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HDF5 documents and links Introduction to HDF5 HDF5 User Guide |
And in this document, the
HDF5 Reference Manual
H5 H5A H5D H5E H5F H5G H5I H5P H5R H5S H5T H5Z Tools Datatypes |
The C Interfaces:
H5Fclose(hid_t file_id
)
H5Fclose terminates access to an HDF5 file
by flushing all data to storage and terminating access
to the file through file_id.
If this is the last file identifier open for the file and no other access identifier is open (e.g., a dataset identifier, group identifier, or shared datatype identifier), the file will be fully closed and access will end.
Delayed close:
Note the following deviation from the above-described behavior.
If H5Fclose is called for a file but one or more
objects within the file remain open, those objects will remain
accessible until they are individually closed.
Thus, if the dataset data_sample is open when
H5Fclose is called for the file containing it,
data_sample will remain open and accessible
(including writable) until it is explicitely closed.
The file will be automatically closed once all objects in the
file have been closed.
Be warned, hoever, that there are circumstances where it is
not possible to delay closing a file.
For example, an MPI-IO file close is a collective call; all of
the processes that opened the file must close it collectively.
The file cannot be closed at some time in the future by each
process in an independent fashion.
Another example is that an application using an AFS token-based
file access privilage may destroy its AFS token after
H5Fclose has returned successfully.
This would make any future access to the file, or any object
within it, illegal.
In such situations, applications must close all open objects
in a file before calling H5Fclose.
It is generally recommended to do so in all cases.
file_id
SUBROUTINE h5fclose_f(file_id, hdferr)
IMPLICIT NONE
INTEGER(HID_T), INTENT(IN) :: file_id ! File identifier
INTEGER, INTENT(OUT) :: hdferr ! Error code
! 0 on success and -1 on failure
END SUBROUTINE h5fclose_f
H5Fcreate(const char *name,
unsigned flags,
hid_t create_id,
hid_t access_id
)
H5Fcreate is the primary function for creating
HDF5 files .
The flags parameter determines whether an
existing file will be overwritten. All newly created files
are opened for both reading and writing. All flags may be
combined with the bit-wise OR operator (`|') to change
the behavior of the H5Fcreate call.
The more complex behaviors of file creation and access
are controlled through the file-creation and file-access
property lists. The value of H5P_DEFAULT for
a property list value indicates that the library should use
the default values for the appropriate property list.
The return value is a file identifier for the newly-created file;
this file identifier should be closed by calling
H5Fclose when it is no longer needed.
Special case -- File creation in the case of an
already-open file:
If a file being created is already opened, by either a
previous H5Fopen or H5Fcreate call,
the HDF5 library may or may not detect that the open file and
the new file are the same physical file.
(See H5Fopen regarding
the limitations in detecting the re-opening of an already-open
file.)
If the library detects that the file is already opened,
H5Fcreate will return a failure, regardless
of the use of H5F_ACC_TRUNC.
If the library does not detect that the file is already opened
and H5F_ACC_TRUNC is not used,
H5Fcreate will return a failure because the file
already exists. Note that this is correct behavior.
But if the library does not detect that the file is already
opened and H5F_ACC_TRUNC is used,
H5Fcreate will truncate the existing file
and return a valid file identifier.
Such a truncation of a currently-opened file will almost
certainly result in errors.
While unlikely, the HDF5 library may not be able to detect,
and thus report, such errors.
Applications should avoid calling H5Fcreate
with an already opened file.
name
flags
H5F_ACC_TRUNC
H5F_ACC_EXCL
H5F_ACC_TRUNC and H5F_ACC_EXCL
are mutually exclusive; use exactly one.
H5F_ACC_DEBUG, prints
debug information. This flag is used only by HDF5 library
developers; it is neither tested nor supported
for use in applications.
create_id
H5P_DEFAULT for default file creation properties.
access_id
access_id.
Use H5P_DEFAULT for default file access properties.
SUBROUTINE h5fcreate_f(name, access_flags, file_id, hdferr, &
creation_prp, access_prp)
IMPLICIT NONE
CHARACTER(LEN=*), INTENT(IN) :: name ! Name of the file
INTEGER, INTENT(IN) :: access_flag ! File access flags
! Possible values are:
! H5F_ACC_RDWR_F
! H5F_ACC_RDONLY_F
! H5F_ACC_TRUNC_F
! H5F_ACC_EXCL_F
! H5F_ACC_DEBUG_F
INTEGER(HID_T), INTENT(OUT) :: file_id ! File identifier
INTEGER, INTENT(OUT) :: hdferr ! Error code
! 0 on success and -1 on failure
INTEGER(HID_T), OPTIONAL, INTENT(IN) :: creation_prp
! File creation propertly
! list identifier, if not
! specified its value is
! H5P_DEFAULT_F
INTEGER(HID_T), OPTIONAL, INTENT(IN) :: access_prp
! File access property list
! identifier, if not
! specified its value is
! H5P_DEFAULT_F
END SUBROUTINE h5fcreate_f
H5Fflush(hid_t object_id,
H5F_scope_t scope
)
H5Fflush causes all buffers associated with a
file to be immediately flushed to disk without removing the
data from the cache.
