#include "hdf5inc.h"
#include "F5F.h"

Macros
#define	F5printf(verbosity, ...)
#define	F5check(HDF5call)
#define	CASEITEM(x, i, refs, name)

Functions
hid_t	F5Acreate (hid_t loc_id, const char *name, hid_t type_id, hid_t space_id, hid_t create_plist)
void	F5T_save_perm_vector (hid_t location, int rank, int perm_vector[])
hid_t	F5I_create_contents (hid_t File_id)
herr_t	F5Glink (hid_t loc_id, H5G_link_t link_type, const char current_name, const char new_name)
herr_t	F5Glink_soft_to_id (hid_t loc_id, hid_t existing_id, const char *linkname)
void	F5I_add_grid (F5Path fpath, const char gridname, const double *time)
void	F5I_add_field (F5Path fpath, const char fieldname)
F5_API void	F5printf (int verbosity, const char *fmt,...)
F5_API void	F5printx (int verbosity, const char sourcefilename, int lineNo, const char FunctionName, const char *fmt,...)
F5_API void	F5print_dimensions (int verbosity, const char *prefix, int rank, const hsize_t dims[])
F5_API herr_t	F_H5Aread (hid_t attr_id, hid_t mem_type_id, void buf, const char name)
F5_API herr_t	F5Aread2 (hid_t attr_id, hid_t mem_type_id, void buf, const char name)
F5_API void	F5print_OpenHandles (hid_t file_id)

Variables
int	F5printf_indent

Macro Definition Documentation

◆ CASEITEM

#define CASEITEM	(	x,
		i,
		refs,
		name )

Value:

case x:\
        printf( " [%ld] %s, open references: %d:\t %s\n", i, #x, refs, name ); \
        break;  \

Definition at line 88 of file F5private.h.

#define CASEITEM(x, i, refs, name)                      \
case x:\
        printf( " [%ld] %s, open references: %d:\t %s\n", i, #x, refs, name ); \
        break;  \
 

Referenced by F5print_OpenHandles().

◆ F5check

#define F5check ( HDF5call )

Value:

{herr_t err = HDF5call; if (err<0) \
F5printf(1, "** %s returned error in %s:%d\n",\
         #HDF5call, __FILE__, __LINE__ ); }

Definition at line 71 of file F5private.h.

#define F5check(HDF5call) {herr_t err = HDF5call; if (err<0) \
                     F5printf(1, "** %s returned error in %s:%d\n",\
                              #HDF5call, __FILE__, __LINE__ ); }

Referenced by F5Tset_field_enum(), and F5Tset_field_ProcArray_enum().

◆ F5printf

#define F5printf	(		verbosity,
			... )

Value:

F5printx(verbosity, __FILE__, __LINE__, __PRETTY_FUNCTION__, __VA_ARGS__)

F5printx

void F5printx(int verbosity, const char *sourcefilename, int lineNo, const char *FunctionName, const char *fmt,...)

Definition F5private.c:368

http://gcc.gnu.org/onlinedocs/cpp/Variadic-Macros.html

Definition at line 60 of file F5private.h.

