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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 = "$Header$";
CCTK_FILEVERSION(CactusPUGHIO_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 given 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
the accumulated return code from @seeroutine IOHDF5Util_DumpVar
(should be 0 for success, or negative if some error occured)
@endreturndesc
@@*/
int IOHDF5Util_DumpGH (const cGH *GH, const int *timers, hid_t file)
{
int dim, groupvarsize, first_vindex, gindex, retval;
cGroup gdata;
cGroupDynamicData gdynamicdata;
char *fullname;
ioRequest *request;
DECLARE_CCTK_PARAMETERS
retval = 0;
/* start CP_PARAMETERS_TIMER timer */
if (timers)
{
CCTK_TimerResetI (timers[CP_PARAMETERS_TIMER]);
CCTK_TimerStartI (timers[CP_PARAMETERS_TIMER]);
}
/* 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 */
IOHDF5Util_DumpParameters (GH, 1, file);
IOHDF5Util_DumpGHExtensions (GH, file);
}
if (CCTK_Equals (verbose, "full"))
{
CCTK_INFO ("Dumping Grid 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--)
{
/* skip empty groups */
if (CCTK_NumVarsInGroupI (gindex) <= 0)
{
continue;
}
/* only dump groups which have storage assigned */
if (CCTK_QueryGroupStorageI (GH, gindex) <= 0)
{
continue;
}
/* get the number of allocated timelevels */
CCTK_GroupData (gindex, &gdata);
gdata.numtimelevels = 0;
gdata.numtimelevels = CCTK_GroupStorageIncrease (GH, 1, &gindex,
&gdata.numtimelevels,NULL);
/* dump all timelevels except the oldest (for multi-level groups) */
if (gdata.numtimelevels > 1)
{
gdata.numtimelevels--;
}
/* skip zero-sized groups */
CCTK_GroupDynamicData (GH, gindex, &gdynamicdata);
groupvarsize = 1;
for (dim = 0; dim < gdynamicdata.dim; dim++)
{
groupvarsize *= gdynamicdata.gsh[dim];
}
if (groupvarsize <= 0)
{
continue;
}
first_vindex = CCTK_FirstVarIndexI (gindex);
/* get the default I/O request for this group */
request = IOUtil_DefaultIORequest (GH, first_vindex, 1);
/* disable checking for old data objects,
disable datatype conversion and downsampling,
request hyperslab output including ghostzones */
request->check_exist = 0;
request->hdatatype = gdata.vartype;
for (request->hdim = 0; request->hdim < request->vdim; request->hdim++)
{
request->downsample[request->hdim] = 1;
}
request->with_ghostzones = 1;
/* loop over all variables in this group */
for (request->vindex = first_vindex;
request->vindex < first_vindex + gdata.numvars;
request->vindex++)
{
/* loop over all allocated timelevels of this variable */
for (request->timelevel = 0;
request->timelevel < gdata.numtimelevels;
request->timelevel++)
{
if (CCTK_Equals (verbose, "full") && file >= 0)
{
fullname = CCTK_FullName (request->vindex);
CCTK_VInfo (CCTK_THORNSTRING, " %s (timelevel %d)",
fullname, request->timelevel);
free (fullname);
}
retval += IOHDF5Util_DumpVar (GH, request, file);
}
} /* 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]);
}
/* free I/O request */
IOUtil_FreeIORequest (&request);
return (retval);
}
/*@@
