Sudden Arity Mismatch when defining non-linear problem

I have been solving the following problem using FEniCSx for over a month now without any issues. All of a sudden, I am getting ArityMismatch: Adding expressions with non-matching form arguments ('v_0',) vs ('conj(v_0)',) when I define the non-linear problem. I do not believe I have changed anything leading up to the problem definition. Here is the code:

L = 4.e-3 
t_step = 60
D = 6.5e-06 
k = 6e-2 

domain = mesh.create_interval(MPI.COMM_WORLD, 100, [0, L])
P1 = ufl.FiniteElement('CG', domain.ufl_cell(), 1)
element = ufl.MixedElement([P1, P1])
V = fem.FunctionSpace(domain, element)

# test functions
v1, v2 = ufl.TestFunctions(V)

# fields to solve for
num_subs = V.num_sub_spaces
spaces = []
maps = []
for i in range(num_subs):
    space_i, map_i = V.sub(i).collapse()
    spaces.append(space_i)
    maps.append(map_i)
    
u = fem.Function(V)
u1 = fem.Function(spaces[0])
u2 = fem.Function(spaces[1])

# concentrations from previous timestep
u_n = fem.Function(V)
u_n1, u_n2 = ufl.split(u_n)

# apply timestep variable to each node in the mesh
dt = fem.Constant(domain, ScalarType(t_step))

# turn floats to Constant objects
D_ = fem.Constant(domain, ScalarType(D))
k_ = fem.Constant(domain, ScalarType(k))

# set initial conditions 
u1.vector.array[:] = C_0 * np.ones(u1.vector.array.shape)
u2.vector.array[:] = N_0 * np.ones(u2.vector.array.shape)
u_n.vector.array[maps[0]] = u1.vector.array
u_n.vector.array[maps[1]] = u2.vector.array

# set initial guess
u.vector.array[maps[0]] = u1.vector.array
u.vector.array[maps[1]] = u2.vector.array

u1, u2 = ufl.split(u)

# function determining if a node is on the tray top
def on_top_boundary(x):
    return(np.isclose(x[0], L))

# must use collapsed subspace to determine boundary DOFs
V0, submap = V.sub(0).collapse()

# determine boundary DOFs
boundary_dofs = fem.locate_dofs_geometrical((V.sub(0),V0), on_top_boundary)

# apply dirichlet BC to boundary DOFs
bc = fem.dirichletbc(ScalarType(C_0), boundary_dofs[0], V.sub(0))

u.x.array[bc.dof_indices()[0]] = bc.value.value

F = (1/dt)*(u1 - u_n1)*v1*ufl.dx + \
    (1/dt)*(u2 - u_n2)*v2*ufl.dx + \
    D_*ufl.inner(ufl.grad(u1), ufl.grad(v1))*ufl.dx + \
    k_*u1*u2*v1*ufl.dx + \
    k_*u1*u2*v2*ufl.dx

problem = fem.petsc.NonlinearProblem(F, u, bcs=[bc])

When I get to this step, it returns:

ArityMismatch                             Traceback (most recent call last)
Input In [8], in <cell line: 7>()
      1 F = (1/dt)*(u1 - u_n1)*v1*ufl.dx + \
      2     (1/dt)*(u2 - u_n2)*v2*ufl.dx + \
      3     D_*ufl.inner(ufl.grad(u1), ufl.grad(v1))*ufl.dx + \
      4     k_*u1*u2*v1*ufl.dx + \
      5     k_*u1*u2*v2*ufl.dx
----> 7 problem = fem.petsc.NonlinearProblem(F, u, bcs=[bc])
      8 solver = nls.petsc.NewtonSolver(MPI.COMM_WORLD, problem)

File /usr/local/dolfinx-complex/lib/python3.10/dist-packages/dolfinx/fem/petsc.py:678, in NonlinearProblem.__init__(self, F, u, bcs, J, form_compiler_params, jit_params)
    656 def __init__(self, F: ufl.form.Form, u: _Function, bcs: typing.List[DirichletBCMetaClass] = [],
    657              J: ufl.form.Form = None, form_compiler_params={}, jit_params={}):
    658     """Initialize solver for solving a non-linear problem using Newton's method, :math:`dF/du(u) du = -F(u)`.
    659 
    660     Args:
   (...)
    676 
    677     """
--> 678     self._L = _create_form(F, form_compiler_params=form_compiler_params,
    679                            jit_params=jit_params)
    681     # Create the Jacobian matrix, dF/du
    682     if J is None:

