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authortradke <tradke@7842ec3a-9562-4be5-9c5b-06ba18f2b668>2002-04-23 14:58:00 +0000
committertradke <tradke@7842ec3a-9562-4be5-9c5b-06ba18f2b668>2002-04-23 14:58:00 +0000
commitb31eef3fee54b3133265c466eec75714d34d4e99 (patch)
treeb7ed2ac60935828bf93f92a829913e63d2352862
parent1111ce1fb848e6490b311b1ec5ba4363765e0333 (diff)
Code cleanup before moving into production mode.
git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOHDF5Util/trunk@58 7842ec3a-9562-4be5-9c5b-06ba18f2b668
Diffstat
-rw-r--r--src/DumpUtils.c306
-rw-r--r--src/DumpVar.c926
-rw-r--r--src/ParseVars.c269
-rw-r--r--src/RecoverVar.c318
-rw-r--r--src/Startup.c206
-rw-r--r--src/ioHDF5UtilGH.h292
-rw-r--r--src/make.configuration.defn20
7 files changed, 977 insertions, 1360 deletions
diff --git a/src/DumpUtils.c b/src/DumpUtils.c
index 0234fea..4ab5688 100644
--- a/src/DumpUtils.c
+++ b/src/DumpUtils.c
@@ -28,12 +28,11 @@ CCTK_FILEVERSION(BetaThorns_IOHDF5Util_DumpUtils_c)
@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.
+ 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
+ @vdesc pointer to CCTK grid hierarchy
@vtype const cGH *
@vio in
@endvar
@@ -54,50 +53,34 @@ CCTK_FILEVERSION(BetaThorns_IOHDF5Util_DumpUtils_c)
(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 IOHDF5Util_DumpGH (const cGH *GH, const int *timers, hid_t file)
{
- int retval, maxdim;
- int first_vindex, vindex, gindex;
- int timelevel, last_timelevel;
+ int first_vindex, gindex, timelevels, retval;
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;
+ ioSlab slab;
DECLARE_CCTK_PARAMETERS
retval = 0;
- 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++)
+ /* set up a hyperslab description for full hyperslabs */
+ slab.vdim = CCTK_MaxDim ();
+ slab.vectors = (CCTK_INT *) calloc (slab.vdim + 6,
+ slab.vdim * sizeof(CCTK_INT));
+ slab.hoffset = slab.vectors + 0*slab.vdim;
+ slab.hsize = slab.vectors + 1*slab.vdim;
+ slab.hsize_chunk = slab.vectors + 2*slab.vdim;
+ slab.origin = slab.vectors + 3*slab.vdim;
+ slab.extent = slab.vectors + 4*slab.vdim;
+ slab.downsample = slab.vectors + 5*slab.vdim;
+ slab.direction = slab.vectors + 6*slab.vdim;
+
+ for (slab.hdim = 0; slab.hdim < slab.vdim; slab.hdim++)
{
- request.length[vindex] = -1;
- request.downsample[vindex] = 1;
+ slab.extent[slab.hdim] = -1;
+ slab.downsample[slab.hdim] = 1;
}
- /* disable output in single precision */
- old_out_single = ioUtilGH->out_single;
- ioUtilGH->out_single = 0;
-
/* start CP_PARAMETERS_TIMER timer */
if (timers)
{
@@ -105,7 +88,7 @@ int IOHDF5Util_DumpGH (const cGH *GH,
CCTK_TimerStartI (timers[CP_PARAMETERS_TIMER]);
}
- /* Great; Now start dumping away! */
+ /* now start dumping away */
if (file >= 0)
{
/* all GH extension variables and parameter stuff which is not
@@ -130,47 +113,45 @@ int IOHDF5Util_DumpGH (const cGH *GH,
/* ... now the variables, sorted by groups */
for (gindex = CCTK_NumGroups () - 1; gindex >= 0; gindex--)
{
- /* only dump groups which belong to an active implementation
- and have storage assigned */
- if (! CCTK_IsImplementationActive (CCTK_ImpFromVarI (CCTK_FirstVarIndexI
- (gindex))) ||
- CCTK_QueryGroupStorageI (GH, gindex) <= 0)
+ /* 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)
+ timelevels = gdata.numtimelevels;
+ if (timelevels > 1)
{
- last_timelevel--;
+ timelevels--;
}
- request.sdim = request.vdim = gdata.dim;
+ slab.hdim = slab.vdim = gdata.dim;
+ slab.check_exist = 0;
+ slab.hdatatype = gdata.vartype;
/* 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++)
+ memset (slab.direction, 0, slab.hdim * slab.vdim * sizeof (int));
+ for (slab.hdim = 0; slab.hdim < slab.vdim; slab.hdim++)
{
- request.direction[vindex * request.vdim + vindex] = 1;
+ slab.direction[slab.hdim * (slab.vdim + 1)] = 1;
}
/* loop over all variables in this group */
first_vindex = CCTK_FirstVarIndexI (gindex);
- for (vindex = first_vindex; vindex < first_vindex + gdata.numvars; vindex++)
+ for (slab.vindex = first_vindex;
+ slab.vindex < first_vindex + gdata.numvars;
+ slab.vindex++)
{
if (verbose && file >= 0)
{
- CCTK_VInfo (CCTK_THORNSTRING, " %s", CCTK_VarName (vindex));
+ CCTK_VInfo (CCTK_THORNSTRING, " %s", CCTK_VarName (slab.vindex));
}
/* loop over all timelevels of this variable */
- for (timelevel = 0; timelevel < last_timelevel; timelevel++)
+ for (slab.timelevel = 0; slab.timelevel < timelevels; slab.timelevel++)
{
- retval += IOHDF5Util_DumpVar (GH, vindex, timelevel, &request, file, 0);
+ retval += IOHDF5Util_DumpVar (GH, &slab, file);
}
} /* end of loop over all variables */
@@ -182,11 +163,8 @@ int IOHDF5Util_DumpGH (const cGH *GH,
CCTK_TimerStopI (timers[CP_VARIABLES_TIMER]);
}
- /* restore output precision flag */
- ioUtilGH->out_single = old_out_single;
-
/* free temporary resources */
- free (request.origin);
+ free (slab.vectors);
return (retval);
}
@@ -210,45 +188,26 @@ int IOHDF5Util_DumpGH (const cGH *GH,
</ul>
@enddesc
@var GH
- @vdesc Pointer to CCTK grid hierarchy
+ @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 *
+ @var slab
+ @vdesc reference to the I/O hyperslab description
+ @vtype const ioSlab *
@vio in
@endvar
@var dataset
- @vdesc the dataset handle where the attributes should be attached to
+ @vdesc the object 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)
+void IOHDF5Util_DumpCommonAttributes (const cGH *GH, const ioSlab *slab,
+ hid_t object)
{
- char *groupname;
int dim, vdim;
+ char *groupname;
CCTK_INT attr_int;
CCTK_REAL *attr_real;
ioHDF5UtilGH *myGH;
@@ -256,27 +215,19 @@ void IOHDF5Util_DumpCommonAttributes (const cGH *GH,
DECLARE_CCTK_PARAMETERS
- /* 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);
+ groupname = CCTK_GroupNameFromVarI (slab->vindex);
+ WRITE_ATTRIBUTE ("groupname", groupname, object, myGH, 0, myGH->HDF5_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);
+ attr_int = CCTK_GroupTypeFromVarI (slab->vindex);
+ WRITE_ATTRIBUTE ("grouptype", &attr_int, object, myGH, 0, HDF5_INT);
+ attr_int = CCTK_NumTimeLevelsFromVarI (slab->vindex);
+ WRITE_ATTRIBUTE ("ntimelevels", &attr_int, object, myGH, 0, HDF5_INT);
+ WRITE_ATTRIBUTE ("global_size", slab->hsize, object, myGH, slab->hdim,
+ HDF5_INT);
+ WRITE_ATTRIBUTE ("time", &GH->cctk_time, object, myGH, 0, HDF5_REAL);
/* attributes describing the underlying grid
These are only stored for CCTK_GF variables if they are associated
@@ -284,9 +235,9 @@ void IOHDF5Util_DumpCommonAttributes (const cGH *GH,
/* 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);
+ vdim = CCTK_GroupDimFromVarI (slab->vindex);
sprintf (coord_system_name, "cart%dd", vdim);
- if (CCTK_GroupTypeFromVarI (vindex) == CCTK_GF &&
+ if (CCTK_GroupTypeFromVarI (slab->vindex) == CCTK_GF &&
CCTK_CoordSystemHandle (coord_system_name) >= 0)
{
attr_real = (CCTK_REAL *) malloc (2 * vdim * sizeof (CCTK_REAL));
@@ -296,45 +247,42 @@ void IOHDF5Util_DumpCommonAttributes (const cGH *GH,
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);
+ WRITE_ATTRIBUTE ("origin", attr_real, object, myGH, vdim, HDF5_REAL);
+ WRITE_ATTRIBUTE ("min_ext", attr_real, object, myGH, vdim, HDF5_REAL);
+ WRITE_ATTRIBUTE ("max_ext", attr_real + vdim, object, myGH, vdim,HDF5_REAL);
+ WRITE_ATTRIBUTE ("delta", GH->cctk_delta_space, object, myGH, vdim,
+ HDF5_REAL);
free (attr_real);
}
#if 0
/* attributes describing the hyperslab */
/* FIXME: what attributes are really needed here ?? ***/
- if (request)
+ if (slab)
{
- attr_real = (CCTK_REAL *) malloc (4 * request->sdim * sizeof (CCTK_REAL));
- for (dim = 0; dim < request->sdim; dim++)
+ attr_real = (CCTK_REAL *) malloc (4 * slab->hdim * sizeof (CCTK_REAL));
+ for (dim = 0; dim < slab->hdim; 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]];
+ attr_real[dim + 0*slab->hdim] =
+ slab->origin[slab->direction[dim]] *
+ GH->cctk_delta_space[slab->direction[dim]];
+ attr_real[dim + 1*slab->hdim] =
+ slab->origin[dim] * GH->cctk_delta_space[dim];
+ attr_real[dim + 2*slab->hdim] =
+ (slab->origin[dim] + slab->actlen[dim]-1) *
+ GH->cctk_delta_space[dim] * slab->downsample[dim];
+ attr_real[dim + 3*slab->hdim] =
+ GH->cctk_delta_space[slab->direction[dim]] *
+ slab->downsample[slab->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);
+ WRITE_ATTRIBUTE ("origin_slab", attr_real + 0*dim, object, myGH, dim,
+ HDF5_REAL);
+ WRITE_ATTRIBUTE ("min_ext_slab", attr_real + 1*dim, object, myGH, dim,
+ HDF5_REAL);
+ WRITE_ATTRIBUTE ("max_ext_slab", attr_real + 2*dim, object, myGH, dim,
+ HDF5_REAL);
+ WRITE_ATTRIBUTE ("delta_slab", attr_real + 3*dim, object, myGH, dim,
+ HDF5_REAL);
free (attr_real);
}
#endif
@@ -351,7 +299,7 @@ void IOHDF5Util_DumpCommonAttributes (const cGH *GH,
attached to the CACTUS_PARAMETERS_GROUP group in the HDF5 file.
@enddesc
@var GH
- @vdesc Pointer to CCTK grid hierarchy
+ @vdesc pointer to CCTK grid hierarchy
@vtype const cGH *
@vio in
@endvar
@@ -380,18 +328,16 @@ void IOHDF5Util_DumpParameters (const cGH *GH, int all, hid_t file)
CCTK_INFO ("Dumping Parameters ...");
}
- /* Get the parameter string buffer */
+ /* get the parameter string buffer */
parameters = IOUtil_GetAllParameters (GH, all);
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));
+ HDF5_ERROR (group = H5Gcreate (file, CACTUS_PARAMETERS_GROUP, 0));
+ WRITE_ATTRIBUTE (ALL_PARAMETERS, parameters, group, myGH, 0,
+ myGH->HDF5_STRING);
+ HDF5_ERROR (H5Gclose (group));
free (parameters);
}
@@ -408,7 +354,7 @@ void IOHDF5Util_DumpParameters (const cGH *GH, int all, hid_t file)
in the HDF5 file.
@enddesc
@var GH
- @vdesc Pointer to CCTK grid hierarchy
+ @vdesc pointer to CCTK grid hierarchy
@vtype const cGH *
@vio in
@endvar
@@ -418,8 +364,7 @@ void IOHDF5Util_DumpParameters (const cGH *GH, int all, hid_t file)
@vio in
@endvar
@@*/
-void IOHDF5Util_DumpGHExtensions (const cGH *GH,
- hid_t file)
+void IOHDF5Util_DumpGHExtensions (const cGH *GH, hid_t file)
{
int value;
hid_t group;
@@ -435,29 +380,24 @@ void IOHDF5Util_DumpGHExtensions (const cGH *GH,
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));
+ HDF5_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);
+ WRITE_ATTRIBUTE ("main_loop_index", &value, group, myGH, 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);
+ 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->scalar_dataspace, 0, myGH->IOHDF5_STRING);
+ WRITE_ATTRIBUTE ("Cactus version", version, group, myGH, 0,myGH->HDF5_STRING);
/* add the parameter filename and the creation date
as file identification attributes */
@@ -466,8 +406,7 @@ void IOHDF5Util_DumpGHExtensions (const cGH *GH,
{
buffer[0] = 0;
CCTK_ParameterFilename (sizeof (buffer), buffer);
- WRITE_ATTRIBUTE ("parameter file", buffer, group,
- myGH->scalar_dataspace, 0, myGH->IOHDF5_STRING);
+ WRITE_ATTRIBUTE ("parameter file", buffer, group, myGH,0,myGH->HDF5_STRING);
}
if (CCTK_Equals (out_fileinfo, "creation date") ||
CCTK_Equals (out_fileinfo, "all"))
@@ -477,11 +416,10 @@ void IOHDF5Util_DumpGHExtensions (const cGH *GH,
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);
+ WRITE_ATTRIBUTE ("creation date", buffer, group, myGH, 0,myGH->HDF5_STRING);
}
- IOHDF5_ERROR (H5Gclose (group));
+ HDF5_ERROR (H5Gclose (group));
}
@@ -494,7 +432,7 @@ void IOHDF5Util_DumpGHExtensions (const cGH *GH,
@enddesc
@var myGH
- @vdesc Pointer to IOHDF5Util's GH extensions
+ @vdesc pointer to IOHDF5Util's GH extensions
@vtype ioHDF5UtilGH *
@vio in
@endvar
@@ -516,30 +454,30 @@ hid_t IOHDF5Util_DataType (const ioHDF5UtilGH *myGH, int cctk_type)
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;
+ 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_INT2
- case CCTK_VARIABLE_INT2: retval = IOHDF5_INT2; break;
+ case CCTK_VARIABLE_INT2: retval = HDF5_INT2; break;
#endif
#ifdef CCTK_INT4
- case CCTK_VARIABLE_INT4: retval = IOHDF5_INT4; break;
+ case CCTK_VARIABLE_INT4: retval = HDF5_INT4; break;
#endif
#ifdef CCTK_INT8
- case CCTK_VARIABLE_INT8: retval = IOHDF5_INT8; break;
+ case CCTK_VARIABLE_INT8: retval = HDF5_INT8; break;
#endif
#ifdef CCTK_REAL4
- case CCTK_VARIABLE_REAL4: retval = IOHDF5_REAL4; break;
- case CCTK_VARIABLE_COMPLEX8: retval = myGH->IOHDF5_COMPLEX8; break;
+ 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 = IOHDF5_REAL8; break;
- case CCTK_VARIABLE_COMPLEX16: retval = myGH->IOHDF5_COMPLEX16; break;
+ 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 = IOHDF5_REAL16; break;
- case CCTK_VARIABLE_COMPLEX32: retval = myGH->IOHDF5_COMPLEX32; break;
+ 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,
diff --git a/src/DumpVar.c b/src/DumpVar.c
index 109df75..96148d9 100644
--- a/src/DumpVar.c
+++ b/src/DumpVar.c
@@ -2,9 +2,9 @@
@file DumpVar.c
@date Fri May 21 1999
@author Thomas Radke
- @desc
+ @desc
Routines for writing variables into HDF5 data or checkpoint files.
- These routines are used by other HDF5 IO methods.
+ These routines are used by other HDF5 I/O methods.
