// ISSUES: // 1. Does not handle unconnected nodes (not connected to any element) // // 2. SideSet distribution factors are klugy and may not fully work in // strange cases // // // Copyright(C) 1999-2022 National Technology & Engineering Solutions // of Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with // NTESS, the U.S. Government retains certain rights in this software. // // See packages/seacas/LICENSE for details #include #if defined PARALLEL_AWARE_EXODUS #include #include #include #include #include #include #include #include #include "vtk_fmt.h" #include VTK_FMT(fmt/ostream.h) #include #include #include #include #include #include #include #include #ifndef _MSC_VER #include #endif #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #undef MPICPP // ======================================================================== // Static internal helper functions // ======================================================================== namespace { const size_t max_line_length = MAX_LINE_LENGTH; const std::string SEP() { return std::string("@"); } // Separator for attribute offset storage const char *complex_suffix[] = {".re", ".im"}; void check_node_owning_processor_data(const Ioss::IntVector &nop, size_t file_node_count) { // Verify that the nop (NodeOwningProcessor) vector is not empty and is of the correct size. // This vector specifies which rank owns each node on this rank // Throws error if problem, otherwise returns quietly. if (file_node_count == 0) { return; } if (nop.empty()) { std::ostringstream errmsg; fmt::print(errmsg, "ERROR: The use of the 'compose' output option requires the definition of " "the 'owning_processor'" " field prior to the output of nodal data. This field has not yet been " "defined so output is not possible." " For more information, contact gdsjaar@sandia.gov.\n"); IOSS_ERROR(errmsg); } else if (nop.size() < file_node_count) { std::ostringstream errmsg; fmt::print(errmsg, "ERROR: The 'owning_processor' data was defined, but it is not the correct size." " Its size is {}, but it must be at least this size {}." " For more information, contact gdsjaar@sandia.gov.\n", nop.size(), file_node_count); IOSS_ERROR(errmsg); } } void get_connectivity_data(int exoid, void *data, ex_entity_type type, ex_entity_id id, int position, int int_size_api) { int ierr = 0; if (int_size_api == 8) { int64_t *conn[3]; conn[0] = nullptr; conn[1] = nullptr; conn[2] = nullptr; conn[position] = static_cast(data); assert(1 == 0 && "Unimplemented fixme"); ierr = ex_get_conn(exoid, type, id, conn[0], conn[1], conn[2]); // FIXME } else { int *conn[3]; conn[0] = nullptr; conn[1] = nullptr; conn[2] = nullptr; conn[position] = static_cast(data); assert(1 == 0 && "Unimplemented fixme"); ierr = ex_get_conn(exoid, type, id, conn[0], conn[1], conn[2]); // FIXME } if (ierr < 0) { Ioex::exodus_error(exoid, __LINE__, __func__, __FILE__); } } template void compute_internal_border_maps(T *entities, T *internal, size_t count, size_t entity_count) { for (size_t ij = 0; ij < count; ij++) { internal[ij] = 1; } for (size_t J = 0; J < entity_count; J++) { internal[entities[J] - 1] = 0; } size_t b = 0; for (size_t ij = 0; ij < count; ij++) { if (internal[ij] == 0) { entities[b++] = ij + 1; } } size_t k = 0; for (size_t ij = 0; ij < count; ij++) { if (internal[ij] == 1) { internal[k++] = ij + 1; } } } template void map_nodeset_id_data(const Ioss::IntVector &owning_processor, Ioss::Int64Vector &owned_nodes, int this_processor, const INT *ids, size_t ids_size, std::vector &file_data) { // Determine which nodes in this nodeset are owned by this processor. // Save this mapping in the "owned_nodes" vector for use in // mapping nodeset field data (df, transient, attributes, ...) for (size_t i = 0; i < ids_size; i++) { INT node = ids[i]; if (owning_processor[node - 1] == this_processor) { file_data.push_back(ids[i]); owned_nodes.push_back(i); } } } template void map_nodeset_data(Ioss::Int64Vector &owned_nodes, const T *data, std::vector &file_data, size_t offset = 0, size_t stride = 1) { // Pull out the locally owned nodeset data for (auto owned_node : owned_nodes) { file_data.push_back(data[stride * owned_node + offset]); } } template void extract_data(std::vector &local_data, T *data, size_t num_entity, size_t offset, size_t comp_count) { local_data.resize(num_entity); if (comp_count == 1 && offset == 0) { for (size_t j = 0; j < num_entity; j++) { local_data[j] = data[j]; } } else { for (size_t j = 0; j < num_entity; j++) { local_data[j] = data[offset]; offset += comp_count; } } } // Ideally, there should only be a single data type for in and out // data, but in the node id map mapping, we have an int64_t coming // in and either an int or int64_t going out... template void filter_owned_nodes(const Ioss::IntVector &owning_processor, int this_processor, const T *data, std::vector &file_data, size_t offset = 0, size_t stride = 1) { size_t index = offset; for (auto op : owning_processor) { if (op == this_processor) { file_data.push_back(data[index]); } index += stride; } } // This version can be used *if* the input and output types are the same *and* the // input `data` can be modified / overwritten. template void filter_owned_nodes(const Ioss::IntVector &owning_processor, int this_processor, T *data) { size_t index = 0; size_t entry = 0; for (auto op : owning_processor) { if (op == this_processor) { data[entry++] = data[index]; } index++; } } template void map_local_to_global_implicit(INT *data, size_t count, const std::vector &global_implicit_map) { for (size_t i = 0; i < count; i++) { data[i] = global_implicit_map[data[i] - 1]; } } void update_processor_offset_property(Ioss::Region *region, const Ioex::Mesh &mesh) { const Ioss::NodeBlockContainer &node_blocks = region->get_node_blocks(); if (!node_blocks.empty()) { node_blocks[0]->property_add( Ioss::Property("_processor_offset", mesh.nodeblocks[0].procOffset)); } const Ioss::EdgeBlockContainer &edge_blocks = region->get_edge_blocks(); for (size_t i = 0; i < edge_blocks.size(); i++) { edge_blocks[i]->property_add( Ioss::Property("_processor_offset", mesh.edgeblocks[i].procOffset)); } const Ioss::FaceBlockContainer &face_blocks = region->get_face_blocks(); for (size_t i = 0; i < face_blocks.size(); i++) { face_blocks[i]->property_add( Ioss::Property("_processor_offset", mesh.faceblocks[i].procOffset)); } int64_t offset = 0; // Offset into global element map... const Ioss::ElementBlockContainer &element_blocks = region->get_element_blocks(); for (size_t i = 0; i < element_blocks.size(); i++) { element_blocks[i]->property_add(Ioss::Property("global_map_offset", offset)); offset += mesh.elemblocks[i].entityCount; element_blocks[i]->property_add( Ioss::Property("_processor_offset", mesh.elemblocks[i].procOffset)); } const Ioss::NodeSetContainer &nodesets = region->get_nodesets(); for (size_t i = 0; i < nodesets.size(); i++) { nodesets[i]->property_add(Ioss::Property("_processor_offset", mesh.nodesets[i].procOffset)); } const Ioss::EdgeSetContainer &edgesets = region->get_edgesets(); for (size_t i = 0; i < edgesets.size(); i++) { edgesets[i]->property_add(Ioss::Property("_processor_offset", mesh.edgesets[i].procOffset)); } const Ioss::FaceSetContainer &facesets = region->get_facesets(); for (size_t i = 0; i < facesets.size(); i++) { facesets[i]->property_add(Ioss::Property("_processor_offset", mesh.facesets[i].procOffset)); } const Ioss::ElementSetContainer &elementsets = region->get_elementsets(); for (size_t i = 0; i < facesets.size(); i++) { elementsets[i]->property_add( Ioss::Property("_processor_offset", mesh.elemsets[i].procOffset)); } const Ioss::SideSetContainer &ssets = region->get_sidesets(); for (size_t i = 0; i < ssets.size(); i++) { ssets[i]->property_add(Ioss::Property("_processor_offset", mesh.sidesets[i].procOffset)); ssets[i]->property_add(Ioss::Property("processor_df_offset", mesh.sidesets[i].dfProcOffset)); // Propagate down to owned sideblocks... const Ioss::SideBlockContainer &side_blocks = ssets[i]->get_side_blocks(); for (auto &block : side_blocks) { block->property_add(Ioss::Property("_processor_offset", mesh.sidesets[i].procOffset)); block->property_add(Ioss::Property("processor_df_offset", mesh.sidesets[i].dfProcOffset)); } } const auto &blobs = region->get_blobs(); for (size_t i = 0; i < blobs.size(); i++) { blobs[i]->property_add(Ioss::Property("_processor_offset", mesh.blobs[i].procOffset)); } } } // namespace namespace Ioex { ParallelDatabaseIO::ParallelDatabaseIO(Ioss::Region *region, const std::string &filename, Ioss::DatabaseUsage db_usage, Ioss_MPI_Comm communicator, const Ioss::PropertyManager &props) : Ioex::BaseDatabaseIO(region, filename, db_usage, communicator, props) { usingParallelIO = true; if (!is_parallel_consistent()) { std::ostringstream errmsg; fmt::print(errmsg, "ERROR: Parallel IO cannot be used in an application that is not guaranteeing " "parallel consistent calls of the get and put field data functions.\n" "The application created this database with a 'false' setting for the " "isParallelConsistent property."); IOSS_ERROR(errmsg); } if (!is_input()) { // Check whether appending to or modifying existing file... if (open_create_behavior() == Ioss::DB_APPEND || open_create_behavior() == Ioss::DB_APPEND_GROUP || open_create_behavior() == Ioss::DB_MODIFY) { // Append to file if it already exists -- See if the file exists. Ioss::FileInfo file = Ioss::FileInfo(get_filename()); fileExists = file.exists(); if (fileExists && myProcessor == 0) { fmt::print(Ioss::WARNING(), "Appending to existing database in parallel single-file " "output mode is a new capability; please check results carefully. File '{}'", get_filename()); } } } } void ParallelDatabaseIO::release_memory__() { free_file_pointer(); nodeMap.release_memory(); edgeMap.release_memory(); faceMap.release_memory(); elemMap.release_memory(); Ioss::Utils::clear(nodeOwningProcessor); Ioss::Utils::clear(nodeGlobalImplicitMap); Ioss::Utils::clear(elemGlobalImplicitMap); nodeGlobalImplicitMapDefined = false; elemGlobalImplicitMapDefined = false; nodesetOwnedNodes.clear(); try { decomp.reset(); } catch (...) { } } bool ParallelDatabaseIO::check_valid_file_ptr(bool write_message, std::string *error_msg, int *bad_count, bool abort_if_error) const { // Check for valid exodus_file_ptr (valid >= 0; invalid < 0) assert(isParallel); int global_file_ptr = util().global_minmax(m_exodusFilePtr, Ioss::ParallelUtils::DO_MIN); if (global_file_ptr < 0) { if (write_message || error_msg != nullptr || bad_count != nullptr) { Ioss::IntVector status; util().all_gather(m_exodusFilePtr, status); std::string open_create = is_input() ? "open input" : "create output"; if (write_message || error_msg != nullptr) { std::vector procs; for (int i = 0; i < util().parallel_size(); i++) { if (status[i] < 0) { procs.push_back(i); } } std::string error_list = Ioss::Utils::format_id_list(procs, "--"); // See which processors could not open/create the file... std::ostringstream errmsg; fmt::print(errmsg, "ERROR: Unable to {} exodus database file '{}' on processors:\n\t{}", open_create, get_filename(), error_list); fmt::print(errmsg, "\n"); if (error_msg != nullptr) { *error_msg = errmsg.str(); } if (write_message && myProcessor == 0) { fmt::print(Ioss::OUTPUT(), "{}", errmsg.str()); } } if (bad_count != nullptr) { *bad_count = std::count_if(status.begin(), status.end(), [](int i) { return i < 0; }); } if (abort_if_error) { std::ostringstream errmsg; fmt::print(errmsg, "ERROR: Cannot {} file '{}'", open_create, get_filename()); IOSS_ERROR(errmsg); } } return false; } return true; } bool ParallelDatabaseIO::open_input_file(bool write_message, std::string *error_msg, int *bad_count, bool abort_if_error) const { int cpu_word_size = sizeof(double); int io_word_size = 0; float version; int mode = exodusMode; if (int_byte_size_api() == 8) { mode |= EX_ALL_INT64_API; } #if defined EX_DISKLESS // Experimental -- in memory read by netcdf library if (properties.exists("MEMORY_READ")) { mode |= EX_DISKLESS; } #endif MPI_Info info = MPI_INFO_NULL; std::string filename = get_filename(); // See bug description in thread at // https://www.open-mpi.org/community/lists/users/2015/01/26167.php and // https://prod.sandia.gov/sierra-trac/ticket/14679 // Kluge is to set cwd to pathname, open file, then set cwd back to original. // // Since several different mpi implementations are based on the // mpich code which introduced this bug, it has been difficult to // create an ifdef'd version of the fix which is only applied to the // buggy mpiio code. Therefore, we always do chdir call. Maybe in several // years, we can remove this code and everything will work... #if !defined(__IOSS_WINDOWS__) Ioss::FileInfo file(filename); std::string path = file.pathname(); filename = file.tailname(); char *current_cwd = getcwd(nullptr, 0); if (!path.empty()) { auto success = chdir(path.c_str()); if (success == -1) { if (write_message || error_msg != nullptr) { std::ostringstream errmsg; fmt::print(errmsg, "ERROR: Directory '{}' does not exist. Error in filename specification.", path); fmt::print(errmsg, "\n"); if (error_msg != nullptr) { *error_msg = errmsg.str(); } if (write_message && myProcessor == 0) { fmt::print(Ioss::OUTPUT(), "{}", errmsg.str()); } if (bad_count != nullptr) { *bad_count = 1; } if (abort_if_error) { IOSS_ERROR(errmsg); } } return false; } } #endif bool do_timer = false; Ioss::Utils::check_set_bool_property(properties, "IOSS_TIME_FILE_OPEN_CLOSE", do_timer); double t_begin = (do_timer ? Ioss::Utils::timer() : 0); int app_opt_val = ex_opts(EX_VERBOSE); m_exodusFilePtr = ex_open_par(filename.c_str(), EX_READ | mode, &cpu_word_size, &io_word_size, &version, util().communicator(), info); if (do_timer) { double t_end = Ioss::Utils::timer(); double duration = util().global_minmax(t_end - t_begin, Ioss::ParallelUtils::DO_MAX); if (myProcessor == 0) { fmt::print(Ioss::DEBUG(), "File Open Time = {}\n", duration); } } #if !defined(__IOSS_WINDOWS__) if (!path.empty()) { chdir(current_cwd); } std::free(current_cwd); #endif bool is_ok = check_valid_file_ptr(write_message, error_msg, bad_count, abort_if_error); if (is_ok) { finalize_file_open(); } ex_opts(app_opt_val); // Reset back to what it was. return is_ok; } bool ParallelDatabaseIO::handle_output_file(bool write_message, std::string *error_msg, int *bad_count, bool overwrite, bool abort_if_error) const { // If 'overwrite' is false, we do not want to overwrite or clobber // the output file if it already exists since the app might be // reading the restart data from this file and then later // clobbering it and then writing restart data to the same // file. So, for output, we first check whether the file exists // and if it it and is writable, assume that we can later create a // new or append to existing file. // if 'overwrite' is true, then clobber/append if (!overwrite) { // check if file exists and is writeable. If so, return true. // Only need to check on processor 0 int int_is_ok = 0; if (myProcessor == 0) { Ioss::FileInfo file(get_filename()); int_is_ok = file.exists() && file.is_writable() ? 1 : 0; } util().broadcast(int_is_ok); if (int_is_ok == 1) { // Note that at this point, we cannot totally guarantee that // we will be able to create the file when needed, but we have // a pretty good chance. We can't guarantee creation without // creating and the app (or calling function) doesn't want us to overwrite... return true; } // File doesn't exist, so fall through and try to // create file since we won't be overwriting anything... } int cpu_word_size = sizeof(double); int io_word_size = 0; float version; int mode = exodusMode; if (int_byte_size_api() == 8) { mode |= EX_ALL_INT64_API; } #if defined EX_DISKLESS // Experimental -- in memory write by netcdf library if (properties.exists("MEMORY_WRITE")) { mode |= EX_DISKLESS; } #endif MPI_Info info = MPI_INFO_NULL; int app_opt_val = ex_opts(EX_VERBOSE); Ioss::DatabaseIO::openDatabase__(); std::string filename = get_dwname(); #if !defined(__IOSS_WINDOWS__) Ioss::FileInfo file(filename); std::string path = file.pathname(); filename = file.tailname(); char *current_cwd = getcwd(nullptr, 0); chdir(path.c_str()); #endif bool do_timer = false; Ioss::Utils::check_set_bool_property(properties, "IOSS_TIME_FILE_OPEN_CLOSE", do_timer); double t_begin = (do_timer ? Ioss::Utils::timer() : 0); if (fileExists) { m_exodusFilePtr = ex_open_par(filename.c_str(), EX_WRITE | mode, &cpu_word_size, &io_word_size, &version, util().communicator(), info); } else { // If the first write for this file, create it... if (int_byte_size_api() == 8) { // Check whether client actually wants 4-byte output on db // - If they specified INTEGER_SIZE_DB and the size isn't 8, // then don't change mode and use the default 4-byte output. if (properties.exists("INTEGER_SIZE_DB")) { if (properties.get("INTEGER_SIZE_DB").get_int() == 8) { mode |= EX_ALL_INT64_DB; } } else { mode |= EX_ALL_INT64_DB; } } m_exodusFilePtr = ex_create_par(filename.c_str(), mode, &cpu_word_size, &dbRealWordSize, util().communicator(), info); } if (do_timer) { double t_end = Ioss::Utils::timer(); double duration = util().global_minmax(t_end - t_begin, Ioss::ParallelUtils::DO_MAX); std::string open_create = fileExists ? "Open" : "Create"; if (myProcessor == 0) { fmt::print(Ioss::DEBUG(), "File {} Time = {}\n", open_create, duration); } } #if !defined(__IOSS_WINDOWS__) chdir(current_cwd); std::free(current_cwd); #endif bool is_ok = check_valid_file_ptr(write_message, error_msg, bad_count, abort_if_error); if (is_ok) { ex_set_max_name_length(m_exodusFilePtr, maximumNameLength); // Check properties handled post-create/open... if (properties.exists("COMPRESSION_METHOD")) { auto method = properties.get("COMPRESSION_METHOD").get_string(); method = Ioss::Utils::lowercase(method); ex_compression_type exo_method = EX_COMPRESS_ZLIB; if (method == "zlib" || method == "libz" || method == "gzip") { exo_method = EX_COMPRESS_ZLIB; } else if (method == "szip") { #if !defined(NC_HAS_SZIP_WRITE) #define NC_HAS_SZIP_WRITE 0 #endif #if NC_HAS_SZIP_WRITE exo_method = EX_COMPRESS_SZIP; #else if (myProcessor == 0) { fmt::print(Ioss::WARNING(), "The NetCDF library does not have SZip compression enabled." " 'zlib' will be used instead.\n\n"); } #endif } else { if (myProcessor == 0) { fmt::print(Ioss::WARNING(), "Unrecognized compression method specified: '{}'." " 'zlib' will be used instead.