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/*@@
@header ioHDF5UtilGH.h
@date Fri Oct 6 2000
@author Thomas Radke
@desc
The GH extensions structure for IOHDF5Util.
@enddesc
@version $Id$
@@*/
#ifndef _IOUTILHDF5_IOUTILHDF5GH_H_
#define _IOUTILHDF5_IOUTILHDF5GH_H_
/* include the HDF5 header file */
#include <hdf5.h>
/*****************************************************************************/
/* some useful macros */
/*****************************************************************************/
/* Check error flags from HDF5 calls */
#define IOHDF5_ERROR(fn_call) \
do \
{ \
int _error_code = fn_call; \
\
\
if (_error_code < 0) \
{ \
CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING, \
"HDF5 call '%s' returned error code %d\n", \
#fn_call, _error_code); \
} \
} while (0)
/* macro for writing an attribute */
#define WRITE_ATTRIBUTE(name, value, dataset, dataspace, dim, datatype) \
do \
{ \
int _len; \
hid_t _attr; \
/* this union is only there to fix a bug in the HDF5 API */ \
union \
{ \
const void *const_val; \
void *non_const_val; \
} _v; \
hsize_t _arrayDim = dim; \
\
\
_v.const_val = value; \
if (H5Tget_class (datatype) == H5T_STRING) \
{ \
_len = strlen ((const char *) _v.const_val); \
if (_len == 0) /* HDF5 doesn't like zero-len strings */ \
{ \
_len++; \
} \
IOHDF5_ERROR (H5Tset_size (datatype, _len)); \
} \
if (_arrayDim > 0) \
{ \
IOHDF5_ERROR (H5Sset_extent_simple (dataspace, 1, \
&_arrayDim, NULL)); \
} \
IOHDF5_ERROR (_attr = H5Acreate (dataset, name, datatype, \
dataspace, H5P_DEFAULT)); \
IOHDF5_ERROR (H5Awrite (_attr, datatype, _v.non_const_val)); \
IOHDF5_ERROR (H5Aclose (_attr)); \
} while (0);
/* macro for reading an attribute */
#define READ_ATTRIBUTE(dataset, attrname, requested_type, buffer) \
do \
{ \
hid_t _attr, _attrtype; \
hsize_t _asize = 0; \
\
\
if ((_attr = H5Aopen_name (dataset, attrname)) < 0) \
{ \
CCTK_WARN (1, "Can't find " attrname " attribute"); \
} \
if (requested_type == H5T_C_S1) \
{ \
IOHDF5_ERROR (_attrtype = H5Aget_type (_attr)); \
IOHDF5_ERROR (_asize = H5Tget_size (_attrtype)); \
if (_asize + 1 >= sizeof (buffer)) \
{ \
CCTK_WARN (1, "Can't read " attrname " attribute (too long)");\
} \
} \
else \
{ \
_attrtype = requested_type; \
} \
if (H5Aread (_attr, _attrtype, buffer) < 0) \
{ \
CCTK_WARN (1, "Can't read " attrname " attribute"); \
} \
if (requested_type == H5T_C_S1) \
{ \
((char *) buffer)[_asize] = 0; \
IOHDF5_ERROR (H5Tclose (_attrtype)); \
} \
IOHDF5_ERROR (H5Aclose (_attr)); \
} while (0)
/***
Define the different datatypes used for HDF5 I/O
NOTE: the complex datatype is defined dynamically at runtime in Startup.c
***/
/* char type is easy */
#define IOHDF5_CHAR H5T_NATIVE_CHAR
/* floating point types are architecture-independent,
ie. a float has always 4 bytes, and a double has 8 bytes
IOHDF5_REAL is used for storing reals of the generic CCTK_REAL type
IOHDF5_REALn is used to explicitely store n-byte reals */
#ifdef CCTK_REAL4
#define IOHDF5_REAL4 H5T_NATIVE_FLOAT
#endif
#ifdef CCTK_REAL8
#define IOHDF5_REAL8 H5T_NATIVE_DOUBLE
#endif
#ifdef CCTK_REAL16
#define IOHDF5_REAL16 (sizeof (CCTK_REAL16) == sizeof (long double) ? \
H5T_NATIVE_LDOUBLE : -1)
#endif
#ifdef CCTK_REAL_PRECISION_16
#define IOHDF5_REAL IOHDF5_REAL16
#elif CCTK_REAL_PRECISION_8
#define IOHDF5_REAL IOHDF5_REAL8
#elif CCTK_REAL_PRECISION_4
#define IOHDF5_REAL IOHDF5_REAL4
#endif
/* integer types are architecture-dependent:
IOHDF5_INT is used for communicating integers of the generic CCTK_INT type
IOHDF5_INTn is used to explicitely communicate n-byte integers */
