[petsc-users] A combined petsc4py, FEniCS, and Firedrake issue

[Justin Chang]

Hi Lawrence,

I just resolved this issue, you're right I did have two petsc4py's
(manually removing the one in /usr/local/... did the trick) and I undid
every installation step i took for Firedrake. Seems the issue was me
installing FEniCS with sudo apt-get install fenics and installing Firedrake
dependencies via sudo pip install ... gave me problems.

Thanks,
Justin

PS - as for the other e-mail, I will get back to you shortly on that



On Tue, Jul 14, 2015 at 3:37 AM, Lawrence Mitchell <
lawrence.mitchell at imperial.ac.uk> wrote:

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> Hi Justin,
>
> On 14/07/15 09:24, Justin Chang wrote:
> > Hi everyone,
> >
> > As the title says, I have an issue regarding all three. Not sure
> > which mailing to post this to but i figured somebody here may
> > help.
> >
> > I was attempting to install Firedrake on my Ubuntu PC, so far it
> > has not worked yet. However, after my failed attempt, i tried to
> > run some of my old FEniCS programs, and something within the Dolfin
> > library has screwed up. Below is the error:
> >
> > Traceback (most recent call last): File "Idealized_reservoir.py",
> > line 8, in <module> from dolfin import * File
> > "/usr/lib/python2.7/dist-packages/dolfin/__init__.py", line 16, in
> > <module> from . import cpp File
> > "/usr/lib/python2.7/dist-packages/dolfin/cpp/__init__.py", line 42,
> > in <module> exec("from . import %s" % module_name) File "<string>",
> > line 1, in <module> File
> > "/usr/lib/python2.7/dist-packages/dolfin/cpp/common.py", line 32,
> > in <module> _common = swig_import_helper() File
> > "/usr/lib/python2.7/dist-packages/dolfin/cpp/common.py", line 28,
> > in swig_import_helper _mod = imp.load_module('_common', fp,
> > pathname, description) File
> > "/usr/local/lib/python2.7/dist-packages/petsc4py/PETSc.py", line 4,
> > in <module> PETSc._initialize() File "PETSc/PETSc.pyx", line 407,
> > in petsc4py.PETSc._initialize (src/petsc4py.PETSc.c:232527) File
> > "PETSc/PETSc.pyx", line 395, in petsc4py.PETSc.register
> > (src/petsc4py.PETSc.c:232364) File "PETSc/Object.pyx", line 257,
> > in petsc4py.PETSc.PyPetscType_Register
> > (src/petsc4py.PETSc.c:64906) ValueError: key: 0, cannot register:
> > <type 'petsc4py.PETSc.Partitioner'>, already registered: None
> >
> > It seems I screwed something up when I attempted to installed
> > petsc4py. The following command was used to install petsc4py per
> > firedrake instructions:
> >
> > sudo pip install
> > git+https://bitbucket.org/mapdes/petsc4py.git@firedrake#egg=petsc4py
> >
> >  I tried uninstalling petsc4py via sudo pip uninstall but it says
> > "Not uninstalling petsc4py at /usr/lib/pymodules/python2.7, owned
> > by OS".
>
> Something funky is going on here, since the petsc4py in the backtrace
> above lives in /usr/local/lib/python2.7/... not
> /usr/lib/pymodules/python2.7
>
> I presume "pip list" doesn't list petsc4py anywhere.
>
>  I
> > reinstalled fenics/dolfin and all of its dependencies but i still
> > get the traceback errors above. I tried to upgrade petsc4py sudo
> > pip install -U --no-deps ... but it says "Can't roll back petsc4py;
> > was not uninstalled".
> >
> > Any idea what I can do here?
>
> This looks a bit like there are two petsc4py versions kicking around.
> Does just importing petsc4py work at all (from petsc4py import PETSc),
> and if so, where does it point to?  (print PETSc.__file__).
>
> Do things work if you manually remove petsc4py from
> /usr/local/lib/python2.7/dist-packages/petsc4py?
>
> Cheers,
>
> Lawrence
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