mhdf_public.h File Reference

#include <H5Tpublic.h>

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Classes
struct	struct_mhdf_Status
	Struct used to return error status. More...
struct	mhdf_EntDesc
struct	mhdf_TagDesc
struct	mhdf_ElemDesc
struct	mhdf_FileDesc

Macros
#define	MHDF_MESSAGE_BUFFER_LEN   160
#define	mhdf_EDGE_TYPE_NAME   "Edge"
	Name to use for edge element. More...
#define	mhdf_TRI_TYPE_NAME   "Tri"
	Name to use for triangle element. More...
#define	mhdf_QUAD_TYPE_NAME   "Quad"
	Name to use for quadrilateral element. More...
#define	mhdf_POLYGON_TYPE_NAME   "Polygon"
	Name to use for general polygon element. More...
#define	mhdf_TET_TYPE_NAME   "Tet"
	Name to use for tetrahedral element. More...
#define	mhdf_PYRAMID_TYPE_NAME   "Pyramid"
	Name to use for quad-based pyramid element. More...
#define	mhdf_PRISM_TYPE_NAME   "Prism"
	Name to use for triangular prism element. More...
#define	mdhf_KNIFE_TYPE_NAME   "Knife"
	Name to use for knife element. More...
#define	mdhf_HEX_TYPE_NAME   "Hex"
	Name to use for quad-sided hexahedral element. More...
#define	mhdf_POLYHEDRON_TYPE_NAME   "Polyhedron"
	Name to use for general polyhedron specified as a arbitrary-length list of faces. More...
#define	mhdf_SEPTAHEDRON_TYPE_NAME   "Septahedron"
	Name to use for hexagonal-based pyramid. More...

Typedefs
typedef struct struct_mhdf_Status	mhdf_Status
	Struct used to return error status. More...
typedef mhdf_Status	MHDF_Status
typedef enum mhdf_TagDataType	MHDF_TagDataType
	Enum for tag data type class. More...
typedef long	mhdf_index_t
	Type used when creating index tables. More...
typedef void *	mhdf_FileHandle
	Opaque handle to an open file. More...
typedef mhdf_FileHandle	MHDF_FileHandle
typedef struct mhdf_EntDesc	MHDF_EntDesc
typedef struct mhdf_TagDesc	MHDF_TagDesc
typedef struct mhdf_ElemDesc	MHDF_ElemDesc
typedef struct mhdf_FileDesc	MHDF_FileDesc

Enumerations
enum	mhdf_TagDataType {   mhdf_OPAQUE = 0 , mhdf_INTEGER , mhdf_FLOAT , mhdf_BITFIELD ,   mhdf_BOOLEAN , mhdf_ENTITY_ID }
	Enum for tag data type class. More...

Functions
int	mhdf_isError (mhdf_Status const *)
	Return 1 if passed status object indicates an error. Zero otherwise. More...
const char *	mhdf_message (mhdf_Status const *)
	Get the error message given a status object. More...
mhdf_FileHandle	mhdf_createFile (const char *filename, int overwrite, const char **elem_type_list, size_t elem_type_list_len, hid_t id_type, mhdf_Status *status)
	Create a new file. More...
mhdf_FileHandle	mhdf_openFile (const char *filename, int writable, unsigned long *max_id, hid_t id_type, mhdf_Status *status)
	Open an existing file. More...
mhdf_FileHandle	mhdf_openFileWithOpt (const char *filename, int writable, unsigned long *max_id, hid_t id_type, hid_t options, mhdf_Status *status)
	Open an existing file with options. More...
int	mhdf_countOpenHandles (mhdf_FileHandle h)
	Get number of open HDF5 objects from file. More...
MHDF_FileDesc *	mhdf_getFileSummary (mhdf_FileHandle file_handle, hid_t file_id_type, mhdf_Status *status, int extraSetInfo)
	Get summary of data tables contained within file. More...
void	mhdf_fixFileDesc (struct mhdf_FileDesc *copy_ptr, const struct mhdf_FileDesc *orig_addr)
	Fix nested pointers for copied/moved FileDesc struct. More...
void	mhdf_closeFile (mhdf_FileHandle handle, mhdf_Status *status)
	Close the file. More...

Macro Definition Documentation

mdhf_HEX_TYPE_NAME

#define mdhf_HEX_TYPE_NAME   "Hex"

Name to use for quad-sided hexahedral element.

Definition at line 44 of file mhdf_public.h.

mdhf_KNIFE_TYPE_NAME

#define mdhf_KNIFE_TYPE_NAME   "Knife"

Name to use for knife element.

Definition at line 42 of file mhdf_public.h.

mhdf_EDGE_TYPE_NAME

#define mhdf_EDGE_TYPE_NAME   "Edge"

Name to use for edge element.

Definition at line 28 of file mhdf_public.h.

MHDF_MESSAGE_BUFFER_LEN

#define MHDF_MESSAGE_BUFFER_LEN   160

Definition at line 10 of file mhdf_public.h.

mhdf_POLYGON_TYPE_NAME

#define mhdf_POLYGON_TYPE_NAME   "Polygon"

Name to use for general polygon element.

Definition at line 34 of file mhdf_public.h.

mhdf_POLYHEDRON_TYPE_NAME

#define mhdf_POLYHEDRON_TYPE_NAME   "Polyhedron"

Name to use for general polyhedron specified as a arbitrary-length list of faces.