@enddesc
@version $Id$
@@*/
@@ -15,77 +15,40 @@
#include "cctk.h"
#include "cctk_Parameters.h"
#include "CactusPUGH/PUGH/src/include/pugh.h"
-#include "CactusPUGH/PUGHSlab/src/NewPUGHSlab.h"
+#include "CactusPUGH/PUGHSlab/src/NewPUGHSlab.h"
#include "CactusBase/IOUtil/src/ioGH.h"
#include "ioHDF5UtilGH.h"
-
/* the rcs ID and its dummy function to use it */
static const char *rcsid = "$Header$";
CCTK_FILEVERSION(BetaThorns_IOHDF5Util_DumpVar_c)
-/* #define DEBUG_ME 1 */
-
-#define IOTAGBASE 20000 /* This may break on more than 2000 processors */
-
-/* info structure describing how to dump a given CCTK variable type */
-typedef struct
-{
- int iohdf5_type; /* the HDF5 type to use */
- int element_size; /* size of a single data element */
-#ifdef CCTK_MPI
- MPI_Datatype mpi_type; /* the data type for MPI communication */
+/********************************************************************
+ ******************** Macro Definitions ************************
+ ********************************************************************/
+/* uncomment the following line to enable some debugging output */
+/* #define IOHDF5UTIL_DEBUG 1 */
+
+/* tag base for MPI messages (this may break on more than 2000 processors) */
+#define MPITAGBASE 20000
+
+
+/********************************************************************
+ ******************** Internal Routines ************************
+ ********************************************************************/
+static int WriteGS (const cGH *GH, const ioSlab *slab, const char *name,
+ hid_t file);
+static int WriteGA (const cGH *GH, const ioSlab *slab, const char *name,
+ hid_t file);
+static int GetLocalHyperslab (const cGH *GH, const ioSlab *slab, void **data,
+ int *free_data);
+static void WriteData (const cGH *GH, const ioSlab *slab, const char *name,
+ const void *data, int proc, hid_t file);
+#if defined(CCTK_MPI) && defined(H5_HAVE_PARALLEL)
+static void WriteDataCollective (const cGH *GH, const ioSlab *slab,
+ const char *name, const void *data,hid_t file);
#endif
-} dumpInfo;
-
-
-/* prototypes of routines defined in this source file */
-static int IOHDF5Util_DumpGS (const cGH *GH,
- int vindex,
- int timelevel,
- int iohdf5_type,
- const ioHDF5Geo_t *request,
- int check_exisiting_objects,
- hid_t file);
-static int IOHDF5Util_DumpGA (const cGH *GH,
- int vindex,
- int timelevel,
- const ioHDF5Geo_t *request,
- const dumpInfo *info,
- int check_exisiting_objects,
- hid_t file);
-static int IOHDF5Util_getDumpData (const cGH *GH,
- int vindex,
- int timelevel,
- const ioHDF5Geo_t *request,
- void **outme,
- int *free_outme,
- CCTK_INT *geom);
-static void IOHDF5Util_procDump (const cGH *GH,
- int vindex,
- int timelevel,
- const ioHDF5Geo_t *request,
- const void *outme,
- const CCTK_INT *geom,
- int proc,
- int iohdf5_type,
- int check_exisiting_objects,
- hid_t file);
-#ifdef CCTK_MPI
-#ifdef H5_HAVE_PARALLEL
-static void IOHDF5Util_collectiveDump (const cGH *GH,
- int vindex,
- int timelevel,
- const ioHDF5Geo_t *request,
- const void *outme,
- const CCTK_INT *geom,
- int hdf5io_type,
- int check_exisiting_objects,
- hid_t file);
-#endif /* H5_HAVE_PARALLEL */
-#endif /* MPI */
-
/*@@
@@ -96,27 +59,17 @@ static void IOHDF5Util_collectiveDump (const cGH *GH,
Generic dump routine, just calls the type-specific dump routine.
@enddesc
- @calls IOHDF5Util_DumpGS
- IOHDF5Util_DumpGA
+ @calls WriteGS
+ WriteGA
@var GH
- @vdesc Pointer to CCTK grid hierarchy
+ @vdesc pointer to CCTK grid hierarchy
@vtype const cGH *
@vio in
@endvar
- @var vindex
- @vdesc index of the variable to be dumped
- @vtype int
- @vio in
- @endvar
- @var timelevel
- @vdesc the timelevel to dump
- @vtype int
- @vio in
- @endvar
- @var request
- @vdesc pointer to the IO request structure
- @vtype const ioHDF5Geo_t *
+ @var slab
+ @vdesc reference to the I/O hyperslab description
+ @vtype const ioSlab *
@vio in
@endvar
@var file
@@ -124,141 +77,83 @@ static void IOHDF5Util_collectiveDump (const cGH *GH,
@vtype hid_t
@vio in
@endvar
- @var check_exisiting_objects
- @vdesc flag indicating if we should check for already existing objects
- before these are created anew
- This might happen for existing files reopened after recovery.
- @vtype int
- @vio in
- @endvar
@returntype int
@returndesc
- -1 if variable has unknown type
- or return code of either
- @seeroutine IOHDF5Util_DumpGS or
- @seeroutine IOHDF5Util_DumpGA
+ -1 if variable has unknown group type
+ or return code of either @seeroutine WriteGS or
+ @seeroutine WriteGA
@endreturndesc
@@*/
-int IOHDF5Util_DumpVar (const cGH *GH,
- int vindex,
- int timelevel,
- const ioHDF5Geo_t *request,
- hid_t file,
- int check_exisiting_objects)
+int IOHDF5Util_DumpVar (const cGH *GH, const ioSlab *slab, hid_t file)
{
- int vtype, gtype;
- pGH *pughGH;
- ioHDF5UtilGH *myGH;
- ioGH *ioUtilGH;
- dumpInfo info;
- int retval;
+ int gtype, retval;
+ char *fullname, *objectname;
- /* Get the handle for PUGH, IOUtil, and IOHDF5Util extensions */
- pughGH = PUGH_pGH (GH);
- ioUtilGH = (ioGH *) CCTK_GHExtension (GH, "IO");
- myGH = (ioHDF5UtilGH *) CCTK_GHExtension (GH, "IOHDF5Util");
+ /* build the unique name for the file object to write */
+ fullname = CCTK_FullName (slab->vindex);
+ objectname = (char *) malloc (strlen (fullname) + 80);
+ sprintf (objectname, "%s timelevel %d at iteration %d",
+ fullname, slab->timelevel, GH->cctk_iteration);
- vtype = CCTK_VarTypeI (vindex);
- /* downgrade the output precision if requested */
- if (ioUtilGH->out_single)
+ /* check whether the object already exists */
+ if (slab->check_exist && file >= 0)
{
- /* Do we only want to downgrade generic CCTK types ? */
-#ifdef CCTK_REAL4
- if (vtype == CCTK_VARIABLE_REAL)
- {
- vtype = CCTK_VARIABLE_REAL4;
- }
- else if (vtype == CCTK_VARIABLE_COMPLEX)
- {
- vtype = CCTK_VARIABLE_COMPLEX8;
- }
-#endif
-#ifdef CCTK_INT4
- if (vtype == CCTK_VARIABLE_INT)
+ H5E_BEGIN_TRY
{
- vtype = CCTK_VARIABLE_INT4;
- }
-#endif
- }
- info.element_size = CCTK_VarTypeSize (vtype);
-#ifdef CCTK_MPI
- info.mpi_type = PUGH_MPIDataType (pughGH, vtype);
-#endif
- info.iohdf5_type = IOHDF5Util_DataType (myGH, vtype);
-
- if (info.element_size <= 0 ||
-#ifdef CCTK_MPI
- info.mpi_type == MPI_DATATYPE_NULL ||
-#endif
- info.iohdf5_type < 0)
- {
- CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
- "Unsupported variable type %d", vtype);
- return (-1);
+ H5Gunlink (file, objectname);
+ } H5E_END_TRY;
}
- /* now branch to the appropriate dump routine */
- gtype = CCTK_GroupTypeFromVarI (vindex);
+ /* branch to the appropriate dump routine */
+ gtype = CCTK_GroupTypeFromVarI (slab->vindex);
if (gtype == CCTK_SCALAR)
{
- retval = IOHDF5Util_DumpGS (GH, vindex, timelevel, info.iohdf5_type,
- request, check_exisiting_objects, file);
+ retval = WriteGS (GH, slab, objectname, file);
}
else if (gtype == CCTK_ARRAY || gtype == CCTK_GF)
{
- retval = IOHDF5Util_DumpGA (GH, vindex, timelevel, request, &info,
- check_exisiting_objects, file);
+ retval = WriteGA (GH, slab, objectname, file);
}
else
{
CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
- "Invalid group type %d", gtype);
+ "Invalid group type %d for variable '%s'", gtype, fullname);
retval = -1;
}
+ /* clean up */
+ free (objectname);
+ free (fullname);
+
return (retval);
}
+/********************************************************************
+ ******************** Internal Routines ************************
+ ********************************************************************/
/*@@
- @routine IOHDF5Util_DumpGS
+ @routine WriteGS
@date May 21 1999
@author Thomas Radke
@desc
- Dumps a CCTK_SCALAR type variable into a HDF5 file.
- @enddesc
+ Writes a CCTK_SCALAR type variable into a HDF5 file.
+ @enddesc
@var GH
- @vdesc Pointer to CCTK grid hierarchy
+ @vdesc pointer to CCTK grid hierarchy
@vtype const cGH *
@vio in
@endvar
- @var vindex
- @vdesc index of the variable to be dumped
- @vtype int
- @vio in
- @endvar
- @var timelevel
- @vdesc the timelevel to dump
- @vtype int
- @vio in
- @endvar
- @var iohdf5_type
- @vdesc the HDF5 datatype
- @vtype int
- @vio in
- @endvar
- @var request
- @vdesc pointer to the IO request structure
- @vtype const ioHDF5Geo_t *
+ @var slab
+ @vdesc reference to the I/O hyperslab description
+ @vtype const ioSlab *
@vio in
@endvar
- @var check_exisiting_objects
- @vdesc flag indicating if we should check for already existing objects
- before these are created anew
- This might happen for existing files reopened after recovery.
- @vtype int
+ @var name
+ @vdesc name of the dataset to write
+ @vtype const char *
@vio in
@endvar
@var file
@@ -272,113 +167,68 @@ int IOHDF5Util_DumpVar (const cGH *GH,
0 for success, or -1 if file handle is invalid
@endreturndesc
@@*/
-static int IOHDF5Util_DumpGS (const cGH *GH,
- int vindex,
- int timelevel,
- int iohdf5_type,
- const ioHDF5Geo_t *request,
- int check_exisiting_objects,
- hid_t file)
+static int WriteGS (const cGH *GH, const ioSlab *slab, const char *name,
+ hid_t file)
{
ioGH *ioUtilGH;
ioHDF5UtilGH *myGH;
- hid_t dataset;
- char *fullname;
- char *datasetname;
- static CCTK_INT global_shape[1] = {0};
-
+ hid_t dataset, hdf5type;
- /* immediately return if file handle is invalid */
- if (file < 0)
- {
- return (-1);
- }
- /* Get the handles for IOHDF5Util and IOUtil extensions */
ioUtilGH = (ioGH *) CCTK_GHExtension (GH, "IO");
myGH = (ioHDF5UtilGH *) CCTK_GHExtension (GH, "IOHDF5Util");
+ /* only I/O processors write data */
if (CCTK_MyProc (GH) != ioUtilGH->ioproc)
{
return (0);
}
- fullname = CCTK_FullName (vindex);
- datasetname = (char *) malloc (strlen (fullname) + 80);
- sprintf (datasetname, "%s timelevel %d at iteration %d",
- fullname, timelevel, GH->cctk_iteration);
-
- /* if restart from recovery delete an already existing dataset
- so that it can be created as anew */
- if (check_exisiting_objects)
+ /* check if file handle is invalid */
+ if (file < 0)
{
- IOHDF5_ERROR (H5Eset_auto (NULL, NULL));
- H5Gunlink (file, datasetname);
- IOHDF5_ERROR (H5Eset_auto (myGH->print_error_fn, myGH->print_error_fn_arg));
+ return (-1);
}
- IOHDF5_ERROR (dataset = H5Dcreate (file, datasetname, iohdf5_type,
- myGH->scalar_dataspace, H5P_DEFAULT));
- IOHDF5_ERROR (H5Dwrite (dataset, iohdf5_type, H5S_ALL, H5S_ALL, H5P_DEFAULT,
- CCTK_VarDataPtrI (GH, timelevel, vindex)));
-
- IOHDF5Util_DumpCommonAttributes (GH, vindex, timelevel, global_shape,
- request, dataset);
+ hdf5type = IOHDF5Util_DataType (myGH, slab->hdatatype);
+ HDF5_ERROR (dataset = H5Dcreate (file, name, hdf5type, myGH->scalar_dataspace,
+ H5P_DEFAULT));
+ HDF5_ERROR (H5Dwrite (dataset, hdf5type, H5S_ALL, H5S_ALL, H5P_DEFAULT,
+ CCTK_VarDataPtrI (GH, slab->timelevel, slab->vindex)));
- IOHDF5_ERROR (H5Dclose (dataset));
+ IOHDF5Util_DumpCommonAttributes (GH, slab, dataset);
- free (datasetname);
- free (fullname);
+ HDF5_ERROR (H5Dclose (dataset));
return (0);
}
/*@@
- @routine IOHDF5Util_DumpGA
+ @routine WriteGA
@date May 21 1999
@author Paul Walker
@desc
- Dumps a CCTK_GF or CCTK_ARRAY type variable into a HDF5 file.
- @enddesc
+ Writes a grid array into a HDF5 file.
+ @enddesc
- @calls IOHDF5Util_getDumpData
- IOHDF5Util_procDump
- IOHDF5Util_collectiveDump
+ @calls GetLocalHyperslab
+ WriteData
+ WriteDataCollective
@var GH
- @vdesc Pointer to CCTK grid hierarchy
+ @vdesc pointer to CCTK grid hierarchy
@vtype const cGH *
@vio in
@endvar
- @var vindex
- @vdesc index of the variable to be dumped
- @vtype int
- @vio in
- @endvar
- @var timelevel
- @vdesc the timelevel to dump
- @vtype int
- @vio in
- @endvar
- @var request
- @vdesc pointer to the IO request structure
- @vtype const ioHDF5Geo_t *
- @vio in
- @endvar
- @var info
- @vdesc info structure describing
- - the HDF5 datatype to store
- - the size of an element of variable
- - the MPI datatype to communicate
- @vtype const dumpInfo *
+ @var slab
+ @vdesc reference to the I/O hyperslab description
+ @vtype const ioSlab *
@vio in
@endvar
- @var check_exisiting_objects
- @vdesc flag indicating if we should check for already existing objects
- before these are created anew
- This might happen for existing files reopened after recovery.
