Asemble_scalar error "LiteralFloat- no array attribute "

dolfinx
,
1

Hello,

I am getting error in assemble_scalar. I am using DOLFINx version: 0.8.0. Please find the MWE.


from dolfinx.fem.petsc import LinearProblem, assemble_matrix
from mpi4py import MPI
import numpy as np
import dolfinx
import basix
from dolfinx.fem import form, petsc, Function, functionspace, locate_dofs_topological, apply_lifting, set_bc
from ufl import as_vector, dot, Cell, as_tensor, SpatialCoordinate, dx
from dolfinx import fem
import petsc4py.PETSc
from dolfinx.io import gmshio
from mpi4py import MPI
import ufl
gdim = 1
shape = "interval"
deg = 1

cell = Cell(shape)
elem= basix.ufl.element("Lagrange", "interval", deg, shape=(1, ))
domain = ufl.Mesh(elem)

x = np.array([-4,-3,-2]) # Reference 0
cells = np.array([[0,1],[1,2]])
dom = dolfinx.mesh.create_mesh(MPI.COMM_WORLD, cells, x, domain)

dx = Measure('dx')(domain=dom)
########################################################
x = SpatialCoordinate(dom)

Eps2=as_tensor([(1,0,0,0,0,0),
                  (0,1,0,0,1,0),
                  (0,0,0,0,0,0),
                  (0,0,1,0,0,0),
                  (0,0,0,x[0],0,0),
                  (0,0,1,0,0,x[0])]) 
E1,E2,E3=3.4400E+03, 3.4400E+03, 3.4400E+03
G12,G13,G23= 1.3230E+03, 1.3230E+03, 1.3230E+03
v12,v13,v23 = 0.3,0.3,0.3

S=np.zeros((6,6))
S[0,0], S[1,1], S[2,2]=1/E1, 1/E2, 1/E3
S[0,1], S[0,2]= -v12/E1, -v13/E1
S[1,0], S[1,2]= -v12/E1, -v23/E2
S[2,0], S[2,1]= -v13/E1, -v23/E2
S[3,3], S[4,4], S[5,5]= 1/G23, 1/G13, 1/G12    
C=as_tensor(np.linalg.inv(S))
DD=np.zeros((6,6))
for s in range(6):
    for k in range(6): 
        f=fem.form(sum([dot(Eps2.T,dot(C,Eps2))[s,k]*dx]))
        DD[s,k]=fem.assemble_scalar(f)

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[5], line 49
     47 for s in range(6):
     48     for k in range(6): 
---> 49         f=fem.form(sum([dot(Eps2.T,dot(C,Eps2))[s,k]*dx]))
     50         DD[s,k]=fem.assemble_scalar(f)

File /usr/lib/petsc/lib/python3/dist-packages/dolfinx/fem/forms.py:249, in form(form, dtype, form_compiler_options, jit_options, entity_maps)
    246         return list(map(lambda sub_form: _create_form(sub_form), form))
    247     return form
--> 249 return _create_form(form)

File /usr/lib/petsc/lib/python3/dist-packages/dolfinx/fem/forms.py:244, in form.<locals>._create_form(form)
    241 """Recursively convert ufl.Forms to dolfinx.fem.Form, otherwise
    242 return form argument"""
    243 if isinstance(form, ufl.Form):
--> 244     return _form(form)
    245 elif isinstance(form, collections.abc.Iterable):
    246     return list(map(lambda sub_form: _create_form(sub_form), form))

File /usr/lib/petsc/lib/python3/dist-packages/dolfinx/fem/forms.py:186, in form.<locals>._form(form)
    184 if mesh is None:
    185     raise RuntimeError("Expecting to find a Mesh in the form.")
--> 186 ufcx_form, module, code = jit.ffcx_jit(
    187     mesh.comm, form, form_compiler_options=form_compiler_options, jit_options=jit_options
    188 )
    190 # For each argument in form extract its function space
    191 V = [arg.ufl_function_space()._cpp_object for arg in form.arguments()]

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

File /usr/lib/petsc/lib/python3/dist-packages/dolfinx/jit.py:201, in ffcx_jit(ufl_object, form_compiler_options, jit_options)
    199 # Switch on type and compile, returning cffi object
    200 if isinstance(ufl_object, ufl.Form):
--> 201     r = ffcx.codegeneration.jit.compile_forms([ufl_object], options=p_ffcx, **p_jit)
    202 elif isinstance(ufl_object, ufl.AbstractFiniteElement):
    203     r = ffcx.codegeneration.jit.compile_elements([ufl_object], options=p_ffcx, **p_jit)

