Undefined reference to...

[Giovar6]

Dear MOOSE users and developers,

I have an issue when compiling my application.
I would start telling that this application was working on another computer, but for different reasons, I had to move to a new computer where it is now installed Ubuntu 20.04.4
MOOSE is installed correctly, and I obtain PASS in most of the tests I have run after installing MOOSE.
Then I created a new application and imported all the code required to perform my simulations.
When I try to compile this new application, however, I get this error:

Checking if header needs updating: /home/giovanni/projects/moose/framework/include/base/MooseRevision.h...
Linking Executable /home/giovanni/projects/mufasa/mufasa-opt...
/home/giovanni/mambaforge3/envs/moose/bin/../lib/gcc/x86_64-conda-linux-gnu/10.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/giovanni/projects/mufasa/lib/libmufasa-opt.so: undefined reference to `InputParameters validParams()'
collect2: error: ld returned 1 exit status
make: *** [/home/giovanni/projects/moose/framework/app.mk:416: /home/giovanni/projects/mufasa/mufasa-opt] Errore 1

I think it is a linking problem, but I don't know how to solve it.
May it be something related to some components that are missing on the computer?
I hope you can help me with this problem.

Giovanni

[GiudGiud]

Hello

so it could be that you have an object where validParams is present in the header but not defined in the source. Usually we would get a little more information about this.

Can you clean up the repo (save everything with git commit, then git clean -xfd) then try to compile again?

Guillaume

[FatimahDzr]

Thank you very much for your reply. I created an application and with the implementation of the src and include files I was able to solve the "not registered" error. However, when I'm trying to run SinteringDilute.i code in tests files of moose, I get this error and I don't know how to fix it. I also tried different codes from the Crow application for sintering but still get the same error:

*** ERROR ***
The following error occurred in the object "MOOSE Problem", of type "FEProblem".

**Variable 'gr0' requested in initial condition 'gr0_IC' does not exist.**

Stack frames: 14
0: libMesh::print_trace(std::ostream&)
1: moose::internal::mooseErrorRaw(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)
2: callMooseErrorRaw(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, MooseApp*)
3: /mnt/c/moose/projects/moose/framework/libmoose-opt.so.0(+0x125d656) [0x7f5fd3a61656]
4: FEProblemBase::addInitialCondition(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, InputParameters&)
5: Action::timedAct()
6: ActionWarehouse::executeActionsWithAction(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)
7: ActionWarehouse::executeAllActions()
8: MooseApp::runInputFile()
9: MooseApp::run()
10: main
11: /lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f5fcbb99d90]
12: __libc_startr_main
13: ../bat-opt(+0x33ef) [0x55b9a441c3ef]
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1
:
system msg for write_line failure : Bad file descriptor

I should point out that the codes run on another old computer with an already compiled Crow application, but with my new application and the lastest version of moose, I get this error.
I would be grateful if you could help me to solve this problem.

[GiudGiud]

what does the input file look like?

[FatimahDzr]

this is the input:
#input file to test the GrandPotentialSinteringMaterial using the dilute energy profile

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 17
  ny = 10
  xmin = 0
  xmax = 660
  ymin = 0
  ymax = 380
[]

[GlobalParams]
  op_num = 2
  var_name_base = gr
  int_width = 40
[]

[Variables]
  [./w]
    [./InitialCondition]
      type = FunctionIC
      variable = w
      function = f_w
    [../]
  [../]
  [./phi]
  [../]
  [./PolycrystalVariables]
  [../]
[]

[AuxVariables]
  [./T]
    order = CONSTANT
    family = MONOMIAL
    [./InitialCondition]
      type = FunctionIC
      variable = T
      function = f_T
    [../]
  [../]
[]

