Merge Pull Request #13547 from trilinos/Trilinos/stk-snapshot

Automatically Merged using Trilinos Pull Request AutoTester
PR Title: b'STK: Snapshot 10-24-24 10:56 from Sierra 5.21.6-321-gf1c5a4d6'
PR Author: alanw0

packages/stk/CHANGELOG.md

@@ -1,8 +1,14 @@
 # CHANGELOG
 
+5.21.6 (STK_VERSION 5210600) 10/25/2024
+  stk_search: fix build-error (instantiation error for morton_lbvh_search) for gcc 13.2
+  stk_util: added parallel/OutputStreams.hpp
+    - which includes the functions outputP0(), output(), output_flush(), set_outputP0(..), reset_default_output_streams().
+
 5.21.5-2 (STK_VERSION 5210502) 10/07/2024
   stk_search: Fixed HIP sort error.
   stk_mesh: add multi-field NGP-FieldBLAS field_fill
+
 5.21.5-1 (STK_VERSION 5210501) 9/27/2024
   stk_mesh: deprecate BulkData::relation_exist
 

packages/stk/stk_balance/stk_balance/balance.cpp

@@ -50,6 +50,7 @@
 #include "stk_tools/transfer_utils/TransientFieldTransferById.hpp"
 #include "stk_util/diag/StringUtil.hpp"
 #include "stk_util/parallel/ParallelReduce.hpp"
+#include "stk_util/parallel/OutputStreams.hpp"
 #include "stk_util/util/ReportHandler.hpp"  // for ThrowRequireMsg
 #include <stk_balance/search_tolerance_algs/SecondShortestEdgeFaceSearchTolerance.hpp>
 #include <stk_io/FillMesh.hpp>
@@ -252,7 +253,7 @@ bool balanceStkMesh(const BalanceSettings& balanceSettings, stk::mesh::BulkData&
   const bool anyElementMovement = balancer.balance(mesh, selectors);
 
   DiagnosticsPrinter diagPrinter(stkMeshBulkData.parallel(), stkMeshBulkData.parallel_size());
-  diagPrinter.print(sierra::Env::outputP0());
+  diagPrinter.print(stk::outputP0());
 
   return anyElementMovement;
 }
@@ -270,7 +271,7 @@ bool balanceStkMesh(const BalanceSettings& balanceSettings, stk::mesh::BulkData&
   const bool anyElementMovement = balancer.balance(mesh);
 
   DiagnosticsPrinter diagPrinter(stkMeshBulkData.parallel(), stkMeshBulkData.parallel_size());
-  diagPrinter.print(sierra::Env::outputP0());
+  diagPrinter.print(stk::outputP0());
 
   return anyElementMovement;
 }
@@ -290,7 +291,7 @@ bool balanceStkMeshNodes(const BalanceSettings& balanceSettings, stk::mesh::Bulk
                                                                         balanceSettings.getNodeBalancerMaxIterations());
 
     DiagnosticsPrinter diagPrinter(stkMeshBulkData.parallel(), stkMeshBulkData.parallel_size());
-    diagPrinter.print(sierra::Env::outputP0());
+    diagPrinter.print(stk::outputP0());
 
     return anyChangedOwnership;
   }

packages/stk/stk_balance/stk_balance/internal/privateDeclarations.cpp

@@ -38,6 +38,7 @@
 #include <stk_mesh/base/SkinMeshUtil.hpp>
 #include <stk_util/environment/Env.hpp>
 #include <stk_util/parallel/ParallelReduce.hpp>
+#include <stk_util/parallel/OutputStreams.hpp>
 #include <stk_util/util/SortAndUnique.hpp>
 #include <algorithm>
 #include <tuple>
@@ -792,7 +793,7 @@ void fill_output_subdomain_field(const stk::mesh::BulkData & bulk, const Balance
 
 void logMessage(MPI_Comm communicator, const std::string &message)
 {
-  stk::log_with_time_and_memory(communicator, message);
+  stk::log_with_time_and_memory(communicator, message, stk::outputP0());
 }
 
 void fill_zoltan2_graph(const BalanceSettings& balanceSettings,

packages/stk/stk_balance/stk_balance/internal/privateDeclarations.hpp

@@ -45,7 +45,7 @@
 #include <stk_mesh/base/CreateFaces.hpp>
 #include <stk_mesh/base/SkinMesh.hpp>
 #include <stk_mesh/baseImpl/elementGraph/BulkDataIdMapper.hpp>
-#include <stk_util/environment/Env.hpp>
+#include <stk_util/parallel/OutputStreams.hpp>
 