Referenced by _F5Gclose(), F5Aget_string(), F5Aget_type(), F5Aopen_name(), F5Asave(), F5Asave_ints(), F5Astore_integer(), F5Awrite_integer(), F5B_new_global_domain(), F5B_permute_dimensions(), F5B_read_chart_domain(), F5B_read_global_chart(), F5Bappend_slice(), F5Bget_timetable_size(), F5Binitialize_path(), F5Bopen_coordinate_domain(), F5close(), F5connect(), F5Dappend(), F5Dcreate(), F5Dset_type_attribute(), F5Fcreate(), F5Ffragment_is_group(), F5Fget_attribute_byname(), F5Fget_attribute_nr_elements(), F5Fget_field_enum(), F5Fget_fragment_attribute(), F5Fget_string_attribute(), F5Fhas_attribute(), F5Fhas_fragment_attribute(), F5file_type(), F5Fis_attribute_of_type(), F5Fis_fragment_attribute_of_type(), F5Fopen(), F5Fopen_group_or_dataset(), F5Fopen_group_or_dataset_attribute(), F5Fopen_or_create_group_or_dataset_attribute(), F5Fread_linear(), F5Fread_linear_fragment(), F5Fset_attribute(), F5Fset_attribute_byname(), F5Fset_fragment_attribute(), F5Fset_string_attribute(), F5FSwrite_fraction(), F5Fwrite_1D(), F5Fwrite_flexible(), F5Fwrite_fraction(), F5Fwrite_fraction_external(), F5Fwrite_fractionS(), F5Fwrite_linear(), F5Fwrite_linear_fraction(), F5FwriteIMAGE(), F5Fwrites(), F5FwriteX(), F5Gappend_external(), F5Gappend_hinted_creation(), F5Gappend_tree(), F5Glink(), F5Glink_soft_to_id(), F5I_add_field(), F5I_add_grid(), F5I_create_contents(), F5iterate_field_fragments(), F5iterate_grid_atlas(), F5iterate_gridevolution(), F5iterate_grids(), F5iterate_grids_per_bundle(), F5iterate_representations(), F5iterate_timeslices(), F5iterate_topologies(), F5iterate_topology_fields(), F5LAget_dimensions(), F5LAsave_dimensions(), F5Lcreate(), F5Lget_space(), F5Lget_type(), F5listen(), F5LreadS(), F5Lset_space(), F5LSwrite_fraction(), F5LTcreate(), F5LTcreate_topology(), F5LTcreateV(), F5LTexpand_dataspace(), F5LTget_index_depth(), F5LTget_skeleton_dimensionality(), F5LTmake_enum_type(), F5LTset_dataspace(), F5LTset_maximal_grid_refinement(), F5Lwrite(), F5Lwrite_fraction(), F5Lwrite_fraction_external(), F5Lwrite_fractionS(), F5Lwrite_linear(), F5LwriteS(), F5Lwrites(), F5LwriteX(), F5print_dimensions(), F5Rcreate_cartesian_nD(), F5Rcreate_relative_vertex_Qrefinement3D(), F5Rcreate_static_cartesian_3D(), F5Rget_timestep(), F5Rset_timestep(), F5Tappend(), F5Tcheck_committed(), F5Tget_field_Array_enum(), F5Tget_field_ProcArray_enum(), F5Tget_index_depth(), F5Tget_space(), F5Tis_convertible(), F5Tmake_precise_tensor(), F5Tpermute_dimensions(), F5Tsave_F5field_enum(), F5Tsave_ProcArray_enum(), F5Tsave_tensor(), F5Tset_field_enum(), F5Tset_field_ProcArray_enum(), F5write_particle_cartesian3Dv(), F5write_particle_cartesian3DvU(), F5write_particle_double_cartesian3Dv(), and F_H5Aread().

Function Documentation

◆ F5Acreate()

hid_t F5Acreate	(	hid_t	loc_id,
		const char *	name,
		hid_t	type_id,
		hid_t	space_id,
		hid_t	create_plist )

Definition at line 11 of file F5private.c.

{
        return H5Acreate2( loc_id, name, type_id, space_id,  create_plist, H5P_DEFAULT );
}

References name.

Referenced by F5Fset_attribute_byname(), and F5T_save_perm_vector().

◆ F5Aread2()

F5_API herr_t F5Aread2	(	hid_t	attr_id,
		hid_t	mem_type_id,
		void *	buf,
		const char *	name )

References F5_API, and name.

◆ F5Glink()

herr_t F5Glink	(	hid_t	loc_id,
		H5G_link_t	link_type,
		const char *	current_name,
		const char *	new_name )

Definition at line 162 of file F5private.c.

{
herr_t  retval;
        H5E_BEGIN_TRY
        retval = H5Glink(loc_id,  link_type,  current_name, new_name);
        H5E_END_TRY
 
        if (retval<0)
                F5printf(30, "F5Glink(,,%s -> %s) FAILED\n", current_name, new_name);
        else
                F5printf(30, "F5Glink(,,%s -> %s) DONE\n", current_name, new_name);
 
        return retval;
}

References F5printf.

Referenced by F5LTcreateV(), F5Rcreate_relative_vertex_Irefinement3D(), F5Rcreate_relative_vertex_Qrefinement3D(), and F5Rlink_default_vertex_topology().

