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idaholab
New add_subdomain_names capability does not work with exodus output if subdomains are not added before output
Bug Description
if the subdomain is not created by the time the mesh is output
libMesh terminating:
ExodusII_IO_Helper: block id 72 not found in block_ids.
Stack frames: 17
0: 0 libmesh_devel.0.dylib 0x000000010e3e2e60 libMesh::print_trace(std::__1::basic_ostream<char, std::__1::char_traits<char>>&) + 1044
1: 1 libmesh_devel.0.dylib 0x000000010e3dfc30 libMesh::MacroFunctions::report_error(char const*, int, char const*, char const*, std::__1::basic_ostream<char, std::__1::char_traits<char>>&) + 272
2: 2 libmesh_devel.0.dylib 0x000000010e9d5670 libMesh::ExodusII_IO_Helper::initialize_element_variables(std::__1::vector<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>>>, std::__1::vector<std::__1::set<unsigned short, std::__1::less<unsigned short>, std::__1::allocator<unsigned short>>, std::__1::allocator<std::__1::set<unsigned short, std::__1::less<unsigned short>, std::__1::allocator<unsigned short>>>> const&) + 1156
3: 3 libmesh_devel.0.dylib 0x000000010e9b880c libMesh::ExodusII_IO::write_element_data(libMesh::EquationSystems const&) + 668
4: 4 libmoose-devel.0.dylib 0x0000000108cf10c8 Exodus::outputElementalVariables() + 304
5: 5 libmoose-devel.0.dylib 0x0000000108ce8d34 AdvancedOutput::output() + 440
6: 6 libmoose-devel.0.dylib 0x0000000108cf075c Exodus::output() + 184
7: 7 libmoose-devel.0.dylib 0x0000000108cefc3c OversampleOutput::outputStep(MooseEnumItem const&) + 760
8: 8 libmoose-devel.0.dylib 0x0000000108d137c0 OutputWarehouse::outputStep(MooseEnumItem) + 216
9: 9 libmoose-devel.0.dylib 0x00000001083ee144 FEProblemBase::outputStep(MooseEnumItem) + 712
10: 10 libmoose-devel.0.dylib 0x0000000107cf2254 Transient::preExecute() + 156
11: 11 libmoose-devel.0.dylib 0x0000000107cf1100 Transient::execute() + 64
12: 12 libmoose-devel.0.dylib 0x0000000108ddc97c MooseApp::executeExecutioner() + 700
13: 13 libmoose-devel.0.dylib 0x0000000108dd4e34 MooseApp::run() + 4584
14: 14 pronghorn-devel 0x000000010447bbf8 void Moose::main<PronghornTestApp>(int, char**) + 152
15: 15 pronghorn-devel 0x000000010447bb54 main + 12
16: 16 dyld 0x0000000181c160e0 start + 2360
[0] ../src/mesh/exodusII_io_helper.C, line 3262, compiled May 15 2024 at 10:58:09
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
Steps to Reproduce
Run with
- exodus output
- add_subdomain_names = 'dummy' in the Mesh block
Impact
Slowing down debugging add_subdomain_names is great for changing the mesh and setting all the missing subdomains there to avoid re-writing the input
[Optional] Diagnostics
No response
no but there;s a workaround. It should work fine when adding dummy variables that are not block restricted
I attempted to add the dummy AuxVariables, but the problem still persisted. The following is my input file.