 #include <Teuchos_ParameterList.hpp>
 #include <stk_balance/internal/StkMeshAdapterForZoltan2.hpp>
@@ -140,14 +140,11 @@ void print_zoltan_statistics(const ZoltanAdapter& stkMeshAdapter, Zoltan2::Evalu
   double localsum = 0.;
   for (size_t i = 0; i< stkMeshAdapter.getLocalNumIDs(); i++) localsum += kdd[i];
 
-  sierra::Env::outputP0() << parallel_rank
+  stk::outputP0() << parallel_rank
                           << " PRINTING METRICS nObj " << stkMeshAdapter.getLocalNumIDs()
                           << " nwgts " << stkMeshAdapter.getNumWeightsPerID()
                           << " sumwgt " << localsum << std::endl;
-  zoltanEvaluateParition.printMetrics(sierra::Env::outputP0());
-  //sierra::Env::outputP0() << parallel_rank
-  //        << " PRINTING GRAPH METRICS" << std::endl;
-  //zoltanEvaluateParition.printGraphMetrics(sierra::Env::outputP0());
+  zoltanEvaluateParition.printMetrics(stk::outputP0());
 }
 
 template <class ZoltanAdapter>

packages/stk/stk_balance/stk_balance/m2n/m2nRebalance.cpp

@@ -39,6 +39,7 @@
 #include <stk_mesh/base/MeshBuilder.hpp>
 #include <stk_io/StkMeshIoBroker.hpp>
 #include <stk_io/FillMesh.hpp>
+#include "stk_util/parallel/OutputStreams.hpp"
 #include "stk_util/environment/Env.hpp"
 #include "stk_util/environment/EnvData.hpp"
 #include "stk_util/environment/OutputLog.hpp"
@@ -52,18 +53,18 @@ void set_output_streams(MPI_Comm comm, const stk::balance::M2NBalanceSettings &
   if (stk::parallel_machine_rank(comm) == 0) {
     const std::string & logName = balanceSettings.get_log_filename();
     if (logName == "cout"  || logName == "cerr") {
-      stk::EnvData::instance().m_outputP0 = stk::get_log_ostream(logName);
+      stk::set_outputP0(stk::get_log_ostream(logName));
     }
     else {
       stk::bind_output_streams("log=\"" + logName + "\"");
-      stk::EnvData::instance().m_outputP0 = stk::get_log_ostream("log");
+      stk::set_outputP0(stk::get_log_ostream("log"));
     }
   }
   else {
-    stk::EnvData::instance().m_outputP0 = &stk::EnvData::instance().m_outputNull;
+    //stk::outputP0() is already a null output stream by default on other MPI ranks.
   }
 
-  Ioss::Utils::set_output_stream(sierra::Env::outputP0());
+  Ioss::Utils::set_output_stream(stk::outputP0());
 }
 
 void print_running_message(const stk::balance::M2NBalanceSettings & balanceSettings, MPI_Comm comm)
@@ -120,7 +121,7 @@ void m2nRebalance(stk::io::StkMeshIoBroker& ioBroker, const stk::balance::M2NBal
 void rebalance_m2n(stk::balance::M2NBalanceSettings &balanceSettings, MPI_Comm comm)
 {
   print_running_message(balanceSettings, comm);
-  print_banner(sierra::Env::outputP0());
+  print_banner(stk::outputP0());
 
   std::shared_ptr<stk::mesh::BulkData> bulk = stk::mesh::MeshBuilder(comm).create();
   stk::io::StkMeshIoBroker ioBroker;

packages/stk/stk_balance/stk_balance/m2n_main/m2nMain.cpp

@@ -38,13 +38,15 @@
 #include <stk_balance/setup/M2NParser.hpp>
 #include "stk_balance/internal/LogUtils.hpp"
 
-#include <stk_util/environment/Env.hpp>
+#include <stk_util/parallel/OutputStreams.hpp>
 #include <stk_util/environment/memory_util.hpp>
 #include <stk_util/util/human_bytes.hpp>
 
 int main(int argc, const char**argv)
 {
     MPI_Init(&argc, const_cast<char***>(&argv));
+    Kokkos::initialize(argc, const_cast<char**>(argv));
+
     MPI_Comm comm = MPI_COMM_WORLD;
     stk::balance::initialize_environment(comm, argv);
 