@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> global grid size
<li> simulation time
<li> bounding box info (if the variable has a coordinate
system associated with it)
</ul>
@enddesc
@var GH
@vdesc pointer to CCTK grid hierarchy
@vtype const cGH *
@vio in
@endvar
@var request
@vdesc reference to the I/O request description
@vtype const ioRequest *
@vio in
@endvar
@var dataset
@vdesc the object handle where the attributes should be attached to
@vtype hid_t
@vio in
@endvar
@@*/
void IOHDF5Util_DumpCommonAttributes (const cGH *GH, const ioRequest *request,
hid_t object)
{
int hdim, vdim, coord_system_handle;
char *groupname;
CCTK_INT iattr;
CCTK_INT *coord_handles;
CCTK_REAL *rattr;
const ioHDF5UtilGH *myGH;
DECLARE_CCTK_PARAMETERS
myGH = CCTK_GHExtension (GH, "IOHDF5Util");
/* attributes describing the variable */
groupname = CCTK_GroupNameFromVarI (request->vindex);
WRITE_ATTRIBUTE ("groupname", groupname, object, myGH, 0, myGH->HDF5_STRING);
coord_system_handle = Coord_GroupSystem (GH, groupname);
free (groupname);
iattr = CCTK_GroupTypeFromVarI (request->vindex);
WRITE_ATTRIBUTE ("grouptype", &iattr, object, myGH, 0, HDF5_INT);
iattr = CCTK_MaxTimeLevelsVI (request->vindex);
WRITE_ATTRIBUTE ("ntimelevels", &iattr, object, myGH, 0, HDF5_INT);
WRITE_ATTRIBUTE ("global_size", request->hsize, object, myGH, request->hdim,
HDF5_INT);
WRITE_ATTRIBUTE ("time", &GH->cctk_time, object, myGH, 0, HDF5_REAL);
/* write bbox attributes if we have coordinate system info */
coord_handles = malloc (request->vdim * sizeof (CCTK_INT));
if (coord_system_handle >= 0 &&
Util_TableGetIntArray (coord_system_handle, request->vdim,
coord_handles, "COORDINATES") >= 0)
{
rattr = calloc (3 * request->vdim, sizeof (CCTK_REAL));
for (vdim = 0; vdim < request->vdim; vdim++)
{
for (hdim = 0; hdim < request->hdim; hdim++)
{
if (request->direction[hdim*request->hdim + vdim])
{
Util_TableGetReal (coord_handles[vdim], &rattr[hdim+0*request->vdim],
"COMPMIN");
if (Util_TableGetReal (coord_handles[vdim],
&rattr[hdim+2*request->vdim], "DELTA") >= 0)
{
rattr[hdim+2*request->vdim] *= request->downsample[hdim];
rattr[hdim+1*request->vdim] = rattr[hdim+0*request->vdim];
rattr[hdim+1*request->vdim] +=
((request->extent[hdim] + request->downsample[hdim]-1)
/ request->downsample[hdim] - 1)
* rattr[hdim+2*request->vdim];
}
}
}
}
WRITE_ATTRIBUTE ("origin", rattr + 0*vdim, object, myGH, vdim, HDF5_REAL);
WRITE_ATTRIBUTE ("min_ext", rattr + 0*vdim, object, myGH, vdim, HDF5_REAL);
WRITE_ATTRIBUTE ("max_ext", rattr + 1*vdim, object, myGH, vdim, HDF5_REAL);
WRITE_ATTRIBUTE ("delta", rattr + 2*vdim, object, myGH, vdim, HDF5_REAL);
free (rattr);
}
free (coord_handles);
}
/*@@
@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 a single dataset
into the CACTUS_PARAMETERS_GROUP group in the HDF5 file.
Note that we used to write the parameters string as a single
attribute attached to the CACTUS_PARAMETERS_GROUP group.
This caused problems with very long strings (HDF5 has a 16k-limit
on the total size of attributes).
