Thank you so much Johannes,
Now Fenics works, although I am still struggling with installing
dolfin-nonnewtonian(I found more recent version of this package called
rheagen).
Now the error message changed to the following:
*$ scons*
/==========================================================
scons: Reading SConscript files ...
scons: done reading SConscript files.
scons: Building targets ...
/usr/bin/c++ -o src/Fluid.os -c -g -O2 -fstack-protector
--param=ssp-buffer-size=4 -Wformat -Werror=format-security
-Wno-deprecated -frounding-math -fopenmp -fPIC -D_FORTIFY_SOURCE=2
-DDOLFIN_VERSION="1.3.0" -DBOOST_UBLAS_NDEBUG -DHAS_HDF5
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE
-D_BSD_SOURCE -DHAS_SLEPC -DHAS_PETSC -DHAS_UMFPACK -DHAS_CHOLMOD
-DHAS_SCOTCH -DHAS_CGAL -DHAS_ZLIB -DHAS_MPI -DHAS_OPENMP -DHAS_QT4
-DHAS_VTK -DHAS_QVTK -I/usr/include/vtk-5.8 -I/usr/include/qt4
-I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include
-I/usr/include/scotch -I/usr/include/suitesparse
-I/usr/lib/petscdir/3.4.2/linux-gnu-c-opt/include
-I/usr/lib/petscdir/3.4.2/include -I/usr/include/eigen3
-I/usr/lib/slepcdir/3.4.2/include
-I/usr/lib/slepcdir/3.4.2/linux-gnu-c-opt/include
-I/usr/lib/slepcdir/3.4.2 -I/usr/include/libxml2 src/Fluid.cpp
src/Fluid.cpp: In member function ‘std::vector<const
dolfin::BoundaryCondition*>
dolfin::Fluid::createBCs(dolfin::FunctionSpace&, bool, bool)’:
src/Fluid.cpp:129:59: error: no matching function for call to
‘std::vector<const
dolfin::BoundaryCondition*>::push_back(dolfin::DirichletBC*)’
*_vel_subdomains, i) );
^
src/Fluid.cpp:129:59: note: candidate is:
In file included from /usr/include/c++/4.8/vector:64:0,
from /usr/include/dolfin/log/Table.h:26,
from /usr/include/dolfin/common/timing.h:25,
from /usr/include/dolfin/common/dolfin_common.h:10,
from /usr/include/dolfin.h:6,
from src/Fluid.h:10,
from src/Fluid.cpp:7:
/usr/include/c++/4.8/bits/stl_vector.h:901:7: note: void
std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = const
dolfin::BoundaryCondition*; _Alloc = std::allocator<const
dolfin::BoundaryCondition*>; std::vector<_Tp, _Alloc>::value_type =
const dolfin::BoundaryCondition*]
push_back(const value_type& __x)
^
/usr/include/c++/4.8/bits/stl_vector.h:901:7: note: no known
conversion for argument 1 from ‘dolfin::DirichletBC*’ to ‘const
dolfin::BoundaryCondition* const&’
src/Fluid.cpp:133:59: error: no matching function for call to
‘std::vector<const
dolfin::BoundaryCondition*>::push_back(dolfin::DirichletBC*)’
*_vel_subdomains, i) );
^
src/Fluid.cpp:133:59: note: candidate is:
In file included from /usr/include/c++/4.8/vector:64:0,
from /usr/include/dolfin/log/Table.h:26,
from /usr/include/dolfin/common/timing.h:25,
from /usr/include/dolfin/common/dolfin_common.h:10,
from /usr/include/dolfin.h:6,
from src/Fluid.h:10,
from src/Fluid.cpp:7:
/usr/include/c++/4.8/bits/stl_vector.h:901:7: note: void
std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = const
dolfin::BoundaryCondition*; _Alloc = std::allocator<const
dolfin::BoundaryCondition*>; std::vector<_Tp, _Alloc>::value_type =
const dolfin::BoundaryCondition*]
push_back(const value_type& __x)
^
/usr/include/c++/4.8/bits/stl_vector.h:901:7: note: no known
conversion for argument 1 from ‘dolfin::DirichletBC*’ to ‘const
dolfin::BoundaryCondition* const&’
src/Fluid.cpp:142:61: error: no matching function for call to
‘std::vector<const
dolfin::BoundaryCondition*>::push_back(dolfin::DirichletBC*)’
*_pinpoint, "pointwise") );
^
src/Fluid.cpp:142:61: note: candidate is:
In file included from /usr/include/c++/4.8/vector:64:0,
from /usr/include/dolfin/log/Table.h:26,
from /usr/include/dolfin/common/timing.h:25,
from /usr/include/dolfin/common/dolfin_common.h:10,
from /usr/include/dolfin.h:6,
from src/Fluid.h:10,
from src/Fluid.cpp:7:
/usr/include/c++/4.8/bits/stl_vector.h:901:7: note: void
std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = const
dolfin::BoundaryCondition*; _Alloc = std::allocator<const
dolfin::BoundaryCondition*>; std::vector<_Tp, _Alloc>::value_type =
