fenics team mailing list archive

[Johannes Ring <johannr@xxxxxxxxx>]

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?

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()
>
>