dolfin team mailing list archive

[Johan Hake <hake@xxxxxxxxx>]

On Thursday 14 August 2008 09:46:00 Johannes Ring wrote:
> On Thu, August 14, 2008 09:42, Anders Logg wrote:
> > On Thu, Aug 14, 2008 at 08:39:25AM +0100, Garth N. Wells wrote:
> >> Johannes Ring wrote:
> >> > On Thu, August 14, 2008 08:52, Garth N. Wells wrote:
> >> >> Anders Logg wrote:
> >> >>> On Wed, Aug 13, 2008 at 08:03:39PM +0100, Garth N. Wells wrote:
> >> >>>> I'm experiencing a puzzling problem wth pyDOLFIN and MPI again.
> >> >>>>
> >> >>>> When I do
> >> >>>>
> >> >>>>      python file.py
> >> >>>>
> >> >>>> where file.py is just
> >> >>>>
> >> >>>>      from dolfin import *
> >> >>>>
> >> >>>>      object = Function("/tmp/fileKFnQpl.xml")
> >> >>>>      plot(object)
> >> >>>>      interactive()
> >> >>>>
> >> >>>> I see a plot as expected, and get
> >> >>>>
> >> >>>>      Plot active, press 'q' to continue.
> >> >>>>
> >> >>>> After pressing 'q', I get
> >> >>>>
> >> >>>>      *** An error occurred in MPI_Attr_get
> >> >>>>      *** after MPI was finalized
> >> >>>>      *** MPI_ERRORS_ARE_FATAL (goodbye)
> >> >>>>      [gnw20pc:2277] Abort before MPI_INIT completed successfully;
> >>
> >> not
> >>
> >> >>>> able to guarantee that all other processes were killed!
> >> >>>>      *** An error occurred in MPI_Comm_rank
> >> >>>>      *** after MPI was finalized
> >> >>>>      *** MPI_ERRORS_ARE_FATAL (goodbye)
> >> >>>>      *** An error occurred in MPI_Type_free
> >> >>>>      *** after MPI was finalized
> >> >>>>      *** MPI_ERRORS_ARE_FATAL (goodbye)
> >> >>>>      Segmentation fault
> >> >>>>
> >> >>>> Somehow, Python appears to be calling MPI_Finalize before DOLFIN
> >>
> >> gets a
> >>
> >> >>>> chance to finalise things correctly. Any ideas/experience on how
> >>
> >> Python
> >>
> >> >>>> interacts with MPI? I've commented out MPI_Finalize() in DOLFIN to
> >>
> >> be
> >>
> >> >>>> sure that DOLFIN is not calling it.
> >> >>>>
> >> >>>> Garth
> >> >>>
> >> >>> Would it help if we just call MPI_Finalized to check before
> >> >>> finalizing? We can add a wrapper for it just like for
> >>
> >> MPI_Initialized.
> >>
> >> >> I've added some annoying debug output to SubSystemsManager. Can you
> >>
> >> tell
> >>
> >> >> me what you see when running
> >> >>
> >> >>      from dolfin import *
> >> >>      x = PETScVector(10)
> >> >>
> >> >> When I run it, the first line of output is
> >> >>
> >> >>      MPI status in initPETSc() 1
> >> >>
> >> >> which indicates that MPI_Initialize is saying that MPI has been
> >> >> initialised before PETSc is initialised, but we haven't initialise
> >>
> >> it.
> >>
> >> >> The same code in C++ gives
> >> >>
> >> >>      MPI status in initPETSc() 0
> >> >>
> >> >> which is the expected result.
> >> >
> >> > I get
> >> >
> >> >>>> from dolfin import *
> >> >>>> x = PETScVector(10)
> >> >
> >> > MPI status in initPETSc() 0
> >> > [simula-x61:17855] mca: base: component_find: unable to open osc
> >>
> >> pt2pt:
> >> > file not found (ignored)
> >> > MPI status in initMPI() 1
> >> >
> >> > Have you compiled Trilinos with MPI support? It seems to be the same
> >> > problems I had with my Ubuntu packages for Trilinos on 64bit. Turning
> >>
> >> off
> >>
> >> > MPI support for Trilinos fixed the problem for me.
> >>
> >> Yes, Trilinos with MPI support was the culprit, even though I disabled
> >> Trilinos (enableTrilinos=no). Trilinos must be placing some files in
> >> /usr/local/lib/ which cause a problem which is nasty. Just removing
> >> Trilinos did the trick. Thanks!
> >>
> >> Garth
> >
> > What about the annoying
> >
> >   mca: base: component_find: unable to open osc pt2pt: file not found
> > (ignored)
> >
> > ?
>
> I'm not sure how to remove it.

I have a serial version of trilinos 8.0.7 compiled localy on my computer, 
which do not produce this output. See:

<http://www.fenics.org/pipermail/dolfin-dev/2008-June/008442.html>

Johan