Merge pull request #28817 from lindsayad/petsc-update

Update petsc to 3.22.1-ish (includes some 3.23 features)

apptainer/petsc.def

@@ -91,4 +91,3 @@ From: {{ APPTAINER_FROM }}
 %files
     {{ MOOSE_DIR }}/scripts/configure_petsc.sh {{ ROOT_BUILD_DIR }}/scripts/configure_petsc.sh
     {{ MOOSE_DIR }}/scripts/update_and_rebuild_petsc.sh {{ ROOT_BUILD_DIR }}/scripts/update_and_rebuild_petsc.sh
-    {{ MOOSE_DIR }}/scripts/tao_restore_viewer.patch {{ ROOT_BUILD_DIR }}/scripts/tao_restore_viewer.patch

conda/libmesh/conda_build_config.yaml

@@ -3,8 +3,8 @@ mpi:
   - openmpi
 
 moose_petsc:
-  - moose-petsc 3.21.5 mpich_1
-  - moose-petsc 3.21.5 openmpi_1
+  - moose-petsc 3.22.1.193.g72c1e49ee3d mpich_0
+  - moose-petsc 3.22.1.193.g72c1e49ee3d openmpi_0
 
 moose_libmesh_vtk:
   - moose-libmesh-vtk 9.3.0 mpich_4

conda/libmesh/meta.yaml

@@ -4,7 +4,7 @@
 #
 # As well as any directions pertaining to modifying those files.
 # ALSO: Follow the directions in scripts/tests/versioner_hashes.yaml
-{% set build = 1 %}
+{% set build = 2 %}
 {% set version = "2024.10.17" %}
 
 package:

conda/moose-dev/conda_build_config.yaml

@@ -3,8 +3,8 @@ mpi:
   - openmpi
 
 moose_libmesh:
-  - moose-libmesh 2024.10.17 mpich_1
-  - moose-libmesh 2024.10.17 openmpi_1
+  - moose-libmesh 2024.10.17 mpich_2
+  - moose-libmesh 2024.10.17 openmpi_2
 
 moose_wasp:
   - moose-wasp 2024.11.13

conda/moose-dev/meta.yaml

@@ -2,7 +2,7 @@
 # REMEMBER TO UPDATE the .yaml files for the following packages:
 #   moose/conda_build_config.yaml
 # As well as any directions pertaining to modifying those files.
-{% set version = "2024.11.14" %}
+{% set version = "2024.11.15" %}
 
 package:
   name: moose-dev

conda/moose/conda_build_config.yaml

@@ -3,7 +3,7 @@ mpi:
   - openmpi
 
 moose_dev:
-  - moose-dev 2024.11.14
+  - moose-dev 2024.11.15
 
 #### Darwin SDK SYSROOT
 CONDA_BUILD_SYSROOT:                                        # [osx]

conda/petsc/meta.yaml

@@ -7,8 +7,8 @@
 #
 # As well as any directions pertaining to modifying those files.
 # ALSO: Follow the directions in scripts/tests/versioner_hashes.yaml
-{% set build = 1 %}
-{% set version = "3.21.5" %}
+{% set build = 0 %}
+{% set version = "3.22.1.193.g72c1e49ee3d" %}
 
 package:
   name: moose-petsc
@@ -20,7 +20,6 @@ source:
   - path: ../functions/retry_build.sh
   - patches:
       - no-cppflags-in-pkgconfig-cflags.patch
-      - ../../scripts/tao_restore_viewer.patch
 
 build:
   number: {{ build }}

framework/doc/packages_config.yml

@@ -10,7 +10,7 @@ maximum_python: 3.11
 mpich: 4.2.1
 openmpi: 4.1.6
 petsc_alt: 3.11.4
-petsc: 3.21.5
+petsc: 3.22.1.193.g72c1e49ee3d
 apptainer_rockylinux: 8.8.20230518
 apptainer_mpich: 3.4.3
 apptainer_gcc: 12.2.1

framework/include/problems/FEProblemBase.h

@@ -2333,9 +2333,9 @@ class FEProblemBase : public SubProblem, public Restartable
   void clearCurrentResidualVectorTags();
 