Definition at line 46 of file mhdf_public.h.

mhdf_PRISM_TYPE_NAME

#define mhdf_PRISM_TYPE_NAME   "Prism"

Name to use for triangular prism element.

Definition at line 40 of file mhdf_public.h.

mhdf_PYRAMID_TYPE_NAME

#define mhdf_PYRAMID_TYPE_NAME   "Pyramid"

Name to use for quad-based pyramid element.

Definition at line 38 of file mhdf_public.h.

mhdf_QUAD_TYPE_NAME

#define mhdf_QUAD_TYPE_NAME   "Quad"

Name to use for quadrilateral element.

Definition at line 32 of file mhdf_public.h.

mhdf_SEPTAHEDRON_TYPE_NAME

#define mhdf_SEPTAHEDRON_TYPE_NAME   "Septahedron"

Name to use for hexagonal-based pyramid.

Definition at line 48 of file mhdf_public.h.

mhdf_TET_TYPE_NAME

#define mhdf_TET_TYPE_NAME   "Tet"

Name to use for tetrahedral element.

Definition at line 36 of file mhdf_public.h.

mhdf_TRI_TYPE_NAME

#define mhdf_TRI_TYPE_NAME   "Tri"

Name to use for triangle element.

Definition at line 30 of file mhdf_public.h.

Typedef Documentation

MHDF_ElemDesc

typedef struct mhdf_ElemDesc MHDF_ElemDesc

MHDF_EntDesc

typedef struct mhdf_EntDesc MHDF_EntDesc

Data common to sets, nodes, and each element type

MHDF_FileDesc

typedef struct mhdf_FileDesc MHDF_FileDesc

mhdf_FileHandle

typedef void* mhdf_FileHandle

Opaque handle to an open file.

Definition at line 73 of file mhdf_public.h.

MHDF_FileHandle

typedef mhdf_FileHandle MHDF_FileHandle

Definition at line 75 of file mhdf_public.h.

mhdf_index_t

typedef long mhdf_index_t

Type used when creating index tables.

The data type used by mhdf_create* functions that create tables if indices (e.g. mhdf_createSetMeta, mhdf_createVarLenTag, etc.).

Definition at line 70 of file mhdf_public.h.

mhdf_Status

typedef struct struct_mhdf_Status mhdf_Status

Struct used to return error status.

MHDF_Status

typedef mhdf_Status MHDF_Status

Definition at line 18 of file mhdf_public.h.

MHDF_TagDataType

typedef enum mhdf_TagDataType MHDF_TagDataType

Enum for tag data type class.

Enumerates known types for tag data

MHDF_TagDesc

typedef struct mhdf_TagDesc MHDF_TagDesc

Struct describing a tag

Enumeration Type Documentation

mhdf_TagDataType

enum mhdf_TagDataType

Enum for tag data type class.

Enumerates known types for tag data

Enumerator
mhdf_OPAQUE	Opaque/unknown type
mhdf_INTEGER	Integer type
mhdf_FLOAT	Floating point value
mhdf_BITFIELD	Bit field
mhdf_BOOLEAN	Boolean values stored as one byte each
mhdf_ENTITY_ID	Global ID referencing another entity in file

Definition at line 55 of file mhdf_public.h.

{
 mhdf_OPAQUE = 0, /**< Opaque/unknown type */
 mhdf_INTEGER, /**< Integer type */
 mhdf_FLOAT, /**< Floating point value */
 mhdf_BITFIELD, /**< Bit field */
 mhdf_BOOLEAN, /**< Boolean values stored as one byte each */
 mhdf_ENTITY_ID /**< Global ID referencing another entity in file */
} MHDF_TagDataType;

Function Documentation

mhdf_closeFile()

void mhdf_closeFile	(	mhdf_FileHandle	handle,
		mhdf_Status *	status
	)

Close the file.

Parameters

handle	The file to close.
status	Passed back status of API call.

Definition at line 438 of file file.c.

{
 FileHandle* file_ptr;
 API_BEGIN;
 
 file_ptr = (FileHandle*)( handle );
 if( !mhdf_check_valid_file( file_ptr, status ) ) return;
 /*
 if (file_ptr->open_handle_count)
 {
 mhdf_setError( status, "Cannot close file with %d open data handles.",
 file_ptr->open_handle_count );
 return;
 }
 */
 
 /* Check for open handles. HDF5 will not actually close the
 file until all handles are closed. */
 if( mhdf_checkOpenHandles( handle, status ) ) return;
 
 if( 0 > H5Fclose( file_ptr->hdf_handle ) )
 {
 mhdf_setFail( status, "H5FClose failed. Invalid handle?" );
 return;
 }
 
 memset( file_ptr, 0, sizeof( FileHandle ) );
 free( file_ptr );
 mhdf_setOkay( status );
 API_END_H( -1 );
}

References API_BEGIN, API_END_H, struct_FileHandle::hdf_handle, mhdf_check_valid_file(), mhdf_checkOpenHandles(), mhdf_setFail(), and mhdf_setOkay().

Referenced by moab::ReadHDF5::clean_up_read(), iMOAB_ReadHeaderInfo(), main(), moab::WriteHDF5Parallel::parallel_create_file(), moab::ReadHDF5::set_up_read(), and moab::WriteHDF5::write_file().

mhdf_countOpenHandles()

int mhdf_countOpenHandles

(

mhdf_FileHandle

h

)

Get number of open HDF5 objects from file.