\n\n", method); } } ex_set_option(m_exodusFilePtr, EX_OPT_COMPRESSION_TYPE, exo_method); } if (properties.exists("COMPRESSION_LEVEL")) { int comp_level = properties.get("COMPRESSION_LEVEL").get_int(); ex_set_option(m_exodusFilePtr, EX_OPT_COMPRESSION_LEVEL, comp_level); } if (properties.exists("COMPRESSION_SHUFFLE")) { int shuffle = properties.get("COMPRESSION_SHUFFLE").get_int(); ex_set_option(m_exodusFilePtr, EX_OPT_COMPRESSION_SHUFFLE, shuffle); } } ex_opts(app_opt_val); // Reset back to what it was. return is_ok; } int ParallelDatabaseIO::get_file_pointer() const { return Ioex::BaseDatabaseIO::get_file_pointer(); } int ParallelDatabaseIO::free_file_pointer() const { int flag; MPI_Initialized(&flag); if (flag == 0) { std::ostringstream errmsg; fmt::print(errmsg, "ERROR: MPI is not initialized."); IOSS_ERROR(errmsg); } // Make sure all file pointers are valid... int fp_min = util().global_minmax(m_exodusFilePtr, Ioss::ParallelUtils::DO_MIN); int fp_max = util().global_minmax(m_exodusFilePtr, Ioss::ParallelUtils::DO_MAX); if (fp_min != fp_max && fp_min < 0) { std::ostringstream errmsg; fmt::print(errmsg, "ERROR: Inconsistent file pointer values."); IOSS_ERROR(errmsg); } return Ioex::BaseDatabaseIO::free_file_pointer(); } void ParallelDatabaseIO::read_meta_data__() { int exoid = get_file_pointer(); // get_file_pointer() must be called first. // APPENDING: // If parallel (single file, not fpp), we have assumptions // that the writing process (ranks, mesh, decomp, vars) is the // same for the original run that created this database and // for this run which is appending to the database so the // defining of the output database should be the same except // we don't write anything since it is already there. We do // need the number of steps though... if (open_create_behavior() == Ioss::DB_APPEND) { get_step_times__(); return; } if (int_byte_size_api() == 8) { decomp = std::unique_ptr( new DecompositionData(properties, util().communicator())); } else { decomp = std::unique_ptr( new DecompositionData(properties, util().communicator())); } assert(decomp != nullptr); decomp->decompose_model(exoid); read_region(); get_elemblocks(); get_step_times__(); get_nodeblocks(); get_edgeblocks(); get_faceblocks(); check_side_topology(); get_nodesets(); get_sidesets(); #if 0 get_edgesets(); get_facesets(); get_elemsets(); #endif get_commsets(); // Add assemblies now that all entities should be defined... consistent across processors // (metadata) get_assemblies(); get_blobs(); handle_groups(); add_region_fields(); if (!is_input() && open_create_behavior() == Ioss::DB_APPEND) { get_map(EX_NODE_BLOCK); get_map(EX_ELEM_BLOCK); } } void ParallelDatabaseIO::read_region() { // Add properties and fields to the 'owning' region. // Also defines member variables of this class... ex_init_params info{}; int error = ex_get_init_ext(get_file_pointer(), &info); if (error < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } spatialDimension = decomp->spatial_dimension(); nodeCount = decomp->ioss_node_count(); edgeCount = 0; faceCount = 0; elementCount = decomp->ioss_elem_count(); m_groupCount[EX_NODE_BLOCK] = 1; m_groupCount[EX_EDGE_BLOCK] = info.num_edge_blk; m_groupCount[EX_FACE_BLOCK] = info.num_face_blk; m_groupCount[EX_ELEM_BLOCK] = info.num_elem_blk; m_groupCount[EX_NODE_SET] = info.num_node_sets; m_groupCount[EX_EDGE_SET] = info.num_edge_sets; m_groupCount[EX_FACE_SET] = info.num_face_sets; m_groupCount[EX_ELEM_SET] = info.num_elem_sets; m_groupCount[EX_SIDE_SET] = info.num_side_sets; m_groupCount[EX_ASSEMBLY] = info.num_assembly; m_groupCount[EX_BLOB] = info.num_blob; // Checks: node, element, blocks > 0; warning if == 0; error if < 0 check_valid_values(); Ioss::Region *this_region = get_region(); // See if any coordinate frames exist on mesh. If so, define them on region. Ioex::add_coordinate_frames(get_file_pointer(), this_region); this_region->property_add( Ioss::Property("global_node_count", static_cast(decomp->global_node_count()))); this_region->property_add( Ioss::Property("global_element_count", static_cast(decomp->global_elem_count()))); this_region->property_add(Ioss::Property(std::string("title"), info.title)); // Get QA records from database and add to qaRecords... int num_qa = ex_inquire_int(get_file_pointer(), EX_INQ_QA); if (num_qa > 0) { struct qa_element { char *qa_record[1][4]; }; auto qa = new qa_element[num_qa]; for (int i = 0; i < num_qa; i++) { for (int j = 0; j < 4; j++) { qa[i].qa_record[0][j] = new char[MAX_STR_LENGTH + 1]; } } ex_get_qa(get_file_pointer(), qa[0].qa_record); for (int i = 0; i < num_qa; i++) { add_qa_record(qa[i].qa_record[0][0], qa[i].qa_record[0][1], qa[i].qa_record[0][2], qa[i].qa_record[0][3]); } for (int i = 0; i < num_qa; i++) { for (int j = 0; j < 4; j++) { delete[] qa[i].qa_record[0][j]; } } delete[] qa; } // Get information records from database and add to informationRecords... int num_info = ex_inquire_int(get_file_pointer(), EX_INQ_INFO); if (num_info > 0) { char **info_rec = Ioss::Utils::get_name_array( num_info, max_line_length); // 'total_lines' pointers to char buffers ex_get_info(get_file_pointer(), info_rec); for (int i = 0; i < num_info; i++) { add_information_record(info_rec[i]); } Ioss::Utils::delete_name_array(info_rec, num_info); } } void ParallelDatabaseIO::get_step_times__() { double last_time = DBL_MAX; int timestep_count = 0; std::vector tsteps(0); { timestep_count = ex_inquire_int(get_file_pointer(), EX_INQ_TIME); if (timestep_count <= 0) { return; } // For an exodusII file, timesteps are global and are stored in the region. // Read the timesteps and add to the region tsteps.resize(timestep_count); int error = ex_get_all_times(get_file_pointer(), tsteps.data()); if (error < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } // See if the "last_written_time" attribute exists and if it // does, check that it matches the largest time in 'tsteps'. Ioex::read_last_time_attribute(get_file_pointer(), &last_time); } // Only add states that are less than or equal to the // 'last_time' value which is either DBL_MAX or the value of // the last time successfully written to the database and // flushed to disk. This is used to avoid corrupt data arising // from a job that crashed during the writing of the last step // on the database. Output a warning message if there is // potentially corrupt data on the database... // Check whether user or application wants to limit the times even further... // One use case is that job is restarting at a time prior to what has been // written to the results file, so want to start appending after // restart time instead of at end time on database. int max_step = properties.get_optional("APPEND_OUTPUT_AFTER_STEP", timestep_count); max_step = std::min(max_step, timestep_count); double max_time = properties.get_optional("APPEND_OUTPUT_AFTER_TIME", std::numeric_limits::max()); last_time = std::min(last_time, max_time); Ioss::Region *this_region = get_region(); for (int i = 0; i < max_step; i++) { if (tsteps[i] <= last_time) { this_region->add_state(tsteps[i] * timeScaleFactor); } else { if (myProcessor == 0 && max_time == std::numeric_limits::max()) { // NOTE: Don't want to warn on all processors if there are // corrupt steps on all databases, but this will only print // a warning if there is a corrupt step on processor // 0... Need better warnings which won't overload in the // worst case... fmt::print(Ioss::WARNING(), "Skipping step {} at time {} in database file\n\t{}.\nThe data for that step " "is possibly corrupt.\n", fmt::group_digits(i + 1), tsteps[i], get_filename()); } } } } const Ioss::Map &ParallelDatabaseIO::get_map(ex_entity_type type) const { switch (type) { case EX_NODE_BLOCK: case EX_NODE_SET: { assert(decomp != nullptr); size_t offset = decomp->decomp_node_offset(); size_t count = decomp->decomp_node_count(); return get_map(nodeMap, nodeCount, offset, count, EX_NODE_MAP, EX_INQ_NODE_MAP); } case EX_ELEM_BLOCK: case EX_ELEM_SET: { assert(decomp != nullptr); size_t offset = decomp->decomp_elem_offset(); size_t count = decomp->decomp_elem_count(); return get_map(elemMap, elementCount, offset, count, EX_ELEM_MAP, EX_INQ_ELEM_MAP); } case EX_FACE_BLOCK: case EX_FACE_SET: return get_map(faceMap, faceCount, 0, 0, EX_FACE_MAP, EX_INQ_FACE_MAP); case EX_EDGE_BLOCK: case EX_EDGE_SET: return get_map(edgeMap, edgeCount, 0, 0, EX_EDGE_MAP, EX_INQ_EDGE_MAP); default: std::ostringstream errmsg; fmt::print(errmsg, "INTERNAL ERROR: Invalid map type. " "Something is wrong in the Ioex::ParallelDatabaseIO::get_map() function. " "Please report.\n"); IOSS_ERROR(errmsg); } } const Ioss::Map &ParallelDatabaseIO::get_map(Ioss::Map &entity_map, int64_t entity_count, int64_t file_offset, int64_t file_count, ex_entity_type entity_type, ex_inquiry inquiry_type) const { // Allocate space for node number map and read it in... // Can be called multiple times, allocate 1 time only if (entity_map.map().empty()) { entity_map.set_size(entity_count); if (is_input()) { Ioss::MapContainer file_data(file_count); int error = 0; // Check whether there is a "original_global_id_map" map on // the database. If so, use it instead of the "node_num_map". bool map_read = false; int map_count = ex_inquire_int(get_file_pointer(), inquiry_type); if (map_count > 0) { char **names = Ioss::Utils::get_name_array(map_count, maximumNameLength); int ierr = ex_get_names(get_file_pointer(), entity_type, names); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } if (map_count == 1 && Ioss::Utils::str_equal(names[0], "original_global_id_map")) { if (int_byte_size_api() == 8) { error = ex_get_partial_num_map(get_file_pointer(), entity_type, 1, file_offset + 1, file_count, file_data.data()); } else { // Ioss stores as 64-bit, read as 32-bit and copy over... Ioss::IntVector tmp_map(file_count); error = ex_get_partial_num_map(get_file_pointer(), entity_type, 1, file_offset + 1, file_count, tmp_map.data()); std::copy(tmp_map.begin(), tmp_map.end(), file_data.begin()); } if (error >= 0) { map_read = true; } } Ioss::Utils::delete_name_array(names, map_count); } if (!map_read) { if (int_byte_size_api() == 8) { error = ex_get_partial_id_map(get_file_pointer(), entity_type, file_offset + 1, file_count, file_data.data()); } else { // Ioss stores as 64-bit, read as 32-bit and copy over... Ioss::IntVector tmp_map(file_count); error = ex_get_partial_id_map(get_file_pointer(), entity_type, file_offset + 1, file_count, tmp_map.data()); std::copy(tmp_map.begin(), tmp_map.end(), file_data.begin()); } } if (error >= 0) { if (entity_type == EX_NODE_MAP) { decomp->communicate_node_data(file_data.data(), &entity_map.map()[1], 1); } else if (entity_type == EX_ELEM_MAP) { decomp->communicate_element_data(file_data.data(), &entity_map.map()[1], 1); } } else { // Clear out the vector... Ioss::MapContainer().swap(entity_map.map()); Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } // Check for sequential node map. // If not, build the reverse G2L node map... entity_map.is_sequential(true); entity_map.build_reverse_map(); } else { // Output database; entity_map.map() not set yet... Build a default map. entity_map.set_default(entity_count); } } return entity_map; } void ParallelDatabaseIO::get_elemblocks() { get_blocks(EX_ELEM_BLOCK, 0, "block"); } void ParallelDatabaseIO::get_faceblocks() { // get_blocks(EX_FACE_BLOCK, 1, "faceblock"); } void ParallelDatabaseIO::get_edgeblocks() { // get_blocks(EX_EDGE_BLOCK, 2, "edgeblock"); } void ParallelDatabaseIO::get_blocks(ex_entity_type entity_type, int rank_offset, const std::string &basename) { // Attributes of an X block are: (X = element, face, or edge) // -- id // -- name // -- X type // -- number of Xs // -- number of attributes per X // -- number of nodes per X (derivable from type) // -- number of faces per X (derivable from type) // -- number of edges per X (derivable from type) // In a parallel execution, it is possible that an X block will have // no Xs on a particular processor... // NOTE: This routine may be called multiple times on a single database. // make sure it is not dependent on being called one time only... // Get exodusII X block metadata if (m_groupCount[entity_type] == 0) { return; } assert(entity_type == EX_ELEM_BLOCK); Ioss::Int64Vector X_block_ids(m_groupCount[entity_type]); int used_blocks = 0; int error; if ((ex_int64_status(get_file_pointer()) & EX_IDS_INT64_API) != 0) { error = ex_get_ids(get_file_pointer(), entity_type, X_block_ids.data()); } else { Ioss::IntVector tmp_set_ids(X_block_ids.size()); error = ex_get_ids(get_file_pointer(), entity_type, tmp_set_ids.data()); if (error >= 0) { std::copy(tmp_set_ids.begin(), tmp_set_ids.end(), X_block_ids.begin()); } } if (error < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } int nvar = std::numeric_limits::max(); // Number of 'block' vars on database. Used to // skip querying if none. int nmap = std::numeric_limits::max(); // Number of 'block' maps on database. Used to // skip querying if none. for (int iblk = 0; iblk < m_groupCount[entity_type]; iblk++) { if (decomp->el_blocks[iblk].global_count() == 0) { continue; } int64_t id = decomp->el_blocks[iblk].id(); bool db_has_name = false; std::string alias = Ioss::Utils::encode_entity_name(basename, id); std::string block_name; if (ignore_database_names()) { block_name = alias; } else { block_name = Ioex::get_entity_name(get_file_pointer(), entity_type, id, basename, maximumNameLength, db_has_name); } if (get_use_generic_canonical_name()) { std::swap(block_name, alias); } std::string save_type = decomp->el_blocks[iblk].topologyType; std::string type = Ioss::Utils::fixup_type(decomp->el_blocks[iblk].topologyType, decomp->el_blocks[iblk].nodesPerEntity, spatialDimension - rank_offset); Ioss::EntityBlock *io_block = nullptr; if (entity_type == EX_ELEM_BLOCK) { auto *eblock = new Ioss::ElementBlock(this, block_name, type, decomp->el_blocks[iblk].ioss_count()); io_block = eblock; io_block->property_add(Ioss::Property("id", id)); io_block->property_add(Ioss::Property("guid", util().generate_guid(id))); io_block->property_add(Ioss::Property("iblk", iblk)); // Sequence in decomp. if (db_has_name) { std::string *db_name = &block_name; if (get_use_generic_canonical_name()) { db_name = &alias; } io_block->property_add(Ioss::Property("db_name", *db_name)); } get_region()->add(eblock); #if 0 } else if (entity_type == EX_FACE_BLOCK) { Ioss::FaceBlock *fblock = new Ioss::FaceBlock(this, block_name, type, block.num_entry); io_block = fblock; io_block->property_add(Ioss::Property("id", id)); io_block->property_add(Ioss::Property("guid", util().generate_guid(id))); if (db_has_name) { std::string *db_name = &block_name; if (get_use_generic_canonical_name()) { db_name = &alias; } io_block->property_add(Ioss::Property("db_name", *db_name)); } get_region()->add(fblock); } else if (entity_type == EX_EDGE_BLOCK) { Ioss::EdgeBlock *eblock = new Ioss::EdgeBlock(this, block_name, type, block.num_entry); io_block = eblock; io_block->property_add(Ioss::Property("id", id)); io_block->property_add(Ioss::Property("guid", util().generate_guid(id))); if (db_has_name) { std::string *db_name = &block_name; if (get_use_generic_canonical_name()) { db_name = &alias; } io_block->property_add(Ioss::Property("db_name", *db_name)); } get_region()->add(eblock); #endif } else { std::ostringstream errmsg; fmt::print(errmsg, "ERROR: Invalid type in get_blocks()"); IOSS_ERROR(errmsg); } #if 0 // See which connectivity options were defined for this block. // X -> Node is always defined. // X -> Face? if (block.num_faces_per_entry > 0 && rank_offset < 1) { std::string storage = "Real["+std::to_string(block.num_faces_per_entry)+"]"; io_block->field_add(Ioss::Field("connectivity_face", io_block->field_int_type(), storage, Ioss::Field::MESH)); } // X -> Edge? if (block.num_edges_per_entry > 0 && rank_offset < 2) { std::string storage = "Real["+std::to_string(block.num_edges_per_entry)+"]"; io_block->field_add(Ioss::Field("connectivity_edge", io_block->field_int_type(), storage, Ioss::Field::MESH)); } #endif // Maintain block order on output database... io_block->property_add(Ioss::Property("original_block_order", used_blocks++)); if (save_type != "null" && save_type != "") { io_block->property_update("original_topology_type", save_type); } io_block->property_add(Ioss::Property( "global_entity_count", static_cast(decomp->el_blocks[iblk].ioss_count()))); if (block_name != alias) { get_region()->add_alias(block_name, alias, io_block->type()); } // Check for additional variables. add_attribute_fields(entity_type, io_block, decomp->el_blocks[iblk].attributeCount, type); if (nvar > 0) { nvar = add_results_fields(entity_type, io_block, iblk); } if (entity_type == EX_ELEM_BLOCK) { if (nmap > 0) { nmap = Ioex::add_map_fields(get_file_pointer(), dynamic_cast(io_block), decomp->el_blocks[iblk].ioss_count(), maximumNameLength); } if (!assemblyOmissions.empty() || !assemblyInclusions.empty()) { update_block_omissions_from_assemblies(); } assert(blockOmissions.empty() || blockInclusions.empty()); // Only one can be non-empty // Handle all block omissions or inclusions... // This only affects the generation of surfaces... if (!blockOmissions.empty()) { for (const auto &name : blockOmissions) { auto block = get_region()->get_element_block(name); if (block) { block->property_add(Ioss::Property(std::string("omitted"), 1)); } } } if (!blockInclusions.empty()) { const auto &blocks = get_region()->get_element_blocks(); for (auto &block : blocks) { block->property_add(Ioss::Property(std::string("omitted"), 1)); } // Now, erase the property on any blocks in the inclusion list... for (const auto &name : blockInclusions) { auto block = get_region()->get_element_block(name); if (block != nullptr) { block->property_erase("omitted"); } } } } } } void ParallelDatabaseIO::compute_node_status() const { // Create a field for all nodes in the model indicating // the connectivity 'status' of the node. The status values are: // 0 -- node not connected to any elements // 1 -- node only connected to omitted elements // 2 -- node only connected to active elements // 3 -- node at border of active and omitted elements. /// \todo Get working for parallel... if (nodeConnectivityStatusCalculated) { return; } nodeConnectivityStatus.resize(nodeCount); const Ioss::ElementBlockContainer &element_blocks = get_region()->get_element_blocks(); assert(Ioss::Utils::check_block_order(element_blocks)); for (Ioss::ElementBlock *block : element_blocks) { unsigned char status = 2; if (Ioss::Utils::block_is_omitted(block)) { status = 1; } int64_t id = block->get_property("id").get_int(); int element_nodes = block->topology()->number_nodes(); int64_t my_element_count = block->entity_count(); int order = block->get_property("iblk").get_int(); if (int_byte_size_api() == 8) { std::vector conn(my_element_count * element_nodes); decomp->get_block_connectivity(get_file_pointer(), conn.data(), id, order, element_nodes); for (auto node : conn) { nodeConnectivityStatus[node - 1] |= status; } } else { std::vector conn(my_element_count * element_nodes); decomp->get_block_connectivity(get_file_pointer(), conn.data(), id, order, element_nodes); for (auto node : conn) { nodeConnectivityStatus[node - 1] |= status; } } } nodeConnectivityStatusCalculated = true; } namespace { void get_element_sides_lists(const std::unique_ptr &decomp, int exoid, int64_t id, int int_byte_size, int64_t number_sides, Ioss::Int64Vector &element, Ioss::Int64Vector &sides) { // Check whether we already populated the element/sides vectors. if (element.empty() && sides.empty() && number_sides > 0) { element.resize(number_sides); sides.resize(number_sides); // Easier below here if the element and sides are a known 64-bit size... // Kluge here to do that... if (int_byte_size == 4) { Ioss::Field side_field("sides", Ioss::Field::INTEGER, IOSS_SCALAR(), Ioss::Field::MESH, number_sides); Ioss::Field elem_field("ids_raw", Ioss::Field::INTEGER, IOSS_SCALAR(), Ioss::Field::MESH, number_sides); Ioss::IntVector e32(number_sides); decomp->get_set_mesh_var(exoid, EX_SIDE_SET, id, elem_field, e32.data()); std::copy(e32.begin(), e32.end(), element.begin()); decomp->get_set_mesh_var(exoid, EX_SIDE_SET, id, side_field, e32.data()); std::copy(e32.begin(), e32.end(), sides.begin()); } else { Ioss::Field