Problem with FunctionSpace "In instant.recompile" after upgrade to Ubuntu 13.04

Have you tried instant-clean?

Johan

On 04/30/2013 08:46 AM, Torbjørn Bækø Ness wrote:
> New question #227829 on DOLFIN:
> https://answers.launchpad.net/dolfin/+question/227829
>
>
> Hi,
> Yesterday I updated from Ubuntu 12.04 LTS to 13.04, and now I get an error when making a FunctionSpace.
>
>
> imt-iw23014324 ~ $ instant-clean
> Removing 0 modules from Instant cache...
> Removing 1 error logs from Instant cache...
> Removing 3 lock files from Instant cache...
> imt-iw23014324 ~ $ ipython
> Python 2.7.4 (default, Apr 19 2013, 18:28:01)
> Type "copyright", "credits" or "license" for more information.
>
> IPython 0.13.2 -- An enhanced Interactive Python.
> ? -> Introduction and overview of IPython's features.
> %quickref -> Quick reference.
> help -> Python's own help system.
> object? -> Details about 'object', use 'object??' for extra details.
>
> In [1]: from dolfin import *
>
> In [2]: mesh = UnitCubeMesh(10,10,10)
>
> In [3]: V = FunctionSpace(mesh, "CG", 2)
> Calling FFC just-in-time (JIT) compiler, this may take some time.
> In instant.recompile: The module did not compile with command 'make VERBOSE=1 ', see '/home/torbjone/.instant/error/instant_module_a49eb348ce456fe60d36eece210766253e9e756c/compile.log'
> ---------------------------------------------------------------------------
> RuntimeError Traceback (most recent call last)
> <ipython-input-3-8b7206211eee> in <module>()
> ----> 1 V = FunctionSpace(mesh, "CG", 2)
>
> /usr/lib/python2.7/dist-packages/dolfin/functions/functionspace.pyc in __init__(self, mesh, family, degree, form_degree, constrained_domain, restriction)
> 388
> 389 # Initialize base class
> --> 390 FunctionSpaceBase.__init__(self, mesh, element, constrained_domain)
> 391
> 392 self.___degree = degree
>
> /usr/lib/python2.7/dist-packages/dolfin/functions/functionspace.pyc in __init__(self, mesh, element, constrained_domain)
> 82
> 83 # JIT-compile element to get ufc_element and ufc_dofmap
> ---> 84 ufc_element, ufc_dofmap = jit(self._ufl_element)
> 85
> 86 # Instantiate DOLFIN FiniteElement and DofMap
>
> /usr/lib/python2.7/dist-packages/dolfin/compilemodules/jit.pyc in mpi_jit(*args, **kwargs)
> 64 # Just call JIT compiler when running in serial
> 65 if MPI.num_processes() == 1:
> ---> 66 return local_jit(*args, **kwargs)
> 67
> 68 # Compile first on process 0
>
> /usr/lib/python2.7/dist-packages/dolfin/compilemodules/jit.pyc in jit(form, form_compiler_parameters, common_cell)
> 152 raise RuntimeError, "Form compiler must implement the jit function."
> 153
> --> 154 return jit_compile(form, parameters=p, common_cell=common_cell)
>
> /usr/lib/python2.7/dist-packages/ffc/jitcompiler.pyc in jit(ufl_object, parameters, common_cell)
> 73 # Check if we get an element or a form
> 74 if isinstance(ufl_object, FiniteElementBase):
> ---> 75 return jit_element(ufl_object, parameters)
> 76 else:
> 77 return jit_form(ufl_object, parameters, common_cell)
>
> /usr/lib/python2.7/dist-packages/ffc/jitcompiler.pyc in jit_element(element, parameters)
> 242
> 243 # Compile form
> --> 244 compiled_form, module, form_data, prefix = jit_form(form, parameters)
> 245
> 246 return _extract_element_and_dofmap(module, prefix, form_data)
>
> /usr/lib/python2.7/dist-packages/ffc/jitcompiler.pyc in jit_form(form, parameters, common_cell)
> 210 cppargs = parameters["cpp_optimize_flags"].split() \
> 211 if parameters["cpp_optimize"] else ["-O0"],
> --> 212 cache_dir = cache_dir)
> 213
> 214 # Remove code
>
> /usr/lib/python2.7/dist-packages/ufc_utils/build.pyc in build_ufc_module(h_files, source_directory, system_headers, swig_binary, swig_path, **kwargs)
> 62 system_headers = system_headers,
> 63 cmake_packages = ["UFC"],
> ---> 64 **kwargs)
> 65
> 66 def extract_declarations(h_files):
>
> /usr/lib/python2.7/dist-packages/instant/build.pyc 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)
> 539
> 540 # Recompile if necessary
> --> 541 recompile(modulename, module_path, new_compilation_checksum, build_system)
> 542
> 543 # --- Load, cache, and return module
>
> /usr/lib/python2.7/dist-packages/instant/build.pyc in recompile(modulename, module_path, new_compilation_checksum, build_system)
> 148 os.remove(compilation_checksum_filename)
> 149 msg = "In instant.recompile: The module did not compile with command '%s', see '%s'"
> --> 150 instant_error(msg % (cmd, compile_log_filename_dest))
> 151
> 152 finally:
>
> /usr/lib/python2.7/dist-packages/instant/output.pyc in instant_error(*message)
> 47 _log.error(*message)
> 48 text = message[0] % message[1:]
> ---> 49 raise RuntimeError(text)
> 50
> 51 def instant_assert(condition, *message):
>
> RuntimeError: In instant.recompile: The module did not compile with command 'make VERBOSE=1 ', see '/home/torbjone/.instant/error/instant_module_a49eb348ce456fe60d36eece210766253e9e756c/compile.log'
>
> In [4]:
>
> The output of "cat /home/torbjone/.instant/error/instant_module_a49eb348ce456fe60d36eece210766253e9e756c/compile.log" is:
>
>
>
> In [4]: cat /home/torbjone/.instant/error/instant_module_a49eb348ce456fe60d36eece210766253e9e756c/compile.log
