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refactor: some more details for mesh import, unify createChild log messages #3476

Merged
merged 6 commits into from
Dec 13, 2024
Merged

refactor: some more details for mesh import, unify createChild log messages #3476

merged 6 commits into from
Dec 13, 2024

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paveltomin
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example output:

Num ranks: 8
GEOS version: 1.1.0 (develop, sha1: b56762c29)
  - c++ compiler: gcc 11.4.0
  - MPI version: Open MPI v4.1.2, package: Debian OpenMPI, ident: 4.1.2, repo rev: v4.1.2, Nov 24, 2021
  - HDF5 version: 1.12.1
  - Conduit version: 0.9.2
  - VTK version: 9.3.1
  - RAJA version: 2024.7.0
  - umpire version: 2024.07.0
  - chai version: 2024.7.0
  - METIS version: 5.1
  - PARAMETIS version: 4.0
  - scotch version: 7.0.3
  - superlu_dist version: 6.3.0
  - suitesparse version: 5.7.9
  - hypre version: 2.32.0
  - Python3 version: 3.10.12
Started at 2024-12-05 16:53:36.596858600
Opened XML file: /home/ptls/GEOS/BB/run_coupled_multiphase_well_seq.xml
Included additionnal XML file: /home/ptls/GEOS/BB/numerical_methods.xml
Included additionnal XML file: /home/ptls/GEOS/BB/poromech_reservoir_solver_seq.xml
Included additionnal XML file: /home/ptls/GEOS/BB/mech_solver.xml
Included additionnal XML file: /home/ptls/GEOS/BB/reservoir_solver.xml
Included additionnal XML file: /home/ptls/GEOS/BB/flow_solver.xml
Included additionnal XML file: /home/ptls/GEOS/BB/mesh_and_wells.xml
Included additionnal XML file: /home/ptls/GEOS/BB/constitutive.xml
Included additionnal XML file: /home/ptls/GEOS/BB/hydrostatic_equilibrium.xml
Included additionnal XML file: /home/ptls/GEOS/BB/mech_init_seq.xml
Included additionnal XML file: /home/ptls/GEOS/BB/mech_bc.xml
Included additionnal XML file: /home/ptls/GEOS/BB/statistics.xml
Included additionnal XML file: /home/ptls/GEOS/BB/output.xml
Events: adding PeriodicEvent solverApplications
FiniteElements: adding FiniteElementSpace FE1
FiniteVolume: adding TwoPointFluxApproximation TPFA
Solvers: adding CompositionalMultiphaseReservoirPoromechanics poromechanicsReservoirSolver
Solvers: adding SolidMechanics_LagrangianFEM mechanicsSolver
Solvers: adding CompositionalMultiphaseReservoir reservoirSolver
Solvers: adding CompositionalMultiphaseFVM flowSolver
Solvers: adding CompositionalMultiphaseWell wellSolver
Mesh: adding VTKMesh mesh
mesh: adding InternalWell well
well: adding Perforation well_perf
Functions: adding TableFunction co2Conc
Functions: adding TableFunction watConc
Functions: adding TableFunction temp
FieldSpecifications: adding HydrostaticEquilibrium initialization
Events: adding SoloEvent mechInit
Tasks: adding CompositionalMultiphaseReservoirPoromechanicsInitialization mechInit
FieldSpecifications: adding FieldSpecification I_min
FieldSpecifications: adding FieldSpecification I_max
FieldSpecifications: adding FieldSpecification J_min
FieldSpecifications: adding FieldSpecification J_max
FieldSpecifications: adding FieldSpecification K_max
Tasks: adding CompositionalMultiphaseStatistics flowStatistics
Tasks: adding SolidMechanicsStatistics mechStatistics
Events: adding PeriodicEvent statistics
statistics: adding PeriodicEvent flowStatistics
statistics: adding PeriodicEvent mechStatistics
Outputs: adding VTK vtkOutput
Events: adding PeriodicEvent outputs
Constitutive: adding PorousElasticIsotropic porousRock
Constitutive: adding ElasticIsotropic rock
Constitutive: adding BiotPorosity rockPorosity
Constitutive: adding ConstantPermeability rockPermeability
Constitutive: adding CO2BrinePhillipsFluid brine
Constitutive: adding BrooksCoreyRelativePermeability relPerm
ElementRegions: adding CellElementRegion Domain
ElementRegions: adding WellElementRegion WellRegion
Functions: adding TableFunction brine_phaseModel1_PhillipsBrineDensity_sat_density_table
Functions: adding TableFunction brine_phaseModel1_PhillipsBrineDensity_sat_pressure_table
Functions: adding TableFunction brine_phaseModel1_PhillipsBrineDensity_table
Functions: adding TableFunction brine_phaseModel1_PhillipsBrineViscosity_table
Functions: adding TableFunction brine_phaseModel2_SpanWagnerCO2Density_table
Functions: adding TableFunction brine_phaseModel2_FenghourCO2Viscosity_table
CO2Solubility: 3 negative solubility values encountered. These will be truncated to zero.
Check out report table with max 5 values.
  Pressure (Pa) Temperature (C) CO2 solubility (mol/kg) H2O solubility (mol/kg) 
         101325             102            -0.000895723                       0 
         101325             112             -0.00547276                       0 
         101325             122              -0.0110234                       0 
Functions: adding TableFunction brine_CO2Solubility_co2Dissolution_table
Functions: adding TableFunction brine_CO2Solubility_waterVaporization_table
poromechanicsReservoirSolver: found CompositionalMultiphaseReservoir solver named reservoirSolver
poromechanicsReservoirSolver: found SolidMechanics_LagrangianFEM solver named mechanicsSolver

