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 < [email protected]> wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > 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 > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1 > > iQEcBAEBAgAGBQJVpMpVAAoJECOc1kQ8PEYvE+QH/R8V9n7a/v18eREO4t06h/X1 > jrYyU3AmYEQUaKHUnDyhS0G3ew4jVUWscSzxqqagnQFZLsegm2ubS5+q22tWn52k > W7ExtrZ1EQl2D2KcivJH0o1cQmmufoV3A3M+VjW4yKhoBWacDK4FabFwu7xWdx5S > RWUWbYHfsjjiTaVFneuFwNZUhwYs4Eofnx4OBRBhji704rUhcqLZhiJDBFJJrnCA > bcRMusvU6Bfq1+xtrmLYZnJqN45vUK4tnXdMQUBJCQi3jBwh+yMB2MLTX2qmoQzO > VvxRS4wC7Cl91tYC7rqh6GzVh5oZNocet+0OQ9+/AwdjDwVa7ppSplMnJAWeQrc= > =Ksbp > -----END PGP SIGNATURE----- >