Definition at line 150 of file file.c.

{
 return H5Fget_obj_count( ( (FileHandle*)file_handle )->hdf_handle, H5F_OBJ_ALL );
}

Referenced by moab::CheckOpenReadHDF5Handles::~CheckOpenReadHDF5Handles(), and moab::CheckOpenWriteHDF5Handles::~CheckOpenWriteHDF5Handles().

mhdf_createFile()

mhdf_FileHandle mhdf_createFile	(	const char *	filename,
		int	overwrite,
		const char **	elem_type_list,
		size_t	elem_type_list_len,
		hid_t	id_type,
		mhdf_Status *	status
	)

Create a new file.

Create a new HDF mesh file. This handle must be closed with mhdf_closeFile to avoid resource loss.

Parameters

filename	The path and name of the file to create
overwrite	If zero, will fail if the specified file already exists. If non-zero, will overwrite an existing file.
elem_type_list	The list of element types that will be stored in the file. If the element name exits as a pre- defined constant (mhdf_type), that constant should be used. If a constant does not exist for the type, a similar naming pattern should be used (accepted name for type, first character uppercase, subsequent characters lowercase.) The element type index passed to mhdf_addElement is then an index into this list. The array may contain null entries to allow the caller some control over the assigned indices without creating dummy types which may confuse readers.
elem_type_list_len	The length of elem_type_list.
id_type	Type to use when creating datasets containing file IDs
status	Passed back status of API call.

Returns

An opaque handle to the file.

Definition at line 37 of file file.c.

{
 FileHandle* file_ptr;
 unsigned int flags;
 unsigned char idx;
 size_t i;
 hid_t enum_id, group_id;
 int rval;
 API_BEGIN;
 
 if( elem_list_len > 255 )
 {
 mhdf_setFail( status, "Element type list too long." );
 return NULL;
 }
 mhdf_setOkay( status );
 
 /* Create struct to hold working data */
 file_ptr = mhdf_alloc_FileHandle( 0, id_type, status );
 if( !file_ptr ) return NULL;
 
 /* Create the file */
 flags = overwrite ? H5F_ACC_TRUNC : H5F_ACC_EXCL;
 file_ptr->hdf_handle = H5Fcreate( filename, flags, H5P_DEFAULT, H5P_DEFAULT );
 if( file_ptr->hdf_handle < 0 )
 {
 mhdf_setFail( status, "Failed to create file \"%s\"", filename );
 free( file_ptr );
 return NULL;
 }
 
 /* Create file structure */
 if( !make_hdf_group( ROOT_GROUP, file_ptr->hdf_handle, 6, status ) ||
 !make_hdf_group( TAG_GROUP, file_ptr->hdf_handle, 0, status ) ||
 !make_hdf_group( ELEMENT_GROUP, file_ptr->hdf_handle, 8, status ) ||
 !make_hdf_group( NODE_GROUP, file_ptr->hdf_handle, 3, status ) ||
 !make_hdf_group( SET_GROUP, file_ptr->hdf_handle, 5, status ) ||
 !make_hdf_group( NODE_TAG_GROUP, file_ptr->hdf_handle, 0, status ) ||
 !make_hdf_group( SET_TAG_GROUP, file_ptr->hdf_handle, 0, status ) )
 {
 H5Fclose( file_ptr->hdf_handle );
 free( file_ptr );
 return NULL;
 }
 
 /* Store the max ID as an attribite on the /tstt/ group */
#if defined( H5Gopen_vers ) && H5Gopen_vers > 1
 group_id = H5Gopen2( file_ptr->hdf_handle, ROOT_GROUP, H5P_DEFAULT );
#else
 group_id = H5Gopen( file_ptr->hdf_handle, ROOT_GROUP );
#endif
 rval = mhdf_create_scalar_attrib( group_id, MAX_ID_ATTRIB, H5T_NATIVE_ULONG, &file_ptr->max_id, status );
 H5Gclose( group_id );
 if( !rval )
 {
 H5Fclose( file_ptr->hdf_handle );
 free( file_ptr );
 return NULL;
 }
 
 /* Create the type name list in file */
 enum_id = H5Tenum_create( H5T_NATIVE_UCHAR );
 if( enum_id < 0 )
 {
 mhdf_setFail( status, "Failed to store elem type list." );
 H5Fclose( file_ptr->hdf_handle );
 free( file_ptr );
 return NULL;
 }
 for( i = 0; i < elem_list_len; ++i )
 {
 if( !elem_type_list[i] || !*elem_type_list[i] ) continue;
 
 idx = (unsigned char)i;
 if( H5Tenum_insert( enum_id, elem_type_list[i], &idx ) < 0 )
 {
 mhdf_setFail( status, "Failed to store elem type list." );
 H5Fclose( file_ptr->hdf_handle );
 free( file_ptr );
 return NULL;
 }
 }
#if defined( H5Tcommit_vers ) && H5Tcommit_vers > 1
 if( H5Tcommit2( file_ptr->hdf_handle, TYPE_ENUM_PATH, enum_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT ) < 0 )
#else
 if( H5Tcommit( file_ptr->hdf_handle, TYPE_ENUM_PATH, enum_id ) < 0 )
#endif
 {
 mhdf_setFail( status, "Failed to store elem type list." );
 H5Fclose( file_ptr->hdf_handle );
 free( file_ptr );
 return NULL;
 }
 H5Tclose( enum_id );
 
 API_END_H( 1 );
 return file_ptr;
}

References API_BEGIN, API_END_H, ELEMENT_GROUP, struct_FileHandle::hdf_handle, make_hdf_group(), struct_FileHandle::max_id, MAX_ID_ATTRIB, mhdf_alloc_FileHandle(), mhdf_create_scalar_attrib(), mhdf_setFail(), mhdf_setOkay(), NODE_GROUP, NODE_TAG_GROUP, ROOT_GROUP, SET_GROUP, SET_TAG_GROUP, TAG_GROUP, and TYPE_ENUM_PATH.

