dolfin team mailing list archive

[Johan Hake <hake@xxxxxxxxx>]

On Sunday 20 September 2009 21:26:14 logg wrote:
> On Fri, Sep 18, 2009 at 01:57:19PM -0000, Johan Hake wrote:
> > On Friday 18 September 2009 15:43:34 KVS wrote:
> > > Public bug reported:
> > >
> > > Hi,
> > > I just build FEniCS with Dorsal and tried to run the poisson.py demo.
> > > Running "python demo.py" works fine, but "mpirun -n 2 python demo.py"
> > > does not. See text below. Is there an easy fix?
> >
> > What version of linux do you use?
> >
> > This looks like the same problem I had a while ago (with jaunty), where
> > mpirun use ssh to submit the different jobs. The problem is that the
> > script is executed without the necessary paths. You need to forward
> > these.
> >
> > My workaround was to set the following alias:
> >
> >   alias mpirun='mpirun -x PYTHONPATH -x LD_LIBRARY_PATH -x
> > PKG_CONFIG_PATH\ -x PATH -x DISPLAY'
> >
> > you might also need to put:
> >
> > Host *
> > ForwardAgent yes
> > ForwardX11 yes
> >
> > in your .ssh/config file to get plotting to work.
> >
> > Johan
> 
> I still find it strange you need to do this. Is this a bug that has
> been fixed in Karmic? 

Yes, that is how I understand it.

See:

   http://www.open-mpi.org/community/lists/users/2009/03/8571.php
   https://bugs.launchpad.net/ubuntu/+source/openmpi/+bug/365122

I have tried to compile the source packages with the suggested bugfix, but 
with no luck.

> Which MPI packages do you have?
> 
>   # dpkg -l | grep mpi | grep -v ompiz | grep -v ompil | grep -v empi |
> awk '{print $2, $3}'

libhdf5-openmpi-1.6.6-0 1.6.6-4ubuntu1
libmpich1.0gf 1.2.7-9ubuntu1
libopenmpi-dbg 1.3-2ubuntu1
libopenmpi-dev 1.3-2ubuntu1
libopenmpi1 1.3-2ubuntu1
libopenmpi1.3 1.3.2-4
openmpi-bin 1.3-2ubuntu1
openmpi-common 1.3-2ubuntu1
openmpi-doc 1.3-2ubuntu1

Johan

>   libopenmpi-dev 1.3.2-3ubuntu1
>   libopenmpi1.3 1.3.2-3ubuntu1
>   mpi-default-bin 0.6
>   openmpi-bin 1.3.2-3ubuntu1
>   openmpi-common 1.3.2-3ubuntu1
>   python-mpi 2.4.11-2ubuntu3


> --
> Anders
> 
> > > Kristian
> > >
> > > kvs@flekktvetann:~/fenics/dolfin/demo/pde/poisson/python$ python
> > > demo.py Solving linear variational problem
> > >   Matrix of size 1089 x 1089 has 7361 nonzero entries.
> > >   Applying boundary conditions to linear system.
> > >   Solving linear system of size 1089 x 1089 (PETSc LU solver, petsc).
> > > Plot active, press 'q' to continue.
> > >
> > > kvs@flekktvetann:~/fenics/dolfin/demo/pde/poisson/python$ mpirun -n 2
> > >  python demo.py kvs@flekktvetann's password:
> > > Traceback (most recent call last):
> > >   File "demo.py", line 20, in <module>
> > >     from dolfin import *
> > > ImportError: No module named dolfin
> > > Traceback (most recent call last):
> > >   File "demo.py", line 20, in <module>
> > >     from dolfin import *
> > > ImportError: No module named dolfin
> > >
> > > ** Affects: dolfin
> > >      Importance: Undecided
> > >          Status: New
>

-- 
Poisson demo in parallel
https://bugs.launchpad.net/bugs/432491
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Status in DOLFIN: New

Bug description:
Hi, 
I just build FEniCS with Dorsal and tried to run the poisson.py demo.
Running "python demo.py" works fine, but "mpirun -n 2 python demo.py" does not.
See text below. Is there an easy fix?

Kristian

kvs@flekktvetann:~/fenics/dolfin/demo/pde/poisson/python$ python demo.py
Solving linear variational problem
  Matrix of size 1089 x 1089 has 7361 nonzero entries.
  Applying boundary conditions to linear system.
  Solving linear system of size 1089 x 1089 (PETSc LU solver, petsc).
Plot active, press 'q' to continue.

kvs@flekktvetann:~/fenics/dolfin/demo/pde/poisson/python$ mpirun -n 2 python demo.py
kvs@flekktvetann's password: 
Traceback (most recent call last):
  File "demo.py", line 20, in <module>
    from dolfin import *
ImportError: No module named dolfin
Traceback (most recent call last):
  File "demo.py", line 20, in <module>
    from dolfin import *
ImportError: No module named dolfin