fenics team mailing list archive

[Johannes Ring <johannr@xxxxxxxxx>]

Hi Lorenzo,

On Mon, May 17, 2010 at 9:30 AM, Lorenzo Isella
<lorenzo.isella@xxxxxxxxx> wrote:
> Anders Logg wrote:
>>
>> This looks like a problem with your MPI/DOLFIN installation, not the
>> script itself.
>>
>> What happens when you write
>>
>>  python -c "import dolfin"
>>
>> ?
>>
>> --
>> Anders
>>
>
> Hi Anders,
> Thanks for helping. Here is the output you wanted
>
> $ python -c "import dolfin"
> Fatal error in MPI_Comm_size: Invalid communicator, error stack:
> MPI_Comm_size(111): MPI_Comm_size(comm=0xb5d0e1c0, size=0x7fff07719fbc)
> failed
> MPI_Comm_size(69).: Invalid communicator

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

> but unfortunately, it still sounds Greek to me.
> Any help is really appreciated.
> Cheers
>
> Lorenzo
>
>
>>
>> On Fri, May 14, 2010 at 04:06:24PM +0200, Lorenzo Isella wrote:
>>
>>>
>>> Dear All,
>>> I have recently installed fenics on my machine (Ubuntu 9.10 amd64
>>> architecture), following the instructions at
>>>
>>> http://www.fenics.org/wiki/Download
>>>
>>>
>>> However, when I try running the first example script from the
>>> excellent tutorial
>>>
>>> http://www.fenics.org/pub/documents/fenics/tutorial/fenics-tutorial.pdf
>>>
>>> which I paste at the end of the email (saved as fenics-test.py),
>>> this is the output I get
>>>
>>>
>>> $ python fenics-test.py
>>> Fatal error in MPI_Comm_size: Invalid communicator, error stack:
>>> MPI_Comm_size(111): MPI_Comm_size(comm=0x227101c0,
>>> size=0x7fff9ea355ec) failed
>>> MPI_Comm_size(69).: Invalid communicator
>>>
>>> I am using a multicore machine and it looks like that something
>>> related to MPI is a problem.
>>> I am not really knowledgeable about parallelization and I am not
>>> interested (as for now) in running fenics in parallel, but I simply
>>> would like to be able to play a bit with this example script.
>>> Any help is really appreciated.
>>> Cheers
>>>
>>> Lorenzo
>>>
>>> ####################################################
>>>
>>>
>>> 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()
>>>
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>
>
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