◆ F5Glink_soft_to_id()

herr_t F5Glink_soft_to_id	(	hid_t	loc_id,
		hid_t	existing_id,
		const char *	linkname )

Definition at line 148 of file F5private.c.

{
char    objname[2048];
herr_t  retval = H5Iget_name(existing_id, objname, sizeof(objname) );
 
        if (retval<1)
                return retval;
 
        F5printf(30, "F5Glink(%s)", linkname);
        retval = H5Glink(loc_id,  H5G_LINK_SOFT, objname, linkname);
        F5printf(30, "~F5Glink()");
        return retval;
}

References F5printf.

◆ F5I_add_field()

void F5I_add_field	(	F5Path *	fpath,
		const char *	fieldname )

Definition at line 178 of file F5private.c.

{
        if (!fpath) return;
 
        if (!fpath->Field_hid)
        {
                F5printf(3, "F5I_add_field(%s): INVALID Field ID %ld",fieldname, (long)fpath->Field_hid); 
                assert(fpath->Field_hid);
                return;
        } 
        F5printf(30, "F5I_add_field(%s)",fieldname);
 
        /* Creating Field Information per Bundle */
        {
hid_t   FieldTable = F5Gappend(fpath->ContentsGroup_hid, FIBER_CONTENT_FIELDS);
hid_t   FieldInfo  = F5Gappend(FieldTable, fieldname);
 
char    gridref[2048] = "/" FIBER_CONTENTS "/" FIBER_CONTENT_GRIDS "/";
char    gridname[2048];
char    *g;
 
        if (fpath->Grid_hid<0)
        {
                F5printf(-1, "F5I_add_field(): FATAL INTERNAL ERROR: No Grid id!");
                return;
        }
        if (H5Iget_name(fpath->Grid_hid, gridname, sizeof(gridname) )<1)
        {
                F5printf(-1, "F5I_add_field(): Could not get name for Grid id!");
                assert(0);
        }
 
        /* /T=1234.5676/myFunnyGrid */
        g = strrchr(gridname, '/');
        if (!g) g = gridname; else g++;
/*      puts(g);        */
        strcat(gridref, g);
 
        /*
         NOTE: This link might already exist!
               If so, it's not an error.
        */
        H5E_BEGIN_TRY
        /*  /TableOfContents/Fields/myFunnyField/myFunnyGrid -> /TableOfContents/Grids/myFunnyGrid   */
        H5Glink(FieldInfo, H5G_LINK_SOFT, gridref , g);
        H5E_END_TRY
 
        H5Gclose( FieldInfo );
        H5Gclose( FieldTable );
        }
}

References F5Path::ContentsGroup_hid, F5Gappend(), F5printf, FIBER_CONTENT_FIELDS, FIBER_CONTENT_GRIDS, FIBER_CONTENTS, F5Path::Field_hid, F5Path::Grid_hid, and H5Gclose.

Referenced by F5Cwrite_regular_surface(), F5Fcreate(), F5FSwrite_fraction(), F5Fwrite_1D(), F5Fwrite_flexible(), F5Fwrite_fraction(), F5Fwrite_fraction_external(), F5Fwrite_fractionS(), F5Fwrite_linear(), F5Fwrite_linear_fraction(), F5FwriteIMAGE(), F5Fwrites(), F5FwriteX(), F5Rcreate_rectilinear(), F5write_particle_cartesian3Dv(), F5write_particle_cartesian3DvU(), and F5write_particle_double_cartesian3Dv().

◆ F5I_add_grid()

void F5I_add_grid	(	F5Path *	fpath,
		const char *	gridname,
		const double *	time )

Definition at line 230 of file F5private.c.