object_id can be any object associated with the file,
including the file itself, a dataset, a group, an attribute, or
a named data type.
scope specifies whether the scope of the flushing
action is global or local. Valid values are
H5F_SCOPE_GLOBAL |
Flushes the entire virtual file. | |
H5F_SCOPE_LOCAL |
Flushes only the specified file. |
H5Fflush flushes the internal HDF5 buffers then
asks the operating system (the OS) to flush the system buffers for the
open files. After that, the OS is responsible for ensuring that
the data is actually flushed to disk.
object_id
scope
SUBROUTINE h5fflush_f(obj_id, new_file_id, hdferr)
IMPLICIT NONE
INTEGER(HID_T), INTENT(IN) :: obj_id ! Object identifier
INTEGER, INTENT(IN) :: scope ! Flag with two possible values:
! H5F_SCOPE_GLOBAL_F
! H5F_SCOPE_LOCAL_F
INTEGER, INTENT(OUT) :: hdferr ! Error code
! 0 on success and -1 on failure
END SUBROUTINE h5fflush_f
H5Fget_access_plist(hid_t file_id)
H5Fget_access_plist returns the
file access property list identifier of the specified file.
See "File Access Properties" in H5P: Property List Interface in this reference manual and "File Access Property Lists" in Files in the HDF5 User's Guide for additional information and related functions.
file_id
SUBROUTINE h5fget_access_plist_f(file_id, fcpl_id, hdferr)
IMPLICIT NONE
INTEGER(HID_T), INTENT(IN) :: file_id ! File identifier
INTEGER(HID_T), INTENT(OUT) :: fapl_id ! File access property list identifier
INTEGER, INTENT(OUT) :: hdferr ! Error code
! 0 on success and -1 on failure
END SUBROUTINE h5fget_access_plist_f
H5Fget_create_plist(hid_t file_id
)
H5Fget_create_plist returns a file creation
property list identifier identifying the creation properties
used to create this file. This function is useful for
duplicating properties when creating another file.
See "File Creation Properties" in H5P: Property List Interface in this reference manual and "File Creation Properties" in Files in the HDF5 User's Guide for additional information and related functions.
file_id
SUBROUTINE h5fget_create_plist_f(file_id, fcpl_id, hdferr)
IMPLICIT NONE
INTEGER(HID_T), INTENT(IN) :: file_id ! File identifier
INTEGER(HID_T), INTENT(OUT) :: fcpl_id ! File creation property list
! identifier
INTEGER, INTENT(OUT) :: hdferr ! Error code
! 0 on success and -1 on failure
END SUBROUTINE h5fget_create_plist_f
H5Fget_freespace(hid_t file_id)
file_id,
H5Fget_freespace returns the amount of space that is
unused by any objects in the file.
Currently, the HDF5 library only tracks free space in a file from a file open or create until that file is closed, so this routine will only report the free space that has been created during that interval.
file_id
SUBROUTINE h5fget_freespace_f(file_id, free_space, hdferr)
IMPLICIT NONE
INTEGER(HID_T), INTENT(IN) :: file_id ! File identifier
INTEGER(HSSIZE_T), INTENT(OUT) :: free_space ! Amount of free space in file
INTEGER, INTENT(OUT) :: hdferr ! Error code
! 0 on success and -1 on failure
END SUBROUTINE h5fget_freespace_f
H5Fget_obj_count(hid_t file_id,
unsigned int types
)
file_id,
and the desired object types, types,
H5Fget_obj_count returns the number of
open object identifiers for the file.
To retrieve a count of open identifiers for open objects in
all HDF5 application files that are currently open,
pass the value H5F_OBJ_ALL in file_id.
The types of objects to be counted are specified
in types as follows:
H5F_OBJ_FILE
| Files only |
H5F_OBJ_DATASET
| Datasets only |
H5F_OBJ_GROUP
| Groups only |
H5F_OBJ_DATATYPE
| Named datatypes only |
H5F_OBJ_ATTR
| Attributes only |
H5F_OBJ_ALL
|
All of the above
(I.e., H5F_OBJ_FILE | H5F_OBJ_DATASET |
H5F_OBJ_GROUP | H5F_OBJ_DATATYPE
| H5F_OBJ_ATTR )
|
OR operator (|).
