'Cell' object has no attribute 'num_sub_entities' when running old dolfinx 0.4.1 code

Errors
1

Hi all,

I recently updated Dolfinx from 0.4.1 to 0.7.2. After that, my old code stopped working throwing an attribute error when trying to form a bilinear form:

AttributeError: 'Cell' object has no attribute 'num_sub_entities'

The full diffusion code that I am running:

import numpy as np
from mpi4py import MPI
from petsc4py import PETSc
from dolfinx import fem, mesh


# Define temporal parameters
t = 0 # Start time
T = 1.0 # Final time
num_steps = 50
dt = T / num_steps # time step size

# Define mesh
nx, ny = 50, 50
domain = mesh.create_rectangle(MPI.COMM_WORLD, [np.array([-2, -2]), np.array([2, 2])],
                               [nx, ny], mesh.CellType.triangle)
V = fem.FunctionSpace(domain, ("CG", 1))


# Create initial condition
def initial_condition(x, a=5):
    return np.exp(-a*(x[0]**2+x[1]**2))
u_n = fem.Function(V)
u_n.name = "u_n"
u_n.interpolate(initial_condition)

# Create boundary condition
fdim = domain.topology.dim - 1
boundary_facets = mesh.locate_entities_boundary(
    domain, fdim, lambda x: np.full(x.shape[1], True, dtype=bool))
bc = fem.dirichletbc(PETSc.ScalarType(0), fem.locate_dofs_topological(V, fdim, boundary_facets), V)



uh = fem.Function(V)
uh.name = "uh"
uh.interpolate(initial_condition)

import ufl
u, v = ufl.TrialFunction(V), ufl.TestFunction(V)
f = fem.Constant(domain, PETSc.ScalarType(0))

D = ufl.as_tensor(((1, 0), (0, 2)))
a = u * v * ufl.dx + dt*ufl.inner(D * ufl.grad(u), ufl.grad(v)) * ufl.dx
L = (u_n + dt * f) * v * ufl.dx

bilinear_form = fem.form(a)
linear_form = fem.form(L)

A = fem.petsc.assemble_matrix(bilinear_form, bcs=[bc])
A.assemble()
b = fem.petsc.create_vector(linear_form)

solver = PETSc.KSP().create(domain.comm)
solver.setOperators(A)
solver.setType(PETSc.KSP.Type.PREONLY)
solver.getPC().setType(PETSc.PC.Type.LU)

for i in range(num_steps):
    t += dt

    print(t)
    D = ufl.as_tensor(((1 - t, 0), (0, 2 - t)))
    a = u * v * ufl.dx + dt*ufl.inner(D * ufl.grad(u), ufl.grad(v)) * ufl.dx
    print('----> Assembling')
    A = fem.petsc.assemble_matrix(fem.form(a), bcs=[bc])
    A.assemble()
    solver.setOperators(A)

    # Update the right hand side reusing the initial vector
    with b.localForm() as loc_b:
        loc_b.set(0)
    fem.petsc.assemble_vector(b, linear_form)

    # Apply Dirichlet boundary condition to the vector
    fem.petsc.apply_lifting(b, [bilinear_form], [[bc]])
    b.ghostUpdate(addv=PETSc.InsertMode.ADD_VALUES, mode=PETSc.ScatterMode.REVERSE)
    fem.petsc.set_bc(b, [bc])

    # Solve linear problem
    solver.solve(b, uh.vector)
    uh.x.scatter_forward()

    # Update solution at previous time step (u_n)
    u_n.x.array[:] = uh.x.array

The full error message:

