IOSS 2.0

Iopx_DatabaseIO.h
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32
33 // -*- Mode: c++ -*-
34 #ifndef IOSS_Iopx_DatabaseIO_h
35 #define IOSS_Iopx_DatabaseIO_h
36
37 #include <Ioss_CodeTypes.h>
38 #include <Ioss_DBUsage.h> // for DatabaseUsage
39 #include <Ioss_Map.h> // for Map
40 #include <Ioss_State.h> // for State
41 #include <exodus/Ioex_DatabaseIO.h> // for DatabaseIO
42 #include <exodusII.h> // for ex_entity_type, etc
43 #include <functional> // for less
44 #include <map> // for map, map<>::value_compare
45 #include <memory>
46 #include <set> // for set
47 #include <stddef.h> // for size_t
48 #include <stdint.h> // for int64_t
49 #include <string> // for string, operator<
50 #include <time.h> // for nullptr, time_t
51 #include <utility> // for pair
52 #include <vector> // for vector
53 namespace Iopx {
54 class DecompositionDataBase;
55 }
56 namespace Iopx {
57 template <typename INT> class DecompositionData;
58 }
59
60 namespace Ioss {
61 class EntityBlock;
62 class ElementTopology;
63 class CommSet;
64 class EdgeBlock;
65 class EdgeSet;
66 class ElementBlock;
67 class ElementSet;
68 class EntitySet;
69 class FaceBlock;
70 class FaceSet;
71 class Field;
72 class GroupingEntity;
73 class NodeBlock;
74 class NodeSet;
75 class PropertyManager;
76 class Region;
77 class SideBlock;
78 class SideSet;
79 class StructuredBlock;
80 } // namespace Ioss
81
82 /** \brief A namespace for the decompose-on-the-fly version of the
83 * parallel exodus database format.
84 */
85 namespace Iopx {
86 class DatabaseIO : public Ioex::DatabaseIO
87 {
88 public:
89 DatabaseIO(Ioss::Region *region, const std::string &filename, Ioss::DatabaseUsage db_usage,
90 MPI_Comm communicator, const Ioss::PropertyManager &properties);
91 DatabaseIO(const DatabaseIO &from) = delete;
92 DatabaseIO &operator=(const DatabaseIO &from) = delete;
93 ~DatabaseIO();
94
95 int get_file_pointer() const override; // Open file and set exodusFilePtr.
96 bool needs_shared_node_information() const override { return true; }
97
98 private:
99 void compute_node_status() const;
100
101 void release_memory__() override;
102
103 void get_step_times__() override;
104
105 bool open_input_file(bool write_message, std::string *error_msg, int *bad_count,
106 bool abort_if_error) const override;
107 bool handle_output_file(bool write_message, std::string *error_msg, int *bad_count,
108 bool overwrite, bool abort_if_error) const override;
109 bool check_valid_file_ptr(bool write_message, std::string *error_msg, int *bad_count,
110 bool abort_if_error) const;
111
112 int64_t get_field_internal(const Ioss::Region *reg, const Ioss::Field &field, void *data,
113 size_t data_size) const override;
114 int64_t get_field_internal(const Ioss::NodeBlock *nb, const Ioss::Field &field, void *data,
115 size_t data_size) const override;
116 int64_t get_field_internal(const Ioss::EdgeBlock *eb, const Ioss::Field &field, void *data,
117 size_t data_size) const override;
118 int64_t get_field_internal(const Ioss::FaceBlock *eb, const Ioss::Field &field, void *data,
119 size_t data_size) const override;
120 int64_t get_field_internal(const Ioss::ElementBlock *eb, const Ioss::Field &field, void *data,
121 size_t data_size) const override;
122 int64_t get_field_internal(const Ioss::StructuredBlock * /* sb */,
123 const Ioss::Field & /* field */, void * /* data */,
124 size_t /* data_size */) const override
125 {
126 return -1;
127 }
128 int64_t get_field_internal(const Ioss::SideBlock *fb, const Ioss::Field &field, void *data,
129 size_t data_size) const override;
130 int64_t get_field_internal(const Ioss::NodeSet *ns, const Ioss::Field &field, void *data,
131 size_t data_size) const override;
132 int64_t get_field_internal(const Ioss::EdgeSet *ns, const Ioss::Field &field, void *data,
133 size_t data_size) const override;
134 int64_t get_field_internal(const Ioss::FaceSet *ns, const Ioss::Field &field, void *data,
135 size_t data_size) const override;