Referenced by moab::WriteHDF5Parallel::parallel_create_file(), and moab::WriteHDF5::serial_create_file().

mhdf_fixFileDesc()

void mhdf_fixFileDesc	(	struct mhdf_FileDesc *	copy_ptr,
		const struct mhdf_FileDesc *	orig_addr
	)

Fix nested pointers for copied/moved FileDesc struct.

This is a utility method to facility copying/moving/communicating struct FileDesc instances. The structure and all data it references are allocated in a single contiguous block of memory of size FileDesc::total_size. As such, the struct can be copied with a single memcpy, packed into a single network packet, communicated with a single MPI call, etc. However, the pointers contained within the struct will not be valid in the copied instance (they will still point into the original instance.) Given a pointer to the copied struct and the address of the original struct, this function will updated all contained pointers.

Definition at line 77 of file file-desc.c.

{
 int i;
 
 API_BEGIN;
 FIX_OFFSET( int*, nodes.dense_tag_indices );
 FIX_OFFSET( int*, sets.dense_tag_indices );
 FIX_OFFSET( struct mhdf_ElemDesc*, elems );
 FIX_OFFSET( struct mhdf_TagDesc*, tags );
 
 FIX_OFFSET( int*, numEntSets );
 FIX_OFFSET( int**, defTagsEntSets );
 FIX_OFFSET( int**, defTagsVals );
 
 for( i = 0; i < 5; i++ )
 {
 if( copy_ptr->defTagsEntSets ) FIX_OFFSET( int*, defTagsEntSets[i] );
 if( copy_ptr->defTagsVals ) FIX_OFFSET( int*, defTagsVals[i] );
 }
 
 if( copy_ptr->elems != NULL )
 {
 for( i = 0; i < copy_ptr->num_elem_desc; ++i )
 {
 FIX_OFFSET( const char*, elems[i].handle );
 FIX_OFFSET( const char*, elems[i].type );
 FIX_OFFSET( int*, elems[i].desc.dense_tag_indices );
 }
 }
 
 if( copy_ptr->tags != NULL )
 {
 for( i = 0; i < copy_ptr->num_tag_desc; ++i )
 {
 FIX_OFFSET( const char*, tags[i].name );
 FIX_OFFSET( void*, tags[i].default_value );
 FIX_OFFSET( void*, tags[i].global_value );
 FIX_OFFSET( int*, tags[i].dense_elem_indices );
 }
 }
 API_END;
}

References API_BEGIN, API_END, mhdf_FileDesc::defTagsEntSets, mhdf_FileDesc::defTagsVals, mhdf_EntDesc::dense_tag_indices, mhdf_FileDesc::elems, FIX_OFFSET, mhdf_FileDesc::nodes, mhdf_FileDesc::num_elem_desc, mhdf_FileDesc::num_tag_desc, mhdf_FileDesc::numEntSets, mhdf_FileDesc::sets, and mhdf_FileDesc::tags.

Referenced by realloc_data(), and moab::ReadHDF5::set_up_read().

mhdf_getFileSummary()

MHDF_FileDesc* mhdf_getFileSummary	(	mhdf_FileHandle	file_handle,
		hid_t	file_id_type,
		mhdf_Status *	status,
		int	extraSetInfo
	)

Get summary of data tables contained within file.

Returned struct, including all pointed-to data, is allocated in a single contiguous block of memory with a size equal to 'total_size'. Caller is responsible for freeing the returned struct FileDesc pointer (and only that pointer, not pointers nexted within the struct!). Caller may copy (e.g. MPI_BCast) entire struct as one contiguous block, assuming all nested pointers in the copy are updated to the correct relative offset from the beginning of the struct.

Definition at line 385 of file file-desc.c.

{
 struct mhdf_FileDesc* result;
 hid_t table_id;
 int i, i1, numtags, j, k, size, *indices, have, num_tag_names = 0;
 unsigned int ui;
 void* ptr;
 char **elem_handles = 0, **tag_names = 0;
 unsigned char *array, *matrix;
 const char* pname[5] = { "PARALLEL_PARTITION", "MATERIAL_SET", "NEUMANN_SET", "DIRICHLET_SET", "GEOM_DIMENSION" };
 
 long* id_list;
 struct mhdf_TagDesc* tag_desc;
 long int nval, junk;
 hid_t table[3];
 hid_t data_type;
 
 API_BEGIN;
 
 mhdf_setOkay( status );
 result = alloc_file_desc( status );
 if( NULL == result ) return NULL;
 
