Adaptive mesh refinement, problem with boundary terms in linear form

[Sven Joachim]

Hello,

when running the attached file the following problem occurs. When I consider

L = inner(f, v)*dx

I can solve a linear elasticity equation with adaptive mesh refinement.

Whenever I include terms with ds in the linear form, like

L = inner(f, v)*dx + inner(g, v)*ds(2)

I receive the following error message:

In instant.recompile: The module did not compile with command 'make VERBOSE=1 ', see '/home/kimmerle/.instant/error/instant_module_f85117a588b102c37e97eb08e8ba64a1195dcf6a/compile.log'
Traceback (most recent call last):
  File "Test_MinimalExample.py", line 57, in <module>
    solve(a == L, u, bc, tol=5.0E-7, M=MF) #Solve adaptively
  File "/usr/lib/python2.7/dist-packages/dolfin/fem/solving.py", line 264, in solve
    _solve_varproblem_adaptive(*args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/dolfin/fem/solving.py", line 339, in _solve_varproblem_adaptive
    solver = AdaptiveLinearVariationalSolver(problem, M)
  File "/usr/lib/python2.7/dist-packages/dolfin/fem/adaptivesolving.py", line 58, in __init__
    ec = generate_error_control(self.problem, goal)
  File "/usr/lib/python2.7/dist-packages/dolfin/fem/adaptivesolving.py", line 150, in generate_error_control
    forms = [Form(form, form_compiler_parameters=p) for form in ufl_forms]
  File "/usr/lib/python2.7/dist-packages/dolfin/fem/form.py", line 56, in __init__
    common_cell)
  File "/usr/lib/python2.7/dist-packages/dolfin/compilemodules/jit.py", line 66, in mpi_jit
    return local_jit(*args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/dolfin/compilemodules/jit.py", line 154, in jit
    return jit_compile(form, parameters=p, common_cell=common_cell)
  File "/usr/lib/python2.7/dist-packages/ffc/jitcompiler.py", line 77, in jit
    return jit_form(ufl_object, parameters, common_cell)
  File "/usr/lib/python2.7/dist-packages/ffc/jitcompiler.py", line 212, in jit_form
    cache_dir = cache_dir)
  File "/usr/lib/python2.7/dist-packages/ufc_utils/build.py", line 64, in build_ufc_module
    **kwargs)
  File "/usr/lib/python2.7/dist-packages/instant/build.py", line 541, in build_module
    recompile(modulename, module_path, new_compilation_checksum, build_system)
  File "/usr/lib/python2.7/dist-packages/instant/build.py", line 150, in recompile
    instant_error(msg % (cmd, compile_log_filename_dest))
  File "/usr/lib/python2.7/dist-packages/instant/output.py", line 49, in instant_error
    raise RuntimeError(text)
RuntimeError: In instant.recompile: The module did not compile with command 'make VERBOSE=1 ', see '/home/kimmerle/.instant/error/instant_module_f85117a588b102c37e97eb08e8ba64a1195dcf6a/compile.log'

By choosing a fine mesh manually, I can solve the problem by FEniCS accurately. The PDE is well-posed and numerical locking effects have been taken care of.

It seams to me that there is a bug or what might be the issue?

I am working with FEniCS v1.2 in python.

Thanks in advance,

SJ

[Marie Rognes (meg-simula)]

FEniCS no longer uses Launchpad for Bugs. Please consult the
documentation on the FEniCS web page for where and how to (re)post your
issue: http://fenicsproject.org/support/#reporting-bugs
<http://fenicsproject.org/support/>

--
Marie

On 06/07/2013 03:49 PM, Sven Joachim wrote:
> Public bug reported:
>
>
> Hello,
>
> when running the attached file the following problem occurs. When I
> consider
>
> L = inner(f, v)*dx
>
> I can solve a linear elasticity equation with adaptive mesh refinement.
>
> Whenever I include terms with ds in the linear form, like
>
> L = inner(f, v)*dx + inner(g, v)*ds(2)
>
> I receive the following error message:
>
>
> In instant.recompile: The module did not compile with command 'make VERBOSE=1 ', see '/home/kimmerle/.instant/error/instant_module_f85117a588b102c37e97eb08e8ba64a1195dcf6a/compile.log'
> Traceback (most recent call last):
> File "Test_MinimalExample.py", line 57, in <module>
> solve(a == L, u, bc, tol=5.0E-7, M=MF) #Solve adaptively
> File "/usr/lib/python2.7/dist-packages/dolfin/fem/solving.py", line 264, in solve
> _solve_varproblem_adaptive(*args, **kwargs)
> File "/usr/lib/python2.7/dist-packages/dolfin/fem/solving.py", line 339, in _solve_varproblem_adaptive
> solver = AdaptiveLinearVariationalSolver(problem, M)
> File "/usr/lib/python2.7/dist-packages/dolfin/fem/adaptivesolving.py", line 58, in __init__
> ec = generate_error_control(self.problem, goal)
> File "/usr/lib/python2.7/dist-packages/dolfin/fem/adaptivesolving.py", line 150, in generate_error_control
> forms = [Form(form, form_compiler_parameters=p) for form in ufl_forms]
> File "/usr/lib/python2.7/dist-packages/dolfin/fem/form.py", line 56, in __init__
> common_cell)
> File "/usr/lib/python2.7/dist-packages/dolfin/compilemodules/jit.py", line 66, in mpi_jit
> return local_jit(*args, **kwargs)
> File "/usr/lib/python2.7/dist-packages/dolfin/compilemodules/jit.py", line 154, in jit
> return jit_compile(form, parameters=p, common_cell=common_cell)
> File "/usr/lib/python2.7/dist-packages/ffc/jitcompiler.py", line 77, in jit
> return jit_form(ufl_object, parameters, common_cell)
> File "/usr/lib/python2.7/dist-packages/ffc/jitcompiler.py", line 212, in jit_form
> cache_dir = cache_dir)
> File "/usr/lib/python2.7/dist-packages/ufc_utils/build.py", line 64, in build_ufc_module
> **kwargs)
> File "/usr/lib/python2.7/dist-packages/instant/build.py", line 541, in build_module
> recompile(modulename, module_path, new_compilation_checksum, build_system)
> File "/usr/lib/python2.7/dist-packages/instant/build.py", line 150, in recompile
> instant_error(msg % (cmd, compile_log_filename_dest))
> File "/usr/lib/python2.7/dist-packages/instant/output.py", line 49, in instant_error
> raise RuntimeError(text)
> RuntimeError: In instant.recompile: The module did not compile with command 'make VERBOSE=1 ', see '/home/kimmerle/.instant/error/instant_module_f85117a588b102c37e97eb08e8ba64a1195dcf6a/compile.log'
>
>
> By choosing a fine mesh manually, I can solve the problem by FEniCS accurately. The PDE is well-posed and numerical locking effects ...

[Sven Joachim (sven-joachim-kimmerle)]

Since it was indicated to me by Garth Wells, that this is rather a question than a bug, I am reposting my issue as a question.

Any help is welcome. Thanks in advance,

SJ