dolfin team mailing list archive

[Johan Hake <hake@xxxxxxxxx>]

On Sunday 20 September 2009 22:03:38 logg wrote:
> On Sun, Sep 20, 2009 at 07:49:48PM -0000, Johan Hake wrote:
> > 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.
> 
> Just upgrade to Karmic. I've been running it for 2 months now. There
> have been some issues but some fixes last week did the trick.

Running parallel jobs on my laptop will not be "the breaking point" for an 
upgrade for me ;)

The fix I suggest work just fine for minor debugging.

I will invalidate this bug as it is not a bug in DOLFIN.

Johan
 
> Note to Kristian: Upgrade to Karmic.
> 
> --
> Anders
> 
> > > 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
>

-- 
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