Almost all working refs idaholab#15444

Fixup a couple of tests refs idaholab#15444

Remove debugging statement refs idaholab#15444

Clang format idaholab#15444

Fixup build error refs idaholab#15444

framework/include/base/MooseApp.h

@@ -891,6 +891,9 @@ class MooseApp : public ConsoleStreamInterface,
   /// Input file names used
   std::vector<std::string> _input_filenames;
 
+  /// Input file name used
+  std::string _input_filename;
+
   /// The output file basename
   std::string _output_file_base;
 
@@ -924,6 +927,9 @@ class MooseApp : public ConsoleStreamInterface,
   /// The PerfGraph object for this applciation
   PerfGraph _perf_graph;
 
+  /// The RankMap is a useful object for determining how
+  const RankMap _rank_map;
+
   /// Input parameter storage structure (this is a raw pointer so the destruction time can be explicitly controlled)
   InputParameterWarehouse * _input_parameter_warehouse;
 

framework/include/utils/MooseUtils.h

@@ -566,6 +566,7 @@ void MaterialPropertyStorageDump(
  * @param prefix The prefix to use for indenting
  * @param message The message that will be indented
  * @param color The color to apply to the prefix (default CYAN)
+ * @param indent_first_line If true this will indent the first line too (default)
  *
  * Takes a message like the following and indents it with another color code (see below)
  *
@@ -584,9 +585,14 @@ void MaterialPropertyStorageDump(
  *
  * Also handles single line color codes
  * COLOR_CYAN sub_app: 0 Nonline |R| = COLOR_GREEN 1.0e-10 COLOR_DEFAULT
+ *
+ * Not indenting the first line is useful in the case where the first line is actually finishing
+ * the line before it.
  */
-void
-indentMessage(const std::string & prefix, std::string & message, const char * color = COLOR_CYAN);
+void indentMessage(const std::string & prefix,
+                   std::string & message,
+                   const char * color = COLOR_CYAN,
+                   bool dont_indent_first_line = true);
 
 /**
  * remove ANSI escape sequences for teminal color from msg

framework/src/actions/CouplingFunctorCheckAction.C

@@ -30,7 +30,7 @@ CouplingFunctorCheckAction::validParams()
 }
 
 CouplingFunctorCheckAction::CouplingFunctorCheckAction(InputParameters parameters)
-    : Action(parameters)
+  : Action(parameters)
 {
   _name = "coupling_functor_check";
 }

framework/src/actions/MeshOnlyAction.C

@@ -36,7 +36,7 @@ MeshOnlyAction::act()
   auto & mesh_ptr = _app.actionWarehouse().mesh();
 
   // Print information about the mesh
-  _console << mesh_ptr->getMesh().get_info(/* verbosity = */ 2);
+  _console << mesh_ptr->getMesh().get_info(/* verbosity = */ 2) << std::endl;
 
   bool should_generate = false;
   // If no argument specified or if the argument following --mesh-only starts

framework/src/actions/SetupMeshCompleteAction.C

@@ -104,12 +104,16 @@ SetupMeshCompleteAction::act()
   }
   else
   {
-    TIME_SECTION("completeSetup", 2, "Completing Mesh Setup");
-
     // Prepare the mesh (may occur multiple times)
-    _mesh->prepare();
+    {
+      TIME_SECTION("completeSetupUndisplaced", 2, "Setting Up Undisplaced Mesh");
+      _mesh->prepare();
+    }
 
     if (_displaced_mesh)
+    {
+      TIME_SECTION("completeSetupDisplaced", 2, "Setting Up Displaced Mesh");
       _displaced_mesh->prepare();
+    }
   }
 }

