bug#57143: python-dolfin-adjoint / FEniCS fails to build

bug#57143: python-dolfin-adjoint / FEniCS fails to build

[Andreas Enge]

Hello,

when updating python-sympy, I noticed that its dependent python-dolfin-adjoint
fails to build. Probably this was also true before, since we do not have a
substitute.

I think the problem was in FEniCS, with an assertion failure, so my
impression was that the code computed a wrong solution.

It would be nice if someone with special knowledge could have a look;
some of the packages in the family also have updates available (but not
dolfin itself if I saw correctly).

Andreas

bug#57143: Test failure in python-dolfin-adjoint

[Andreas Enge]

Hello,

below are more details on the current test failure of python-dolfin-adjoint
version 2019.1.0. Maybe an option would be to try to update to a newer
version? There is 2019.1.2.

Andreas


=================================== FAILURES ===================================
_____________________________ test_read_checkpoint _____________________________

    def test_read_checkpoint():
        with stop_annotating():
            N = 15
            mesh = UnitSquareMesh(N, N)
            V = FunctionSpace(mesh, "CG", 1)
            x = SpatialCoordinate(mesh)
            v = project(x[0]*x[1]*cos(x[1]), V)
            out = XDMFFile(file_from_curr_dir("scalar.xdmf"))
            out.write_checkpoint(v, "u", 0.0)
            out.close()
            exact = assemble(v*dx)

        mesh = UnitSquareMesh(N, N)
        V = FunctionSpace(mesh, "CG", 1)
        v = Function(V)
        c = Control(v)
        J = assemble(v*dx)
        infile = XDMFFile(file_from_curr_dir("scalar.xdmf"))
        u = Function(V)
>       infile.read_checkpoint(u,'u', -1)

tests/fenics_adjoint/test_io.py:38:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <dolfin.cpp.io.XDMFFile object at 0x7fffb58557f0>
args = (Coefficient(FunctionSpace(Mesh(VectorElement(FiniteElement('Lagrange', triangle, 1), dim=2), 38754), FiniteElement('Lagrange', triangle, 1)), 38769), 'u', -1)
kwargs = {}, annotate = True

    def XDMFFile_read_checkpoint(self, *args, **kwargs):
        annotate = annotate_tape(kwargs)
>       output = __XDMFFile_read_checkpoint__(self, *args, **kwargs)
E       RuntimeError: basic_string::_M_construct null not valid

/gnu/store/p7hjddizapgmdk62dpvmrdkac0d4l3r9-python-dolfin-adjoint-2019.1.0/lib/python3.10/site-packages/fenics_adjoint/types/io.py:48: RuntimeError
----------------------------- Captured stdout call -----------------------------
Calling FFC just-in-time (JIT) compiler, this may take some time.
------------------------------ Captured log call -------------------------------
Level 25 FFC:log.py:127 Calling FFC just-in-time (JIT) compiler, this may take some time.
INFO     FFC:log.py:127 Compiling form ffc_form_e905624fad7a62b101d5d4bc784070d31ec0cc46

INFO     FFC:log.py:127 Compiler stage 1: Analyzing form(s)
INFO     FFC:log.py:127 -----------------------------------
DEBUG    FFC:log.py:127   Preprocessing form using 'uflacs' representation family.
INFO     FFC:log.py:127
INFO     FFC:log.py:127   Geometric dimension:       2
  Number of cell subdomains: 0
  Rank:                      1
  Arguments:                 '(v_0)'
  Number of coefficients:    0
  Coefficients:              '[]'
  Unique elements:           'CG1(?,?), Vector<2 x CG1(?,?)>'
  Unique sub elements:       'CG1(?,?), Vector<2 x CG1(?,?)>'

INFO     FFC:log.py:127   representation:    auto --> uflacs
INFO     FFC:log.py:127   quadrature_rule:   auto --> default
INFO     FFC:log.py:127   quadrature_degree: auto --> 6
INFO     FFC:log.py:127   quadrature_degree: 6
INFO     FFC:log.py:127
INFO     FFC:log.py:127 Compiler stage 1 finished in 0.00596237 seconds.