side_field("sides", Ioss::Field::INT64, IOSS_SCALAR(), Ioss::Field::MESH, number_sides); Ioss::Field elem_field("ids_raw", Ioss::Field::INT64, IOSS_SCALAR(), Ioss::Field::MESH, number_sides); decomp->get_set_mesh_var(exoid, EX_SIDE_SET, id, elem_field, element.data()); decomp->get_set_mesh_var(exoid, EX_SIDE_SET, id, side_field, sides.data()); } } } } // namespace void ParallelDatabaseIO::get_sidesets() { // This function creates all sidesets (surfaces) for a // model. Note that a sideset contains 1 or more sideblocks // which are homogeneous (same topology). In serial execution, // this is fairly straightforward since there are no null sets and // we have all the information we need. (...except see below for // surface evolution). // // However, in a parallel execution, we have the possibility that a // side set will have no sides or distribution factors on // a particular processor. We then don't know the block topology of // the block(s) contained in this set. We could do some // communication and get a good idea of the topologies that are in // the set. if (m_groupCount[EX_SIDE_SET] > 0) { check_side_topology(); // Get exodusII sideset metadata // Get the names (may not exist) of all sidesets and see if they are actually // side "blocks" (perhaps written by IO system for a restart). In that case, // they were split by a previous run and we need to reconstruct the side "set" // that may contain one or more of them. Ioex::SideSetMap ss_map; Ioex::SideSetSet ss_set; { int error; for (const auto &ss : decomp->side_sets) { int64_t id = ss.id(); std::vector ss_name(maximumNameLength + 1); error = ex_get_name(get_file_pointer(), EX_SIDE_SET, id, ss_name.data()); if (error < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } if (ss_name[0] != '\0') { Ioss::Utils::fixup_name(ss_name.data()); Ioex::decode_surface_name(ss_map, ss_set, ss_name.data()); } } } // Create sidesets for each entry in the ss_set... These are the // sidesets which were probably written by a previous run of the // IO system and are already split into homogeneous pieces... { for (auto &ss_name : ss_set) { auto *side_set = new Ioss::SideSet(this, ss_name); get_region()->add(side_set); int64_t id = Ioex::extract_id(ss_name); if (id > 0) { side_set->property_add(Ioss::Property("id", id)); side_set->property_add(Ioss::Property("guid", util().generate_guid(id))); } } } for (int iss = 0; iss < m_groupCount[EX_SIDE_SET]; iss++) { int64_t id = decomp->side_sets[iss].id(); std::string sid; Ioex::TopologyMap topo_map; Ioex::TopologyMap side_map; // Used to determine side consistency Ioss::SurfaceSplitType split_type = splitType; std::string side_set_name; Ioss::SideSet *side_set = nullptr; bool db_has_name = false; { std::string alias = Ioss::Utils::encode_entity_name("surface", id); if (ignore_database_names()) { side_set_name = alias; } else { side_set_name = Ioex::get_entity_name(get_file_pointer(), EX_SIDE_SET, id, "surface", maximumNameLength, db_has_name); } if (side_set_name == "universal_sideset") { split_type = Ioss::SPLIT_BY_DONT_SPLIT; } bool in_ss_map = false; auto SSM = ss_map.find(side_set_name); if (SSM != ss_map.end()) { in_ss_map = true; std::string ess_name = (*SSM).second; side_set = get_region()->get_sideset(ess_name); Ioss::Utils::check_non_null(side_set, "sideset", ess_name, __func__); } else { if (get_use_generic_canonical_name()) { std::swap(side_set_name, alias); } side_set = new Ioss::SideSet(this, side_set_name); side_set->property_add(Ioss::Property("id", id)); side_set->property_add(Ioss::Property("guid", util().generate_guid(id))); if (db_has_name) { std::string *db_name = &side_set_name; if (get_use_generic_canonical_name()) { db_name = &alias; } side_set->property_add(Ioss::Property("db_name", *db_name)); } get_region()->add(side_set); get_region()->add_alias(side_set_name, alias, Ioss::SIDESET); get_region()->add_alias(side_set_name, Ioss::Utils::encode_entity_name("sideset", id), Ioss::SIDESET); } // split_type = SPLIT_BY_ELEMENT_BLOCK; // split_type = SPLIT_BY_TOPOLOGIES; // split_type = SPLIT_BY_DONT_SPLIT; // Determine how many side blocks compose this side set. int64_t number_sides = decomp->side_sets[iss].ioss_count(); // FIXME: Support- number_distribution_factors = decomp->side_sets[iss].df_count(); Ioss::Int64Vector element; Ioss::Int64Vector sides; if (!blockOmissions.empty() || !blockInclusions.empty()) { get_element_sides_lists(decomp, get_file_pointer(), id, int_byte_size_api(), number_sides, element, sides); Ioex::filter_element_list(get_region(), element, sides, true); number_sides = element.size(); assert(element.size() == sides.size()); } if (split_type == Ioss::SPLIT_BY_TOPOLOGIES && sideTopology.size() == 1) { // There is only one side type for all elements in the model topo_map[std::make_pair(sideTopology[0].first->name(), sideTopology[0].second)] = number_sides; } else if (split_type == Ioss::SPLIT_BY_DONT_SPLIT) { const Ioss::ElementTopology *mixed_topo = Ioss::ElementTopology::factory("unknown"); topo_map[std::make_pair(std::string("unknown"), mixed_topo)] = number_sides; } else if (in_ss_map) { std::vector tokens = Ioss::tokenize(side_set_name, "_"); assert(tokens.size() >= 4); // The sideset should have only a single topology which is // given by the sideset name... const Ioss::ElementTopology *side_topo = Ioss::ElementTopology::factory(tokens[tokens.size() - 2]); assert(side_topo != nullptr); const Ioss::ElementTopology *element_topo = Ioss::ElementTopology::factory(tokens[tokens.size() - 3], true); std::string name; if (element_topo != nullptr) { name = element_topo->name(); } else { // -4 -3 -2 -1 // Name is of the form name_block_id_sidetopo_id name = tokens[tokens.size() - 4] + "_" + tokens[tokens.size() - 3]; } topo_map[std::make_pair(name, side_topo)] = number_sides; // We want the id to match the id on the sideset in this // case so that the generated name will match the current // name. Instead of converting from string to int back to // string, we just set a variable to query later. sid = tokens[tokens.size() - 1]; } else if (split_type == Ioss::SPLIT_BY_TOPOLOGIES) { // There are multiple side types in the model. // Iterate through the elements in the sideset, determine // their parent element block using the blocks element // topology and the side number, determine the side // type. for (auto &side_topo : sideTopology) { topo_map[std::make_pair(side_topo.first->name(), side_topo.second)] = 0; side_map[std::make_pair(side_topo.first->name(), side_topo.second)] = 0; } get_element_sides_lists(decomp, get_file_pointer(), id, int_byte_size_api(), number_sides, element, sides); Ioex::separate_surface_element_sides(element, sides, get_region(), topo_map, side_map, split_type, side_set_name); } else if (split_type == Ioss::SPLIT_BY_ELEMENT_BLOCK) { // There are multiple side types in the model. Iterate // through the elements in the sideset, determine their parent // element block using blocks element topology and the side // number, determine the side type. // Seed the topo_map map with name, side_topo> // pairs so we are sure that all processors have the same // starting topo_map (size and order). const Ioss::ElementBlockContainer &element_blocks = get_region()->get_element_blocks(); assert(Ioss::Utils::check_block_order(element_blocks)); for (Ioss::ElementBlock *block : element_blocks) { if (!Ioss::Utils::block_is_omitted(block)) { const std::string &name = block->name(); const Ioss::ElementTopology *common_ftopo = block->topology()->boundary_type(0); if (common_ftopo != nullptr) { // All sides of this element block's topology have the same topology topo_map[std::make_pair(name, common_ftopo)] = 0; side_map[std::make_pair(name, common_ftopo)] = 0; } else { // The sides have different topology, iterate over // them and create an entry for the unique side // topology types int par_dim = block->topology()->parametric_dimension(); if (par_dim == 2 || par_dim == 3) { int64_t my_side_count = block->topology()->number_boundaries(); for (int64_t ii = 0; ii < my_side_count; ii++) { const Ioss::ElementTopology *topo = block->topology()->boundary_type(ii + 1); topo_map[std::make_pair(name, topo)] = 0; side_map[std::make_pair(name, topo)] = 0; } } } } } get_element_sides_lists(decomp, get_file_pointer(), id, int_byte_size_api(), number_sides, element, sides); Ioex::separate_surface_element_sides(element, sides, get_region(), topo_map, side_map, split_type, side_set_name); } } // End of first step in splitting. Check among all processors // to see which potential splits have sides in them... Ioss::Int64Vector global_side_counts(topo_map.size()); { int64_t i = 0; for (auto &topo : topo_map) { global_side_counts[i++] = topo.second; } // If splitting by element block, also sync the side_map // information which specifies whether the sideset has // consistent sides for all elements. Only really used for // shells, but easier to just set the value on all surfaces // in the element block split case. if (side_map.size() == topo_map.size()) { global_side_counts.resize(topo_map.size() + side_map.size()); for (auto &side : side_map) { global_side_counts[i++] = side.second; } } // See if any processor has non-zero count for the topo_map counts // For the side_map, need the max value. util().global_array_minmax(global_side_counts, Ioss::ParallelUtils::DO_MAX); } // Create Side Blocks int64_t i = 0; for (auto &topo : topo_map) { if (global_side_counts[i++] > 0) { const std::string topo_or_block_name = topo.first.first; const Ioss::ElementTopology *side_topo = topo.first.second; assert(side_topo != nullptr); #if 0 if (side_topo->parametric_dimension() == topology_dimension-1 || split_type == Ioss::SPLIT_BY_DONT_SPLIT ) { #else if (true) { #endif int64_t my_side_count = topo.second; std::string side_block_name = "surface_" + topo_or_block_name + "_" + side_topo->name(); if (split_type == Ioss::SPLIT_BY_DONT_SPLIT) { side_block_name = side_set_name; } else { if (db_has_name) { side_block_name = side_set->name() + "_" + topo_or_block_name + "_" + side_topo->name(); } else { if (sid.empty()) { side_block_name = Ioss::Utils::encode_entity_name(side_block_name, id); } else { side_block_name += "_"; side_block_name += sid; } } } Ioss::ElementBlock *block = nullptr; // Need to get elem_topo.... const Ioss::ElementTopology *elem_topo = nullptr; if (split_type == Ioss::SPLIT_BY_TOPOLOGIES) { elem_topo = Ioss::ElementTopology::factory(topo_or_block_name); } else if (split_type == Ioss::SPLIT_BY_ELEMENT_BLOCK) { block = get_region()->get_element_block(topo_or_block_name); if (block == nullptr || Ioss::Utils::block_is_omitted(block)) { std::ostringstream errmsg; fmt::print(errmsg, "INTERNAL ERROR: Could not find element block '{}'. Something is wrong " "in the Ioex::ParallelDatabaseIO class. Please report.\n", topo_or_block_name); IOSS_ERROR(errmsg); } elem_topo = block->topology(); } if (split_type == Ioss::SPLIT_BY_DONT_SPLIT) { // Most likely this is "unknown", but can be a true // topology if there is only a single element block in // the model. elem_topo = Ioss::ElementTopology::factory(topo_or_block_name); } assert(elem_topo != nullptr); auto *side_block = new Ioss::SideBlock(this, side_block_name, side_topo->name(), elem_topo->name(), my_side_count); assert(side_block != nullptr); side_block->property_add(Ioss::Property("id", id)); side_block->property_add(Ioss::Property("guid", util().generate_guid(id))); side_set->add(side_block); // Note that all sideblocks within a specific // sideset might have the same id. // If splitting by element block, need to set the // element block member on this side block. if (split_type == Ioss::SPLIT_BY_ELEMENT_BLOCK) { side_block->set_parent_element_block(block); } // If we calculated whether the element side is // consistent for all sides in this block, then // tell the block which side it is, or that they are // inconsistent. If it wasn't calculated above, then it // will be calculated on the fly when/if requested. // This is to avoid reading the sideset bulk data in // cases where we don't need to read it, but if we are // already reading it (to split the sidesets), then use // the data when we have it. if (!side_map.empty()) { // Set a property indicating which element side // (1-based) all sides in this block are applied to. // If they are not all assigned to the same element // side, indicate this with a side equal to 0. // // (note: 'i' has already been incremented earlier in // the loop. We need previous value here...) int side = global_side_counts[i - 1 + topo_map.size()]; if (side == 999) { side = 0; } assert(side <= elem_topo->number_boundaries()); side_block->set_consistent_side_number(side); } // Add an alias... get_region()->add_alias(side_block); if (split_type != Ioss::SPLIT_BY_DONT_SPLIT && side_set_name != "universal_sideset") { std::string storage = "Real["; storage += std::to_string(side_topo->number_nodes()); storage += "]"; side_block->field_add(Ioss::Field("distribution_factors", Ioss::Field::REAL, storage, Ioss::Field::MESH)); } if (side_set_name == "universal_sideset") { side_block->field_add(Ioss::Field("side_ids", side_block->field_int_type(), "scalar", Ioss::Field::MESH)); } int num_attr = 0; { int ierr = ex_get_attr_param(get_file_pointer(), EX_SIDE_SET, 1, &num_attr); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } // Add additional fields add_attribute_fields(EX_SIDE_SET, side_block, num_attr, ""); add_results_fields(EX_SIDE_SET, side_block, iss); } } } } } } // namespace Ioex template void ParallelDatabaseIO::get_sets(ex_entity_type type, int64_t count, const std::string &base, const T * /* set_type */) { // Attributes of a Xset are: // -- id // -- name // -- number of nodes // -- number of distribution factors (see next comment) // ----the #distribution factors should equal #Xs or 0, any // other value does not make sense. If it is 0, then a substitute // list will be created returning 1.0 for the factor // In a parallel execution, it is possible that a Xset will have // no Xs or distribution factors on a particular processor... // Get exodusII Xset metadata for (int64_t ins = 0; ins < count; ins++) { int64_t id = decomp->node_sets[ins].id(); int num_attr = 0; int ierr = ex_get_attr_param(get_file_pointer(), type, id, &num_attr); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } bool db_has_name = false; std::string Xset_name; std::string alias = Ioss::Utils::encode_entity_name(base + "list", id); if (ignore_database_names()) { Xset_name = alias; } else { Xset_name = Ioex::get_entity_name(get_file_pointer(), type, id, base + "list", maximumNameLength, db_has_name); } if (get_use_generic_canonical_name()) { std::swap(Xset_name, alias); } T *Xset = new T(this, Xset_name, decomp->node_sets[ins].ioss_count()); Xset->property_add(Ioss::Property("id", id)); Xset->property_add(Ioss::Property("guid", util().generate_guid(id))); if (db_has_name) { std::string *db_name = &Xset_name; if (get_use_generic_canonical_name()) { db_name = &alias; } Xset->property_add(Ioss::Property("db_name", *db_name)); } get_region()->add(Xset); get_region()->add_alias(Xset_name, alias, Xset->type()); get_region()->add_alias(Xset_name, Ioss::Utils::encode_entity_name(base + "set", id), Xset->type()); add_attribute_fields(type, Xset, num_attr, ""); add_results_fields(type, Xset, ins); } } void ParallelDatabaseIO::get_nodesets() { get_sets(EX_NODE_SET, m_groupCount[EX_NODE_SET], "node", (Ioss::NodeSet *)nullptr); } void ParallelDatabaseIO::get_edgesets() { get_sets(EX_EDGE_SET, m_groupCount[EX_EDGE_SET], "edge", (Ioss::EdgeSet *)nullptr); } void ParallelDatabaseIO::get_facesets() { get_sets(EX_FACE_SET, m_groupCount[EX_FACE_SET], "face", (Ioss::FaceSet *)nullptr); } void ParallelDatabaseIO::get_elemsets() { get_sets(EX_ELEM_SET, m_groupCount[EX_ELEM_SET], "element", (Ioss::ElementSet *)nullptr); } void ParallelDatabaseIO::get_commsets() { // Attributes of a commset are: // -- id (property) // -- name (property) // -- number of node--CPU pairs (field) // In a parallel execution, it is possible that a commset will have // no nodes on a particular processor... // If this is a serial execution, there will be no communication // nodesets, just return an empty container. if (isParallel) { // Create a single node commset Ioss::CommSet *commset = new Ioss::CommSet(this, "commset_node", "node", decomp->get_commset_node_size()); commset->property_add(Ioss::Property("id", 1)); commset->property_add(Ioss::Property("guid", util().generate_guid(1))); get_region()->add(commset); } } int64_t ParallelDatabaseIO::get_field_internal(const Ioss::Region *reg, const Ioss::Field &field, void *data, size_t data_size) const { return Ioex::BaseDatabaseIO::get_field_internal(reg, field, data, data_size); } int64_t ParallelDatabaseIO::get_field_internal(const Ioss::NodeBlock *nb, const Ioss::Field &field, void *data, size_t data_size) const { size_t num_to_get = field.verify(data_size); #ifndef NDEBUG int64_t my_node_count = field.raw_count(); assert(my_node_count == nodeCount); #endif Ioss::Field::RoleType role = field.get_role(); if (role == Ioss::Field::MESH) { if (field.get_name() == "mesh_model_coordinates_x" || field.get_name() == "mesh_model_coordinates_y" || field.get_name() == "mesh_model_coordinates_z" || field.get_name() == "mesh_model_coordinates") { decomp->get_node_coordinates(get_file_pointer(), reinterpret_cast(data), field); } else if (field.get_name() == "ids") { // Map the local ids in this node block // (1...node_count) to global node ids. get_map(EX_NODE_BLOCK).map_implicit_data(data, field, num_to_get, 0); } // The 1..global_node_count id. In a parallel-decomposed run, // it maps the node back to its implicit position in the serial // undecomposed mesh file. This is ONLY provided for backward- // compatibility and should not be used unless absolutely required. else if (field.get_name() == "implicit_ids") { size_t offset = decomp->decomp_node_offset(); size_t count = decomp->decomp_node_count(); if (int_byte_size_api() == 4) { std::vector file_ids(count); std::iota(file_ids.begin(), file_ids.end(), offset + 1); decomp->communicate_node_data(file_ids.data(), reinterpret_cast(data), 1); } else { std::vector file_ids(count); std::iota(file_ids.begin(), file_ids.end(), offset + 1); decomp->communicate_node_data(file_ids.data(), reinterpret_cast(data), 1); } } else if (field.get_name() == "connectivity") { // Do nothing, just handles an idiosyncrasy of the GroupingEntity } else if (field.get_name() == "connectivity_raw") { // Do nothing, just handles an idiosyncrasy of the GroupingEntity } else if (field.get_name() == "node_connectivity_status") { compute_node_status(); char *status = static_cast(data); std::copy(nodeConnectivityStatus.begin(), nodeConnectivityStatus.end(), status); } else if (field.get_name() == "owning_processor") { // If parallel, then set the "locally_owned" property on the nodeblocks. Ioss::CommSet *css = get_region()->get_commset("commset_node"); int *idata = static_cast(data); // Owning processor field is 4-byte int always for (int64_t i = 0; i < nodeCount; i++) { idata[i] = myProcessor; } if (int_byte_size_api() == 8) { // Cannot call: // `css->get_field_data("entity_processor_raw", ent_proc);` // directly since it will cause a deadlock (in threaded code), // expand out into corresponding `get_field_internal` call. Ioss::Field ep_field = css->get_field("entity_processor_raw"); std::vector ent_proc(ep_field.raw_count() * ep_field.get_component_count(Ioss::Field::InOut::INPUT)); size_t ep_data_size = ent_proc.size() * sizeof(int64_t); get_field_internal(css, ep_field, ent_proc.data(), ep_data_size); for (size_t i = 0; i < ent_proc.size(); i += 2) { int64_t node = ent_proc[i + 0]; int64_t proc = ent_proc[i + 1]; if (proc < idata[node - 1]) { idata[node - 1] = proc; } } } else { Ioss::Field ep_field = css->get_field("entity_processor_raw"); std::vector ent_proc(ep_field.raw_count() * ep_field.get_component_count(Ioss::Field::InOut::INPUT)); size_t ep_data_size = ent_proc.size() * sizeof(int); get_field_internal(css, ep_field, ent_proc.data(), ep_data_size); for (size_t i = 0; i < ent_proc.size(); i += 2) { int node = ent_proc[i + 0]; int proc = ent_proc[i + 1]; if (proc < idata[node - 1]) { idata[node - 1] = proc; } } } } else { num_to_get = Ioss::Utils::field_warning(nb, field, "input"); } } else if (role == Ioss::Field::TRANSIENT) { // Check if the specified field exists on this node block. // Note that 'higher-order' storage types (e.g. SYM_TENSOR) // exist on the database as scalars with the appropriate // extensions. // Read in each component of the variable and transfer into // 'data'. Need temporary storage area of size 'number of // nodes in this block. num_to_get = read_transient_field(EX_NODE_BLOCK, m_variables[EX_NODE_BLOCK], field, nb, data); } else if (role == Ioss::Field::ATTRIBUTE) { num_to_get = read_attribute_field(EX_NODE_BLOCK, field, nb, data); } return num_to_get; } int64_t ParallelDatabaseIO::get_field_internal(const Ioss::Blob *blob, const Ioss::Field &field, void *data, size_t data_size) const { { Ioss::SerializeIO serializeIO__(this); size_t num_to_get = field.verify(data_size); if (num_to_get > 0) { Ioss::Field::RoleType role = field.get_role(); if (role == Ioss::Field::MESH) { if (field.get_name() == "ids") { // Map the local ids in this node block // (1...node_count) to global node ids. // get_map(EX_BLOB).map_implicit_data(data, field, num_to_get, 0); } else if (field.get_name() == "connectivity") { // Do nothing, just handles an idiosyncrasy of the GroupingEntity } else if (field.get_name() == "connectivity_raw") { // Do nothing, just handles an idiosyncrasy of the GroupingEntity } else { num_to_get = Ioss::Utils::field_warning(blob, field, "input"); } } else if (role == Ioss::Field::TRANSIENT) { // Check if the specified field exists on this blob. // Note that 'higher-order' storage types (e.g. SYM_TENSOR) // exist on the database as scalars with the appropriate // extensions. // Read in each component of the variable and transfer into // 'data'. Need temporary storage area of size 'number of // items in this blob. num_to_get = read_transient_field(EX_BLOB, m_variables[EX_BLOB], field, blob, data); } else if (role == Ioss::Field::ATTRIBUTE) { num_to_get = read_attribute_field(EX_BLOB, field, blob, data); } else if (role == Ioss::Field::REDUCTION) { get_reduction_field(EX_BLOB, field, blob, data); } } return num_to_get; } } int64_t ParallelDatabaseIO::get_field_internal(const Ioss::Assembly *assembly, const Ioss::Field &field, void *data, size_t data_size) const { { Ioss::SerializeIO serializeIO__(this); size_t num_to_get = field.verify(data_size); if (num_to_get > 0) { Ioss::Field::RoleType role = field.get_role(); if (role == Ioss::Field::MESH) { if (field.get_name() == "ids") { // Map the local ids in this node block // (1...node_count) to global node ids. // get_map(EX_ASSEMBLY).map_implicit_data(data, field, num_to_get, 0); } else if (field.get_name() == "connectivity") { // Do nothing, just handles an idiosyncrasy of the GroupingEntity } else if (field.get_name() == "connectivity_raw") { // Do nothing, just handles an idiosyncrasy of the GroupingEntity } else { num_to_get = Ioss::Utils::field_warning(assembly, field, "input"); } } else if (role == Ioss::Field::TRANSIENT) { // Check if the specified field exists on this assembly. // Note that 'higher-order' storage types (e.g. SYM_TENSOR) // exist on the database as scalars with the appropriate // extensions. // Read in each component of the variable and transfer into // 'data'. Need temporary storage area of size 'number of // items in this assembly. num_to_get = read_transient_field(EX_ASSEMBLY, m_variables[EX_ASSEMBLY], field, assembly, data); } else if (role == Ioss::Field::ATTRIBUTE) { num_to_get = read_attribute_field(EX_ASSEMBLY, field, assembly, data); } } return num_to_get; } } int64_t ParallelDatabaseIO::get_field_internal(const Ioss::ElementBlock *eb, const Ioss::Field &field, void *data, size_t data_size) const { size_t num_to_get = field.verify(data_size); int64_t id = Ioex::get_id(eb, EX_ELEM_BLOCK, &ids_); size_t my_element_count = eb->entity_count(); Ioss::Field::RoleType role = field.get_role(); if (role == Ioss::Field::MESH) { // Handle the MESH fields required for an ExodusII file model. // (The 'genesis' portion) if (field.get_name() == "connectivity" || field.get_name() == "connectivity_raw") { int element_nodes = eb->topology()->number_nodes(); assert(field.get_component_count(Ioss::Field::InOut::INPUT) == element_nodes); int order = eb->get_property("iblk").get_int(); // The connectivity is stored in a 1D array. // The element_node index varies fastet decomp->get_block_connectivity(get_file_pointer(), data, id, order, element_nodes); if (field.get_name() == "connectivity") { get_map(EX_NODE_BLOCK).map_data(data, field, num_to_get * element_nodes); } } #if 0 else if (field.get_name() == "connectivity_face") { int face_count = field.get_component_count(Ioss::Field::InOut::INPUT); // The connectivity is stored in a 1D array. // The element_face index varies fastest if (my_element_count > 0) { get_connectivity_data(get_file_pointer(), data, EX_ELEM_BLOCK, id, 2, int_byte_size_api()); get_map(EX_FACE_BLOCK).map_data(data, field, num_to_get*face_count); } } else if (field.get_name() == "connectivity_edge") { int edge_count = field.get_component_count(Ioss::Field::InOut::INPUT); // The connectivity is stored in a 1D array. // The element_edge index varies fastest if (my_element_count > 0) { get_connectivity_data(get_file_pointer(), data, EX_ELEM_BLOCK, id, 1, int_byte_size_api()); get_map(EX_EDGE_BLOCK).map_data(data, field, num_to_get*edge_count); } } #endif else if (field.get_name() == "ids" || field.get_name() == "implicit_ids") { // Map the local ids in this element block // (eb_offset+1...eb_offset+1+my_element_count) to global element ids. get_map(EX_ELEM_BLOCK).map_implicit_data(data, field, num_to_get, eb->get_offset()); } else if (field.get_name() == "skin") { // This is (currently) for the skinned body. It maps the // side element on the skin to the original element/local // side number. It is a two component field, the first // component is the global id of the underlying element in // the initial mesh and its local side number (1-based). if (field.is_type(Ioss::Field::INTEGER)) { Ioss::IntVector element(my_element_count); Ioss::IntVector side(my_element_count); int *el_side = reinterpret_cast(data); // FIX: Hardwired map ids.... size_t eb_offset = eb->get_offset(); assert(1 == 0 && "Unimplemented FIXME"); ex_get_partial_num_map(get_file_pointer(), EX_ELEM_MAP, 1, eb_offset + 1, my_element_count, element.data()); // FIXME ex_get_partial_num_map(get_file_pointer(), EX_ELEM_MAP, 2, eb_offset + 1, my_element_count, side.data()); // FIXME int index = 0; for (size_t i = 0; i < my_element_count; i++) { el_side[index++] = element[i]; el_side[index++] = side[i]; } } else { Ioss::Int64Vector element(my_element_count); Ioss::Int64Vector side(my_element_count); int64_t *el_side = reinterpret_cast(data); // FIX: Hardwired map ids.... size_t eb_offset = eb->get_offset(); assert(1 == 0 && "Unimplemented FIXME"); ex_get_partial_num_map(get_file_pointer(), EX_ELEM_MAP, 1, eb_offset + 1, my_element_count, element.data()); // FIXME ex_get_partial_num_map(get_file_pointer(), EX_ELEM_MAP, 2, eb_offset + 1, my_element_count, side.data()); // FIXME size_t index = 0; for (size_t i = 0; i < my_element_count; i++) { el_side[index++] = element[i]; el_side[index++] = side[i]; } } } else { num_to_get = Ioss::Utils::field_warning(eb, field, "input"); } } else if (role == Ioss::Field::ATTRIBUTE) { num_to_get = read_attribute_field(EX_ELEM_BLOCK, field, eb, data); } else if (role == Ioss::Field::TRANSIENT) { // Check if the specified field exists on this element block. // Note that 'higher-order' storage types (e.g. SYM_TENSOR) // exist on the database as scalars with the appropriate // extensions. // Read in each component of the variable and transfer into // 'data'. Need temporary storage area of size 'number of // elements in this block. num_to_get = read_transient_field(EX_ELEM_BLOCK, m_variables[EX_ELEM_BLOCK], field, eb, data); } else if (role == Ioss::Field::REDUCTION) { num_to_get = Ioss::Utils::field_warning(eb, field, "input reduction"); } return num_to_get; } int64_t ParallelDatabaseIO::get_field_internal(const Ioss::FaceBlock *eb, const Ioss::Field &field, void *data, size_t data_size) const { size_t num_to_get = field.verify(data_size); int64_t id = Ioex::get_id(eb, EX_FACE_BLOCK, &ids_); size_t my_face_count = eb->entity_count(); Ioss::Field::RoleType role = field.get_role(); if (role == Ioss::Field::MESH) { // Handle the MESH fields required for an ExodusII file model. // (The 'genesis' portion) if (field.get_name() == "connectivity") { int face_nodes = eb->topology()->number_nodes(); assert(field.get_component_count(Ioss::Field::InOut::INPUT) == face_nodes); // The connectivity is stored in a 1D array. // The face_node index varies fastet if (my_face_count > 0) { get_connectivity_data(get_file_pointer(), data, EX_FACE_BLOCK, id, 0, int_byte_size_api()); get_map(EX_NODE_BLOCK).map_data(data, field, num_to_get * face_nodes); } } else if (field.get_name() == "connectivity_edge") { int edge_count = field.get_component_count(Ioss::Field::InOut::INPUT); // The connectivity is stored in a 1D array. // The face_edge index varies fastest if (my_face_count > 0) { get_connectivity_data(get_file_pointer(), data, EX_FACE_BLOCK, id, 1, int_byte_size_api()); get_map(EX_EDGE_BLOCK).map_data(data, field, num_to_get * edge_count); } } else if (field.get_name() == "connectivity_raw") { // "connectivity_raw" has nodes in local id space (1-based) assert(field.get_component_count(Ioss::Field::InOut::INPUT) == eb->topology()->number_nodes()); // The connectivity is stored in a 1D array. // The face_node index varies fastet if (my_face_count > 0) { get_connectivity_data(get_file_pointer(), data, EX_FACE_BLOCK, id, 0, int_byte_size_api()); } } else if (field.get_name() == "ids") { // Map the local ids in this face block // (eb_offset+1...eb_offset+1+my_face_count) to global face ids. get_map(EX_FACE_BLOCK).map_implicit_data(data, field, num_to_get, eb->get_offset()); } else { num_to_get = Ioss::Utils::field_warning(eb, field, "input"); } } else if (role == Ioss::Field::ATTRIBUTE) { num_to_get = read_attribute_field(EX_FACE_BLOCK, field, eb, data); } else if (role == Ioss::Field::TRANSIENT) { // Check if the specified field exists on this element block. // Note that 'higher-order' storage types (e.g. SYM_TENSOR) // exist on the database as scalars with the appropriate // extensions. // Read in each component of the variable and transfer into // 'data'. Need temporary storage area of size 'number of // elements in this block. num_to_get = read_transient_field(EX_FACE_BLOCK, m_variables[EX_FACE_BLOCK], field, eb, data); } else if (role == Ioss::Field::REDUCTION) { num_to_get = Ioss::Utils::field_warning(eb, field, "input reduction"); } return num_to_get; } int64_t ParallelDatabaseIO::get_field_internal(const Ioss::EdgeBlock *eb, const Ioss::Field &field, void *data, size_t data_size) const { size_t num_to_get = field.verify(data_size); int64_t id = Ioex::get_id(eb, EX_EDGE_BLOCK, &ids_); int64_t my_edge_count = eb->entity_count(); Ioss::Field::RoleType role = field.get_role(); if (role == Ioss::Field::MESH) { // Handle the MESH fields required for an ExodusII file model. // (The 'genesis' portion) if (field.get_name() == "connectivity") { int edge_nodes = eb->topology()->number_nodes(); assert(field.get_component_count(Ioss::Field::InOut::INPUT) == edge_nodes); // The connectivity is stored in a 1D array. // The edge_node index varies fastet if (my_edge_count > 0) { get_connectivity_data(get_file_pointer(), data, EX_EDGE_BLOCK, id, 0, int_byte_size_api()); get_map(EX_NODE_BLOCK).map_data(data, field, num_to_get * edge_nodes); } } else if (field.get_name() == "connectivity_raw") { // "connectivity_raw" has nodes in local id space (1-based) assert(field.get_component_count(Ioss::Field::InOut::INPUT) == eb->topology()->number_nodes()); // The connectivity is stored in a 1D array. // The edge_node index varies fastet if (my_edge_count > 0) { get_connectivity_data(get_file_pointer(), data, EX_EDGE_BLOCK, id, 0, int_byte_size_api()); } } else if (field.get_name() == "ids") { // Map the local ids in this edge block // (eb_offset+1...eb_offset+1+my_edge_count) to global edge ids. get_map(EX_EDGE_BLOCK).map_implicit_data(data, field, num_to_get, eb->get_offset()); } else { num_to_get = Ioss::Utils::field_warning(eb, field, "input"); } } else if (role == Ioss::Field::ATTRIBUTE) { num_to_get = read_attribute_field(EX_EDGE_BLOCK, field, eb, data); } else if (role == Ioss::Field::TRANSIENT) { // Check if the specified field exists on this element block. // Note that 'higher-order' storage types (e.g. SYM_TENSOR) // exist on the database as scalars with the appropriate // extensions. // Read in each component of the variable and transfer into // 'data'. Need temporary storage area of size 'number of // elements in this block. num_to_get = read_transient_field(EX_EDGE_BLOCK, m_variables[EX_EDGE_BLOCK], field, eb, data); } else if (role == Ioss::Field::REDUCTION) { num_to_get = Ioss::Utils::field_warning(eb, field, "input reduction"); } return num_to_get; } int64_t ParallelDatabaseIO::get_Xset_field_internal(ex_entity_type type, const Ioss::EntitySet *ns, const Ioss::Field &field, void *data, size_t data_size) const { int ierr; size_t num_to_get = field.verify(data_size); Ioss::Field::RoleType role = field.get_role(); // Find corresponding set in file decomp class... if (role == Ioss::Field::MESH) { int64_t id = Ioex::get_id(ns, type, &ids_); if (field.get_name() == "ids" || field.get_name() == "ids_raw") { if (field.get_type() == Ioss::Field::INTEGER) { ierr = decomp->get_set_mesh_var(get_file_pointer(), EX_NODE_SET, id, field, static_cast(data)); } else { ierr = decomp->get_set_mesh_var(get_file_pointer(), EX_NODE_SET, id, field, static_cast(data)); } if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } if (field.get_name() == "ids") { // Convert the local node ids to global ids get_map(EX_NODE_BLOCK).map_data(data, field, num_to_get); } } else if (field.get_name() == "orientation") { if (field.get_type() == Ioss::Field::INTEGER) { ierr = decomp->get_set_mesh_var(get_file_pointer(), EX_NODE_SET, id, field, static_cast(data)); } else { ierr = decomp->get_set_mesh_var(get_file_pointer(), EX_NODE_SET, id, field, static_cast(data)); } if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } else if (field.get_name() == "distribution_factors") { ierr = decomp->get_set_mesh_double(get_file_pointer(), EX_NODE_SET, id, field, static_cast(data)); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } } else if (role == Ioss::Field::ATTRIBUTE) { num_to_get = read_attribute_field(type, field, ns, data); } else if (role == Ioss::Field::TRANSIENT) { // Check if the specified field exists on this node block. // Note that 'higher-order' storage types (e.g. SYM_TENSOR) // exist on the database as scalars with the appropriate // extensions. // Read in each component of the variable and transfer into // 'data'. Need temporary storage area of size 'number of // nodes in this block. num_to_get = read_transient_field(type, m_variables[type], field, ns, data); } return num_to_get; } int64_t ParallelDatabaseIO::get_field_internal(const Ioss::NodeSet *ns, const Ioss::Field &field, void *data, size_t data_size) const { return get_Xset_field_internal(EX_NODE_SET, ns, field, data, data_size); } int64_t ParallelDatabaseIO::get_field_internal(const Ioss::EdgeSet *ns, const Ioss::Field &field, void *data, size_t data_size) const { return get_Xset_field_internal(EX_EDGE_SET, ns, field, data, data_size); } int64_t ParallelDatabaseIO::get_field_internal(const Ioss::FaceSet *ns, const Ioss::Field &field, void *data, size_t data_size) const { return get_Xset_field_internal(EX_FACE_SET, ns, field, data, data_size); } int64_t ParallelDatabaseIO::get_field_internal(const Ioss::ElementSet *ns, const Ioss::Field &field, void *data, size_t data_size) const { return get_Xset_field_internal(EX_ELEM_SET, ns, field, data, data_size); } int64_t ParallelDatabaseIO::get_field_internal(const Ioss::SideSet *ss, const Ioss::Field &field, void *data, size_t data_size) const { size_t num_to_get = field.verify(data_size); if (field.get_name() == "ids") { // Do nothing, just handles an idiosyncrasy of the GroupingEntity // However, make sure that the caller gets a consistent answer, i.e., don't leave the buffer // full of junk memset(data, 0x00, data_size); } else { num_to_get = Ioss::Utils::field_warning(ss, field, "input"); } return num_to_get; } int64_t ParallelDatabaseIO::get_field_internal(const Ioss::CommSet *cs, const Ioss::Field &field, void *data, size_t data_size) const { size_t num_to_get = field.verify(data_size); // Return the pair if (field.get_name() == "entity_processor" || field.get_name() == "entity_processor_raw") { // Check type -- node or side std::string type = cs->get_property("entity_type").get_string(); if (type == "node") { bool do_map = field.get_name() == "entity_processor"; // Convert local node id to global node id and store in 'data' const Ioss::MapContainer &map = get_map(EX_NODE_BLOCK).map(); if (int_byte_size_api() == 4) { decomp->get_node_entity_proc_data(static_cast(data), map, do_map); } else { decomp->get_node_entity_proc_data(static_cast(data), map, do_map); } } else { std::ostringstream errmsg; fmt::print(errmsg, "ERROR: Invalid commset type {}", type); IOSS_ERROR(errmsg); } } else if (field.get_name() == "ids") { // Do nothing, just handles an idiosyncrasy of the GroupingEntity } else { num_to_get = Ioss::Utils::field_warning(cs, field, "input"); } return num_to_get; } int64_t ParallelDatabaseIO::get_field_internal(const Ioss::SideBlock *sb, const Ioss::Field &field, void *data, size_t data_size) const { int64_t num_to_get = field.verify(data_size); int ierr = 0; int64_t id = Ioex::get_id(sb, EX_SIDE_SET, &ids_); int64_t entity_count = sb->entity_count(); if (num_to_get != entity_count) { std::ostringstream errmsg; fmt::print(errmsg, "ERROR: Partial field input not yet implemented for side blocks"); IOSS_ERROR(errmsg); } auto &set = decomp->get_decomp_set(EX_SIDE_SET, id); int64_t number_sides = set.ioss_count(); int64_t number_distribution_factors = set.df_count(); Ioss::Field::RoleType role = field.get_role(); if (role == Ioss::Field::MESH) { // In exodusII, we may have split the sideset into multiple // side blocks if there are multiple side topologies in the // sideset. Because of this, the passed in 'data' may not be // large enough to hold the data residing in the sideset and we // may need to allocate a temporary array... This can be checked // by comparing the size of the sideset with the 'side_count' of // the side block. // Get size of data stored on the file... // FIX 64: FIX THIS -- STORING INT IN DOUBLE WON'T WORK if (field.get_name() == "side_ids" && sb->name() == "universal_sideset") { // The side ids are being stored as the distribution factor // field on the universal sideset. There should be no other // side sets that request this field... (Eventually, // create an id field to store this info. if (number_distribution_factors == num_to_get) { std::vector real_ids(num_to_get); Ioss::Field df_field("distribution_factor", Ioss::Field::REAL, "scalar", Ioss::Field::MESH, num_to_get); decomp->get_set_mesh_double(get_file_pointer(), EX_SIDE_SET, id, df_field, real_ids.data()); if (field.get_type() == Ioss::Field::INTEGER) { // Need to convert 'double' to 'int' for Sierra use... int *ids = static_cast(data); for (int64_t i = 0; i < num_to_get; i++) { ids[i] = static_cast(real_ids[i]); } } else { // Need to convert 'double' to 'int' for Sierra use... int64_t *ids = static_cast(data); for (int64_t i = 0; i < num_to_get; i++) { ids[i] = static_cast(real_ids[i]); } } } } else if (field.get_name() == "side_ids") { } else if (field.get_name() == "ids") { // In exodusII, the 'side set' is stored as a sideset. A // sideset has a list of elements and a corresponding local // element side (1-based) The side id is: side_id = // 10*element_id + local_side_number This assumes that all // sides in a sideset are boundary sides. Since we // only have a single array, we need to allocate an extra array // to store all of the data. Note also that the element_id is // the global id but only the local id is stored so we need to // map from local_to_global prior to generating the side id... Ioss::Field el_side = sb->get_field("element_side"); std::vector element_side(2 * number_sides * int_byte_size_api()); get_field_internal(sb, el_side, element_side.data(), element_side.size()); // At this point, have the 'element_side' data containing // the global element ids and the sides... Iterate // through to generate the ids... if (int_byte_size_api() == 4) { int64_t int_max = std::numeric_limits::max(); int *ids = static_cast(data); int *els = reinterpret_cast(element_side.data()); size_t idx = 0; for (int64_t iel = 0; iel < 2 * entity_count; iel += 2) { int64_t new_id = static_cast(10) * els[iel] + els[iel + 1]; if (new_id > int_max) { std::ostringstream errmsg; fmt::print(errmsg, "ERROR: accessing the sideset field 'ids'\n" "\t\thas exceeded the integer bounds for entity {}, local side id {}.