-------------------------------------------------------------------------------------
|                          mechanicsSolver: linear solver                           |
-------------------------------------------------------------------------------------
|  Parameter                                                      |  Value          |
-------------------------------------------------------------------------------------
|  Log level                                                      |  1              |
|  Linear solver type                                             |  gmres          |
|  Preconditioner type                                            |  amg            |
|  Stop if error                                                  |  1              |
|  Maximum iterations                                             |  200            |
|  Maximum iterations before restart                              |  200            |
|  Use adaptive tolerance                                         |  0              |
|  Relative convergence tolerance                                 |  0.0001         |
|  AMG                                                            |                 |
|    Smoother sweeps                                              |  1              |
|    Smoother type                                                |  l1sgs          |
|    Relaxation factor for the smoother                           |  1              |
|    Coarsest level solver/smoother type                          |  direct         |
|    Coarsening algorithm                                         |  HMIS           |
|    Interpolation algorithm                                      |  extendedI      |
|    Interpolation maximum number of nonzeros per row             |  4              |
|    Number of functions                                          |  1              |
|    Number of paths for aggressive coarsening                    |  1              |
|    Number of levels for aggressive coarsening                   |  0              |
|    Aggressive interpolation algorithm                           |  multipass      |
|    Strength-of-connection threshold                             |  0.8            |
|    Apply separate component filter for multi-variable problems  |  0              |
|    Near null space approximation                                |  constantModes  |
-------------------------------------------------------------------------------------



--------------------------------------------------
|         reservoirSolver: linear solver         |
--------------------------------------------------
|  Parameter                          |  Value   |
--------------------------------------------------
|  Log level                          |  1       |
|  Linear solver type                 |  gmres   |
|  Preconditioner type                |  mgr     |
|  Stop if error                      |  1       |
|  Maximum iterations                 |  200     |
|  Maximum iterations before restart  |  200     |
|  Use adaptive tolerance             |  0       |
|  Relative convergence tolerance     |  0.0001  |
--------------------------------------------------


reservoirSolver: found CompositionalMultiphaseFVM solver named flowSolver
reservoirSolver: found CompositionalMultiphaseWell solver named wellSolver