{
hid_t   GridsTable     ;
hid_t   GridInfo       ;
 
TimeTableEntry GridTimeInfo;
 
        if (!fpath) return;
 
        F5printf(30, "F5I_add_grid(%s,t=%g)@%d", gridname, *time, (int)(fpath->ContentsGroup_hid) );
 
        GridsTable     = F5Gappend(fpath->ContentsGroup_hid, FIBER_CONTENT_GRIDS);
 
        F5printf(30, "F5I_add_grid(%s,t=%g): grid table %d", gridname, *time, (int)(GridsTable) );
 
        GridInfo       = F5Gappend(GridsTable, gridname);
 
        if (time)
                GridTimeInfo.TimeValue = *time;
 
        GridTimeInfo.TimesliceName[0] = '/';
        F5I_timegroup(time, GridTimeInfo.TimesliceName+1, F5_TIMESLICE_NAME_LENGTH-2 );
 
#if     0
        if (time)
        {
        double  T = *time;
                printf("F5I_add_grid(T=%g) TimeTableEntry={%g, %s})\n",
                       T,
                       GridTimeInfo.TimeValue,
                       GridTimeInfo.TimesliceName);
 
                assert( GridTimeInfo.TimeValue == *time);
        }
        else
                printf("F5I_add_grid() TimeTableEntry={(undefined),%s})\n",
                       GridTimeInfo.TimesliceName );
#endif
 
 
 
/*
  Note: We could link here directly to the respective grid.
        However, then we cannot get the concrete time for which the grid is valid,
        because grid groups don't have a time attribute by themselves such that
        the same grid object can be shared among multiple timesteps.
        For the same reason, it does not have a backlink to the slice group where
        it is contained.
        Thus, when browsing via grid types, it is required to specify the grid name
        twice:
 
         /TableOfContents/Grids/MyFunnyGrid/T=1234.5676/MyFunnyGrid/
 
*/
        H5E_BEGIN_TRY
        /* ln -s /TableOfContents/Grids/MyFunnyGrid/T=1234.5676 -> /T=1234.5676   */
        H5Glink(GridInfo, H5G_LINK_SOFT, GridTimeInfo.TimesliceName, GridTimeInfo.TimesliceName+1);
        H5E_END_TRY
 
        if (time)
        {
/*
  ln -s /T=1234.5676/MyFunnyGrid/F5::TimeTable -> /TableOfContents/Grids/MyFunnyGrid/
 */
        herr_t  timetableError;
 
                H5E_BEGIN_TRY
                timetableError = H5Lcreate_hard( GridsTable, gridname, /* targetname */
                                                 fpath->Grid_hid, F5_TIMETABLE_NAME, /* linkname */
                                                 H5P_DEFAULT, H5P_DEFAULT);
                H5E_END_TRY
 
                if (timetableError>=0)
                {
                        F5Bappend_timetable(GridInfo, fpath->ContentsGroup_hid, &GridTimeInfo, 1);
                }
        }
 
        H5Gclose(GridsTable);
        H5Gclose(GridInfo);
}

References F5Path::ContentsGroup_hid, F5_TIMESLICE_NAME_LENGTH, F5_TIMETABLE_NAME, F5Bappend_timetable(), F5Gappend(), F5I_timegroup(), F5printf, FIBER_CONTENT_GRIDS, F5Path::Grid_hid, H5Gclose, _TimeTableEntry::TimesliceName, and _TimeTableEntry::TimeValue.

Referenced by F5LTcreateV().

◆ F5I_create_contents()

hid_t F5I_create_contents ( hid_t File_id )

Definition at line 103 of file F5private.c.

{
hid_t   TOC_id;
hid_t   G_id;
 
        if (File_id<0)
        {
                F5printf(0, "F5I_create_contents(): Invalid File!\n");
                return -1;
        }
 
        F5printf(30, "F5I_create_contents(%d): mkgroup %s", File_id, FIBER_CONTENTS) ;
        TOC_id = F5Gappend(File_id, FIBER_CONTENTS);
 
        if (TOC_id<0)
                return -1;
 
        H5E_BEGIN_TRY
        H5Adelete(TOC_id, FIBER_VERSION_ATTRIBUTE_NAME);
        H5E_END_TRY
 
        F5Asave_version(TOC_id, FIBER_MAJOR_VERSION, FIBER_MINOR_VERSION, FIBER_RELEASE_VERSION);
 
        G_id = F5Gappend(TOC_id, FIBER_CONTENT_GRIDS);
        assert(G_id>0);
        H5Gclose( G_id);
        G_id = F5Gappend(TOC_id, FIBER_CONTENT_FIELDS);
        H5Gclose( G_id);
 
        H5Gset_comment(File_id, FIBER_CONTENTS,
                       "All file objects in reverse order for easier browsing. ");
 