@@ -58,10 +60,12 @@ int main(int argc, const char**argv)
 
     size_t hwmMax = 0, hwmMin = 0, hwmAvg = 0;
     stk::get_memory_high_water_mark_across_processors(comm, hwmMax, hwmMin, hwmAvg);
-    sierra::Env::outputP0() << "Memory HWM across procs, max/min/avg: "
-                            << stk::human_bytes(hwmMax) << " / "
-                            << stk::human_bytes(hwmMin) << " / "
-                            << stk::human_bytes(hwmAvg) << std::endl;
+    stk::outputP0() << "Memory HWM across procs, max/min/avg: "
+                    << stk::human_bytes(hwmMax) << " / "
+                    << stk::human_bytes(hwmMin) << " / "
+                    << stk::human_bytes(hwmAvg) << std::endl;
+
+    Kokkos::finalize();
     MPI_Finalize();
     return 0;
 }

packages/stk/stk_balance/stk_balance/setup/LifeCycle.cpp

@@ -33,6 +33,7 @@
 
 #include "LifeCycle.hpp"
 
+#include "stk_util/parallel/OutputStreams.hpp"
 #include "stk_util/environment/Env.hpp"
 #include "stk_util/environment/EnvData.hpp"
 #include "stk_util/environment/OutputLog.hpp"
@@ -81,7 +82,7 @@ void LifeCycle::run()
   }
 
   print_running_message();
-  print_banner(sierra::Env::outputP0());
+  print_banner(stk::outputP0());
 
   if (is_serial_no_op()) {
     print_serial_no_op_message();
@@ -132,14 +133,14 @@ bool LifeCycle::rebalance_will_corrupt_data(const stk::io::StkMeshIoBroker & ioB
   if (isRebalancing && sameInputAndOutputFile && sameInputAndOutputProcCount) {
     if (hasTransientFieldData) {
       willCorruptData = true;
-      sierra::Env::outputP0()
+      stk::outputP0()
           << "Aborting rebalance: Overwriting input files that contain transient fields will" << std::endl
           << "lead to data corruption.  Please specify a different outputDirectory." << std::endl;
     }
 
     if (has64BitIds) {
       willCorruptData = true;
-      sierra::Env::outputP0()
+      stk::outputP0()
           << "Aborting rebalance: Overwriting input files that contain 64-bit IDs will" << std::endl
           << "lead to data corruption.  Please specify a different outputDirectory." << std::endl;
     }
@@ -162,7 +163,7 @@ void LifeCycle::balance()
   io.write(mesh);
 
   DiagnosticsPrinter diagPrinter(m_comm, m_settings.get_num_output_processors());
-  diagPrinter.print(sierra::Env::outputP0());
+  diagPrinter.print(stk::outputP0());
 }
 
 void LifeCycle::rebalance()
@@ -187,26 +188,26 @@ void LifeCycle::rebalance()
   stk::balance::rebalance(ioBroker, m_settings);
 
   DiagnosticsPrinter diagPrinter(m_comm, m_settings.get_num_output_processors());
-  diagPrinter.print(sierra::Env::outputP0());
+  diagPrinter.print(stk::outputP0());
 }
 
 void LifeCycle::set_output_streams()
 {
   if (m_isProc0) {
     const std::string & logName = m_settings.get_log_filename();
     if (logName == "cout"  || logName == "cerr") {
-      stk::EnvData::instance().m_outputP0 = stk::get_log_ostream(logName);
+      stk::set_outputP0(stk::get_log_ostream(logName));
     }
     else {
       stk::bind_output_streams("log=\"" + logName + "\"");
-      stk::EnvData::instance().m_outputP0 = stk::get_log_ostream("log");
+      stk::set_outputP0(stk::get_log_ostream("log"));
     }
   }
   else {
-    stk::EnvData::instance().m_outputP0 = &stk::EnvData::instance().m_outputNull;
+    //stk::outputP0() is already a null output stream by default on other MPI ranks.
   }
 
