On Thu, May 29, 2014 at 10:02 PM, Christopher DeMars <[email protected]> wrote: > I think I've successfully cleaned out any fenics related stuff from > /usr/local. I purged then reinstalled fenics from the ppa. > > Now python is returning a novel error. Any ideas short of a total reformat > of my computer (which isn't viable at this time)? > > > > > In [1]: run Lshape > Set the environment variable CBCCFD to the location of /cbcpdesys/cbc/cfd > 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/paradox/.instant/error/ffc_form_b71eb25668e7c5158b0a24c305b338c0bbd5659f/compile.log' > --------------------------------------------------------------------------- > RuntimeError Traceback (most recent call last) > > /home/paradox/SparkleShare/sediment/sed3d/software/cbcpdesys/cbc/cfd/problems/Lshape.py > in <module>() > 102 #solver = icns.NSFullySegregated(problem, solver_parameters) > 103 #solver = icns.NSCoupled(problem, solver_parameters) > --> 104 solver = icns.NSSegregated(problem, solver_parameters) > 105 solver.pdesubsystems['u'].prm['monitor_convergence'] = True > 106 solver.pdesubsystems['p'].prm['monitor_convergence'] = True > > /usr/local/lib/python2.7/dist-packages/cbc/cfd/icns/NSSegregated.py in > __init__(self, problem, parameters) > 11 NSSolver.__init__(self, system_composition=[['u'], ['p']], > 12 problem=problem, > ---> 13 parameters=parameters) > 14 > 15 def define(self): > > /usr/local/lib/python2.7/dist-packages/cbc/cfd/icns/NSSolver.py in > __init__(self, system_composition, problem, parameters) > 71 > 72 def __init__(self, system_composition, problem, parameters): > ---> 73 PDESystem.__init__(self, system_composition, problem, > parameters) > 74 self.correction = None # For Reynolds stress models > 75 self.resultfile = {} # Files used to store the > solution > > /usr/local/lib/python2.7/dist-packages/cbc/pdesys/PDESystem.py in > __init__(self, system_composition, problem, parameters) > 108 > 109 # Create all FunctionSpaces, Functions, Test-TrialFunctions > etc. > --> 110 self.setup() > 111 > 112 def setup(self): > > > /usr/local/lib/python2.7/dist-packages/cbc/cfd/icns/NSSolver.py in > setup(self) > 76 > 77 def setup(self): > ---> 78 PDESystem.setup(self) > 79 self.problem.NS_solver = self # rename, same as > problem.pdesystems['Navier-Stokes'] > 80 # Create some short forms > > /usr/local/lib/python2.7/dist-packages/cbc/pdesys/PDESystem.py in > setup(self) > 125 > 126 self.define_function_spaces(self.mesh, self.prm['degree'], > --> 127 self.prm['space'], self.prm['family'], > cons) > 128 self.setup_subsystems() > 129 if self.prm['time_integration'] == 'Steady': > > /usr/local/lib/python2.7/dist-packages/cbc/pdesys/PDESystem.py in > define_function_spaces(self, mesh, degree, space, family, cons) > 140 """Define functionspaces for names and system_names""" > 141 V = self.V = dict((name, space[name](mesh, family[name], > degree[name], > --> 142 **cons[name])) for name in self.names + > ['dq']) > 143 > 144 # Add function space for compound functions for the sub > systems > > /usr/local/lib/python2.7/dist-packages/cbc/pdesys/PDESystem.py in > <genexpr>((name,)) > 140 """Define functionspaces for names and system_names""" > 141 V = self.V = dict((name, space[name](mesh, family[name], > degree[name], > --> 142 **cons[name])) for name in self.names + > ['dq']) > 143 > 144 # Add function space for compound functions for the sub > systems > > > /usr/lib/python2.7/dist-packages/dolfin/functions/functionspace.pyc in > __init__(self, mesh, family, degree, dim, form_degree, constrained_domain, > restriction) > 560 > 561 # Initialize base class > --> 562 FunctionSpaceBase.