\n" "\t\tTry using 64-bit mode to read the file '{}'.\n", els[iel], els[iel + 1], get_filename()); IOSS_ERROR(errmsg); } ids[idx++] = static_cast(new_id); } } else { int64_t *ids = static_cast(data); int64_t *els = reinterpret_cast(element_side.data()); size_t idx = 0; for (int64_t iel = 0; iel < 2 * entity_count; iel += 2) { int64_t new_id = 10 * els[iel] + els[iel + 1]; ids[idx++] = new_id; } } } else if (field.get_name() == "element_side" || field.get_name() == "element_side_raw") { // In exodusII, the 'side set' is stored as a sideset. A sideset // has a list of elements and a corresponding local element side // (1-based) // Since we only have a single array, we need to allocate an extra // array to store all of the data. Note also that the element_id // is the global id but only the local id is stored so we need to // map from local_to_global prior to generating the side id... // Get the element number map (1-based)... const Ioss::MapContainer &map = get_map(EX_ELEM_BLOCK).map(); // Allocate space for local side number and element numbers // numbers. // See if edges or faces... int64_t side_offset = Ioss::Utils::get_side_offset(sb); if (sb->owner()->block_count() == 1 && number_sides == entity_count) { if (int_byte_size_api() == 4) { int *element_side = static_cast(data); decomp->get_set_mesh_var(get_file_pointer(), EX_SIDE_SET, id, field, element_side); for (int64_t iel = 1; iel < 2 * entity_count; iel += 2) { element_side[iel] = element_side[iel] - side_offset; } } else { int64_t *element_side = static_cast(data); decomp->get_set_mesh_var(get_file_pointer(), EX_SIDE_SET, id, field, element_side); for (int64_t iel = 1; iel < 2 * entity_count; iel += 2) { element_side[iel] = element_side[iel] - side_offset; } } } else { // Need a larger vector to get the entire sideset and then filter down to the correct // size... std::vector element(number_sides * int_byte_size_api()); std::vector sides(number_sides * int_byte_size_api()); if (int_byte_size_api() == 4) { Ioss::Field elem_field("ids", Ioss::Field::INTEGER, "scalar", Ioss::Field::MESH, number_sides); Ioss::Field side_field("sides", Ioss::Field::INTEGER, "scalar", Ioss::Field::MESH, number_sides); decomp->get_set_mesh_var(get_file_pointer(), EX_SIDE_SET, id, elem_field, reinterpret_cast(element.data())); decomp->get_set_mesh_var(get_file_pointer(), EX_SIDE_SET, id, side_field, reinterpret_cast(sides.data())); } else { Ioss::Field elem_field("ids", Ioss::Field::INT64, "scalar", Ioss::Field::MESH, number_sides); Ioss::Field side_field("sides", Ioss::Field::INT64, "scalar", Ioss::Field::MESH, number_sides); decomp->get_set_mesh_var(get_file_pointer(), EX_SIDE_SET, id, elem_field, reinterpret_cast(element.data())); decomp->get_set_mesh_var(get_file_pointer(), EX_SIDE_SET, id, side_field, reinterpret_cast(sides.data())); } Ioss::IntVector is_valid_side; Ioss::Utils::calculate_sideblock_membership(is_valid_side, sb, int_byte_size_api(), element.data(), sides.data(), number_sides, get_region()); int64_t index = 0; if (int_byte_size_api() == 4) { int *element_side = static_cast(data); int *element32 = reinterpret_cast(element.data()); int *sides32 = reinterpret_cast(sides.data()); for (int64_t iel = 0; iel < number_sides; iel++) { if (is_valid_side[iel] == 1) { // This side belongs in the side block element_side[index++] = element32[iel]; element_side[index++] = sides32[iel] - side_offset; } } } else { int64_t *element_side = static_cast(data); int64_t *element64 = reinterpret_cast(element.data()); int64_t *sides64 = reinterpret_cast(sides.data()); for (int64_t iel = 0; iel < number_sides; iel++) { if (is_valid_side[iel] == 1) { // This side belongs in the side block element_side[index++] = element64[iel]; element_side[index++] = sides64[iel] - side_offset; } } } assert(index / 2 == entity_count); } if (field.get_name() == "element_side") { if (int_byte_size_api() == 4) { int *element_side = static_cast(data); for (int64_t iel = 0; iel < 2 * entity_count; iel += 2) { element_side[iel] = map[element_side[iel]]; } } else { int64_t *element_side = static_cast(data); for (int64_t iel = 0; iel < 2 * entity_count; iel += 2) { element_side[iel] = map[element_side[iel]]; } } } } else if (field.get_name() == "connectivity") { // The side connectivity needs to be generated 'on-the-fly' from // the element number and local side of that element. A sideset // can span multiple element blocks, and contain multiple side // types; the side block contains side of similar topology. ierr = get_side_connectivity(sb, id, entity_count, data, true); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } else if (field.get_name() == "connectivity_raw") { // The side connectivity needs to be generated 'on-the-fly' from // the element number and local side of that element. A sideset // can span multiple element blocks, and contain multiple side // types; the side block contains side of similar topology. ierr = get_side_connectivity(sb, id, entity_count, data, false); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } else if (field.get_name() == "distribution_factors") { ierr = get_side_distributions(sb, id, entity_count, static_cast(data), data_size / sizeof(double)); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } else { num_to_get = Ioss::Utils::field_warning(sb, field, "input"); } } else if (role == Ioss::Field::TRANSIENT) { // Check if the specified field exists on this block. // Note that 'higher-order' storage types (e.g. SYM_TENSOR) // exist on the database as scalars with the appropriate // extensions. if (sb->owner()->block_count() == 1 && number_sides == entity_count) { num_to_get = read_transient_field(EX_SIDE_SET, m_variables[EX_SIDE_SET], field, sb, data); } else { // Need to read all values for the specified field and then // filter down to the elements actually in this side block. Ioss::IntVector is_valid_side; // Need a larger vector to get the entire sideset and then filter down to the correct size... std::vector element(number_sides * int_byte_size_api()); std::vector sides(number_sides * int_byte_size_api()); if (int_byte_size_api() == 4) { Ioss::Field elem_field("ids", Ioss::Field::INTEGER, "scalar", Ioss::Field::MESH, number_sides); Ioss::Field side_field("sides", Ioss::Field::INTEGER, "scalar", Ioss::Field::MESH, number_sides); decomp->get_set_mesh_var(get_file_pointer(), EX_SIDE_SET, id, elem_field, reinterpret_cast(element.data())); decomp->get_set_mesh_var(get_file_pointer(), EX_SIDE_SET, id, side_field, reinterpret_cast(sides.data())); } else { Ioss::Field elem_field("ids", Ioss::Field::INT64, "scalar", Ioss::Field::MESH, number_sides); Ioss::Field side_field("sides", Ioss::Field::INT64, "scalar", Ioss::Field::MESH, number_sides); decomp->get_set_mesh_var(get_file_pointer(), EX_SIDE_SET, id, elem_field, reinterpret_cast(element.data())); decomp->get_set_mesh_var(get_file_pointer(), EX_SIDE_SET, id, side_field, reinterpret_cast(sides.data())); } Ioss::Utils::calculate_sideblock_membership(is_valid_side, sb, int_byte_size_api(), element.data(), sides.data(), number_sides, get_region()); num_to_get = read_ss_transient_field(field, id, data, is_valid_side); } } return num_to_get; } int64_t ParallelDatabaseIO::write_attribute_field(ex_entity_type type, const Ioss::Field &field, const Ioss::GroupingEntity *ge, void *data) const { std::string att_name = ge->name() + SEP() + field.get_name(); int64_t num_entity = ge->entity_count(); int64_t offset = field.get_index(); int64_t id = Ioex::get_id(ge, type, &ids_); assert(offset > 0); assert(offset - 1 + field.get_component_count(Ioss::Field::InOut::OUTPUT) <= ge->get_property("attribute_count").get_int()); size_t proc_offset = ge->get_optional_property("_processor_offset", 0); int64_t file_count = ge->get_optional_property("locally_owned_count", num_entity); Ioss::Field::BasicType ioss_type = field.get_type(); assert(ioss_type == Ioss::Field::REAL || ioss_type == Ioss::Field::INTEGER || ioss_type == Ioss::Field::INT64); int comp_count = field.get_component_count(Ioss::Field::InOut::OUTPUT); if (type == EX_NODAL) { for (int i = 0; i < comp_count; i++) { std::vector file_data; file_data.reserve(file_count); check_node_owning_processor_data(nodeOwningProcessor, file_count); if (ioss_type == Ioss::Field::REAL) { filter_owned_nodes(nodeOwningProcessor, myProcessor, static_cast(data), file_data, i, comp_count); } else if (ioss_type == Ioss::Field::INTEGER) { filter_owned_nodes(nodeOwningProcessor, myProcessor, static_cast(data), file_data, i, comp_count); } else if (ioss_type == Ioss::Field::INT64) { filter_owned_nodes(nodeOwningProcessor, myProcessor, static_cast(data), file_data, i, comp_count); } int ierr = ex_put_partial_one_attr(get_file_pointer(), type, id, proc_offset + 1, file_count, offset + i, file_data.data()); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } } else if (type == EX_NODE_SET) { for (int i = 0; i < comp_count; i++) { std::vector file_data; file_data.reserve(file_count); if (ioss_type == Ioss::Field::REAL) { map_nodeset_data(nodesetOwnedNodes[ge], static_cast(data), file_data, i, comp_count); } else if (ioss_type == Ioss::Field::INTEGER) { map_nodeset_data(nodesetOwnedNodes[ge], static_cast(data), file_data, i, comp_count); } else if (ioss_type == Ioss::Field::INT64) { map_nodeset_data(nodesetOwnedNodes[ge], static_cast(data), file_data, i, comp_count); } int ierr = ex_put_partial_one_attr(get_file_pointer(), type, id, proc_offset + 1, file_count, offset + i, file_data.data()); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } } else { assert(file_count == num_entity); std::vector file_data(file_count); for (int i = 0; i < comp_count; i++) { if (ioss_type == Ioss::Field::REAL) { extract_data(file_data, static_cast(data), num_entity, i, comp_count); } else if (ioss_type == Ioss::Field::INTEGER) { extract_data(file_data, static_cast(data), num_entity, i, comp_count); } else if (ioss_type == Ioss::Field::INT64) { extract_data(file_data, static_cast(data), num_entity, i, comp_count); } int ierr = ex_put_partial_one_attr(get_file_pointer(), type, id, proc_offset + 1, file_count, offset + i, file_data.data()); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } } return num_entity; } int64_t ParallelDatabaseIO::read_attribute_field(ex_entity_type type, const Ioss::Field &field, const Ioss::GroupingEntity *ge, void *data) const { int64_t num_entity = ge->entity_count(); int attribute_count = ge->get_property("attribute_count").get_int(); int64_t id = Ioex::get_id(ge, type, &ids_); Ioss::Field::BasicType ioss_type = field.get_type(); if (ioss_type == Ioss::Field::INTEGER || ioss_type == Ioss::Field::INT64) { std::ostringstream errmsg; fmt::print(errmsg, "INTERNAL ERROR: Integer attribute fields are not yet handled for read. " "Please report.\n"); IOSS_ERROR(errmsg); } std::string att_name = ge->name() + SEP() + field.get_name(); int64_t offset = field.get_index(); assert(offset - 1 + field.get_component_count(Ioss::Field::InOut::INPUT) <= attribute_count); if (offset == 1 && field.get_component_count(Ioss::Field::InOut::INPUT) == attribute_count) { // Read all attributes in one big chunk... int ierr = decomp->get_attr(get_file_pointer(), type, id, attribute_count, static_cast(data)); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } else { // Read a subset of the attributes. If scalar, read one; // if higher-order (vector3d, ..) read each component and // put into correct location... if (field.get_component_count(Ioss::Field::InOut::INPUT) == 1) { int ierr = decomp->get_one_attr(get_file_pointer(), type, id, offset, static_cast(data)); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } else { // Multi-component... // Need a local memory space to read data into and // then push that into the user-supplied data block... std::vector local_data(num_entity); int comp_count = field.get_component_count(Ioss::Field::InOut::INPUT); double *rdata = static_cast(data); for (int i = 0; i < comp_count; i++) { int ierr = decomp->get_one_attr(get_file_pointer(), type, id, offset + i, local_data.data()); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } size_t k = i; for (int64_t j = 0; j < num_entity; j++) { rdata[k] = local_data[j]; k += comp_count; } } } } return num_entity; } int64_t ParallelDatabaseIO::read_transient_field(ex_entity_type type, const Ioex::VariableNameMap &variables, const Ioss::Field &field, const Ioss::GroupingEntity *ge, void *data) const { // Read into a double variable since that is all ExodusII can store... size_t num_entity = ge->entity_count(); std::vector temp(num_entity); size_t step = get_current_state(); // get number of components, cycle through each component // and add suffix to base 'field_name'. Look up index // of this name in 'nodeVariables' map size_t comp_count = field.get_component_count(Ioss::Field::InOut::INPUT); for (size_t i = 0; i < comp_count; i++) { std::string var_name = get_component_name(field, Ioss::Field::InOut::INPUT, i + 1); // Read the variable... int64_t id = Ioex::get_id(ge, type, &ids_); int ierr = 0; auto var_iter = variables.find(var_name); if (var_iter == variables.end()) { std::ostringstream errmsg; fmt::print(errmsg, "ERROR: Could not find field '{}'\n", var_name); IOSS_ERROR(errmsg); } size_t var_index = var_iter->second; assert(var_index > 0); if (type == EX_BLOB) { size_t offset = ge->get_property("_processor_offset").get_int(); ierr = ex_get_partial_var(get_file_pointer(), step, type, var_index, id, offset + 1, num_entity, temp.data()); } else { ierr = decomp->get_var(get_file_pointer(), step, type, var_index, id, num_entity, temp); } if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } // Transfer to 'data' array. size_t k = 0; if (field.get_type() == Ioss::Field::INTEGER) { int *ivar = static_cast(data); for (size_t j = i; j < num_entity * comp_count; j += comp_count) { ivar[j] = static_cast(temp[k++]); } } else if (field.get_type() == Ioss::Field::INT64) { // FIX 64 UNSAFE int64_t *ivar = static_cast(data); for (size_t j = i; j < num_entity * comp_count; j += comp_count) { ivar[j] = static_cast(temp[k++]); } } else if (field.get_type() == Ioss::Field::REAL) { double *rvar = static_cast(data); for (size_t j = i; j < num_entity * comp_count; j += comp_count) { rvar[j] = temp[k++]; } } else { std::ostringstream errmsg; fmt::print(errmsg, "IOSS_ERROR: Field storage type must be either integer or double.\n" " Field '{}' is invalid.\n", field.get_name()); IOSS_ERROR(errmsg); } assert(k == num_entity); } return num_entity; } int64_t ParallelDatabaseIO::read_ss_transient_field(const Ioss::Field &field, int64_t id, void *variables, Ioss::IntVector &is_valid_side) const { size_t num_valid_sides = 0; size_t my_side_count = is_valid_side.size(); std::vector temp(my_side_count); size_t step = get_current_state(); // get number of components, cycle through each component // and add suffix to base 'field_name'. Look up index // of this name in 'nodeVariables' map size_t comp_count = field.get_component_count(Ioss::Field::InOut::INPUT); for (size_t i = 0; i < comp_count; i++) { std::string var_name = get_component_name(field, Ioss::Field::InOut::INPUT, i + 1); // Read the variable... int ierr = 0; auto var_iter = m_variables[EX_SIDE_SET].find(var_name); if (var_iter == m_variables[EX_SIDE_SET].end()) { std::ostringstream errmsg; fmt::print(errmsg, "ERROR: Could not find Sideset field '{}'\n", var_name); IOSS_ERROR(errmsg); } size_t var_index = var_iter->second; assert(var_index > 0); ierr = decomp->get_var(get_file_pointer(), step, EX_SIDE_SET, var_index, id, my_side_count, temp); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } // Transfer to 'variables' array. size_t j = i; if (field.get_type() == Ioss::Field::INTEGER) { int *ivar = static_cast(variables); for (size_t k = 0; k < my_side_count; k++) { if (is_valid_side[k] == 1) { ivar[j] = static_cast(temp[k]); j += comp_count; } } } else if (field.get_type() == Ioss::Field::INT64) { // FIX 64 UNSAFE int64_t *ivar = static_cast(variables); for (size_t k = 0; k < my_side_count; k++) { if (is_valid_side[k] == 1) { ivar[j] = static_cast(temp[k]); j += comp_count; } } } else if (field.get_type() == Ioss::Field::REAL) { double *rvar = static_cast(variables); for (size_t k = 0; k < my_side_count; k++) { if (is_valid_side[k] == 1) { rvar[j] = temp[k]; j += comp_count; } } } else { std::ostringstream errmsg; fmt::print(errmsg, "IOSS_ERROR: Field storage type must be either integer or double.\n" " Field '{}' is invalid.