        H5Gset_comment(TOC_id, FIBER_CONTENT_GRIDS,
                       "All grids and their sequences.");
 
        {
        hid_t param_space_id = F5Gappend(TOC_id, FIBER_PARAMETER_SPACE);
        hid_t time_param_id  = F5Gappend(param_space_id, FIBER_HDF5_TIME_ATTRIB);
                H5Gclose(time_param_id);
                H5Gclose(param_space_id);
        }
        F5printf(30, "~F5I_create_contents()") ;
        return TOC_id;
}

References F5Asave_version(), F5Gappend(), F5printf, FIBER_CONTENT_FIELDS, FIBER_CONTENT_GRIDS, FIBER_CONTENTS, FIBER_HDF5_TIME_ATTRIB, FIBER_MAJOR_VERSION, FIBER_MINOR_VERSION, FIBER_PARAMETER_SPACE, FIBER_RELEASE_VERSION, FIBER_VERSION_ATTRIBUTE_NAME, and H5Gclose.

Referenced by F5LTcreateV().

◆ F5print_dimensions()

F5_API void F5print_dimensions	(	int	verbosity,
		const char *	prefix,
		int	rank,
		const hsize_t	dims[] )

Definition at line 394 of file F5private.c.

{
        if (rank==3)
                F5printf(verbosity, "%s(%ux%ux%u)", prefix,
                (int)dims[0], (int)dims[1], (int)dims[2]);
        else if(rank==2)
                F5printf(verbosity, "%s(%ux%u)", prefix,
                         (int)dims[0], (int)dims[1]);
        else if (rank==1)
                F5printf(verbosity, "%s(%u)", prefix,
                         (int)dims[0]);
        
}

References F5printf.

Referenced by F5Fwrite_fraction(), and F5Fwrite_fractionS().

◆ F5print_OpenHandles()

F5_API void F5print_OpenHandles ( hid_t file_id )

Definition at line 410 of file F5private.c.

{
        puts("F5print_OpenHandles"); fflush(stdout);
 
ssize_t obj_nr;
        obj_nr = H5Fget_obj_count( file_id, H5F_OBJ_ALL );
 
        if( obj_nr < 0 )
                puts("F5print_OpenHandles() Error retrieving number of open objects" );
 
        printf( "Open HDF5 object handles: %ld \n", obj_nr );
 
hid_t* objs = (hid_t*)calloc( obj_nr, sizeof( hid_t )  );
 
ssize_t check = H5Fget_obj_ids( file_id, H5F_OBJ_ALL, -1, objs );
        assert( check == obj_nr );
 
ssize_t i;
        for( i = 0; i < obj_nr; ++i)
        {
        htri_t valid;
                valid = H5Iis_valid( objs[i] ) ;
 
                if( valid == 0 )
                {
                        printf( " [%ld] is invalid!\n");
                        continue;
                }
                else if( valid < 0 )
                {
                        printf( " [%ld] Error on validness check!\n");
                        continue;
                }
 
        H5I_type_t type;
                type = H5Iget_type( objs[i] );
                if( type < 0)
                        puts( "Error retrieving type of open object." );
 
 
        int refs;
                refs = H5Iget_ref( objs[i] );
 
        char name_buf[512];
                H5Iget_name( objs[i], name_buf, 512 );
 
 
                switch( type )
                {
                CASEITEM( H5I_FILE, i, refs, name_buf )
                CASEITEM( H5I_GROUP, i, refs , name_buf )
                CASEITEM( H5I_DATATYPE, i, refs , name_buf )
                CASEITEM( H5I_DATASPACE, i, refs , name_buf )
                CASEITEM( H5I_DATASET, i, refs , name_buf )
                CASEITEM( H5I_ATTR, i, refs , name_buf )
                CASEITEM( H5I_BADID, i, refs , name_buf )
 
                default:
                        printf (" [%ld]: unknown type\n", i);
                }
        }
 
        free(objs);
}

References CASEITEM, and free().

◆ F5printf()

F5_API void F5printf	(	int	verbosity,
		const char *	fmt,
			... )

Definition at line 352 of file F5private.c.

