dolfin team mailing list archive

[Nuno David Lopes <ndl@xxxxxxxxxxxxxx>]

Thank you very much.
This last e-mail made the subject more clear to me.
In fact i was calling ./app  
I thougt PETSc should do all the parallel work from the inside of the ./app.

Still with 
$mpirun -np 2 ./app  
(2-core PC)
i get the same top results.: Cpu0=100% Cpu1=0%

By the way  i get  the following message from Dolfin:
_____________________________________________
Initializing PETSc (ignoring command-line arguments)
_____________________________________________
Could this be the reason for PETSc not going into parallel?

Or could it still be a problem with dolfin compilation?

P.S:
Installing mpich with apt-get i get the following apps:
mpicc
mpiCC
mpicxx
mpif77
mpif90
and 
mpirun 

 
On Monday 02 June 2008, Johannes Ring wrote:
> On Mon, June 2, 2008 Nuno David Lopes wrote:
> > Finally i could install it:
> > _________________________________________________________________________
> > petsc:
> > $./config/configure.py --with-cc=gcc --with-fc=gfortran\\
> > --download-umfpack=1 --download-hypre=1 --with-mpi-dir=/usr/lib/mpich
> > --with-shared=1
> > dolfin:
> > $scons enablePetsc=1 --withPetscDir=$PETSC _ DIR --enableMpi=1
>
> Note that we don't use dashes when specifying options to scons. The above
> line should therefore be like this:
>
> $scons enablePetsc=1 withPetscDir=$PETSC_DIR enableMpi=1
>
> > the --download-mpich=1 in PETSc didn't work because scons::DOLFIN
> > still didn't find the MPICH stuff.
>
> Then the problem is probably that we are unable to locate a MPI C++
> compiler on your system. As I said earlier, we only look for mpicxx,
> mpic++, and mpiCC. Using --download-mpich=1 when configuring PETSc, you
> will only get mpicc which is normally just a MPI C compiler. As far as I
> can remember, the mpicc compiler you get should also work as a C++
> compiler. You can try this by defining the CXX environment variable,
> giving the complete path to the mpicc compiler that was downloaded and
> installed by PETSc. An alternative is to configure PETSc with the
> --with-clanguage=C++ option. This should produce a MPI C++ compiler when
> using --download-mpich=1.
>
> > And i've really change the PATHs to the
> > downloaded mpich dir.
> > Probably it should be good to have a scons option "withMpiDir= " like for
> > the
> > other packages.
> >
> > I've also tried with lam or openmpi...
> >
> > But still I can't see the PETSc parallel system solving in my codes?
>
> Did you start your codes with mpirun or mpiexec? If you just do, e.g.,
>
>   ./app
>
> when starting your application, you won't be running in parallel. Try with
>
>   mpirun -np 2 ./app
>
> or
>
>   mpiexec -np 2 ./app
>
> This should run two copies of your program in parallel.
>
> Johannes
>
> > (I really don't know much about parallel algorithms...so sorry if i'm
> > saying
> > something that doesn't make sense)
> > but what i get when i run top at the time the program is solving a system
> > is
> > still a
> > --------------------
> > Cpu0 : 0.0%
> > Cpu1 :100.%
> > -------------------
> > it seems that petsc isn't allocating the two cores at the same time...so
> > it
> > isn't really parallel, and there aren't really any advantage on it.
> > Is this a know issue? Like an mpich bug or something..
> > Should i try again with opemmpi like was suggested?
> >
> > Thanks
> >
> > On Monday 02 June 2008, Jed Brown wrote:
> >> On Mon 2008-06-02 08:29, Johannes Ring wrote:
> >> > On Fri, May 30, 2008 Nuno David Lopes wrote:
> >> > > Ok, i have mpich on my system, petsc (without hypre)  compiled
> >> > > with --download-mpich=1, it all works, my code compiles and runs
> >> > > etc.... Everything is running with the exception that MPI isn't
> >> > > working...
> >> > >
> >> > > ..................scons: Reading SConscript files ...
> >> > > Using options from scons/options.cache
> >> > > MPI not found (might not work if PETSc uses MPI).
> >> > > ....................................................................
> >> > >... .
> >> >
> >> > The reason you get this warning is that we are unable to locate mpirun
> >>
> >> or
> >>
> >> > an MPI C++ compiler (we look for mpic++, mpicxx, and mpiCC) on your
> >> > system. This might be a bit limiting, so I added mpiexec and orterun
> >>
> >> as
> >>
> >> > alternatives for mpirun. Please try again with the latest from the hg
> >> > repository.
> >>
> >> When PETSc installs mpich, it doesn't automatically put it in your path
> >> so
> >> you will have to specify the path explicitly when you configure Dolfin.
> >>
> >> In terms of Dolfin configuration, it's not really a good idea to just
> >> use
> >> any random MPI implementation that may be in your path.  You can get the
> >> correct implementation from PETSc (CC,CXX,MPIEXEC in
> >> $PETSC_DIR/bmake/$PETSC_ARCH/petscconf).  This would be especially nice
> >> if
> >> you have multiple PETSc builds with different MPI implementations (i.e.
> >> OpenMPI with a debugging build for development/testing and vendor MPI
> >> with
> >> optimized build for production runs).
> >>
> >> Jed
> >
> > --
> > Nuno David Lopes
> >
> > e-mail:ndl@xxxxxxxxxxxxxx        (FCUL/CMAF)
> >            nlopes@xxxxxxxxxxxxxxx    (ISEL)
> > http://ptmat.ptmat.fc.ul.pt/%7Endl/
> > _______________________________________________
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> > DOLFIN-dev@xxxxxxxxxx
> > http://www.fenics.org/mailman/listinfo/dolfin-dev
>
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-- 
Nuno David Lopes

e-mail:ndl@xxxxxxxxxxxxxx        (FCUL/CMAF)
           nlopes@xxxxxxxxxxxxxxx    (ISEL)
http://ptmat.ptmat.fc.ul.pt/%7Endl/