Merge branch 'matthewhoffman/mali/enable_thermal_solver' (PR #6559)

Activate MALI thermal solver and update configuration to be relevant to both AIS and GIS grids

This PR updates a number of details about the MALI configuration to
support both Antarctica and Greenland Ice Sheet configurations:
* Enables the MALI thermal solver, which is needed to allow evolving
  calving fronts, in preparation for enabling calving
* Adds new logic to make the albany_input.yaml file specific to a mesh.
  This is needed because AIS and GIS meshes use different solver
  boundary conditions that are specified in that file.
* Enables config_remove_icebergs and config_remove_small_islands, two
  options that improve convergence of the velocity solver and are
  typically used in standalone MALI simulations
* Adds additional fields to the MALI history files related to the now
  activated thermal solver, as well as ice-shelf basal melting. Also
  updates the MALI globalStats files to write out all global stats
  instead of the subset that was hardcoded before.
* Updates the
    ERS_Ld5.TL319_oQU240wLI_ais20.MPAS_LISIO_JRA1p5.mpaso-ocn_glcshelf
  test to the MALI ais8to30 grid that was recently added. When the mesh
  was added, the test was failing due to issues with the thermal solver,
  but those have been resolved between MALI thermal solver bug fix and
  improved iceberg handling #6547 and this PR, so we can now update that
  test to the newer mesh.

[NML] for all configurations with MALI
[non-BFB] for all configurations with active MALI

Author: jonbob

cime_config/tests.py

@@ -304,7 +304,7 @@
             "SMS.ne30_f19_g16_rx1.A",
             "ERS_Ld5.T62_oQU120.CMPASO-NYF",
             "ERS.f09_g16_g.MALISIA",
-            "ERS_Ld5.TL319_oQU240wLI_ais20.MPAS_LISIO_JRA1p5.mpaso-ocn_glcshelf",
+            "ERS_Ld5.TL319_oQU240wLI_ais8to30.MPAS_LISIO_JRA1p5.mpaso-ocn_glcshelf",
             "SMS_P12x2.ne4pg2_oQU480.WCYCL1850NS.allactive-mach_mods",
             "ERS_Ln9.ne4pg2_ne4pg2.F2010-MMF1.eam-mmf_crmout",
             )