> -- The C compiler identification is GNU 4.7.3
> -- The CXX compiler identification is GNU 4.7.3
> -- Check for working C compiler: /usr/bin/cc
> -- Check for working C compiler: /usr/bin/cc -- works
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Check for working CXX compiler: /usr/bin/c++
> -- Check for working CXX compiler: /usr/bin/c++ -- works
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> -- Found SWIG: /usr/bin/swig2.0 (found version "2.0.8")
> -- Configuring done
> -- Generating done
> CMake Warning:
> Manually-specified variables were not used by the project:
>
> DEBUG
>
>
> -- Build files have been written to: /tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c
> /usr/bin/cmake -H/tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c -B/tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c --check-build-system CMakeFiles/Makefile.cmake 0
> /usr/bin/cmake -E cmake_progress_start /tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c/CMakeFiles /tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c/CMakeFiles/progress.marks
> make -f CMakeFiles/Makefile2 all
> make[1]: Entering directory `/tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c'
> make -f CMakeFiles/_instant_module_a49eb348ce456fe60d36eece210766253e9e756c.dir/build.make CMakeFiles/_instant_module_a49eb348ce456fe60d36eece210766253e9e756c.dir/depend
> make[2]: Entering directory `/tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c'
> /usr/bin/cmake -E cmake_progress_report /tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c/CMakeFiles 1
> [ 50%] Swig source
> /usr/bin/cmake -E make_directory /tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c
> /usr/bin/swig2.0 -python -module instant_module_a49eb348ce456fe60d36eece210766253e9e756c -shadow -modern -modernargs -fastdispatch -fvirtual -nosafecstrings -noproxydel -fastproxy -fastinit -fastunpack -fastquery -nobuildnone -outdir /tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c -c++ -I/usr/include -I/usr/include/python2.7 -I/usr/include/i386-linux-gnu/python2.7 -I/usr/include -I/tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c -o /tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c/instant_module_a49eb348ce456fe60d36eece210766253e9e756cPYTHON_wrap.cxx /tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c/instant_module_a49eb348ce456fe60d36eece210766253e9e756c.i
> cd /tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c /tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c /tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c /tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c /tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c/CMakeFiles/_instant_module_a49eb348ce456fe60d36eece210766253e9e756c.dir/DependInfo.cmake --color=
> Dependee "/tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c/CMakeFiles/_instant_module_a49eb348ce456fe60d36eece210766253e9e756c.dir/DependInfo.cmake" is newer than depender "/tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c/CMakeFiles/_instant_module_a49eb348ce456fe60d36eece210766253e9e756c.dir/depend.internal".
> Dependee "/tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c/CMakeFiles/_instant_module_a49eb348ce456fe60d36eece210766253e9e756c.dir/depend.internal".
> Scanning dependencies of target _instant_module_a49eb348ce456fe60d36eece210766253e9e756c
> make[2]: Leaving directory `/tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c'
> make -f CMakeFiles/_instant_module_a49eb348ce456fe60d36eece210766253e9e756c.dir/build.make CMakeFiles/_instant_module_a49eb348ce456fe60d36eece210766253e9e756c.dir/build
> make[2]: Entering directory `/tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c'
> /usr/bin/cmake -E cmake_progress_report /tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c/CMakeFiles 2
> [100%] Building CXX object CMakeFiles/_instant_module_a49eb348ce456fe60d36eece210766253e9e756c.dir/instant_module_a49eb348ce456fe60d36eece210766253e9e756cPYTHON_wrap.cxx.o
> /usr/bin/c++ -D_instant_module_a49eb348ce456fe60d36eece210766253e9e756c_EXPORTS -fPIC -I/usr/include/python2.7 -I/usr/include/i386-linux-gnu/python2.7 -I/tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c -o CMakeFiles/_instant_module_a49eb348ce456fe60d36eece210766253e9e756c.dir/instant_module_a49eb348ce456fe60d36eece210766253e9e756cPYTHON_wrap.cxx.o -c /tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c/instant_module_a49eb348ce456fe60d36eece210766253e9e756cPYTHON_wrap.cxx
> make[2]: *** No rule to make target `/usr/lib/i386-linux-gnu/libpython2.7.so', needed by `_instant_module_a49eb348ce456fe60d36eece210766253e9e756c.so'. Stop.
> make[2]: Leaving directory `/tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c'
> make[1]: *** [CMakeFiles/_instant_module_a49eb348ce456fe60d36eece210766253e9e756c.dir/all] Error 2
> make[1]: Leaving directory `/tmp/tmp8uqFSf2013-4-30-08-38_instant/instant_module_a49eb348ce456fe60d36eece210766253e9e756c'
> make: *** [all] Error 2
>
> Any idea what's wrong?
>
>
> You received this question notification because you are a member of
> DOLFIN Team, which is an answer contact for DOLFIN.
>

