianness. As of HDF 1.8.6, this works
* with all data types Not just H5T_INTEGER. See
* https://www.hdfgroup.org/HDF5/doc/RM/RM_H5T.html#Datatype-GetOrder */
if((order = H5Tget_order(hdf_typeid)) < 0)
return NC_EHDFERR;
@ -452,7 +451,8 @@ nc4_open_file(const char *path, int mode, void* parameters, NC *nc)
nc4_chunk_cache_preemption) < 0)
BAIL(NC_EHDFERR);
LOG((4, "%s: set HDF raw chunk cache to size %d nelems %d preemption %f",
__func__, nc4_chunk_cache_size, nc4_chunk_cache_nelems, nc4_chunk_cache_preemption));
__func__, nc4_chunk_cache_size, nc4_chunk_cache_nelems,
nc4_chunk_cache_preemption));
#endif /* USE_PARALLEL4 */
/* The NetCDF-3.x prototype contains an mode option NC_SHARE for
@ -602,7 +602,7 @@ read_var(NC_GRP_INFO_T *grp, hid_t datasetid, const char *obj_name,
{
NC_VAR_INFO_T *var = NULL;
hid_t access_pid = 0;
int incr_id_rc = 0; /* Whether the dataset ID's ref count has been incremented */
int incr_id_rc = 0; /* Whether dataset ID's ref count has been incremented */
int d;
H5Z_filter_t filter;
int num_filters;
@ -628,7 +628,8 @@ read_var(NC_GRP_INFO_T *grp, hid_t datasetid, const char *obj_name,
{
/* Allocate space for the name. */
if(finalname) {free(finalname); finalname = NULL;}
if (!(finalname = malloc(((strlen(obj_name) - strlen(NON_COORD_PREPEND))+ 1) * sizeof(char))))
if (!(finalname = malloc(((strlen(obj_name) -
strlen(NON_COORD_PREPEND))+ 1) * sizeof(char))))
BAIL(NC_ENOMEM);
strcpy(finalname, &obj_name[strlen(NON_COORD_PREPEND)]);
} else
@ -640,8 +641,8 @@ read_var(NC_GRP_INFO_T *grp, hid_t datasetid, const char *obj_name,
/* Fill in what we already know. */
var->hdf_datasetid = datasetid;
H5Iinc_ref(var->hdf_datasetid); /* Increment number of objects using ID */
incr_id_rc++; /* Indicate that we've incremented the ref. count (for errors) */
H5Iinc_ref(var->hdf_datasetid); /* Increment number of objects using ID */
incr_id_rc++; /* Indicate that we've incremented the ref. count (for errors) */
var->created = NC_TRUE;
/* Get the current chunk cache settings. */
@ -696,7 +697,8 @@ read_var(NC_GRP_INFO_T *grp, hid_t datasetid, const char *obj_name,
case H5Z_FILTER_DEFLATE:
var->deflate = NC_TRUE;
if (cd_nelems != CD_NELEMS_ZLIB || cd_values_zip[0] > NC_MAX_DEFLATE_LEVEL)
if (cd_nelems != CD_NELEMS_ZLIB ||
cd_values_zip[0] > NC_MAX_DEFLATE_LEVEL)
BAIL(NC_EHDFERR);
var->deflate_level = cd_values_zip[0];
break;
@ -799,14 +801,15 @@ read_var(NC_GRP_INFO_T *grp, hid_t datasetid, const char *obj_name,
if (num_scales && ndims)
{
/* Allocate space to remember whether the dimscale has been attached
* for each dimension. */
if (NULL == (var->dimscale_attached = calloc(ndims, sizeof(nc_bool_t))))
/* Allocate space to remember whether the dimscale has been
* attached for each dimension. */
if (!(var->dimscale_attached = calloc(ndims, sizeof(nc_bool_t))))
BAIL(NC_ENOMEM);
/* Store id information allowing us to match hdf5
* dimscales to netcdf dimensions. */
if (NULL == (var->dimscale_hdf5_objids = malloc(ndims * sizeof(struct hdf5_objid))))
if (!(var->dimscale_hdf5_objids = malloc(ndims *
sizeof(struct hdf5_objid))))
BAIL(NC_ENOMEM);
for (d = 0; d < var->ndims; d++)