136 int64_t get_field_internal(const Ioss::ElementSet *ns, const Ioss::Field &field, void *data,
137 size_t data_size) const override;
138 int64_t get_field_internal(const Ioss::SideSet *fs, const Ioss::Field &field, void *data,
139 size_t data_size) const override;
140 int64_t get_field_internal(const Ioss::CommSet *cs, const Ioss::Field &field, void *data,
141 size_t data_size) const override;
142
143 int64_t put_field_internal(const Ioss::Region *reg, const Ioss::Field &field, void *data,
144 size_t data_size) const override;
145 int64_t put_field_internal(const Ioss::NodeBlock *nb, const Ioss::Field &field, void *data,
146 size_t data_size) const override;
147 int64_t put_field_internal(const Ioss::EdgeBlock *eb, const Ioss::Field &field, void *data,
148 size_t data_size) const override;
149 int64_t put_field_internal(const Ioss::FaceBlock *eb, const Ioss::Field &field, void *data,
150 size_t data_size) const override;
151 int64_t put_field_internal(const Ioss::ElementBlock *eb, const Ioss::Field &field, void *data,
152 size_t data_size) const override;
153 int64_t put_field_internal(const Ioss::SideBlock *fb, const Ioss::Field &field, void *data,
154 size_t data_size) const override;
155 int64_t put_field_internal(const Ioss::NodeSet *ns, const Ioss::Field &field, void *data,
156 size_t data_size) const override;
157 int64_t put_field_internal(const Ioss::EdgeSet *ns, const Ioss::Field &field, void *data,
158 size_t data_size) const override;
159 int64_t put_field_internal(const Ioss::FaceSet *ns, const Ioss::Field &field, void *data,
160 size_t data_size) const override;
161 int64_t put_field_internal(const Ioss::ElementSet *ns, const Ioss::Field &field, void *data,
162 size_t data_size) const override;
163 int64_t put_field_internal(const Ioss::SideSet *fs, const Ioss::Field &field, void *data,
164 size_t data_size) const override;
165 int64_t put_field_internal(const Ioss::CommSet *cs, const Ioss::Field &field, void *data,
166 size_t data_size) const override;
167 int64_t put_field_internal(const Ioss::StructuredBlock * /* sb */,
168 const Ioss::Field & /* field */, void * /* data */,
169 size_t /* data_size */) const override
170 {
171 return -1;
172 }
173
174 int64_t put_Xset_field_internal(ex_entity_type type, const Ioss::EntitySet *ns,
175 const Ioss::Field &field, void *data, size_t data_size) const;
176 int64_t get_Xset_field_internal(ex_entity_type type, const Ioss::EntitySet *ns,
177 const Ioss::Field &field, void *data, size_t data_size) const;
178
179 int free_file_pointer() const override;
180
181 int64_t read_nodal_coordinates();
182 void read_elements(const Ioss::ElementBlock &block);
183
184 void create_implicit_global_map() const;
185 void output_node_map() const;
186
187 // Metadata-related functions.
188 void read_meta_data__() override;
189
190 int64_t read_transient_field(ex_entity_type type, const Ioex::VariableNameMap &variables,
191 const Ioss::Field &field, const Ioss::GroupingEntity *ge,
192 void *data) const;
193
194 int64_t read_attribute_field(ex_entity_type type, const Ioss::Field &field,
195 const Ioss::GroupingEntity *ge, void *data) const;
196
197 int64_t write_attribute_field(ex_entity_type type, const Ioss::Field &field,
198 const Ioss::GroupingEntity *ge, void *data) const;
199
200 // Handles subsetting of side blocks.
201 int64_t read_ss_transient_field(const Ioss::Field &field, int64_t id, void *variables,
202 std::vector<int> &is_valid_side) const;
203
204 // Should be made more generic again so can rejoin with write_element_transient field
205 void write_nodal_transient_field(ex_entity_type type, const Ioss::Field &field,
206 const Ioss::NodeBlock *nb, int64_t count,
207 void *variables) const;
208 // Should be made more generic again so can rejoin with write_nodal_transient field
209 void write_entity_transient_field(ex_entity_type type, const Ioss::Field &field,
210 const Ioss::GroupingEntity *ge, int64_t count,
211 void *variables) const;
212 void write_meta_data() override;
213
214 // Read related metadata and store it in the region...