- @vtype int
+ @var name
+ @vdesc name of the dataset to write
+ @vtype const char *
@vio in
@endvar
@var file
@@ -390,45 +240,36 @@ static int IOHDF5Util_DumpGS (const cGH *GH,
@returntype int
@returndesc
0 for success
- or returncode of @seeroutine IOHDF5Util_getDumpData
+ or returncode of @seeroutine GetLocalHyperslab
@endreturndesc
@@*/
-static int IOHDF5Util_DumpGA (const cGH *GH,
- int vindex,
- int timelevel,
- const ioHDF5Geo_t *request,
- const dumpInfo *info,
- int check_exisiting_objects,
- hid_t file)
+static int WriteGA (const cGH *GH, const ioSlab *slab, const char *name,
+ hid_t file)
{
ioGH *ioUtilGH;
- pGH *pughGH;
- int myproc;
- int nprocs;
- CCTK_INT *geom; /* Lower bounds, sizes and global shape of data */
- void *outme; /* The data pointer to dump ... */
- int free_outme; /* and whether it needs freeing */
- int retval;
+ ioHDF5UtilGH *myGH;
+ int myproc, nprocs, retval;
+ void *data; /* The data pointer to dump ... */
+ int free_data; /* and whether it needs freeing */
#ifdef CCTK_MPI
void *tmpd;
- int incoming;
- int outgoing;
- int i, j;
+ int i, j, incoming, outgoing;
+ MPI_Comm comm;
MPI_Status ms;
+ MPI_Datatype mpitype;
#endif
DECLARE_CCTK_PARAMETERS
- /* Get the handles for PUGH and IOUtil extensions */
- pughGH = PUGH_pGH (GH);
+ myGH = (ioHDF5UtilGH *) CCTK_GHExtension (GH, "IOHDF5Util");
ioUtilGH = (ioGH *) CCTK_GHExtension (GH, "IO");
- /* allocate the geometry buffer */
- geom = (CCTK_INT *) malloc (3 * request->sdim * sizeof (CCTK_INT));
-
- /* Get the pointer to the data we want to output (includes downsampling) */
- retval = IOHDF5Util_getDumpData (GH, vindex, timelevel, request, &outme,
- &free_outme, geom);
+#ifdef CCTK_MPI
+ mpitype = PUGH_MPIDataType (PUGH_pGH (GH), slab->hdatatype);
+#endif
+
+ /* get the pointer to the data we want to output (includes downsampling) */
+ retval = GetLocalHyperslab (GH, slab, &data, &free_data);
if (retval < 0)
{
return (retval);
@@ -441,87 +282,82 @@ static int IOHDF5Util_DumpGA (const cGH *GH,
#ifdef H5_HAVE_PARALLEL
if (ioUtilGH->unchunked)
{
- IOHDF5Util_collectiveDump (GH, vindex, timelevel, request, outme, geom,
- info->iohdf5_type, check_exisiting_objects,file);
- if (free_outme)
+ WriteDataCollective (GH, slab, name, data, file);
+ if (free_data)
{
- free (outme);
+ free (data);
}
- free (geom);
return (0);
}
#endif
#endif
- /* Dump data held on IO processor */
+ /* dump data held on I/O processor */
if (myproc == ioUtilGH->ioproc)
{
- IOHDF5Util_procDump (GH, vindex, timelevel, request, outme, geom,
- myproc, info->iohdf5_type, check_exisiting_objects,
- file);
+ WriteData (GH, slab, name, data, myproc, file);
}
#ifdef CCTK_MPI
+ comm = PUGH_pGH (GH)->PUGH_COMM_WORLD;
if (myproc == ioUtilGH->ioproc)
{
- /* Dump data from all other processors */
+ /* dump data from all other processors */
for (i = myproc+1; i < myproc+ioUtilGH->ioproc_every && i < nprocs; i++)
{
- /* receive geometry */
- CACTUS_MPI_ERROR (MPI_Recv (geom, 3*request->sdim, PUGH_MPI_INT, i,
- 2*i + IOTAGBASE + 1, pughGH->PUGH_COMM_WORLD,
- &ms));
+ /* receive geometry (this assumes the geometry arrays
+ to be contiguous starting at hoffset */
+ CACTUS_MPI_ERROR (MPI_Recv (slab->hoffset, 3*slab->hdim, PUGH_MPI_INT, i,
+ 2*i + MPITAGBASE + 1, comm, &ms));
- incoming = geom[request->sdim];
- for (j = 1; j < request->sdim; j++)
+ incoming = 1;
+ for (j = 0; j < slab->hdim; j++)
{
- incoming *= geom[request->sdim + j];
+ incoming *= slab->hsize_chunk[slab->hdim + j];
}
/* receive data */
+ tmpd = NULL;
if (incoming > 0)
{
- tmpd = malloc (incoming * info->element_size);
- CACTUS_MPI_ERROR (MPI_Recv (tmpd, incoming, info->mpi_type, i,
- 2*i + IOTAGBASE, pughGH->PUGH_COMM_WORLD,
- &ms));
+ tmpd = malloc (incoming * CCTK_VarTypeSize (slab->hdatatype));
+ CACTUS_MPI_ERROR (MPI_Recv (tmpd, incoming, mpitype, i,
+ 2*i + MPITAGBASE, comm, &ms));
}
- else
- {
- tmpd = NULL;
- }
- IOHDF5Util_procDump (GH, vindex, timelevel, request, tmpd, geom, i,
- info->iohdf5_type, check_exisiting_objects, file);
+
+ /* write data */
+ WriteData (GH, slab, name, tmpd, i, file);
+
if (tmpd)
{
free (tmpd);
}
- } /* End loop over processors */
+ } /* end loop over processors */
}
else
{
-
- /* Send the geometry and data from the non-IO processors
- * to the IO processors
+ /*
+ * send the geometry and data from non-I/O processors to the I/O processors
*/
- outgoing = geom[request->sdim];
- for (i = 1; i < request->sdim; i++)
+ outgoing = 1;
+ for (i = 0; i < slab->hdim; i++)
{
- outgoing *= geom[request->sdim + i];
+ outgoing *= slab->hsize_chunk[slab->hdim + i];
}
- /* send geometry */
- CACTUS_MPI_ERROR (MPI_Send (geom, 3*request->sdim, PUGH_MPI_INT,
- ioUtilGH->ioproc, 2*myproc + IOTAGBASE + 1,
- pughGH->PUGH_COMM_WORLD));
+ /* send geometry (this assumes the geometry arrays
+ to be contiguous starting at hoffset */
+ CACTUS_MPI_ERROR (MPI_Send (slab->hoffset, 3*slab->hdim, PUGH_MPI_INT,
+ ioUtilGH->ioproc, 2*myproc + MPITAGBASE + 1,
+ comm));
+ /* send data */
if (outgoing > 0)
{
- /* send data if outgoing>0 */
- CACTUS_MPI_ERROR (MPI_Send (outme, outgoing, info->mpi_type,
- ioUtilGH->ioproc, 2*myproc + IOTAGBASE,
- pughGH->PUGH_COMM_WORLD));
-#ifdef DEBUG_ME
+ CACTUS_MPI_ERROR (MPI_Send (data, outgoing, mpitype,
+ ioUtilGH->ioproc, 2*myproc + MPITAGBASE,
+ comm));
+#ifdef IOHDF5UTIL_DEBUG
printf ("Processor %d sent %d data points\n", myproc, outgoing);
#endif
}
@@ -532,118 +368,95 @@ static int IOHDF5Util_DumpGA (const cGH *GH,
#endif
/* free allocated resources */
- if (free_outme)
+ if (free_data)
{
- free (outme);
+ free (data);
}
- free (geom);
return (retval);
}
-/**************************************************************************/
-/* local functions */
-/**************************************************************************/
-static int IOHDF5Util_getDumpData (const cGH *GH,
- int vindex,
- int timelevel,
- const ioHDF5Geo_t *request,
- void **outme,
- int *free_outme,
- CCTK_INT *geom)
+static int GetLocalHyperslab (const cGH *GH, const ioSlab *slab, void **data,
+ int *free_data)
{
int i, retval;
- int cctk_output_type;
- ioGH *ioUtilGH;
- int *hsizes, *hsizes_global, *hsizes_offset; /* geometry information */
char *fullname;
-
-
- /* get GH extension for IOUtil */
- ioUtilGH = (ioGH *) CCTK_GHExtension (GH, "IO");
-
- /* determine the datatype for the hyperslab */
- cctk_output_type = CCTK_VarTypeI (vindex);
- if (ioUtilGH->out_single)
- {
-#ifdef CCTK_INT4
- if (cctk_output_type == CCTK_VARIABLE_INT)
- {
- cctk_output_type = CCTK_VARIABLE_INT4;
- }
-#endif
-#ifdef CCTK_REAL4
- if (cctk_output_type == CCTK_VARIABLE_REAL)
- {
- cctk_output_type = CCTK_VARIABLE_REAL4;
- }
- else if (cctk_output_type == CCTK_VARIABLE_COMPLEX)
- {
- cctk_output_type = CCTK_VARIABLE_COMPLEX8;
- }
-#endif
- }
- /* FIXME */
- /* allocate array to hold size information of request */
- hsizes = (int *) malloc (3 * request->sdim * sizeof (int));
- hsizes_global = hsizes + 1*request->sdim;
- hsizes_offset = hsizes + 2*request->sdim;
#if 0
- FIXME: what is this for ???
- /* Get the start indeces for the request from origin. */
- /* Slab_start from the geo structure is not a true start index,
- it is currently used as the intersection point of three surfaces,
- that's why two entries have to be set to zero in the case of a
- surface (one entry for line)
- FIXME */
- for (i = 0; i < vdim; i++)
+ mapping = Hyperslab_DefineLocalMappingByIndex (GH, vindex, slab->hdim,
+ slab->direction, slab->origin,
+ slab->extent, slab->downsample,
+ -1, NULL, slab->hsize_local,
+ slab->hsize_global,
+ slab->hoffset_global);
+ const cGH *GH,
+ CCTK_INT vindex,
+ CCTK_INT hdim,
+ const CCTK_INT *direction /* vdim*hdim */,
+ const CCTK_INT *origin /* vdim */,
+ const CCTK_INT *extent /* hdim */,
+ const CCTK_INT *downsample /* hdim */,
+ CCTK_INT table_handle,
+ t_hslabConversionFn conversion_fn,
+ CCTK_INT *hsize_local, /* hdim */
+ CCTK_INT *hsize_global, /* hdim */
+ CCTK_INT *hoffset_global /* hdim */);
+
+ if (mapping < 0)
{
- slabstart[i] = request->origin[i];
+ fullname = CCTK_FullName (vindex);
+ CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
+ "Failed to extract hyperslab for variable '%s'", fullname);
+ free (fullname);
}
- for (i = 0; i < request->sdim; i++)
- {
- slabstart[request->direction[i]] = 0;
- }
-#endif
- retval = NewHyperslab_GetLocalHyperslab (GH, vindex, timelevel, request->sdim,
- cctk_output_type, NULL, request->origin,
- request->direction, request->length,
- request->downsample, outme, free_outme,
+#else
+{
+ int *hsizes, *hsizes_global, *hsizes_offset; /* geometry information */
+
+ /* allocate array to hold size information of request */
+ hsizes = (int *) malloc (3 * slab->hdim * sizeof (int));
+ hsizes_global = hsizes + 1*slab->hdim;
+ hsizes_offset = hsizes + 2*slab->hdim;
+
+ retval = NewHyperslab_GetLocalHyperslab (GH, slab->vindex, slab->timelevel, slab->hdim,
+ slab->hdatatype, NULL, slab->origin,
+ slab->direction, slab->extent,
+ slab->downsample, data, free_data,
hsizes, hsizes_global, hsizes_offset);
if (retval == 0)
{
- for (i = 0; i < request->sdim; i++)
+ for (i = 0; i < slab->hdim; i++)
{
- geom[i + 0*request->sdim] = hsizes_offset[i];
- geom[i + 1*request->sdim] = hsizes[i];
- geom[i + 2*request->sdim] = hsizes_global[i];
- request->actlen[i] = hsizes_global[i];
+ slab->hoffset[i] = hsizes_offset[i];
+ slab->hsize[i] = hsizes_global[i];
+ slab->hsize_chunk[i] = hsizes[i];
}
}
else
{
- fullname = CCTK_FullName (vindex);
+ fullname = CCTK_FullName (slab->vindex);
CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
"Failed to extract hyperslab for variable '%s'", fullname);
free (fullname);
}
free (hsizes);
+}
+#endif
return (retval);
}
/*@@
- @routine IOHDF5Util_procDump
+ @routine WriteData
@author Thomas Radke
@date May 21 1999
@desc
- All IO processors dump the data of their group into the file,
+ All I/O processors dump the data of their group into the file,
either as one chunk per processor or unchunked
(depending on parameter "unchunked").
@enddesc
@@ -651,78 +464,44 @@ static int IOHDF5Util_getDumpData (const cGH *GH,
@calls IOHDF5Util_DumpCommonAttributes
@var GH
- @vdesc Pointer to CCTK grid hierarchy
+ @vdesc pointer to CCTK grid hierarchy
@vtype const cGH *
@vio in
@endvar
- @var vindex
- @vdesc global index of the variable to be dumped
- @vtype int
- @vio in
- @endvar
- @var timelevel
- @vdesc the timelevel to store
- @vtype int
+ @var slab
+ @vdesc reference to the I/O hyperslab description
+ @vtype const ioSlab *
@vio in
@endvar
- @var request
- @vdesc pointer to the IO request structure
- @vtype const ioHDF5Geo_t *
+ @var name
+ @vdesc name of the dataset to write
+ @vtype const char *
@vio in
@endvar
- @var outme
+ @var data
@vdesc pointer to the chunk to dump
@vtype const void *
@vio in
@endvar
- @var geom
- @vdesc bounds and sizes of the output
- @vtype const CCTK_INT[3*dim]
- @vio in
- @vcomment geom[0*dim..1*dim-1]: lower bounds
- geom[1*dim..2*dim-1]: (local) data sizes
- geom[2*dim..3*dim-1]: global space
- @endvar
@var proc
@vdesc the processor which's chunk is to be dumped
@vtype int
@vio in
@endvar
- @var hdf5io_type
- @vdesc the HDF5 datatype identifier
- @vtype int
- @vio in
- @endvar
- @var check_exisiting_objects
- @vdesc flag indicating if we should check for already existing objects
- before these are created anew
- This might happen for existing files reopened after recovery.
