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/*@@
@file DumpUtils.c
@date Fri Oct 6 2000
@author Thomas Radke
@desc
Utility routines for dumping data into HDF5 files.
@enddesc
@version $Id$
@@*/
#include <stdlib.h>
#include "cctk.h"
#include "cctk_Version.h"
#include "cctk_Parameters.h"
#include "CactusBase/IOUtil/src/ioGH.h"
#include "CactusBase/IOUtil/src/ioutil_CheckpointRecovery.h"
#include "ioHDF5UtilGH.h"
/* the rcs ID and its dummy function to use it */
static const char *rcsid = "$Id$";
CCTK_FILEVERSION(BetaThorns_IOHDF5Util_DumpUtils_c)
/*@@
@routine IOHDF5Util_DumpGH
@date Tue Oct 10 2000
@author Thomas Radke
@desc
Dump all variables of the given GH along with
the global attributes and parameters
to the (already opened) HDF5 checkpoint file.
@enddesc
@var GH
@vdesc Pointer to CCTK grid hierarchy
@vtype const cGH *
@vio in
@endvar
@var timers
@vdesc array of timers for timing the checkpointing
@vtype const int *
@vio in
@endvar
@var file
@vdesc HDF5 file handle
@vtype hid_t
@vio in
@endvar
@returntype int
@returndesc
always 0 (for success)
@endreturndesc
@@*/
int IOHDF5Util_DumpGH (const cGH *GH,
const int *timers,
hid_t file)
{
DECLARE_CCTK_PARAMETERS
int maxdim;
int first_vindex, vindex, gindex;
int timelevel, last_timelevel;
cGroup gdata;
int old_out_single;
ioGH *ioUtilGH;
ioHDF5Geo_t request;
/*** FIXME: can CCTK_SyncGroup() have a 'const cGH *' parameter ?? ***/
union
{
const cGH *const_ptr;
cGH *non_const_ptr;
} GH_fake_const;
GH_fake_const.const_ptr = GH;
/* Get the GH extension for IOUtil */
ioUtilGH = (ioGH *) CCTK_GHExtension (GH, "IO");
maxdim = CCTK_MaxDim ();
request.origin = (int *) calloc (4 + maxdim, maxdim * sizeof (int));
request.length = request.origin + 1 * maxdim;
request.downsample = request.origin + 2 * maxdim;
request.actlen = request.origin + 3 * maxdim;
request.direction = request.origin + 4 * maxdim;
for (vindex = 0; vindex < maxdim; vindex++)
{
request.length[vindex] = -1;
request.downsample[vindex] = 1;
}
/* disable output in single precision */
old_out_single = ioUtilGH->out_single;
ioUtilGH->out_single = 0;
/* sync all active groups */
for (vindex = CCTK_NumGroups () - 1; vindex >= 0; vindex--)
{
if (CCTK_IsImplementationActive (
CCTK_ImpFromVarI (CCTK_FirstVarIndexI (vindex))))
{
CCTK_SyncGroupI (GH_fake_const.non_const_ptr, vindex);
}
}
/* start CP_PARAMETERS_TIMER timer */
if (timers)
{
CCTK_TimerResetI (timers[CP_PARAMETERS_TIMER]);
CCTK_TimerStartI (timers[CP_PARAMETERS_TIMER]);
}
/* Great; Now start dumping away! */
if (file >= 0)
{
/* all GH extension variables and parameter stuff which is not
specific to any dataset goes into dedicated groups */
if (out3D_parameters)
{
IOHDF5Util_DumpParameters (GH, file);
}
IOHDF5Util_DumpGHExtensions (GH, file);
}
if (verbose)
{
CCTK_INFO ("Dumping variables ...");
}
/* stop CP_PARAMETERS_TIMER timer and start CP_VARIABLES_TIMER */
if (timers)
{
CCTK_TimerStopI (timers[CP_PARAMETERS_TIMER]);
CCTK_TimerResetI (timers[CP_VARIABLES_TIMER]);
CCTK_TimerStartI (timers[CP_VARIABLES_TIMER]);
}
/* ... now the variables, sorted by groups */
for (gindex = CCTK_NumGroups () - 1; gindex >= 0; gindex--)
{
/* only dump groups which have storage assigned */
if (CCTK_QueryGroupStorageI (GH, gindex) <= 0)
{
continue;
}
/* sync the group */
CCTK_SyncGroupI (GH_fake_const.non_const_ptr, gindex);
/* dump all timelevels except the oldest (for multi-level groups) */