   /**
-   * Clear the current Jacobian vector tag data structure ... if someone creates it
+   * Clear the current Jacobian matrix tag data structure ... if someone creates it
    */
-  void clearCurrentJacobianVectorTags() {}
+  void clearCurrentJacobianMatrixTags() {}
 
   using SubProblem::doingPRefinement;
   virtual void doingPRefinement(bool doing_p_refinement,

framework/include/systems/DumpObjectsNonlinearSystem.h

@@ -28,7 +28,7 @@ class DumpObjectsNonlinearSystem : public NonlinearSystemBase
 
   virtual NonlinearSolver<Number> * nonlinearSolver() override { return NULL; }
   virtual void solve() override {}
-  virtual void stopSolve(const ExecFlagType &) override {}
+  virtual void stopSolve(const ExecFlagType &, const std::set<TagID> &) override {}
   virtual bool converged() override { return true; }
   virtual NumericVector<Number> & RHS() override { return *_dummy; }
   virtual SNES getSNES() override { return nullptr; }

framework/include/systems/LinearSystem.h

@@ -50,7 +50,8 @@ class LinearSystem : public SolverSystem, public PerfGraphInterface
   /**
    * Quit the current solve as soon as possible.
    */
-  virtual void stopSolve(const ExecFlagType & exec_flag) override;
+  virtual void stopSolve(const ExecFlagType & exec_flag,
+                         const std::set<TagID> & vector_tags_to_close) override;
 
   /**
    * Compute the right hand side and the system matrix of the system for given tags.

framework/include/systems/NonlinearEigenSystem.h

@@ -41,7 +41,8 @@ class NonlinearEigenSystem : public NonlinearSystemBase
   /**
    * Quit the current solve as soon as possible.
    */
-  virtual void stopSolve(const ExecFlagType & exec_flag) override;
+  virtual void stopSolve(const ExecFlagType & exec_flag,
+                         const std::set<TagID> & vector_tags_to_close) override;
 
   /**
    * Returns the current nonlinear iteration number.  In libmesh, this is

framework/include/systems/NonlinearSystem.h

@@ -37,7 +37,8 @@ class NonlinearSystem : public NonlinearSystemBase, public NonlinearImplicitSyst
   /**
    * Quit the current solve as soon as possible.
    */
-  virtual void stopSolve(const ExecFlagType & exec_flag) override;
+  virtual void stopSolve(const ExecFlagType & exec_flag,
+                         const std::set<TagID> & vector_tags_to_close) override;
 
   /**
    * Returns the current nonlinear iteration number.  In libmesh, this is

framework/include/systems/SolverSystem.h

@@ -36,7 +36,8 @@ class SolverSystem : public SystemBase
   /**
    * Quit the current solve as soon as possible.
    */
-  virtual void stopSolve(const ExecFlagType & exec_flag) = 0;
+  virtual void stopSolve(const ExecFlagType & exec_flag,
+                         const std::set<TagID> & vector_tags_to_close) = 0;
 
   /**
    * Set the solution to a given vector.

framework/src/problems/EigenProblem.C

@@ -296,8 +296,8 @@ EigenProblem::computeResidualTag(const NumericVector<Number> & soln,
   // specific system tags that we need for this instance
   _nl_eigen->disassociateDefaultVectorTags();
 
-  // Clear FE tags and first add the specific tag associated with the residual
-  _fe_vector_tags.clear();
+  // add the specific tag associated with the residual
+  mooseAssert(_fe_vector_tags.empty(), "This should be empty indicating a clean starting state");
   _fe_vector_tags.insert(tag);
 
   // Add any other user-added vector residual tags if they have associated vectors
@@ -312,6 +312,7 @@ EigenProblem::computeResidualTag(const NumericVector<Number> & soln,
 
   setCurrentNonlinearSystem(_nl_eigen->number());
   computeResidualTags(_fe_vector_tags);
+  _fe_vector_tags.clear();
 
   _nl_eigen->disassociateVectorFromTag(residual, tag);
 }
@@ -329,8 +330,8 @@ EigenProblem::computeResidualAB(const NumericVector<Number> & soln,
   // specific system tags that we need for this instance
   _nl_eigen->disassociateDefaultVectorTags();
 
-  // Clear FE tags and first add the specific tags associated with the residual
-  _fe_vector_tags.clear();
+  // add the specific tags associated with the residual
+  mooseAssert(_fe_vector_tags.empty(), "This should be empty indicating a clean starting state");
   _fe_vector_tags.insert(tagA);
   _fe_vector_tags.insert(tagB);
 
@@ -346,6 +347,7 @@ EigenProblem::computeResidualAB(const NumericVector<Number> & soln,
   _nl_eigen->setSolution(soln);
 
   computeResidualTags(_fe_vector_tags);
+  _fe_vector_tags.clear();
 
   _nl_eigen->disassociateVectorFromTag(residualA, tagA);
   _nl_eigen->disassociateVectorFromTag(residualB, tagB);

framework/src/problems/FEProblemBase.C

@@ -6265,10 +6265,10 @@ FEProblemBase::checkExceptionAndStopSolve(bool print_message)
       // SNESSetFunctionDomainError() or directly inserting NaNs in the
       // residual vector to let PETSc >= 3.6 return DIVERGED_NANORINF.
       if (_current_nl_sys)
-        _current_nl_sys->stopSolve(_current_execute_on_flag);
+        _current_nl_sys->stopSolve(_current_execute_on_flag, _fe_vector_tags);
 
       if (_current_linear_sys)
-        _current_nl_sys->stopSolve(_current_execute_on_flag);
+        _current_linear_sys->stopSolve(_current_execute_on_flag, _fe_vector_tags);
 