 /* get node info */
 have = mhdf_haveNodes( file_handle, status );
 if( mhdf_isError( status ) )
 {
 free( result );
 return NULL;
 }
 if( have )
 {
 table_id = mhdf_openNodeCoords( file_handle, &result->nodes.count, &result->nodes.vals_per_ent,
 &result->nodes.start_id, status );
 if( table_id < 0 )
 {
 free( result );
 return NULL;
 }
 mhdf_closeData( file_handle, table_id, status );
 }
 else
 {
 result->nodes.count = 0;
 result->nodes.vals_per_ent = 0;
 result->nodes.start_id = 0;
 }
 
 /* get set info */
 result->sets.vals_per_ent = -1;
 have = mhdf_haveSets( file_handle, &result->have_set_contents, &result->have_set_children,
 &result->have_set_parents, status );
 if( mhdf_isError( status ) )
 {
 free( result );
 return NULL;
 }
 if( have )
 {
 table_id = mhdf_openSetMeta( file_handle, &result->sets.count, &result->sets.start_id, status );
 if( table_id < 0 )
 {
 free( result );
 return NULL;
 }
 mhdf_closeData( file_handle, table_id, status );
 }
 else
 {
 result->sets.count = 0;
 result->sets.start_id = 0;
 }
 
 /* get element list */
 elem_handles = mhdf_getElemHandles( file_handle, &ui, status );
 if( elem_handles == NULL )
 {
 free( result );
 return NULL;
 }
 result->num_elem_desc = ui;
 
 /* allocate array of element descriptors */
 size = result->num_elem_desc * sizeof( struct mhdf_ElemDesc );
 ptr = realloc_data( &result, size, status, sizeof( char* ) );
 if( NULL == ptr )
 {
 free( elem_handles );
 return NULL;
 }
 memset( ptr, 0, size );
 result->elems = ptr;
 
 /* Initialize each element descriptor */
 for( i = 0; i < result->num_elem_desc; ++i )
 {
 result = get_elem_desc( file_handle, result, elem_handles[i], i, status );
 if( NULL == result )
 {
 free( elem_handles );
 return NULL;
 }
 }
 
 /* get tag list */
 tag_names = mhdf_getTagNames( file_handle, &num_tag_names, status );
 if( mhdf_isError( status ) )
 {
 free( elem_handles );
 free( result );
 return NULL;
 }
 
 /* allocate array of tag descriptors */
 size = num_tag_names * sizeof( struct mhdf_TagDesc );
 ptr = realloc_data( &result, size, status, sizeof( char* ) );
 if( NULL == ptr )
 {
 free( elem_handles );
 free_string_list( tag_names, result->num_tag_desc );
 return NULL;
 }
 memset( ptr, 0, size );
 result->tags = ptr;
 result->num_tag_desc = num_tag_names;
 memset( result->tags, 0, size );
 
 /* Initialize each tag descriptor */
 for( i = 0; i < result->num_tag_desc; ++i )
 {
 result = get_tag_desc( file_handle, result, tag_names[i], i, file_id_type, status );
 if( NULL == result )
 {
 free( elem_handles );
 free_string_list( tag_names, num_tag_names );
 return NULL;
 }
 }
 
 /* Determine which dense tags are present */
 
 size = ( 2 + result->num_elem_desc ) * result->num_tag_desc;
 array = mhdf_malloc( size, status );
 if( NULL == array )
 {
 free( elem_handles );
 free_string_list( tag_names, num_tag_names );
 free( result );
 return NULL;
 }
 memset( array, 0, size );
 matrix = array + ( 2 * result->num_tag_desc );
 
 for( j = 0; j < result->num_tag_desc; ++j )
 {
 if( mhdf_haveDenseTag( file_handle, tag_names[j], mhdf_node_type_handle(), status ) )
 matrix[-1 * result->num_tag_desc + j] = 1;
 if( mhdf_haveDenseTag( file_handle, tag_names[j], mhdf_set_type_handle(), status ) )
 matrix[-2 * result->num_tag_desc + j] = 1;
 for( i = 0; i < result->num_elem_desc; ++i )
 if( mhdf_haveDenseTag( file_handle, tag_names[j], elem_handles[i], status ) )
 matrix[i * result->num_tag_desc + j] = 1;
 }
 free( elem_handles );
 free_string_list( tag_names, result->num_tag_desc );
 
 /* Populate dense tag lists for element types */
 for( i = -2; i < result->num_elem_desc; ++i )
 {
 size = 0;
 for( j = 0; j < result->num_tag_desc; ++j )
 size += matrix[i * result->num_tag_desc + j];
 if( !size )
 {
 indices = NULL;
 }
 else
 {
 indices = realloc_data( &result, size * sizeof( int ), status, sizeof( int ) );
 if( NULL == indices )
 {
 free( array );
 return NULL;
 }
 
 k = 0;
 for( j = 0; j < result->num_tag_desc; ++j )
 if( matrix[i * result->num_tag_desc + j] ) indices[k++] = j;
 assert( k == size );
 }
 
 if( i == -2 )
 {
 result->sets.dense_tag_indices = indices;
 result->sets.num_dense_tags = size;
 }
 else if( i == -1 )
 {
 result->nodes.dense_tag_indices = indices;
 result->nodes.num_dense_tags = size;
 }
 else
 {
 result->elems[i].desc.dense_tag_indices = indices;
 result->elems[i].desc.num_dense_tags = size;
 }
 }
 
