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Add support for Exodus IOSS properties related to field interpretatio…
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…n to the Catalyst IOSS Database (sandialabs#456)

* Refactored testing infrastructure to add transient unstructured fields

* First test failing, for wrong reason

* Test Fixture completed. First failing test done.

* Added failing tests for all 5 Props. Need to update Frwrk for Sur_Split_type

* Refactored get*block() to be public

* Added failing list for SURFACE_SPLIT_TYPE. Compromises made

* Fixed conduit error related to scoping. Refactored tests a bit

* Implemented Exodus IOSS properties. Removed asserts. Finished verifying fields

* Refactored readField() to not have DatabaseIO as parameter
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@ajpelle @tokusanya
ajpelle authored and tokusanya committed Jul 16, 2024
1 parent f185aa3 commit eb5eb69
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Showing 11 changed files with 710 additions and 26 deletions.
110 changes: 97 additions & 13 deletions packages/seacas/libraries/ioss/src/catalyst/Iocatalyst_DatabaseIO.C
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
#include <tokenize.h>

#include "Ioss_CommSet.h" // for CommSet
#include "Ioss_CodeTypes.h" // for IOSS_SCALAR()
#include "Ioss_DBUsage.h" // for DatabaseUsage, etc
#include "Ioss_DatabaseIO.h" // for DatabaseIO
#include "Ioss_EdgeBlock.h" // for EdgeBlock
Expand Down Expand Up @@ -141,6 +142,8 @@ namespace Iocatalyst {
inline static const std::string RANGEEND = "m_rangeEnd";
inline static const std::string FACE = "m_face";

inline static const std::string SURFACESPLITTYPE = "surface_split_type";

std::string getValuePath(const std::string &prop)
{
return detail::PROPERTIES + detail::FS + prop + detail::FS + detail::VALUE;
Expand Down Expand Up @@ -305,12 +308,17 @@ namespace Iocatalyst {

bool defineModel(Ioss::Region *region)
{
assert(region->model_defined());
if(!region->model_defined()) {
std::ostringstream errmsg;
errmsg << "Catalyst Write in defineModel(): model isn't defined in region"<<"\n";
IOSS_ERROR(errmsg);
}

auto &node = this->DBNode;
node = conduit_cpp::Node();

node[detail::getAPISizePath()].set_int8(region->get_database()->int_byte_size_api());
node[detail::SURFACESPLITTYPE].set_int8(region->get_database()->get_surface_split_type());
RegionContainer rc;
rc.push_back(region);
this->defineEntityGroup(node[detail::REGION], rc);
Expand Down Expand Up @@ -810,6 +818,24 @@ namespace Iocatalyst {
template <typename GroupingEntityT>
bool readFields(const conduit_cpp::Node &&parent, GroupingEntityT *block) const
{
//Assumption: count = entity_count (in block)
Ioss::DatabaseIO *dbase = block->get_database();
Ioss::EntityType b_t = block->type();
bool is_entity_block = false;
if(b_t == Ioss::EntityType::ELEMENTBLOCK ||
b_t == Ioss::EntityType::EDGEBLOCK ||
b_t == Ioss::EntityType::FACEBLOCK ||
b_t == Ioss::EntityType::NODEBLOCK ||
b_t == Ioss::EntityType::SIDEBLOCK ||
b_t == Ioss::EntityType::STRUCTUREDBLOCK) {
is_entity_block = true;
}
const int FNAME_MAX_LENGTH = 255;
size_t field_count = 0;
char **field_names =
Ioss::Utils::get_name_array(parent.number_of_children(), FNAME_MAX_LENGTH);
size_t entity_count = 0;

for (conduit_index_t idx = 0, max = parent.number_of_children(); idx < max; ++idx) {
auto &&child = parent[idx];
const auto name = child.name();
Expand All @@ -819,17 +845,43 @@ namespace Iocatalyst {
const auto index = child[detail::INDEX].as_int64();
const auto storage = child[detail::STORAGE].as_string();
if (!block->field_exists(name)) {
block->field_add(
if(storage == IOSS_SCALAR() && role==Ioss::Field::TRANSIENT && is_entity_block) {
//Add to get_fields() call
char field_name[FNAME_MAX_LENGTH + 1];
Ioss::Utils::copy_string(field_name, name, FNAME_MAX_LENGTH + 1);
Ioss::Utils::copy_string(field_names[field_count++], field_name, FNAME_MAX_LENGTH + 1);
if(entity_count == 0)
entity_count = count;
}
else {
block->field_add(
Ioss::Field(name, type, storage, role, count, index).set_zero_copy_enabled());
}
}
else {
// TODO verify field details.
auto field = block->get_fieldref(name);
if (!field.has_transform()) {
// Verify field details.
auto field_block = block->get_fieldref(name);
if (!field_block.has_transform()) {
block->get_fieldref(name).set_zero_copy_enabled();
}
assert(field.get_type() == type);
auto f = block->get_fieldref(name);
auto field_conduit = Ioss::Field(name, type, storage, role, count, index).set_zero_copy_enabled();
if(field_block != field_conduit) {
std::ostringstream errmsg;
errmsg << "Catalyst Read: Field '"<<name<<"' from conduit "<<
"already exists in block '"<<block->name().c_str()<<
"' of type '"<<block->type_string()<<"' and differs from it\n";
IOSS_ERROR(errmsg);
}
}
}