components/mpas-albany-landice/bld/namelist_files/albany_input.ais20km.yaml

@@ -0,0 +1,231 @@
+%YAML 1.1
+---
+ANONYMOUS:
+
+# Discretization Description
+  Discretization:
+    #Exodus Output File Name: albany_output.exo
+
+  Piro:
+#   Nonlinear Solver Information
+    NOX:
+      Nonlinear Solver: Line Search Based
+      Line Search:
+        Full Step:
+          Full Step: 1.0e+00
+        Method: Backtrack
+      Solver Options:
+        Status Test Check Type: Minimal
+      Status Tests:
+        Test Type: Combo
+        Combo Type: OR
+        Number of Tests: 2
+        Test 0:
+          Test Type: Combo
+          Combo Type: AND
+          Number of Tests: 2
+          Test 0:
+            Test Type: NormF
+            Norm Type: Two Norm
+            Scale Type: Unscaled
+            Tolerance: 1.0e-03
+          Test 1:
+            Test Type: RelativeNormF
+            Norm Type: Two Norm
+            Tolerance: 0.9999
+        Test 1:
+          Test Type: MaxIters
+          Maximum Iterations: 100
+      Printing:
+        Output Precision: 3
+        Output Processor: 0
+        Output Information:
+          Error: true
+          Warning: true
+          Outer Iteration: true
+          Parameters: false
+          Details: false
+          Linear Solver Details: false
+          Stepper Iteration: true
+          Stepper Details: true
+          Stepper Parameters: true
+
+      Direction:
+        Method: Newton
+        Newton:
+          Forcing Term Method: Type 2
+          Rescue Bad Newton Solve: true
+          Linear Solver:
+            Write Linear System: false
+            Tolerance: 1.0e-8
+
+          Stratimikos Linear Solver:
+            Stratimikos:
+
+#             Linear Solver Information
+              Linear Solver Type: Belos
+              Linear Solver Types:
+                Belos:
+                  Solver Type: Block GMRES
+                  Solver Types:
+                    Block GMRES:
+                      Output Frequency: 20
+                      Output Style: 1
+                      Verbosity: 33
+                      Maximum Iterations: 200
+                      Block Size: 1
+                      Num Blocks: 200
+                      Flexible Gmres: false
+                  VerboseObject:
+                    Output File: none
+                    Verbosity Level: low
+
+#             Preconditioner Information
+              Preconditioner Type: MueLu
+              Preconditioner Types:
+
+                Ifpack2:
+                  Overlap: 1
+                  Prec Type: ILUT
+
+                MueLu:
+                  Matrix:
+                    PDE equations: 2
+                  Factories:
+                    myLineDetectionFact:
+                      factory: LineDetectionFactory
+                      'linedetection: orientation': coordinates
+                    mySemiCoarsenPFact1:
+                      factory: SemiCoarsenPFactory
+                      'semicoarsen: coarsen rate': 14
+                    UncoupledAggregationFact2:
+                      factory: UncoupledAggregationFactory
+                      'aggregation: ordering': graph
+                      'aggregation: max selected neighbors': 0
+                      'aggregation: min agg size': 3
+                      'aggregation: phase3 avoid singletons': true
+                    MyCoarseMap2:
+                      factory: CoarseMapFactory
+                      Aggregates: UncoupledAggregationFact2
+                    myTentativePFact2:
+                      'tentative: calculate qr': true
+                      factory: TentativePFactory
+                      Aggregates: UncoupledAggregationFact2
+                      CoarseMap: MyCoarseMap2
+                    mySaPFact2:
+                      'sa: eigenvalue estimate num iterations': 10
+                      'sa: damping factor': 1.33333e+00
+                      factory: SaPFactory
+                      P: myTentativePFact2
+                    myTransferCoordinatesFact:
+                      factory: CoordinatesTransferFactory
+                      CoarseMap: MyCoarseMap2
+                      Aggregates: UncoupledAggregationFact2
+                    myTogglePFact:
+                      factory: TogglePFactory
+                      'semicoarsen: number of levels': 2
+                      TransferFactories:
+                        P1: mySemiCoarsenPFact1
+                        P2: mySaPFact2
+                        Ptent1: mySemiCoarsenPFact1
+                        Ptent2: myTentativePFact2
+                        Nullspace1: mySemiCoarsenPFact1
+                        Nullspace2: myTentativePFact2
+                    myRestrictorFact:
+                      factory: TransPFactory
+                      P: myTogglePFact
+                    myToggleTransferCoordinatesFact:
+                      factory: ToggleCoordinatesTransferFactory
+                      Chosen P: myTogglePFact
+                      TransferFactories:
+                        Coordinates1: mySemiCoarsenPFact1
+                        Coordinates2: myTransferCoordinatesFact
+                    myRAPFact:
+                      factory: RAPFactory
+                      P: myTogglePFact
+                      R: myRestrictorFact
+                      TransferFactories:
+                        For Coordinates: myToggleTransferCoordinatesFact
+                    myRepartitionHeuristicFact:
+                      factory: RepartitionHeuristicFactory
+                      A: myRAPFact
+                      'repartition: min rows per proc': 3000
+                      'repartition: max imbalance': 1.327e+00
+                      'repartition: start level': 1
+                    myZoltanInterface:
+                      factory: ZoltanInterface
+                      A: myRAPFact
+                      Coordinates: myToggleTransferCoordinatesFact
+                      number of partitions: myRepartitionHeuristicFact
+                    myRepartitionFact:
+                      factory: RepartitionFactory
+                      A: myRAPFact
+                      Partition: myZoltanInterface
+                      'repartition: remap parts': true
+                      number of partitions: myRepartitionHeuristicFact
+                    myRebalanceProlongatorFact:
+                      factory: RebalanceTransferFactory
+                      type: Interpolation
+                      P: myTogglePFact
+                      Coordinates: myToggleTransferCoordinatesFact
+                      Nullspace: myTogglePFact
+                    myRebalanceRestrictionFact:
+                      factory: RebalanceTransferFactory
+                      type: Restriction
+                      R: myRestrictorFact
+                    myRebalanceAFact:
+                      factory: RebalanceAcFactory
+                      A: myRAPFact
+                      TransferFactories: { }
+                    mySmoother1:
+                      factory: TrilinosSmoother
+                      type: LINESMOOTHING_BANDEDRELAXATION
+                      'smoother: pre or post': both
+                      ParameterList:
+                        'relaxation: type': Gauss-Seidel
+                        'relaxation: sweeps': 1
+                        'relaxation: damping factor': 1.0
+                    mySmoother3:
+                      factory: TrilinosSmoother
+                      type: RELAXATION
+                      'smoother: pre or post': both
+                      ParameterList:
+                        'relaxation: type': Gauss-Seidel
+                        'relaxation: sweeps': 1
+                        'relaxation: damping factor': 1.0
+                    mySmoother4:
+                      factory: TrilinosSmoother
+                      type: RELAXATION
+                      'smoother: pre or post': pre
+                      ParameterList:
+                        'relaxation: type': Gauss-Seidel
+                        'relaxation: sweeps': 4
+                        'relaxation: damping factor': 1.0
+                  Hierarchy:
+                    max levels: 7
+                    'coarse: max size': 2000
+                    verbosity: None
+                    Finest:
+                      Smoother: mySmoother1
+                      CoarseSolver: mySmoother4
+                      P: myRebalanceProlongatorFact
+                      Nullspace: myRebalanceProlongatorFact
+                      CoarseNumZLayers: myLineDetectionFact
+                      LineDetection_Layers: myLineDetectionFact
+                      LineDetection_VertLineIds: myLineDetectionFact
+                      A: myRebalanceAFact
+                      Coordinates: myRebalanceProlongatorFact
+                      Importer: myRepartitionFact
+                    All:
+                      startLevel: 1
+                      Smoother: mySmoother4
+                      CoarseSolver: mySmoother4
+                      P: myRebalanceProlongatorFact
+                      Nullspace: myRebalanceProlongatorFact
+                      CoarseNumZLayers: myLineDetectionFact
+                      LineDetection_Layers: myLineDetectionFact
+                      LineDetection_VertLineIds: myLineDetectionFact
+                      A: myRebalanceAFact
+                      Coordinates: myRebalanceProlongatorFact
+                      Importer: myRepartitionFact
+