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Fix performance regression in libMesh unstructured mesh tallies (#3577)
This commit is contained in:
Kevin Sawatzky
GitHub
parent
8f36ff2b3a
commit
ed433fe1cd
2 changed files with 101 additions and 57 deletions
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@ -990,25 +990,26 @@ public:
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libMesh::MeshBase* mesh_ptr() const { return m_; };
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protected:
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// Methods
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//! Translate a bin value to an element reference
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virtual const libMesh::Elem& get_element_from_bin(int bin) const;
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//! Translate an element pointer to a bin index
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virtual int get_bin_from_element(const libMesh::Elem* elem) const;
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libMesh::MeshBase* m_; //!< pointer to libMesh MeshBase instance, always set
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//!< during intialization
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private:
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void initialize() override;
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void set_mesh_pointer_from_filename(const std::string& filename);
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void build_eqn_sys();
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// Methods
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//! Translate a bin value to an element reference
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const libMesh::Elem& get_element_from_bin(int bin) const;
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//! Translate an element pointer to a bin index
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int get_bin_from_element(const libMesh::Elem* elem) const;
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// Data members
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unique_ptr<libMesh::MeshBase> unique_m_ =
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nullptr; //!< pointer to the libMesh MeshBase instance, only used if mesh is
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//!< created inside OpenMC
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libMesh::MeshBase* m_; //!< pointer to libMesh MeshBase instance, always set
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//!< during intialization
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vector<unique_ptr<libMesh::PointLocatorBase>>
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pl_; //!< per-thread point locators
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unique_ptr<libMesh::EquationSystems>
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@ -1022,8 +1023,34 @@ private:
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libMesh::BoundingBox bbox_; //!< bounding box of the mesh
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libMesh::dof_id_type
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first_element_id_; //!< id of the first element in the mesh
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};
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class AdaptiveLibMesh : public LibMesh {
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public:
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// Constructor
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AdaptiveLibMesh(
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libMesh::MeshBase& input_mesh, double length_multiplier = 1.0);
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// Overridden methods
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int n_bins() const override;
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void add_score(const std::string& var_name) override;
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void set_score_data(const std::string& var_name, const vector<double>& values,
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const vector<double>& std_dev) override;
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void write(const std::string& filename) const override;
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protected:
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// Overridden methods
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int get_bin_from_element(const libMesh::Elem* elem) const override;
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const libMesh::Elem& get_element_from_bin(int bin) const override;
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private:
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// Data members
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const libMesh::dof_id_type num_active_; //!< cached number of active elements
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const bool adaptive_; //!< whether this mesh has adaptivity enabled or not
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std::vector<libMesh::dof_id_type>
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bin_to_elem_map_; //!< mapping bin indices to dof indices for active
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//!< elements
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109
src/mesh.cpp
109
src/mesh.cpp
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@ -3219,7 +3219,7 @@ void MOABMesh::write(const std::string& base_filename) const
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const std::string LibMesh::mesh_lib_type = "libmesh";
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LibMesh::LibMesh(pugi::xml_node node) : UnstructuredMesh(node), adaptive_(false)
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LibMesh::LibMesh(pugi::xml_node node) : UnstructuredMesh(node)
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{
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// filename_ and length_multiplier_ will already be set by the
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// UnstructuredMesh constructor
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@ -3230,7 +3230,6 @@ LibMesh::LibMesh(pugi::xml_node node) : UnstructuredMesh(node), adaptive_(false)
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// create the mesh from a pointer to a libMesh Mesh
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LibMesh::LibMesh(libMesh::MeshBase& input_mesh, double length_multiplier)
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: adaptive_(input_mesh.n_active_elem() != input_mesh.n_elem())
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{
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if (!dynamic_cast<libMesh::ReplicatedMesh*>(&input_mesh)) {
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fatal_error("At present LibMesh tallies require a replicated mesh. Please "
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@ -3244,7 +3243,6 @@ LibMesh::LibMesh(libMesh::MeshBase& input_mesh, double length_multiplier)
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// create the mesh from an input file
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LibMesh::LibMesh(const std::string& filename, double length_multiplier)
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: adaptive_(false)
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{
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n_dimension_ = 3;
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set_mesh_pointer_from_filename(filename);
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@ -3307,21 +3305,6 @@ void LibMesh::initialize()
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auto first_elem = *m_->elements_begin();
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first_element_id_ = first_elem->id();
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// if the mesh is adaptive elements aren't guaranteed by libMesh to be
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// contiguous in ID space, so we need to map from bin indices (defined over
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// active elements) to global dof ids
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if (adaptive_) {
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bin_to_elem_map_.reserve(m_->n_active_elem());
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elem_to_bin_map_.resize(m_->n_elem(), -1);
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for (auto it = m_->active_elements_begin(); it != m_->active_elements_end();
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it++) {
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auto elem = *it;
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bin_to_elem_map_.push_back(elem->id());
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elem_to_bin_map_[elem->id()] = bin_to_elem_map_.size() - 1;
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}
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}
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// bounding box for the mesh for quick rejection checks
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bbox_ = libMesh::MeshTools::create_bounding_box(*m_);
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libMesh::Point ll = bbox_.min();
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@ -3379,7 +3362,7 @@ std::string LibMesh::library() const
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int LibMesh::n_bins() const