INFO     FFC:log.py:127 Compiler stage 2: Computing intermediate representation
INFO     FFC:log.py:127 -------------------------------------------------------
INFO     FFC:log.py:127   Computing representation of 0 elements
INFO     FFC:log.py:127   Computing representation of 0 dofmaps
INFO     FFC:log.py:127   Computing representation of 0 coordinate mappings
INFO     FFC:log.py:127   Computing representation of integrals
INFO     FFC:log.py:127   Computing uflacs representation
DEBUG    FFC:log.py:127   Reusing element from cache
DEBUG    FFC:log.py:127   Reusing element from cache
DEBUG    FFC:log.py:127   Reusing element from cache
DEBUG    FFC:log.py:127   Reusing element from cache
DEBUG    FFC:log.py:127   Reusing element from cache
DEBUG    FFC:log.py:127   Reusing element from cache
DEBUG    FFC:log.py:127   Reusing element from cache
DEBUG    FFC:log.py:127   Reusing element from cache
DEBUG    FFC:log.py:127   Reusing element from cache
DEBUG    FFC:log.py:127   Reusing element from cache
DEBUG    FFC:log.py:127   Reusing element from cache
DEBUG    FFC:log.py:127   Reusing element from cache
DEBUG    FFC:log.py:127   Reusing element from cache
DEBUG    UFL:log.py:127 Blocks of each mode:
  1	full
INFO     FFC:log.py:127   Computing representation of forms
INFO     FFC:log.py:127
INFO     FFC:log.py:127 Compiler stage 2 finished in 0.0164835 seconds.

INFO     FFC:log.py:127 Compiler stage 3: Optimizing intermediate representation
INFO     FFC:log.py:127 --------------------------------------------------------
INFO     FFC:log.py:127   Optimizing uflacs representation
INFO     FFC:log.py:127
INFO     FFC:log.py:127 Compiler stage 3 finished in 0.000202894 seconds.

INFO     FFC:log.py:127 Compiler stage 4: Generating code
INFO     FFC:log.py:127 ---------------------------------
INFO     FFC:log.py:127   Generating code for 0 finite_element(s)
INFO     FFC:log.py:127   Generating code for 0 dofmap(s)
INFO     FFC:log.py:127   Generating code for 0 coordinate_mapping(s)
INFO     FFC:log.py:127   Generating code for integrals
INFO     FFC:log.py:127   Generating code from ffc.uflacs representation
INFO     FFC:log.py:127   Generating code for forms
INFO     FFC:log.py:127
INFO     FFC:log.py:127 Compiler stage 4 finished in 0.00399137 seconds.

INFO     FFC:log.py:127 Compiler stage 4.1 finished in 9.53674e-07 seconds.

INFO     FFC:log.py:127 Compiler stage 5: Formatting code
INFO     FFC:log.py:127 ---------------------------------
INFO     FFC:log.py:127
INFO     FFC:log.py:127 Compiler stage 5 finished in 0.000437498 seconds.

INFO     FFC:log.py:127 FFC finished in 0.0274181 seconds.
=============================== warnings summary ===============================
../../../gnu/store/v36c8jmb0316czxkqajpkai70kjkmkfy-fenics-2019.1.0.post0/lib/python3.10/site-packages/dolfin_utils/test/fixtures.py:96
  /gnu/store/v36c8jmb0316czxkqajpkai70kjkmkfy-fenics-2019.1.0.post0/lib/python3.10/site-packages/dolfin_utils/test/fixtures.py:96: PytestDeprecationWarning: @pytest.yield_fixture is deprecated.
  Use @pytest.fixture instead; they are the same.
    @pytest.yield_fixture(scope="function")

../../../gnu/store/v36c8jmb0316czxkqajpkai70kjkmkfy-fenics-2019.1.0.post0/lib/python3.10/site-packages/dolfin_utils/test/fixtures.py:230
  /gnu/store/v36c8jmb0316czxkqajpkai70kjkmkfy-fenics-2019.1.0.post0/lib/python3.10/site-packages/dolfin_utils/test/fixtures.py:230: PytestDeprecationWarning: @pytest.yield_fixture is deprecated.
  Use @pytest.fixture instead; they are the same.
    @pytest.yield_fixture(scope="function")

../../../gnu/store/v36c8jmb0316czxkqajpkai70kjkmkfy-fenics-2019.1.0.post0/lib/python3.10/site-packages/dolfin_utils/test/fixtures.py:255
  /gnu/store/v36c8jmb0316czxkqajpkai70kjkmkfy-fenics-2019.1.0.post0/lib/python3.10/site-packages/dolfin_utils/test/fixtures.py:255: PytestDeprecationWarning: @pytest.yield_fixture is deprecated.
  Use @pytest.fixture instead; they are the same.
    def pushpop_parameters():

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED tests/fenics_adjoint/test_io.py::test_read_checkpoint - RuntimeError: ...
= 1 failed, 125 passed, 9 skipped, 1 xfailed, 3 warnings in 839.66s (0:13:59) ==