CCTK_GroupData (gindex, &gdata);
last_timelevel = gdata.numtimelevels;
if (last_timelevel > 1)
{
last_timelevel--;
}
request.sdim = request.vdim = gdata.dim;
/* set the hyperslab directions (orthogonal to all axes) */
memset (request.direction, 0, request.sdim * request.vdim * sizeof (int));
for (vindex = 0; vindex < request.sdim; vindex++)
{
request.direction[vindex * request.vdim + vindex] = 1;
}
/* loop over all variables in this group */
first_vindex = CCTK_FirstVarIndexI (gindex);
for (vindex = first_vindex; vindex < first_vindex + gdata.numvars; vindex++)
{
if (verbose && file >= 0)
{
CCTK_VInfo (CCTK_THORNSTRING, " %s", CCTK_VarName (vindex));
}
/* loop over all timelevels of this variable */
for (timelevel = 0; timelevel < last_timelevel; timelevel++)
{
IOHDF5Util_DumpVar (GH, vindex, timelevel, &request, file, 0);
}
} /* end of loop over all variables */
} /* end of loop over all groups */
/* stop CP_VARIABLES_TIMER timer */
if (timers)
{
CCTK_TimerStopI (timers[CP_VARIABLES_TIMER]);
}
/* restore output precision flag */
ioUtilGH->out_single = old_out_single;
/* free temporary resources */
free (request.origin);
return (0);
}
/*@@
@routine IOHDF5Util_DumpCommonAttributes
@date May 21 1999
@author Thomas Radke
@desc
Add "Common" attributes to the given dataset, these are:
<ul>
<li> the variable's groupname
<li> the grouptype
<li> number of timelevels
<li> simulation time
<li> origin
<li> bounding box
<li> gridspacings
<li> global grid size
</ul>
@enddesc
@var GH
@vdesc Pointer to CCTK grid hierarchy
@vtype const cGH *
@vio in
@endvar
@var vindex
@vdesc CCTK index of the variable to dump
@vtype int
@vio in
@endvar
@var timelevel
@vdesc timelevel of the variable to dump
@vtype int
@vio in
@endvar
@var global_shape
@vdesc global shape of the grid
@vtype CCTK_INT []
@vio in
@endvar
@var request
@vdesc pointer to IO request structure describing the hyperslab
@vtype ioHDF5Geo_t *
@vio in
@endvar
@var dataset
@vdesc the dataset handle where the attributes should be attached to
@vtype hid_t
@vio in
@endvar
@@*/
void IOHDF5Util_DumpCommonAttributes (const cGH *GH,
int vindex,
int timelevel,
const CCTK_INT *global_shape,
const ioHDF5Geo_t *request,
hid_t dataset)
{
DECLARE_CCTK_PARAMETERS
char *groupname;
int dim, vdim;
CCTK_INT attr_int;
CCTK_REAL *attr_real;
ioHDF5UtilGH *myGH;
char coord_system_name[20];
/* prevent compiler warning about unused parameter */
timelevel = timelevel;
/* Get the handle for IOHDF5Util extensions */
myGH = (ioHDF5UtilGH *) CCTK_GHExtension (GH, "IOHDF5Util");
/* attributes describing the variable */
groupname = CCTK_GroupNameFromVarI (vindex);
WRITE_ATTRIBUTE ("groupname", groupname, dataset,
myGH->scalar_dataspace, 0, myGH->IOHDF5_STRING);
free (groupname);
attr_int = CCTK_GroupTypeFromVarI (vindex);
WRITE_ATTRIBUTE ("grouptype", &attr_int, dataset,
myGH->scalar_dataspace, 0, IOHDF5_INT);
attr_int = CCTK_NumTimeLevelsFromVarI (vindex);
WRITE_ATTRIBUTE ("ntimelevels", &attr_int, dataset,
myGH->scalar_dataspace, 0, IOHDF5_INT);
WRITE_ATTRIBUTE ("global_size", global_shape, dataset,
myGH->array_dataspace, request->sdim, IOHDF5_INT);
WRITE_ATTRIBUTE ("time", &GH->cctk_time, dataset,
myGH->scalar_dataspace, 0, IOHDF5_REAL);
/* attributes describing the underlying grid
These are only stored for CCTK_GF variables if they are associated
with coordinates. */
/* FIXME: This is hardcoded for cartesian coordinate systems.