- @vtype int
- @vio in
- @endvar
@var file
@vdesc the HDF5 file handle
@vtype hid_t
@vio in
@endvar
@@*/
-static void IOHDF5Util_procDump (const cGH *GH,
- int vindex,
- int timelevel,
- const ioHDF5Geo_t *request,
- const void *outme,
- const CCTK_INT *geom,
- int proc,
- int iohdf5_type,
- int check_exisiting_objects,
- hid_t file)
+static void WriteData (const cGH *GH, const ioSlab *slab, const char *name,
+ const void *data, int proc, hid_t file)
{
- int i, sdim;
- int myproc;
+ int i, myproc;
ioGH *ioUtilGH;
ioHDF5UtilGH *myGH;
- hid_t group, dataset, memspace, filespace, plist;
- char *fullname, *datasetname, *chunkname;
+ hid_t hdf5type, group, dataset, memspace, filespace, plist;
+ char *chunkname;
hssize_t *chunk_origin;
hsize_t *chunk_dims, *file_dims;
hsize_t buffersize;
@@ -738,160 +517,132 @@ static void IOHDF5Util_procDump (const cGH *GH,
ioUtilGH = (ioGH *) CCTK_GHExtension (GH, "IO");
myGH = (ioHDF5UtilGH *) CCTK_GHExtension (GH, "IOHDF5Util");
- sdim = request->sdim;
- myproc = CCTK_MyProc (GH);
-
- chunk_origin = (hssize_t *) malloc (sdim * sizeof (hssize_t));
- chunk_dims = (hsize_t *) malloc (2*sdim * sizeof (hsize_t));
- file_dims = chunk_dims + sdim;
-
- /* HDF5 needs it in reverse order */
- for (i = 0; i < sdim; i++)
+ /* copy the size arrays from CCTK_INT to appropriate types
+ note that HDF5 wants elements in reverse order */
+ chunk_origin = (hssize_t *) malloc (slab->hdim * sizeof (hssize_t));
+ chunk_dims = (hsize_t *) malloc (2*slab->hdim * sizeof (hsize_t));
+ file_dims = chunk_dims + slab->hdim;
+ for (i = 0; i < slab->hdim; i++)
{
- chunk_origin[i] = geom[1*sdim - 1 - i];
- chunk_dims [i] = geom[2*sdim - 1 - i];
- file_dims [i] = geom[3*sdim - 1 - i];
+ chunk_origin[i] = slab->hoffset[slab->hdim - 1 - i];
+ file_dims [i] = slab->hsize[slab->hdim - 1 - i];
+ chunk_dims [i] = slab->hsize_chunk[slab->hdim - 1 - i];
}
- /* build the unique dataset name from the variable's full name,
- the timelevel and the current iteration number */
- fullname = CCTK_FullName (vindex);
- datasetname = (char *) malloc (strlen (fullname) + 80);
- sprintf (datasetname, "%s timelevel %d at iteration %d",
- fullname, timelevel, GH->cctk_iteration);
-
- /* if restart from recovery delete an already existing dataset
- so that it can be created as anew */
- if (proc == myproc && check_exisiting_objects)
- {
- IOHDF5_ERROR (H5Eset_auto (NULL, NULL));
- H5Gunlink (file, datasetname);
- IOHDF5_ERROR (H5Eset_auto (myGH->print_error_fn, myGH->print_error_fn_arg));
- }
+ myproc = CCTK_MyProc (GH);
- if (outme)
+ memspace = -1;
+ if (data)
{
/* create the memspace according to chunk dims */
- IOHDF5_ERROR (memspace = H5Screate_simple (sdim, chunk_dims, NULL));
- }
- else
- {
- memspace = -1;
+ HDF5_ERROR (memspace = H5Screate_simple (slab->hdim, chunk_dims, NULL));
}
+ hdf5type = IOHDF5Util_DataType (myGH, slab->hdatatype);
if (ioUtilGH->unchunked)
{
/* create the (global) filespace and set the hyperslab for the chunk */
- IOHDF5_ERROR (filespace = H5Screate_simple (sdim, file_dims, NULL));
- IOHDF5_ERROR (H5Sselect_hyperslab (filespace, H5S_SELECT_SET,
- chunk_origin, NULL, chunk_dims, NULL));
-
- /* the IO processor creates the dataset and adds the common attributes
+ HDF5_ERROR (filespace = H5Screate_simple (slab->hdim, file_dims, NULL));
+ HDF5_ERROR (H5Sselect_hyperslab (filespace, H5S_SELECT_SET, chunk_origin,
+ NULL, chunk_dims, NULL));
+
+ /* the I/O processor creates the dataset and adds the common attributes
when writing its own data, otherwise the dataset is reopened */
if (proc == myproc)
{
- IOHDF5_ERROR (plist = H5Pcreate (H5P_DATASET_CREATE));
+ HDF5_ERROR (plist = H5Pcreate (H5P_DATASET_CREATE));
/* enable compression for chunked dataset if compression was requested */
if (compression_level)
{
- IOHDF5_ERROR (H5Pset_chunk (plist, sdim, chunk_dims));
- IOHDF5_ERROR (H5Pset_deflate (plist, compression_level));
+ HDF5_ERROR (H5Pset_chunk (plist, slab->hdim, chunk_dims));
+ HDF5_ERROR (H5Pset_deflate (plist, compression_level));
}
- IOHDF5_ERROR (dataset = H5Dcreate (file, datasetname,
- iohdf5_type, filespace, plist));
- IOHDF5_ERROR (H5Pclose (plist));
- IOHDF5Util_DumpCommonAttributes (GH, vindex, timelevel, &geom[2*sdim],
- request, dataset);
+ HDF5_ERROR (dataset = H5Dcreate (file, name, hdf5type, filespace, plist));
+ HDF5_ERROR (H5Pclose (plist));
+ IOHDF5Util_DumpCommonAttributes (GH, slab, dataset);
}
else
{
- IOHDF5_ERROR (dataset = H5Dopen (file, datasetname));
+ HDF5_ERROR (dataset = H5Dopen (file, name));
}
if (memspace >= 0)
{
/* increase the buffer size if the default isn't sufficient */
- IOHDF5_ERROR (plist = H5Pcreate (H5P_DATASET_XFER));
+ HDF5_ERROR (plist = H5Pcreate (H5P_DATASET_XFER));
buffersize = H5Dget_storage_size (dataset);
if (buffersize > H5Pget_buffer (plist, NULL, NULL))
{
- IOHDF5_ERROR (H5Pset_buffer (plist, buffersize, NULL, NULL));
+ HDF5_ERROR (H5Pset_buffer (plist, buffersize, NULL, NULL));
}
/* write the data */
- IOHDF5_ERROR (H5Dwrite (dataset, iohdf5_type, memspace, filespace,
- plist, outme));
+ HDF5_ERROR (H5Dwrite (dataset, hdf5type, memspace, filespace, plist,
+ data));
/* close the transfer property list */
- IOHDF5_ERROR (H5Pclose (plist));
+ HDF5_ERROR (H5Pclose (plist));
}
/* close the file dataspace */
- IOHDF5_ERROR (H5Sclose (filespace));
+ HDF5_ERROR (H5Sclose (filespace));
}
else
{
- /* the IO processor creates the chunk group and adds common attributes */
+ /* the I/O processor creates the chunk group and adds common attributes */
if (proc == myproc)
{
- IOHDF5_ERROR (group = H5Gcreate (file, datasetname, 0));
- IOHDF5Util_DumpCommonAttributes (GH, vindex, timelevel, &geom[2*sdim],
- request, group);
- IOHDF5_ERROR (H5Gclose (group));
+ HDF5_ERROR (group = H5Gcreate (file, name, 0));
+ IOHDF5Util_DumpCommonAttributes (GH, slab, group);
+ HDF5_ERROR (H5Gclose (group));
}
+ dataset = -1;
if (memspace >= 0)
{
/* now the chunk dataset for each processor is created within the group */
- chunkname = (char *) malloc (strlen (datasetname) + 20);
- sprintf (chunkname, "%s/chunk%d", datasetname, proc - myproc);
- IOHDF5_ERROR (plist = H5Pcreate (H5P_DATASET_CREATE));
+ chunkname = (char *) malloc (strlen (name) + 20);
+ sprintf (chunkname, "%s/chunk%d", name, proc - myproc);
+ HDF5_ERROR (plist = H5Pcreate (H5P_DATASET_CREATE));
/* enable compression for chunked dataset if compression was requested */
if (compression_level)
{
- IOHDF5_ERROR (H5Pset_chunk (plist, sdim, chunk_dims));
- IOHDF5_ERROR (H5Pset_deflate (plist, compression_level));
- }
+ HDF5_ERROR (H5Pset_chunk (plist, slab->hdim, chunk_dims));
+ HDF5_ERROR (H5Pset_deflate (plist, compression_level));
+ }
/* create the chunk dataset and dump the chunk data */
- IOHDF5_ERROR (dataset = H5Dcreate (file, chunkname,
- iohdf5_type, memspace, plist));
- IOHDF5_ERROR (H5Pclose (plist));
- IOHDF5_ERROR (H5Dwrite (dataset, iohdf5_type, H5S_ALL, H5S_ALL,
- H5P_DEFAULT, outme));
+ HDF5_ERROR (dataset = H5Dcreate (file, chunkname, hdf5type, memspace,
+ plist));
+ HDF5_ERROR (H5Pclose (plist));
+ HDF5_ERROR (H5Dwrite (dataset, hdf5type, H5S_ALL, H5S_ALL, H5P_DEFAULT,
+ data));
/* add the "origin" attribute for the chunk */
- WRITE_ATTRIBUTE ("chunk_origin", geom, dataset, myGH->array_dataspace,
- sdim, IOHDF5_INT);
+ WRITE_ATTRIBUTE ("chunk_origin", slab->hoffset, dataset, myGH, slab->hdim,
+ HDF5_INT);
free (chunkname);
}
- else
- {
- dataset = -1;
- }
}
/* close the dataset and the memspace */
if (dataset >= 0)
{
- IOHDF5_ERROR (H5Dclose (dataset));
+ HDF5_ERROR (H5Dclose (dataset));
}
if (memspace >= 0)
{
- IOHDF5_ERROR (H5Sclose (memspace));
+ HDF5_ERROR (H5Sclose (memspace));
}
/* free allocated resources */
- free (datasetname);
- free (fullname);
free (chunk_origin);
free (chunk_dims);
}
-#ifdef CCTK_MPI
-#ifdef H5_HAVE_PARALLEL
+#if defined(CCTK_MPI) && defined(H5_HAVE_PARALLEL)
/*@@
- @routine IOHDF5Util_collectiveDump
+ @routine WriteDataCollective
@author Thomas Radke
@date May 21 1999
@desc
@@ -901,70 +652,36 @@ static void IOHDF5Util_procDump (const cGH *GH,
@calls IOHDF5Util_DumpCommonAttributes
@var GH
- @vdesc Pointer to CCTK grid hierarchy
+ @vdesc pointer to CCTK grid hierarchy
@vtype const cGH *
@vio in
@endvar
- @var vindex
- @vdesc global index of the variable to be dumped
- @vtype int
+ @var slab
+ @vdesc reference to the I/O hyperslab description
+ @vtype const ioSlab *
@vio in
@endvar
- @var timelevel
- @vdesc the timelevel to store
- @vtype int
+ @var name
+ @vdesc name of the dataset to write
+ @vtype const char *
@vio in
@endvar
- @var request
- @vdesc pointer to the IO request structure
- @vtype const ioHDF5Geo_t *
- @vio in
- @endvar
- @var outme
+ @var data
@vdesc pointer to the chunk to dump
@vtype const void *
@vio in
@endvar
- @var geom
- @vdesc bounds and sizes of the output
- @vtype const CCTK_INT[3*dim]
- @vio in
- @vcomment geom[0*dim..1*dim-1]: lower bounds
- geom[1*dim..2*dim-1]: (local) data sizes
- geom[2*dim..3*dim-1]: global space
- @endvar
- @var hdf5io_type
- @vdesc the HDF5 datatype identifier
- @vtype int
- @vio in
- @endvar
- @var check_exisiting_objects
- @vdesc flag indicating if we should check for already existing objects
- before these are created anew
- This might happen for existing files reopened after recovery.
- @vtype int
- @vio in
- @endvar
@var file
@vdesc the HDF5 file handle
@vtype hid_t
@vio in
@endvar
@@*/
-static void IOHDF5Util_collectiveDump (const cGH *GH,
- int vindex,
- int timelevel,
- const ioHDF5Geo_t *request,
- const void *outme,
- const CCTK_INT *geom,
- int hdf5io_type,
- int check_exisiting_objects,
- hid_t file)
+static void WriteDataCollective (const cGH *GH, const ioSlab *slab,
+ const char *name, const void *data, hid_t file)
{
int i, dim;
- ioHDF5UtilGH *myGH;
- hid_t dataset, memspace, filespace, plist;
- char *fullname, *datasetname;
+ hid_t hdf5type, dataset, memspace, filespace, plist;
hssize_t *chunk_origin;
hsize_t *chunk_dims, *file_dims;
hsize_t buffersize;
@@ -977,84 +694,63 @@ static void IOHDF5Util_collectiveDump (const cGH *GH,
return;
}
- myGH = (ioHDF5UtilGH *) CCTK_GHExtension (GH, "IOHDF5Util");
-
- /* get the dimension of the variable */
- chunk_origin = (hssize_t *) malloc (request->sdim * sizeof (hssize_t));
- chunk_dims = (hsize_t *) malloc (2*request->sdim * sizeof (hsize_t));
- file_dims = chunk_dims + request->sdim;
-
- /* HDF5 needs it in reverse order */
- for (i = 0; i < request->sdim; i++)
+ /* copy the size arrays from CCTK_INT to appropriate types
+ note that HDF5 wants elements in reverse order */
+ chunk_origin = (hssize_t *) malloc (slab->hdim * sizeof (hssize_t));
+ chunk_dims = (hsize_t *) malloc (2*slab->hdim * sizeof (hsize_t));
+ file_dims = chunk_dims + slab->hdim;
+ for (i = 0; i < slab->hdim; i++)
{
- chunk_origin[i] = geom[1*request->sdim - 1 - i];
- chunk_dims [i] = geom[2*request->sdim - 1 - i];
- file_dims [i] = geom[3*request->sdim - 1 - i];
+ chunk_origin[i] = slab->hoffset[slab->hdim - 1 - i];
+ chunk_dims [i] = slab->hsize_chunk[slab->hdim - 1 - i];
+ file_dims [i] = slab->hsize_global[slab->hdim - 1 - i];
}
- /* build the unique dataset name */
- fullname = CCTK_FullName (vindex);
- datasetname = (char *) malloc (strlen (fullname) + 80);
- sprintf (datasetname, "%s timelevel %d at iteration %d",
- fullname, timelevel, GH->cctk_iteration);
-
/* create the memspace according to chunk dims */
- IOHDF5_ERROR (memspace = H5Screate_simple (request->sdim, chunk_dims, NULL));
+ HDF5_ERROR (memspace = H5Screate_simple (slab->hdim, chunk_dims, NULL));
/* create the (global) filespace and set the hyperslab for the chunk */
- IOHDF5_ERROR (filespace = H5Screate_simple (request->sdim, file_dims, NULL));
- IOHDF5_ERROR (H5Sselect_hyperslab (filespace, H5S_SELECT_SET,
- chunk_origin, NULL, chunk_dims, NULL));
+ HDF5_ERROR (filespace = H5Screate_simple (slab->hdim, file_dims, NULL));
+ HDF5_ERROR (H5Sselect_hyperslab (filespace, H5S_SELECT_SET, chunk_origin,
+ NULL, chunk_dims, NULL));
- /* the IO processor creates the dataset and adds the common attributes
+ /* the I/O processor creates the dataset and adds the common attributes
when writing its own data, otherwise the dataset is reopened */
- /* if restart from recovery delete an already existing group
- so that it can be created as anew */
- if (check_exisiting_objects)
- {
- IOHDF5_ERROR (H5Eset_auto (NULL, NULL));
- H5Gunlink (file, datasetname);
- IOHDF5_ERROR (H5Eset_auto (myGH->print_error_fn, myGH->print_error_fn_arg));
- }
+ hdf5type = IOHDF5Util_DataType (myGH, slab->hdatatype);
+
/* enable compression for chunked dataset if compression was requested */
- IOHDF5_ERROR (plist = H5Pcreate (H5P_DATASET_CREATE));
+ HDF5_ERROR (plist = H5Pcreate (H5P_DATASET_CREATE));
if (compression_level)
{
- IOHDF5_ERROR (H5Pset_chunk (plist, request->sdim, chunk_dims));
- IOHDF5_ERROR (H5Pset_deflate (plist, compression_level));
+ HDF5_ERROR (H5Pset_chunk (plist, slab->hdim, chunk_dims));
+ HDF5_ERROR (H5Pset_deflate (plist, compression_level));
}
- IOHDF5_ERROR (dataset = H5Dcreate (file, datasetname, hdf5io_type, filespace,
- plist));
- IOHDF5_ERROR (H5Pclose (plist));
+ HDF5_ERROR (dataset = H5Dcreate (file, name, hdf5type, filespace, plist));
+ HDF5_ERROR (H5Pclose (plist));
if (CCTK_MyProc (GH) == 0)
{
- IOHDF5Util_DumpCommonAttributes (GH, vindex, timelevel,
- &geom[2*request->sdim], request, dataset);
+ IOHDF5Util_DumpCommonAttributes (GH, slab, dataset);
}
/* increase the buffer size if the default isn't sufficient */
- IOHDF5_ERROR (plist = H5Pcreate (H5P_DATASET_XFER));
+ HDF5_ERROR (plist = H5Pcreate (H5P_DATASET_XFER));
buffersize = H5Dget_storage_size (dataset);
if (buffersize > H5Pget_buffer (plist, NULL, NULL))
{
- IOHDF5_ERROR (H5Pset_buffer (plist, buffersize, NULL, NULL));
+ HDF5_ERROR (H5Pset_buffer (plist, buffersize, NULL, NULL));
}
/* write the data */
- IOHDF5_ERROR (H5Dwrite (dataset, hdf5io_type, memspace, filespace, plist,
- outme));
+ HDF5_ERROR (H5Dwrite (dataset, hdf5type, memspace, filespace, plist, data));
/* close resources */
- IOHDF5_ERROR (H5Pclose (plist));
- IOHDF5_ERROR (H5Sclose (filespace));
- IOHDF5_ERROR (H5Dclose (dataset));
- IOHDF5_ERROR (H5Sclose (memspace));
+ HDF5_ERROR (H5Pclose (plist));
+ HDF5_ERROR (H5Sclose (filespace));
+ HDF5_ERROR (H5Dclose (dataset));
+ HDF5_ERROR (H5Sclose (memspace));
/* free allocated resources */
- free (datasetname);
- free (fullname);
free (chunk_origin);
free (chunk_dims);
}
-#endif /* H5_HAVE_PARALLEL */
-#endif /* MPI */
+#endif /* CCTK_MPI && H5_HAVE_PARALLEL */
diff --git a/src/ParseVars.c b/src/ParseVars.c
index fb70525..de99c3e 100644
--- a/src/ParseVars.c
+++ b/src/ParseVars.c
@@ -10,12 +10,12 @@
#include <stdlib.h>
#include <string.h>
-#include <stdio.h>
#include "cctk.h"
#include "util_String.h"
#include "cctk_Parameters.h"
#include "cctk_GNU.h"
+#include "CactusBase/IOUtil/src/ioGH.h"
#include "ioHDF5UtilGH.h"
@@ -24,13 +24,15 @@ static const char *rcsid = "$Id$";
CCTK_FILEVERSION(BetaThorns_IOHDF5Util_ParseVars_c)
+typedef struct
+{
+ const cGH *GH;
+ ioSlab **slablist;
+} info_t;
+
/* prototypes of routines defined in this source file */
-void IOHDF5Util_ParseVarsForOutput (const char *output_varstring,
- ioHDF5Geo_t *output_request_list[]);
-static void IOHDF5Util_ParseOutputRequest (int vindex,
- const char *optstring,
- void *arg);
-static ioHDF5Geo_t *IOHDF5Util_DefaultIORequest (int vindex);
+static void SetOutputVar (int vindex, const char *optstring, void *arg);
+static ioSlab *DefaultIOHyperslab (const cGH *GH, int vindex);
/* prototypes of external routines for which no header files exist */
int CCTK_RegexMatch (const char *string,
@@ -54,9 +56,8 @@ int CCTK_RegexMatch (const char *string,
special keyword "all" which indicates that output is requested
on all variables.