Traceback (most recent call last):
  File "test.py", line 50, in <module>
    bilinear_form = fem.form(a)
  File "/usr/lib/petsc/lib/python3/dist-packages/dolfinx/fem/forms.py", line 188, in form
    return _create_form(form)
  File "/usr/lib/petsc/lib/python3/dist-packages/dolfinx/fem/forms.py", line 183, in _create_form
    return _form(form)
  File "/usr/lib/petsc/lib/python3/dist-packages/dolfinx/fem/forms.py", line 141, in _form
    ufcx_form, module, code = jit.ffcx_jit(mesh.comm, form,
  File "/usr/lib/petsc/lib/python3/dist-packages/dolfinx/jit.py", line 56, in mpi_jit
    return local_jit(*args, **kwargs)
  File "/usr/lib/petsc/lib/python3/dist-packages/dolfinx/jit.py", line 204, in ffcx_jit
    r = ffcx.codegeneration.jit.compile_forms([ufl_object], options=p_ffcx, **p_jit)
  File "/usr/lib/python3/dist-packages/ffcx/codegeneration/jit.py", line 199, in compile_forms
    raise e
  File "/usr/lib/python3/dist-packages/ffcx/codegeneration/jit.py", line 190, in compile_forms
    impl = _compile_objects(decl, forms, form_names, module_name, p, cache_dir,
  File "/usr/lib/python3/dist-packages/ffcx/codegeneration/jit.py", line 260, in _compile_objects
    _, code_body = ffcx.compiler.compile_ufl_objects(ufl_objects, prefix=module_name, options=options)
  File "/usr/lib/python3/dist-packages/ffcx/compiler.py", line 102, in compile_ufl_objects
    ir = compute_ir(analysis, object_names, prefix, options, visualise)
  File "/usr/lib/python3/dist-packages/ffcx/ir/representation.py", line 197, in compute_ir
    irs = [_compute_integral_ir(fd, i, analysis.element_numbers, integral_names, finite_element_names,
  File "/usr/lib/python3/dist-packages/ffcx/ir/representation.py", line 197, in <listcomp>
    irs = [_compute_integral_ir(fd, i, analysis.element_numbers, integral_names, finite_element_names,
  File "/usr/lib/python3/dist-packages/ffcx/ir/representation.py", line 492, in _compute_integral_ir
    integral_ir = compute_integral_ir(itg_data.domain.ufl_cell(), itg_data.integral_type,
  File "/usr/lib/python3/dist-packages/ffcx/ir/integral.py", line 84, in compute_integral_ir
    mt_table_reference = build_optimized_tables(
  File "/usr/lib/python3/dist-packages/ffcx/ir/elementtables.py", line 361, in build_optimized_tables
    t = get_ffcx_table_values(quadrature_rule.points, cell,
  File "/usr/lib/python3/dist-packages/ffcx/ir/elementtables.py", line 117, in get_ffcx_table_values
    num_entities = cell.num_sub_entities(entity_dim)
AttributeError: 'Cell' object has no attribute 'num_sub_entities'

Would appreciate any insights into how to resolve it…

2

Could you print the version of ufl, ffcx and Basix installed on your pc?

3

It seems like Basix was not installed. After installing it, here are the versions:

>>> import ufl, ffcx, basix
>>> ufl.__version__
'2023.2.0'
>>> ffcx.__version__
'0.7.0'
>>> basix.__version__
'0.0.13'

However, now I cannot import dolfinx due to the missing basix.ufl, although my dolfinx is version 0.7.2 (2:0.7.0.2~ppa1~jammy1 from Ubuntu PPA) and I think it should include this package already (e.g., Cahn-Hilliard - Where is basix.ufl? - #2 by dokken). The full error message:

Traceback (most recent call last):
  File "test.py", line 7, in <module>
    from dolfinx import fem, mesh, geometry
  File "/usr/lib/petsc/lib/python3/dist-packages/dolfinx/__init__.py", line 40, in <module>
    from dolfinx import fem, geometry, graph, io, jit, la, log, mesh, nls, plot
  File "/usr/lib/petsc/lib/python3/dist-packages/dolfinx/fem/__init__.py", line 12, in <module>
    from dolfinx.fem.assemble import (apply_lifting, assemble_matrix,
  File "/usr/lib/petsc/lib/python3/dist-packages/dolfinx/fem/assemble.py", line 22, in <module>
    from dolfinx.fem.forms import Form
  File "/usr/lib/petsc/lib/python3/dist-packages/dolfinx/fem/forms.py", line 17, in <module>
    from dolfinx import default_scalar_type, jit
  File "/usr/lib/petsc/lib/python3/dist-packages/dolfinx/jit.py", line 17, in <module>
    import ffcx.codegeneration.jit
  File "/usr/lib/python3/dist-packages/ffcx/codegeneration/jit.py", line 21, in <module>
    import ffcx.naming
  File "/usr/lib/python3/dist-packages/ffcx/naming.py", line 16, in <module>
    from .element_interface import convert_element
  File "/usr/lib/python3/dist-packages/ffcx/element_interface.py", line 12, in <module>
    import basix.ufl
ModuleNotFoundError: No module named 'basix.ufl'
4

This is not the correct version of Basix.
Basix should be installable from apt, see FEniCS PPA : “FEniCS Packages Team” team