mpi problem in fresh install ubuntu 16.04

[Sebastian Gonzalez pintor]

Hi, 

I have a fresh install of Ubuntu 16.04, and I installed Fenics through the PPA repositories. When I try to run, for example d1_p2D.py
I get the following error:

me@mycomputer:~/fenics-example/stationary/poisson $ python d1_p2D.py 

Reading DOLFIN parameters from file "dolfin_parameters.xml".

[segonpin-maths:07514] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_shmem_sysv: /usr/lib/openmpi/lib/openmpi/mca_shmem_sysv.so: undefined symbol: opal_show_help (ignored)

[segonpin-maths:07514] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_shmem_posix: /usr/lib/openmpi/lib/openmpi/mca_shmem_posix.so: undefined symbol: opal_shmem_base_framework (ignored)

[segonpin-maths:07514] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_shmem_mmap: /usr/lib/openmpi/lib/openmpi/mca_shmem_mmap.so: undefined symbol: opal_show_help (ignored)

--------------------------------------------------------------------------

It looks like opal_init failed for some reason; your parallel process is

likely to abort.  There are many reasons that a parallel process can

fail during opal_init; some of which are due to configuration or

environment problems.  This failure appears to be an internal failure;

here's some additional information (which may only be relevant to an

Open MPI developer):

  opal_shmem_base_select failed

  --> Returned value -1 instead of OPAL_SUCCESS

--------------------------------------------------------------------------

--------------------------------------------------------------------------

It looks like orte_init failed for some reason; your parallel process is

likely to abort.  There are many reasons that a parallel process can

fail during orte_init; some of which are due to configuration or

environment problems.  This failure appears to be an internal failure;

here's some additional information (which may only be relevant to an

Open MPI developer):

  opal_init failed

  --> Returned value Error (-1) instead of ORTE_SUCCESS

--------------------------------------------------------------------------

--------------------------------------------------------------------------

It looks like MPI_INIT failed for some reason; your parallel process is

likely to abort.  There are many reasons that a parallel process can

fail during MPI_INIT; some of which are due to configuration or environment

problems.  This failure appears to be an internal failure; here's some

additional information (which may only be relevant to an Open MPI

developer):

  ompi_mpi_init: ompi_rte_init failed

  --> Returned "Error" (-1) instead of "Success" (0)

--------------------------------------------------------------------------

*** An error occurred in MPI_Init_thread

*** on a NULL communicator

*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,

***    and potentially your MPI job)

[segonpin-maths:7514] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed!

I have look for similar errors in the previous questions but I did not find anything. Any idea about how can it be fixed?

[Garth N. Wells]

Looks like something is wrong with your MPI installation. Try
compiling and running a MPI 'hello world' program, e.g.
http://mpitutorial.com/tutorials/mpi-hello-world/.

Garth


On 14 October 2016 at 15:29, Sebastian Gonzalez pintor

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[Sebastian Gonzalez pintor]

Hi Garth,

Thaks for the quick answer. I have downloaded the code you suggested

$ git clone https://github.com/wesleykendall/mpitutorial

compiled the example

$ cd mpitutorial/tutorials/mpi-hello-world/code/

$ make

mpicc -o mpi_hello_world mpi_hello_world.c

and the code seems to run without problems

$ cd ../../
$ ./run.py mpi_hello_world

mpirun -n 4  ./mpi-hello-world/code/mpi_hello_world

Hello world from processor segonpin-maths, rank 1 out of 4 processors

Hello world from processor segonpin-maths, rank 2 out of 4 processors

Hello world from processor segonpin-maths, rank 0 out of 4 processors

Hello world from processor segonpin-maths, rank 3 out of 4 processors

Any other idea that can help to identify the problem?

Sebas

[Sebastian Gonzalez pintor]

Because the error makes some reference to the file "dolfin_parameters.xml", I have moved the file to a different folder and run it there instead. The file is the following one

from dolfin import *

# Create mesh and define function space
mesh = UnitSquare(6, 4)
#mesh = UnitCube(6, 4, 5)
V = FunctionSpace(mesh, 'Lagrange', 1)

# Define boundary conditions
u0 = Expression('1 + x[0]*x[0] + 2*x[1]*x[1]')

def u0_boundary(x, on_boundary):
    return on_boundary

bc = DirichletBC(V, u0, u0_boundary)

# Define variational problem
u = TrialFunction(V)
v = TestFunction(V)
f = Constant(-6.0)
a = inner(nabla_grad(u), nabla_grad(v))*dx
L = f*v*dx

# Compute solution
u = Function(V)
solve(a == L, u, bc)

# Plot solution and mesh
plot(u)
plot(mesh)

# Dump solution to file in VTK format
file = File('poisson.pvd')
file << u

# Hold plot
interactive()

And when I run it the error now is

$ python poisson.py 

Traceback (most recent call last):

  File "poisson.py", line 4, in <module>

    mesh = UnitSquare(6, 4)

NameError: name 'UnitSquare' is not defined

Aborted (core dumped)

I do not really understand why the error is different, but this one makes me think that there is some problem loading dolfin... I do not know if you know any simpler test.

[Jan Blechta]

d1_2D.py comes from very outdated tutorial. Start with the new tutorial
or documented demos.

https://fenicsproject.org/documentation/dolfin/2016.1.0/python/demo/index.html
http://hplgit.github.io/fenics-tutorial/doc/web/index.html

Jan


On Fri, 14 Oct 2016 08:01:14 -0700 (PDT)

Sebastian Gonzalez pintor <sego...@gmail.com> wrote:

[Sebastian Gonzalez pintor]

Hi,

I run the new file and it worked fine:

$ wget https://fenicsproject.org/documentation/dolfin/2016.1.0/python/_downloads/demo_poisson.py

$ python demo_poisson.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.

Calling DOLFIN just-in-time (JIT) compiler, this may take some time.

Calling FFC just-in-time (JIT) compiler, this may take some time.

Calling FFC just-in-time (JIT) compiler, this may take some time.

Solving linear variational problem.

Thanks for your help, and sorry for wasting your time with such a silly question. I did not find the new tutorial at all. 

Sebas.

[Anders Logg]

The new tutorial is being prepared and will be made available here within a couple of weeks: https://fenicsproject.org/tutorial

You can find the latest draft of the tutorial here:

https://github.com/hplgit/fenics-tutorial/blob/master/pub/pdf/fenics-tutorial1-4print.pdf

--

Anders

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