For example, the expression (H5F_OBJ_DATASET|H5F_OBJ_GROUP) would call for
datasets and groups.
file_id
H5F_OBJ_ALL for all currently-open HDF5 files.
types
SUBROUTINE h5fget_obj_count_f(file_id, obj_type, obj_count, hdferr)
IMPLICIT NONE
INTEGER(HID_T), INTENT(IN) :: file_id ! File identifier
INTEGER, INTENT(IN) :: obj_type ! Object types, possible values are:
! H5F_OBJ_FILE_F
! H5F_OBJ_GROUP_F
! H5F_OBJ_DATASET_F
! H5F_OBJ_DATATYPE_F
! H5F_OBJ_ALL_F
INTEGER, INTENT(OUT) :: obj_count ! Number of opened objects
INTEGER, INTENT(OUT) :: hdferr ! Error code
! 0 on success and -1 on failure
END SUBROUTINE h5fget_obj_count_f
H5Fget_obj_ids(hid_t file_id,
unsigned int types,
int max_objs,
hid_t *obj_id_list
)
file_id and
the type of objects to be identified, types,
H5Fget_obj_ids returns the list of identifiers
for all open HDF5 objects fitting the specified criteria.
To retrieve identifiers for open objects in all HDF5 application
files that are currently open, pass the value
H5F_OBJ_ALL in file_id.
The types of object identifiers to be retrieved are specified
in types using the codes listed for the same
parameter in H5Fget_obj_count
To retrieve identifiers for all open objects, pass a negative value
for the max_objs.
file_id
H5F_OBJ_ALL for all currently-open HDF5 files.
types
max_objs
obj_id_list.
obj_id_list
obj_id_list if successful;
otherwise returns a negative value.
SUBROUTINE h5fget_obj_ids_f(file_id, obj_type, max_objs, obj_ids, hdferr)
IMPLICIT NONE
INTEGER(HID_T), INTENT(IN) :: file_id ! File identifier
INTEGER, INTENT(IN) :: obj_type ! Object types, possible values are:
! H5F_OBJ_FILE_F
! H5F_OBJ_GROUP_F
! H5F_OBJ_DATASET_F
! H5F_OBJ_DATATYPE_F
! H5F_OBJ_ALL_F
INTEGER, INTENT(IN) :: max_objs ! Maximum number of object
! identifiers to retrieve
INTEGER(HID_T), DIMENSION(*), INTENT(OUT) :: obj_ids
! Array of requested object
! identifiers
INTEGER, INTENT(OUT) :: hdferr ! Error code
! 0 on success and -1 on failure
END SUBROUTINE h5fget_obj_ids_f
H5Fget_vfd_handle(hid_t file_id,
hid_t fapl_id,
void *file_handle
)
file_id and
the file access property list fapl_id,
H5Fget_vfd_handle returns a pointer to the file handle
from the low-level file driver currently being used by the
HDF5 library for file I/O.
This file handle is dynamic and is valid only while the file remains open; it will be invalid if the file is closed and reopened or opened during a subsequent session.
file_id
fapl_id
H5P_DEFAULT.
For the FAMILY or MULTI drivers,
this value should be defined through the property list
functions:
H5Pset_family_offset for the FAMILY
driver and H5Pset_multi_type for the
MULTI driver.
file_handle
H5Fis_hdf5(const char *name
)
H5Fis_hdf5 determines whether a file is in
the HDF5 format.
name
TRUE,
or 0 (zero), for FALSE.
Otherwise returns a negative value.
SUBROUTINE h5fis_hdf5_f(name, status, hdferr)
IMPLICIT NONE
CHARACTER(LEN=*), INTENT(IN) :: name ! Name of the file
LOGICAL, INTENT(OUT) :: status ! This parameter indicates
! whether file is an HDF5 file
! ( TRUE or FALSE )
INTEGER, INTENT(OUT) :: hdferr ! Error code
! 0 on success and -1 on failure
END SUBROUTINE h5fis_hdf5_f
H5Fmount(hid_t loc_id,
const char *name,
hid_t child_id,
hid_t plist_id
)
H5Fmount mounts the file specified by
child_id onto the group specified by
loc_id and name using
the mount properties plist_id.
Note that loc_id is either a file or group identifier
and name is relative to loc_id.
loc_id
name is defined.
name
child_id
is to be mounted.
child_id
plist_id
SUBROUTINE h5fmount_f(loc_id, name, child_id, hdferr)
IMPLICIT NONE
INTEGER(HID_T), INTENT(IN) :: loc_id ! File or group identifier
CHARACTER(LEN=*), INTENT(IN):: name ! Group name at locationloc_id
INTEGER(HID_T), INTENT(IN) :: child_id ! File(to be mounted) identifier
INTEGER, INTENT(OUT) :: hdferr ! Error code
! 0 on success and -1 on failure
END SUBROUTINE h5fmount_f
H5Fopen(const char *name,
unsigned flags,
hid_t access_id
)
H5Fopen opens an existing file and is the primary
function for accessing existing HDF5 files.
