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Merge pull request iraikov#6 from iraikov/feature/aggregate_append
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Fixes and improvements to parallel append
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@iraikov
iraikov authored Jul 20, 2023
2 parents 54c0b38 + 767b08e commit e646078
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Showing 17 changed files with 971 additions and 311 deletions.
127 changes: 6 additions & 121 deletions include/cell/append_tree.hh
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Original file line number Diff line number Diff line change
Expand Up @@ -62,146 +62,31 @@ namespace neuroh5
/*****************************************************************************
* Save tree data structures to HDF5
*****************************************************************************/
template <class T>
int append_trees
(
MPI_Comm comm,
const std::string& file_name,
MPI_Comm io_comm,
hid_t loc,
const std::string& pop_name,
const CELL_IDX_T& pop_start,
std::forward_list<neurotree_t> &tree_list,
const set<size_t> &io_rank_set,
CellPtr ptr_type = CellPtr(PtrOwner),
const size_t chunk_size = 4000,
const size_t value_chunk_size = 4000
)
{
herr_t status;

unsigned int rank, size;
throw_assert_nomsg(MPI_Comm_size(comm, (int*)&size) == MPI_SUCCESS);
throw_assert_nomsg(MPI_Comm_rank(comm, (int*)&rank) == MPI_SUCCESS);


std::vector<SEC_PTR_T> sec_ptr;
std::vector<TOPO_PTR_T> topo_ptr;
std::vector<ATTR_PTR_T> attr_ptr;

std::vector<CELL_IDX_T> all_index_vector;
std::vector<SECTION_IDX_T> all_src_vector, all_dst_vector;
std::vector<COORD_T> all_xcoords, all_ycoords, all_zcoords; // coordinates of nodes
std::vector<REALVAL_T> all_radiuses; // Radius
std::vector<LAYER_IDX_T> all_layers; // Layer
std::vector<SECTION_IDX_T> all_sections; // Section
std::vector<PARENT_NODE_IDX_T> all_parents; // Parent
std::vector<SWC_TYPE_T> all_swc_types; // SWC Types

if (ptr_type.type == PtrNone)
{
status = build_singleton_tree_datasets(comm,
tree_list,
all_src_vector, all_dst_vector,
all_xcoords, all_ycoords, all_zcoords,
all_radiuses, all_layers, all_sections,
all_parents, all_swc_types);
}
else
{
status = build_tree_datasets(comm,
tree_list,
sec_ptr, topo_ptr, attr_ptr,
all_index_vector, all_src_vector, all_dst_vector,
all_xcoords, all_ycoords, all_zcoords,
all_radiuses, all_layers, all_sections,
all_parents, all_swc_types);
throw_assert_nomsg(status >= 0);
}


throw_assert_nomsg(append_cell_index (comm, file_name, pop_name, pop_start,
hdf5::TREES, all_index_vector) == 0);

const data::optional_hid dflt_data_type;
const data::optional_hid coord_data_type(COORD_H5_NATIVE_T);
const data::optional_hid layer_data_type(LAYER_IDX_H5_NATIVE_T);
const data::optional_hid parent_node_data_type(PARENT_NODE_IDX_H5_NATIVE_T);
const data::optional_hid section_data_type(SECTION_IDX_H5_NATIVE_T);
const data::optional_hid swc_data_type(SWC_TYPE_H5_NATIVE_T);

string attr_ptr_owner_path = hdf5::cell_attribute_path(hdf5::TREES, pop_name, hdf5::X_COORD) + "/" + hdf5::ATTR_PTR;
string sec_ptr_owner_path = hdf5::cell_attribute_path(hdf5::TREES, pop_name, hdf5::SRCSEC) + "/" + hdf5::SEC_PTR;

append_cell_attribute (comm, file_name, hdf5::TREES, pop_name, pop_start, hdf5::X_COORD,
all_index_vector, attr_ptr, all_xcoords,
coord_data_type, IndexShared,
CellPtr (PtrOwner, hdf5::ATTR_PTR),
chunk_size, value_chunk_size);
append_cell_attribute (comm, file_name, hdf5::TREES, pop_name, pop_start, hdf5::Y_COORD,
all_index_vector, attr_ptr, all_ycoords,
coord_data_type, IndexShared,
CellPtr (PtrShared, attr_ptr_owner_path),
chunk_size, value_chunk_size);
append_cell_attribute (comm, file_name, hdf5::TREES, pop_name, pop_start, hdf5::Z_COORD,
all_index_vector, attr_ptr, all_zcoords,
coord_data_type, IndexShared,
CellPtr (PtrShared, attr_ptr_owner_path),
chunk_size, value_chunk_size);
append_cell_attribute (comm, file_name, hdf5::TREES, pop_name, pop_start, hdf5::RADIUS,
all_index_vector, attr_ptr, all_radiuses,
dflt_data_type, IndexShared,
CellPtr (PtrShared, attr_ptr_owner_path),
chunk_size, value_chunk_size);
append_cell_attribute (comm, file_name, hdf5::TREES, pop_name, pop_start, hdf5::LAYER,
all_index_vector, attr_ptr, all_layers,
layer_data_type, IndexShared,
CellPtr (PtrShared, attr_ptr_owner_path),
chunk_size, value_chunk_size);
append_cell_attribute (comm, file_name, hdf5::TREES, pop_name, pop_start, hdf5::PARENT,
all_index_vector, attr_ptr, all_parents,
parent_node_data_type, IndexShared,
CellPtr (PtrShared, attr_ptr_owner_path),
chunk_size, value_chunk_size);

append_cell_attribute (comm, file_name, hdf5::TREES, pop_name, pop_start, hdf5::SWCTYPE,
all_index_vector, attr_ptr, all_swc_types,
swc_data_type, IndexShared,
CellPtr (PtrShared, attr_ptr_owner_path),
chunk_size, value_chunk_size);
append_cell_attribute (comm, file_name, hdf5::TREES, pop_name, pop_start, hdf5::SRCSEC,
all_index_vector, topo_ptr, all_src_vector,
section_data_type, IndexShared,
CellPtr (PtrOwner, hdf5::SEC_PTR),
chunk_size, value_chunk_size);
append_cell_attribute (comm, file_name, hdf5::TREES, pop_name, pop_start, hdf5::DSTSEC,
all_index_vector, topo_ptr, all_dst_vector,
section_data_type, IndexShared,
CellPtr (PtrShared, sec_ptr_owner_path),
chunk_size, value_chunk_size);

append_cell_attribute (comm, file_name, hdf5::TREES, pop_name, pop_start, hdf5::SECTION,
all_index_vector, sec_ptr, all_sections,
section_data_type, IndexShared,
CellPtr (PtrOwner, hdf5::SEC_PTR),
chunk_size, value_chunk_size);


return 0;
}
);

template<class T>
int append_trees
(
MPI_Comm comm,
const std::string& file_name,
const std::string& pop_name,
const CELL_IDX_T& pop_start,
std::forward_list<neurotree_t> &tree_list,
size_t io_size,
const size_t chunk_size,
const size_t value_chunk_size
)
{
return append_trees<T>(comm, file_name, pop_name, pop_start, tree_list,
CellPtr(PtrOwner), chunk_size, value_chunk_size);
}
);

}
}
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