@enddesc
- @history
- @endhistory
- @var var_list
+
+ @var out_vars
@vdesc list of variables and/or group names
@vtype const char *
@vio in
@@ -67,50 +68,50 @@ int CCTK_RegexMatch (const char *string,
@vio out
@endvar
@@*/
-
-void IOHDF5Util_ParseVarsForOutput (const char *output_varstring,
- ioHDF5Geo_t *output_request_list[])
+void IOHDF5Util_ParseVarsForOutput (const cGH *GH, const char *out_vars,
+ ioSlab *slablist[])
{
int i;
+ info_t info;
- /* free current list of output requests */
+ /* free current list of hyperslabs */
for (i = CCTK_NumVars () - 1; i >= 0; i--)
{
- if (output_request_list[i])
+ if (slablist[i])
{
- free (output_request_list[i]->origin);
- free (output_request_list[i]);
- output_request_list[i] = NULL;
+ free (slablist[i]->vectors);
+ free (slablist[i]);
+ slablist[i] = NULL;
}
}
- /* generate new list of output requests */
- CCTK_TraverseString (output_varstring, IOHDF5Util_ParseOutputRequest,
- output_request_list, CCTK_GROUP_OR_VAR);
+ /* generate new list of hyperslabs */
+ info.GH = GH;
+ info.slablist = slablist;
+ CCTK_TraverseString (out_vars, SetOutputVar, &info, CCTK_GROUP_OR_VAR);
}
-static void IOHDF5Util_ParseOutputRequest (int vindex,
- const char *optstring,
- void *arg)
+static void SetOutputVar (int vindex, const char *optstring, void *arg)
{
+ info_t *info;
regmatch_t gmatch[6], *dmatch;
int i, j, bytes, matched;
char *token, *separator, *fullname;
char *substring, *parsestring, *regexstring;
- ioHDF5Geo_t **output_requests, *new_request;
+ ioSlab *slab;
DECLARE_CCTK_PARAMETERS
- output_requests = (ioHDF5Geo_t **) arg;
+ info = (info_t *) arg;
- /* allocate a new IO request structure and initialize it with defaults */
- new_request = IOHDF5Util_DefaultIORequest (vindex);
+ /* allocate a new I/O hyperslab structure and initialize it with defaults */
+ slab = DefaultIOHyperslab (info->GH, vindex);
if (! optstring)
{
- output_requests[vindex] = new_request;
+ info->slablist[vindex] = slab;
return;
}
@@ -119,7 +120,7 @@ static void IOHDF5Util_ParseOutputRequest (int vindex,
"\\{([0-9]*)\\}" /* dimension */
"\\{([0-9,()]+)*\\}" /* direction */
"\\{([0-9,]+)*\\}" /* origin */
- "\\{([-0-9,]+)*\\}" /* length */
+ "\\{([-0-9,]+)*\\}" /* extent */
"\\{([0-9,]+)*\\}", /* downsample */
6, gmatch);
if (matched <= 0)
@@ -129,7 +130,7 @@ static void IOHDF5Util_ParseOutputRequest (int vindex,
"Couldn't parse hyperslab options '%s' for variable '%s'",
optstring, fullname);
free (fullname);
- free (new_request);
+ free (slab);
return;
}
@@ -137,15 +138,15 @@ static void IOHDF5Util_ParseOutputRequest (int vindex,
bytes = (int) (gmatch[1].rm_eo - gmatch[1].rm_so);
if (gmatch[1].rm_so != -1 && bytes > 0)
{
- new_request->sdim = atoi (optstring + gmatch[1].rm_so);
- if (new_request->sdim <= 0 || new_request->sdim > new_request->vdim)
+ slab->hdim = atoi (optstring + gmatch[1].rm_so);
+ if (slab->hdim <= 0 || slab->hdim > slab->vdim)
{
fullname = CCTK_FullName (vindex);
CCTK_VWarn (2, __LINE__, __FILE__, CCTK_THORNSTRING,
"Invalid dimension given %d in hyperslab options '%s' "
- "for variable '%s'", new_request->sdim, optstring, fullname);
+ "for variable '%s'", slab->hdim, optstring, fullname);
free (fullname);
- free (new_request);
+ free (slab);
return;
}
}
@@ -157,15 +158,15 @@ static void IOHDF5Util_ParseOutputRequest (int vindex,
substring = strdup (optstring + gmatch[2].rm_so);
substring[bytes] = 0;
- dmatch = (regmatch_t *) malloc ((new_request->sdim + 1) *
+ dmatch = (regmatch_t *) malloc ((slab->hdim + 1) *
sizeof (regmatch_t));
- regexstring = (char *) malloc (new_request->sdim * sizeof ("\\(([0-9,]+)\\)"));
+ regexstring = (char *) malloc (slab->hdim * sizeof ("\\(([0-9,]+)\\)"));
regexstring[0] = 0;
- for (i = 0; i < new_request->sdim; i++)
+ for (i = 0; i < slab->hdim; i++)
{
strcat (regexstring, "\\(([0-9,]+)\\)");
}
- matched = CCTK_RegexMatch (substring, regexstring, new_request->sdim + 1,
+ matched = CCTK_RegexMatch (substring, regexstring, slab->hdim + 1,
dmatch);
free (regexstring);
if (matched <= 0)
@@ -176,11 +177,11 @@ static void IOHDF5Util_ParseOutputRequest (int vindex,
"for variable '%s'.", optstring, fullname);
free (fullname);
free (dmatch);
- free (new_request);
+ free (slab);
return;
}
- for (j = 0; j < new_request->sdim; j++)
+ for (j = 0; j < slab->hdim; j++)
{
i = 0;
bytes = (int) (dmatch[j + 1].rm_eo - dmatch[j + 1].rm_so);
@@ -193,25 +194,25 @@ static void IOHDF5Util_ParseOutputRequest (int vindex,
while ((separator = strchr (token, ',')) != NULL)
{
*separator = 0;
- new_request->direction[j * new_request->vdim + i] = atoi (token);
- if (++i >= new_request->vdim)
+ slab->direction[j * slab->vdim + i] = atoi (token);
+ if (++i >= slab->vdim)
{
break;
}
token = separator + 1;
}
- new_request->direction[j * new_request->vdim + i++] = atoi (token);
+ slab->direction[j * slab->vdim + i++] = atoi (token);
free (parsestring);
}
free (substring);
- if (i < new_request->vdim)
+ if (i < slab->vdim)
{
fullname = CCTK_FullName (vindex);
CCTK_VWarn (2, __LINE__, __FILE__, CCTK_THORNSTRING,
"Direction vectors are incomplete or missing in hyperslab "
"options '%s' for variable '%s'.", optstring, fullname);
free (fullname);
- free (new_request);
+ free (slab);
return;
}
}
@@ -229,24 +230,24 @@ static void IOHDF5Util_ParseOutputRequest (int vindex,
while ((separator = strchr (token, ',')) != NULL)
{
*separator = 0;
- new_request->origin[i] = atoi (token);
- if (++i >= new_request->vdim)
+ slab->origin[i] = atoi (token);
+ if (++i >= slab->vdim)
{
break;
}
token = separator + 1;
}
- new_request->origin[i++] = atoi (token);
+ slab->origin[i++] = atoi (token);
free (substring);
- if (i < new_request->vdim)
+ if (i < slab->vdim)
{
fullname = CCTK_FullName (vindex);
CCTK_VWarn (2, __LINE__, __FILE__, CCTK_THORNSTRING,
"Origin vector is incomplete or missing in hyperslab "
"options '%s' for variable '%s'.", optstring, fullname);
free (fullname);
- free (new_request);
+ free (slab);
return;
}
}
@@ -263,24 +264,24 @@ static void IOHDF5Util_ParseOutputRequest (int vindex,
while ((separator = strchr (token, ',')) != NULL)
{
*separator = 0;
- new_request->length[i] = atoi (token);
- if (++i >= new_request->sdim)
+ slab->extent[i] = atoi (token);
+ if (++i >= slab->hdim)
{
break;
}
token = separator + 1;
}
- new_request->length[i++] = atoi (token);
+ slab->extent[i++] = atoi (token);
free (substring);
- if (i < new_request->sdim)
+ if (i < slab->hdim)
{
fullname = CCTK_FullName (vindex);
CCTK_VWarn (2, __LINE__, __FILE__, CCTK_THORNSTRING,
"Length vector is incomplete or missing in hyperslab "
"options '%s' for variable '%s'.", optstring, fullname);
free (fullname);
- free (new_request);
+ free (slab);
return;
}
}
@@ -297,134 +298,114 @@ static void IOHDF5Util_ParseOutputRequest (int vindex,
while ((separator = strchr (token, ',')) != NULL)
{
*separator = 0;
- new_request->downsample[i] = atoi (token);
- if (++i >= new_request->sdim)
+ slab->downsample[i] = atoi (token);
+ if (++i >= slab->hdim)
{
break;
}
token = separator + 1;
}
- new_request->downsample[i++] = atoi (token);
+ slab->downsample[i++] = atoi (token);
free (substring);
- if (i < new_request->sdim)
+ if (i < slab->hdim)
{
fullname = CCTK_FullName (vindex);
CCTK_VWarn (2, __LINE__, __FILE__, CCTK_THORNSTRING,
"Downsampling vector is incomplete or missing in hyperslab "
"options '%s' for variable '%s'.", optstring, fullname);
free (fullname);
- free (new_request);
+ free (slab);
return;
}
}
- /* assign the output request */
- output_requests[vindex] = new_request;
-
-
-#ifdef IOHDF5UTIL_DEBUG
- printf("Geometry Data: \n");
- printf(" Argument/Slab dimension: %d / %d \n", new_request->vdim,new_request->sdim);
- printf(" Origin: ");
- for (i=0;i<new_request->vdim;i++)
- printf("%s %d ", new_request->origin[i]);
- printf("\n Downs : ");
- for (i=0;i<new_request->sdim;i++)
- printf(" %d ", new_request->downsample[i]);
- printf("\n Length: ");
- for (i=0;i<new_request->sdim;i++)
- printf(" %d ", new_request->length[i]);
- printf("\n Dirs : ");
- for (i=0;i<new_request->sdim;i++)
- printf(" %d ", new_request->direction[i]);
- printf("\n\n");
-#endif
+ /* assign the new hyperslab */
+ info->slablist[vindex] = slab;
}
-static ioHDF5Geo_t *IOHDF5Util_DefaultIORequest (int vindex)
+static ioSlab *DefaultIOHyperslab (const cGH *GH, int vindex)
{
+ ioSlab *slab;
+ int *extent_int;
+ const ioGH *ioUtilGH;
DECLARE_CCTK_PARAMETERS
- int i;
- ioHDF5Geo_t *request;
-#if 0
- const char *argument, *token;
-#endif
- /* allocate a new IO request structure */
- request = (ioHDF5Geo_t *) malloc (sizeof (ioHDF5Geo_t));
+ ioUtilGH = (const ioGH *) CCTK_GHExtension (GH, "IO");
- /* get the variable's dimension
- set it also to be the default hyperslab dimension */
- request->vdim = request->sdim = CCTK_GroupDimFromVarI (vindex);
+ /* allocate a new I/O hyperslab structure */
+ slab = (ioSlab *) malloc (sizeof (ioSlab));
- request->origin = (int *) calloc (4 + request->sdim,
- request->vdim * sizeof (int));
- request->length = request->origin + 1 * request->vdim;
- request->downsample = request->origin + 2 * request->vdim;
- request->actlen = request->origin + 3 * request->vdim;
- request->direction = request->origin + 4 * request->vdim;
+ /* fill out the basics */
+ slab->vindex = vindex;
+ slab->timelevel = 0;
+ slab->check_exist = ioUtilGH->recovered;
- for (i = 0; i < request->vdim; i++)
+ /* get the hyperslab datatype (will be single-precision if requested) */
+ slab->hdatatype = CCTK_VarTypeI (vindex);
+ if (ioUtilGH->out_single)
{
- request->length[i] = -1;
- request->direction[i * request->vdim + i] = 1;
+ if (slab->hdatatype == CCTK_VARIABLE_REAL)
+ {
+ slab->hdatatype = CCTK_VARIABLE_REAL4;
+ }
+ else if (slab->hdatatype == CCTK_VARIABLE_COMPLEX)
+ {
+ slab->hdatatype = CCTK_VARIABLE_COMPLEX8;
+ }
+#ifdef CCTK_INT2
+ else if (slab->hdatatype == CCTK_VARIABLE_INT)
+ {
+ slab->hdatatype = CCTK_VARIABLE_INT2;
+ }
+#endif
+ }
+
+ /* get the variable's dimension and extents */
+ slab->vdim = CCTK_GroupDimFromVarI (vindex);
+ extent_int = (int *) malloc (slab->vdim * sizeof (int));
+ CCTK_GroupgshVI (GH, slab->vdim, extent_int, vindex);
+
+ /* allocate the arrays all in one go
+ only initialize those which are mandatory for the Hyperslab API */
+ slab->vectors = (CCTK_INT *) calloc (slab->vdim + 6,
+ slab->vdim * sizeof (CCTK_INT));
+ slab->hoffset = slab->vectors + 0*slab->vdim;
+ slab->hsize = slab->vectors + 1*slab->vdim;
+ slab->hsize_chunk = slab->vectors + 2*slab->vdim;
+ slab->origin = slab->vectors + 3*slab->vdim;
+ slab->extent = slab->vectors + 4*slab->vdim;
+ slab->downsample = slab->vectors + 5*slab->vdim;
+ slab->direction = slab->vectors + 6*slab->vdim;
+
+ for (slab->hdim = 0; slab->hdim < slab->vdim; slab->hdim++)
+ {
+ slab->extent[slab->hdim] = extent_int[slab->hdim];
+ slab->direction[slab->hdim] = slab->hdim * (slab->vdim + 1);
/* take the downsampling parameters from IOUtil */
- if (i == 0)
+ if (slab->hdim == 0)
{
- request->downsample[i] = out3D_downsample_x;
+ slab->downsample[slab->hdim] = out3D_downsample_x;
}
- else if (i == 1)
+ else if (slab->hdim == 1)
{
- request->downsample[i] = out3D_downsample_y;
+ slab->downsample[slab->hdim] = out3D_downsample_y;
}
- else if (i == 2)
+ else if (slab->hdim == 2)
{
- request->downsample[i] = out3D_downsample_z;
+ slab->downsample[slab->hdim] = out3D_downsample_z;
}
else
{
- request->downsample[i] = 1;
+ slab->downsample[slab->hdim] = 1;
}
}
-#if 0
- FIXME: parse default hyperslab parameters
- /* Origin */
- i=0;
- argument = origin;
- while((token = Util_StrSep(&argument,","))) {
- request->origin[i++]=atoi(token);
- }
- request->downsample[i] = atoi(argument);
-
- /* Direction */
- i=0;
- argument = direction;
- while((token = Util_StrSep(&argument,","))) {
- request->direction[i++]=atoi(token);
- }
- request->downsample[i] = atoi(argument);
-
- /* Downsample */
- i=0;
- argument = downsampling;
- while((token = Util_StrSep(&argument,","))) {
- request->downsample[i++]=atoi(token);
- }
- request->downsample[i] = atoi(argument);
-
- /* Length */
- i=0;
- argument = length;
- while((token = Util_StrSep(&argument,","))) {
- request->length[i++]=atoi(token);
- }
- request->length[i] = atoi(argument);
-#endif
+ /* clean up */
+ free (extent_int);
- return (request);
+ return (slab);
}
diff --git a/src/RecoverVar.c b/src/RecoverVar.c
index 852a78e..95d9835 100644
--- a/src/RecoverVar.c
+++ b/src/RecoverVar.c
@@ -20,15 +20,21 @@
#include "CactusPUGH/PUGH/src/include/pugh.h"
#include "ioHDF5UtilGH.h"
-
/* the rcs ID and its dummy function to use it */
static const char *rcsid = "$Id$";
CCTK_FILEVERSION(BetaThorns_IOHDF5Util_RecoverVar_c)
-/* MPI tag base */
-#define STARTUPBASE 1001
+
+/********************************************************************
+ ******************** Macro Definitions ************************
+ ********************************************************************/
+/* tag base for MPI messages */
+#define MPITAGBASE 1001
+/********************************************************************
+ ******************** Internal Typedefs ************************
+ ********************************************************************/
typedef struct
{
cGH *GH;
@@ -42,47 +48,53 @@ typedef struct
{
iterate_info_t *it_info;
int element_size;
- int iohdf5_type;
+ int hdf5type;
#ifdef CCTK_MPI
MPI_Datatype mpi_type;
#endif
} recover_info_t;
-/* local function prototypes */
-static herr_t processDataset (hid_t group,
- const char *datasetname,
- void *arg);
+/********************************************************************
+ ******************** Internal Routines ************************
+ ********************************************************************/
+static herr_t processDataset (hid_t group, const char *datasetname, void *arg);
/*@@
- @routine IOHDF5Util_RecoverVariables
- @date Fri Jun 19 09:19:48 1998
- @author Tom Goodale
- @desc
- Reads in data from an open HDF5 file.
