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Diffstat (limited to 'Carpet/CarpetIOHDF5/src/Output.cc')
-rw-r--r--Carpet/CarpetIOHDF5/src/Output.cc99
1 files changed, 68 insertions, 31 deletions
diff --git a/Carpet/CarpetIOHDF5/src/Output.cc b/Carpet/CarpetIOHDF5/src/Output.cc
index 675c51bc6..62f9d9778 100644
--- a/Carpet/CarpetIOHDF5/src/Output.cc
+++ b/Carpet/CarpetIOHDF5/src/Output.cc
@@ -72,18 +72,25 @@ int WriteVarUnchunked (const cGH* const cctkGH,
BEGIN_MAP_LOOP (cctkGH, group.grouptype) {
// Collect the set of all components' bboxes
ibset bboxes;
- BEGIN_COMPONENT_LOOP (cctkGH, group.grouptype) {
+ for (int c=0; c<arrdata.at(gindex).at(Carpet::map).hh->components(refinementlevel); ++c) {
// Using "interior" removes ghost zones and refinement boundaries.
+#if 0
bboxes += arrdata.at(gindex).at(Carpet::map).dd->
- boxes.at(mglevel).at(refinementlevel).at(component).interior;
- } END_COMPONENT_LOOP;
+ boxes.at(mglevel).at(refinementlevel).at(c).interior;
+#endif
+ bboxes += arrdata.at(gindex).at(Carpet::map).dd->
+ boxes.at(mglevel).at(refinementlevel).at(c).exterior;
+ }
// Normalise the set, i.e., try to represent the set with fewer bboxes.
- //
+ bboxes.normalize();
+
+#if 0
// According to Cactus conventions, DISTRIB=CONSTANT arrays
// (including grid scalars) are assumed to be the same on all
// processors and are therefore stored only by processor 0.
- if (group.disttype != CCTK_DISTRIB_CONSTANT) bboxes.normalize();
+ if (group.disttype != CCTK_DISTRIB_CONSTANT);
+#endif
// Loop over all components in the bbox set
int bbox_id = 0;
@@ -150,6 +157,11 @@ int WriteVarUnchunked (const cGH* const cctkGH,
HDF5_ERROR (H5Pset_chunk (plist, group.dim, shape));
HDF5_ERROR (H5Pset_deflate (plist, compression_lvl));
}
+ // enable checksums if requested
+ if (use_checksums) {
+ HDF5_ERROR (H5Pset_chunk (plist, group.dim, shape));
+ HDF5_ERROR (H5Pset_filter (plist, H5Z_FILTER_FLETCHER32, 0, 0, NULL));
+ }
HDF5_ERROR (dataset = H5Dcreate (outfile, datasetname.str().c_str(),
filedatatype, dataspace, plist));
HDF5_ERROR (H5Pclose (plist));
@@ -160,24 +172,33 @@ int WriteVarUnchunked (const cGH* const cctkGH,
BEGIN_COMPONENT_LOOP (cctkGH, group.grouptype) {
// Get the intersection of the current component with this combination
// (use either the interior or exterior here, as we did above)
+ gh const * const hh = arrdata.at(gindex).at(Carpet::map).hh;
+ dh const * const dd = arrdata.at(gindex).at(Carpet::map).dd;
+#if 0
ibbox const overlap = *bbox &
- arrdata.at(gindex).at(Carpet::map).dd->
- boxes.at(mglevel).at(refinementlevel).at(component).interior;
+ dd->boxes.at(mglevel).at(refinementlevel).at(component).interior;
+#endif
+ ibbox const overlap = *bbox &
+ dd->boxes.at(mglevel).at(refinementlevel).at(component).exterior;
// Continue if this component is not part of this combination
if (overlap.empty()) continue;
// Copy the overlap to the local processor
const ggf* ff = arrdata.at(gindex).at(Carpet::map).data.at(var);
- const gdata* const data = (*ff) (request->timelevel,
- refinementlevel,
- component, mglevel);
+ const gdata* const data =
+ local_component >= 0
+ ? (*ff) (request->timelevel, refinementlevel,
+ local_component, mglevel)
+ : NULL;
+ // TODO: This does not work; data may be NULL
gdata* const processor_component =
data->make_typed (request->vindex, error_centered, op_sync);
processor_component->allocate (overlap, 0);
for (comm_state state; not state.done(); state.step()) {
- processor_component->copy_from (state, data, overlap);
+ int const p = hh->processor(refinementlevel,component);
+ processor_component->copy_from (state, data, overlap, 0, p);
}
// Write data
@@ -207,12 +228,7 @@ int WriteVarUnchunked (const cGH* const cctkGH,
// before HDF5-1.6.4 the H5Sselect_hyperslab() function expected
// the 'start' argument to be of type 'hssize_t'
-#if (H5_VERS_MAJOR == 1 && \
- (H5_VERS_MINOR < 6 || (H5_VERS_MINOR == 6 && H5_VERS_RELEASE < 4)))
- hssize_t overlaporigin[dim];
-#else
- hsize_t overlaporigin[dim];
-#endif
+ slice_start_size_t overlaporigin[dim];
for (int d = 0; d < group.dim; ++d) {
assert (group.dim-1-d>=0 and group.dim-1-d<dim);
overlaporigin[group.dim-1-d] =
@@ -321,8 +337,10 @@ int WriteVarChunkedSequential (const cGH* const cctkGH,
BEGIN_MAP_LOOP (cctkGH, group.grouptype) {
BEGIN_COMPONENT_LOOP (cctkGH, group.grouptype) {
// Using "exterior" includes ghost zones and refinement boundaries.