-  Ioss::Utils::set_output_stream(sierra::Env::outputP0());
+  Ioss::Utils::set_output_stream(stk::outputP0());
 }
 
 void LifeCycle::print_parse_error(const char* what) const
@@ -225,7 +226,7 @@ void LifeCycle::print_balance_error(const char* what) const
 
 void LifeCycle::print_serial_no_op_message() const
 {
-  sierra::Env::outputP0()
+  stk::outputP0()
     << "Aborting balance: Rewriting the same input serial mesh file.  Please specify" << std::endl
     << "a different outputDirectory if you wish to copy the input file to an output" << std::endl
     << "file of the same name." << std::endl;

packages/stk/stk_doc_tests/stk_io/readInitialConditionNodalSubset.cpp

@@ -90,8 +90,9 @@ TEST(StkMeshIoBrokerHowTo, readInitialConditionNodalSubset)
     stk::mesh::MetaData &meta_data = stkIo.meta_data();
 
     // Declare the nodal "temperature" field. Exists on all nodes.
+    constexpr int numStates = 1;
     stk::mesh::Field<double> &temperature =
-        stkIo.meta_data().declare_field<double>(stk::topology::NODE_RANK, appFieldName,1);
+        stkIo.meta_data().declare_field<double>(stk::topology::NODE_RANK, appFieldName,numStates);
 
     // "NodeBlock_1" is the name of the node field on the input mesh.
     stk::io::MeshField mf(temperature, dbFieldNameShell);

packages/stk/stk_integration_tests/stk_balance/IntegrationTestCoincidentElems.cpp

@@ -91,6 +91,8 @@ class CoincidentElems : public stk::unit_test_util::MeshFixture
 
 TEST_F(CoincidentElems, balance_coincidentsNotSplit)
 {
+  if (stk::parallel_machine_size(MPI_COMM_WORLD) != 2) { GTEST_SKIP(); }
+
   setup_empty_mesh(stk::mesh::BulkData::NO_AUTO_AURA);
   std::string meshDesc =
       "0,1,HEX_8,1,2,3,4,5,6,7,8\n"

packages/stk/stk_io/example/io_mesh.cpp

@@ -47,8 +47,7 @@
 #include <stk_mesh/base/CreateFaces.hpp>
 #include <stk_util/Version.hpp>                                 // for versi...
 #include <stk_util/command_line/CommandLineParserParallel.hpp>  // for Comma...
-#include <stk_util/environment/Env.hpp>                         // for outputP0
-#include <stk_util/environment/EnvData.hpp>                     // for EnvData
+#include <stk_util/parallel/OutputStreams.hpp>
 #include <stk_util/environment/LogWithTimeAndMemory.hpp>        // for log_w...
 #include <stk_util/environment/memory_util.hpp>                 // for get_c...
 #include <stk_util/parallel/Parallel.hpp>                       // for paral...
@@ -81,10 +80,7 @@
 
 void set_output_streams(MPI_Comm comm)
 {
-  if (stk::parallel_machine_rank(comm) != 0) {
-    stk::EnvData::instance().m_outputP0 = &stk::EnvData::instance().m_outputNull;
-  }
-  Ioss::Utils::set_output_stream(sierra::Env::outputP0());
+  Ioss::Utils::set_output_stream(stk::outputP0());
 }
 
 class IoMeshDriver
@@ -289,14 +285,14 @@ class IoMeshDriver
     // For each global field name on the input database, determine the type of the field
     // and define that same global field on the results, restart, history, and heartbeat outputs.
     if (!global_fields.empty()) {
-      sierra::Env::outputP0() << "Adding " << global_fields.size() << " global fields:\n";
+      stk::outputP0() << "Adding " << global_fields.size() << " global fields:\n";
     }
 
     auto io_region = ioBroker.get_input_ioss_region();
 
     for (size_t i=0; i < global_fields.size(); i++) {
       const Ioss::Field &input_field = io_region->get_fieldref(global_fields[i]);
-      sierra::Env::outputP0() << "\t" << input_field.get_name() << " of type " << input_field.raw_storage()->name() << "\n";
+      stk::outputP0() << "\t" << input_field.get_name() << " of type " << input_field.raw_storage()->name() << "\n";
 
       if (input_field.raw_storage()->component_count() == 1) {
 	double val = 0.0;
@@ -446,7 +442,7 @@ class IoMeshDriver
       ioBroker.property_add(Ioss::Property("DECOMPOSITION_METHOD", decomp_method));
     }
     else {
-      sierra::Env::outputP0()<<"decomposition not specified, defaulting to file-per-processor mode for mesh-read."<<std::endl;
+      stk::outputP0()<<"decomposition not specified, defaulting to file-per-processor mode for mesh-read."<<std::endl;
     }
 
