For the package listing from fenics-packages/fenics ppa, I only have the following packages show up:
python-petsc4py dolfin-dev dolfin-doc dolfin-bin python-dolfin python-dolfin-dbg libdolfin1.3-dev libdolfin1.3 libdolfin1.3-dbg Do I need to import the old 'saucy' packages somehow that haven't migrated over to 'trusty'? --Christopher On Fri, May 30, 2014 at 11:31 AM, Johannes Ring <[email protected]> wrote: > ufc.h is installed by the ufc package and you should find it in > /usr/include. > > Johannes > On May 30, 2014 6:53 PM, "Christopher DeMars" <[email protected]> > wrote: > >> 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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