framework/src/base/MooseApp.C

@@ -305,14 +305,14 @@ MooseApp::MooseApp(InputParameters parameters)
     _pars(parameters),
     _type(getParam<std::string>("_type")),
     _comm(getParam<std::shared_ptr<Parallel::Communicator>>("_comm")),
-    _rank_map(*_comm, _perf_graph),
     _file_base_set_by_user(false),
     _output_position_set(false),
     _start_time_set(false),
     _start_time(0.0),
     _global_time_offset(0.0),
     _output_warehouse(*this),
     _perf_graph(type() + " (" + name() + ')', *this, getParam<bool>("perf_graph_live_all")),
+    _rank_map(*_comm, _perf_graph),
     _input_parameter_warehouse(new InputParameterWarehouse()),
     _action_factory(*this),
     _action_warehouse(*this, _syntax, _action_factory),

framework/src/outputs/MaterialPropertyDebugOutput.C

@@ -49,7 +49,7 @@ MaterialPropertyDebugOutput::output(const ExecFlagType & /*type*/)
   }
 
   _console << "\n\nConsumed Material Properties:\n";
-  _console << std::setw(ConsoleUtils::console_field_width) << consumed.str() << '\n';
+  _console << std::setw(ConsoleUtils::console_field_width) << consumed.str() << std::endl;
 }
 
 void

framework/src/outputs/OutputWarehouse.C

@@ -29,8 +29,7 @@ OutputWarehouse::OutputWarehouse(MooseApp & app)
     _output_exec_flag(EXEC_CUSTOM),
     _force_output(false),
     _logging_requested(false),
-    _last_message_ended_in_newline(true),
-    _num_printed(0)
+    _last_message_ended_in_newline(true)
 {
   // Set the reserved names
   _reserved.insert("none"); // allows 'none' to be used as a keyword in 'outputs' parameter
@@ -216,8 +215,9 @@ OutputWarehouse::mooseConsole(std::ostringstream & buffer)
 
       // If that last message ended in newline then this one may need
       // to start with indenting
-      if (_last_message_ended_in_newline && _app.multiAppLevel() > 0)
-        MooseUtils::indentMessage(_app.name(), message);
+      // Note that we only indent the first line if the last message ended in new line
+      if (_app.multiAppLevel() > 0)
+        MooseUtils::indentMessage(_app.name(), message, COLOR_CYAN, _last_message_ended_in_newline);
 
       Moose::out << message << std::flush;
       buffer.clear();

framework/src/problems/FEProblemBase.C

@@ -985,7 +985,7 @@ FEProblemBase::initialSetup()
   // Call initialSetup on the MultiApps
   if (_multi_apps.hasObjects())
   {
-    TIME_SECTION("initialSetupMultiApps", 2, "Initializing MultiApps");
+    TIME_SECTION("initialSetupMultiApps", 2, "Initializing MultiApps", false);
     _multi_apps.initialSetup();
   }
 

framework/src/utils/MooseUtils.C

@@ -645,7 +645,8 @@ removeColor(std::string & msg)
 void
 indentMessage(const std::string & prefix,
               std::string & message,
-              const char * color /*= COLOR_CYAN*/)
+              const char * color /*= COLOR_CYAN*/,
+              bool indent_first_line)
 {
   // First we need to see if the message we need to indent (with color) also contains color codes
   // that span lines.
@@ -658,20 +659,28 @@ indentMessage(const std::string & prefix,
 
   bool ends_in_newline = message.empty() ? true : message.back() == '\n';
 
+  bool first = true;
+
   std::istringstream iss(message);
   for (std::string line; std::getline(iss, line);) // loop over each line
   {
     const static pcrecpp::RE match_color(".*(\\33\\[3\\dm)((?!\\33\\[3\\d)[^\n])*");
     pcrecpp::StringPiece line_piece(line);
     match_color.FindAndConsume(&line_piece, &color_code);
-    colored_message += color + prefix + ": " + curr_color + line;
+
+    if (!first || indent_first_line)
+      colored_message += color + prefix + ": " + curr_color;
+
+    colored_message += line;
 