File /usr/local/dolfinx-complex/lib/python3.10/dist-packages/dolfinx/fem/forms.py:168, in form(form, dtype, form_compiler_params, jit_params)
    165         return list(map(lambda sub_form: _create_form(sub_form), form))
    166     return form
--> 168 return _create_form(form)

File /usr/local/dolfinx-complex/lib/python3.10/dist-packages/dolfinx/fem/forms.py:163, in form.<locals>._create_form(form)
    160 """Recursively convert ufl.Forms to dolfinx.fem.Form, otherwise
    161 return form argument"""
    162 if isinstance(form, ufl.Form):
--> 163     return _form(form)
    164 elif isinstance(form, collections.abc.Iterable):
    165     return list(map(lambda sub_form: _create_form(sub_form), form))

File /usr/local/dolfinx-complex/lib/python3.10/dist-packages/dolfinx/fem/forms.py:137, in form.<locals>._form(form)
    134 if mesh is None:
    135     raise RuntimeError("Expecting to find a Mesh in the form.")
--> 137 ufcx_form, module, code = jit.ffcx_jit(mesh.comm, form,
    138                                        form_compiler_params=form_compiler_params,
    139                                        jit_params=jit_params)
    141 # For each argument in form extract its function space
    142 V = [arg.ufl_function_space()._cpp_object for arg in form.arguments()]

File /usr/local/dolfinx-complex/lib/python3.10/dist-packages/dolfinx/jit.py:56, in mpi_jit_decorator.<locals>.mpi_jit(comm, *args, **kwargs)
     51 @functools.wraps(local_jit)
     52 def mpi_jit(comm, *args, **kwargs):
     53 
     54     # Just call JIT compiler when running in serial
     55     if comm.size == 1:
---> 56         return local_jit(*args, **kwargs)
     58     # Default status (0 == ok, 1 == fail)
     59     status = 0

File /usr/local/dolfinx-complex/lib/python3.10/dist-packages/dolfinx/jit.py:204, in ffcx_jit(ufl_object, form_compiler_params, jit_params)
    202 # Switch on type and compile, returning cffi object
    203 if isinstance(ufl_object, ufl.Form):
--> 204     r = ffcx.codegeneration.jit.compile_forms([ufl_object], parameters=p_ffcx, **p_jit)
    205 elif isinstance(ufl_object, ufl.FiniteElementBase):
    206     r = ffcx.codegeneration.jit.compile_elements([ufl_object], parameters=p_ffcx, **p_jit)

File /usr/local/lib/python3.10/dist-packages/ffcx/codegeneration/jit.py:168, in compile_forms(forms, parameters, cache_dir, timeout, cffi_extra_compile_args, cffi_verbose, cffi_debug, cffi_libraries)
    165     for name in form_names:
    166         decl += form_template.format(name=name)
--> 168     impl = _compile_objects(decl, forms, form_names, module_name, p, cache_dir,
    169                             cffi_extra_compile_args, cffi_verbose, cffi_debug, cffi_libraries)
    170 except Exception:
    171     # remove c file so that it will not timeout next time
    172     c_filename = cache_dir.joinpath(module_name + ".c")

File /usr/local/lib/python3.10/dist-packages/ffcx/codegeneration/jit.py:232, in _compile_objects(decl, ufl_objects, object_names, module_name, parameters, cache_dir, cffi_extra_compile_args, cffi_verbose, cffi_debug, cffi_libraries)
    228 import ffcx.compiler
    230 # JIT uses module_name as prefix, which is needed to make names of all struct/function
    231 # unique across modules
--> 232 _, code_body = ffcx.compiler.compile_ufl_objects(ufl_objects, prefix=module_name, parameters=parameters)
    234 ffibuilder = cffi.FFI()
    235 ffibuilder.set_source(module_name, code_body, include_dirs=[ffcx.codegeneration.get_include_path()],
    236                       extra_compile_args=cffi_extra_compile_args, libraries=cffi_libraries)

File /usr/local/lib/python3.10/dist-packages/ffcx/compiler.py:97, in compile_ufl_objects(ufl_objects, object_names, prefix, parameters, visualise)
     95 # Stage 1: analysis
     96 cpu_time = time()
---> 97 analysis = analyze_ufl_objects(ufl_objects, parameters)
     98 _print_timing(1, time() - cpu_time)
    100 # Stage 2: intermediate representation