A better solution would be to be able to query the coordinate
system which is associated with the variable. */
vdim = CCTK_GroupDimFromVarI (vindex);
sprintf (coord_system_name, "cart%dd", vdim);
if (CCTK_GroupTypeFromVarI (vindex) == CCTK_GF &&
CCTK_CoordSystemHandle (coord_system_name) >= 0)
{
attr_real = (CCTK_REAL *) malloc (2 * vdim * sizeof (CCTK_REAL));
for (dim = 0; dim < vdim; dim++)
{
CCTK_CoordRange (GH, &attr_real[dim], &attr_real[dim + vdim], dim + 1,
NULL, coord_system_name);
}
WRITE_ATTRIBUTE ("origin", attr_real, dataset,
myGH->array_dataspace, vdim, IOHDF5_REAL);
WRITE_ATTRIBUTE ("min_ext", attr_real, dataset,
myGH->array_dataspace, vdim, IOHDF5_REAL);
WRITE_ATTRIBUTE ("max_ext", attr_real + vdim, dataset,
myGH->array_dataspace, vdim, IOHDF5_REAL);
WRITE_ATTRIBUTE ("delta", GH->cctk_delta_space, dataset,
myGH->array_dataspace, vdim, IOHDF5_REAL);
free (attr_real);
}
#if 0
/* attributes describing the hyperslab */
/* FIXME: what attributes are really needed here ?? ***/
if (request)
{
attr_real = (CCTK_REAL *) malloc (4 * request->sdim * sizeof (CCTK_REAL));
for (dim = 0; dim < request->sdim; dim++)
{
attr_real[dim + 0*request->sdim] =
request->origin[request->direction[dim]] *
GH->cctk_delta_space[request->direction[dim]];
attr_real[dim + 1*request->sdim] =
request->origin[dim] * GH->cctk_delta_space[dim];
attr_real[dim + 2*request->sdim] =
(request->origin[dim] + request->actlen[dim]-1) *
GH->cctk_delta_space[dim] * request->downsample[dim];
attr_real[dim + 3*request->sdim] =
GH->cctk_delta_space[request->direction[dim]] *
request->downsample[request->direction[dim]];
}
WRITE_ATTRIBUTE ("origin_slab", attr_real + 0*dim, dataset,
myGH->array_dataspace, dim, IOHDF5_REAL);
WRITE_ATTRIBUTE ("min_ext_slab", attr_real + 1*dim, dataset,
myGH->array_dataspace, dim, IOHDF5_REAL);
WRITE_ATTRIBUTE ("max_ext_slab", attr_real + 2*dim, dataset,
myGH->array_dataspace, dim, IOHDF5_REAL);
WRITE_ATTRIBUTE ("delta_slab", attr_real + 3*dim, dataset,
myGH->array_dataspace, dim, IOHDF5_REAL);
free (attr_real);
}
#endif
}
/*@@
@routine IOHDF5Util_DumpParameters
@date Thu Jan 20 2000
@author Thomas Radke
@desc
Collects the parameters of all active implementations
into a single string and writes it as an attribute
attached to the CACTUS_PARAMETERS_GROUP group in the HDF5 file.
@enddesc
@var GH
@vdesc Pointer to CCTK grid hierarchy
@vtype const cGH *
@vio in
@endvar
@var file
@vdesc the HDF5 file handle
@vtype hid_t
@vio in
@endvar
@@*/
void IOHDF5Util_DumpParameters (const cGH *GH,
hid_t file)
{
DECLARE_CCTK_PARAMETERS
ioHDF5UtilGH *myGH;
char *parameters;
hid_t group;
if (verbose)
{
CCTK_INFO ("Dumping Parameters ...");
}
/* Get the parameter string buffer */
parameters = IOUtil_GetAllParameters (GH);
if (parameters)
{
/* Get the handle for IOHDF5Util extensions */
myGH = (ioHDF5UtilGH *) CCTK_GHExtension (GH, "IOHDF5Util");
IOHDF5_ERROR (group = H5Gcreate (file, CACTUS_PARAMETERS_GROUP, 0));
WRITE_ATTRIBUTE (ALL_PARAMETERS, parameters, group,
myGH->scalar_dataspace, 0, myGH->IOHDF5_STRING);
IOHDF5_ERROR (H5Gclose (group));
free (parameters);
}
}
/*@@
@routine IOHDF5Util_DumpGHExtensions
@date Thu Jan 20 2000
@author Thomas Radke
@desc
Attaches the current values of important flesh and IO variables
as attributes to the GLOBAL_ATTRIBUTES_GROUP group
in the HDF5 file.