[ICs]
  [./phi_IC]
    type = SpecifiedSmoothCircleIC
    variable = phi
    x_positions = '190 470'
    y_positions = '190 190'
    z_positions = '  0   0'
    radii = '150 150'
    invalue = 0
    outvalue = 1
  [../]
  [./gr0_IC]
    type = SmoothCircleIC
    variable = gr0
    x1 = 190
    y1 = 190
    z1 = 0
    radius = 150
    invalue = 1
    outvalue = 0
  [../]
  [./gr1_IC]
    type = SmoothCircleIC
    variable = gr1
    x1 = 470
    y1 = 190
    z1 = 0
    radius = 150
    invalue = 1
    outvalue = 0
  [../]
[]

[Functions]
  [./f_T]
    type = ConstantFunction
    value = 1600
  [../]
  [./f_w]
    type = ParsedFunction
    value = '1.515e-7 * x'
  [../]
[]

[Materials]
  # Free energy coefficients for parabolic curve
  [./kv]
    type = ParsedMaterial
    f_name = kv
    args = 'T'
    constant_names = 'a b'
    constant_expressions = '-0.025 1571.6'
    function = 'a*T + b'
  [../]
  # Diffusivity and mobilities
  [./chiD]
    type = GrandPotentialTensorMaterial
    f_name = chiD
    solid_mobility = L
    void_mobility = Lv
    chi = chi
    surface_energy = 19.7
    c = phi
    T = T
    D0 = 2.0e11
    GBmob0 = 1.4759e9
    Q = 2.77
    Em = 2.40
    bulkindex = 1
    gbindex = 20
    surfindex = 100
  [../]
  # Equilibrium vacancy concentration
  [./cs_eq]
    type = DerivativeParsedMaterial
    f_name = cs_eq
    args = 'gr0 gr1 T'
    constant_names = 'Ef Egb kB'
    constant_expressions = '2.69 2.1 8.617343e-5'
    function = 'bnds:=gr0^2 + gr1^2; cb:=exp(-Ef/kB/T); cgb:=exp(-(Ef-Egb)/kB/T);
                cb + 4.0*(cgb-cb)*(1.0 - bnds)^2'
  [../]
  # Everything else
  [./sintering]
    type = GrandPotentialSinteringMaterial
    chemical_potential = w
    void_op = phi
    Temperature = T
    surface_energy = 19.7
    grainboundary_energy = 9.86
    void_energy_coefficient = kv
    equilibrium_vacancy_concentration = cs_eq
    solid_energy_model = DILUTE
    outputs = exodus
  [../]

  # Concentration is only meant for output
  [./c]
    type = ParsedMaterial
    f_name = c
    material_property_names = 'hs rhos hv rhov'
    constant_names = 'Va'
    constant_expressions = '0.04092'
    function = 'Va*(hs*rhos + hv*rhov)'
    outputs = exodus
  [../]
[]

[Kernels]
  [./dt_gr0]
    type = TimeDerivative
    variable = gr0
  [../]
  [./dt_gr1]
    type = TimeDerivative
    variable = gr1
  [../]
  [./dt_phi]
    type = TimeDerivative
    variable = phi
  [../]
  [./dt_w]
    type = TimeDerivative
    variable = w
  [../]
[]

[AuxKernels]
  [./T_aux]
    type = FunctionAux
    variable = T
    function = f_T
  [../]
[]

[Executioner]
  type = Transient
  scheme = bdf2
  solve_type = JFNK
  dt = 1
  num_steps = 2
  nl_abs_tol = 1e-10
[]

[Outputs]
  exodus = true
[]

[GiudGiud]

This is probably just a name mismatch. Turn off the IC and run the input to just create the exodus output.
Then open it and look at the variable name. Maybe it's gr_0 instead of gr0

[ykvishal]

@FatimahDzr Recently, I (re)installed MOOSE, and your input file works perfectly. Here are the images of gr0 and gr1. May be something is wrong with your app.

[FatimahDzr]

thank you very much. Now I can run the moose sintering input files. However, in running the crow input files such as below, I hit an error regarding the "PolycrystalSinteringKernel". I found a header file for that to implement but I couldn't find any source file to make it run. I don't know if I can replace it with another kernel or not.