--------------------------------------------------
|           flowSolver: linear solver            |
--------------------------------------------------
|  Parameter                          |  Value   |
--------------------------------------------------
|  Log level                          |  1       |
|  Linear solver type                 |  gmres   |
|  Preconditioner type                |  mgr     |
|  Stop if error                      |  1       |
|  Maximum iterations                 |  200     |
|  Maximum iterations before restart  |  200     |
|  Use adaptive tolerance             |  0       |
|  Relative convergence tolerance     |  0.0001  |
--------------------------------------------------


Functions: adding TableFunction wellControl_ConstantBHP_table
Functions: adding TableFunction wellControl_ConstantTotalRate_table
Functions: adding TableFunction wellControl_ConstantPhaseRate_table
Functions: adding TableFunction wellControl_ConstantMassRate_table
Functions: adding TableFunction WellControls_OpenStatus_table
VTKMesh 'mesh': reading the dataset...
VTKMesh 'mesh': reading mesh from /home/ptls/GEOS/BB/BB_base.vtu
[PW0BMYGN:05471] 7 more processes have sent help message help-btl-vader.txt / cma-permission-denied
[PW0BMYGN:05471] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
VTKMesh 'mesh': redistributing mesh...
Generating global Ids from VTK mesh
Rank 0: Local mesh size: 334073
VTKMesh 'mesh': finding neighbor ranks...
Rank 1: Local mesh size: 338212
Rank 2: Local mesh size: 349243
Rank 7: Local mesh size: 345264
Rank 4: Local mesh size: 340307
Rank 6: Local mesh size: 345318
Rank 3: Local mesh size: 355210
Rank 5: Local mesh size: 348593
VTKMesh 'mesh': done!
VTKMesh 'mesh': generating GEOS mesh data structure
VTKMesh 'mesh': preprocessing...
VTKMesh 'mesh': writing nodes...
VTKMesh 'mesh': writing cells...
Importing cell block 11_hexahedra
VTKMesh 'mesh': writing surfaces...
Importing surface 4
Importing surface 3
Importing surface 2
Importing surface 5
Importing surface 7
Importing surface 6
VTKMesh 'mesh': building connectivity maps...
VTKMesh 'mesh': done!
Number of nodes: 2677338
  Number of elems: 2756220
          Polygon:  158820
             C3D8: 2597400
Load balancing:    min    avg    max
(element/rank): 334073 344527 355210

-----------------------------------------------------------------------------
|                         Well 'well' Element Table                         |
-----------------------------------------------------------------------------
|  Element no.  |   CoordX  |    CoordY  |  CoordZ  |     Prev  |     Next  |
|               |           |            |          |  Element  |  Element  |
-----------------------------------------------------------------------------
|            0  |  -410500  |  -3274500  |   -2165  |           |           |
-----------------------------------------------------------------------------



-------------------------------------------------------------------------
|                     Well 'well' Perforation Table                     |
-------------------------------------------------------------------------
|  Perforation no.  |                 Coordinates  |  Well element no.  |
-------------------------------------------------------------------------
|                0  |  [-410500, -3274500, -2230]  |                 0  |
-------------------------------------------------------------------------