@enddesc
@var GH
@vdesc pointer to CCTK grid hierarchy
@vtype const cGH *
@vio in
@endvar
@var all
@vdesc flag indicating whether to save all parameters or just the ones
which have been set before
@vtype int
@vio in
@endvar
@var file
@vdesc the HDF5 file handle
@vtype hid_t
@vio in
@endvar
@@*/
void IOHDF5Util_DumpParameters (const cGH *GH, int all, hid_t file)
{
ioHDF5UtilGH *myGH;
char *parameters;
hid_t group, dataspace, dataset;
hsize_t size;
DECLARE_CCTK_PARAMETERS
if (CCTK_Equals (verbose, "full"))
{
CCTK_INFO ("Dumping Parameters ...");
}
/* get the parameter string buffer */
parameters = IOUtil_GetAllParameters (GH, all);
if (parameters)
{
myGH = CCTK_GHExtension (GH, "IOHDF5Util");
size = strlen (parameters) + 1;
HDF5_ERROR (group = H5Gcreate (file, CACTUS_PARAMETERS_GROUP, 0));
HDF5_ERROR (dataspace = H5Screate_simple (1, &size, NULL));
HDF5_ERROR (dataset = H5Dcreate (group, ALL_PARAMETERS, H5T_NATIVE_UCHAR,
dataspace, H5P_DEFAULT));
HDF5_ERROR (H5Dwrite (dataset, H5T_NATIVE_CHAR, H5S_ALL, H5S_ALL,
H5P_DEFAULT, parameters));
HDF5_ERROR (H5Dclose (dataset));
HDF5_ERROR (H5Sclose (dataspace));
HDF5_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)
{
int value;
hid_t group;
char buffer[128];
const char *version;
const ioGH *ioUtilGH;
const ioHDF5UtilGH *myGH;
DECLARE_CCTK_PARAMETERS
if (CCTK_Equals (verbose, "full"))
{
CCTK_INFO ("Dumping GH extensions ...");
}
ioUtilGH = CCTK_GHExtension (GH, "IO");
myGH = CCTK_GHExtension (GH, "IOHDF5Util");
HDF5_ERROR (group = H5Gcreate (file, GLOBAL_ATTRIBUTES_GROUP, 0));
value = CCTK_MainLoopIndex ();
WRITE_ATTRIBUTE ("main_loop_index", &value, group, myGH, 0, H5T_NATIVE_INT);
value = CCTK_nProcs (GH);
WRITE_ATTRIBUTE ("nprocs", &value, group, myGH, 0, H5T_NATIVE_INT);
WRITE_ATTRIBUTE ("ioproc_every", &ioUtilGH->ioproc_every, group, myGH, 0,
H5T_NATIVE_INT);
WRITE_ATTRIBUTE ("unchunked", &ioUtilGH->unchunked, group, myGH, 0,
H5T_NATIVE_INT);
WRITE_ATTRIBUTE ("cctk_time", &GH->cctk_time, group, myGH, 0, HDF5_REAL);
WRITE_ATTRIBUTE ("cctk_iteration", &GH->cctk_iteration, group, myGH, 0,
H5T_NATIVE_INT);
version = CCTK_FullVersion ();
WRITE_ATTRIBUTE ("Cactus version", version, group, myGH, 0,myGH->HDF5_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,0,myGH->HDF5_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, 0,myGH->HDF5_STRING);
}
HDF5_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 = HDF5_CHAR; break;
case CCTK_VARIABLE_INT: retval = HDF5_INT; break;
case CCTK_VARIABLE_REAL: retval = HDF5_REAL; break;
case CCTK_VARIABLE_COMPLEX: retval = myGH->HDF5_COMPLEX; break;
#ifdef CCTK_INT1
case CCTK_VARIABLE_INT1: retval = HDF5_INT1; break;
#endif
#ifdef CCTK_INT2
case CCTK_VARIABLE_INT2: retval = HDF5_INT2; break;
#endif
#ifdef CCTK_INT4
case CCTK_VARIABLE_INT4: retval = HDF5_INT4; break;
#endif
#ifdef CCTK_INT8
case CCTK_VARIABLE_INT8: retval = HDF5_INT8; break;
#endif
#ifdef CCTK_REAL4
case CCTK_VARIABLE_REAL4: retval = HDF5_REAL4; break;
case CCTK_VARIABLE_COMPLEX8: retval = myGH->HDF5_COMPLEX8; break;
#endif
#ifdef CCTK_REAL8
case CCTK_VARIABLE_REAL8: retval = HDF5_REAL8; break;
case CCTK_VARIABLE_COMPLEX16: retval = myGH->HDF5_COMPLEX16; break;
#endif
#ifdef CCTK_REAL16
case CCTK_VARIABLE_REAL16: retval = HDF5_REAL16; break;
case CCTK_VARIABLE_COMPLEX32: retval = myGH->HDF5_COMPLEX32; break;
#endif
default: CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
"Unsupported CCTK variable datatype %d", cctk_type);
retval = -1;
}
return (retval);
}
|