215 void read_region();
216 void get_edgeblocks();
217 void get_faceblocks();
218 void get_elemblocks();
219 void get_blocks(ex_entity_type entity_type, int rank_offset, const std::string &basename);
220
221 void get_sidesets();
222
223 template <typename T>
224 void get_sets(ex_entity_type type, int64_t count, const std::string &base, const T *);
225 void get_nodesets();
226 void get_edgesets();
227 void get_facesets();
228 void get_elemsets();
229
230 void get_commsets();
231
232 void check_valid_values() const;
233
234 // ID Mapping functions.
235 const Ioss::Map &get_map(ex_entity_type type) const;
236 const Ioss::Map &get_map(Ioss::Map &entity_map, int64_t entityCount, int64_t file_offset,
237 int64_t file_count, ex_entity_type entity_type,
238 ex_inquiry inquiry_type) const;
239
240 // Internal data handling
241 int64_t handle_node_ids(void *ids, int64_t num_to_get, size_t offset, size_t count) const;
242 int64_t handle_element_ids(const Ioss::ElementBlock *eb, void *ids, size_t num_to_get,
243 size_t offset, size_t count) const;
244 int64_t handle_face_ids(const Ioss::FaceBlock *eb, void *ids, size_t num_to_get) const;
245 int64_t handle_edge_ids(const Ioss::EdgeBlock *eb, void *ids, size_t num_to_get) const;
246
247 int64_t get_side_connectivity(const Ioss::SideBlock *fb, int64_t id, int64_t side_count,
248 void *fconnect, bool map_ids) const;
249 int64_t get_side_distributions(const Ioss::SideBlock *fb, int64_t id, int64_t my_side_count,
250 double *dist_fact, size_t data_size) const;
251
252 int64_t get_side_field(const Ioss::SideBlock *ef_blk, const Ioss::Field &field, void *data,
253 size_t data_size) const;
254 int64_t put_side_field(const Ioss::SideBlock *fb, const Ioss::Field &field, void *data,
255 size_t data_size) const;
256
257 // Private member data...
258 mutable std::unique_ptr<DecompositionDataBase> decomp;
259
260 mutable Ioss::IntVector nodeOwningProcessor; // Processor that owns each node on this processor
261 mutable Ioss::Int64Vector
262 nodeGlobalImplicitMap; // Position of this node in the global-implicit ordering
263 mutable Ioss::Int64Vector
264 elemGlobalImplicitMap; // Position of this element in the global-implicit ordering
265
266 // Contains the indices of all owned nodes in each nodeset on this processor to pull data
267 // from the global list down to the file list.
268 // NOTE: Even though map type is GroupingEntity*, it is only valid
269 // for a GroupingEntity* which is a NodeSet*
270 mutable std::map<const Ioss::GroupingEntity *, Ioss::Int64Vector> nodesetOwnedNodes;
271
272 mutable bool metaDataWritten{false};
273 };
274 } // namespace Iopx
275 #endif
Ioss_DBUsage.h
Iopx::DatabaseIO::open_input_file
bool open_input_file(bool write_message, std::string *error_msg, int *bad_count, bool abort_if_error) const override
Definition: Iopx_DatabaseIO.C:337
Iopx::DatabaseIO::put_field_internal
int64_t put_field_internal(const Ioss::Region *reg, const Ioss::Field &field, void *data, size_t data_size) const override
Definition: Iopx_DatabaseIO.C:3106
Iopx::DatabaseIO::get_commsets
void get_commsets()
Definition: Iopx_DatabaseIO.C:1609
Ioss::Field
Holds metadata for bulk data associated with a GroupingEntity.