     // Only add a newline to the last line if it had one to begin with!
     if (!iss.eof() || ends_in_newline)
       colored_message += "\n";
 
     if (!color_code.empty())
       curr_color = color_code; // remember last color of this line
+
+    first = false;
   }
   message = colored_message;
 }

framework/src/utils/PerfGraphLivePrint.C

@@ -99,7 +99,8 @@ PerfGraphLivePrint::printStats(PerfGraph::SectionIncrement & section_increment_s
       (_last_printed_increment &&
        _last_printed_increment != &section_increment_start)) // Print Finished
   {
-    if ((_last_printed_increment->_state == PerfGraph::IncrementState::printed &&
+    if ((_last_printed_increment &&
+         _last_printed_increment->_state == PerfGraph::IncrementState::printed &&
          _id_to_section_info[_last_printed_increment->_id]._print_dots))
       _console << '\n';
 
@@ -268,7 +269,7 @@ PerfGraphLivePrint::start()
       continue;
 
     // The last entry in the current execution list for convenience
-    _current_execution_list_last = _current_execution_list_end - 1 >= 0
+    _current_execution_list_last = static_cast<long int>(_current_execution_list_end) - 1 >= 0
                                        ? _current_execution_list_end - 1
                                        : MAX_EXECUTION_LIST_SIZE;
 

modules/contact/src/constraints/MechanicalContactConstraint.C

@@ -401,13 +401,14 @@ MechanicalContactConstraint::AugmentedLagrangianContactConverged()
   _communicator.max(converged);
 
   if (converged == 1)
-    _console
-      << "The Augmented Lagrangian contact tangential sliding enforcement is NOT satisfied " << std::endl;
+    _console << "The Augmented Lagrangian contact tangential sliding enforcement is NOT satisfied "
+             << std::endl;
   else if (converged == 2)
-    _console
-      << "The Augmented Lagrangian contact tangential sliding enforcement is NOT satisfied "  << std::endl;
+    _console << "The Augmented Lagrangian contact tangential sliding enforcement is NOT satisfied "
+             << std::endl;
   else if (converged == 3)
-    _console << "The Augmented Lagrangian contact frictional force enforcement is NOT satisfied "  << std::endl;
+    _console << "The Augmented Lagrangian contact frictional force enforcement is NOT satisfied "
+             << std::endl;
   else
     return true;
 

modules/geochemistry/src/outputs/GeochemicalModelInterrogator.C

@@ -267,7 +267,8 @@ GeochemicalModelInterrogator::outputTemperature(const std::string & eqm_species)
     rhs = -std::log10(getActivity(eqm_species));
   else
   {
-    _console << "Not enough activites known to compute equilibrium temperature for reaction\n  " << std::flush;
+    _console << "Not enough activites known to compute equilibrium temperature for reaction\n  "
+             << std::flush;
     outputReaction(eqm_species);
     return;
   }
@@ -280,8 +281,8 @@ GeochemicalModelInterrogator::outputTemperature(const std::string & eqm_species)
         rhs += _mgd.eqm_stoichiometry(row, i) * std::log10(getActivity(sp));
       else
       {
-        _console
-          << "Not enough activites known to compute equilibrium temperature for reaction\n  " << std::flush;
+        _console << "Not enough activites known to compute equilibrium temperature for reaction\n  "
+                 << std::flush;
         outputReaction(eqm_species);
         return;
       }

modules/misc/src/userobjects/RigidBodyModes3D.C

@@ -67,7 +67,8 @@ RigidBodyModes3D::RigidBodyModes3D(const InputParameters & parameters)
   if (_modes.size() > 6)
   {
     std::stringstream err;
-    err << "Expected between 0 and 6 rigid body modes, got " << _modes.size() << " instead" << std::endl;
+    err << "Expected between 0 and 6 rigid body modes, got " << _modes.size() << " instead"
+        << std::endl;
     mooseError(err.str());
   }
   for (std::set<std::string>::const_iterator it = _modes.begin(); it != _modes.end(); ++it)

modules/phase_field/src/userobjects/EBSDReader.C

@@ -337,8 +337,7 @@ EBSDReader::readFile()
     if (!data_quality_ok)
       _console << COLOR_YELLOW << "EBSD data may not be reliable"
                << "\n"
-               << COLOR_DEFAULT
-               << std::flush;
+               << COLOR_DEFAULT << std::flush;
 