{
@ -820,8 +823,6 @@ read_var(NC_GRP_INFO_T *grp, hid_t datasetid, const char *obj_name,
/* Read variable attributes. */
var->atts_not_read = 1;
/* if ((retval = nc4_read_var_atts(grp, var))) */
/* BAIL(retval); */
/* Is this a deflated variable with a chunksize greater than the
* current cache size? */
@ -1002,11 +1003,13 @@ read_hdf5_att(NC_GRP_INFO_T *grp, hid_t attid, NC_ATT_INFO_T *att)
/* Get type of attribute in file. */
if ((file_typeid = H5Aget_type(attid)) < 0)
return NC_EATTMETA;
if ((att->native_hdf_typeid = H5Tget_native_type(file_typeid, H5T_DIR_DEFAULT)) < 0)
if ((att->native_hdf_typeid = H5Tget_native_type(file_typeid,
H5T_DIR_DEFAULT)) < 0)
BAIL(NC_EHDFERR);
if ((att_class = H5Tget_class(att->native_hdf_typeid)) < 0)
BAIL(NC_EATTMETA);
if (att_class == H5T_STRING && !H5Tis_variable_str(att->native_hdf_typeid))
if (att_class == H5T_STRING &&
!H5Tis_variable_str(att->native_hdf_typeid))
{
fixed_len_string++;
if (!(fixed_size = H5Tget_size(att->native_hdf_typeid)))
@ -1059,7 +1062,8 @@ read_hdf5_att(NC_GRP_INFO_T *grp, hid_t attid, NC_ATT_INFO_T *att)
if ((space_class = H5Sget_simple_extent_type(spaceid)) < 0)
BAIL(NC_EATTMETA);
/* Check for NULL HDF5 dataspace class (should be weeded out earlier) */
/* Check for NULL HDF5 dataspace class (should be weeded out
* earlier) */
if (H5S_NULL == space_class)
BAIL(NC_EATTMETA);
@ -1081,7 +1085,8 @@ read_hdf5_att(NC_GRP_INFO_T *grp, hid_t attid, NC_ATT_INFO_T *att)
attribute. */
if (dims[0])
{
if ((retval = nc4_get_typelen_mem(grp->nc4_info, att->nc_typeid, &type_size)))
if ((retval = nc4_get_typelen_mem(grp->nc4_info, att->nc_typeid,
&type_size)))
return retval;
if (att_class == H5T_VLEN)
{
@ -1295,7 +1300,8 @@ read_type(NC_GRP_INFO_T *grp, hid_t hdf_typeid, char *type_name)
assert(grp && type_name);
LOG((4, "%s: type_name %s grp->hdr.name %s", __func__, type_name, grp->hdr.name));
LOG((4, "%s: type_name %s grp->hdr.name %s", __func__, type_name,
grp->hdr.name));
/* What is the native type for this platform? */
if ((native_typeid = H5Tget_native_type(hdf_typeid, H5T_DIR_DEFAULT)) < 0)
@ -1313,7 +1319,7 @@ read_type(NC_GRP_INFO_T *grp, hid_t hdf_typeid, char *type_name)
/* Remember common info about this type. */
type->committed = NC_TRUE;
type->hdf_typeid = hdf_typeid;
H5Iinc_ref(type->hdf_typeid); /* Increment number of objects using ID */
H5Iinc_ref(type->hdf_typeid); /* Increment number of objects using ID */
type->native_hdf_typeid = native_typeid;
/* What is the class of this type, compound, vlen, etc. */
@ -1355,7 +1361,8 @@ read_type(NC_GRP_INFO_T *grp, hid_t hdf_typeid, char *type_name)
if ((member_hdf_typeid = H5Tget_member_type(type->native_hdf_typeid, m)) < 0)
return NC_EHDFERR;
if ((member_native_typeid = H5Tget_native_type(member_hdf_typeid, H5T_DIR_DEFAULT)) < 0)
if ((member_native_typeid = H5Tget_native_type(member_hdf_typeid,
H5T_DIR_DEFAULT)) < 0)
return NC_EHDFERR;
/* Get the name of the member.*/
@ -1568,7 +1575,8 @@ read_type(NC_GRP_INFO_T *grp, hid_t hdf_typeid, char *type_name)
}
/**
* @internal Callback function for reading attributes. This is used by read_var().