File /usr/local/lib/python3.10/dist-packages/ffcx/analysis.py:85, in analyze_ufl_objects(ufl_objects, parameters)
     82     else:
     83         raise TypeError("UFL objects not recognised.")
---> 85 form_data = tuple(_analyze_form(form, parameters) for form in forms)
     86 for data in form_data:
     87     elements += [convert_element(e) for e in data.unique_sub_elements]

File /usr/local/lib/python3.10/dist-packages/ffcx/analysis.py:85, in <genexpr>(.0)
     82     else:
     83         raise TypeError("UFL objects not recognised.")
---> 85 form_data = tuple(_analyze_form(form, parameters) for form in forms)
     86 for data in form_data:
     87     elements += [convert_element(e) for e in data.unique_sub_elements]

File /usr/local/lib/python3.10/dist-packages/ffcx/analysis.py:168, in _analyze_form(form, parameters)
    165 complex_mode = "_Complex" in parameters["scalar_type"]
    167 # Compute form metadata
--> 168 form_data = ufl.algorithms.compute_form_data(
    169     form,
    170     do_apply_function_pullbacks=True,
    171     do_apply_integral_scaling=True,
    172     do_apply_geometry_lowering=True,
    173     preserve_geometry_types=(ufl.classes.Jacobian,),
    174     do_apply_restrictions=True,
    175     do_append_everywhere_integrals=False,  # do not add dx integrals to dx(i) in UFL
    176     complex_mode=complex_mode)
    178 # Determine unique quadrature degree, quadrature scheme and
    179 # precision per each integral data
    180 for id, integral_data in enumerate(form_data.integral_data):
    181     # Iterate through groups of integral data. There is one integral
    182     # data for all integrals with same domain, itype, subdomain_id
   (...)
    188 
    189     # Extract precision

File /usr/local/lib/python3.10/dist-packages/ufl/algorithms/compute_form_data.py:407, in compute_form_data(form, do_apply_function_pullbacks, do_apply_integral_scaling, do_apply_geometry_lowering, preserve_geometry_types, do_apply_default_restrictions, do_apply_restrictions, do_estimate_degrees, do_append_everywhere_integrals, complex_mode)
    403 # TODO: This is a very expensive check... Replace with something
    404 # faster!
    405 preprocessed_form = reconstruct_form_from_integral_data(self.integral_data)
--> 407 check_form_arity(preprocessed_form, self.original_form.arguments(), complex_mode)  # Currently testing how fast this is
    409 # TODO: This member is used by unit tests, change the tests to
    410 # remove this!
    411 self.preprocessed_form = preprocessed_form

File /usr/local/lib/python3.10/dist-packages/ufl/algorithms/check_arities.py:177, in check_form_arity(form, arguments, complex_mode)
    175 def check_form_arity(form, arguments, complex_mode=False):
    176     for itg in form.integrals():
--> 177         check_integrand_arity(itg.integrand(), arguments, complex_mode)

File /usr/local/lib/python3.10/dist-packages/ufl/algorithms/check_arities.py:159, in check_integrand_arity(expr, arguments, complex_mode)
    156 arguments = tuple(sorted(set(arguments),
    157                          key=lambda x: (x.number(), x.part())))
    158 rules = ArityChecker(arguments)
--> 159 arg_tuples = map_expr_dag(rules, expr, compress=False)
    160 args = tuple(a[0] for a in arg_tuples)
    161 if args != arguments:

File /usr/local/lib/python3.10/dist-packages/ufl/corealg/map_dag.py:36, in map_expr_dag(function, expression, compress, vcache, rcache)
     17 def map_expr_dag(function, expression,
     18                  compress=True,
     19                  vcache=None,
     20                  rcache=None):
     21     """Apply a function to each subexpression node in an expression DAG.
     22 
     23     If *compress* is ``True`` (default) the output object from
   (...)
     34     Return the result of the final function call.
     35     """
---> 36     result, = map_expr_dags(function, [expression], compress=compress,
     37                             vcache=vcache,
     38                             rcache=rcache)
     39     return result

