[petsc-users] is something wrong with nnz ?

[jean-frederic thebault]

OK, Im not familiar with debugger (!!) but I will try to see something with
valgrind... I thougth I have already checked the prototypes of all
functions when upgrading with petsc-3.1.p8 and petsc-3.2.p5, but will do
that again.

Thanks anyway.
Best Regards.
John

Le 23 novembre 2011 17:44, Satish Balay <balay at mcs.anl.gov> a écrit :

> > [1]PETSC ERROR: d_nnz cannot be less than 0: local row 78 value
> -750763693!
>
> There is something wrong in your code. You'll have to verify the
> prototypes of all functions - with the petsc-3.2 documentation.
>
> And valgrind is an easy way to pinpoint to the problem source. [also a
> debugger should show you whats going wrong]
>
> Satish
>
>
> On Wed, 23 Nov 2011, jean-frederic thebault wrote:
>
> > Well, actually, when I call MatSetFromOption, with the right arguments,
> the
> > whole simulation is running, but there are some PETSC-ERROR about nnz,
> and
> > when I comment the calling of MatSetFromOption, the simulation (program)
> > stop at the first calculation. This time, I'm putting in this email the
> > log-file with calling of MatSetFromOption (then with PETSC-ERROR on
> nnz)...
> >
> > Le 23 novembre 2011 17:17, Satish Balay <balay at mcs.anl.gov> a écrit :
> >
> > > Since you get a SEGV - I would suggest running the code in the
> > > debugger - to check where its crashing.
> > >
> > > Also run with valgrind to see where problems start.. Mostlikely the
> > > issues would be change in prototypes for PETSc functions - between
> > > releases.
> > >
> > > Satish
> > >
> > > On Wed, 23 Nov 2011, jean-frederic thebault wrote:
> > >
> > > > Thanks for your response.
> > > >
> > > > Sorry about that, to reduce the size of the log file, unfortunetly,
> I did
> > > > took out the bad lines... In the out.log I've put in this email, I've
> > > make
> > > > sure there are...
> > > >
> > > > Actually, I don't use MatSetOption, but MatSetFromOption instead.
> > > However,
> > > > when I called MatSetFromOption, the PETSC_COMM_WORLD was missing. But
> > > now,
> > > > it's getting worse !! (as you could see in the out.log included in
> this
> > > > email).
> > > >
> > > > Le 23 novembre 2011 15:55, Jed Brown <jedbrown at mcs.anl.gov> a écrit
> :
> > > >
> > > > >  On Wed, Nov 23, 2011 at 08:24, jean-frederic thebault <
> > > > > jean-frederic at thebault-net.com> wrote:
> > > > >
> > > > >> I'm wondering what's wrong in my code. I'm using PETSc to solve a
> > > linear
> > > > >> system, and willing to use a multi-processor computer. 9 years
> ago, I
> > > used
> > > > >> petsc-2.1.3 with success. Few weeks ago, I've update petsc with
> the
> > > 3.1-p8
> > > > >> version and made the necessary changes to work with. No problem.
> And
> > > > >> recently, I've migrate to petsc-3.2-p5. Compilation is OK. But
> when I
> > > do
> > > > >> simulation, now, I have some PETSC-ERROR in the log file, even
> using
> > > only
> > > > >> one processor (see the out.log file in this email).
> > > > >>
> > > > >
> > > > > You are calling MatSetOption() with the wrong number of arguments.
> C
> > > > > compilers tell you about this, but Fortran compilers do not.
> > > > >
> > > > >
> > > > >
> > >
> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatSetOption.html
> > > > >
> > > > >
> > > > >> However, I think I defined MatMPI and VecMPI correctly, according
> to
> > > the
> > > > >> doc. The log file tell that something wrong with the nnz which
> should
> > > not
> > > > >> be greater than row length (??).
> > > > >>
> > > > >
> > > > > The log you sent does not say anything about nnz. Fix the call to
> > > > > MatSetOption().
> > > > >
> > > > >  And also, with the previous version of PETSc I've used, the were
> no
> > > > >> problem using -pc_type bjacobi and -sub_pc_type sor, juste to
> solve
> > > linear
> > > > >> system doing parallel computations and because SOR is not
> > > parallelized. But
> > > > >> now, when I use -pc_type bjacobi and -sub_pc_type sor, with 3
> rank, I
> > > > >> experiment some convergence problem during my simulation.
> > > > >>
> > > > >
> > > > > These options should do the same thing they used to do. Make sure
> you
> > > are
> > > > > assembling correctly. If it's still confusing, run the old and new
> > > code with
> > > > >
> > > > > -ksp_monitor_true_residual -ksp_converged_reason -ksp_view -pc_type
> > > > > bjacobi -sub_pc_type sor
> > > > >
> > > > > and send the output of both for us to look at.
> > > > >
> > > > > Also note that you can use -pc_type sor even in parallel. There are
> > > > > options for local iterations and full iterations.
> > > > >
> > > >
> > >
> >
>
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