//Apply Exodus Properties to Scalar Fields in Entity Blocks
if(field_count > 0) {
std::vector<Ioss::Field> fields;
Ioss::Utils::get_fields(entity_count, field_names, field_count, Ioss::Field::TRANSIENT,
dbase, nullptr, fields);
for (const auto &field : fields) {
block->field_add(field.set_zero_copy_enabled());
}
}

Expand Down Expand Up @@ -1039,6 +1091,12 @@ namespace Iocatalyst {
auto &node = this->DBNode;
region->get_database()->set_int_byte_size_api(
static_cast<Ioss::DataSize>(node[detail::getAPISizePath()].as_int8()));
const auto write_split_type =
static_cast<Ioss::SurfaceSplitType>(node[detail::SURFACESPLITTYPE].as_int8());
if(write_split_type != region->get_database()->get_surface_split_type()) {
static_cast<DatabaseIO*>(region->get_database())->set_split_type_changed(true);
}

auto tpath = detail::REGION + detail::FS + detail::TIME;
if (node.has_path(tpath)) {
region->add_state(node[tpath].to_float64());
Expand All @@ -1048,8 +1106,14 @@ namespace Iocatalyst {
this->readEntityGroup<Ioss::ElementBlock>(node[detail::ELEMENTBLOCKS], region);
this->readEntityGroup<Ioss::EdgeBlock>(node[detail::EDGEBLOCKS], region);
this->readEntityGroup<Ioss::FaceBlock>(node[detail::FACEBLOCKS], region);
this->readEntityGroup<Ioss::SideBlock>(node[detail::SIDEBLOCKS], region);
this->readEntityGroup<Ioss::SideSet>(node[detail::SIDESETS], region);

bool surface_split_changed =
static_cast<DatabaseIO*>(region->get_database())->split_type_changed();
if(!surface_split_changed) {
this->readEntityGroup<Ioss::SideBlock>(node[detail::SIDEBLOCKS], region);
this->readEntityGroup<Ioss::SideSet>(node[detail::SIDESETS], region);
}

this->readEntityGroup<Ioss::NodeSet>(node[detail::NODESETS], region);
this->readEntityGroup<Ioss::EdgeSet>(node[detail::EDGESETS], region);
this->readEntityGroup<Ioss::FaceSet>(node[detail::FACESETS], region);
Expand Down Expand Up @@ -1116,11 +1180,19 @@ namespace Iocatalyst {

bool DatabaseIO::end_nl(Ioss::State state)
{
assert(this->dbState == state);
if(this->dbState != state) {
std::ostringstream errmsg;
errmsg << "Catalyst: dbState != state in end_nl"<<"\n";
IOSS_ERROR(errmsg);
}

if (!is_input()) {
auto region = this->get_region();
assert(region != nullptr);
if(region == nullptr) {
std::ostringstream errmsg;
errmsg << "Catalyst: region is nullptr in end_nl"<<"\n";
IOSS_ERROR(errmsg);
}

auto &impl = (*this->Impl.get());
switch (state) {
Expand Down Expand Up @@ -1180,7 +1252,11 @@ namespace Iocatalyst {
void DatabaseIO::read_meta_data_nl()
{
auto region = this->get_region();
assert(region != nullptr);
if(region == nullptr) {
std::ostringstream errmsg;
errmsg << "Catalyst: region is nullptr in read_meta_data_nl()"<<"\n";
IOSS_ERROR(errmsg);
}

auto &impl = (*this->Impl.get());
impl.readModel(region);
Expand All @@ -1189,7 +1265,11 @@ namespace Iocatalyst {
void DatabaseIO::get_step_times_nl()
{
auto region = this->get_region();
assert(region != nullptr);
if(region == nullptr) {
std::ostringstream errmsg;
errmsg << "Catalyst: region is nullptr in get_step_times_nl()"<<"\n";
IOSS_ERROR(errmsg);
}