 /* Populate dense tag lists for each tag */
 for( j = 0; j < result->num_tag_desc; ++j )
 {
 size = 0;
 for( i = -2; i < result->num_elem_desc; ++i )
 size += matrix[i * result->num_tag_desc + j];
 if( !size )
 {
 indices = 0;
 }
 else
 {
 indices = realloc_data( &result, size * sizeof( int ), status, sizeof( int ) );
 if( NULL == ptr )
 {
 free( array );
 return NULL;
 }
 
 k = 0;
 for( i = -2; i < result->num_elem_desc; ++i )
 if( matrix[i * result->num_tag_desc + j] ) indices[k++] = i;
 assert( k == size );
 }
 
 result->tags[j].num_dense_indices = size;
 result->tags[j].dense_elem_indices = indices;
 }
 
 if( extraSetInfo )
 {
 /* open the table for parallel partitions, material sets, neumann sets,
 * dirichlet sets
 * to determine number of parts, etc
 * this is needed for iMOAB and VisIt plugin */
 const int NPRIMARY_SETS = 5;
 ptr = realloc_data( &result, NPRIMARY_SETS * sizeof( int ), status, sizeof( int ) );
 if( NULL == ptr || mhdf_isError( status ) )
 {
 free( array );
 return NULL;
 }
 result->numEntSets = ptr;
 for( i = 0; i < NPRIMARY_SETS; ++i )
 result->numEntSets[i] = 0;
 
 ptr = realloc_data( &result, NPRIMARY_SETS * sizeof( int* ), status, sizeof( int* ) );
 if( NULL == ptr || mhdf_isError( status ) )
 {
 free( array );
 return NULL;
 }
 result->defTagsEntSets = ptr;
 
 ptr = realloc_data( &result, NPRIMARY_SETS * sizeof( int* ), status, sizeof( int* ) );
 if( NULL == ptr || mhdf_isError( status ) )
 {
 free( array );
 return NULL;
 }
 result->defTagsVals = ptr;
 numtags = result->num_tag_desc;
 
 for( i = 0; i < numtags; i++ )
 {
 tag_desc = &( result->tags[i] );
 for( k = 0; k < NPRIMARY_SETS; k++ ) /* number of default tags to consider */
 {
 if( strcmp( pname[k], tag_desc->name ) == 0 )
 {
 if( tag_desc->have_sparse )
 {
 mhdf_openSparseTagData( file_handle, pname[k], &nval, &junk, table, status );
 if( mhdf_isError( status ) )
 {
 free( array );
 return NULL;
 }
 /* for sparse tags, read */
 result->numEntSets[k] = nval;
 if( nval <= 0 ) continue; /* do not do anything */
 
 ptr = realloc_data( &result, nval * sizeof( int ), status, sizeof( int ) );
 if( NULL == ptr || mhdf_isError( status ) )
 {
 free( array );
 return NULL;
 }
 memset( ptr, 0, nval * sizeof( int ) );
 result->defTagsEntSets[k] = ptr;
 tag_desc = &( result->tags[i] );
 
 ptr = realloc_data( &result, nval * sizeof( int ), status, sizeof( int ) );
 if( NULL == ptr || mhdf_isError( status ) )
 {
 free( array );
 return NULL;
 }
 memset( ptr, 0, nval * sizeof( int ) );
 result->defTagsVals[k] = ptr;
 tag_desc = &( result->tags[i] ); /* this is because the tag might point to
 something else*/
 
 /* make room for the long array type
 is it long or something else? */
 id_list = mhdf_malloc( nval * sizeof( long ), status );
 /* fill the id with values, then convert to int type (-set start)
 
 mhdf_read_data( table_id, offset, count, int_type, id_list, H5P_DEFAULT,
 status );*/
 
 data_type = H5Dget_type( table[0] );
 
 mhdf_read_data( table[0], 0, nval, data_type, id_list, H5P_DEFAULT, status );
 if( mhdf_isError( status ) )
 {
 free( array );
 return NULL;
 }
 H5Tclose( data_type );
 
 for( i1 = 0; i1 < nval; i1++ )
 result->defTagsEntSets[k][i1] = (int)( id_list[i1] - result->sets.start_id + 1 );
 /* now read values, integer type */
 data_type = H5Dget_type( table[1] );
 mhdf_read_data( table[1], 0, nval, data_type, result->defTagsVals[k], H5P_DEFAULT, status );
 if( mhdf_isError( status ) )
 {
 free( array );
 return NULL;
 }
 H5Tclose( data_type );
 mhdf_closeData( file_handle, table[0], status );
 if( mhdf_isError( status ) )
 {
 free( array );
 return NULL;
 }
 mhdf_closeData( file_handle, table[1], status );
 if( mhdf_isError( status ) )
 {
 free( array );
 return NULL;
 }
 free( id_list );
 }
 else if( 0 == k || 1 == k )
 { /* parallel partition or material sets should still work if dense
 could be dense tags on sets */
 if( !mhdf_haveDenseTag( file_handle, pname[k], mhdf_set_type_handle(), status ) ) continue;
 table[0] =
 mhdf_openDenseTagData( file_handle, pname[k], mhdf_set_type_handle(), &nval, status );
 if( mhdf_isError( status ) )
 {
 continue; /* do not error out if not a dense tag either */
 }
 result->numEntSets[k] = nval;
 if( nval <= 0 ) continue; /* do not do anything */
 