       // and close Aux system (we MUST do this here; see #11525)
       _aux->solution().close();
@@ -6300,8 +6300,9 @@ FEProblemBase::resetState()
   ADReal::do_derivatives = true;
   _current_execute_on_flag = EXEC_NONE;
 
+  // Clear the VectorTags and MatrixTags
   clearCurrentResidualVectorTags();
-  clearCurrentJacobianVectorTags();
+  clearCurrentJacobianMatrixTags();
 
   _safe_access_tagged_vectors = true;
   _safe_access_tagged_matrices = true;
@@ -6639,54 +6640,35 @@ FEProblemBase::computeResidual(const NumericVector<Number> & soln,
   _current_nl_sys->associateVectorToTag(residual, _current_nl_sys->residualVectorTag());
   const auto & residual_vector_tags = getVectorTags(Moose::VECTOR_TAG_RESIDUAL);
 
+  mooseAssert(_fe_vector_tags.empty(), "This should be empty indicating a clean starting state");
   // We filter out tags which do not have associated vectors in the current nonlinear
   // system. This is essential to be able to use system-dependent residual tags.
   selectVectorTagsFromSystem(*_current_nl_sys, residual_vector_tags, _fe_vector_tags);
 
   computeResidualInternal(soln, residual, _fe_vector_tags);
+  _fe_vector_tags.clear();
 }
 
 void
 FEProblemBase::computeResidualAndJacobian(const NumericVector<Number> & soln,
                                           NumericVector<Number> & residual,
                                           SparseMatrix<Number> & jacobian)
 {
-  // vector tags
-  {
-    _current_nl_sys->associateVectorToTag(residual, _current_nl_sys->residualVectorTag());
-    const auto & residual_vector_tags = getVectorTags(Moose::VECTOR_TAG_RESIDUAL);
-
-    // We filter out tags which do not have associated vectors in the current nonlinear
-    // system. This is essential to be able to use system-dependent residual tags.
-    selectVectorTagsFromSystem(*_current_nl_sys, residual_vector_tags, _fe_vector_tags);
-
-    setCurrentResidualVectorTags(_fe_vector_tags);
-  }
-
-  // matrix tags
-  {
-    _fe_matrix_tags.clear();
-
-    auto & tags = getMatrixTags();
-    for (auto & tag : tags)
-      _fe_matrix_tags.insert(tag.second);
-  }
-
   try
   {
     try
     {
       // vector tags
-      {
-        _current_nl_sys->associateVectorToTag(residual, _current_nl_sys->residualVectorTag());
-        const auto & residual_vector_tags = getVectorTags(Moose::VECTOR_TAG_RESIDUAL);
+      _current_nl_sys->associateVectorToTag(residual, _current_nl_sys->residualVectorTag());
+      const auto & residual_vector_tags = getVectorTags(Moose::VECTOR_TAG_RESIDUAL);
 
-        // We filter out tags which do not have associated vectors in the current nonlinear
-        // system. This is essential to be able to use system-dependent residual tags.
-        selectVectorTagsFromSystem(*_current_nl_sys, residual_vector_tags, _fe_vector_tags);
+      mooseAssert(_fe_vector_tags.empty(),
+                  "This should be empty indicating a clean starting state");
+      // We filter out tags which do not have associated vectors in the current nonlinear
+      // system. This is essential to be able to use system-dependent residual tags.
+      selectVectorTagsFromSystem(*_current_nl_sys, residual_vector_tags, _fe_vector_tags);
 
-        setCurrentResidualVectorTags(_fe_vector_tags);
-      }
+      setCurrentResidualVectorTags(_fe_vector_tags);
 
       // matrix tags
       {
@@ -6793,6 +6775,8 @@ FEProblemBase::computeResidualAndJacobian(const NumericVector<Number> & soln,
   }
 
   resetState();
+  _fe_vector_tags.clear();
+  _fe_matrix_tags.clear();
 }
 
 void

framework/src/systems/LinearSystem.C

@@ -281,13 +281,10 @@ LinearSystem::solve()
 }
 
 void
-LinearSystem::stopSolve(const ExecFlagType & /*exec_flag*/)
+LinearSystem::stopSolve(const ExecFlagType & /*exec_flag*/,
+                        const std::set<TagID> & vector_tags_to_close)
 {
   // We close the containers in case the solve restarts from a failed iteration
+  closeTaggedVectors(vector_tags_to_close);
   _linear_implicit_system.matrix->close();
-  _linear_implicit_system.rhs->close();
-  if (_rhs_time)
-    _rhs_time->close();
-  if (_rhs_non_time)
-    _rhs_non_time->close();
 }