@enddesc
@var GH
@vdesc Pointer to CCTK grid hierarchy
@vtype const cGH *
@vio in
@endvar
@var file
@vdesc the HDF5 file handle
@vtype hid_t
@vio in
@endvar
@@*/
void IOHDF5Util_DumpGHExtensions (const cGH *GH,
hid_t file)
{
DECLARE_CCTK_PARAMETERS
int value;
hid_t group;
char buffer[128];
const char *version;
ioGH *ioUtilGH;
ioHDF5UtilGH *myGH;
if (verbose)
{
CCTK_INFO ("Dumping GH extensions ...");
}
/* Get the handles for IOUtil and IOHDF5 extensions */
ioUtilGH = (ioGH *) CCTK_GHExtension (GH, "IO");
myGH = (ioHDF5UtilGH *) CCTK_GHExtension (GH, "IOHDF5Util");
IOHDF5_ERROR (group = H5Gcreate (file, GLOBAL_ATTRIBUTES_GROUP, 0));
value = CCTK_MainLoopIndex ();
WRITE_ATTRIBUTE ("main_loop_index", &value, group,
myGH->scalar_dataspace, 0, H5T_NATIVE_INT);
value = CCTK_nProcs (GH);
WRITE_ATTRIBUTE ("nprocs", &value, group,
myGH->scalar_dataspace, 0, H5T_NATIVE_INT);
WRITE_ATTRIBUTE ("ioproc_every", &ioUtilGH->ioproc_every, group,
myGH->scalar_dataspace, 0, H5T_NATIVE_INT);
WRITE_ATTRIBUTE ("unchunked", &ioUtilGH->unchunked, group,
myGH->scalar_dataspace, 0, H5T_NATIVE_INT);
WRITE_ATTRIBUTE ("cctk_time", &GH->cctk_time, group,
myGH->scalar_dataspace, 0, IOHDF5_REAL);
WRITE_ATTRIBUTE ("cctk_iteration", &GH->cctk_iteration, group,
myGH->scalar_dataspace, 0, H5T_NATIVE_INT);
version = CCTK_FullVersion ();
WRITE_ATTRIBUTE ("Cactus version", version, group,
myGH->scalar_dataspace, 0, myGH->IOHDF5_STRING);
/* add the parameter filename and the creation date
as file identification attributes */
if (CCTK_Equals (out_fileinfo, "parameter filename") ||
CCTK_Equals (out_fileinfo, "all"))
{
buffer[0] = 0;
CCTK_ParameterFilename (sizeof (buffer), buffer);
WRITE_ATTRIBUTE ("parameter file", buffer, group,
myGH->scalar_dataspace, 0, myGH->IOHDF5_STRING);
}
if (CCTK_Equals (out_fileinfo, "creation date") ||
CCTK_Equals (out_fileinfo, "all"))
{
buffer[0] = 0;
Util_CurrentDate (sizeof (buffer), buffer);
value = strlen (buffer) + 1;
buffer[value-1] = ' ';
Util_CurrentTime (sizeof (buffer) - value, buffer + value);
WRITE_ATTRIBUTE ("creation date", buffer, group,
myGH->scalar_dataspace, 0, myGH->IOHDF5_STRING);
}
IOHDF5_ERROR (H5Gclose (group));
}
/*@@
@routine IOHDF5Util_DataType
@author Thomas Radke
@date Mon 11 June 2001
@desc
Returns the HDF5 datatype for a given CCTK datatype
@enddesc
@var myGH
@vdesc Pointer to IOHDF5Util's GH extensions
@vtype ioHDF5UtilGH *
@vio in
@endvar
@var cctk_type
@vdesc CCTK datatype
@vtype int
@vio in
@endvar
@returntype hid_t
@returndesc
the appropriate HDF5 datatype for success, or -1 otherwise
@endreturndesc
@@*/
hid_t IOHDF5Util_DataType (const ioHDF5UtilGH *myGH, int cctk_type)
{
hid_t retval;
switch (cctk_type)
{
case CCTK_VARIABLE_CHAR: retval = IOHDF5_CHAR; break;
case CCTK_VARIABLE_INT: retval = IOHDF5_INT; break;
case CCTK_VARIABLE_REAL: retval = IOHDF5_REAL; break;
case CCTK_VARIABLE_COMPLEX: retval = myGH->IOHDF5_COMPLEX; break;
#ifdef CCTK_INT2
case CCTK_VARIABLE_INT2: retval = IOHDF5_INT2; break;
#endif
#ifdef CCTK_INT4
case CCTK_VARIABLE_INT4: retval = IOHDF5_INT4; break;
#endif
#ifdef CCTK_INT8
case CCTK_VARIABLE_INT8: retval = IOHDF5_INT8; break;
#endif
#ifdef CCTK_REAL4
case CCTK_VARIABLE_REAL4: retval = IOHDF5_REAL4; break;
case CCTK_VARIABLE_COMPLEX8: retval = myGH->IOHDF5_COMPLEX8; break;
#endif
#ifdef CCTK_REAL8
case CCTK_VARIABLE_REAL8: retval = IOHDF5_REAL8; break;
case CCTK_VARIABLE_COMPLEX16: retval = myGH->IOHDF5_COMPLEX16; break;
#endif
#ifdef CCTK_REAL16
case CCTK_VARIABLE_REAL16: retval = IOHDF5_REAL16; break;
case CCTK_VARIABLE_COMPLEX32: retval = myGH->IOHDF5_COMPLEX32; break;
#endif
default: CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
"Unsupported CCTK variable datatype %d", cctk_type);
retval = -1;
}
return (retval);
}
|