[GlobalParams]
  var_name_base = gr
  op_num = 2.0
  block = 0
  #displacements = 'disp_x disp_y disp_z'
  #use_displaced_mesh = true
  #outputs = exodus
[]

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 50
  ny = 40
  #nz = 15
  xmax = 100.0
  ymax = 80.0
  #zmax = 60.0
  #uniform_refine = 1
  elem_type = QUAD4
[]

[Variables]
  [./c]
  [../]
  [./w]
  [../]
  [./PolycrystalVariables]
  [../]
[]

[AuxVariables]
  [./bnds]
  [../]
  [./total_en]
    order = CONSTANT
    family = MONOMIAL
  [../]
[]

[Kernels]
  [./cres]
    type = SplitCHParsed
    variable = c
    kappa_name = kappa_c
    w = w
    f_name = F
    args = 'gr0  gr1'
  [../]
  [./wres]
    type = SplitCHWRes
    variable = w
    mob_name = M
  [../]
  [./time]
    type = CoupledTimeDerivative
    variable = w
    v = c
  [../]
  [./PolycrystalSinteringKernel]
    c = c
    consider_rigidbodymotion = false
    anisotropic = false
    #grain_force = grain_force
    #grain_tracker_object = grain_center
    #grain_volumes = grain_volumes
    #translation_constant = 10.0
    #rotation_constant = 1.0
  [../]
  #[./motion]
  #  type = MultiGrainRigidBodyMotion
  #  variable = w
  #  c = c
  #  v = 'gr0 gr1   '
  #  grain_force = grain_force
  #  grain_tracker_object = grain_center
  #  grain_volumes = grain_volumes
  #  translation_constant = 10.0
  #  rotation_constant = 1.0
  #[../]
[]

[AuxKernels]
  [./bnds]
    type = BndsCalcAux
    variable = bnds
    v = 'gr0 gr1 '
  [../]
  [./Total_en]
    type = TotalFreeEnergy
    variable = total_en
    kappa_names = 'kappa_c kappa_op kappa_op'
    interfacial_vars = 'c  gr0 gr1'
  [../]
[]

[BCs]
  [./flux]
    type = CahnHilliardFluxBC
    variable = w
    boundary = 'top bottom left right'
    flux = '0 0 0'
    mob_name = M
    args = 'c'
  [../]
[]

[Materials]
  [./free_energy]
    type = SinteringFreeEnergy
    block = 0
    c = c
    v = 'gr0 gr1'
    #f_name = S
    derivative_order = 2
    output_properties = 'S'
    outputs = exodus
  [../]
  [./mob]
    type = SinteringMobility
    T = 673.0
    int_width = 2
    Qv = 1.97
    #Qvc = 2.3
    Qgb = 2.4
    Qs = 2.4
    #Qgbm = 1.08
    Dgb0 = 10
    Dsurf0 = 100
    #Dvap0 = 4.0e-7
    Dvol0 = 0.67e-4
    c = c
    v = 'gr0 gr1'
    Vm = 1.71e-29
    length_scale = 1e-09
    time_scale = 0.1
    bulkindex = 1.0
    surfindex = 1.0
    gbindex = 1.0
    outputs = exodus
  [../]
  [./constant_mat]
    type = GenericConstantMaterial
    block = 0
    prop_names = '  A       B     L   kappa_op  kappa_c'
    prop_values = '25.436 2.466 10.68  7.397     13.951 '
  [../]
[]