{
va_list argptr;
int     i;
        if (verbosity > F5verbosity() )
                return;
 
        va_start(argptr, fmt);
        for(i = 0; i<F5printf_indent; i++)
                putc(' ',stderr);
        vfprintf(stderr, fmt, argptr);
        putc('\n',stderr);
        fflush(stderr);
        va_end(argptr);
}

References F5printf_indent.

◆ F5printx()

F5_API void F5printx	(	int	verbosity,
		const char *	sourcefilename,
		int	lineNo,
		const char *	FunctionName,
		const char *	fmt,
			... )

Definition at line 368 of file F5private.c.

{
va_list argptr;
int     i;
int     EffectiveVerbosity = F5verbosity();
        if (EffectiveVerbosity<0) EffectiveVerbosity = -EffectiveVerbosity;
        if (verbosity > EffectiveVerbosity)
                return;
 
        if (F5verbosity()<0)
        {
                fprintf(stderr, "%s:%d [%s]\t", sourcefilename, lineNo, FunctionName);
        }
 
        va_start(argptr, fmt);
        for(i = 0; i<F5printf_indent; i++)
                putc(' ',stderr);
        vfprintf(stderr, fmt, argptr);
        putc('\n',stderr);
        fflush(stderr);
        va_end(argptr);
}

References F5printf_indent.

◆ F5T_save_perm_vector()

void F5T_save_perm_vector	(	hid_t	location,
		int	rank,
		int	perm_vector[] )

Definition at line 879 of file F5Bchart.c.

{
        if (!perm_vector)
        {
                puts("F5T_save_perm_vector()");
                return;
        }
 
        /* Save the memory layout ordering attribute */
        /* Possible optimization: Save only if perm_vector is not FORTRAN ordering */
        {
        hsize_t Tdims = rank;
        hid_t   index_ds = H5Screate_simple(1, &Tdims, &Tdims ) ;
        hid_t   Rank_id = F5Acreate(location, FIBER_HDF5_CHART_MEMLAYOUT, H5T_NATIVE_INT, index_ds, 0);
                H5Awrite(Rank_id, H5T_NATIVE_INT, perm_vector );
                H5Aclose(Rank_id);
                H5Sclose(index_ds);
        }
}

References F5Acreate(), and FIBER_HDF5_CHART_MEMLAYOUT.

Referenced by F5B_save_global_chart(), and F5file_type().

◆ F_H5Aread()

F5_API herr_t F_H5Aread	(	hid_t	attr_id,
		hid_t	mem_type_id,
		void *	buf,
		const char *	name )

Definition at line 332 of file F5private.c.

{
        F5printf(50, "Reading attribute `%s'", name);
        return H5Aread(attr_id, mem_type_id, buf);
}

References F5printf, and name.

Referenced by F5Aget_ints(), F5Aget_string(), F5Aget_version(), F5B_read_chart_domain(), F5Fget_attribute_byname(), F5Fread_attr_data(), F5LAget_dimensions(), F5Lget_space(), F5Lread_linear(), F5Rget_timestep(), F5Tget_field_Array_enum(), and F5Tget_field_ProcArray_enum().

Variable Documentation

◆ F5printf_indent

int F5printf_indent

extern

Definition at line 349 of file F5private.c.

Referenced by F5Fcreate(), F5Fread_linear(), F5Fread_linear_fragment(), F5FSwrite_fraction(), F5Fwrite_flexible(), F5Fwrite_fraction(), F5Fwrite_fraction_external(), F5Fwrite_fractionS(), F5Fwrite_linear(), F5FwriteIMAGE(), F5Fwrites(), F5LTcreateV(), F5printf(), F5printx(), F5Rcreate_cartesian_nD(), and if().

Macros

Functions

Variables

Macro Definition Documentation

◆ CASEITEM

◆ F5check

◆ F5printf

Function Documentation

◆ F5Acreate()

◆ F5Aread2()

◆ F5Glink()

◆ F5Glink_soft_to_id()

◆ F5I_add_field()

◆ F5I_add_grid()

◆ F5I_create_contents()

◆ F5print_dimensions()

◆ F5print_OpenHandles()

◆ F5printf()

◆ F5printx()

◆ F5T_save_perm_vector()

◆ F_H5Aread()

Variable Documentation

◆ F5printf_indent