* @internal Callback function for reading attributes. This is used by
* read_var().
*
* @param loc_id HDF5 attribute ID.
* @param att_name Name of the attrigute.
@ -1582,7 +1590,8 @@ read_type(NC_GRP_INFO_T *grp, hid_t hdf_typeid, char *type_name)
* @return ::NC_EBADTYPID Can't read attribute type.
*/
static herr_t
att_read_var_callbk(hid_t loc_id, const char *att_name, const H5A_info_t *ainfo, void *att_data)
att_read_var_callbk(hid_t loc_id, const char *att_name,
const H5A_info_t *ainfo, void *att_data)
{
hid_t attid = 0;
@ -1687,11 +1696,11 @@ read_scale(NC_GRP_INFO_T *grp, hid_t datasetid, const char *obj_name,
const H5G_stat_t *statbuf, hsize_t scale_size, hsize_t max_scale_size,
NC_DIM_INFO_T **dim)
{
NC_DIM_INFO_T *new_dim; /* Dimension added to group */
NC_DIM_INFO_T *new_dim; /* Dimension added to group */
char dimscale_name_att[NC_MAX_NAME + 1] = ""; /* Dimscale name, for checking if dim without var */
htri_t attr_exists = -1; /* Flag indicating hidden attribute exists */
hid_t attid = -1; /* ID of hidden attribute (to store dim ID) */
int dimscale_created = 0; /* Remember if a dimension was created (for error recovery) */
htri_t attr_exists = -1; /* Flag indicating hidden attribute exists */
hid_t attid = -1; /* ID of hidden attribute (to store dim ID) */
int dimscale_created = 0; /* Remember if a dimension was created (for error recovery) */
short initial_next_dimid = grp->nc4_info->next_dimid;/* Retain for error recovery */
int retval;
size_t len = 0;
@ -1758,7 +1767,8 @@ read_scale(NC_GRP_INFO_T *grp, hid_t datasetid, const char *obj_name,
new_dim->len = *lenp;
}
/* Hold open the dataset, since the dimension doesn't have a coordinate variable */
/* Hold open the dataset, since the dimension doesn't have a
* coordinate variable */
new_dim->hdf_dimscaleid = datasetid;
H5Iinc_ref(new_dim->hdf_dimscaleid); /* Increment number of objects using ID */
}
@ -1768,7 +1778,8 @@ read_scale(NC_GRP_INFO_T *grp, hid_t datasetid, const char *obj_name,
*dim = new_dim;
exit:
/* Close the hidden attribute, if it was opened (error, or no error) */
/* Close the hidden attribute, if it was opened (error, or no
* error) */
if (attid > 0 && H5Aclose(attid) < 0)
BAIL2(NC_EHDFERR);
@ -1927,7 +1938,8 @@ nc4_rec_read_metadata_cb(hid_t grpid, const char *name, const H5L_info_t *info,
/* Learn all about this dataset, which may be a dimscale
* (i.e. dimension metadata), or real data. */
if ((retval = read_dataset(udata->grp, oinfo.oid, oinfo.oname, &oinfo.statbuf)))
if ((retval = read_dataset(udata->grp, oinfo.oid, oinfo.oname,
&oinfo.statbuf)))
{
/* Allow NC_EBADTYPID to transparently skip over datasets
* which have a datatype that netCDF-4 doesn't undertand