Ubuntu
fenics package

FEniCS 1.0 and Ubuntu 11.10 (with Swig 2.0.4)

Asked by Tim Berger

I have updated to Ubuntu 11.10 yesterday and now I get the following error message when I try to execute my FEniCS program:
    left = compile_subdomains('(std::abs(x[0]) < 1e-03) && on_boundary')
  File "/usr/lib/python2.7/dist-packages/dolfin/compilemodules/subdomains.py", line 185, in compile_subdomains
    subdomains = compile_subdomain_code("\n".join(all_code), classnames)
  File "/usr/lib/python2.7/dist-packages/dolfin/compilemodules/subdomains.py", line 119, in compile_subdomain_code
    use_numpy_typemaps=False)
  File "/usr/lib/python2.7/dist-packages/dolfin/compilemodules/jit.py", line 62, in mpi_jit
    return local_jit(*args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/dolfin/compilemodules/compilemodule.py", line 362, in compile_extension_module
    instant_kwargs = configure_instant()
  File "/usr/lib/python2.7/dist-packages/dolfin/compilemodules/compilemodule.py", line 194, in configure_instant
    """%ufc.__swigversion__
OSError: The python extension module of UFC was not compiled with the present version of swig.
Install swig version 2.0.1 or recompile UFC with present swig

I have tried to follow the suggestion. But the Synaptics paket manager seems offers only Swig 2.0.4 and 1.3. Further the paket manager and the update program of Ubuntu are not able to find FEniCS paket sources for the new Ubunutu version.

Are you able to tell when an FEniCS/Dolfin update will be ready?
I would appreciate any hint . Because I think about making a roll-back to the previous Ubuntu. But I have not done such a thing before and I think that this may also take some time effort and maybe you are faster updating than me doing the roll-back.

Or is there a way to switch only this Swig back to version 2.0.1?

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Tim Berger
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Revision history for this message
Tim Berger (tim-berger) said : 		#1

I have tried the Python way to define the boundaries. But the problem occurs only later:

    V = VectorFunctionSpace(mesh, 'CG', 1)
  File "/usr/lib/python2.7/dist-packages/dolfin/functions/functionspace.py", line 456, in __init__
    FunctionSpaceBase.__init__(self, mesh, element)
  File "/usr/lib/python2.7/dist-packages/dolfin/functions/functionspace.py", line 72, in __init__
    ufc_element, ufc_dofmap = jit(self._ufl_element)
  File "/usr/lib/python2.7/dist-packages/dolfin/compilemodules/jit.py", line 62, in mpi_jit
    return local_jit(*args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/dolfin/compilemodules/jit.py", line 105, in jit
    """%cpp.__swigversion__
OSError: PyDOLFIN was not compiled with the present version of swig.
Install swig version 2.0.1 or recompiled PyDOLFIN with present swig

Revision history for this message
Tim Berger (tim-berger) said : 		#2

The boundary definition is now:
    class left_boundary(SubDomain):

        def inside(self, x, on_boundary) :

            return on_boundary and (abs(x[0]) < tol)

    left = left_boundary()
instead of:
left = compile_subdomains('(std::abs(x[0]) < 1e-03) && on_boundary')

Revision history for this message
actionparsnip (andrew-woodhead666) said : 		#3

I suggest reporting a bug

Revision history for this message
Tim Berger (tim-berger) said : 		#4

Is it really bug? I don't know. But it looks like a incompatibility between (the version of Swig which comes with) the new Ubuntu version and the last stable FEniCS release. I guess if one would compile FEniCS with the current Swig it would probably work with the new Ubuntu. But I have not enough experience to do such thing (that is also one reason why I'm using Ubuntu with its colorful desktop environment).
Should a create a bug report anyway? Where should I create it? Here or some place else like the Dolfin answers page?

Revision history for this message
Tim Berger (tim-berger) said : 		#5

I thought a lot about this problem today and I should probably mention that I'm using the 64bit version of Ubuntu 11.10.
During the update to the new Ubuntu version the name of this version which is part of the software source folder has been changed automatically and when I check for updates I get always the error message that this FEniCS source does not exist (404).

Revision history for this message
Tim Berger (tim-berger) said : 		#6

Here are the message from the Ubuntu software upgrade program:
W:Failed to fetch http://ppa.launchpad.net/fenics-packages/fenics-dev/ubuntu/dists/oneiric/main/source/Sources 404 Not Found
, W:Failed to fetch http://ppa.launchpad.net/fenics-packages/fenics-dev/ubuntu/dists/oneiric/main/binary-amd64/Packages 404 Not Found
, W:Failed to fetch http://ppa.launchpad.net/fenics-packages/fenics-dev/ubuntu/dists/oneiric/main/binary-i386/Packages 404 Not Found
, W:Failed to fetch http://ppa.launchpad.net/fenics/ppa/ubuntu/dists/oneiric/main/source/Sources 404 Not Found
, W:Failed to fetch http://ppa.launchpad.net/fenics/ppa/ubuntu/dists/oneiric/main/binary-amd64/Packages 404 Not Found
, W:Failed to fetch http://ppa.launchpad.net/fenics/ppa/ubuntu/dists/oneiric/main/binary-i386/Packages 404 Not Found

Revision history for this message
Tim Berger (tim-berger) said : 		#7

The FEniCS files have been updated today. The new versions of the files solve this problem. Thank you.