This is the same problem as reported here:

https://answers.launchpad.net/fenics/+question/227822

Thanks Johannes Ring, that solved my question.

Maybe I spoke too fast here, I have a new error message now:

/home/torbjone/work/moi_verification/elec_size/elec_impact.py in superposition_electrode_fem(solver_params, charges_pos, elec_pos, sigma_T, sigma_S, magnitudes, mesh_dict, elec_name, elec_r)
     74 point = Point(pos[0], pos[1], pos[2])
     75 delta = PointSource(V, point, magnitudes[idx])
---> 76 delta.apply(b)
     77
     78 solve(A, phi.vector(), b, solver_params["linear_solver"],

RuntimeError:

*** -------------------------------------------------------------------------
*** DOLFIN encountered an error. If you are not able to resolve this issue
*** using the information listed below, you can ask for help at
***
*** https://answers.launchpad.net/dolfin
***
*** Remember to include the error message listed below and, if possible,
*** include a *minimal* running example to reproduce the error.
***
*** -------------------------------------------------------------------------
*** Error: Unable to create intersection operator.
*** Reason: IntersectionOperatorImplementation is not available, DOLFIN has been compiled without CGAL.
*** Where: This error was encountered inside IntersectionOperator.cpp.
*** Process: 0
*** -------------------------------------------------------------------------

imt-iw23014324 ~/work/moi_verification/elec_size(master) $

I have googled it but the 'standard' answer seems to be to install FEniCS with PPA, but that is what I have done.
When runing has_cgal() dolfin confirmes that it's false.

This is a different issue. DOLFIN 1.2.0 requires CGAL >= 4.1, while Ubuntu 13.04 only has CGAL 4.0.2. I will add CGAL 4.1 to the PPA for Ubuntu 13.04 and rebuild the DOLFIN packages.

There was some CGAL stuff in the software update this morning, but it didn't seem to change anything. Should it have?

No, it is not fixed yet. I'll let you know.

Thanks Johannes Ring, that solved my question.