\n", field.get_name()); IOSS_ERROR(errmsg); } if (i + 1 == comp_count) { num_valid_sides = j / comp_count; } } return num_valid_sides; } int64_t ParallelDatabaseIO::get_side_connectivity(const Ioss::SideBlock *sb, int64_t id, int64_t /*unused*/, void *fconnect, bool map_ids) const { // Get size of data stored on the file... ex_set set_param[1]; set_param[0].id = id; set_param[0].type = EX_SIDE_SET; set_param[0].entry_list = nullptr; set_param[0].extra_list = nullptr; set_param[0].distribution_factor_list = nullptr; int ierr = ex_get_sets(get_file_pointer(), 1, set_param); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } int64_t number_sides = set_param[0].num_entry; // Allocate space for element and local side number assert(number_sides > 0); // Need a larger vector to get the entire sideset and then filter down to the correct size... std::vector element(number_sides * int_byte_size_api()); std::vector side(number_sides * int_byte_size_api()); if (int_byte_size_api() == 4) { Ioss::Field elem_field("ids", Ioss::Field::INTEGER, "scalar", Ioss::Field::MESH, number_sides); Ioss::Field side_field("sides", Ioss::Field::INTEGER, "scalar", Ioss::Field::MESH, number_sides); decomp->get_set_mesh_var(get_file_pointer(), EX_SIDE_SET, id, elem_field, reinterpret_cast(element.data())); decomp->get_set_mesh_var(get_file_pointer(), EX_SIDE_SET, id, side_field, reinterpret_cast(side.data())); } else { Ioss::Field elem_field("ids", Ioss::Field::INT64, "scalar", Ioss::Field::MESH, number_sides); Ioss::Field side_field("sides", Ioss::Field::INT64, "scalar", Ioss::Field::MESH, number_sides); decomp->get_set_mesh_var(get_file_pointer(), EX_SIDE_SET, id, elem_field, reinterpret_cast(element.data())); decomp->get_set_mesh_var(get_file_pointer(), EX_SIDE_SET, id, side_field, reinterpret_cast(side.data())); } Ioss::IntVector is_valid_side; Ioss::Utils::calculate_sideblock_membership(is_valid_side, sb, int_byte_size_api(), (void *)element.data(), (void *)side.data(), number_sides, get_region()); std::vector elconnect; int64_t elconsize = 0; // Size of currently allocated connectivity block Ioss::ElementBlock *conn_block = nullptr; // Block that we currently // have connectivity for Ioss::ElementBlock *block = nullptr; int *element32 = nullptr; int64_t *element64 = nullptr; int *side32 = nullptr; int64_t *side64 = nullptr; int *elconn32 = nullptr; int64_t *elconn64 = nullptr; int *fconn32 = nullptr; int64_t *fconn64 = nullptr; if (int_byte_size_api() == 4) { element32 = reinterpret_cast(element.data()); side32 = reinterpret_cast(side.data()); fconn32 = reinterpret_cast(fconnect); } else { element64 = reinterpret_cast(element.data()); side64 = reinterpret_cast(side.data()); fconn64 = reinterpret_cast(fconnect); } Ioss::IntVector side_elem_map; // Maps the side into the elements // connectivity array int64_t current_side = -1; int nelnode = 0; int nfnodes = 0; int ieb = 0; size_t offset = 0; for (int64_t iel = 0; iel < number_sides; iel++) { if (is_valid_side[iel] == 1) { int64_t elem_id = 0; if (int_byte_size_api() == 4) { elem_id = element32[iel]; } else { elem_id = element64[iel]; } // ensure we have correct connectivity block = get_region()->get_element_block(elem_id); if (conn_block != block) { int64_t nelem = block->entity_count(); nelnode = block->topology()->number_nodes(); // Used to map element number into position in connectivity array. // E.g., element 97 is the (97-offset)th element in this block and // is stored in array index (97-offset-1). offset = block->get_offset() + 1; if (elconsize < nelem * nelnode) { elconsize = nelem * nelnode; elconnect.resize(elconsize * int_byte_size_api()); if (int_byte_size_api() == 4) { elconn32 = reinterpret_cast(elconnect.data()); } else { elconn64 = reinterpret_cast(elconnect.data()); } } if (map_ids) { get_field_internal(block, block->get_field("connectivity"), elconnect.data(), nelem * nelnode * int_byte_size_api()); } else { get_field_internal(block, block->get_field("connectivity_raw"), elconnect.data(), nelem * nelnode * int_byte_size_api()); } conn_block = block; current_side = -1; } // NOTE: Element connectivity is returned with nodes in global id space if "map_ids" false, // otherwise it is in local space. int64_t side_id = 0; if (int_byte_size_api() == 4) { side_id = side32[iel]; } else { side_id = side64[iel]; } if (current_side != side_id) { side_elem_map = block->topology()->boundary_connectivity(side_id); current_side = side_id; nfnodes = block->topology()->boundary_type(side_id)->number_nodes(); } for (int inode = 0; inode < nfnodes; inode++) { size_t index = (elem_id - offset) * nelnode + side_elem_map[inode]; if (int_byte_size_api() == 4) { fconn32[ieb++] = elconn32[index]; } else { fconn64[ieb++] = elconn64[index]; } } } } return ierr; } // Get distribution factors for the specified side block int64_t ParallelDatabaseIO::get_side_distributions(const Ioss::SideBlock *sb, int64_t id, int64_t my_side_count, double *dist_fact, size_t /* data_size */) const { // Allocate space for elements and local side numbers // Get size of data stored on the file... auto &set = decomp->get_decomp_set(EX_SIDE_SET, id); int64_t number_sides = set.ioss_count(); int64_t number_distribution_factors = set.df_count(); const Ioss::ElementTopology *ftopo = sb->topology(); int nfnodes = ftopo->number_nodes(); if (set.distributionFactorConstant) { // Fill in the array with the constant value... for (int64_t i = 0; i < nfnodes * my_side_count; i++) { dist_fact[i] = set.distributionFactorValue; } return 0; } // Take care of the easy situation -- If 'side_count' == // 'number_sides' then the sideset is stored in a single sideblock // and all distribution factors on the database are transferred // 1-to-1 into 'dist_fact' array. int64_t entity_count = sb->entity_count(); if (sb->owner()->block_count() == 1 && number_sides == entity_count) { assert(number_sides == 0 || number_distribution_factors % number_sides == 0); assert(number_sides == 0 || number_distribution_factors / number_sides == nfnodes); if (number_sides * nfnodes != number_distribution_factors && number_sides != number_distribution_factors) { std::ostringstream errmsg; fmt::print(errmsg, "ERROR: SideBlock '{}' has incorrect distribution factor count.\n" "\tThere are {} '{}' sides with {} nodes per side, but there are {}" " distribution factors which is not correct.\n" "\tThere should be either {} or {} distribution factors.\n", sb->name(), number_sides, ftopo->name(), nfnodes, number_distribution_factors, number_sides, number_sides * nfnodes); IOSS_ERROR(errmsg); } std::string storage = "Real[" + std::to_string(nfnodes) + "]"; Ioss::Field dist("distribution_factors", Ioss::Field::REAL, storage, Ioss::Field::MESH, number_sides); decomp->get_set_mesh_double(get_file_pointer(), EX_SIDE_SET, id, dist, dist_fact); return 0; } std::string storage = "Real[" + std::to_string(nfnodes) + "]"; Ioss::Field field("distribution_factors", Ioss::Field::REAL, storage, Ioss::Field::MESH, number_distribution_factors / nfnodes); std::vector dist(number_distribution_factors); decomp->get_set_mesh_double(get_file_pointer(), EX_SIDE_SET, id, field, dist.data()); // Another easy situation (and common for exodusII) is if the input // distribution factors are all the same value (typically 1). In // that case, we only have to fill in the output array with that // value. { double value = number_distribution_factors > 0 ? dist[0] : 0.0; bool constant = true; for (auto df : dist) { if (df != value) { constant = false; break; } } constant = util().global_minmax(constant ? 1 : 0, Ioss::ParallelUtils::DO_MIN); if (constant) { if (value == 0.0) { value = 1.0; // Take care of some buggy mesh generators } for (int64_t j = 0; j < my_side_count * nfnodes; j++) { dist_fact[j] = value; } return 0; } } // If we get to here, the underlying sideset contains multiple side // topologies and the distribution factors are non-constant. Need to // allocate space to store all distribution factors and then pull // out those that are applied to sides with the correct topology. // Allocate space for element and local side number (this is bulk // data...) //---- std::vector element(number_sides * int_byte_size_api()); std::vector sides(number_sides * int_byte_size_api()); if (int_byte_size_api() == 4) { Ioss::Field elem_field("ids", Ioss::Field::INTEGER, "scalar", Ioss::Field::MESH, number_sides); Ioss::Field side_field("sides", Ioss::Field::INTEGER, "scalar", Ioss::Field::MESH, number_sides); decomp->get_set_mesh_var(get_file_pointer(), EX_SIDE_SET, id, elem_field, reinterpret_cast(element.data())); decomp->get_set_mesh_var(get_file_pointer(), EX_SIDE_SET, id, side_field, reinterpret_cast(sides.data())); } else { Ioss::Field elem_field("ids", Ioss::Field::INT64, "scalar", Ioss::Field::MESH, number_sides); Ioss::Field side_field("sides", Ioss::Field::INT64, "scalar", Ioss::Field::MESH, number_sides); decomp->get_set_mesh_var(get_file_pointer(), EX_SIDE_SET, id, elem_field, reinterpret_cast(element.data())); decomp->get_set_mesh_var(get_file_pointer(), EX_SIDE_SET, id, side_field, reinterpret_cast(sides.data())); } //---- Ioss::IntVector is_valid_side; Ioss::Utils::calculate_sideblock_membership(is_valid_side, sb, int_byte_size_api(), element.data(), sides.data(), number_sides, get_region()); int64_t ieb = 0; // counter for distribution factors in this sideblock int64_t idb = 0; // counter for distribution factors read from database Ioss::ElementBlock *block = nullptr; int *element32 = nullptr; int64_t *element64 = nullptr; int *side32 = nullptr; int64_t *side64 = nullptr; if (int_byte_size_api() == 4) { element32 = reinterpret_cast(element.data()); side32 = reinterpret_cast(sides.data()); } else { element64 = reinterpret_cast(element.data()); side64 = reinterpret_cast(sides.data()); } for (int64_t iel = 0; iel < number_sides; iel++) { int64_t elem_id = 0; int64_t side_id = 0; if (int_byte_size_api() == 4) { elem_id = element32[iel]; side_id = side32[iel]; } else { elem_id = element64[iel]; side_id = side64[iel]; } if (block == nullptr || !block->contains(elem_id)) { block = get_region()->get_element_block(elem_id); } if (block == nullptr) { std::ostringstream errmsg; fmt::print(errmsg, "INTERNAL ERROR: Could not find element block containing element with id {}." " Something is wrong in the Ioex::ParallelDatabaseIO class. Please report.\n", elem_id); IOSS_ERROR(errmsg); } const Ioss::ElementTopology *topo = block->topology()->boundary_type(side_id); if (topo == nullptr) { std::ostringstream errmsg; fmt::print(errmsg, "INTERNAL ERROR: Could not find topology of element block boundary. " "Something is wrong in the Ioex::ParallelDatabaseIO class. Please report.\n"); IOSS_ERROR(errmsg); } int nside_nodes = topo->number_nodes(); if (is_valid_side[iel] == 1) { // This side belongs in the sideblock for (int64_t i = 0; i < nside_nodes; i++) { dist_fact[ieb++] = dist[idb++]; } } else { // Skip over unused 'dist' factors idb += topo->number_nodes(); } } assert(ieb == my_side_count * nfnodes); // If the following assert fails, it may be due to bug in Patran // which writes too many distribution factors to the database in a // mixed element case. Note that this is checked earlier also with a // better error message. assert(idb == number_distribution_factors); return 0; } int64_t ParallelDatabaseIO::put_field_internal(const Ioss::Region *reg, const Ioss::Field &field, void *data, size_t data_size) const { return Ioex::BaseDatabaseIO::put_field_internal(reg, field, data, data_size); } int64_t ParallelDatabaseIO::put_field_internal(const Ioss::NodeBlock *nb, const Ioss::Field &field, void *data, size_t data_size) const { size_t num_to_get = field.verify(data_size); size_t proc_offset = nb->get_optional_property("_processor_offset", 0); size_t file_count = nb->get_optional_property("locally_owned_count", num_to_get); Ioss::Field::RoleType role = field.get_role(); if (role == Ioss::Field::MESH) { if (field.get_name() == "owning_processor") { // Set the nodeOwningProcessor vector for all nodes on this processor. // Value is the processor that owns the node. // NOTE: The owning_processor field is always int32 nodeOwningProcessor.reserve(num_to_get); int *owned = (int *)data; for (size_t i = 0; i < num_to_get; i++) { nodeOwningProcessor.push_back(owned[i]); } // Now create the "implicit local" to "implicit global" // map which maps data from its local implicit position // to its implicit (1..num_global_node) position in the // global file. This is needed for the global-to-local // mapping of element connectivity and nodeset nodelists. create_implicit_global_map(); } else if (field.get_name() == "mesh_model_coordinates_x") { double *rdata = static_cast(data); std::vector file_data; file_data.reserve(file_count); check_node_owning_processor_data(nodeOwningProcessor, file_count); filter_owned_nodes(nodeOwningProcessor, myProcessor, rdata, file_data); int ierr = ex_put_partial_coord_component(get_file_pointer(), proc_offset + 1, file_count, 1, file_data.data()); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } else if (field.get_name() == "mesh_model_coordinates_y") { double *rdata = static_cast(data); std::vector file_data; file_data.reserve(file_count); check_node_owning_processor_data(nodeOwningProcessor, file_count); filter_owned_nodes(nodeOwningProcessor, myProcessor, rdata, file_data); int ierr = ex_put_partial_coord_component(get_file_pointer(), proc_offset + 1, file_count, 2, file_data.data()); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } else if (field.get_name() == "mesh_model_coordinates_z") { double *rdata = static_cast(data); std::vector file_data; file_data.reserve(file_count); check_node_owning_processor_data(nodeOwningProcessor, file_count); filter_owned_nodes(nodeOwningProcessor, myProcessor, rdata, file_data); int ierr = ex_put_partial_coord_component(get_file_pointer(), proc_offset + 1, file_count, 3, file_data.data()); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } else if (field.get_name() == "mesh_model_coordinates") { // Data required by upper classes store x0, y0, z0, ... xn, yn, zn // Data stored in exodusII file is x0, ..., xn, y0, ..., yn, z0, ..., zn // so we have to allocate some scratch memory to read in the data // and then map into supplied 'data' std::vector x; std::vector y; std::vector z; x.reserve(file_count > 0 ? file_count : 1); if (spatialDimension > 1) { y.reserve(file_count > 0 ? file_count : 1); } if (spatialDimension == 3) { z.reserve(file_count > 0 ? file_count : 1); } // Cast 'data' to correct size -- double double *rdata = static_cast(data); check_node_owning_processor_data(nodeOwningProcessor, file_count); filter_owned_nodes(nodeOwningProcessor, myProcessor, rdata, x, 0, spatialDimension); if (spatialDimension > 1) { filter_owned_nodes(nodeOwningProcessor, myProcessor, rdata, y, 1, spatialDimension); } if (spatialDimension == 3) { filter_owned_nodes(nodeOwningProcessor, myProcessor, rdata, z, 2, spatialDimension); } int ierr = ex_put_partial_coord(get_file_pointer(), proc_offset + 1, file_count, x.data(), y.data(), z.data()); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } else if (field.get_name() == "ids") { // The ids coming in are the global ids; their position is the // local id -1 (That is, data[0] contains the global id of local // node 1) // Another 'const-cast' since we are modifying the database just // for efficiency; which the client does not see... handle_node_ids(data, num_to_get, proc_offset, file_count); } else if (field.get_name() == "connectivity") { // Do nothing, just handles an idiosyncrasy of the GroupingEntity } else if (field.get_name() == "connectivity_raw") { // Do nothing, just handles an idiosyncrasy of the GroupingEntity } else if (field.get_name() == "node_connectivity_status") { // Do nothing, input only field. } else if (field.get_name() == "implicit_ids") { // Do nothing, input only field. } else { return Ioss::Utils::field_warning(nb, field, "mesh output"); } } else if (role == Ioss::Field::TRANSIENT) { // Check if the specified field exists on this node block. // Note that 'higher-order' storage types (e.g. SYM_TENSOR) // exist on the database as scalars with the appropriate // extensions. // Transfer each component of the variable into 'data' and then // output. Need temporary storage area of size 'number of // nodes in this block. write_nodal_transient_field(EX_NODE_BLOCK, field, nb, num_to_get, data); } else if (role == Ioss::Field::REDUCTION) { store_reduction_field(EX_NODE_BLOCK, field, nb, data); } return num_to_get; } int64_t ParallelDatabaseIO::put_field_internal(const Ioss::Blob *blob, const Ioss::Field &field, void *data, size_t data_size) const { { Ioss::SerializeIO serializeIO__(this); size_t num_to_get = field.verify(data_size); if (num_to_get > 0) { Ioss::Field::RoleType role = field.get_role(); if (role == Ioss::Field::MESH) { if (field.get_name() == "ids") { // The ids coming in are the global ids; their position is the // local id -1 (That is, data[0] contains the global id of local // node 1) // handle_node_ids(data, num_to_get); } else if (field.get_name() == "connectivity") { // Do nothing, just handles an idiosyncrasy of the GroupingEntity } else if (field.get_name() == "connectivity_raw") { // Do nothing, just handles an idiosyncrasy of the GroupingEntity } else if (field.get_name() == "node_connectivity_status") { // Do nothing, input only field. } else if (field.get_name() == "implicit_ids") { // Do nothing, input only field. } else { return Ioss::Utils::field_warning(blob, field, "mesh output"); } } else if (role == Ioss::Field::TRANSIENT) { // Check if the specified field exists on this node block. // Note that 'higher-order' storage types (e.g. SYM_TENSOR) // exist on the database as scalars with the appropriate // extensions. // Transfer each component of the variable into 'data' and then // output. Need temporary storage area of size 'number of // nodes in this block. write_entity_transient_field(EX_BLOB, field, blob, num_to_get, data); } else if (role == Ioss::Field::REDUCTION) { store_reduction_field(EX_BLOB, field, blob, data); } else if (role == Ioss::Field::ATTRIBUTE) { num_to_get = write_attribute_field(EX_BLOB, field, blob, data); } } return num_to_get; } } int64_t ParallelDatabaseIO::put_field_internal(const Ioss::Assembly *assembly, const Ioss::Field &field, void *data, size_t data_size) const { { Ioss::SerializeIO serializeIO__(this); size_t num_to_get = field.verify(data_size); if (num_to_get > 0) { Ioss::Field::RoleType role = field.get_role(); if (role == Ioss::Field::MESH) { if (field.get_name() == "ids") { // The ids coming in are the global ids; their position is the // local id -1 (That is, data[0] contains the global id of local // node 1) // handle_node_ids(data, num_to_get); } else if (field.get_name() == "connectivity") { // Do nothing, just handles an idiosyncrasy of the GroupingEntity } else if (field.get_name() == "connectivity_raw") { // Do nothing, just handles an idiosyncrasy of the GroupingEntity } else if (field.get_name() == "node_connectivity_status") { // Do nothing, input only field. } else if (field.get_name() == "implicit_ids") { // Do nothing, input only field. } else { return Ioss::Utils::field_warning(assembly, field, "mesh output"); } } else if (role == Ioss::Field::TRANSIENT) { // Check if the specified field exists on this node block. // Note that 'higher-order' storage types (e.g. SYM_TENSOR) // exist on the database as scalars with the appropriate // extensions. // Transfer each component of the