File /usr/local/lib/python3.10/dist-packages/ufl/corealg/map_dag.py:99, in map_expr_dags(function, expressions, compress, vcache, rcache)
     97     r = handlers[v._ufl_typecode_](v)
     98 else:
---> 99     r = handlers[v._ufl_typecode_](v, *[vcache[u] for u in v.ufl_operands])
    101 # Optionally check if r is in rcache, a memory optimization
    102 # to be able to keep representation of result compact
    103 if compress:

File /usr/local/lib/python3.10/dist-packages/ufl/algorithms/check_arities.py:48, in ArityChecker.sum(self, o, a, b)
     46 def sum(self, o, a, b):
     47     if a != b:
---> 48         raise ArityMismatch("Adding expressions with non-matching form arguments {0} vs {1}.".format(_afmt(a), _afmt(b)))
     49     return a

ArityMismatch: Adding expressions with non-matching form arguments ('v_0',) vs ('conj(v_0)',).

Any idea what might be causing this? And why it seemingly started happening out of the blue?

You seem to be running DOLFINx is complex mode (i.e. defined with complex valued degrees of freedom). To write variational forms for such problems, you need to consistently use ufl.inner as explained in:
https://jorgensd.github.io/dolfinx-tutorial/chapter1/complex_mode.html#variational-problem

That is interesting. I have not defined any functions or parameters with complex numbers. Would you happen to know why it defaulted to complex mode?

No, But you can inspect your $PYTHONPATH and $PETSC_ARCH to see what they are set to.
As you are using the docker image you can call
source /usr/local/bin/dolfinx-real-mode to change it back.

When I call $PYTHONPATH I get /usr/local/dolfinx-real/lib/python3.10/dist-packages:/usr/local/lib:: not found and $PETSC_ARCH is linux-gnu-real-32: not found. Does this mean they are set to real mode? I’m not sure what the not found is about. When I call source /usr/local/bin/dolfinx-real-mode in the container’s terminal I get source: not found.

Try source dolfinx-real-mode.

Im not sure why/how it picks up the complex-mode dolfinx as its not in your Python path.

Same result: source: not found. I pulled a new Docker image and ran it in there and still have the same issue.

I also printed sys.path and got the following:

['/root',
 '',
 '/usr/local/dolfinx-complex/lib/python3.10/dist-packages',
 '/usr/local/dolfinx-real/lib/python3.10/dist-packages',
 '/usr/local/lib',
 '/root',
 '/usr/lib/python310.zip',
 '/usr/lib/python3.10',
 '/usr/lib/python3.10/lib-dynload',
 '/usr/local/lib/python3.10/dist-packages',
 '/usr/lib/python3/dist-packages']

I then deliberately removed '/usr/local/dolfinx-complex/lib/python3.10/dist-packages' from the path and ran the script, but somehow still get the same error.

I cannot reproduce your issue running the following commands:

docker pull dolfinx/dolfinx
Using default tag: latest
latest: Pulling from dolfinx/dolfinx
405f018f9d1d: Already exists 
4f4fb700ef54: Already exists 
386f7a6b5f73: Already exists 
b3ec56910bbb: Already exists 
5659da0f2533: Already exists 
234abc5288f0: Already exists 
d0e189c145b0: Already exists 
9471e8d8b282: Already exists 
fc7e58205b26: Already exists 
4f3c2f613f03: Already exists 
bb6481e4f2e4: Already exists 
42bed89592d0: Already exists 
cade438157a3: Pull complete 
141b92052441: Pull complete 
Digest: sha256:9ebac7eb88f6255f7385d99c9ce4e4f11d290e0f398aec6b9623b587d9c1e47d
Status: Downloaded newer image for dolfinx/dolfinx:latest
docker.io/dolfinx/dolfinx:latest
docker run -it -v $(pwd):/home/fenics/shared -w /home/fenics/shared --rm  dolfinx/dolfinx:latest
root@30fa60082082:/home/fenics/shared# echo $PYTHONPATH 
/usr/local/dolfinx-real/lib/python3.10/dist-packages:/usr/local/lib:
root@30fa60082082:/home/fenics/shared# python3 -c "from petsc4py import PETSc; print(PETSc.ScalarType)"
<class 'numpy.float64'>
root@30fa60082082:/home/fenics/shared# source dolfinx-real-mode
root@30fa60082082:/home/fenics/shared# which dolfinx-real-mode
/usr/local/bin/dolfinx-real-mode