[Postprocessors]
  [./mat_D]
    type = ElementIntegralMaterialProperty
    mat_prop = D
  [../]
  [./elem_c]
    type = ElementIntegralVariablePostprocessor
    variable = c
  [../]
  [./elem_bnds]
    type = ElementIntegralVariablePostprocessor
    variable = bnds
  [../]
  [./total_energy]
    type = ElementIntegralVariablePostprocessor
    variable = total_en
  [../]
  [./free_en]
    type = ElementIntegralMaterialProperty
    mat_prop = F
  [../]
  [./dofs]
    type = NumDOFs
  [../]
  [./tstep]
    type = TimestepSize
  [../]
  #[./run_time]
  #  type = RunTime
  #  time_type = active
  #[../]
  [./int_area]
    type = InterfaceAreaPostprocessor
    variable = c
  [../]
  [./grain_size_gr0]
    type = ElementIntegralVariablePostprocessor
    variable = gr0
  [../]
  [./grain_size_gr1]
    type = ElementIntegralVariablePostprocessor
    variable = gr1
  [../]
  [./gb_area]
    type = GrainBoundaryArea
  [../]
  [./neck]
    type = NeckAreaPostprocessor
  [../]
  [./gb0_area]
    type = GrainBoundaryArea
    v = gr0
  [../]
  [./gb1_area]
    type = GrainBoundaryArea
    v = gr1
  [../]
  [./c_int_area]
    type = GrainBoundaryArea
    v = c
  [../]
[]

[Preconditioning]
  [./SMP]
    type = SMP
    coupled_groups = 'c,w c,gr0,gr1'
  [../]
[]


[Executioner]
  # Preconditioned JFNK (default)
  type = Transient
  scheme = BDF2
  solve_type = NEWTON
  petsc_options_iname = '-pc_type -ksp_grmres_restart -sub_ksp_type -sub_pc_type -pc_asm_overlap'
  petsc_options_value = 'asm         31   preonly   ilu      1'
  l_max_its = 20
  nl_max_its = 20
  l_tol = 1.0e-3
  nl_rel_tol = 1.0e-8
  nl_abs_tol = 1e-10
  end_time = 10000
  #dt = 0.01
  #[./Adaptivity]
  #  refine_fraction = 0.7
  #  coarsen_fraction = 0.1
  #  max_h_level = 2
  #  initial_adaptivity = 1
  #[../]
  [./TimeStepper]
    type = IterationAdaptiveDT
    dt = 0.01
    growth_factor = 1.5
  [../]
[]

[Adaptivity]
  marker = bound_adapt
  max_h_level = 2
  [./Indicators]
    [./error]
      type = GradientJumpIndicator
      variable = bnds
    [../]
  [../]
  [./Markers]
    [./bound_adapt]
      type = ValueRangeMarker
      lower_bound = 0.01
      upper_bound = 0.95
      variable = bnds
    [../]
  [../]
[]

[Outputs]
  print_linear_residuals = true
  print_perf_log = true
  gnuplot = true
  [./console]
    type = Console
    perf_log = true
  [../]
  [./exodus]
    type = Exodus
    elemental_as_nodal = true
  [../]
[]

[ICs]
  [./ic_gr1]
    int_width = 2.0
    x1 = 33.0
    y1 = 30.0
    z1 = 0.0
    radius = 20.0
    outvalue = 0.0
    variable = gr1
    invalue = 1.0
    3D_spheres = true
    type = SmoothCircleIC
  [../]
  [./multip]
    x_positions = '33.0 70.0'
    int_width = 2.0
    z_positions = '0.0 0.0'
    y_positions = '30.0 50.0 '
    radii = '20.0 20.0'
    3D_spheres = true
    outvalue = 0.001
    variable = c
    invalue = 0.999
    type = SpecifiedSmoothCircleIC
    block = 0
  [../]
  [./ic_gr0]
    int_width = 2.0
    x1 = 70.0
    y1 = 50.0
    z1 = 0.0
    radius = 20.0
    outvalue = 0.0
    variable = gr0
    invalue = 1.0
    3D_spheres = true
    type = SmoothCircleIC
  [../]
[]

[Debug]
  show_var_residual_norms = true
[]

[GiudGiud]

what error are you hitting?

[FatimahDzr]

Thanks for the reply. I don't get any error right now when I delete the PolycrystalSinteringKernel in the code. So I can see the results for the concentration as :

But in the case of "bnds" output, there is no change in the results:

I searched to find out about the deleted kernel, but I couldn't find anything related. I'm not sure that this result is due to that.