Definition: Ioss_Field.h:47
Iopx::DatabaseIO::get_facesets
void get_facesets()
Definition: Iopx_DatabaseIO.C:1599
Iopx::DatabaseIO::handle_element_ids
int64_t handle_element_ids(const Ioss::ElementBlock *eb, void *ids, size_t num_to_get, size_t offset, size_t count) const
Definition: Iopx_DatabaseIO.C:3624
Ioss_Map.h
Ioss::IntVector
std::vector< int > IntVector
Definition: Ioss_CodeTypes.h:51
Ioex::VariableNameMap
std::map< std::string, int, std::less< std::string > > VariableNameMap
Definition: Ioex_DatabaseIO.h:80
Iopx::DatabaseIO::read_attribute_field
int64_t read_attribute_field(ex_entity_type type, const Ioss::Field &field, const Ioss::GroupingEntity *ge, void *data) const
Definition: Iopx_DatabaseIO.C:2559
Iopx::DatabaseIO::metaDataWritten
bool metaDataWritten
Definition: Iopx_DatabaseIO.h:272
Iopx::DatabaseIO::read_nodal_coordinates
int64_t read_nodal_coordinates()
Iopx::DatabaseIO::get_Xset_field_internal
int64_t get_Xset_field_internal(ex_entity_type type, const Ioss::EntitySet *ns, const Ioss::Field &field, void *data, size_t data_size) const
Definition: Iopx_DatabaseIO.C:2019
Iopx::DatabaseIO::get_field_internal
int64_t get_field_internal(const Ioss::Region *reg, const Ioss::Field &field, void *data, size_t data_size) const override
Definition: Iopx_DatabaseIO.C:1633
Iopx::DatabaseIO::put_field_internal
int64_t put_field_internal(const Ioss::StructuredBlock *, const Ioss::Field &, void *, size_t) const override
Definition: Iopx_DatabaseIO.h:167
Ioss::EdgeBlock
A collection of element edges with the same topology.
Definition: Ioss_EdgeBlock.h:53
Ioss::DatabaseUsage
DatabaseUsage
Specifies how an Ioss::DatabaseIO object will be used.
Definition: Ioss_DBUsage.h:40
Ioss
The main namespace for the Ioss library.
Definition: Ioad_DatabaseIO.C:66
Ioex::DatabaseIO
Definition: Ioex_DatabaseIO.h:96
Iopx::DatabaseIO::check_valid_values
void check_valid_values() const
Definition: Iopx_DatabaseIO.C:4558
anonymous_namespace{Iovs_DatabaseIO.C}::entity_type
entity_type
Definition: Iovs_DatabaseIO.C:81
Iopx::DatabaseIO::get_edgesets
void get_edgesets()
Definition: Iopx_DatabaseIO.C:1594
Ioss::Region
A grouping entity that contains other grouping entities.
Definition: Ioss_Region.h:98
Ioss::NodeSet
A collection of nodes.
Definition: Ioss_NodeSet.h:53
Ioex_DatabaseIO.h
Ioss::FaceSet
A collection of element faces.
Definition: Ioss_FaceSet.h:54
Ioss::StructuredBlock
A structured zone – i,j,k.
Definition: Ioss_StructuredBlock.h:103
Iopx
A namespace for the decompose-on-the-fly version of the parallel exodus database format.
Definition: Iopx_DatabaseIO.C:233
Iopx::DatabaseIO::create_implicit_global_map
void create_implicit_global_map() const
Definition: Iopx_DatabaseIO.C:4493
Iopx::DatabaseIO::elemGlobalImplicitMap
Ioss::Int64Vector elemGlobalImplicitMap
Definition: Iopx_DatabaseIO.h:264
Iopx::DatabaseIO::write_meta_data
void write_meta_data() override
Definition: Iopx_DatabaseIO.C:4246
Ioss::PropertyManager
A collection of Ioss::Property objects.
Definition: Ioss_PropertyManager.h:49
Ioss::EdgeSet
A collection of element edges.
Definition: Ioss_EdgeSet.h:54
Ioss::ElementSet
A collection of elements.
Definition: Ioss_ElementSet.h:54
Ioss::CommSet
Definition: Ioss_CommSet.h:51
Iopx::DatabaseIO::read_region
void read_region()
Definition: Iopx_DatabaseIO.C:589
Iopx::DatabaseIO::get_nodesets
void get_nodesets()
Definition: Iopx_DatabaseIO.C:1589
Iopx::DatabaseIO::get_file_pointer
int get_file_pointer() const override
Definition: Iopx_DatabaseIO.C:525
Iopx::DatabaseIO::output_node_map
void output_node_map() const
Definition: Iopx_DatabaseIO.C:4520
Ioss::FaceBlock
A collection of element faces with the same topology.
