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Catalyst API 2 (#461)
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Fixed crash bug when IOSS field suffix separator is empty.

Added tests for case when reading from Conduit files written
by Catalyst IOSS database.

Changed time step selection when reading from Conduit files to use
the IOSS integer property CATALYST_READER_TIME_STEP instead of IOSS
database filename.
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@tjotaha
tjotaha authored Jun 12, 2024
1 parent 2d2a558 commit b03564a
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Showing 5 changed files with 270 additions and 164 deletions.
147 changes: 75 additions & 72 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 @@ -70,6 +70,7 @@ namespace Iocatalyst {
inline static const std::string BOUNDARYCONDS = "boundaryconditions";
inline static const std::string CATCONDNODE = "CATALYST_CONDUIT_NODE";
inline static const std::string CATDUMPDIR = "CATALYST_DATA_DUMP_DIRECTORY";
inline static const std::string CATREADTIMESTEP = "CATALYST_READER_TIME_STEP";
inline static const std::string COMPONENTCOUNT = "component_count";
inline static const std::string COMPONENTDEGREE = "component_degree";
inline static const std::string COUNT = "count";
Expand Down Expand Up @@ -115,7 +116,6 @@ namespace Iocatalyst {
inline static const std::string ROLE = "role";
inline static const std::string SHALLOWCOPYFIELDS = "SHALLOW_COPY_FIELDS";
inline static const std::string SIDEBLOCKS = "sideblocks";
inline static const std::string STATETIME = "state_time";
inline static const std::string STORAGE = "storage";
inline static const std::string TIME = "time";
inline static const std::string TOPOLOGYTYPE = "topology_type";
Expand Down Expand Up @@ -289,6 +289,7 @@ namespace Iocatalyst {
conduit_cpp::Node DBNode;
mutable Ioss::Map NodeMap;
std::map<std::string, Ioss::SideBlock *> sideBlocks;
char read_db_field_separator;

public:
conduit_cpp::Node &databaseNode() { return this->DBNode; }
Expand Down Expand Up @@ -348,9 +349,8 @@ namespace Iocatalyst {
bool readTime(Ioss::Region *region)
{
auto &node = this->DBNode;
if (node.has_child(detail::STATETIME)) {
const auto time = node[detail::STATETIME].as_float64();
region->add_state(time);
if (node.has_path(getTimePath())) {
region->add_state(node[getTimePath()].as_float64());
}
return true;
}
Expand Down Expand Up @@ -585,6 +585,8 @@ namespace Iocatalyst {
return retVal;
}

std::string getTimePath() { return detail::DATABASE + detail::FS + detail::TIME; }

Ioss::Map &get_node_map(const Ioss::DatabaseIO *dbase) const
{
if (this->NodeMap.defined()) {
Expand Down Expand Up @@ -818,96 +820,93 @@ namespace Iocatalyst {

std::vector<std::string> getScalarNamesFromNonScalarField(const Ioss::Field &field) const
{
int ncomp = field.get_component_count(Ioss::Field::InOut::INPUT);
int ncomp = field.get_component_count(Ioss::Field::InOut::INPUT);
std::vector<std::string> fnames;
for(int i=1; i<=ncomp; i++){
fnames.push_back(field.get_component_name(i, Ioss::Field::InOut::INPUT));
for (int i = 1; i <= ncomp; i++) {
if (read_db_field_separator == '\0') {
fnames.push_back(
field.get_component_name(i, Ioss::Field::InOut::INPUT, read_db_field_separator));
}
else {
fnames.push_back(field.get_component_name(i, Ioss::Field::InOut::INPUT));
}
}
return fnames;
}

template <typename T>
std::vector<T> getInterweavedScalarDataFromConduitNode(const std::vector<std::string> fnames, conduit_cpp::Node &node) const
std::vector<T> getInterweavedScalarDataFromConduitNode(const std::vector<std::string> fnames,
conduit_cpp::Node &node) const
{
int ncomp = fnames.size();
auto &&t_node = node[fnames[0] + detail::FS + detail::VALUE];
int num_get = t_node.number_of_elements();
std::vector<T> vals(ncomp*num_get);
for(int i=0; i<num_get; i++) {
for(int j=0; j<ncomp; j++){
int ncomp = fnames.size();
auto &&t_node = node[fnames[0] + detail::FS + detail::VALUE];
int num_get = t_node.number_of_elements();
std::vector<T> vals(ncomp * num_get);