Here is the code:

[GlobalParams]
  var_name_base = gr
  op_num = 2.0
  int_width = 2.0
  #en_ratio = 1
[]

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 80
  ny = 40
  nz = 0
  xmin = 0.0
  xmax = 40.0
  ymin = 0.0
  ymax = 20.0
  zmax = 0
  elem_type = QUAD4
[]

[Variables]
  [./c]
    #scaling = 10
  [../]
  [./w]
  [../]
  [./PolycrystalVariables]
  [../]
[]

[ICs]
  [./ic_gr1]
    int_width = 2.0
    x1 = 25.0
    y1 = 10.0
    radius = 7.4
    outvalue = 0.0
    variable = gr1
    invalue = 1.0
    type = SmoothCircleIC
  [../]
  [./multip]
    x_positions = '10.0 25.0'
    int_width = 2.0
    z_positions = '0 0'
    y_positions = '10.0 10.0 '
    radii = '7.4 7.4'
    3D_spheres = false
    outvalue = 0.001
    variable = c
    invalue = 0.999
    type = SpecifiedSmoothCircleIC
    block = 0
  [../]
  [./ic_gr0]
    int_width = 2.0
    x1 = 10.0
    y1 = 10.0
    radius = 7.4
    outvalue = 0.0
    variable = gr0
    invalue = 1.0
    type = SmoothCircleIC
  [../]
[]

[AuxVariables]
  [./bnds]
  [../]
  [./total_en]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./unique_grains]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./var_indices]
    order = CONSTANT
    family = MONOMIAL
  [../]
  [./centroids]
    order = CONSTANT
    family = MONOMIAL
  [../]
[]

[Kernels]
  [./cres]
    type = SplitCHParsed
    variable = c
    kappa_name = kappa_c
    w = w
    f_name = F
    args = 'gr0 gr1'
  [../]
  [./wres]
    type = SplitCHWRes
    variable = w
    mob_name = D
  [../]
  [./time]
    type = CoupledTimeDerivative
    variable = w
    v = c
  [../]
  [./PolycrystalSinteringKernel]
    c = c
    consider_rigidbodymotion = false
    anisotropic = false
    grain_force = grain_force
    grain_tracker_object = grain_center
    grain_volumes = grain_volumes
    translation_constant = 10.0
    rotation_constant = 1.0
  [../]
[]

[AuxKernels]
  [./bnds]
    type = BndsCalcAux
    variable = bnds
    v = 'gr0 gr1'
  [../]
  [./Total_en]
    type = TotalFreeEnergy
    variable = total_en
    kappa_names = 'kappa_c kappa_op kappa_op'
    interfacial_vars = 'c  gr0 gr1'
  [../]
  [./unique_grains]
    type = FeatureFloodCountAux
    variable = unique_grains
    flood_counter = grain_center
    field_display = UNIQUE_REGION
    execute_on = timestep_begin
  [../]
  [./var_indices]
    type = FeatureFloodCountAux
    variable = var_indices
    flood_counter = grain_center
    field_display = VARIABLE_COLORING
    execute_on = timestep_begin
  [../]
  [./centroids]
    type = FeatureFloodCountAux
    variable = centroids
    execute_on = timestep_begin
    field_display = CENTROID
    flood_counter = grain_center
  [../]
[]

[BCs]
  # [./flux]
  #   type = CahnHilliardFluxBC
  #   variable = w
  #   boundary = 'top bottom left right'
  #   flux = '0 0 0'
  #   mob_name = D
  #   args = 'c'
  # [../]
[]

[Functions]
  [./load]
    type = ConstantFunction
    value = 0.01
  [../]
[]

