Classes
struct	mhdf_EntDesc
struct	mhdf_TagDesc
struct	mhdf_ElemDesc
struct	mhdf_FileDesc
Typedefs
typedef void *	mhdf_FileHandle
	Opaque handle to an open file.
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
Functions
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.
mhdf_FileHandle	mhdf_openFile (const char filename, int writable, unsigned long max_id, hid_t id_type, mhdf_Status *status)
	Open an existing file.
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.
int	mhdf_countOpenHandles (mhdf_FileHandle h)
	Get number of open HDF5 objects from file.
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.
void	mhdf_fixFileDesc (struct mhdf_FileDesc copy_ptr, const struct mhdf_FileDesc orig_addr)
	Fix nested pointers for copied/moved FileDesc struct.
void	mhdf_closeFile (mhdf_FileHandle handle, mhdf_Status *status)
	Close the file.
Variables
char	struct_mhdf_Status::message [MHDF_MESSAGE_BUFFER_LEN]
long	mhdf_EntDesc::start_id
long	mhdf_EntDesc::count
int	mhdf_EntDesc::vals_per_ent
int *	mhdf_EntDesc::dense_tag_indices
int	mhdf_EntDesc::num_dense_tags
const char *	mhdf_TagDesc::name
enum mhdf_TagDataType	mhdf_TagDesc::type
int	mhdf_TagDesc::size
int	mhdf_TagDesc::bytes
int	mhdf_TagDesc::storage
int	mhdf_TagDesc::have_sparse
void *	mhdf_TagDesc::default_value
int	mhdf_TagDesc::default_value_size
void *	mhdf_TagDesc::global_value
int	mhdf_TagDesc::global_value_size
int *	mhdf_TagDesc::dense_elem_indices
int	mhdf_TagDesc::num_dense_indices
const char *	mhdf_ElemDesc::handle
const char *	mhdf_ElemDesc::type
int	mhdf_ElemDesc::have_adj
struct mhdf_EntDesc	mhdf_ElemDesc::desc
struct mhdf_EntDesc	mhdf_FileDesc::nodes
struct mhdf_EntDesc	mhdf_FileDesc::sets
int	mhdf_FileDesc::have_set_contents
int	mhdf_FileDesc::have_set_children
int	mhdf_FileDesc::have_set_parents
struct mhdf_ElemDesc *	mhdf_FileDesc::elems
int	mhdf_FileDesc::num_elem_desc
struct mhdf_TagDesc *	mhdf_FileDesc::tags
int	mhdf_FileDesc::num_tag_desc
int *	mhdf_FileDesc::numEntSets
int **	mhdf_FileDesc::defTagsEntSets
int **	mhdf_FileDesc::defTagsVals
size_t	mhdf_FileDesc::total_size
unsigned char *	mhdf_FileDesc::offset

Typedef Documentation

typedef struct mhdf_ElemDesc MHDF_ElemDesc

typedef struct mhdf_EntDesc MHDF_EntDesc

Data common to sets, nodes, and each element type

typedef struct mhdf_FileDesc MHDF_FileDesc

typedef void* mhdf_FileHandle

Opaque handle to an open file.

Definition at line 87 of file mhdf_public.h.

typedef mhdf_FileHandle MHDF_FileHandle

Definition at line 89 of file mhdf_public.h.

typedef struct mhdf_TagDesc MHDF_TagDesc

Struct describing a tag

Function Documentation

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.

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().

{
    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 );
}

int mhdf_countOpenHandles ( mhdf_FileHandle h )

Get number of open HDF5 objects from file.

Definition at line 150 of file file.c.

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

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

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 (Common element type names.), 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.

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().

{
    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;
}

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.

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().

{
    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;
}

MHDF_FileDesc* mhdf_getFileSummary	(	mhdf_FileHandle	file_handle,
		hid_t	file_id_type,
		mhdf_Status *	status,
		int	extraSetInfo
	)		`[read]`

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.

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().

{
    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;
}

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.

References mhdf_openFileWithOpt().

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

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

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.

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().

{
    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;
}