auto &impl = (*this->Impl.get());
impl.readTime(region);
Expand Down Expand Up @@ -1420,6 +1500,7 @@ namespace Iocatalyst {
int64_t DatabaseIO::get_field_internal(const Ioss::SideBlock *sb, const Ioss::Field &field,
void *data, size_t data_size) const
{
if(split_type_changed()) { return -1; }
auto &impl = (*this->Impl.get());
return impl.getField(detail::SIDEBLOCKS, sb, field, data, data_size);
}
Expand Down Expand Up @@ -1450,6 +1531,7 @@ namespace Iocatalyst {
int64_t DatabaseIO::get_field_internal(const Ioss::SideSet *ss, const Ioss::Field &field,
void *data, size_t data_size) const
{
if(split_type_changed()) { return -1; }
auto &impl = (*this->Impl.get());
return impl.getField(detail::SIDESETS, ss, field, data, data_size);
}
Expand Down Expand Up @@ -1531,6 +1613,7 @@ namespace Iocatalyst {
int64_t DatabaseIO::get_zc_field_internal(const Ioss::SideBlock *sb, const Ioss::Field &field,
void **data, size_t *data_size) const
{
if(split_type_changed()) { return -1; }
auto &impl = (*this->Impl.get());
return impl.getFieldZeroCopy(detail::SIDEBLOCKS, sb, field, data, data_size);
}
Expand Down Expand Up @@ -1561,6 +1644,7 @@ namespace Iocatalyst {
int64_t DatabaseIO::get_zc_field_internal(const Ioss::SideSet *ss, const Ioss::Field &field,
void **data, size_t *data_size) const
{
if(split_type_changed()) { return -1; }
auto &impl = (*this->Impl.get());
return impl.getFieldZeroCopy(detail::SIDESETS, ss, field, data, data_size);
}
Expand Down
4 changes: 4 additions & 0 deletions packages/seacas/libraries/ioss/src/catalyst/Iocatalyst_DatabaseIO.h
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Original file line number Diff line number Diff line change
Expand Up @@ -85,6 +85,9 @@ namespace Iocatalyst {

std::string get_catalyst_dump_dir() const;

void set_split_type_changed(bool split_type_changed) { split_type_c = split_type_changed; }
IOSS_NODISCARD bool split_type_changed() const { return split_type_c; }

private:
bool open_group_nl(const std::string & /* group_name */) override { return false; }
bool create_subgroup_nl(const std::string & /* group_name */) override { return false; }
Expand Down Expand Up @@ -202,5 +205,6 @@ namespace Iocatalyst {
class ImplementationT;
std::unique_ptr<ImplementationT> Impl;
bool useDeepCopy;
bool split_type_c{false};
};
} // namespace Iocatalyst
20 changes: 20 additions & 0 deletions packages/seacas/libraries/ioss/src/catalyst_tests/Iocatalyst_BlockMesh.C
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Original file line number Diff line number Diff line change
Expand Up @@ -291,4 +291,24 @@ namespace Iocatalyst {
return (extents.i + offset) * (extents.j + offset) * (extents.k + offset);
}

std::map<std::string, double>* BlockMesh::getTransientCellFieldMap()
{
return &(this->transientCellFields);
}

std::map<std::string, double>* BlockMesh::getTransientPointFieldMap()
{
return &(this->transientPointFields);
}

void BlockMesh::addTransientCellField(std::string f_name, double f_value)
{
this->transientCellFields.insert({ f_name, f_value });
}

void BlockMesh::addTransientPointField(std::string f_name, double f_value)
{
this->transientPointFields.insert({ f_name, f_value });
}

} // namespace Iocatalyst
9 changes: 9 additions & 0 deletions packages/seacas/libraries/ioss/src/catalyst_tests/Iocatalyst_BlockMesh.h
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Original file line number Diff line number Diff line change
Expand Up @@ -82,6 +82,12 @@ namespace Iocatalyst {
static Extent getCoordsForID(ID id, Extent bounds);
static ID getIDfromCoords(Extent coords, Extent bounds);

void addTransientCellField(std::string f_name, double f_value);
void addTransientPointField(std::string f_name, double f_value);

std::map<std::string, double>* getTransientCellFieldMap();
std::map<std::string, double>* getTransientPointFieldMap();

private:
Partition partition;
Extent origin;
Expand All @@ -98,6 +104,9 @@ namespace Iocatalyst {
int getNumInBlockMesh(unsigned int offset) const;
ID id;
static ID _id;

std::map<std::string, double> transientCellFields;
std::map<std::string, double> transientPointFields;
};

} // namespace Iocatalyst
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