for (int i = 0; i < num_get; i++) {
for (int j = 0; j < ncomp; j++) {
std::string path_to_value = fnames[j] + detail::FS + detail::VALUE;
auto &&child_value = node[path_to_value];
vals[i*ncomp + j] =
reinterpret_cast<const T *>(child_value.element_ptr(0))[i];
auto &&child_value = node[path_to_value];
vals[i * ncomp + j] = reinterpret_cast<const T *>(child_value.element_ptr(0))[i];
}
}
return vals;
}

template <typename T>
void addFieldNodeAndDataToConduitNode(const Ioss::Field &field, void *data, conduit_cpp::Node &node) const
void addFieldNodeAndDataToConduitNode(const Ioss::Field &field, void *data,
conduit_cpp::Node &node) const
{
int ncomp = field.get_component_count(Ioss::Field::InOut::INPUT);
int num_get = field.raw_count();
int ncomp = field.get_component_count(Ioss::Field::InOut::INPUT);
int num_get = field.raw_count();
node[field.get_name()] = conduit_cpp::Node();
auto &&f_node = node[field.get_name()];
auto &&f_node = node[field.get_name()];
f_node[detail::ROLE].set(static_cast<std::int8_t>(field.get_role()));
f_node[detail::TYPE].set(static_cast<std::int8_t>(field.get_type()));
f_node[detail::COUNT].set(static_cast<std::int64_t>(field.raw_count()));
f_node[detail::INDEX].set(static_cast<std::int64_t>(field.get_index()));
f_node[detail::COMPONENTCOUNT].set(static_cast<std::int64_t>(ncomp));
f_node[detail::STORAGE].set(field.raw_storage()->name());
f_node[detail::VALUE].set(static_cast< T *>(data), ncomp * num_get);
f_node[detail::VALUE].set(static_cast<T *>(data), ncomp * num_get);
}

void combineScalarFieldsInConduitNodeToNonScalarField(
const Ioss::Field &field, conduit_cpp::Node &node) const
void combineScalarFieldsInConduitNodeToNonScalarField(const Ioss::Field &field,
conduit_cpp::Node &node) const
{
std::vector<std::string> fnames =
this->getScalarNamesFromNonScalarField(field);
std::vector<std::string> fnames = this->getScalarNamesFromNonScalarField(field);

switch (field.get_type()) {
case Ioss::Field::BasicType::DOUBLE:
this->addFieldNodeAndDataToConduitNode<double>(
field,
this->getInterweavedScalarDataFromConduitNode<double>(fnames, node).data(),
node
);
break;
case Ioss::Field::BasicType::DOUBLE:
this->addFieldNodeAndDataToConduitNode<double>(
field, this->getInterweavedScalarDataFromConduitNode<double>(fnames, node).data(),
node);
break;

case Ioss::Field::BasicType::INT32:
this->addFieldNodeAndDataToConduitNode<std::int32_t>(
field,
this->getInterweavedScalarDataFromConduitNode<std::int32_t>(fnames, node).data(),
node
);
break;
case Ioss::Field::BasicType::INT32:
this->addFieldNodeAndDataToConduitNode<std::int32_t>(
field, this->getInterweavedScalarDataFromConduitNode<std::int32_t>(fnames, node).data(),
node);
break;

case Ioss::Field::BasicType::INT64:
this->addFieldNodeAndDataToConduitNode<std::int64_t>(
field,
this->getInterweavedScalarDataFromConduitNode<std::int64_t>(fnames, node).data(),
node
);
break;
case Ioss::Field::BasicType::INT64:
this->addFieldNodeAndDataToConduitNode<std::int64_t>(
field, this->getInterweavedScalarDataFromConduitNode<std::int64_t>(fnames, node).data(),
node);
break;