variable into 'data' and then // output. Need temporary storage area of size 'number of // nodes in this block. write_entity_transient_field(EX_ASSEMBLY, field, assembly, num_to_get, data); } else if (role == Ioss::Field::REDUCTION) { store_reduction_field(EX_ASSEMBLY, field, assembly, data); } else if (role == Ioss::Field::ATTRIBUTE) { num_to_get = write_attribute_field(EX_ASSEMBLY, field, assembly, data); } } return num_to_get; } } int64_t ParallelDatabaseIO::put_field_internal(const Ioss::ElementBlock *eb, const Ioss::Field &field, void *data, size_t data_size) const { size_t num_to_get = field.verify(data_size); int ierr = 0; // Get the element block id and element count int64_t id = Ioex::get_id(eb, EX_ELEM_BLOCK, &ids_); int64_t my_element_count = eb->entity_count(); Ioss::Field::RoleType role = field.get_role(); size_t proc_offset = eb->get_optional_property("_processor_offset", 0); size_t file_count = eb->get_optional_property("locally_owned_count", num_to_get); if (role == Ioss::Field::MESH) { // Handle the MESH fields required for an ExodusII file model. // (The 'genesis' portion) if (field.get_name() == "connectivity") { // Map element connectivity from global node id to local node id. int element_nodes = eb->topology()->number_nodes(); // Maps global to local nodeMap.reverse_map_data(data, field, num_to_get * element_nodes); // Maps local to "global_implicit" if (int_byte_size_api() == 4) { map_local_to_global_implicit(reinterpret_cast(data), num_to_get * element_nodes, nodeGlobalImplicitMap); } else { map_local_to_global_implicit(reinterpret_cast(data), num_to_get * element_nodes, nodeGlobalImplicitMap); } ierr = ex_put_partial_conn(get_file_pointer(), EX_ELEM_BLOCK, id, proc_offset + 1, file_count, data, nullptr, nullptr); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } else if (field.get_name() == "connectivity_edge") { // Map element connectivity from global edge id to local edge id. int element_edges = field.get_component_count(Ioss::Field::InOut::OUTPUT); edgeMap.reverse_map_data(data, field, num_to_get * element_edges); ierr = ex_put_conn(get_file_pointer(), EX_ELEM_BLOCK, id, nullptr, data, nullptr); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } else if (field.get_name() == "connectivity_face") { // Map element connectivity from global face id to local face id. int element_faces = field.get_component_count(Ioss::Field::InOut::OUTPUT); faceMap.reverse_map_data(data, field, num_to_get * element_faces); ierr = ex_put_conn(get_file_pointer(), EX_ELEM_BLOCK, id, nullptr, nullptr, data); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } else if (field.get_name() == "connectivity_raw") { // Element connectivity is already in local node id, map local to "global_implicit" int element_nodes = eb->topology()->number_nodes(); if (int_byte_size_api() == 4) { map_local_to_global_implicit(reinterpret_cast(data), num_to_get * element_nodes, nodeGlobalImplicitMap); } else { map_local_to_global_implicit(reinterpret_cast(data), num_to_get * element_nodes, nodeGlobalImplicitMap); } ierr = ex_put_partial_conn(get_file_pointer(), EX_ELEM_BLOCK, id, proc_offset + 1, file_count, data, nullptr, nullptr); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } else if (field.get_name() == "ids") { size_t glob_map_offset = eb->get_property("global_map_offset").get_int(); handle_element_ids(eb, data, num_to_get, glob_map_offset + proc_offset, file_count); } else if (field.get_name() == "implicit_ids") { // Do nothing, input only field. } else if (field.get_name() == "skin") { // This is (currently) for the skinned body. It maps the // side element on the skin to the original element/local // side number. It is a two component field, the first // component is the global id of the underlying element in // the initial mesh and its local side number (1-based). // FIX: Hardwired map ids.... int map_count = ex_inquire_int(get_file_pointer(), EX_INQ_ELEM_MAP); if (map_count == 0) { // This needs to be fixed... Currently hardwired.... ierr = ex_put_map_param(get_file_pointer(), 0, 2); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } std::vector element(my_element_count * int_byte_size_api()); std::vector side(my_element_count * int_byte_size_api()); if (int_byte_size_api() == 4) { int *el_side = reinterpret_cast(data); int *element32 = reinterpret_cast(element.data()); int *side32 = reinterpret_cast(side.data()); int index = 0; for (int i = 0; i < my_element_count; i++) { element32[i] = el_side[index++]; side32[i] = el_side[index++]; } } else { int64_t *el_side = reinterpret_cast(data); int64_t *element64 = reinterpret_cast(element.data()); int64_t *side64 = reinterpret_cast(side.data()); int64_t index = 0; for (int64_t i = 0; i < my_element_count; i++) { element64[i] = el_side[index++]; side64[i] = el_side[index++]; } } size_t eb_offset = eb->get_offset() + proc_offset; ierr = ex_put_partial_num_map(get_file_pointer(), EX_ELEM_MAP, 1, eb_offset + 1, file_count, element.data()); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } ierr = ex_put_partial_num_map(get_file_pointer(), EX_ELEM_MAP, 2, eb_offset + 1, file_count, side.data()); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } if (map_count == 0) { // NOTE: ex_put_*num_map must be called prior to defining the name... ierr = ex_put_name(get_file_pointer(), EX_ELEM_MAP, 1, "skin:parent_element_id"); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } ierr = ex_put_name(get_file_pointer(), EX_ELEM_MAP, 2, "skin:parent_element_side_number"); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } } else { num_to_get = Ioss::Utils::field_warning(eb, field, "mesh output"); } } else if (role == Ioss::Field::ATTRIBUTE) { num_to_get = write_attribute_field(EX_ELEM_BLOCK, field, eb, data); } else if (role == Ioss::Field::TRANSIENT) { // Check if the specified field exists on this element block. // Note that 'higher-order' storage types (e.g. SYM_TENSOR) // exist on the database as scalars with the appropriate // extensions. // Transfer each component of the variable into 'data' and then // output. Need temporary storage area of size 'number of // elements in this block. auto global_entity_count = eb->get_property("global_entity_count").get_int(); if (global_entity_count > 0) { write_entity_transient_field(EX_ELEM_BLOCK, field, eb, my_element_count, data); } } else if (role == Ioss::Field::REDUCTION) { store_reduction_field(EX_ELEM_BLOCK, field, eb, data); } return num_to_get; } int64_t ParallelDatabaseIO::put_field_internal(const Ioss::FaceBlock *eb, const Ioss::Field &field, void *data, size_t data_size) const { size_t num_to_get = field.verify(data_size); int ierr = 0; // Get the face block id and face count int64_t id = Ioex::get_id(eb, EX_FACE_BLOCK, &ids_); int64_t my_face_count = eb->entity_count(); Ioss::Field::RoleType role = field.get_role(); if (role == Ioss::Field::MESH) { // Handle the MESH fields required for an ExodusII file model. // (The 'genesis' portion) if (field.get_name() == "connectivity") { if (my_face_count > 0) { // Map face connectivity from global node id to local node id. int face_nodes = eb->topology()->number_nodes(); nodeMap.reverse_map_data(data, field, num_to_get * face_nodes); ierr = ex_put_conn(get_file_pointer(), EX_FACE_BLOCK, id, data, nullptr, nullptr); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } } else if (field.get_name() == "connectivity_edge") { if (my_face_count > 0) { // Map face connectivity from global edge id to local edge id. // Do it in 'data' ... int face_edges = field.get_component_count(Ioss::Field::InOut::OUTPUT); edgeMap.reverse_map_data(data, field, num_to_get * face_edges); ierr = ex_put_conn(get_file_pointer(), EX_FACE_BLOCK, id, nullptr, data, nullptr); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } } else if (field.get_name() == "connectivity_raw") { // Do nothing, input only field. } else if (field.get_name() == "ids") { handle_face_ids(eb, data, num_to_get); } else { num_to_get = Ioss::Utils::field_warning(eb, field, "mesh output"); } } else if (role == Ioss::Field::ATTRIBUTE) { num_to_get = write_attribute_field(EX_FACE_BLOCK, field, eb, data); } else if (role == Ioss::Field::TRANSIENT) { // Check if the specified field exists on this face block. // Note that 'higher-order' storage types (e.g. SYM_TENSOR) // exist on the database as scalars with the appropriate // extensions. // Transfer each component of the variable into 'data' and then // output. Need temporary storage area of size 'number of // faces in this block. write_entity_transient_field(EX_FACE_BLOCK, field, eb, my_face_count, data); } else if (role == Ioss::Field::REDUCTION) { store_reduction_field(EX_FACE_BLOCK, field, eb, data); } return num_to_get; } int64_t ParallelDatabaseIO::put_field_internal(const Ioss::EdgeBlock *eb, const Ioss::Field &field, void *data, size_t data_size) const { size_t num_to_get = field.verify(data_size); int ierr = 0; // Get the edge block id and edge count int64_t id = Ioex::get_id(eb, EX_EDGE_BLOCK, &ids_); int64_t my_edge_count = eb->entity_count(); Ioss::Field::RoleType role = field.get_role(); if (role == Ioss::Field::MESH) { // Handle the MESH fields required for an ExodusII file model. (The 'genesis' portion) if (field.get_name() == "connectivity") { if (my_edge_count > 0) { // Map edge connectivity from global node id to local node id. int edge_nodes = eb->topology()->number_nodes(); nodeMap.reverse_map_data(data, field, num_to_get * edge_nodes); ierr = ex_put_conn(get_file_pointer(), EX_EDGE_BLOCK, id, data, nullptr, nullptr); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } } else if (field.get_name() == "connectivity_raw") { // Do nothing, input only field. } else if (field.get_name() == "ids") { handle_edge_ids(eb, data, num_to_get); } else { num_to_get = Ioss::Utils::field_warning(eb, field, "mesh output"); } } else if (role == Ioss::Field::ATTRIBUTE) { num_to_get = write_attribute_field(EX_EDGE_BLOCK, field, eb, data); } else if (role == Ioss::Field::TRANSIENT) { // Check if the specified field exists on this edge block. // Note that 'higher-order' storage types (e.g. SYM_TENSOR) // exist on the database as scalars with the appropriate // extensions. // Transfer each component of the variable into 'data' and then // output. Need temporary storage area of size 'number of // edges in this block. write_entity_transient_field(EX_EDGE_BLOCK, field, eb, my_edge_count, data); } else if (role == Ioss::Field::REDUCTION) { store_reduction_field(EX_EDGE_BLOCK, field, eb, data); } return num_to_get; } int64_t ParallelDatabaseIO::handle_node_ids(void *ids, int64_t num_to_get, size_t /* offset */, size_t /*count*/) const { /*! * There are two modes we need to support in this routine: * 1. Initial definition of node map (local->global) and * nodeMap.reverse (global->local). * 2. Redefinition of node map via 'reordering' of the original * map when the nodes on this processor are the same, but their * order is changed (or count because of ghosting) * * So, there will be two maps the 'nodeMap.map' map is a 'direct lookup' * map which maps current local position to global id and the * 'nodeMap.reverse' is an associative lookup which maps the * global id to 'original local'. There is also a * 'nodeMap.reorder' which is direct lookup and maps current local * position to original local. * The ids coming in are the global ids; their position is the * "local id-1" (That is, data[0] contains the global id of local * node 1 in this node block). * * int local_position = nodeMap.reverse[NodeMap[i+1]] * (the nodeMap.map and nodeMap.reverse are 1-based) * * To determine which map to update on a call to this function, we * use the following hueristics: * -- If the database state is 'STATE_MODEL:', then update the * 'nodeMap.reverse' and 'nodeMap.map' * * -- If the database state is not STATE_MODEL, then leave the * 'nodeMap.reverse' and 'nodeMap.map' alone since they correspond to the * information already written to the database. [May want to add a * STATE_REDEFINE_MODEL] * * -- In both cases, update the nodeMap.reorder * * NOTE: The mapping is done on TRANSIENT fields only; MODEL fields * should be in the original order... */ nodeMap.set_size(num_to_get); bool in_define = (dbState == Ioss::STATE_MODEL) || (dbState == Ioss::STATE_DEFINE_MODEL); if (int_byte_size_api() == 4) { nodeMap.set_map(static_cast(ids), num_to_get, 0, in_define); } else { nodeMap.set_map(static_cast(ids), num_to_get, 0, in_define); } nodeMap.set_defined(true); return num_to_get; } int64_t ParallelDatabaseIO::handle_element_ids(const Ioss::ElementBlock *eb, void *ids, size_t num_to_get, size_t offset, size_t count) const { if (dbState == Ioss::STATE_MODEL) { if (elemGlobalImplicitMap.empty()) { elemGlobalImplicitMap.resize(elementCount); } // Build the implicit_global map used to map an elements // local-implicit position to the global-implicit // position. Primarily used for sideset elements. 'count' // Elements starting at 'eb_offset' map to the global implicit // position of 'offset' int64_t eb_offset = eb->get_offset(); for (size_t i = 0; i < count; i++) { elemGlobalImplicitMap[eb_offset + i] = offset + i + 1; } elemGlobalImplicitMapDefined = true; } elemMap.set_size(elementCount); return handle_block_ids(eb, EX_ELEM_MAP, elemMap, ids, num_to_get, offset); } int64_t ParallelDatabaseIO::handle_face_ids(const Ioss::FaceBlock *eb, void *ids, size_t num_to_get) const { faceMap.set_size(faceCount); return handle_block_ids(eb, EX_FACE_MAP, faceMap, ids, num_to_get, 0); } int64_t ParallelDatabaseIO::handle_edge_ids(const Ioss::EdgeBlock *eb, void *ids, size_t num_to_get) const { edgeMap.set_size(edgeCount); return handle_block_ids(eb, EX_EDGE_MAP, edgeMap, ids, num_to_get, 0); } void ParallelDatabaseIO::write_nodal_transient_field(ex_entity_type /* type */, const Ioss::Field &field, const Ioss::NodeBlock *nb, int64_t count, void *variables) const { Ioss::Field::BasicType ioss_type = field.get_type(); assert(ioss_type == Ioss::Field::REAL || ioss_type == Ioss::Field::INTEGER || ioss_type == Ioss::Field::INT64 || ioss_type == Ioss::Field::COMPLEX); // Note that if the field's basic type is COMPLEX, then each component of // the VariableType is a complex variable consisting of a real and // imaginary part. Since exodus cannot handle complex variables, // we have to output a (real and imaginary) X (number of // components) fields. For example, if V is a 3d vector of complex // data, the data in the 'variables' array are v_x, v.im_x, v_y, // v.im_y, v_z, v.im_z which need to be output in six separate // exodus fields. These fields were already defined in // "write_results_metadata". std::vector temp(count); int step = get_current_state(); step = get_database_step(step); // get number of components, cycle through each component // and add suffix to base 'field_name'. Look up index // of this name in 'm_variables[EX_NODE_BLOCK]' map int comp_count = field.get_component_count(Ioss::Field::InOut::OUTPUT); int re_im = 1; if (ioss_type == Ioss::Field::COMPLEX) { re_im = 2; } for (int complex_comp = 0; complex_comp < re_im; complex_comp++) { std::string field_name = field.get_name(); if (re_im == 2) { field_name += complex_suffix[complex_comp]; } for (int i = 0; i < comp_count; i++) { std::string var_name = get_component_name(field, Ioss::Field::InOut::OUTPUT, i + 1); auto var_iter = m_variables[EX_NODE_BLOCK].find(var_name); if (var_iter == m_variables[EX_NODE_BLOCK].end()) { std::ostringstream errmsg; fmt::print(errmsg, "ERROR: Could not find nodal variable '{}'\n", var_name); IOSS_ERROR(errmsg); } int var_index = var_iter->second; size_t begin_offset = (re_im * i) + complex_comp; size_t stride = re_im * comp_count; size_t num_out = 0; if (ioss_type == Ioss::Field::REAL || ioss_type == Ioss::Field::COMPLEX) { num_out = nodeMap.map_field_to_db_scalar_order(static_cast(variables), temp, begin_offset, count, stride, 0); } else if (ioss_type == Ioss::Field::INTEGER) { num_out = nodeMap.map_field_to_db_scalar_order(static_cast(variables), temp, begin_offset, count, stride, 0); } else if (ioss_type == Ioss::Field::INT64) { num_out = nodeMap.map_field_to_db_scalar_order(static_cast(variables), temp, begin_offset, count, stride, 0); } if (num_out != static_cast(nodeCount)) { std::ostringstream errmsg; fmt::print(errmsg, "ERROR: Problem outputting nodal variable '{}' with index = {} to file '{}' on " "processor {}\n" "\tShould have output {} values, but instead only output {} values.