Bug#863828: python3-instant: undefined symbol: PyClass_Type during interpolate

[Drew Parsons]

On Thu, 1 Jun 2017 10:39:37 +0200 Johannes Ring <johannr at simula.no>
wrote:
> On Thu, Jun 1, 2017 at 10:24 AM, Drew Parsons <dparsons at debian.org>
wrote:
> > Should the vtk section in UseDOLFIN.cmake be controlled with some
> > python3 test, so VTK is still pulled in for python2?
> 
> Yes, we can do that, although I believe the vtk section in
> UseDOLFIN.cmake is not important. I will make a patch.


It's still failing, with python-ffc 2016.2.0-3 and libdolfin-dev
2016.2.0-4 (with UseDOLFIN.cmake patched).

In [4]: u = interpolate(Expression('x[0] + x[1]', degree=1), V)
Calling DOLFIN just-in-time (JIT) compiler, this may take some time.
--- Instant: compiling ---
In instant.import_module_directly: Failed to import module 'dolfin_ee8f3791ac0429f005de8924557ccde25f2d90f2' from '/home/drew/.cache/instant/python3.5/cache/dolfin_ee8f3791ac0429f005de8924557ccde25f2d90f2';
ImportError:dynamic module does not define module export function (PyInit__dolfin_ee8f3791ac0429fd87a23c24557ccde25f2d90f2);
Failed to import module found in cache. Modulename: 'dolfin_ee8f3791ac0429fd87a23c24557ccde25f2d90f2';
Path: '/home/useruser/.cache/instant/python3.5/cache/dolfin_ee8f3791ac0429fd87a23c24557ccde25f2d90f2';
ImportError:dynamic module does not define module export function (PyInit__dolfin_ee8f3791ac0429fd87a23c24557ccde25f2d90f2);
---------------------------------------------------------------------------
AssertionError                            Traceback (most recent call last)
<ipython-input-4-e06382777336> in <module>()
----> 1 u = interpolate(Expression('x[0] + x[1]', degree=1), V)

/usr/lib/python3/dist-packages/dolfin/functions/expression.py in __new__(cls, cppcode, *args, **kwargs)
    652         cpp_base, members = compile_expressions([cppcode],
    653                                                 [generic_function_members],
--> 654                                                 mpi_comm=kwargs.get("mpi_comm"))
    655         cpp_base, members = cpp_base[0], members[0]
    656 

/usr/lib/python3/dist-packages/dolfin/compilemodules/expressions.py in compile_expressions(cppargs, generic_function_members, mpi_comm)
    212         "\n\n".join(code_snippets), classnames,
    213         additional_declarations="\n".join(additional_declarations),
--> 214         mpi_comm=mpi_comm)
    215 
    216     return expression_classes, all_members

/usr/lib/python3/dist-packages/dolfin/compilemodules/expressions.py in compile_expression_code(code, classnames, module_name, additional_declarations, mpi_comm)
    139     compiled_module = compile_extension_module(
    140         code, additional_declarations=additional_declarations,
--> 141         mpi_comm=mpi_comm)
    142 
    143     # Get the compiled class

/usr/lib/python3/dist-packages/dolfin/compilemodules/jit.py in mpi_jit(*args, **kwargs)
     66         # Just call JIT compiler when running in serial
     67         if MPI.size(mpi_comm) == 1:
---> 68             return local_jit(*args, **kwargs)
     69 
     70         # Compile first on process 0

/usr/lib/python3/dist-packages/dolfin/compilemodules/compilemodule.py in compile_extension_module(code, module_name, additional_declarations, additional_system_headers, mpi_comm, **instant_kwargs)
    470             code=code,
    471             additional_declarations=additional_declarations,
--> 472             **instant_kwargs)
    473 
    474     sys.stdout.flush()

/usr/lib/python3/dist-packages/instant/build.py in build_module(modulename, source_directory, code, init_code, additional_definitions, additional_declarations, sources, wrap_headers, local_headers, system_headers, include_dirs, library_dirs, libraries, swigargs, swig_include_dirs, cppargs, lddargs, object_files, arrays, generate_interface, generate_setup, cmake_packages, signature, cache_dir)
    585 
    586         # Import module and place in memory cache
--> 587         module = import_and_cache_module(module_path, modulename, moduleids)
    588 
    589         if not module:

/usr/lib/python3/dist-packages/instant/cache.py in import_and_cache_module(path, modulename, moduleids)
     90     module, e = import_module_directly(path, modulename)
     91     instant_assert(module is not None, "Failed to import module found in cache. Modulename: '%s';\nPath: '%s';\n%s:%s;" % (modulename, path, type(e).__name__,
---> 92                                                                                                                            e))
     93     for moduleid in moduleids:
     94         place_module_in_memory_cache(moduleid, module)

/usr/lib/python3/dist-packages/instant/output.py in instant_assert(condition, *message)
    101         _log.error(*message)
    102         text = message[0] % message[1:]
--> 103         raise AssertionError(text)
    104 
    105 

AssertionError: Failed to import module found in cache. Modulename: 'dolfin_ee8f3791ac0429fd87a23c24557ccde25f2d90f2';
Path: '/home/user/.cache/instant/python3.5/cache/dolfin_ee8f3791ac0429fd87a23c24557ccde25f2d90f2';
ImportError:dynamic module does not define module export function (PyInit__dolfin_ee8f3791ac0429fd87a23cd87a23c24557ccde25f2d90f2);