     // compute eigen values and eigen vectors
     Eigen::EigenSolver<Eigen::MatrixXd> EigenSolver(quat_mat * weight * quat_mat.transpose());

modules/tensor_mechanics/src/materials/ADSingleVariableReturnMappingSolution.C

@@ -404,5 +404,6 @@ ADSingleVariableReturnMappingSolution::outputIterationSummary(std::stringstream
   if (iter_output)
     *iter_output << "In " << total_it << " iterations the residual went from "
                  << MetaPhysicL::raw_value(_initial_residual) << " to "
-                 << MetaPhysicL::raw_value(_residual) << " in '" << _svrms_name << "'." << std::endl;
+                 << MetaPhysicL::raw_value(_residual) << " in '" << _svrms_name << "'."
+                 << std::endl;
 }

modules/tensor_mechanics/src/userobjects/TensorMechanicsPlasticMohrCoulombMulti.C

@@ -68,7 +68,8 @@ TensorMechanicsPlasticMohrCoulombMulti::TensorMechanicsPlasticMohrCoulombMulti(
     mooseError("Value of 'shift' in TensorMechanicsPlasticMohrCoulombMulti must not be negative\n");
   if (_shift > _f_tol)
     _console << "WARNING: value of 'shift' in TensorMechanicsPlasticMohrCoulombMulti is probably "
-      "set too high" << std::endl;
+                "set too high"
+             << std::endl;
   if (LIBMESH_DIM != 3)
     mooseError("TensorMechanicsPlasticMohrCoulombMulti is only defined for LIBMESH_DIM=3");
   MooseRandom::seed(0);

modules/tensor_mechanics/src/userobjects/TensorMechanicsPlasticTensileMulti.C

@@ -59,7 +59,8 @@ TensorMechanicsPlasticTensileMulti::TensorMechanicsPlasticTensileMulti(
     mooseError("Value of 'shift' in TensorMechanicsPlasticTensileMulti must not be negative\n");
   if (_shift > _f_tol)
     _console << "WARNING: value of 'shift' in TensorMechanicsPlasticTensileMulti is probably set "
-      "too high" << std::endl;
+                "too high"
+             << std::endl;
   if (LIBMESH_DIM != 3)
     mooseError("TensorMechanicsPlasticTensileMulti is only defined for LIBMESH_DIM=3");
   MooseRandom::seed(0);

modules/tensor_mechanics/src/utils/MultiPlasticityDebugger.C

@@ -516,7 +516,8 @@ MultiPlasticityDebugger::checkSolution(const RankFourTensor & E_inv)
     L2_numer += Utility::pow<2>(orig_rhs[i] - fd_times_x[i]);
     L2_denom += Utility::pow<2>(orig_rhs[i] + fd_times_x[i]);
   }
-  Moose::err << "\nRelative L2norm of these is " << std::sqrt(L2_numer / L2_denom) / 0.5 << std::endl;
+  Moose::err << "\nRelative L2norm of these is " << std::sqrt(L2_numer / L2_denom) / 0.5
+             << std::endl;
 }
 
 void

test/tests/postprocessors/perf_graph_data/perf_graph.i

@@ -41,25 +41,25 @@
     type = PerfGraphData
     section_name = FEProblem::computeResidualInternal
     data_type = CALLS
-    execute_on = 'INITIAL TIMESTEP_END'
+    execute_on = 'TIMESTEP_END'
   []
   [self]
     type = PerfGraphData
     section_name = FEProblem::computeResidualInternal
     data_type = SELF
-    execute_on = 'INITIAL TIMESTEP_END'
+    execute_on = 'TIMESTEP_END'
   []
   [children]
     type = PerfGraphData
     section_name = FEProblem::computeResidualInternal
     data_type = CHILDREN
-    execute_on = 'INITIAL TIMESTEP_END'
+    execute_on = 'TIMESTEP_END'
   []
   [total]
     type = PerfGraphData
     section_name = FEProblem::computeResidualInternal
     data_type = TOTAL
-    execute_on = 'INITIAL TIMESTEP_END'
+    execute_on = 'TIMESTEP_END'
   []
 []