test.i
[Problem]
kernel_coverage_check = false
material_coverage_check = false
boundary_restricted_node_integrity_check = false
[]
new_domain_blocks = '1001 1002'
[Mesh]
[box]
type = GeneratedMeshGenerator
dim = 3
nx = 10
ny = 10
nz = 10
xmin = 0
xmax = 1
ymin = 0
ymax = 1
zmin = 0
zmax = 1
[]
[box1]
type = SubdomainBoundingBoxGenerator
input = box
block_id = 1
bottom_left = '0 0.5 0'
top_right = '1 1 1'
[]
add_subdomain_ids = '${new_domain_blocks}'
[]
[GlobalParams]
displacements = 'disp_x disp_y disp_z'
[]
[Variables]
[disp_x]
block = '${new_domain_blocks}'
[]
[disp_y]
block = '${new_domain_blocks}'
[]
[disp_z]
block = '${new_domain_blocks}'
[]
[porepressure]
block = '${new_domain_blocks}'
[]
[]
[AuxVariables]
[dummy]
[]
[]
# ===== Tensor mechanics for all active domain blocks =====
[Physics]
[SolidMechanics]
[QuasiStatic]
[all]
strain = SMALL
incremental = true
block = '${new_domain_blocks}'
add_variables = false
[]
[]
[]
[]
[FluidProperties]
[the_simple_fluid]
type = SimpleFluidProperties
thermal_expansion = 0.0
bulk_modulus = 2e9
viscosity = 1e-3
density0 = 1000
[]
[]
[PorousFlowFullySaturated]
coupling_type = HydroMechanical
displacements = 'disp_x disp_y disp_z'
porepressure = porepressure
biot_coefficient = 1.0
gravity = '0 -9.8 0'
fp = the_simple_fluid
block = '${new_domain_blocks}'
add_darcy_aux = false
[]
# ===== Boundary Conditions =====
[BCs]
[archor_x]
type = DirichletBC
boundary = 'bottom'
variable = disp_x
value = 0
[]
[archor_y]
type = DirichletBC
boundary = 'bottom'
variable = disp_y
value = 0
[]
[archor_z]
type = DirichletBC
boundary = 'bottom'
variable = disp_z
value = 0
[]
[]
# ===== Materials (linear-elastic to keep it simple) =====
[Materials]
[elasticity_tensor1]
type = ComputeIsotropicElasticityTensor
youngs_modulus = 50E6 # 50 MPa
poissons_ratio = 0.3
block = '${new_domain_blocks}'
[]
[stress]
type = ComputeFiniteStrainElasticStress
block = '${new_domain_blocks}'
[]
[density1]
type = GenericConstantMaterial
prop_names = density
prop_values = 2000
block = '${new_domain_blocks}'
[]
[porosity_soil]
type = PorousFlowPorosityConst # only the initial value of this is used
porosity = 0.2
PorousFlowDictator = dictator
block = '${new_domain_blocks}'
[]
[biot_modulus]
type = PorousFlowConstantBiotModulus
PorousFlowDictator = dictator
biot_coefficient = 1.0
block = '${new_domain_blocks}'
[]
[permeability_soil]
type = PorousFlowPermeabilityConst
permeability = '1e-14 0 0 0 1e-14 0 0 0 1e-14'
PorousFlowDictator = dictator
block = '${new_domain_blocks}'
[]
[]
[MeshModifiers]
[m1]
type = TimedSubdomainModifier
times = '200 300'
blocks_from = '0 1'
blocks_to = '1001 1002'
[]
[]
# ===== Executioner =====
[Executioner]
type = Transient
end_time = 500
dt = 100
solve_type = 'PJFNK'
nl_abs_tol = 1E-5
nl_max_its = 400
l_tol = 1E-8
l_max_its = 200
[]
[Outputs]
exodus = true
[]
libMesh terminating:
ExodusII_IO_Helper: block id 1001 not found in block_ids.
Stack frames: 17
0: libMesh::print_trace(std::ostream&)
1: libMesh::MacroFunctions::report_error(char const*, int, char const*, char const*, std::ostream&)
2: libMesh::ExodusII_IO_Helper::initialize_element_variables(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, std::vector<std::set<unsigned short, std::less<unsigned short>, std::allocator<unsigned short> >, std::allocator<std::set<unsigned short, std::less<unsigned short>, std::allocator<unsigned short> > > > const&)
3: libMesh::ExodusII_IO::write_element_data(libMesh::EquationSystems const&)
4: Exodus::outputElementalVariables()
5: AdvancedOutput::output()
6: Exodus::output()
7: OversampleOutput::outputStep(MooseEnumItem const&)
8: OutputWarehouse::outputStep(MooseEnumItem)
9: FEProblemBase::outputStep(MooseEnumItem)
10: TransientBase::preExecute()
11: TransientBase::execute()
12: MooseApp::executeExecutioner()
13: MooseApp::run()
14: ../../porous_flow-opt(+0x40e8) [0x559442e7b0e8]
15: __libc_start_main
16: ../../porous_flow-opt(+0x438a) [0x559442e7b38a]
[0] ../src/mesh/exodusII_io_helper.C, line 3273, compiled Jan 4 2025 at 01:18:42
Abort(1) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
In your model, all the physics is acting on the blocks added via add_subdomain_ids; the same with the (regular) variables. You could try to swap this (using the new and empty blocks without physics) and then the AuxVariables-trick should work.
The example given in https://github.com/idaholab/moose/discussions/26941 uses the blocks created via add_subdomain_ids without physics.