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'
make[2]: ***
[ffc_form_b71eb25668e7c5158b0a24c305b338c0bbd5659fPYTHON_wrap.cxx] Error 1
make[2]: Leaving directory
`/tmp/tmp9K06tX2014-5-29-12-59_instant_dc69080b0724c43ba7e4f2ffda69942354ba0b6a/ffc_form_b71eb25668e7c5158b0a24c305b338c0bbd5659f'
make[1]: ***
[CMakeFiles/_ffc_form_b71eb25668e7c5158b0a24c305b338c0bbd5659f.dir/all]
Error 2
make[1]: Leaving directory
`/tmp/tmp9K06tX2014-5-29-12-59_instant_dc69080b0724c43ba7e4f2ffda69942354ba0b6a/ffc_form_b71eb25668e7c5158b0a24c305b338c0bbd5659f'
make: *** [all] Error 2
On Thu, May 29, 2014 at 9:49 AM, Johannes Ring <[email protected]> wrote:
> [Please keep fenics-support in Cc]
>
> On Thu, May 29, 2014 at 6:13 PM, Christopher DeMars
> <[email protected]> wrote:
> > I have been beating my head against this problem for the last 2+ days.
> >
> > I'll start with the ppa error. I will send the other errors along later
> > since the build fails at the very end of a long compile.
> >
> > First, my environment:
> >
> > $ lsb_release -a
> > LSB Version:
> >
> core-2.0-amd64:core-2.0-noarch:core-3.0-amd64:core-3.0-noarch:core-3.1-amd64:core-3.1-noarch:core-3.2-amd64:core-3.2-noarch:core-4.0-amd64:core-4.0-noarch
> > Distributor ID: Ubuntu
> > Description: Ubuntu 14.04 LTS
> > Release: 14.04
> > Codename: trusty
> >
> >
> >
> > Next, how I installed fenics a couple of minutes ago:
> >
> > sudo ppa-purge ppa:fenics-packages/fenics-dev
> > sudo ppa-purge ppa:fenics-packages/fenics
> > sudo apt-get autoremove
> > sudo add-apt-repository ppa:fenics-packages/fenics
> > sudo apt-get update
> > sudo apt-get dist-upgrade
> > sudo apt-get install fenics
> >
> >
> >
> > Lastly, the error:
> >
> > $ ipython
> > Python 2.7.6 (default, Mar 22 2014, 22:59:56)
> > Type "copyright", "credits" or "license" for more information.
> >
> > In [1]: run Lshape
> > Set the environment variable CBCCFD to the location of /cbcpdesys/cbc/cfd
> >
> ---------------------------------------------------------------------------
> > TypeError Traceback (most recent call
> last)
> > /usr/lib/python2.7/dist-packages/IPython/utils/py3compat.pyc in
> > execfile(fname, *where)
> > 202 else:
> > 203 filename = fname
> > --> 204 __builtin__.execfile(filename, *where)
> >
> >
> /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)
> > 106
> > 107 # Create all FunctionSpaces, Functions,
> Test-TrialFunctions
> > etc.
> > --> 108 self.setup()
> > 109
> > 110 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)
> > 119
> > 120 self.define_function_spaces(self.mesh,
> self.prm['degree'],
> > --> 121 self.prm['space'],
> self.prm['family'],
> > symmetry)
> > 122 self.setup_subsystems()
> > 123 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, symmetry)
> > 134 """Define functionspaces for names and system_names"""
> > 135 V = self.V = dict((name, space[name](mesh, family[name],
> > degree[name],
> > --> 136 **symmetry[name])) for name in
> self.names
> > + ['dq'])
> > 137
> > 138 # Add function space for compound functions for the sub
> > systems
> >
> > /usr/local/lib/python2.7/dist-packages/cbc/pdesys/PDESystem.py in
> > <genexpr>((name,))
> > 134 """Define functionspaces for names and system_names"""
> > 135 V = self.V = dict((name, space[name](mesh, family[name],
> > degree[name],
> > --> 136 **symmetry[name])) for name in
> self.names
> > + ['dq'])
> > 137
> > 138 # 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)
> >
> >
> > TypeError: jit() got an unexpected keyword argument 'common_cell'
>
> I see that you are running the Lshape.py from the CBC.PDESys package.
> Are you using the development version of CBC.PDESYS? I tried it now in
> a clean Ubuntu 14.04 machine and it worked fine. Here is what I did:
>
> sudo add-apt-repository -y ppa:fenics-packages/fenics
> sudo apt-get update
> sudo apt-get -y install fenics
> bzr branch lp:cbcpdesys
> cd cbcpdesys
> export PYTHONPATH=$PWD:$PYTHONPATH
> cd cbc
> export PYTHONPATH=$PWD:$PYTHONPATH
> cd cfd/problems
> python Lshape.py
>
> Maybe you have some files in /usr/local that are interfering with the
> FEniCS installation from the FEniCS PPA?
>
> Johannes
>
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