case Ioss::Field::BasicType::CHARACTER:
this->addFieldNodeAndDataToConduitNode<std::int8_t>(
field,
this->getInterweavedScalarDataFromConduitNode<char>(fnames, node).data(),
node
);
break;
default:
std::ostringstream errmsg;
fmt::print(errmsg, "ERROR in {} on read: {}, unsupported field type: {}\n", __func__,
field.get_name(), field.type_string());
IOSS_ERROR(errmsg);
case Ioss::Field::BasicType::CHARACTER:
this->addFieldNodeAndDataToConduitNode<std::int8_t>(
field, this->getInterweavedScalarDataFromConduitNode<char>(fnames, node).data(), node);
break;
default:
std::ostringstream errmsg;
fmt::print(errmsg, "ERROR in {} on read: {}, unsupported field type: {}\n", __func__,
field.get_name(), field.type_string());
IOSS_ERROR(errmsg);
}
//Remove Related Scalars from Conduit Node
for(int i=0; i<fnames.size(); i++) {

// Remove Related Scalars from Conduit Node
for (int i = 0; i < fnames.size(); i++) {
node.remove(fnames[i]);
}
}
Expand Down Expand Up @@ -976,7 +975,7 @@ namespace Iocatalyst {
}

for (const auto &field : fields) {
if(field.raw_storage()->name() != IOSS_SCALAR()) {
if (field.raw_storage()->name() != IOSS_SCALAR()) {
this->combineScalarFieldsInConduitNodeToNonScalarField(field, parent);
}
}
Expand All @@ -992,6 +991,7 @@ namespace Iocatalyst {
{
for (conduit_index_t idx = 0, max = parent.number_of_children(); idx < max; ++idx) {
auto &&child = parent[idx];

this->readProperties(child[detail::PROPERTIES], region);

// read fields (meta-data only)
Expand Down Expand Up @@ -1193,10 +1193,10 @@ namespace Iocatalyst {
if (write_split_type != region->get_database()->get_surface_split_type()) {
static_cast<DatabaseIO *>(region->get_database())->set_split_type_changed(true);
}
read_db_field_separator = region->get_database()->get_field_separator();

auto tpath = detail::REGION + detail::FS + detail::TIME;
if (node.has_path(tpath)) {
region->add_state(node[tpath].to_float64());
if (node.has_path(getTimePath())) {
region->add_state(node[getTimePath()].to_float64());
}
this->readEntityGroup<Ioss::Region>(node[detail::REGION], region);
this->readEntityGroup<Ioss::NodeBlock>(node[detail::NODEBLOCKS], region);
Expand Down Expand Up @@ -1239,14 +1239,17 @@ namespace Iocatalyst {
if (is_input()) {
auto &pm = get_property_manager();
if (pm.exists(detail::CATCONDNODE)) {
auto c_node_ptr = reinterpret_cast<conduit_node *>(
get_property_manager().get(detail::CATCONDNODE).get_pointer());
auto c_node_ptr =
reinterpret_cast<conduit_node *>(pm.get(detail::CATCONDNODE).get_pointer());
this->Impl->setDatabaseNode(c_node_ptr);
}
else {
// we'll use filename as the location for the data dumps and read those.
int timestep = 1;
if (pm.exists(detail::CATREADTIMESTEP)) {
timestep = pm.get(detail::CATREADTIMESTEP).get_int();
}
std::ostringstream path;
path << get_catalyst_dump_dir() << detail::EXECUTE_INVC << filename
path << get_catalyst_dump_dir() << detail::EXECUTE_INVC << timestep
<< detail::PARAMS_CONDUIT_BIN << util().parallel_size() << detail::DOT
<< util().parallel_rank();
auto &root = this->Impl->root();
Expand Down Expand Up @@ -1333,7 +1336,7 @@ namespace Iocatalyst {
// invoke catalyst.
auto &impl = (*this->Impl.get());
auto &dbaseNode = this->Impl->databaseNode();
dbaseNode[detail::REGION + detail::FS + detail::TIME].set_float64(time);
dbaseNode[this->Impl->getTimePath()].set_float64(time);
conduit_cpp::Node node;
CatalystManager::getInstance().execute(catPipeID, state, time, impl.databaseNode());
}
Expand Down
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