File /usr/lib/python3/dist-packages/ffcx/codegeneration/jit.py:276, in compile_forms(forms, options, cache_dir, timeout, cffi_extra_compile_args, cffi_verbose, cffi_debug, cffi_libraries, visualise)
    274     except Exception:
    275         pass
--> 276     raise e
    278 obj, module = _load_objects(cache_dir, module_name, form_names)
    279 return obj, module, (decl, impl)

File /usr/lib/python3/dist-packages/ffcx/codegeneration/jit.py:256, in compile_forms(forms, options, cache_dir, timeout, cffi_extra_compile_args, cffi_verbose, cffi_debug, cffi_libraries, visualise)
    253     for name in form_names:
    254         decl += form_template.format(name=name)
--> 256     impl = _compile_objects(
    257         decl,
    258         forms,
    259         form_names,
    260         module_name,
    261         p,
    262         cache_dir,
    263         cffi_extra_compile_args,
    264         cffi_verbose,
    265         cffi_debug,
    266         cffi_libraries,
    267         visualise=visualise,
    268     )
    269 except Exception as e:
    270     try:
    271         # remove c file so that it will not timeout next time

File /usr/lib/python3/dist-packages/ffcx/codegeneration/jit.py:383, in _compile_objects(decl, ufl_objects, object_names, module_name, options, cache_dir, cffi_extra_compile_args, cffi_verbose, cffi_debug, cffi_libraries, visualise)
    379 libraries = _libraries + cffi_libraries if cffi_libraries is not None else _libraries
    381 # JIT uses module_name as prefix, which is needed to make names of all struct/function
    382 # unique across modules
--> 383 _, code_body = ffcx.compiler.compile_ufl_objects(
    384     ufl_objects, prefix=module_name, options=options, visualise=visualise
    385 )
    387 ffibuilder = cffi.FFI()
    389 ffibuilder.set_source(
    390     module_name,
    391     code_body,
   (...)
    394     libraries=libraries,
    395 )

File /usr/lib/python3/dist-packages/ffcx/compiler.py:118, in compile_ufl_objects(ufl_objects, options, object_names, prefix, visualise)
    116 # Stage 3: code generation
    117 cpu_time = time()
--> 118 code = generate_code(ir, options)
    119 _print_timing(3, time() - cpu_time)
    121 # Stage 4: format code

File /usr/lib/python3/dist-packages/ffcx/codegeneration/codegeneration.py:58, in generate_code(ir, options)
     54 code_finite_elements = [
     55     finite_element_generator(element_ir, options) for element_ir in ir.elements
     56 ]
     57 code_dofmaps = [dofmap_generator(dofmap_ir, options) for dofmap_ir in ir.dofmaps]
---> 58 code_integrals = [integral_generator(integral_ir, options) for integral_ir in ir.integrals]
     59 code_forms = [form_generator(form_ir, options) for form_ir in ir.forms]
     60 code_expressions = [
     61     expression_generator(expression_ir, options) for expression_ir in ir.expressions
     62 ]

File /usr/lib/python3/dist-packages/ffcx/codegeneration/codegeneration.py:58, in <listcomp>(.0)
     54 code_finite_elements = [
     55     finite_element_generator(element_ir, options) for element_ir in ir.elements
     56 ]
     57 code_dofmaps = [dofmap_generator(dofmap_ir, options) for dofmap_ir in ir.dofmaps]
---> 58 code_integrals = [integral_generator(integral_ir, options) for integral_ir in ir.integrals]
     59 code_forms = [form_generator(form_ir, options) for form_ir in ir.forms]
     60 code_expressions = [
     61     expression_generator(expression_ir, options) for expression_ir in ir.expressions
     62 ]

File /usr/lib/python3/dist-packages/ffcx/codegeneration/C/integrals.py:41, in generator(ir, options)
     38 ig = IntegralGenerator(ir, backend)
     40 # Generate code ast for the tabulate_tensor body
---> 41 parts = ig.generate()
     43 # Format code as string
     44 CF = CFormatter(options["scalar_type"])

File /usr/lib/python3/dist-packages/ffcx/codegeneration/integral_generator.py:166, in IntegralGenerator.generate(self)
    162     all_preparts += self.generate_piecewise_partition(rule)
    164     # Generate code to integrate reusable blocks of final
    165     # element tensor
--> 166     all_quadparts += self.generate_quadrature_loop(rule)
    168 # Collect parts before, during, and after quadrature loops
    169 parts += all_preparts

