fenics team mailing list archive

[Lorenzo Isella <lorenzo.isella@xxxxxxxxx>]

> 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.

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.
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()