#ifdef CCTK_INT8
#define IOHDF5_INT8 (sizeof (CCTK_INT8) == sizeof (int) ? H5T_NATIVE_INT : \
sizeof (CCTK_INT8) == sizeof (long) ? H5T_NATIVE_LONG :\
sizeof (CCTK_INT8) == sizeof (long long) ? \
H5T_NATIVE_LLONG : -1)
#endif
#ifdef CCTK_INT4
#define IOHDF5_INT4 (sizeof (CCTK_INT4) == sizeof (int) ? H5T_NATIVE_INT : \
sizeof (CCTK_INT4) == sizeof (short) ? \
H5T_NATIVE_SHORT : -1)
#endif
#ifdef CCTK_INT2
#define IOHDF5_INT2 (sizeof (CCTK_INT2) == sizeof (short) ? \
H5T_NATIVE_SHORT : -1)
#endif
#ifdef CCTK_INTEGER_PRECISION_8
#define IOHDF5_INT IOHDF5_INT8
#elif CCTK_INTEGER_PRECISION_4
#define IOHDF5_INT IOHDF5_INT4
#elif CCTK_INTEGER_PRECISION_2
#define IOHDF5_INT IOHDF5_INT2
#endif
/* Constants to index timers within the timers array */
#define CP_PARAMETERS_TIMER 0
#define CP_VARIABLES_TIMER 1
#define CP_TOTAL_TIMER 2
#define RECOVERY_TIMER 3
#define IOHDF5_NUM_TIMERS 4
/* names of the groups that hold global attributes and parameters */
#define GLOBAL_ATTRIBUTES_GROUP "Global Attributes"
#define CACTUS_PARAMETERS_GROUP "Cactus Parameters"
#define ALL_PARAMETERS "All Parameters"
#ifdef __cplusplus
extern "C"
{
#endif
/* Geometry information structure for output variable */
typedef struct
{
int vdim;
int sdim;
int *direction;
int *origin;
int *length;
int *downsample;
int *actlen; /* actual index slab length (by PUGHSlab)*/
} ioHDF5Geo_t;
/* Structure describing a given recovery file */
typedef struct
{
int is_HDF5_file; /* flag indicating valid file info */
hid_t file; /* HDF5 file handle */
char *filename; /* complete file name for recovery */
int nprocs; /* number of total processors */
int ioproc; /* the associated IO processor */
int ioproc_every; /* how many IO processors there are */
int unchunked; /* whether data was written chunked or unchunked */
int has_version; /* whether file contains a Cactus version ID
(this is used to distinguish checkpoint files
with old/new timelevel naming scheme) */
} fileinfo_t;
/* IOHDF5Util GH extension structure */
typedef struct
{
/* while HDF5 error output is disabled
we keep the original error printing routine and its argument in here */
H5E_auto_t print_error_fn;
void *print_error_fn_arg;
/* predefined dataspaces for writing scalar and array attributes */
hid_t scalar_dataspace, array_dataspace;
/* predefined datatype for writing CCTK_COMPLEX types */
hid_t IOHDF5_COMPLEX,
IOHDF5_COMPLEX8,
IOHDF5_COMPLEX16,
IOHDF5_COMPLEX32;
/* predefined datatype for writing C string string attributes */
hid_t IOHDF5_STRING;
} ioHDF5UtilGH;
/* exported functions */
hid_t IOHDF5Util_DataType (const ioHDF5UtilGH *myGH, int cctk_type);
void IOHDF5Util_ParseVarsForOutput (const char *output_varstring,
ioHDF5Geo_t *output_request_list[]);
void IOHDF5Util_DumpParameters (const cGH *GH, int all, hid_t group);
void IOHDF5Util_DumpGHExtensions (const cGH *GH, hid_t group);
int IOHDF5Util_DumpGH (const cGH *GH, const int *timers, hid_t file);
void IOHDF5Util_DumpCommonAttributes (const cGH *GH,
int vindex,
int timelevel,
const CCTK_INT *global_shape,
const ioHDF5Geo_t *slab,
hid_t dataset);
int IOHDF5Util_DumpVar (const cGH *GH,
int vindex,
int timelevel,
const ioHDF5Geo_t *slab,
hid_t file,
int check_exisiting_objects);
int IOHDF5Util_RecoverParameters (const fileinfo_t *filenfo);
int IOHDF5Util_RecoverGHextensions (cGH *GH,
const fileinfo_t *filenfo);
int IOHDF5Util_RecoverVariables (cGH *GH,
const fileinfo_t *filenfo);
#ifdef __cplusplus
} // extern "C"
#endif
#endif /* _IOUTILHDF5_IOUTILHDF5GH_H_ */
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