 /*
 * if dense parallel partition or material set, we know what to expect
 */
 result->numEntSets[k] = nval; /* k could be 0 or 1 */
 if( nval <= 0 ) continue; /* do not do anything */
 
 ptr = realloc_data( &result, nval * sizeof( int ), status, sizeof( int ) );
 if( NULL == ptr || mhdf_isError( status ) )
 {
 free( array );
 return NULL;
 }
 memset( ptr, 0, nval * sizeof( int ) );
 result->defTagsEntSets[k] = ptr;
 tag_desc = &( result->tags[i] );
 
 ptr = realloc_data( &result, nval * sizeof( int ), status, sizeof( int ) );
 if( NULL == ptr || mhdf_isError( status ) )
 {
 free( array );
 return NULL;
 }
 memset( ptr, 0, nval * sizeof( int ) );
 result->defTagsVals[k] = ptr;
 tag_desc = &( result->tags[i] ); /* this is because the tag might point to
 something else*/
 
 for( i1 = 0; i1 < nval; i1++ )
 {
 result->defTagsEntSets[k][i1] = i1 + 1;
 /*result -> defTagsVals[k][i1] = i1; we know how the partition looks
 * like */
 }
 /* fill in the data with the dense tag values
 because dense, sets will be in order
 
 we know it has to be integer */
 mhdf_readTagValues( table[0], 0, nval, H5T_NATIVE_INT, result->defTagsVals[k], status );
 if( mhdf_isError( status ) )
 {
 free( array );
 return NULL;
 }
 mhdf_closeData( file_handle, table[0], status );
 if( mhdf_isError( status ) )
 {
 free( array );
 return NULL;
 }
 }
 }
 }
 }
 }
 /* Compact memory and return */
 free( array );
 result->total_size = result->offset - (unsigned char*)result;
 
 API_END;
 return result;
}

References alloc_file_desc(), API_BEGIN, API_END, mhdf_EntDesc::count, mhdf_FileDesc::defTagsEntSets, mhdf_FileDesc::defTagsVals, mhdf_TagDesc::dense_elem_indices, mhdf_EntDesc::dense_tag_indices, mhdf_ElemDesc::desc, mhdf_FileDesc::elems, free_string_list(), get_elem_desc(), get_tag_desc(), mhdf_FileDesc::have_set_children, mhdf_FileDesc::have_set_contents, mhdf_FileDesc::have_set_parents, mhdf_TagDesc::have_sparse, mhdf_closeData(), mhdf_getElemHandles(), mhdf_getTagNames(), mhdf_haveDenseTag(), mhdf_haveNodes(), mhdf_haveSets(), mhdf_isError(), mhdf_malloc(), mhdf_node_type_handle(), mhdf_openDenseTagData(), mhdf_openNodeCoords(), mhdf_openSetMeta(), mhdf_openSparseTagData(), mhdf_read_data(), mhdf_readTagValues(), mhdf_set_type_handle(), mhdf_setOkay(), mhdf_TagDesc::name, mhdf_FileDesc::nodes, mhdf_TagDesc::num_dense_indices, mhdf_EntDesc::num_dense_tags, mhdf_FileDesc::num_elem_desc, mhdf_FileDesc::num_tag_desc, mhdf_FileDesc::numEntSets, mhdf_FileDesc::offset, realloc_data(), mhdf_FileDesc::sets, size, mhdf_EntDesc::start_id, mhdf_FileDesc::tags, mhdf_FileDesc::total_size, and mhdf_EntDesc::vals_per_ent.

Referenced by iMOAB_ReadHeaderInfo(), main(), and moab::ReadHDF5::set_up_read().

mhdf_isError()

int mhdf_isError

(

mhdf_Status const *

status

)

Return 1 if passed status object indicates an error. Zero otherwise.

MOAB, a Mesh-Oriented datABase, is a software component for creating, storing and accessing finite element mesh data.

Copyright 2004 Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software.

This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.

Definition at line 26 of file status.c.

{
 return !!status->message[0];
}

References struct_mhdf_Status::message.

Referenced by alloc_file_desc(), check_valid_adjacencies(), check_valid_elem_conn(), check_valid_parents_children(), check_valid_poly_conn(), check_valid_set_contents(), check_valid_sets(), check_valid_tag(), check_valid_var_len_tag(), moab::ReadHDF5::create_tag(), get_elem_desc(), get_tag_desc(), iMOAB_ReadHeaderInfo(), moab::ReadHDF5::is_error(), main(), mhdf_getFileSummary(), moab::ReadHDF5::read_qa(), moab::ReadHDF5::read_tag_values_all(), moab::ReadHDF5::read_tag_values_partial(), realloc_data(), moab::ReadHDF5::set_up_read(), and moab::WriteHDF5::write_file().

mhdf_message()

const char* mhdf_message

(

mhdf_Status const *

status

)

Get the error message given a status object.

Definition at line 31 of file status.c.

{
 return status->message;
}

References struct_mhdf_Status::message.

Referenced by check_valid_adjacencies(), check_valid_elem_conn(), check_valid_parents_children(), check_valid_poly_conn(), check_valid_set_contents(), check_valid_sets(), check_valid_tag(), check_valid_var_len_tag(), moab::ReadHDF5::create_tag(), iMOAB_ReadHeaderInfo(), moab::ReadHDF5::is_error(), main(), moab::WriteHDF5Parallel::parallel_create_file(), moab::ReadHDF5::read_qa(), moab::ReadHDF5::read_tag_values_all(), moab::ReadHDF5::read_tag_values_partial(), moab::ReadHDF5::set_up_read(), and moab::WriteHDF5::write_file().

mhdf_openFile()

mhdf_FileHandle mhdf_openFile	(	const char *	filename,
		int	writable,
		unsigned long *	max_id,
		hid_t	id_type,
		mhdf_Status *	status
	)

Open an existing file.