__init__(self, mesh, element, > constrained_domain=constrained_domain) > 563 > 564 class TensorFunctionSpace(FunctionSpaceBase): > > /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) > 58 # Just call JIT compiler when running in serial > 59 if MPI.num_processes() == 1: > ---> 60 return local_jit(*args, **kwargs) > 61 > 62 # Compile first on process 0 > > /usr/lib/python2.7/dist-packages/dolfin/compilemodules/jit.pyc in jit(form, > form_compiler_parameters, common_cell) > 120 raise RuntimeError, "Form compiler must implement the jit > function." > 121 > --> 122 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) > 74 # Check if we get an element or a form > 75 if isinstance(ufl_object, FiniteElementBase): > ---> 76 return jit_element(ufl_object, parameters) > 77 else: > 78 return jit_form(ufl_object, parameters, common_cell) > > /usr/lib/python2.7/dist-packages/ffc/jitcompiler.pyc in jit_element(element, > parameters) > 250 > 251 # Compile form > --> 252 compiled_form, module, form_data, prefix = jit_form(form, > parameters) > 253 > 254 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) > 219 cppargs = parameters["cpp_optimize_flags"].split() \ > 220 if parameters["cpp_optimize"] else ["-O0"], > --> 221 cache_dir = cache_dir) > 222 > 223 # Remove code > > /usr/lib/python2.7/dist-packages/ufc_utils/build.pyc in > build_ufc_module(h_files, source_directory, system_headers, **kwargs) > 71 system_headers = > system_headers, > 72 cmake_packages = ["UFC"], > ---> 73 **kwargs) > 74 > 75 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) > 540 > 541 # Recompile if necessary > --> 542 recompile(modulename, module_path, new_compilation_checksum, > build_system) > 543 > 544 # --- Load, cache, and return module > > /usr/lib/python2.7/dist-packages/instant/build.pyc in recompile(modulename, > module_path, new_compilation_checksum, build_system) > 149 os.remove(compilation_checksum_filename) > 150 msg = "In instant.recompile: The module did not > compile with command '%s', see '%s'" > --> 151 instant_error(msg % (cmd, > compile_log_filename_dest)) > 152 > 153 finally: > > /usr/lib/python2.7/dist-packages/instant/output.pyc in > instant_error(*message) > 55 _log.error(*message) > 56 text = message[0] % message[1:] > ---> 57 raise RuntimeError(text) > 58 > 59 def instant_assert(condition, *message): > > RuntimeError: In instant.recompile: The module did not compile with command > 'make VERBOSE=1', see > '/home/paradox/.instant/error/ffc_form_b71eb25668e7c5158b0a24c305b338c0bbd5659f/compile.log' > > > > > > This is the referenced compile.log: > > > -- The C compiler identification is GNU 4.8.2 > -- The CXX compiler identification is GNU 4.8.2 > -- 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 "2.0.11") > -- Configuring done > -- Generating done > CMake Warning: > Manually-specified variables were not used by the project: > > DEBUG > > > -- Build files have been written to: > /tmp/tmp9K06tX2014-5-29-12-59_instant_dc69080b0724c43ba7e4f2ffda69942354ba0b6a/ffc_form_b71eb25668e7c5158b0a24c305b338c0bbd5659f > /usr/bin/cmake > -H/tmp/tmp9K06tX2014-5-29-12-59_instant_dc69080b0724c43ba7e4f2ffda69942354ba0b6a/ffc_form_b71eb25668e7c5158b0a24c305b338c0bbd5659f > -B/tmp/tmp9K06tX2014-5-29-12-59_instant_dc69080b0724c43ba7e4f2ffda69942354ba0b6a/ffc_form_b71eb25668e7c5158b0a24c305b338c0bbd5659f > --check-build-system CMakeFiles/Makefile.cmake 0 > /usr/bin/cmake -E cmake_progress_start > /tmp/tmp9K06tX2014-5-29-12-59_instant_dc69080b0724c43ba7e4f2ffda69942354ba0b6a/ffc_form_b71eb25668e7c5158b0a24c305b338c0bbd5659f/CMakeFiles > /tmp/tmp9K06tX2014-5-29-12-59_instant_dc69080b0724c43ba7e4f2ffda69942354ba0b6a/ffc_form_b71eb25668e7c5158b0a24c305b338c0bbd5659f/CMakeFiles/progress.marks > make -f CMakeFiles/Makefile2 all > make[1]: Entering directory > `/tmp/tmp9K06tX2014-5-29-12-59_instant_dc69080b0724c43ba7e4f2ffda69942354ba0b6a/ffc_form_b71eb25668e7c5158b0a24c305b338c0bbd5659f' > make -f > CMakeFiles/_ffc_form_b71eb25668e7c5158b0a24c305b338c0bbd5659f.dir/build.make > CMakeFiles/_ffc_form_b71eb25668e7c5158b0a24c305b338c0bbd5659f.dir/depend > make[2]: Entering directory > `/tmp/tmp9K06tX2014-5-29-12-59_instant_dc69080b0724c43ba7e4f2ffda69942354ba0b6a/ffc_form_b71eb25668e7c5158b0a24c305b338c0bbd5659f' > /usr/bin/cmake -E cmake_progress_report > /tmp/tmp9K06tX2014-5-29-12-59_instant_dc69080b0724c43ba7e4f2ffda69942354ba0b6a/ffc_form_b71eb25668e7c5158b0a24c305b338c0bbd5659f/CMakeFiles > 1 > [ 50%] Swig source > /usr/bin/cmake -E make_directory > /tmp/tmp9K06tX2014-5-29-12-59_instant_dc69080b0724c43ba7e4f2ffda69942354ba0b6a/ffc_form_b71eb25668e7c5158b0a24c305b338c0bbd5659f > /usr/bin/swig2.0 -python -module > ffc_form_b71eb25668e7c5158b0a24c305b338c0bbd5659f -shadow -modern > -modernargs -fastdispatch -fvirtual -nosafecstrings -noproxydel -fastproxy > -fastinit -fastunpack -fastquery -nobuildnone -c++ -fcompact -O -I. -small > -outdir > /tmp/tmp9K06tX2014-5-29-12-59_instant_dc69080b0724c43ba7e4f2ffda69942354ba0b6a/ffc_form_b71eb25668e7c5158b0a24c305b338c0bbd5659f > -c++ -I/usr/local/include > -I/tmp/tmp9K06tX2014-5-29-12-59_instant_dc69080b0724c43ba7e4f2ffda69942354ba0b6a/ffc_form_b71eb25668e7c5158b0a24c305b338c0bbd5659f/. > -I/usr/include/python2.7 > -I/tmp/tmp9K06tX2014-5-29-12-59_instant_dc69080b0724c43ba7e4f2ffda69942354ba0b6a/ffc_form_b71eb25668e7c5158b0a24c305b338c0bbd5659f > -o > /tmp/tmp9K06tX2014-5-29-12-59_instant_dc69080b0724c43ba7e4f2ffda69942354ba0b6a/ffc_form_b71eb25668e7c5158b0a24c305b338c0bbd5659f/ffc_form_b71eb25668e7c5158b0a24c305b338c0bbd5659fPYTHON_wrap.cxx > /tmp/tmp9K06tX2014-5-29-12-59_instant_dc69080b0724c43ba7e4f2ffda69942354ba0b6a/ffc_form_b71eb25668e7c5158b0a24c305b338c0bbd5659f/ffc_form_b71eb25668e7c5158b0a24c305b338c0bbd5659f.i > /tmp/tmp9K06tX2014-5-29-12-59_instant_dc69080b0724c43ba7e4f2ffda69942354ba0b6a/ffc_form_b71eb25668e7c5158b0a24c305b338c0bbd5659f/ffc_form_b71eb25668e7c5158b0a24c305b338c0bbd5659f.i:40: > Error: Unable to find 'ufc.h'
This is the error - it cannot find ufc.h. Probably because it is using -I/usr/local/include instead of -I/usr/include. Are you sure you have cleaned out every FEniCS related files in /usr/local? Anything in /usr/local/share/ufc? Johannes _______________________________________________ fenics-support mailing list [email protected] http://fenicsproject.org/mailman/listinfo/fenics-support