- @enddesc
- @var GH
- @vdesc Pointer to CCTK grid hierarchy
- @vtype cGH *
- @vio in
- @endvar
- @var fileinfo
- @vdesc pointer to info structure describing the HDF5 file
- @vtype const fileinfo_t *
- @vio in
- @endvar
+ @routine IOHDF5Util_RecoverVariables
+ @date Fri Jun 19 09:19:48 1998
+ @author Tom Goodale
+ @desc
+ Reads in data from an open HDF5 file.
+ @enddesc
+ @var GH
+ @vdesc Pointer to CCTK grid hierarchy
+ @vtype cGH *
+ @vio in
+ @endvar
+ @var fileinfo
+ @vdesc pointer to info structure describing the HDF5 file
+ @vtype const fileinfo_t *
+ @vio in
+ @endvar
+
+ @returntype int
+ @returndesc
+ 0 for success
+ @endreturndesc
@@*/
-int IOHDF5Util_RecoverVariables (cGH *GH,
- const fileinfo_t *fileinfo)
+int IOHDF5Util_RecoverVariables (cGH *GH, const fileinfo_t *fileinfo)
{
- DECLARE_CCTK_PARAMETERS
+ iterate_info_t info;
#ifdef CCTK_MPI
- pGH *pughGH; /* PUGH extension handle */
- int proc; /* looper */
- CCTK_INT var_info[3]; /* communication buffer for MPI */
+ pGH *pughGH;
+ CCTK_INT var_info[3];
+ MPI_Status ms;
+ MPI_Datatype mpi_type;
+ int vindex, timelevel, proc, npoints;
#endif
- iterate_info_t info; /* info to pass down to the iterator routine */
+ DECLARE_CCTK_PARAMETERS
info.GH = GH;
@@ -92,12 +104,11 @@ int IOHDF5Util_RecoverVariables (cGH *GH,
info.has_version = fileinfo->has_version;
#ifdef CCTK_MPI
- /* Get the handle for PUGH extensions */
pughGH = PUGH_pGH (GH);
- /* Now process the datasets.
+ /* now process the datasets:
All IO processors read the datasets from their checkpoint file,
- verify their contents and communicate them to the non-IO processors. */
+ verify their contents and communicate them to the non-I/O processors. */
/* At first the code for the IO processors.
This holds also for the single processor case. */
@@ -106,7 +117,7 @@ int IOHDF5Util_RecoverVariables (cGH *GH,
#endif /* CCTK_MPI */
/* iterate over all datasets starting from "/" in the HDF5 file */
- IOHDF5_ERROR (H5Giterate (fileinfo->file, "/", NULL, processDataset,&info));
+ HDF5_ERROR (H5Giterate (fileinfo->file, "/", NULL, processDataset, &info));
#ifdef CCTK_MPI
/* To signal completion to the non-IO processors
@@ -119,28 +130,23 @@ int IOHDF5Util_RecoverVariables (cGH *GH,
proc++)
{
CACTUS_MPI_ERROR (MPI_Send (var_info, 3, PUGH_MPI_INT, proc,
- STARTUPBASE, pughGH->PUGH_COMM_WORLD));
+ MPITAGBASE, pughGH->PUGH_COMM_WORLD));
}
}
else
{
-
- /* And here the code for non-IO processors: */
- MPI_Datatype mpi_type;
- MPI_Status ms;
- int vindex, timelevel, npoints;
-
- /* They don't know how many datasets there are, because the IO processors
+ /* And here the code for non-I/O processors: */
+ /* They don't know how many datasets there are, because the I/O processors
could skip some on the fly during their consistency checks.
- The IO Processor sends the index of the variable to be processed next.
- So, all non-IO processors execute a loop where the termination condition
+ The I/O Processor sends the index of the variable to be processed next.
+ So, all non-I/O processors execute a loop where the termination condition
is when an invalid index was received.
*/
while (1)
{
/* receive the next variable index from my IO processor */
CACTUS_MPI_ERROR (MPI_Recv (var_info, 3, PUGH_MPI_INT, fileinfo->ioproc,
- STARTUPBASE, pughGH->PUGH_COMM_WORLD, &ms));
+ MPITAGBASE, pughGH->PUGH_COMM_WORLD, &ms));
vindex = var_info[0]; timelevel = var_info[1]; npoints = var_info[2];
/* check for termination condition */
@@ -159,7 +165,7 @@ int IOHDF5Util_RecoverVariables (cGH *GH,
/* receive following data from my IO processor */
CACTUS_MPI_ERROR (MPI_Recv (GH->data[vindex][timelevel], npoints,
- mpi_type, fileinfo->ioproc, STARTUPBASE,
+ mpi_type, fileinfo->ioproc, MPITAGBASE,
pughGH->PUGH_COMM_WORLD, &ms));
}
}
@@ -172,10 +178,9 @@ int IOHDF5Util_RecoverVariables (cGH *GH,
/* NOTE: Although we could read the GH extensions from multiple recovery files
in parallel, this is done only on by processor 0 here.
Broadcasting the GH extensions is found faster than
- sending it in a loop from each IO processor to all the non IOs
+ sending it in a loop from each I/O processor to all the non I/Os
(don't have subcommunicators yet) */
-int IOHDF5Util_RecoverGHextensions (cGH *GH,
- const fileinfo_t *fileinfo)
+int IOHDF5Util_RecoverGHextensions (cGH *GH, const fileinfo_t *fileinfo)
{
hid_t group;
CCTK_REAL4 real4Buffer;
@@ -191,13 +196,11 @@ int IOHDF5Util_RecoverGHextensions (cGH *GH,
if (int4Buffer[0])
{
+ READ_ATTRIBUTE (group, "cctk_iteration", HDF5_INT4, &int4Buffer[1]);
+ READ_ATTRIBUTE (group, "main_loop_index", HDF5_INT4, &int4Buffer[2]);
+ READ_ATTRIBUTE (group, "cctk_time", HDF5_REAL4, &real4Buffer);
- READ_ATTRIBUTE (group, "cctk_iteration", IOHDF5_INT4, &int4Buffer[1]);
- READ_ATTRIBUTE (group, "main_loop_index", IOHDF5_INT4, &int4Buffer[2]);
- READ_ATTRIBUTE (group, "cctk_time", IOHDF5_REAL4, &real4Buffer);
-
- IOHDF5_ERROR (H5Gclose (group));
-
+ HDF5_ERROR (H5Gclose (group));
}
else
{
@@ -226,7 +229,7 @@ int IOHDF5Util_RecoverGHextensions (cGH *GH,
CCTK_SetMainLoopIndex ((int) int4Buffer[2]);
}
- /* Return 0 for success otherwise negative */
+ /* return 0 for success otherwise negative */
return (int4Buffer[0] ? 0 : -1);
}
@@ -238,19 +241,18 @@ int IOHDF5Util_RecoverGHextensions (cGH *GH,
(don't have subcommunicators yet) */
int IOHDF5Util_RecoverParameters (const fileinfo_t *fileinfo)
{
- DECLARE_CCTK_PARAMETERS
hid_t group, attr, atype;
char *parameters;
CCTK_INT4 parameterSize;
- cGH *GH = NULL; /* There's no cGH set up yet so we pass
- a NULL pointer to CCTK_MyProc() */
+ DECLARE_CCTK_PARAMETERS
+
/* To make the compiler happy */
group = attr = 0;
parameters = NULL;
parameterSize = 0;
- if (CCTK_MyProc (GH) == 0)
+ if (CCTK_MyProc (NULL) == 0)
{
if (verbose)
{
@@ -268,12 +270,12 @@ int IOHDF5Util_RecoverParameters (const fileinfo_t *fileinfo)
if (group > 0 && attr > 0)
{
- IOHDF5_ERROR (atype = H5Aget_type (attr));
+ HDF5_ERROR (atype = H5Aget_type (attr));
parameterSize = H5Tget_size (atype);
parameters = (char *) malloc (parameterSize + 1);
- IOHDF5_ERROR (H5Aread (attr, atype, parameters));
+ HDF5_ERROR (H5Aread (attr, atype, parameters));
parameters[parameterSize] = 0;
- IOHDF5_ERROR (H5Tclose (atype));
+ HDF5_ERROR (H5Tclose (atype));
}
else
{
@@ -283,11 +285,11 @@ int IOHDF5Util_RecoverParameters (const fileinfo_t *fileinfo)
if (attr > 0)
{
- IOHDF5_ERROR (H5Aclose (attr));
+ HDF5_ERROR (H5Aclose (attr));
}
if (group > 0)
{
- IOHDF5_ERROR (H5Gclose (group));
+ HDF5_ERROR (H5Gclose (group));
}
}
@@ -303,7 +305,7 @@ int IOHDF5Util_RecoverParameters (const fileinfo_t *fileinfo)
if (parameterSize > 0)
{
#ifdef CCTK_MPI
- if (CCTK_MyProc (GH) != 0)
+ if (CCTK_MyProc (NULL) != 0)
{
parameters = (char *) malloc (parameterSize + 1);
}
@@ -317,14 +319,14 @@ int IOHDF5Util_RecoverParameters (const fileinfo_t *fileinfo)
free (parameters);
}
- /* Return positive value for success otherwise negative */
+ /* return positive value for success otherwise negative */
return (parameterSize > 0 ? 1 : -1);
}
-/************************************************************************/
-/* local routines */
-/************************************************************************/
+/********************************************************************
+ ******************** Internal Routines ************************
+ ********************************************************************/
/* local routine GetCommonAttributes() reads in the next dataset's attributes
and verifies them:
@@ -341,7 +343,6 @@ int IOHDF5Util_RecoverParameters (const fileinfo_t *fileinfo)
If successful, the global variable index, the group type and the timelevel
to restore are stored in {*vindex, *gtype, *timelevel}, and 0 is returned.
*/
-
static int GetCommonAttributes (cGH *GH,
hid_t dataset,
const char *datasetname,
@@ -426,9 +427,9 @@ static int GetCommonAttributes (cGH *GH,
if the dataset is a chunk group */
if (is_group)
{
- IOHDF5_ERROR (dataset = H5Dopen (dataset, "chunk0"));
+ HDF5_ERROR (dataset = H5Dopen (dataset, "chunk0"));
}
- IOHDF5_ERROR (datatype = H5Dget_type (dataset));
+ HDF5_ERROR (datatype = H5Dget_type (dataset));
/* The CCTK variable type defines do not correlate with the HDF5 defines
so compare them explicitely here. */
@@ -444,7 +445,7 @@ static int GetCommonAttributes (cGH *GH,
strncmp (CCTK_VarTypeName (group_static_data.vartype),
"CCTK_VARIABLE_COMPLEX", 21) == 0);
- IOHDF5_ERROR (H5Tclose (datatype));
+ HDF5_ERROR (H5Tclose (datatype));
if (! flag)
{
CCTK_VWarn (2, __LINE__, __FILE__, CCTK_THORNSTRING,
@@ -453,44 +454,36 @@ static int GetCommonAttributes (cGH *GH,
}
/* verify the dims and sizes */
- IOHDF5_ERROR (dataspace = H5Dget_space (dataset));
- IOHDF5_ERROR (ndims_stored = H5Sget_simple_extent_ndims (dataspace));
+ HDF5_ERROR (dataspace = H5Dget_space (dataset));
+ HDF5_ERROR (ndims_stored = H5Sget_simple_extent_ndims (dataspace));
dims_stored = (hsize_t *) malloc (ndims_stored * sizeof (hsize_t));
- IOHDF5_ERROR (rank_stored = H5Sget_simple_extent_dims (dataspace,
+ HDF5_ERROR (rank_stored = H5Sget_simple_extent_dims (dataspace,
dims_stored, NULL));
/* scalars are stored as rank 0 in HDF5 but have rank 1 in Cactus */
if (rank_stored == 0)
{
rank_stored = 1;
}
- IOHDF5_ERROR (H5Sclose (dataspace));
+ HDF5_ERROR (H5Sclose (dataspace));
- flag = 0;
- if (group_static_data.dim != (int) rank_stored)
- {
- flag = 1;
- }
- switch (group_static_data.grouptype)
+ flag = group_static_data.dim != (int) rank_stored;
+ if (group_static_data.grouptype == CCTK_ARRAY ||
+ group_static_data.grouptype == CCTK_GF)
{
- case CCTK_SCALAR:
- break;
- case CCTK_ARRAY:
- case CCTK_GF:
- if (CCTK_GroupDynamicData (GH, groupindex, &group_dynamic_data) != 0)
- {
- CCTK_VWarn (2, __LINE__, __FILE__, CCTK_THORNSTRING,
- "Cannot get dynamic group data for '%s'", fullvarname);
- return (-1);
- }
- dims = unchunked ? group_dynamic_data.gsh : group_dynamic_data.lsh;
- for (i = 0; i < group_static_data.dim; i++)
+ if (CCTK_GroupDynamicData (GH, groupindex, &group_dynamic_data) != 0)
+ {
+ CCTK_VWarn (2, __LINE__, __FILE__, CCTK_THORNSTRING,
+ "Cannot get dynamic group data for '%s'", fullvarname);
+ return (-1);
+ }
+ dims = unchunked ? group_dynamic_data.gsh : group_dynamic_data.lsh;
+ for (i = 0; i < group_static_data.dim; i++)
+ {
+ if (dims[group_static_data.dim - i - 1] != (int) dims_stored[i])
{
- if (dims[group_static_data.dim - i - 1] != (int) dims_stored[i])
- {
- flag = 1;
- }
+ flag = 1;
}
- break;
+ }
}
free (dims_stored);
@@ -511,7 +504,7 @@ static int GetCommonAttributes (cGH *GH,
/* close the first chunk if the dataset is a chunk group */
if (is_group)
{
- IOHDF5_ERROR (H5Dclose (dataset));
+ HDF5_ERROR (H5Dclose (dataset));
}
*grouptype = group_static_data.grouptype;
@@ -520,30 +513,27 @@ static int GetCommonAttributes (cGH *GH,
}
-static int IOHDF5Util_RestoreGS (hid_t dataset,
- int vindex,
- int timelevel,
+static int IOHDF5Util_RestoreGS (hid_t dataset, int vindex, int timelevel,
recover_info_t *rec_info)
{
void *data;
#ifdef CCTK_MPI
int proc;
CCTK_INT var_info[3];
- pGH *pughGH;
+ MPI_Comm comm;
#endif
data = CCTK_VarDataPtrI (rec_info->it_info->GH, timelevel, vindex);
/* read the data into the local variable ... */
- IOHDF5_ERROR (H5Dread (dataset, rec_info->iohdf5_type, H5S_ALL, H5S_ALL,
- H5P_DEFAULT, data));
+ HDF5_ERROR (H5Dread (dataset, rec_info->hdf5type, H5S_ALL, H5S_ALL,
+ H5P_DEFAULT, data));
#ifdef CCTK_MPI
/* ... and communicate it for the MPI case */
- /* Get the handle for PUGH extensions */
- pughGH = PUGH_pGH (rec_info->it_info->GH);
+ comm = PUGH_pGH (rec_info->it_info->GH)->PUGH_COMM_WORLD;
/* set the variable's index and the timelevel */
var_info[0] = vindex; var_info[1] = timelevel; var_info[2] = 1;
@@ -554,10 +544,10 @@ static int IOHDF5Util_RestoreGS (hid_t dataset,
proc < CCTK_nProcs (rec_info->it_info->GH);
proc++)
{
- CACTUS_MPI_ERROR (MPI_Send (var_info, 3, PUGH_MPI_INT, proc,
- STARTUPBASE, pughGH->PUGH_COMM_WORLD));
- CACTUS_MPI_ERROR (MPI_Send (data, 1, rec_info->mpi_type, proc,
- STARTUPBASE, pughGH->PUGH_COMM_WORLD));
+ CACTUS_MPI_ERROR (MPI_Send (var_info, 3, PUGH_MPI_INT, proc, MPITAGBASE,
+ comm));
+ CACTUS_MPI_ERROR (MPI_Send (data, 1, rec_info->mpi_type, proc, MPITAGBASE,
+ comm));
}
#endif /* CCTK_MPI */
@@ -565,26 +555,28 @@ static int IOHDF5Util_RestoreGS (hid_t dataset,
}
-static int IOHDF5Util_RestoreGA (hid_t dataset,
- int vindex,
- int timelevel,
+static int IOHDF5Util_RestoreGA (hid_t dataset, int vindex, int timelevel,
recover_info_t *rec_info)
{
#ifdef CCTK_MPI
- int proc, npoints;
+ int i, dim, proc, npoints;
CCTK_INT var_info[3];
pGH *pughGH;
void *buffer, *data;
- hid_t filespace, memspace;
+ hid_t filespace, memspace, chunk;
pGExtras *extras;
+ char chunkname[32];
+ hssize_t *chunk_origin;
+ hsize_t *chunk_dims;
#endif
/* single processor case is easy: just read the whole dataset */
if (CCTK_nProcs (rec_info->it_info->GH) == 1)
{
- IOHDF5_ERROR (H5Dread (dataset, rec_info->iohdf5_type, H5S_ALL,
- H5S_ALL, H5P_DEFAULT, rec_info->it_info->GH->data[vindex][timelevel]));
+ HDF5_ERROR (H5Dread (dataset, rec_info->hdf5type, H5S_ALL, H5S_ALL,
+ H5P_DEFAULT,
+ rec_info->it_info->GH->data[vindex][timelevel]));
return (0);
}
@@ -628,24 +620,17 @@ static int IOHDF5Util_RestoreGA (hid_t dataset,
if (! rec_info->it_info->unchunked)
{
- hid_t chunk;
- char chunkname[32];
-
/* Chunked data is stored as separate chunk datasets within a group.
