dolfin team mailing list archive

[Johan Hake <hake@xxxxxxxxx>]

On Thursday 14 August 2008 17:34:49 Anders Logg wrote:
> On Thu, Aug 14, 2008 at 01:44:31PM +0200, Johan Hake wrote:
> > 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>
>
> I don't think this has anything to do with Trilinos. I had it long
> time before I installed Trilinos.

Ok, but when I compiled dolfin with the simula trilinos package, I got the 
message, and it was gone using my own compilation. 

Just an observation.

Johan