const dolfin::BoundaryCondition*]
push_back(const value_type& __x)
^
/usr/include/c++/4.8/bits/stl_vector.h:901:7: note: no known
conversion for argument 1 from ‘dolfin::DirichletBC*’ to ‘const
dolfin::BoundaryCondition* const&’
src/Fluid.cpp: In member function ‘void
dolfin::Fluid::destroyBCs(std::vector<const dolfin::BoundaryCondition*>&)’:
src/Fluid.cpp:151:17: warning: possible problem detected in invocation
of delete operator: [enabled by default]
delete bcs[i];
^
src/Fluid.cpp:151:17: warning: invalid use of incomplete type ‘class
dolfin::BoundaryCondition’ [enabled by default]
In file included from /usr/include/dolfin/fem/dolfin_fem.h:34:0,
from /usr/include/dolfin.h:20,
from src/Fluid.h:10,
from src/Fluid.cpp:7:
/usr/include/dolfin/fem/VariationalProblem.h:32:9: warning: forward
declaration of ‘class dolfin::BoundaryCondition’ [enabled by default]
class BoundaryCondition;
^
src/Fluid.cpp:151:17: note: neither the destructor nor the
class-specific operator delete will be called, even if they are declared
when the class is defined
delete bcs[i];
^
scons: *** [src/Fluid.os] Error 1
scons: building terminated because of errors.
You will need to set library path
*export
LD_LIBRARY_PATH="/home/vasiliy/Dropbox/FEM/rheagen-0.2.0/src:$LD_LIBRARY_PATH"*
Or on a Mac
export
DYLD_LIBRARY_PATH="/home/vasiliy/Dropbox/FEM/rheagen-0.2.0/src:$DYLD_LIBRARY_PATH"
/
===================================
I have added the line (expot LD_LIBRARY_PATH) to my .bashrc, and did
"source ~/.bashrc" although it still shows this error. Is that because
the package is obsolete and syntax in modern fenics differs from the
previous one?
Thanks for the help,
Vasiliy.
On 14-02-19 05:24 AM, Johannes Ring wrote:
On Tue, Feb 18, 2014 at 10:24 PM, Vasiliy <[email protected]> wrote:
Dear Fenics users,
I had a working version of fenics on my ubuntu 13.04. Then I upgraded it to
13.10 Saucy Salamander and reinstalled fenics.
When I try to run some simulations it shows an error:
$ python demo_poisson.py
Incompatible swig versions detected. UFC swig version is not the same as
extension module swig version: '2.0.10' != '2.0.8'
Traceback (most recent call last):
File "demo_poisson.py", line 41, in <module>
V = FunctionSpace(mesh, "Lagrange", 1)
File "/usr/lib/python2.7/dist-packages/dolfin/functions/functionspace.py",
line 403, in __init__
FunctionSpaceBase.__init__(self, mesh, element, constrained_domain)
File "/usr/lib/python2.7/dist-packages/dolfin/functions/functionspace.py",
line 84, in __init__
ufc_element, ufc_dofmap = jit(self._ufl_element)
File "/usr/lib/python2.7/dist-packages/dolfin/compilemodules/jit.py", line
60, in mpi_jit
return local_jit(*args, **kwargs)
File "/usr/lib/python2.7/dist-packages/dolfin/compilemodules/jit.py", line
122, in jit
return jit_compile(form, parameters=p, common_cell=common_cell)
File "/usr/lib/python2.7/dist-packages/ffc/jitcompiler.py", line 76, in
jit
return jit_element(ufl_object, parameters)
File "/usr/lib/python2.7/dist-packages/ffc/jitcompiler.py", line 252, in
jit_element
compiled_form, module, form_data, prefix = jit_form(form, parameters)
File "/usr/lib/python2.7/dist-packages/ffc/jitcompiler.py", line 181, in
jit_form
check_swig_version(module)
File "/usr/lib/python2.7/dist-packages/ffc/jitcompiler.py", line 148, in
check_swig_version
(ufc.__swigversion__, compiled_module.swigversion))
File "<string>", line 1, in <lambda>
File "/usr/lib/python2.7/dist-packages/ufl/log.py", line 154, in error
raise self._exception_type(self._format_raw(*message))
Exception: Incompatible swig versions detected. UFC swig version is not the
same as extension module swig version: '2.0.10' != '2.0.8'
't
I tried to reinstall the SWIG (the older version '2.0.8' ) installing it
from the source but it didn't help.
Do you know any ideas how to make it work?
SWIG 2.0.10 is the version in Ubuntu 13.10 and the one you should use.
Have you tried to run instant-clean?
Johannes
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