So open, read and close the separate chunks here. */
sprintf (chunkname, "chunk%d", proc - rec_info->it_info->ioproc);
- IOHDF5_ERROR (chunk = H5Dopen (dataset, chunkname));
- IOHDF5_ERROR (H5Dread (chunk, rec_info->iohdf5_type, H5S_ALL,
- H5S_ALL, H5P_DEFAULT, data));
- IOHDF5_ERROR (H5Dclose (chunk));
+ HDF5_ERROR (chunk = H5Dopen (dataset, chunkname));
+ HDF5_ERROR (H5Dread (chunk, rec_info->hdf5type, H5S_ALL, H5S_ALL,
+ H5P_DEFAULT, data));
+ HDF5_ERROR (H5Dclose (chunk));
}
else
{
- int i, dim;
- hssize_t *chunk_origin;
- hsize_t *chunk_dims;
-
/* get the dimension of the variable */
dim = CCTK_GroupDimI (CCTK_GroupIndexFromVarI (vindex));
chunk_origin = (hssize_t *) malloc (dim * sizeof (hssize_t));
@@ -659,16 +644,16 @@ static int IOHDF5Util_RestoreGA (hid_t dataset,
chunk_origin[dim - 1 - i] = extras->lb[proc][i];
}
- IOHDF5_ERROR (filespace = H5Dget_space (dataset));
- IOHDF5_ERROR (memspace = H5Screate_simple (dim, chunk_dims, NULL));
- IOHDF5_ERROR (H5Sselect_hyperslab (filespace, H5S_SELECT_SET,
+ HDF5_ERROR (filespace = H5Dget_space (dataset));
+ HDF5_ERROR (memspace = H5Screate_simple (dim, chunk_dims, NULL));
+ HDF5_ERROR (H5Sselect_hyperslab (filespace, H5S_SELECT_SET,
chunk_origin, NULL, chunk_dims, NULL));
- IOHDF5_ERROR (H5Dread (dataset, rec_info->iohdf5_type, memspace,
- filespace, H5P_DEFAULT, data));
+ HDF5_ERROR (H5Dread (dataset, rec_info->hdf5type, memspace, filespace,
+ H5P_DEFAULT, data));
- IOHDF5_ERROR (H5Sclose (memspace));
- IOHDF5_ERROR (H5Sclose (filespace));
+ HDF5_ERROR (H5Sclose (memspace));
+ HDF5_ERROR (H5Sclose (filespace));
free (chunk_dims);
free (chunk_origin);
@@ -679,9 +664,9 @@ static int IOHDF5Util_RestoreGA (hid_t dataset,
{
var_info[2] = extras->rnpoints[proc];
CACTUS_MPI_ERROR (MPI_Send (var_info, 3, PUGH_MPI_INT, proc,
- STARTUPBASE, pughGH->PUGH_COMM_WORLD));
+ MPITAGBASE, pughGH->PUGH_COMM_WORLD));
CACTUS_MPI_ERROR (MPI_Send (data, extras->rnpoints[proc],
- rec_info->mpi_type, proc, STARTUPBASE,
+ rec_info->mpi_type, proc, MPITAGBASE,
pughGH->PUGH_COMM_WORLD));
}
}
@@ -693,20 +678,17 @@ static int IOHDF5Util_RestoreGA (hid_t dataset,
}
-static herr_t processDataset (hid_t group,
- const char *datasetname,
- void *arg)
+static herr_t processDataset (hid_t group, const char *datasetname, void *arg)
{
- DECLARE_CCTK_PARAMETERS
- pGH *pughGH;
ioGH *ioUtilGH;
ioHDF5UtilGH *myGH;
- int vindex, vtype, gtype, timelevel;
+ int vindex, vtype, gtype, timelevel, is_group;
iterate_info_t *it_info = (iterate_info_t *) arg;
recover_info_t rec_info;
hid_t dataset;
H5G_stat_t object_info;
- int is_group;
+ char *fullname;
+ DECLARE_CCTK_PARAMETERS
/* skip the global attributes and GH extensions groups */
@@ -716,20 +698,15 @@ static herr_t processDataset (hid_t group,
return (0);
}
- /* Get the handle for PUGH, IOUtil, and IOHDF5Util extensions */
- pughGH = PUGH_pGH (it_info->GH);
- ioUtilGH = (ioGH *) CCTK_GHExtension (it_info->GH, "IO");
- myGH = (ioHDF5UtilGH *) CCTK_GHExtension (it_info->GH, "IOHDF5Util");
-
- IOHDF5_ERROR (H5Gget_objinfo (group, datasetname, 0, &object_info));
+ HDF5_ERROR (H5Gget_objinfo (group, datasetname, 0, &object_info));
is_group = object_info.type == H5G_GROUP;
if (is_group)
{
- IOHDF5_ERROR (dataset = H5Gopen (group, datasetname));
+ HDF5_ERROR (dataset = H5Gopen (group, datasetname));
}
else
{
- IOHDF5_ERROR (dataset = H5Dopen (group, datasetname));
+ HDF5_ERROR (dataset = H5Dopen (group, datasetname));
}
/* read in the dataset's attributes and verify them */
@@ -742,42 +719,43 @@ static herr_t processDataset (hid_t group,
return (0);
}
+ ioUtilGH = (ioGH *) CCTK_GHExtension (it_info->GH, "IO");
+ myGH = (ioHDF5UtilGH *) CCTK_GHExtension (it_info->GH, "IOHDF5Util");
+
/* if we read in initial data via the file reader interface
check whether the user wants to have this variable restored */
if (ioUtilGH->do_inVars && ! ioUtilGH->do_inVars[vindex])
{
if (verbose)
{
- char *varname = CCTK_FullName (vindex);
-
+ fullname = CCTK_FullName (vindex);
CCTK_VInfo (CCTK_THORNSTRING, "Ignoring variable '%s' for file reader "
- "recovery", varname);
- free (varname);
+ "recovery", fullname);
+ free (fullname);
}
return (0);
}
if (verbose)
{
- char *varname = CCTK_FullName (vindex);
-
+ fullname = CCTK_FullName (vindex);
CCTK_VInfo (CCTK_THORNSTRING, "Restoring variable '%s' (timelevel %d)",
- varname, timelevel);
- free (varname);
+ fullname, timelevel);
+ free (fullname);
}
vtype = CCTK_VarTypeI (vindex);
rec_info.it_info = it_info;
rec_info.element_size = CCTK_VarTypeSize (vtype);
#ifdef CCTK_MPI
- rec_info.mpi_type = PUGH_MPIDataType (pughGH, vtype);
+ rec_info.mpi_type = PUGH_MPIDataType (PUGH_pGH (it_info->GH), vtype);
#endif
- rec_info.iohdf5_type = IOHDF5Util_DataType (myGH, vtype);
+ rec_info.hdf5type = IOHDF5Util_DataType (myGH, vtype);
if (rec_info.element_size <= 0 ||
#ifdef CCTK_MPI
rec_info.mpi_type == MPI_DATATYPE_NULL ||
#endif
- rec_info.iohdf5_type < 0)
+ rec_info.hdf5type < 0)
{
CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
"Unsupported variable datatype %d", vtype);
@@ -802,11 +780,11 @@ static herr_t processDataset (hid_t group,
if (is_group)
{
- IOHDF5_ERROR (H5Gclose (dataset));
+ HDF5_ERROR (H5Gclose (dataset));
}
else
{
- IOHDF5_ERROR (H5Dclose (dataset));
+ HDF5_ERROR (H5Dclose (dataset));
}
return (0);
diff --git a/src/Startup.c b/src/Startup.c
index 710e35c..9fe875c 100644
--- a/src/Startup.c
+++ b/src/Startup.c
@@ -2,9 +2,9 @@
@file Startup.c
@date Fri Oct 6 2000
@author Thomas Radke
- @desc
+ @desc
Startup and termination routines for IOHDF5Util.
- @enddesc
+ @enddesc
@version $Id$
@@*/
@@ -20,25 +20,32 @@
static const char *rcsid = "$Id$";
CCTK_FILEVERSION(BetaThorns_IOHDF5Util_Startup_c)
-/* prototypes of routines defined in this source file */
+
+/********************************************************************
+ ******************** External Routines ************************
+ ********************************************************************/
void IOHDF5Util_Startup (void);
-void IOHDF5Util_Terminate (cGH *GH);
-static void *IOHDF5Util_SetupGH (tFleshConfig *config,
- int convergence_level,
- cGH *GH);
+void IOHDF5Util_Terminate (const cGH *GH);
- /*@@
- @routine IOHDF5Util_Startup
- @date Fri Oct 6 2000
- @author Thomas Radke
- @desc
- The startup registration routine for IOHDF5Util.
- Registers the GH extensions needed for IOHDF5Util
- and the routine to set it up.
- @enddesc
+/********************************************************************
+ ******************** Internal Routines ************************
+ ********************************************************************/
+static void *IOHDF5Util_SetupGH (tFleshConfig *config, int conv_level, cGH *GH);
+
- @calls CCTK_RegisterGHExtensionSetupGH
+ /*@@
+ @routine IOHDF5Util_Startup
+ @date Fri Oct 6 2000
+ @author Thomas Radke
+ @desc
+ The startup registration routine for IOHDF5Util.
+ Registers the GH extensions needed for IOHDF5Util
+ and the routine to set it up.
+ @enddesc
+
+ @calls CCTK_RegisterGHExtension
+ CCTK_RegisterGHExtensionSetupGH
@@*/
void IOHDF5Util_Startup (void)
{
@@ -62,20 +69,21 @@ void IOHDF5Util_Startup (void)
/*@@
- @routine IOHDF5Util_Terminate
- @date Fri Oct 6 2000
- @author Thomas Radke
- @desc
- The termination registration routine for IOHDF5Util.
- It frees any resources kept on the GH extensions.
- @enddesc
+ @routine IOHDF5Util_Terminate
+ @date Fri Oct 6 2000
+ @author Thomas Radke
+ @desc
+ The termination registration routine for IOHDF5Util.
+ It frees any resources kept on the GH extensions.
+ @enddesc
+
@var GH
- @vdesc Pointer to CCTK GH
- @vtype cGH *
+ @vdesc Pointer to CCTK grid hierarchy
+ @vtype const cGH *
@vio in
@endvar
@@*/
-void IOHDF5Util_Terminate (cGH *GH)
+void IOHDF5Util_Terminate (const cGH *GH)
{
ioHDF5UtilGH *myGH;
@@ -86,117 +94,135 @@ void IOHDF5Util_Terminate (cGH *GH)
/* close the dataspaces used to write scalar and array attributes */
if (myGH->scalar_dataspace >= 0)
{
- IOHDF5_ERROR (H5Sclose (myGH->scalar_dataspace));
+ HDF5_ERROR (H5Sclose (myGH->scalar_dataspace));
}
if (myGH->array_dataspace >= 0)
{
- IOHDF5_ERROR (H5Sclose (myGH->array_dataspace));
+ HDF5_ERROR (H5Sclose (myGH->array_dataspace));
}
/* close the predefined complex and string datatypes */
- if (myGH->IOHDF5_COMPLEX >= 0)
+ if (myGH->HDF5_COMPLEX >= 0)
{
- IOHDF5_ERROR (H5Tclose (myGH->IOHDF5_COMPLEX));
+ HDF5_ERROR (H5Tclose (myGH->HDF5_COMPLEX));
}
#ifdef CCTK_REAL4
- if (myGH->IOHDF5_COMPLEX8 >= 0)
+ if (myGH->HDF5_COMPLEX8 >= 0)
{
- IOHDF5_ERROR (H5Tclose (myGH->IOHDF5_COMPLEX8));
+ HDF5_ERROR (H5Tclose (myGH->HDF5_COMPLEX8));
}
#endif
#ifdef CCTK_REAL8
- if (myGH->IOHDF5_COMPLEX16 >= 0)
+ if (myGH->HDF5_COMPLEX16 >= 0)
{
- IOHDF5_ERROR (H5Tclose (myGH->IOHDF5_COMPLEX16));
+ HDF5_ERROR (H5Tclose (myGH->HDF5_COMPLEX16));
}
#endif
#ifdef CCTK_REAL16
- if (myGH->IOHDF5_COMPLEX32 >= 0)
+ if (myGH->HDF5_COMPLEX32 >= 0)
{
- IOHDF5_ERROR (H5Tclose (myGH->IOHDF5_COMPLEX32));
+ HDF5_ERROR (H5Tclose (myGH->HDF5_COMPLEX32));
}
#endif
- if (myGH->IOHDF5_STRING >= 0)
+ if (myGH->HDF5_STRING >= 0)
{
- IOHDF5_ERROR (H5Tclose (myGH->IOHDF5_STRING));
+ HDF5_ERROR (H5Tclose (myGH->HDF5_STRING));
}
}
}
-/****************************************************************************/
-/* local routines */
-/****************************************************************************/
+/********************************************************************
+ ******************** Internal Routines ************************
+ ********************************************************************/
/*@@
- @routine IOHDF5Util_SetupGH
- @date Fri Oct 6 2000
- @author Thomas Radke
- @desc
- Allocate a GH extension structure for IOHDF5Util and set it up.
- @enddesc
-
- @returntype void *
+ @routine IOHDF5Util_SetupGH
+ @date Fri Oct 6 2000
+ @author Thomas Radke
+ @desc
+ Allocates and sets up IOHDF5Util's GH extension structure.