Definition: Ioss_FaceBlock.h:53
Iopx::DatabaseIO::needs_shared_node_information
bool needs_shared_node_information() const override
Determine whether the database needs information about process ownership of nodes.
Definition: Iopx_DatabaseIO.h:96
Ioss::DatabaseIO::properties
Ioss::PropertyManager properties
Definition: Ioss_DatabaseIO.h:578
Iopx::DatabaseIO::get_side_distributions
int64_t get_side_distributions(const Ioss::SideBlock *fb, int64_t id, int64_t my_side_count, double *dist_fact, size_t data_size) const
Definition: Iopx_DatabaseIO.C:2915
Iopx::DatabaseIO::get_sets
void get_sets(ex_entity_type type, int64_t count, const std::string &base, const T *)
Definition: Iopx_DatabaseIO.C:1531
Iopx::DatabaseIO::handle_output_file
bool handle_output_file(bool write_message, std::string *error_msg, int *bad_count, bool overwrite, bool abort_if_error) const override
Definition: Iopx_DatabaseIO.C:404
Ioss::DatabaseIO::DatabaseIO
DatabaseIO()=delete
Iopx::DatabaseIO::write_nodal_transient_field
void write_nodal_transient_field(ex_entity_type type, const Ioss::Field &field, const Ioss::NodeBlock *nb, int64_t count, void *variables) const
Definition: Iopx_DatabaseIO.C:3658
Iopx::DatabaseIO::get_elemsets
void get_elemsets()
Definition: Iopx_DatabaseIO.C:1604
Iopx::DatabaseIO::get_map
const Ioss::Map & get_map(ex_entity_type type) const
Definition: Iopx_DatabaseIO.C:748
Iopx::DecompositionData
Definition: Iopx_DatabaseIO.h:57
Iopx::DatabaseIO::handle_edge_ids
int64_t handle_edge_ids(const Ioss::EdgeBlock *eb, void *ids, size_t num_to_get) const
Definition: Iopx_DatabaseIO.C:3652
Iopx::DatabaseIO::get_field_internal
int64_t get_field_internal(const Ioss::StructuredBlock *, const Ioss::Field &, void *, size_t) const override
Definition: Iopx_DatabaseIO.h:122
Iopx::DatabaseIO::decomp
std::unique_ptr< DecompositionDataBase > decomp
Definition: Iopx_DatabaseIO.h:258
Ioss::Int64Vector
std::vector< int64_t > Int64Vector
Definition: Ioss_CodeTypes.h:52
Iopx::DatabaseIO::get_side_field
int64_t get_side_field(const Ioss::SideBlock *ef_blk, const Ioss::Field &field, void *data, size_t data_size) const
Ioss_State.h
Ioss::SideBlock
A collection of element sides having the same topology.
Definition: Ioss_SideBlock.h:59
Iopx::DatabaseIO::nodeOwningProcessor
Ioss::IntVector nodeOwningProcessor
Definition: Iopx_DatabaseIO.h:260
Iopx::DatabaseIO::check_valid_file_ptr
bool check_valid_file_ptr(bool write_message, std::string *error_msg, int *bad_count, bool abort_if_error) const
Definition: Iopx_DatabaseIO.C:290
Iopx::DatabaseIO::read_transient_field
int64_t read_transient_field(ex_entity_type type, const Ioex::VariableNameMap &variables, const Ioss::Field &field, const Ioss::GroupingEntity *ge, void *data) const
Definition: Iopx_DatabaseIO.C:2622
Ioss::EntitySet
Base class for all 'set'-type grouping entities, which means that members of the set are not necessar...
Definition: Ioss_EntitySet.h:61
Iopx::DatabaseIO::nodesetOwnedNodes
std::map< const Ioss::GroupingEntity *, Ioss::Int64Vector > nodesetOwnedNodes
Definition: Iopx_DatabaseIO.h:270
Iopx::DatabaseIO::get_side_connectivity
int64_t get_side_connectivity(const Ioss::SideBlock *fb, int64_t id, int64_t side_count, void *fconnect, bool map_ids) const
Definition: Iopx_DatabaseIO.C:2762
Ioss::ElementBlock
A collection of elements having the same topology.