MPI Partition information:
  MeshBody: mesh MeshLevel: TPFA

  |------------------------------------------------------------------------------------------------------------------------------------------------|
  |                |             Nodes             |             Edges             |             Faces             |             Elems             |
  |------------------------------------------------------------------------------------------------------------------------------------------------|
  |min(local/total)|             0.91              |             0.92              |             0.94              |             0.95              | 
  |max(local/total)|             0.97              |             0.97              |             0.97              |             0.97              | 
  |------------------------------------------------------------------------------------------------------------------------------------------------|
  |      Rank      |     local     |     ghost     |     local     |     ghost     |     local     |     ghost     |     local     |     ghost     |
  |----------------|---------------|---------------|---------------|---------------|---------------|---------------|---------------|---------------|
  |            min |       328,807 |         9,821 |       970,635 |        29,197 |       954,599 |        28,930 |       312,933 |         9,554 |
  |            max |       342,214 |        33,033 |     1,022,073 |        84,451 |     1,017,444 |        70,143 |       337,585 |        18,724 |
  |------------------------------------------------------------------------------------------------------------------------------------------------|
  |              0 |       328,970 |        10,820 |       970,635 |        32,156 |       954,599 |        31,852 |       312,933 |        10,516 | 
  |              1 |       330,889 |        22,700 |       982,182 |        60,921 |       971,772 |        53,928 |       320,479 |        15,706 | 
  |              3 |       342,214 |        33,033 |     1,022,073 |        84,451 |     1,017,444 |        70,143 |       337,585 |        18,724 | 
  |              2 |       340,565 |        12,441 |     1,007,353 |        34,565 |       993,155 |        31,912 |       326,367 |         9,787 | 
  |              5 |       335,364 |        27,581 |     1,001,754 |        69,835 |       997,318 |        57,276 |       330,927 |        15,020 | 
  |              6 |       336,240 |        24,671 |     1,000,610 |        64,797 |       992,518 |        55,810 |       328,148 |        15,683 | 
  |              4 |       334,291 |         9,821 |       986,639 |        29,197 |       970,639 |        28,930 |       318,290 |         9,554 | 
  |------------------------------------------------------------------------------------------------------------------------------------------------|
  |              7 |       328,807 |        21,201 |       980,301 |        52,483 |       974,165 |        41,629 |       322,671 |        10,346 | 
  MeshBody: mesh MeshLevel: FE1

  |------------------------------------------------------------------------------------------------------------------------------------------------|
  |                |             Nodes             |             Edges             |             Faces             |             Elems             |
  |------------------------------------------------------------------------------------------------------------------------------------------------|
  |min(local/total)|             0.91              |             0.92              |             0.94              |             0.95              | 
  |max(local/total)|             0.97              |             0.97              |             0.97              |             0.97              | 
  |------------------------------------------------------------------------------------------------------------------------------------------------|
  |      Rank      |     local     |     ghost     |     local     |     ghost     |     local     |     ghost     |     local     |     ghost     |
  |----------------|---------------|---------------|---------------|---------------|---------------|---------------|---------------|---------------|
  |            min |       328,807 |         9,821 |       970,635 |        29,197 |       954,599 |        28,930 |       312,933 |         9,554 |
  |            max |       342,214 |        33,033 |     1,022,073 |        84,451 |     1,017,444 |        70,143 |       337,585 |        18,724 |
  |------------------------------------------------------------------------------------------------------------------------------------------------|
  |              0 |       328,970 |        10,820 |       970,635 |        32,156 |       954,599 |        31,852 |       312,933 |        10,516 | 
  |              1 |       330,889 |        22,700 |       982,182 |        60,921 |       971,772 |        53,928 |       320,479 |        15,706 | 
  |              2 |       340,565 |        12,441 |     1,007,353 |        34,565 |       993,155 |        31,912 |       326,367 |         9,787 | 
  |              3 |       342,214 |        33,033 |     1,022,073 |        84,451 |     1,017,444 |        70,143 |       337,585 |        18,724 | 
  |              5 |       335,364 |        27,581 |     1,001,754 |        69,835 |       997,318 |        57,276 |       330,927 |        15,020 | 
  |              4 |       334,291 |         9,821 |       986,639 |        29,197 |       970,639 |        28,930 |       318,290 |         9,554 | 
  |              7 |       328,807 |        21,201 |       980,301 |        52,483 |       974,165 |        41,629 |       322,671 |        10,346 | 
  |------------------------------------------------------------------------------------------------------------------------------------------------|
  |              6 |       336,240 |        24,671 |     1,000,610 |        64,797 |       992,518 |        55,810 |       328,148 |        15,683 | 
regionQuadrature: meshBodyName, meshLevelName, regionName, subRegionName = mesh, Level0, Domain, 11_hexahedra
mesh/Level0/Domain/11_hexahedra/brine allocated 8 quadrature points
mesh/Level0/Domain/11_hexahedra/porousRock allocated 8 quadrature points
mesh/Level0/Domain/11_hexahedra/relPerm allocated 8 quadrature points
regionQuadrature: meshBodyName, meshLevelName, regionName, subRegionName = mesh, Level0, WellRegion, WellRegionUniqueSubRegion
mesh/Level0/WellRegion/WellRegionUniqueSubRegion/brine allocated 1 quadrature points
mesh/Level0/WellRegion/WellRegionUniqueSubRegion/relPerm allocated 1 quadrature points
mesh: importing field data from mesh dataset
  mesh level = Level0
  volumic fields on Domain/11_hexahedra
    DENSITY -> rock_density
    PERM -> rockPermeability_permeability
    PORO -> rockPorosity_referencePorosity
    bulkM -> rock_bulkModulus
    shearM -> rock_shearModulus
  mesh level = TPFA
  volumic fields on Domain/11_hexahedra
    DENSITY -> rock_density
    PERM -> rockPermeability_permeability
    PORO -> rockPorosity_referencePorosity
    bulkM -> rock_bulkModulus
    shearM -> rock_shearModulus
  mesh level = FE1
  volumic fields on Domain/11_hexahedra
    DENSITY -> rock_density
    PERM -> rockPermeability_permeability
    PORO -> rockPorosity_referencePorosity
    bulkM -> rock_bulkModulus
    shearM -> rock_shearModulus
Functions: adding TableFunction initialization_11_hexahedra_water_table