+ @enddesc
+
+ @calls CCTK_RegisterIOMethod
+ CCTK_RegisterIOMethodOutputGH
+ CCTK_RegisterIOMethodOutputVarAs
+ CCTK_RegisterIOMethodTimeToOutput
+ CCTK_RegisterIOMethodTriggerOutput
+
+ @var config
+ @vdesc the CCTK configuration as provided by the flesh
+ @vtype tFleshConfig *
+ @vio unused
+ @endvar
+ @var conv_level
+ @vdesc the convergence level
+ @vtype int
+ @vio unused
+ @endvar
+ @var GH
+ @vdesc Pointer to CCTK grid hierarchy
+ @vtype cGH *
+ @vio unused
+ @endvar
+
+ @returntype void *
@returndesc
- pointer to the allocated GH extension structure
+ pointer to the allocated GH extension structure
@endreturndesc
@@*/
-static void *IOHDF5Util_SetupGH (tFleshConfig *config,
- int convergence_level,
- cGH *GH)
+static void *IOHDF5Util_SetupGH (tFleshConfig *config, int conv_level, cGH *GH)
{
- DECLARE_CCTK_PARAMETERS
ioHDF5UtilGH *myGH;
+ DECLARE_CCTK_PARAMETERS
/* suppress compiler warnings about unused variables */
- config = config;
- convergence_level = convergence_level;
- GH = GH;
+ (void) (config + 0);
+ (void) (conv_level + 0);
+ (void) (GH + 0);
+ /* allocate the GH extension */
myGH = (ioHDF5UtilGH *) malloc (sizeof (ioHDF5UtilGH));
- /* save the original error printing routine and its argument */
- IOHDF5_ERROR (H5Eget_auto (&myGH->print_error_fn, &myGH->print_error_fn_arg));
-
/* predefine dataspaces for writing scalar and array attributes */
/* the dimension of the array dataspace is set when used */
- IOHDF5_ERROR (myGH->scalar_dataspace = H5Screate (H5S_SCALAR));
- IOHDF5_ERROR (myGH->array_dataspace = H5Screate (H5S_SIMPLE));
-
- /* predefine IOHDF5_COMPLEX datatypes */
- IOHDF5_ERROR (myGH->IOHDF5_COMPLEX =
- H5Tcreate (H5T_COMPOUND, sizeof (CCTK_COMPLEX)));
- IOHDF5_ERROR (H5Tinsert (myGH->IOHDF5_COMPLEX, "real",
- offsetof (CCTK_COMPLEX, Re), IOHDF5_REAL));
- IOHDF5_ERROR (H5Tinsert (myGH->IOHDF5_COMPLEX, "imag",
- offsetof (CCTK_COMPLEX, Im), IOHDF5_REAL));
+ HDF5_ERROR (myGH->scalar_dataspace = H5Screate (H5S_SCALAR));
+ HDF5_ERROR (myGH->array_dataspace = H5Screate (H5S_SIMPLE));
+
+ /* predefine HDF5_COMPLEX datatypes */
+ HDF5_ERROR (myGH->HDF5_COMPLEX =
+ H5Tcreate (H5T_COMPOUND, sizeof (CCTK_COMPLEX)));
+ HDF5_ERROR (H5Tinsert (myGH->HDF5_COMPLEX, "real",
+ offsetof (CCTK_COMPLEX, Re), HDF5_REAL));
+ HDF5_ERROR (H5Tinsert (myGH->HDF5_COMPLEX, "imag",
+ offsetof (CCTK_COMPLEX, Im), HDF5_REAL));
#ifdef CCTK_REAL4
- IOHDF5_ERROR (myGH->IOHDF5_COMPLEX8 =
- H5Tcreate (H5T_COMPOUND, sizeof (CCTK_COMPLEX8)));
- IOHDF5_ERROR (H5Tinsert (myGH->IOHDF5_COMPLEX8, "real",
- offsetof (CCTK_COMPLEX8, Re), IOHDF5_REAL4));
- IOHDF5_ERROR (H5Tinsert (myGH->IOHDF5_COMPLEX8, "imag",
- offsetof (CCTK_COMPLEX8, Im), IOHDF5_REAL4));
+ HDF5_ERROR (myGH->HDF5_COMPLEX8 =
+ H5Tcreate (H5T_COMPOUND, sizeof (CCTK_COMPLEX8)));
+ HDF5_ERROR (H5Tinsert (myGH->HDF5_COMPLEX8, "real",
+ offsetof (CCTK_COMPLEX8, Re), HDF5_REAL4));
+ HDF5_ERROR (H5Tinsert (myGH->HDF5_COMPLEX8, "imag",
+ offsetof (CCTK_COMPLEX8, Im), HDF5_REAL4));
#endif
#ifdef CCTK_REAL8
- IOHDF5_ERROR (myGH->IOHDF5_COMPLEX16 =
- H5Tcreate (H5T_COMPOUND, sizeof (CCTK_COMPLEX16)));
- IOHDF5_ERROR (H5Tinsert (myGH->IOHDF5_COMPLEX16, "real",
- offsetof (CCTK_COMPLEX16, Re), IOHDF5_REAL8));
- IOHDF5_ERROR (H5Tinsert (myGH->IOHDF5_COMPLEX16, "imag",
- offsetof (CCTK_COMPLEX16, Im), IOHDF5_REAL8));
+ HDF5_ERROR (myGH->HDF5_COMPLEX16 =
+ H5Tcreate (H5T_COMPOUND, sizeof (CCTK_COMPLEX16)));
+ HDF5_ERROR (H5Tinsert (myGH->HDF5_COMPLEX16, "real",
+ offsetof (CCTK_COMPLEX16, Re), HDF5_REAL8));
+ HDF5_ERROR (H5Tinsert (myGH->HDF5_COMPLEX16, "imag",
+ offsetof (CCTK_COMPLEX16, Im), HDF5_REAL8));
#endif
#ifdef CCTK_REAL16
- IOHDF5_ERROR (myGH->IOHDF5_COMPLEX32 =
- H5Tcreate (H5T_COMPOUND, sizeof (CCTK_COMPLEX32)));
- IOHDF5_ERROR (H5Tinsert (myGH->IOHDF5_COMPLEX32, "real",
- offsetof (CCTK_COMPLEX32, Re), IOHDF5_REAL16));
- IOHDF5_ERROR (H5Tinsert (myGH->IOHDF5_COMPLEX32, "imag",
- offsetof (CCTK_COMPLEX32, Im), IOHDF5_REAL16));
+ HDF5_ERROR (myGH->HDF5_COMPLEX32 =
+ H5Tcreate (H5T_COMPOUND, sizeof (CCTK_COMPLEX32)));
+ HDF5_ERROR (H5Tinsert (myGH->HDF5_COMPLEX32, "real",
+ offsetof (CCTK_COMPLEX32, Re), HDF5_REAL16));
+ HDF5_ERROR (H5Tinsert (myGH->HDF5_COMPLEX32, "imag",
+ offsetof (CCTK_COMPLEX32, Im), HDF5_REAL16));
#endif
/* predefine a C string datatype */
- IOHDF5_ERROR (myGH->IOHDF5_STRING = H5Tcopy (H5T_C_S1));
+ HDF5_ERROR (myGH->HDF5_STRING = H5Tcopy (H5T_C_S1));
return (myGH);
}
diff --git a/src/ioHDF5UtilGH.h b/src/ioHDF5UtilGH.h
index dfdb31e..62dc98a 100644
--- a/src/ioHDF5UtilGH.h
+++ b/src/ioHDF5UtilGH.h
@@ -3,88 +3,87 @@
@date Fri Oct 6 2000
@author Thomas Radke
@desc
- The GH extensions structure for IOHDF5Util.
+ The GH extensions structure for thorn IOHDF5Util.
@enddesc
- @version $Id$
+ @version $Header$
@@*/
#ifndef _IOUTILHDF5_IOUTILHDF5GH_H_
-#define _IOUTILHDF5_IOUTILHDF5GH_H_
+#define _IOUTILHDF5_IOUTILHDF5GH_H_ 1
-/* 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; \
+/********************************************************************
+ ******************** Macro Definitions ************************
+ ********************************************************************/
+/* check return code of HDF5 call and print a warning in case of an error */
+#define HDF5_ERROR(fn_call) \
+ { \
+ 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 \
+ if (_error_code < 0) \
{ \
- 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; \
+ CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING, \
+ "HDF5 call '%s' returned error code %d", \
+ #fn_call, _error_code); \
+ } \
+ }
+
+/* append an attribute to a given file object */
+#define WRITE_ATTRIBUTE(name, value, object, ioHDF5UtilGH, dim, datatype) \
+ { \
+ int _len; \
+ hid_t _attr, _dataspace; \
+ /* 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 _dim = 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) \
+ _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 */ \
{ \
- IOHDF5_ERROR (H5Sset_extent_simple (dataspace, 1, \
- &_arrayDim, NULL)); \
+ _len++; \
} \
- 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 \
+ HDF5_ERROR (H5Tset_size (datatype, _len)); \
+ } \
+ if (_dim > 0) \
{ \
- hid_t _attr, _attrtype; \
- hsize_t _asize = 0; \
+ _dataspace = ioHDF5UtilGH->array_dataspace; \
+ HDF5_ERROR (H5Sset_extent_simple (_dataspace, 1, &_dim, NULL)); \
+ } \
+ else \
+ { \
+ _dataspace = ioHDF5UtilGH->scalar_dataspace; \
+ } \
+ HDF5_ERROR (_attr = H5Acreate (object, name, datatype, _dataspace, \
+ H5P_DEFAULT)); \
+ HDF5_ERROR (H5Awrite (_attr, datatype, _v.non_const_val)); \
+ HDF5_ERROR (H5Aclose (_attr)); \
+ }
+
+/* read an attribute in a given file object */
+#define READ_ATTRIBUTE(object, attrname, requested_type, buffer) \
+ { \
+ hid_t _attr, _attrtype; \
+ hsize_t _asize = 0; \
\
\
- if ((_attr = H5Aopen_name (dataset, attrname)) < 0) \
- { \
- CCTK_WARN (1, "Can't find " attrname " attribute"); \
- } \
+ _attr = H5Aopen_name (object, attrname); \
+ if (_attr >= 0) \
+ { \
if (requested_type == H5T_C_S1) \
{ \
- IOHDF5_ERROR (_attrtype = H5Aget_type (_attr)); \
- IOHDF5_ERROR (_asize = H5Tget_size (_attrtype)); \
+ HDF5_ERROR (_attrtype = H5Aget_type (_attr)); \
+ HDF5_ERROR (_asize = H5Tget_size (_attrtype)); \
if (_asize + 1 >= sizeof (buffer)) \
{ \
CCTK_WARN (1, "Can't read " attrname " attribute (too long)");\
@@ -96,81 +95,84 @@
} \
if (H5Aread (_attr, _attrtype, buffer) < 0) \
{ \
- CCTK_WARN (1, "Can't read " attrname " attribute"); \
+ CCTK_WARN (1, "Can't read '" attrname "' attribute"); \
} \
if (requested_type == H5T_C_S1) \
{ \
((char *) buffer)[_asize] = 0; \
- IOHDF5_ERROR (H5Tclose (_attrtype)); \
+ HDF5_ERROR (H5Tclose (_attrtype)); \
} \
- IOHDF5_ERROR (H5Aclose (_attr)); \
- } while (0)
+ HDF5_ERROR (H5Aclose (_attr)); \
+ } \
+ else \
+ { \
+ CCTK_WARN (1, "Can't find '" attrname "' attribute"); \
+ } \
+ }
-/***
- Define the different datatypes used for HDF5 I/O
- NOTE: the complex datatype is defined dynamically at runtime in Startup.c
+/*** 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
+#define HDF5_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 */
+ HDF5_REAL is used for storing reals of the generic CCTK_REAL type
+ HDF5_REALn is used to explicitely store n-byte reals */
#ifdef CCTK_REAL4
-#define IOHDF5_REAL4 H5T_NATIVE_FLOAT
+#define HDF5_REAL4 H5T_NATIVE_FLOAT
#endif
#ifdef CCTK_REAL8
-#define IOHDF5_REAL8 H5T_NATIVE_DOUBLE
+#define HDF5_REAL8 H5T_NATIVE_DOUBLE
#endif
#ifdef CCTK_REAL16
-#define IOHDF5_REAL16 (sizeof (CCTK_REAL16) == sizeof (long double) ? \
- H5T_NATIVE_LDOUBLE : -1)
+#define HDF5_REAL16 (sizeof (CCTK_REAL16) == sizeof (long double) ? \
+ H5T_NATIVE_LDOUBLE : -1)
#endif
#ifdef CCTK_REAL_PRECISION_16
-#define IOHDF5_REAL IOHDF5_REAL16
+#define HDF5_REAL HDF5_REAL16
#elif CCTK_REAL_PRECISION_8
-#define IOHDF5_REAL IOHDF5_REAL8
+#define HDF5_REAL HDF5_REAL8
#elif CCTK_REAL_PRECISION_4
-#define IOHDF5_REAL IOHDF5_REAL4
+#define HDF5_REAL HDF5_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 */
+ HDF5_INT is used for communicating integers of the generic CCTK_INT type
+ HDF5_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)
+#define HDF5_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)
+#define HDF5_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)
+#define HDF5_INT2 (sizeof (CCTK_INT2) == sizeof (short) ? \
+ H5T_NATIVE_SHORT : -1)
#endif
#ifdef CCTK_INTEGER_PRECISION_8
-#define IOHDF5_INT IOHDF5_INT8
+#define HDF5_INT HDF5_INT8
#elif CCTK_INTEGER_PRECISION_4
-#define IOHDF5_INT IOHDF5_INT4
+#define HDF5_INT HDF5_INT4
#elif CCTK_INTEGER_PRECISION_2
-#define IOHDF5_INT IOHDF5_INT2
+#define HDF5_INT HDF5_INT2
#endif
-/* Constants to index timers within the timers array */
+/* constants to index timers within the timers array */
#define CP_PARAMETERS_TIMER 0
#define CP_VARIABLES_TIMER 1
#define CP_TOTAL_TIMER 2
@@ -188,82 +190,86 @@ extern "C"
{
#endif
-/* Geometry information structure for output variable */
+/* structure for hyperslab descriptions of output variables */
typedef struct
{
- int vdim;
- int sdim;
- int *direction;
- int *origin;
- int *length;
- int *downsample;
- int *actlen; /* actual index slab length (by PUGHSlab)*/
-} ioHDF5Geo_t;
+ /* index and timelevel of the variable */
+ int vindex, timelevel;
+
+ /* dimensionality of the variable and the hyperslab */
+ int vdim, hdim;
+ /* CCTK datatype for the hyperslab */
+ int hdatatype;
-/* Structure describing a given recovery file */
+ /* flag indicating wheter check whether an object to be written already
+ exists (and remove it in that case) */
+ int check_exist;
+
+ /* pointer to allocated buffers */
+ CCTK_INT *vectors;
+
+ /* hyperslab mapping parameters */
+ CCTK_INT *origin, *direction, *extent, *downsample;
+
+ /* offset and sizes of hyperslab into the variable's dataspace */
+ CCTK_INT *hoffset, *hsize, *hsize_chunk;
+
+} ioSlab;
+
+
+/* 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) */
+ /* flag indicating valid file info */
+ int is_HDF5_file;
+
+ /* HDF5 file handle */
+ hid_t file;
+
+ /* complete file name for recovery */
+ char *filename;
+
+ /* number of total and I/O processors, the associated IO processor,
+ flag telling whether data was written chunked or unchunked */
+ int nprocs, ioproc_every, ioproc, unchunked;
+
+ /* whether file contains a Cactus version ID (used to distinguish checkpoint
+ files with old/new timelevel naming scheme) */
+ int has_version;
+
} fileinfo_t;
-/* IOHDF5Util GH extension structure */
+/* IOHDF5Util's 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;
+ hid_t HDF5_COMPLEX, HDF5_COMPLEX8, HDF5_COMPLEX16, HDF5_COMPLEX32;
/* predefined datatype for writing C string string attributes */
- hid_t IOHDF5_STRING;
+ hid_t HDF5_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_ParseVarsForOutput (const cGH *GH, const char *output_varstring,
+ ioSlab *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,
+void IOHDF5Util_DumpCommonAttributes (const cGH *GH, const ioSlab *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_DumpVar (const cGH *GH, const ioSlab *slab, hid_t file);
+
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);
+int IOHDF5Util_RecoverGHextensions (cGH *GH, const fileinfo_t *filenfo);
+int IOHDF5Util_RecoverVariables (cGH *GH, const fileinfo_t *filenfo);
#ifdef __cplusplus
} // extern "C"
diff --git a/src/make.configuration.defn b/src/make.configuration.defn
index 135342a..8879748 100644
--- a/src/make.configuration.defn
+++ b/src/make.configuration.defn
@@ -1,20 +1,12 @@
# make.configuration.defn for IOHDF5Util
+# $Header$
-# make sure that IOHDF5Util was configured with HDF5 and PUGH
-
-ifeq ($(strip $(HDF5_LIBS)), )
-$(NAME): MissingHDF5
-.pseudo: MissingHDF5
-MissingHDF5:
- @echo "IOHDF5Util: requires HDF5"
- @echo "IOHDF5Util: Please configure with HDF5 or remove IOHDF5Util from Thornlist !"
- exit 2
+# make sure that IOHDF5Util was configured with HDF5
+ifeq ($(strip $(HDF5_LIBS)),)
+ $(error "IOHDF5Util requires HDF5. Please configure with HDF5 or remove IOHDF5Util from Thornlist !"
endif
+# make sure that IOHDF5Util was configured with PUGH
ifeq ($(findstring CactusPUGH/PUGH,$(THORNS)),)
-.pseudo: MissingPUGHinIOHDF5Util
-MissingPUGHinIOHDF5Util:
- @echo "IOHDF5Util: requires PUGH"
- @echo "IOHDF5Util: Please add CactusPUGH/PUGH or remove IOHDF5Util from Thornlist !"
- exit 2
+ $(error "IOHDF5Util requires PUGH. Please add CactusPUGH/PUGH or remove IOHDF5Util from Thornlist !"
endif
generated by cgit v1.2.3 (git 2.39.1) at 2024-05-19 03:48:13 +0000