I have double checked /usr/local and am confident I cleaned everything out.
I purged and reinstalled fenics and company using apt, but the ufc.h header is nowhere to be found on my machine except for the ffc source directory in my downloads folder. What package is ufc.h supplied under? Thank you for your time, this is super frustrating --Christopher On Fri, May 30, 2014 at 3:30 AM, Johannes Ring <[email protected]> wrote: > 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 >
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