The parameter access_id is a file access property
list identifier or H5P_DEFAULT if the
default I/O access parameters are to be used
The flags argument determines whether writing
to an existing file will be allowed.
The file is opened with read and write permission if
flags is set to H5F_ACC_RDWR.
All flags may be combined with the bit-wise OR operator (`|')
to change the behavior of the file open call.
More complex behaviors of file access are controlled
through the file-access property list.
The return value is a file identifier for the open file;
this file identifier should be closed by calling
H5Fclose when it is no longer needed.
Special case -- Multiple opens:
A file can often be opened with a new H5Fopen
call without closing an already-open identifier established
in a previous H5Fopen or H5Fcreate
call. Each such H5Fopen call will return a
unique identifier and the file can be accessed through any
of these identifiers as long as the identifier remains valid.
In such multiply-opened cases, all the open calls should
use the same flags argument.
In some cases, such as files on a local Unix file system, the HDF5 library can detect that a file is multiply opened and will maintain coherent access among the file identifiers.
But in many other cases, such as parallel file systems or networked file systems, it is not always possible to detect multiple opens of the same physical file. In such cases, HDF5 will treat the file identifiers as though they are accessing different files and will be unable to maintain coherent access. Errors are likely to result in these cases. While unlikely, the HDF5 library may not be able to detect, and thus report, such errors.
It is generally recommended that applications avoid multiple opens of the same file.
name
flags
H5F_ACC_RDWR
H5F_ACC_RDONLY
H5F_ACC_RDWR and H5F_ACC_RDONLY
are mutually exclusive; use exactly one.
H5F_ACC_DEBUG, prints
debug information. This flag is used only by HDF5 library
developers; it is neither tested nor supported
for use in applications.
access_id
access_id.
Use H5P_DEFAULT for default file access properties.
SUBROUTINE h5fopen_f(name, access_flags, file_id, hdferr, &
access_prp)
IMPLICIT NONE
CHARACTER(LEN=*), INTENT(IN) :: name ! Name of the file
INTEGER, INTENT(IN) :: access_flag ! File access flags
! Possible values are:
! H5F_ACC_RDWR_F
! H5F_ACC_RDONLY_F
INTEGER(HID_T), INTENT(OUT) :: file_id ! File identifier
INTEGER, INTENT(OUT) :: hdferr ! Error code
! 0 on success and -1 on failure
INTEGER(HID_T), OPTIONAL, INTENT(IN) :: access_prp
! File access property list
! identifier
END SUBROUTINE h5fopen_f
H5Freopen(hid_t file_id
)
H5Freopen returns a new file identifier for an
already-open HDF5 file, as specified by file_id.
Both identifiers share caches and other information.
The only difference between the identifiers is that the
new identifier is not mounted anywhere and no files are
mounted on it.
Note that there is no circumstance under which
H5Freopen can actually open a closed file;
the file must already be open and have an active
file_id. E.g., one cannot close a file with
H5Fclose (file_id) then use
H5Freopen (file_id) to reopen it.
The new file identifier should be closed by calling
H5Fclose when it is no longer needed.
file_id
SUBROUTINE h5freopen_f(file_id, new_file_id, hdferr)
IMPLICIT NONE
INTEGER(HID_T), INTENT(IN) :: file_id ! File identifier
INTEGER(HID_T), INTENT(OUT) :: new_file_id ! New file identifier
INTEGER, INTENT(OUT) :: hdferr ! Error code
! 0 on success and -1 on failure
END SUBROUTINE h5freopen_f
H5Funmount(hid_t loc_id,
const char *name
)
H5Funmount
dissassociates the mount point's file
from the file mounted there. This function
does not close either file.
The mount point can be either the group in the parent or the root group of the mounted file (both groups have the same name). If the mount point was opened before the mount then it is the group in the parent; if it was opened after the mount then it is the root group of the child.
Note that loc_id is either a file or group identifier
and name is relative to loc_id.
loc_id
name
SUBROUTINE h5funmount_f(loc_id, name, child_id, hdferr)
IMPLICIT NONE
INTEGER(HID_T), INTENT(IN) :: loc_id ! File or group identifier
CHARACTER(LEN=*), INTENT(IN):: name ! Group name at location loc_id
INTEGER, INTENT(OUT) :: hdferr ! Error code
! 0 on success and -1 on failure
END SUBROUTINE h5funmount_f
|
HDF5 documents and links Introduction to HDF5 HDF5 User Guide |
And in this document, the
HDF5 Reference Manual
H5 H5A H5D H5E H5F H5G H5I H5P H5R H5S H5T H5Z Tools Datatypes |