------------------------- TIMESTEP START -------------------------

@paveltomin paveltomin added type: cleanup / refactor Non-functional change (NFC) flag: ready for review flag: no rebaseline Does not require rebaseline labels Dec 5, 2024
@paveltomin paveltomin self-assigned this Dec 5, 2024
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@CusiniM, @MelReyCG, @andrea-borio, @castelletto1, @corbett5, @cssherman, @dkachuma, @rrsettgast, @ryar9534, and/or @wrtobin please review

@paveltomin paveltomin added ci: run CUDA builds Allows to triggers (costly) CUDA jobs ci: run integrated tests Allows to run the integrated tests in GEOS CI ci: run code coverage enables running of the code coverage CI jobs and removed flag: ready for review labels Dec 12, 2024
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codecov bot commented Dec 13, 2024 •
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Codecov Report

Attention: Patch coverage is 65.45455% with 19 lines in your changes missing coverage. Please review.

Project coverage is 56.89%. Comparing base (da4cd7f) to head (c6f0b81).
Report is 1 commits behind head on develop.

Files with missing lines Patch % Lines
src/coreComponents/mesh/MeshManager.cpp 42.30% 15 Missing ⚠️
src/coreComponents/events/EventBase.cpp 0.00% 1 Missing ⚠️
src/coreComponents/mesh/ExternalDataSourceBase.cpp 0.00% 1 Missing ⚠️
.../coreComponents/mesh/ExternalDataSourceManager.cpp 0.00% 1 Missing ⚠️
src/coreComponents/mesh/ParticleManager.cpp 0.00% 1 Missing ⚠️
Additional details and impacted files 
@@           Coverage Diff            @@
##           develop    #3476   +/-   ##
========================================
  Coverage    56.89%   56.89%           
========================================
  Files         1154     1154           
  Lines        99871    99878    +7     
========================================
+ Hits         56821    56830    +9     
+ Misses       43050    43048    -2

☔ View full report in Codecov by Sentry.
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@paveltomin paveltomin merged commit b5ea7ce into develop Dec 13, 2024
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@paveltomin paveltomin deleted the pt/log-impr branch December 13, 2024 17:47
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@untereiner untereiner untereiner approved these changes

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ci: run code coverage enables running of the code coverage CI jobs ci: run CUDA builds Allows to triggers (costly) CUDA jobs ci: run integrated tests Allows to run the integrated tests in GEOS CI flag: no rebaseline Does not require rebaseline type: cleanup / refactor Non-functional change (NFC)
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