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{
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return m_->n_active_elem();
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return m_->n_elem();
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}
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int LibMesh::n_surface_bins() const
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@ -3402,14 +3385,6 @@ int LibMesh::n_surface_bins() const
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void LibMesh::add_score(const std::string& var_name)
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{
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if (adaptive_) {
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warning(fmt::format(
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"Exodus output cannot be provided as unstructured mesh {} is adaptive.",
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this->id_));
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return;
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}
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if (!equation_systems_) {
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build_eqn_sys();
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}
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@ -3445,14 +3420,6 @@ void LibMesh::remove_scores()
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void LibMesh::set_score_data(const std::string& var_name,
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const vector<double>& values, const vector<double>& std_dev)
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{
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if (adaptive_) {
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warning(fmt::format(
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"Exodus output cannot be provided as unstructured mesh {} is adaptive.",
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this->id_));
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return;
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}
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if (!equation_systems_) {
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build_eqn_sys();
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}
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@ -3496,14 +3463,6 @@ void LibMesh::set_score_data(const std::string& var_name,
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void LibMesh::write(const std::string& filename) const
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{
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if (adaptive_) {
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warning(fmt::format(
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"Exodus output cannot be provided as unstructured mesh {} is adaptive.",
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this->id_));
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return;
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}
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write_message(fmt::format(
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"Writing file: {}.e for unstructured mesh {}", filename, this->id_));
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libMesh::ExodusII_IO exo(*m_);
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@ -3537,8 +3496,7 @@ int LibMesh::get_bin(Position r) const
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int LibMesh::get_bin_from_element(const libMesh::Elem* elem) const
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{
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int bin =
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adaptive_ ? elem_to_bin_map_[elem->id()] : elem->id() - first_element_id_;
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int bin = elem->id() - first_element_id_;
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if (bin >= n_bins() || bin < 0) {
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fatal_error(fmt::format("Invalid bin: {}", bin));
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}
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@ -3553,7 +3511,7 @@ std::pair<vector<double>, vector<double>> LibMesh::plot(
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const libMesh::Elem& LibMesh::get_element_from_bin(int bin) const
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{
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return adaptive_ ? m_->elem_ref(bin_to_elem_map_.at(bin)) : m_->elem_ref(bin);
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return m_->elem_ref(bin);
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}
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double LibMesh::volume(int bin) const
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@ -3561,6 +3519,65 @@ double LibMesh::volume(int bin) const
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return this->get_element_from_bin(bin).volume();
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}
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AdaptiveLibMesh::AdaptiveLibMesh(
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libMesh::MeshBase& input_mesh, double length_multiplier)
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: LibMesh(input_mesh, length_multiplier), num_active_(m_->n_active_elem())
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{
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// if the mesh is adaptive elements aren't guaranteed by libMesh to be
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// contiguous in ID space, so we need to map from bin indices (defined over
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// active elements) to global dof ids
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bin_to_elem_map_.reserve(num_active_);
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elem_to_bin_map_.resize(m_->n_elem(), -1);
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for (auto it = m_->active_elements_begin(); it != m_->active_elements_end();
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it++) {
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auto elem = *it;
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bin_to_elem_map_.push_back(elem->id());
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elem_to_bin_map_[elem->id()] = bin_to_elem_map_.size() - 1;
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}
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}
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int AdaptiveLibMesh::n_bins() const
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{
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return num_active_;
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}
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void AdaptiveLibMesh::add_score(const std::string& var_name)
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{
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warning(fmt::format(
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"Exodus output cannot be provided as unstructured mesh {} is adaptive.",
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this->id_));
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}
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void AdaptiveLibMesh::set_score_data(const std::string& var_name,
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const vector<double>& values, const vector<double>& std_dev)
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{
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warning(fmt::format(
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"Exodus output cannot be provided as unstructured mesh {} is adaptive.",
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this->id_));
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}
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void AdaptiveLibMesh::write(const std::string& filename) const
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{
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warning(fmt::format(
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"Exodus output cannot be provided as unstructured mesh {} is adaptive.",
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this->id_));
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}
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int AdaptiveLibMesh::get_bin_from_element(const libMesh::Elem* elem) const
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{
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int bin = elem_to_bin_map_[elem->id()];
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if (bin >= n_bins() || bin < 0) {
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fatal_error(fmt::format("Invalid bin: {}", bin));
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}
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return bin;
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}
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const libMesh::Elem& AdaptiveLibMesh::get_element_from_bin(int bin) const
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{
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return m_->elem_ref(bin_to_elem_map_.at(bin));
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}
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#endif // OPENMC_LIBMESH_ENABLED
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//==============================================================================
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