Open an existing HDF mesh file. This handle must be closed with mhdf_closeFile to avoid resource loss.

Parameters

filename	The path and name of the file to open
writable	If non-zero, open read-write. Otherwise read-only.
status	Passed back status of API call.
max_id	Used to pass back the maximum global ID used in the file. Provided as an indication to the caller of the size of the mesh. This parameter is optional. NULL may be passed.
id_type	Type to use when creating datasets containing file IDs

Returns

An opaque handle to the file.

Definition at line 141 of file file.c.

{
 return mhdf_openFileWithOpt( filename, writeable, max_id_out, id_type, H5P_DEFAULT, status );
}

References mhdf_openFileWithOpt().

Referenced by iMOAB_ReadHeaderInfo(), main(), and moab::ReadHDF5::set_up_read().

mhdf_openFileWithOpt()

mhdf_FileHandle mhdf_openFileWithOpt	(	const char *	filename,
		int	writable,
		unsigned long *	max_id,
		hid_t	id_type,
		hid_t	options,
		mhdf_Status *	status
	)

Open an existing file with options.

Open an existing HDF mesh file. This handle must be closed with mhdf_closeFile to avoid resource loss. This function allows the calling application to specify the HDF5 access property list that is passed to the HDF5 H5Fopen API. If this is passed as H5P_DEFAULT, the behavior is the same as mhdf_openFile . This argument is typically used to specify a parallel context for for writing the file in parallel.

Parameters

filename	The path and name of the file to open
writable	If non-zero, open read-write. Otherwise read-only.
status	Passed back status of API call.
max_id	Used to pass back the maximum global ID used in the file. Provided as an indication to the caller of the size of the mesh. This parameter is optional. NULL may be passed.
options	The HDF5 access property list to use when opening the file. See the HDF5 documentation for H5Fopen.
id_type	Type to use when creating datasets containing file IDs

Returns

An opaque handle to the file.

Definition at line 277 of file file.c.

{
 FileHandle* file_ptr;
 unsigned int flags;
 hid_t group_id;
 int check_is_hdf5 = 1;
#ifdef MOAB_HAVE_HDF5_PARALLEL
 herr_t err;
 MPI_Comm comm;
 MPI_Info info;
#endif
 API_BEGIN;
 
 /* Check if file is HDF5 */
 /* Don't do this because it can't handle MPI-IO driver code that
 passes options via prefixes on the file name. */
#ifdef MOAB_HAVE_HDF5_PARALLEL
 if( access_prop != H5P_DEFAULT )
 {
 err = H5Pget_fapl_mpio( access_prop, &comm, &info );
 if( err >= 0 )
 {
 check_is_hdf5 = 0;
 /* MPI Documentation is inconsistent with regards to whether
 or not the above call dup's these, but my testing with 1.8.3
 indicates that at least for that version they are not.
 MPI_Comm_free(&comm);
 MPI_Info_free(&info); */
 }
 }
#endif
 if( check_is_hdf5 && H5Fis_hdf5( filename ) <= 0 )
 {
 mhdf_setFail( status, "%s: File is not HDF5", filename );
 return NULL;
 }
 
 /* Create struct to hold working data */
 file_ptr = mhdf_alloc_FileHandle( 0, id_type, status );
 if( !file_ptr )
 {
 mhdf_setFail( status, "Memory allocation failed" );
 return NULL;
 }
 
 /* Create the file */
 flags = writable ? H5F_ACC_RDWR : H5F_ACC_RDONLY;
 file_ptr->hdf_handle = H5Fopen( filename, flags, access_prop );
 if( file_ptr->hdf_handle < 0 )
 {
 mhdf_setFail( status, "Failed to open file \"%s\"", filename );
 free( file_ptr );
 return NULL;
 }
 
 /* Check for TSTT data in file */
#if defined( H5Gopen_vers ) && H5Gopen_vers > 1
 group_id = H5Gopen2( file_ptr->hdf_handle, ROOT_GROUP, H5P_DEFAULT );
#else
 group_id = H5Gopen( file_ptr->hdf_handle, ROOT_GROUP );
#endif
 if( group_id < 0 )
 {
 mhdf_setFail( status, "Invalid file \"%s\"\n", filename );
 H5Fclose( file_ptr->hdf_handle );
 free( file_ptr );
 return NULL;
 }
 H5Gclose( group_id );
 
 /* Get max id */
 if( !scan_for_max_id( file_ptr, status ) )
 {
 H5Fclose( file_ptr->hdf_handle );
 mhdf_setFail( status, "Internal error reading file" );
 free( file_ptr );
 return NULL;
 }
 
 if( max_id_out ) *max_id_out = file_ptr->max_id;
 
 mhdf_setOkay( status );
 API_END_H( 1 );
 return file_ptr;
}

References API_BEGIN, API_END_H, struct_FileHandle::hdf_handle, struct_FileHandle::max_id, mhdf_alloc_FileHandle(), mhdf_setFail(), mhdf_setOkay(), ROOT_GROUP, and scan_for_max_id().

Referenced by mhdf_openFile(), moab::WriteHDF5Parallel::parallel_create_file(), and moab::ReadHDF5::set_up_read().