framework/src/systems/NonlinearEigenSystem.C

@@ -385,7 +385,7 @@ NonlinearEigenSystem::attachSLEPcCallbacks()
 }
 
 void
-NonlinearEigenSystem::stopSolve(const ExecFlagType &)
+NonlinearEigenSystem::stopSolve(const ExecFlagType &, const std::set<TagID> &)
 {
   mooseError("did not implement yet \n");
 }

framework/src/systems/NonlinearSystem.C

@@ -231,29 +231,22 @@ NonlinearSystem::solve()
 }
 
 void
-NonlinearSystem::stopSolve(const ExecFlagType & exec_flag)
+NonlinearSystem::stopSolve(const ExecFlagType & exec_flag,
+                           const std::set<TagID> & vector_tags_to_close)
 {
   PetscNonlinearSolver<Real> & solver =
       static_cast<PetscNonlinearSolver<Real> &>(*sys().nonlinear_solver);
 
   if (exec_flag == EXEC_LINEAR || exec_flag == EXEC_POSTCHECK)
   {
-    auto ierr = SNESSetFunctionDomainError(solver.snes());
-    LIBMESH_CHKERR(ierr);
+    LibmeshPetscCall(SNESSetFunctionDomainError(solver.snes()));
 
     // Clean up by getting vectors into a valid state for a
-    // (possible) subsequent solve.  There may be more than just
-    // these...
-    _nl_implicit_sys.rhs->close();
-    if (_Re_time)
-      _Re_time->close();
-    _Re_non_time->close();
+    // (possible) subsequent solve.
+    closeTaggedVectors(vector_tags_to_close);
   }
   else if (exec_flag == EXEC_NONLINEAR)
-  {
-    auto ierr = SNESSetJacobianDomainError(solver.snes());
-    LIBMESH_CHKERR(ierr);
-  }
+    LibmeshPetscCall(SNESSetJacobianDomainError(solver.snes()));
   else
     mooseError("Unsupported execute flag: ", Moose::stringify(exec_flag));
 }

modules/porous_flow/test/tests/energy_conservation/heat01.i

@@ -68,7 +68,7 @@
     type = SMP
     full = true
     petsc_options_iname = '-ksp_type -pc_type -snes_atol -snes_rtol -snes_max_it'
-    petsc_options_value = 'bcgs bjacobi 1 1 10000'
+    petsc_options_value = 'bcgs bjacobi 1 .999 10000'
   []
 []
 

modules/porous_flow/test/tests/energy_conservation/heat02.i

@@ -117,7 +117,7 @@
     type = SMP
     full = true
     petsc_options_iname = '-ksp_type -pc_type -snes_atol -snes_rtol -snes_max_it'
-    petsc_options_value = 'bcgs bjacobi 1 1 10000'
+    petsc_options_value = 'bcgs bjacobi 1 .999 10000'
   []
 []
 

modules/porous_flow/test/tests/mass_conservation/mass01.i

@@ -90,7 +90,7 @@
     type = SMP
     full = true
     petsc_options_iname = '-ksp_type -pc_type -snes_atol -snes_rtol -snes_max_it'
-    petsc_options_value = 'bcgs bjacobi 1 1 10000'
+    petsc_options_value = 'bcgs bjacobi 1 .999 10000'
   []
 []
 

modules/porous_flow/test/tests/mass_conservation/mass02.i

@@ -107,7 +107,7 @@
     type = SMP
     full = true
     petsc_options_iname = '-ksp_type -pc_type -snes_atol -snes_rtol -snes_max_it'
-    petsc_options_value = 'bcgs bjacobi 1 1 10000'
+    petsc_options_value = 'bcgs bjacobi 1 .999 10000'
   []
 []
 

modules/richards/test/tests/mass/m01.i

@@ -102,7 +102,7 @@
     type = SMP
     full = true
     petsc_options_iname = '-ksp_type -pc_type -snes_atol -snes_rtol -snes_max_it'
-    petsc_options_value = 'bcgs bjacobi 1 1 10000'
+    petsc_options_value = 'bcgs bjacobi 1 .999 10000'
   [../]
 []
 

modules/richards/test/tests/mass/m_fu_01.i

@@ -102,7 +102,7 @@
     type = SMP
     full = true
     petsc_options_iname = '-ksp_type -pc_type -snes_atol -snes_rtol -snes_max_it'
-    petsc_options_value = 'bcgs bjacobi 1 1 10000'
+    petsc_options_value = 'bcgs bjacobi 1 .999 10000'
   [../]
 []