[Materials]
  [./free_energy]
    type = SinteringFreeEnergy
    block = 0
    c = c
    v = 'gr0 gr1'
    #f_name = S
    derivative_order = 2
    #outputs = console
  [../]
  [./CH_mat]
    type = PFDiffusionGrowth
    block = 0
    rho = c
    v = 'gr0 gr1'
    outputs = console
  [../]
  [./constant_mat]
    type = GenericConstantMaterial
    block = 0
    prop_names = '  A    B   L   kappa_op kappa_c'
    prop_values = '16.0 1.0 1.0  0.5      1.0    '
  [../]
[]

[VectorPostprocessors]
  [./grain_volumes]
    type = FeatureVolumeVectorPostprocessor
    flood_counter = grain_center
    execute_on = 'initial timestep_begin'
  [../]
[]

[UserObjects]
  [./grain_center]
    type = GrainTracker
    outputs = none
    compute_var_to_feature_map = true
    execute_on = 'initial timestep_begin'
  [../]
[]

[Postprocessors]
  [./elem_c]
    type = ElementIntegralVariablePostprocessor
    variable = c
  [../]
  [./elem_bnds]
    type = ElementIntegralVariablePostprocessor
    variable = bnds
  [../]
  [./total_energy]
    type = ElementIntegralVariablePostprocessor
    variable = total_en
  [../]
  [./free_en]
    type = ElementIntegralMaterialProperty
    mat_prop = F
  [../]
  [./dofs]
    type = NumDOFs
    system = 'NL'
  [../]
  [./tstep]
    type = TimestepSize
  [../]
  # [./run_time]
  #   type = RunTime
  #   time_type = active
  # [../]
  [./int_area]
    type = InterfaceAreaPostprocessor
    variable = c
  [../]
  [./grain_size_gr0]
    type = ElementIntegralVariablePostprocessor
    variable = gr0
  [../]
  [./grain_size_gr1]
    type = ElementIntegralVariablePostprocessor
    variable = gr1
  [../]
  [./gb_area]
    type = GrainBoundaryArea
  [../]
[]

[Preconditioning]
  [./SMP]
    type = SMP
    coupled_groups = 'c,w c,gr0,gr1 '
  [../]
[]

[Executioner]
  # Preconditioned JFNK (default)
  type = Transient
  scheme = BDF2
  solve_type = NEWTON
  petsc_options_iname = '-pc_type -ksp_grmres_restart -sub_ksp_type -sub_pc_type -pc_asm_overlap'
  petsc_options_value = 'asm         31   preonly   lu      1'
  l_max_its = 20
  nl_max_its = 20
  nl_abs_tol = 1e-10
  nl_rel_tol = 1e-08
  l_tol = 1e-04
  end_time = 20
  #dt = 0.01
  [./TimeStepper]
    type = IterationAdaptiveDT
    dt = 0.01
    growth_factor = 1.2
  [../]
[]

[Adaptivity]
  marker = bound_adapt
  max_h_level = 2
  [./Indicators]
    [./error]
      type = GradientJumpIndicator
      variable = bnds
    [../]
  [../]
  [./Markers]
    [./bound_adapt]
      type = ValueRangeMarker
      lower_bound = 0.01
      upper_bound = 0.99
      variable = bnds
    [../]
  [../]
[]

[Outputs]
  print_linear_residuals = true
  csv = true
  gnuplot = true
  print_perf_log = true
  [./console]
    type = Console
    perf_log = true
  [../]
  [./exodus]
    type = Exodus
    elemental_as_nodal = true
  [../]
[]

[Debug]
  show_var_residual_norms = true
[]

[GiudGiud]

@dschwen @SudiptaBiswas
I m not familiar with bnds

[SudiptaBiswas]

@FatimahDzr By removing the PolycrystalSinteringKernel you are no longer solving for the order parameters. That's why you don't see the bnds variable evolve. What was the issue/error with PolycrystalSinteringKernel ?

[jackeggemeyer]

@SudiptaBiswas When trying to run this test, it asks for the user to define what type PolycrystalSinteringKernel is.
Kernels/PolycrystalSinteringKernel/type'
Doc String: "A string representing the Moose Object that will be built by this Action"