File /usr/lib/python3/dist-packages/ffcx/codegeneration/integral_generator.py:271, in IntegralGenerator.generate_quadrature_loop(self, quadrature_rule)
    268 definitions, intermediates_0 = self.generate_varying_partition(quadrature_rule)
    270 # Generate dofblock parts, some of this will be placed before or after quadloop
--> 271 tensor_comp, intermediates_fw = self.generate_dofblock_partition(quadrature_rule)
    272 assert all([isinstance(tc, L.Section) for tc in tensor_comp])
    274 # Check if we only have Section objects

File /usr/lib/python3/dist-packages/ffcx/codegeneration/integral_generator.py:385, in IntegralGenerator.generate_dofblock_partition(self, quadrature_rule)
    383 intermediates = []
    384 for blockmap in block_groups:
--> 385     block_quadparts, intermediate = self.generate_block_parts(
    386         quadrature_rule, blockmap, block_groups[blockmap]
    387     )
    388     intermediates += intermediate
    390     # Add computations

File /usr/lib/python3/dist-packages/ffcx/codegeneration/integral_generator.py:504, in IntegralGenerator.generate_block_parts(self, quadrature_rule, blockmap, blocklist)
    500         assert all(isinstance(o, L.Symbol) for o in output)
    502         intermediates += [L.VariableDecl(fw, fw_rhs)]
--> 504 var = fw if isinstance(fw, L.Symbol) else fw.array
    505 vars += [var]
    506 assert not blockdata.transposed, "Not handled yet"

AttributeError: 'LiteralFloat' object has no attribute 'array'

I don’t understand how to remove the Literal Form error. However, assembling constant matrix C doesn’t make error.

Q2. How can I add subdomain data for the above interval mesh. The MeshFunction is not supoorted in dolfinx.

Any help is greatly appreciated.

2

For the first issue, it seems to be a bug in DOLFINx that means that one cannot access a component of a transposed tensor.
MWE:

from mpi4py import MPI
import dolfinx
import ufl

mesh = dolfinx.mesh.create_unit_square(MPI.COMM_WORLD, 1, 1)
C = ufl.as_tensor([[1, 0, 0], [0, 1, 1], [0, 0, 1]])

int = ufl.transpose(C)[0, 1]
dx = ufl.Measure("dx", domain=mesh)
form = dolfinx.fem.form(int * dx)

In DOLFINx you use MeshTags, which is very similar to MeshFunction in legacy Dolfin. There are plenty of tutorials and demos using it.

1 Like
3

Thanks for your response. The error is still there if I do not use the transpose.

f=fem.form(sum([dot(Eps2,dot(C,Eps2))[s,k]*dx]))

The error doesn’t appear on using only single dot function dot(C,Eps2).

after defining meshtags for a mesh, do I need to update dx as

mesh_tags=dolfinx.mesh.meshtags(mesh, mesh.topology.dim, cells, np.array(matid[0]))
dx = Measure('dx')(domain=mesh, subdomain_data=mesh_tags)

or defining meshtags in line 1 is the final step.

4

I’ve added an issue at:

and wills he how far I can get with debugging it tonight.

I am not sure if your input to meshtags here make sense. What is cells and matid[0]?
Yes, you would have to supply the mesh_tags as subdomain-data to the Measure if you want to use it.

1 Like
5

@bagla0 PR for resolving the issue has been submitted at: Remove zero Lexpr check by jorgensd · Pull Request #701 · FEniCS/ffcx · GitHub

1 Like
6

@dokken ,

I find the issue is closed and updated to main branch of ffcx. How can get this recent update reflected in my dolfinx code? My code still shows same error.

I have updated fenicsx but, nothing changes.

7

How did you update your DOLFINx installation?

8

I have an ubuntu system. Using:

sudo apt upgrade
sudo apt update
sudo apt install fenicsx
9

You would need to wait for the next release (0.9.0) to get the update through apt.

10

@dokken
Can I get back to previous v08 release where it was working in my ubuntu?
Kindly tell any procedure to do so as that it could work as in previous dolfinx version?

What would be the approx. wait time?

11

See: software installation - How to install specific version of some package? - Ask Ubuntu
and
https://packages.ubuntu.com/noble/python3-dolfinx

12

If you started with dolfinx 0.8.0, your updated installation will still be a 0.8.0 version. We may have had to refresh the package upload due to technical maintenance, but we definitely didn’t upgrade dolfinx to a new released version (because there isn’t one).

If you feel adventorous, you may want to open the file reported at Remove zero Lexpr check by jorgensd · Pull Request #701 · FEniCS/ffcx · GitHub in your system and comment out the three lines you see highlighted in red. If you don’t know where ffcx is installed, a simple

python3 -c 'import ffcx, os; print(os.path.dirname(ffcx.__file__))'

will tell you its path.