- ibbox& bbox = arrdata.at(gindex).at(Carpet::map).dd->
- boxes.at(mglevel).at(refinementlevel).at(component).exterior;
+ gh const * const hh = arrdata.at(gindex).at(Carpet::map).hh;
+ dh const * const dd = arrdata.at(gindex).at(Carpet::map).dd;
+ ibbox const& bbox =
+ dd->boxes.at(mglevel).at(refinementlevel).at(component).exterior;
// Get the shape of the HDF5 dataset (in Fortran index order)
hsize_t shape[dim];
@@ -338,14 +356,19 @@ int WriteVarChunkedSequential (const cGH* const cctkGH,
// Copy the overlap to the local processor
const ggf* ff = arrdata.at(gindex).at(Carpet::map).data.at(var);
- const gdata* const data = (*ff) (request->timelevel, refinementlevel,
- component, mglevel);
+ const gdata* const data =
+ local_component >= 0
+ ? (*ff) (request->timelevel, refinementlevel,
+ local_component, mglevel)
+ : NULL;
+ // TODO: This does not work; data may be NULL
gdata* const processor_component =
- data->make_typed (request->vindex,error_centered, op_sync);
+ data->make_typed (request->vindex, error_centered, op_sync);
processor_component->allocate (bbox, 0);
for (comm_state state; not state.done(); state.step()) {
- processor_component->copy_from (state, data, bbox);
+ int const p = hh->processor(refinementlevel,component);
+ processor_component->copy_from (state, data, bbox, 0, p);
}
// Write data on I/O processor 0
@@ -412,6 +435,11 @@ int WriteVarChunkedSequential (const cGH* const cctkGH,
HDF5_ERROR (H5Pset_chunk (plist, group.dim, shape));
HDF5_ERROR (H5Pset_deflate (plist, compression_lvl));
}
+ // enable checksums if requested
+ if (use_checksums) {
+ HDF5_ERROR (H5Pset_chunk (plist, group.dim, shape));
+ HDF5_ERROR (H5Pset_filter (plist, H5Z_FILTER_FLETCHER32, 0, 0, NULL));
+ }
HDF5_ERROR (dataspace = H5Screate_simple (group.dim, shape, NULL));
HDF5_ERROR (dataset = H5Dcreate (outfile, datasetname.str().c_str(),
filedatatype, dataspace, plist));
@@ -479,13 +507,17 @@ int WriteVarChunkedParallel (const cGH* const cctkGH,
out_single_precision and not called_from_checkpoint));
// Traverse all maps
- BEGIN_MAP_LOOP (cctkGH, group.grouptype) {
+ BEGIN_LOCAL_MAP_LOOP (cctkGH, group.grouptype) {
BEGIN_LOCAL_COMPONENT_LOOP (cctkGH, group.grouptype) {
- const ggf* ff = arrdata.at(gindex).at(Carpet::map).data.at(var);
- const ibbox& bbox = (*ff) (request->timelevel, refinementlevel,
- group.disttype == CCTK_DISTRIB_CONSTANT ?
- 0 : component, mglevel)->extent();
+ // const ggf* ff = arrdata.at(gindex).at(Carpet::map).data.at(var);
+ // const ibbox& bbox = (*ff) (request->timelevel, refinementlevel,
+ // group.disttype == CCTK_DISTRIB_CONSTANT ?
+ // 0 : component, mglevel)->extent();
+ const dh* dd = arrdata.at(gindex).at(Carpet::map).dd;
+ const ibbox& bbox =
+ dd->boxes.AT(mglevel).AT(refinementlevel)
+ .AT(group.disttype == CCTK_DISTRIB_CONSTANT ? 0 : component).exterior;
// Don't create zero-sized components
if (bbox.empty()) continue;
@@ -499,8 +531,8 @@ int WriteVarChunkedParallel (const cGH* const cctkGH,
MPI_Datatype datatype;
switch (group.vartype) {
-#define TYPECASE(N,T) \
- case N: { T dummy; datatype = dist::datatype(dummy); } break;
+#define TYPECASE(N,T) \
+ case N: { T dummy; datatype = dist::mpi_datatype(dummy); } break;
#include "carpet_typecase.hh"
#undef TYPECASE
default: assert (0 and "invalid datatype");
@@ -565,6 +597,11 @@ int WriteVarChunkedParallel (const cGH* const cctkGH,
HDF5_ERROR (H5Pset_chunk (plist, group.dim, shape));
HDF5_ERROR (H5Pset_deflate (plist, compression_lvl));
}
+ // enable checksums if requested
+ if (use_checksums) {
+ HDF5_ERROR (H5Pset_chunk (plist, group.dim, shape));
+ HDF5_ERROR (H5Pset_filter (plist, H5Z_FILTER_FLETCHER32, 0, 0, NULL));
+ }
HDF5_ERROR (dataspace = H5Screate_simple (group.dim, shape, NULL));
HDF5_ERROR (dataset = H5Dcreate (outfile, datasetname.str().c_str(),
filedatatype, dataspace, plist));
@@ -581,7 +618,7 @@ int WriteVarChunkedParallel (const cGH* const cctkGH,
if (data != mydata) free (data);
} END_LOCAL_COMPONENT_LOOP;
- } END_MAP_LOOP;
+ } END_LOCAL_MAP_LOOP;
free (fullname);
generated by cgit v1.2.3 (git 2.39.1) at 2024-06-04 18:10:48 +0000