fenics team mailing list archive

[Johan Hake <johan.hake@xxxxxxxxx>]

On Tuesday May 18 2010 01:57:26 Johannes Ring wrote:
> On Tue, May 18, 2010 at 10:35 AM, Lorenzo Isella
> 
> <lorenzo.isella@xxxxxxxxx> wrote:
> >> Is it possible that your computer is set up with a different MPI
> >> implementation than OpenMPI as default? Try to run
> >> 
> >>  update-alternatives --display mpi
> >> 
> >> If your default is not OpenMPI you should run
> >> 
> >>  sudo update-alternatives --config mpi
> >> 
> >> and select it from the list.
> >> 
> >> Johannes
> > 
> > Hello Johannes,
> > Yes, that could be the case
> > 
> > $ update-alternatives --display mpi
> > mpi - auto mode
> > link currently points to /usr/include/mpich2
> > /usr/include/mpich2 - priority 40
> > slave libmpi++.so: /usr/lib/libmpichcxx.so
> > slave libmpi.so: /usr/lib/libmpich.so
> > slave mpic++: /usr/bin/mpic++.mpich2
> > slave mpic++.1.gz: /usr/share/man/man1/mpic++.mpich2.1.gz
> > slave mpicc: /usr/bin/mpicc.mpich2
> > slave mpicc.1.gz: /usr/share/man/man1/mpicc.mpich2.1.gz
> > slave mpicxx: /usr/bin/mpicxx.mpich2
> > slave mpicxx.1.gz: /usr/share/man/man1/mpicxx.mpich2.1.gz
> > slave mpif77: /usr/bin/mpif77.mpich2
> > slave mpif77.1.gz: /usr/share/man/man1/mpif77.mpich2.1.gz
> > slave mpif90: /usr/bin/mpif90.mpich2
> > slave mpif90.1.gz: /usr/share/man/man1/mpif90.mpich2.1.gz
> > /usr/lib/openmpi/include - priority 40
> > slave libmpi++.so: /usr/lib/openmpi/lib/libmpi_cxx.so
> > slave libmpi.so: /usr/lib/openmpi/lib/libmpi.so
> > slave mpiCC: /usr/bin/mpic++.openmpi
> > slave mpiCC.1.gz: /usr/share/man/man1/mpiCC.openmpi.1.gz
> > slave mpic++: /usr/bin/mpic++.openmpi
> > slave mpic++.1.gz: /usr/share/man/man1/mpic++.openmpi.1.gz
> > slave mpicc: /usr/bin/mpicc.openmpi
> > slave mpicc.1.gz: /usr/share/man/man1/mpicc.openmpi.1.gz
> > slave mpicxx: /usr/bin/mpic++.openmpi
> > slave mpicxx.1.gz: /usr/share/man/man1/mpicxx.openmpi.1.gz
> > slave mpif77: /usr/bin/mpif77.openmpi
> > slave mpif77.1.gz: /usr/share/man/man1/mpif77.openmpi.1.gz
> > slave mpif90: /usr/bin/mpif90.openmpi
> > slave mpif90.1.gz: /usr/share/man/man1/mpif90.openmpi.1.gz
> > Current `best' version is /usr/include/mpich2.
> > 
> > So, it looks like I am using mpich2
> > 
> > and then
> > 
> > $ sudo update-alternatives --config mpi
> > [sudo] password for lorenzo:
> > There are 2 choices for the alternative mpi (providing /usr/include/mpi).
> > 
> >  Selection    Path                      Priority   Status
> > ------------------------------------------------------------
> > * 0            /usr/include/mpich2        40        auto mode
> >  1            /usr/include/mpich2        40        manual mode
> >  2            /usr/lib/openmpi/include   40        manual mode
> > 
> > Press enter to keep the current choice[*], or type selection number: 2
> > update-alternatives: using /usr/lib/openmpi/include to provide
> > /usr/include/mpi (mpi) in manual mode.
> 
> Looks good.
> 
> > However, when I try the example script, I now get an error
> > 
> > $ python fenics-test.py
> > Calling FFC just-in-time (JIT) compiler, this may take some time.
> > Calling DOLFIN just-in-time (JIT) compiler, this may take some time.
> > Traceback (most recent call last):
> >  File "fenics-test.py", line 6, in <module>
> >   u0 = Expression("1 + x[0]*x[0] + 2*x[1]*x[1]", V=V)
> > TypeError: __init__() got an unexpected keyword argument 'V'
> > 
> > where fenics_test.py is reported at the end of the email. What is going
> > wrong? It seems to me that the script below is the exact copy of the
> > example.
> 
> I think this script is a bit too old for your copy of DOLFIN (version
> 0.9.7). I guess the tutorial you posted in your first post, that is
> 
>   http://www.fenics.org/pub/documents/fenics/tutorial/fenics-tutorial.pdf
> 
> is not the latest copy of the FEniCS tutorial. However, I'm not sure
> where to obtain the latest copy. Anyone else?

Not sure of this either, but just remove: ", V=V", in the instantiation of the 
Expresssion and you should be fine.

Johan

> Johannes
> 
> > Can anyone help me out?
> > Many thanks
> > 
> > Lorenzo
> > 
> > 
> > 
> > ########################################
> > #########################################
> > ##########################################
> > 
> > #fenics_test.py
> > 
> > from dolfin import *
> > # Create mesh and define function space
> > mesh = UnitSquare(6, 4)
> > V = FunctionSpace(mesh, "CG", 1)
> > # Define boundary conditions
> > u0 = Expression("1 + x[0]*x[0] + 2*x[1]*x[1]", V=V)
> > 
> > class Boundary(SubDomain): # define the Dirichlet boundary
> >   def inside(self, x, on_boundary):
> >       return on_boundary
> > 
> > u0_boundary = Boundary()
> > bc = DirichletBC(V, u0, u0_boundary)
> > # Define variational problem
> > v = TestFunction(V)
> > u = TrialFunction(V)
> > f = Constant(mesh, -6.0)
> > a = dot(grad(u), grad(v))*dx
> > L = f*v*dx
> > # Compute solution
> > problem = VariationalProblem(a, L, bc)
> > u = problem.solve()
> > # Plot solution and mesh
> > plot(u)
> > plot(mesh)
> > # Dump solution to file in VTK format
> > file = File("poisson.pvd")
> > file << u
> > # Hold plot
> > interactive()
> 
> _______________________________________________
> Mailing list: https://launchpad.net/~fenics
> Post to     : fenics@xxxxxxxxxxxxxxxxxxx
> Unsubscribe : https://launchpad.net/~fenics
> More help   : https://help.launchpad.net/ListHelp