Definition: Ioss_ElementBlock.h:48
Iopx::DatabaseIO::put_side_field
int64_t put_side_field(const Ioss::SideBlock *fb, const Ioss::Field &field, void *data, size_t data_size) const
Iopx::DatabaseIO::handle_node_ids
int64_t handle_node_ids(void *ids, int64_t num_to_get, size_t offset, size_t count) const
Definition: Iopx_DatabaseIO.C:3570
Iopx::DatabaseIO::read_ss_transient_field
int64_t read_ss_transient_field(const Ioss::Field &field, int64_t id, void *variables, std::vector< int > &is_valid_side) const
Definition: Iopx_DatabaseIO.C:2688
Iopx::DatabaseIO::get_step_times__
void get_step_times__() override
Definition: Iopx_DatabaseIO.C:673
Ioss::Map
Definition: Ioss_Map.h:52
Iopx::DatabaseIO::nodeGlobalImplicitMap
Ioss::Int64Vector nodeGlobalImplicitMap
Definition: Iopx_DatabaseIO.h:262
Iopx::DatabaseIO::release_memory__
void release_memory__() override
Definition: Iopx_DatabaseIO.C:272
Iopx::DatabaseIO::read_elements
void read_elements(const Ioss::ElementBlock &block)
anonymous_namespace{cth_pressure_map.C}::data
std::vector< char > data
Definition: cth_pressure_map.C:74
Iopx::DatabaseIO::compute_node_status
void compute_node_status() const
Definition: Iopx_DatabaseIO.C:1076
Iopx::DatabaseIO::write_attribute_field
int64_t write_attribute_field(ex_entity_type type, const Ioss::Field &field, const Ioss::GroupingEntity *ge, void *data) const
Definition: Iopx_DatabaseIO.C:2461
Iopx::DatabaseIO
Definition: Iopx_DatabaseIO.h:86
Iopx::DatabaseIO::get_edgeblocks
void get_edgeblocks()
Definition: Iopx_DatabaseIO.C:871
Iopx::DatabaseIO::put_Xset_field_internal
int64_t put_Xset_field_internal(ex_entity_type type, const Ioss::EntitySet *ns, const Ioss::Field &field, void *data, size_t data_size) const
Definition: Iopx_DatabaseIO.C:3883
Iopx::DatabaseIO::get_faceblocks
void get_faceblocks()
Definition: Iopx_DatabaseIO.C:866
Iopx::DatabaseIO::get_sidesets
void get_sidesets()
Definition: Iopx_DatabaseIO.C:1124
Iopx::DatabaseIO::~DatabaseIO
~DatabaseIO()
Ioss::NodeBlock
A collection of all nodes in the region.
Definition: Ioss_NodeBlock.h:53
Iopx::DatabaseIO::handle_face_ids
int64_t handle_face_ids(const Ioss::FaceBlock *eb, void *ids, size_t num_to_get) const
Definition: Iopx_DatabaseIO.C:3646
Iopx::DatabaseIO::get_blocks
void get_blocks(ex_entity_type entity_type, int rank_offset, const std::string &basename)
Definition: Iopx_DatabaseIO.C:876
MPI_Comm
int MPI_Comm
Definition: Ioss_CodeTypes.h:96
Iopx::DatabaseIO::free_file_pointer
int free_file_pointer() const override
Definition: Iopx_DatabaseIO.C:527
Ioss::SideSet
A collection of element sides.
Definition: Ioss_SideSet.h:53
Ioss::GroupingEntity
Base class for all 'grouping' entities. The following derived classes are typical:
Definition: Ioss_GroupingEntity.h:93
Ioss_CodeTypes.h
Iopx::DatabaseIO::get_elemblocks
void get_elemblocks()
Definition: Iopx_DatabaseIO.C:864
Iopx::DatabaseIO::read_meta_data__
void read_meta_data__() override
Definition: Iopx_DatabaseIO.C:548
Iopx::DatabaseIO::write_entity_transient_field
void write_entity_transient_field(ex_entity_type type, const Ioss::Field &field, const Ioss::GroupingEntity *ge, int64_t count, void *variables) const
Definition: Iopx_DatabaseIO.C:3764
Iopx::DatabaseIO::operator=
DatabaseIO & operator=(const DatabaseIO &from)=delete