     if (compose_output) {
@@ -552,10 +548,10 @@ int main(int argc, const char** argv)
       returnCode = 1;
       break;
     case stk::CommandLineParser::ParseHelpOnly:
-      sierra::Env::outputP0() << cmdLine.get_usage() << std::endl;
+      stk::outputP0() << cmdLine.get_usage() << std::endl;
       break;
     case stk::CommandLineParser::ParseVersionOnly:
-      sierra::Env::outputP0() << "STK Version: " << stk::version_string() << std::endl;
+      stk::outputP0() << "STK Version: " << stk::version_string() << std::endl;
       break;
     default: break;
     }

packages/stk/stk_io/stk_io/FillMesh.cpp

@@ -21,11 +21,9 @@ void fill_mesh_preexisting(stk::io::StkMeshIoBroker & stkIo,
     stkIo.add_mesh_database(meshSpec, purpose);
     stkIo.create_input_mesh();
     stkIo.add_all_mesh_fields_as_input_fields();
-    stkIo.populate_bulk_data();
-
-    if(stkIo.check_integer_size_requirements() == 8) {
-        bulkData.set_large_ids_flag(true);
-    }
+    const bool delayFieldDataAllocation = true;
+    stkIo.populate_mesh(delayFieldDataAllocation);
+    stkIo.populate_field_data();
 }
 
 void fill_mesh_with_auto_decomp(const std::string &meshSpec, stk::mesh::BulkData &bulkData, stk::io::StkMeshIoBroker &stkIo)

packages/stk/stk_io/stk_io/IOHelpers.cpp

@@ -180,6 +180,14 @@ void communicate_shared_side_entity_fields(const stk::mesh::BulkData& bulk,
     }
 }
 
+stk::mesh::EntityRank get_side_rank(Ioss::Region* region, Ioss::SideBlock *block)
+{
+    bool useShellAllFaceSides = region->property_exists("ENABLE_ALL_FACE_SIDES_SHELL");
+    int par_dimen = block->topology()->parametric_dimension();
+    stk::mesh::EntityRank side_rank = par_dimen == 1 ? stk::topology::EDGE_RANK : stk::topology::FACE_RANK;
+    return (block->parent_element_topology()->is_shell() && useShellAllFaceSides) ? stk::topology::FACE_RANK : side_rank;
+}
+
 template <typename INT>
 void process_surface_entity_df(const Ioss::SideSet* sset, stk::mesh::BulkData & bulk)
 {
@@ -215,7 +223,7 @@ void process_surface_entity_df(const Ioss::SideSet* sset, stk::mesh::BulkData &
             //       be the same and this could fail (a sideset of mixed edges and faces)
             int par_dimen = block->topology()->parametric_dimension();
 
-            stk::mesh::EntityRank side_rank = par_dimen == 1 ? stk::topology::EDGE_RANK : stk::topology::FACE_RANK;
+            stk::mesh::EntityRank side_rank = get_side_rank(region, block);
 
             // Would be nice to do:
             //    std::vector<stk::mesh::Entity> sides ;
@@ -242,15 +250,15 @@ void process_surface_entity_df(const Ioss::SideSet* sset, stk::mesh::BulkData &
                 stk::topology elemTopo = bulk.bucket(elem).topology();
                 if(par_dimen == 0)
                 {
-                  stk::topology faceTopo = elemTopo.sub_topology(elemTopo.side_rank(), elemSide);
+                  stk::topology sideTopo = elemTopo.sub_topology(elemTopo.side_rank(elemSide), elemSide);
 
-                  Ioss::ElementTopology *ioss_topo = Ioss::ElementTopology::factory(faceTopo.name(), false);
+                  Ioss::ElementTopology *ioss_topo = Ioss::ElementTopology::factory(sideTopo.name(), false);
                   par_dimen = ioss_topo->parametric_dimension();
-                  side_rank = par_dimen == 1 ? stk::topology::EDGE_RANK : stk::topology::FACE_RANK;
+                  side_rank = get_side_rank(region, block);
                 }
                 STKIORequire(par_dimen == 1 || par_dimen == 2);
 
-                if (par_dimen == 1) {
+                if (par_dimen == 1 && side_rank == stk::topology::EDGE_RANK) {
                   // conversion from face ordinal to edge ordinal for shells
                   if (elemTopo.is_shell()) {
                     elemSide -= elemTopo.num_faces();