\n", var_name, var_index, get_filename(), myProcessor, fmt::group_digits(nodeCount), fmt::group_digits(num_out)); IOSS_ERROR(errmsg); } // Write the variable... size_t proc_offset = nb->get_optional_property("_processor_offset", 0); size_t file_count = nb->get_optional_property("locally_owned_count", num_out); check_node_owning_processor_data(nodeOwningProcessor, file_count); filter_owned_nodes(nodeOwningProcessor, myProcessor, temp.data()); int ierr = ex_put_partial_var(get_file_pointer(), step, EX_NODE_BLOCK, var_index, 0, proc_offset + 1, file_count, temp.data()); if (ierr < 0) { std::ostringstream errmsg; fmt::print(errmsg, "Problem outputting nodal variable '{}' with index = {} on processor {}\n", var_name, var_index, myProcessor); Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__, errmsg.str()); } } } } void ParallelDatabaseIO::write_entity_transient_field(ex_entity_type type, const Ioss::Field &field, const Ioss::GroupingEntity *ge, int64_t count, void *variables) const { static Ioss::Map non_element_map; // Used as an empty map for ge->type() != element block. std::vector temp(count); int step = get_current_state(); step = get_database_step(step); Ioss::Map *map = nullptr; int64_t eb_offset = 0; if (ge->type() == Ioss::ELEMENTBLOCK) { const Ioss::ElementBlock *elb = dynamic_cast(ge); Ioss::Utils::check_dynamic_cast(elb); eb_offset = elb->get_offset(); map = &elemMap; } else { map = &non_element_map; } Ioss::Field::BasicType ioss_type = field.get_type(); assert(ioss_type == Ioss::Field::REAL || ioss_type == Ioss::Field::INTEGER || ioss_type == Ioss::Field::INT64 || ioss_type == Ioss::Field::COMPLEX); // Note that if the field's basic type is COMPLEX, then each component of // the VariableType is a complex variable consisting of a real and // imaginary part. Since exodus cannot handle complex variables, // we have to output a (real and imaginary) X (number of // components) fields. For example, if V is a 3d vector of complex // data, the data in the 'variables' array are v_x, v.im_x, v_y, // v.im_y, v_z, v.im_z which need to be output in six separate // exodus fields. These fields were already defined in // "write_results_metadata". // get number of components, cycle through each component // and add suffix to base 'field_name'. Look up index // of this name in 'm_variables[type]' map int comp_count = field.get_component_count(Ioss::Field::InOut::OUTPUT); int re_im = 1; if (ioss_type == Ioss::Field::COMPLEX) { re_im = 2; } for (int complex_comp = 0; complex_comp < re_im; complex_comp++) { std::string field_name = field.get_name(); if (re_im == 2) { field_name += complex_suffix[complex_comp]; } for (int i = 0; i < comp_count; i++) { std::string var_name = get_component_name(field, Ioss::Field::InOut::OUTPUT, i + 1); auto var_iter = m_variables[type].find(var_name); if (var_iter == m_variables[type].end()) { std::ostringstream errmsg; fmt::print(errmsg, "ERROR: Could not find field '{}'\n", var_name); IOSS_ERROR(errmsg); } int var_index = var_iter->second; assert(var_index > 0); // var is a [count,comp,re_im] array; re_im = 1(real) or 2(complex) // beg_offset = (re_im*i)+complex_comp // number_values = count // stride = re_im*comp_count int64_t begin_offset = (re_im * i) + complex_comp; int64_t stride = re_im * comp_count; if (ioss_type == Ioss::Field::REAL || ioss_type == Ioss::Field::COMPLEX) { map->map_field_to_db_scalar_order(static_cast(variables), temp, begin_offset, count, stride, eb_offset); } else if (ioss_type == Ioss::Field::INTEGER) { map->map_field_to_db_scalar_order(static_cast(variables), temp, begin_offset, count, stride, eb_offset); } else if (ioss_type == Ioss::Field::INT64) { map->map_field_to_db_scalar_order(static_cast(variables), temp, begin_offset, count, stride, eb_offset); } // Write the variable... size_t proc_offset = ge->get_optional_property("_processor_offset", 0); size_t file_count = ge->get_optional_property("locally_owned_count", count); int64_t id = Ioex::get_id(ge, type, &ids_); int ierr; if (type == EX_SIDE_SET) { size_t offset = ge->get_property("set_offset").get_int(); ierr = ex_put_partial_var(get_file_pointer(), step, type, var_index, id, proc_offset + offset + 1, count, temp.data()); } else if (type == EX_NODE_SET) { std::vector file_data; file_data.reserve(file_count); map_nodeset_data(nodesetOwnedNodes[ge], temp.data(), file_data); ierr = ex_put_partial_var(get_file_pointer(), step, type, var_index, id, proc_offset + 1, file_count, file_data.data()); } else { ierr = ex_put_partial_var(get_file_pointer(), step, type, var_index, id, proc_offset + 1, file_count, temp.data()); } if (ierr < 0) { std::ostringstream extra_info; fmt::print(extra_info, "Outputting component {} of field '{}' at step {} on {} '{}'.", i, field_name, fmt::group_digits(step), ge->type_string(), ge->name()); Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__, extra_info.str()); } } } } int64_t ParallelDatabaseIO::put_Xset_field_internal(ex_entity_type type, const Ioss::EntitySet *ns, const Ioss::Field &field, void *data, size_t data_size) const { size_t entity_count = ns->entity_count(); size_t num_to_get = field.verify(data_size); int64_t id = Ioex::get_id(ns, type, &ids_); Ioss::Field::RoleType role = field.get_role(); if (role == Ioss::Field::MESH) { void *out_data = data; std::vector i32data; std::vector i64data; std::vector dbldata; size_t proc_offset = ns->get_optional_property("_processor_offset", 0); size_t file_count = ns->get_optional_property("locally_owned_count", num_to_get); if (field.get_name() == "ids" || field.get_name() == "ids_raw") { // Map node id from global node id to local node id. // Do it in 'data' ... if (field.get_name() == "ids") { nodeMap.reverse_map_data(data, field, num_to_get); } if (type == EX_NODE_SET) { nodesetOwnedNodes[ns].reserve(file_count); if (int_byte_size_api() == 4) { i32data.reserve(file_count); check_node_owning_processor_data(nodeOwningProcessor, file_count); map_nodeset_id_data(nodeOwningProcessor, nodesetOwnedNodes[ns], myProcessor, reinterpret_cast(data), num_to_get, i32data); assert(i32data.size() == file_count); // Maps local to "global_implicit" map_local_to_global_implicit(i32data.data(), file_count, nodeGlobalImplicitMap); out_data = i32data.data(); } else { i64data.reserve(file_count); check_node_owning_processor_data(nodeOwningProcessor, file_count); map_nodeset_id_data(nodeOwningProcessor, nodesetOwnedNodes[ns], myProcessor, reinterpret_cast(data), num_to_get, i64data); assert(i64data.size() == file_count); map_local_to_global_implicit(i64data.data(), file_count, nodeGlobalImplicitMap); out_data = i64data.data(); } } int ierr = ex_put_partial_set(get_file_pointer(), type, id, proc_offset + 1, file_count, out_data, nullptr); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } else if (field.get_name() == "orientation") { int ierr = ex_put_partial_set(get_file_pointer(), type, id, proc_offset + 1, file_count, nullptr, out_data); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } else if (field.get_name() == "distribution_factors") { int ierr = 0; if (type == EX_NODE_SET) { map_nodeset_data(nodesetOwnedNodes[ns], reinterpret_cast(data), dbldata); ierr = ex_put_partial_set_dist_fact(get_file_pointer(), type, id, proc_offset + 1, file_count, dbldata.data()); } else { ierr = ex_put_partial_set_dist_fact(get_file_pointer(), type, id, proc_offset + 1, num_to_get, static_cast(out_data)); } if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } else { num_to_get = Ioss::Utils::field_warning(ns, field, "output"); } } else if (role == Ioss::Field::TRANSIENT) { // Check if the specified field exists on this element block. // Note that 'higher-order' storage types (e.g. SYM_TENSOR) // exist on the database as scalars with the appropriate // extensions. // Transfer each component of the variable into 'data' and then // output. Need temporary storage area of size 'number of // elements in this block. write_entity_transient_field(type, field, ns, entity_count, data); } else if (role == Ioss::Field::ATTRIBUTE) { num_to_get = write_attribute_field(type, field, ns, data); } else if (role == Ioss::Field::REDUCTION) { store_reduction_field(type, field, ns, data); } return num_to_get; } int64_t ParallelDatabaseIO::put_field_internal(const Ioss::NodeSet *ns, const Ioss::Field &field, void *data, size_t data_size) const { return put_Xset_field_internal(EX_NODE_SET, ns, field, data, data_size); } int64_t ParallelDatabaseIO::put_field_internal(const Ioss::EdgeSet *ns, const Ioss::Field &field, void *data, size_t data_size) const { return put_Xset_field_internal(EX_EDGE_SET, ns, field, data, data_size); } int64_t ParallelDatabaseIO::put_field_internal(const Ioss::FaceSet *ns, const Ioss::Field &field, void *data, size_t data_size) const { return put_Xset_field_internal(EX_FACE_SET, ns, field, data, data_size); } int64_t ParallelDatabaseIO::put_field_internal(const Ioss::ElementSet *ns, const Ioss::Field &field, void *data, size_t data_size) const { return put_Xset_field_internal(EX_ELEM_SET, ns, field, data, data_size); } int64_t ParallelDatabaseIO::put_field_internal(const Ioss::SideSet *ss, const Ioss::Field &field, void * /* data */, size_t data_size) const { size_t num_to_get = field.verify(data_size); if (field.get_name() == "ids") { // Do nothing, just handles an idiosyncrasy of the GroupingEntity } else { num_to_get = Ioss::Utils::field_warning(ss, field, "output"); } return num_to_get; } int64_t ParallelDatabaseIO::put_field_internal(const Ioss::CommSet * /*cs*/, const Ioss::Field &field, void * /*data*/, size_t data_size) const { size_t num_to_get = field.verify(data_size); return num_to_get; } int64_t ParallelDatabaseIO::put_field_internal(const Ioss::SideBlock *sb, const Ioss::Field &field, void *data, size_t data_size) const { size_t num_to_get = field.verify(data_size); int64_t id = Ioex::get_id(sb, EX_SIDE_SET, &ids_); size_t entity_count = sb->entity_count(); size_t offset = sb->get_property("set_offset").get_int(); Ioss::Field::RoleType role = field.get_role(); if (role == Ioss::Field::MESH) { if (field.get_name() == "side_ids" && sb->name() == "universal_sideset") { // The side ids are being stored as the distribution factor // field on the universal sideset. There should be no other // side sets that request this field... (Eventually, // create an id field to store this info. // Need to convert 'ints' to 'double' for storage on mesh... // FIX 64 if (field.get_type() == Ioss::Field::INTEGER) { int *ids = static_cast(data); std::vector real_ids(num_to_get); for (size_t i = 0; i < num_to_get; i++) { real_ids[i] = static_cast(ids[i]); } int ierr = ex_put_partial_set_dist_fact(get_file_pointer(), EX_SIDE_SET, id, offset + 1, entity_count, real_ids.data()); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } else { int64_t *ids = static_cast(data); std::vector real_ids(num_to_get); for (size_t i = 0; i < num_to_get; i++) { real_ids[i] = static_cast(ids[i]); } int ierr = ex_put_partial_set_dist_fact(get_file_pointer(), EX_SIDE_SET, id, offset + 1, entity_count, real_ids.data()); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } } else if (field.get_name() == "side_ids") { } else if (field.get_name() == "ids") { // ============================================================= // NOTE: Code is currently commented out since we have // redundant ways of getting the data (element/side) out to // the database. The 'ids' field method relies on a numbering // kluge, so for now trying the 'element_side' field... // ============================================================= } else if (field.get_name() == "distribution_factors") { int ierr; size_t df_offset = sb->get_property("set_df_offset").get_int(); size_t proc_df_offset = sb->get_property("processor_df_offset").get_int(); size_t df_count = sb->get_property("distribution_factor_count").get_int(); ierr = ex_put_partial_set_dist_fact(get_file_pointer(), EX_SIDE_SET, id, proc_df_offset + df_offset + 1, df_count, static_cast(data)); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } else if (field.get_name() == "element_side") { // In exodusII, the 'side block' is stored as a sideset. A // sideset has a list of elements and a corresponding local // element side (1-based) // The 'data' passed into the function is stored as a // 2D vector e0,f0,e1,f1,... (e=element, f=side) // To avoid overwriting the passed in data, we allocate // two arrays to store the data for this sideset. // The element_id passed in is the global id; we need to // output the local id. // Allocate space for local side number and element numbers // numbers. // See if edges or faces... size_t side_offset = Ioss::Utils::get_side_offset(sb); size_t index = 0; size_t proc_offset = sb->get_optional_property("_processor_offset", 0); if (field.get_type() == Ioss::Field::INTEGER) { Ioss::IntVector element(num_to_get); Ioss::IntVector side(num_to_get); int *el_side = reinterpret_cast(data); for (size_t i = 0; i < num_to_get; i++) { element[i] = elemMap.global_to_local(el_side[index++]); side[i] = el_side[index++] + side_offset; } map_local_to_global_implicit(element.data(), num_to_get, elemGlobalImplicitMap); int ierr = ex_put_partial_set(get_file_pointer(), EX_SIDE_SET, id, proc_offset + offset + 1, num_to_get, element.data(), side.data()); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } else { Ioss::Int64Vector element(num_to_get); Ioss::Int64Vector side(num_to_get); int64_t *el_side = reinterpret_cast(data); for (size_t i = 0; i < num_to_get; i++) { element[i] = elemMap.global_to_local(el_side[index++]); side[i] = el_side[index++] + side_offset; } map_local_to_global_implicit(element.data(), num_to_get, elemGlobalImplicitMap); int ierr = ex_put_partial_set(get_file_pointer(), EX_SIDE_SET, id, proc_offset + offset + 1, num_to_get, element.data(), side.data()); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } } else if (field.get_name() == "element_side_raw") { // In exodusII, the 'side block' is stored as a sideset. A // sideset has a list of elements and a corresponding local // element side (1-based) // The 'data' passed into the function is stored as a // 2D vector e0,f0,e1,f1,... (e=element, f=side) // To avoid overwriting the passed in data, we allocate // two arrays to store the data for this sideset. // The element_id passed in is the local id. // See if edges or faces... size_t side_offset = Ioss::Utils::get_side_offset(sb); size_t index = 0; if (field.get_type() == Ioss::Field::INTEGER) { Ioss::IntVector element(num_to_get); Ioss::IntVector side(num_to_get); int *el_side = reinterpret_cast(data); for (size_t i = 0; i < num_to_get; i++) { element[i] = el_side[index++]; side[i] = el_side[index++] + side_offset; } int ierr = ex_put_partial_set(get_file_pointer(), EX_SIDE_SET, id, offset + 1, entity_count, element.data(), side.data()); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } else { Ioss::Int64Vector element(num_to_get); Ioss::Int64Vector side(num_to_get); int64_t *el_side = reinterpret_cast(data); for (size_t i = 0; i < num_to_get; i++) { element[i] = el_side[index++]; side[i] = el_side[index++] + side_offset; } int ierr = ex_put_partial_set(get_file_pointer(), EX_SIDE_SET, id, offset + 1, entity_count, element.data(), side.data()); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } } else if (field.get_name() == "connectivity") { // Do nothing, just handles an idiosyncrasy of the GroupingEntity } else if (field.get_name() == "connectivity_raw") { // Do nothing, just handles an idiosyncrasy of the GroupingEntity } else { num_to_get = Ioss::Utils::field_warning(sb, field, "output"); } } else if (role == Ioss::Field::TRANSIENT) { // Check if the specified field exists on this block. // Note that 'higher-order' storage types (e.g. SYM_TENSOR) // exist on the database as scalars with the appropriate // extensions. // Transfer each component of the variable into 'data' and then // output. Need temporary storage area of size 'number of // entities in this block. write_entity_transient_field(EX_SIDE_SET, field, sb, entity_count, data); } else if (role == Ioss::Field::ATTRIBUTE) { num_to_get = write_attribute_field(EX_SIDE_SET, field, sb, data); } else if (role == Ioss::Field::REDUCTION) { store_reduction_field(EX_SIDE_SET, field, sb, data); } return num_to_get; } void ParallelDatabaseIO::write_meta_data(Ioss::IfDatabaseExistsBehavior behavior) { Ioss::Region *region = get_region(); common_write_meta_data(behavior); char the_title[max_line_length + 1]; // Title... if (region->property_exists("title")) { std::string title_str = region->get_property("title").get_string(); Ioss::Utils::copy_string(the_title, title_str); } else { Ioss::Utils::copy_string(the_title, "IOSS Default Output Title"); } bool file_per_processor = false; Ioex::Mesh mesh(spatialDimension, the_title, util(), file_per_processor); mesh.populate(region); if (behavior != Ioss::DB_APPEND && behavior != Ioss::DB_MODIFY) { if (!properties.exists("OMIT_QA_RECORDS")) { put_qa(); } if (!properties.exists("OMIT_INFO_RECORDS")) { put_info(); } // Write the metadata to the exodusII file... Ioex::Internals data(get_file_pointer(), maximumNameLength, util()); mesh.comm.outputNemesis = false; int ierr = data.write_meta_data(mesh); if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } metaDataWritten = true; // Set the processor offset property. Specifies where in the global list, the data from this // processor begins... update_processor_offset_property(region, mesh); if (behavior != Ioss::DB_APPEND && behavior != Ioss::DB_MODIFY) { output_node_map(); output_other_meta_data(); } } void ParallelDatabaseIO::create_implicit_global_map() const { // If the node is locally owned, then its position is basically // determined by removing all shared nodes from the list and // then compressing the list. This location plus the proc_offset // gives its location in the global-implicit file. // // Do this over in the DecompositionData class since it has // several utilities in place for MPI communication. DecompositionData compose(Ioss::PropertyManager(), util().communicator()); int64_t locally_owned_count = 0; int64_t processor_offset = 0; compose.create_implicit_global_map(nodeOwningProcessor, nodeGlobalImplicitMap, nodeMap, &locally_owned_count, &processor_offset); nodeGlobalImplicitMapDefined = true; const Ioss::NodeBlockContainer &node_blocks = get_region()->get_node_blocks(); if (!node_blocks[0]->property_exists("locally_owned_count")) { node_blocks[0]->property_add(Ioss::Property("locally_owned_count", locally_owned_count)); } if (!node_blocks[0]->property_exists("_processor_offset")) { node_blocks[0]->property_add(Ioss::Property("_processor_offset", processor_offset)); } output_node_map(); } void ParallelDatabaseIO::output_node_map() const { // Write the partial nodemap to the database... This is called // two times -- once from create_implicit_global_map() and once // from write_meta_data(). It will only output the map if // the metadata has been written to the output database AND if // the nodeMap.map and nodeGlobalImplicitMap are defined. if (metaDataWritten) { const Ioss::NodeBlockContainer &node_blocks = get_region()->get_node_blocks(); if (node_blocks.empty()) { return; } assert(node_blocks[0]->property_exists("_processor_offset")); assert(node_blocks[0]->property_exists("locally_owned_count")); size_t processor_offset = node_blocks[0]->get_property("_processor_offset").get_int(); size_t locally_owned_count = node_blocks[0]->get_property("locally_owned_count").get_int(); int ierr = 0; if (nodeMap.defined() && nodeGlobalImplicitMapDefined) { if (int_byte_size_api() == 4) { std::vector file_ids; file_ids.reserve(locally_owned_count); check_node_owning_processor_data(nodeOwningProcessor, locally_owned_count); filter_owned_nodes(nodeOwningProcessor, myProcessor, &nodeMap.map()[1], file_ids); ierr = ex_put_partial_id_map(get_file_pointer(), EX_NODE_MAP, processor_offset + 1, locally_owned_count, file_ids.data()); } else { std::vector file_ids; file_ids.reserve(locally_owned_count); check_node_owning_processor_data(nodeOwningProcessor, locally_owned_count); filter_owned_nodes(nodeOwningProcessor, myProcessor, &nodeMap.map()[1], file_ids); ierr = ex_put_partial_id_map(get_file_pointer(), EX_NODE_MAP, processor_offset + 1, locally_owned_count, file_ids.data()); } } if (ierr < 0) { Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__); } } } void ParallelDatabaseIO::check_valid_values() const { std::vector counts{nodeCount, elementCount, m_groupCount[EX_ELEM_BLOCK]}; std::vector all_counts; util().all_gather(counts, all_counts); // Get minimum value in `all_counts`. If >0, then don't need to check further... auto min_val = *std::min_element(all_counts.begin(), all_counts.end()); if (myProcessor == 0) { size_t proc_count = all_counts.size() / 3; if (min_val < 0) { static std::array label{"node", "element", "element block"}; // Error on one or more of the counts... for (size_t j = 0; j < 3; j++) { std::vector bad_proc; for (size_t i = 0; i < proc_count; i++) { if (all_counts[3 * i + j] < 0) { bad_proc.push_back(i); } } if (!bad_proc.empty()) { std::ostringstream errmsg; fmt::print(errmsg, "ERROR: Negative {} count on {} processor{}:\n\t{}\n\n", label[j], bad_proc.size(), bad_proc.size() > 1 ? "s" : "", Ioss::Utils::format_id_list(bad_proc, ":")); IOSS_ERROR(errmsg); } } } // Now check for warning (count == 0) if (min_val <= 0) { static std::array label{"nodes or elements", "elements", "element blocks"}; // Possible warning on one or more of the counts... // Note that it is possible to have nodes on a processor with no elements, // but not possible to have elements if no nodes... for (size_t j = 0; j < 3; j++) { std::vector bad_proc; for (size_t i = 0; i < proc_count; i++) { if (all_counts[3 * i + j] == 0) { bad_proc.push_back(i); } } if (!bad_proc.empty()) { fmt::print(Ioss::WARNING(), "No {} on processor{}:\n\t{}\n\n", label[j], bad_proc.size() > 1 ? "s" : "", Ioss::Utils::format_id_list(bad_proc, ":")); if (j == 0) { break; } } } } } else { // All other processors; need to abort if negative count if (min_val < 0) { std::ostringstream errmsg; IOSS_ERROR(errmsg); } } } } // namespace Ioex #else const char ioss_exodus_parallel_database_unused_symbol_dummy = '\0'; #endif