[petsc-users] loosing preallocation information
Ethan Coon
ecoon at lanl.gov
Mon Mar 7 09:48:20 CST 2011
On Mon, 2011-03-07 at 15:41 +0100, Alexander Grayver wrote:
> It works! Great, Matt.
>
> I guess there is no other way to know all these small issues but to
> get all possible errors? :)
>
PETSc in Fortran has a lot of oddities due to the difference between the
languages (this "null pointer" thing and different ways of looking at
array bounds being the primary two). If you haven't seen it yet, you
should really look through Chapter 10 of the manual
http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manual.pdf
which explains most of them. Trust me when I say it will save you a lot
of frustrated time (speaking as someone who learned it the hard way!)
Ethan
> Jed, Matt, thank you a lot!
>
> On 07.03.2011 15:35, Matthew Knepley wrote:
> > On Mon, Mar 7, 2011 at 8:04 AM, Alexander Grayver
> > <agrayver at gfz-potsdam.de> wrote:
> > Jed, but why do I get in line 3003 in
> > src/mat/impls/aij/seq/aij.c at all? As far as understand, if
> > I don't pass nnz (NULL in C/C++ or PETSC_NULL in fortran) I
> > have to avoid this loop in aij.c code.
> >
> >
> >
> > This is the problem. Fortran does not allow this kind of flexible
> > checking, so there are different kinds of "NULL"s. You
> > need to pass PETSC_NULL_INTEGER for nnz.
> >
> >
> > Matt
> >
> > I don't have much experience with valgrind. Could you
> > provide me with right parameters to run my code under
> > valgrind?
> > Thanks a lot for your help.
> >
> >
> > On 07.03.2011 14:59, Jed Brown wrote:
> > > Looks like a memory error. Best bet is to run in Valgrind.
> > >
> > > > On Mar 7, 2011 5:52 AM, "Alexander Grayver"
> > > > <agrayver at gfz-potsdam.de> wrote:
> > > >
> > > > Hi Jed,
> > > >
> > > > It's getting even stranger.
> > > >
> > > > When I run this code under linux I've got error:
> > > >
> > > > [0]PETSC ERROR: --------------------- Error Message
> > > > ------------------------------------
> > > > [0]PETSC ERROR: Argument out of range!
> > > > [0]PETSC ERROR: nnz cannot be greater than row length:
> > > > local row 98 value 1455203639 rowlength 343!
> > > > [0]PETSC ERROR:
> > > > ------------------------------------------------------------------------
> > > > [0]PETSC ERROR: Petsc Release Version 3.1.0, Patch 7,
> > > > Mon Dec 20 14:26:37 CST 2010
> > > > [0]PETSC ERROR: See docs/changes/index.html for recent
> > > > updates.
> > > > [0]PETSC ERROR: See docs/faq.html for hints about
> > > > trouble shooting.
> > > > [0]PETSC ERROR: See docs/index.html for manual pages.
> > > > [0]PETSC ERROR:
> > > > ------------------------------------------------------------------------
> > > > [0]PETSC
> > > > ERROR: /home/mt/agrayver/mt-soft/multiem/INV3D/_tiger/em_model on a openmpi-i named glic by agrayver Mon Mar 7 14:49:43 2011
> > > > [0]PETSC ERROR: Libraries linked
> > > > from /panfs/panfs.gfz-hpcc.cluster/home/mt/agrayver/lib/petsc-3.1-p7/openmpi-intel-complex-debug/lib
> > > > [0]PETSC ERROR: Configure run at Fri Mar 4 12:43:58
> > > > 2011
> > > > [0]PETSC ERROR: Configure options
> > > > --with-petsc-arch=openmpi-intel-complex-debug
> > > > --with-mpi-dir=/opt/mpi/intel/openmpi-1.4.2
> > > > --with-scalar-type=complex
> > > > --with-blas-lapack-dir=/opt/intel/Compiler/11.1/072/mkl/lib/em64t --with-precision=double --with-x=0
> > > > [0]PETSC ERROR:
> > > > ------------------------------------------------------------------------
> > > > [0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line
> > > > 3003 in src/mat/impls/aij/seq/aij.c
> > > > [0]PETSC ERROR: MatCreateSeqAIJ() line 2906 in
> > > > src/mat/impls/aij/seq/aij.c
> > > >
> > > >
> > > > Then I traced it under debugger both on Windows and
> > > > Linux and realized that it doesn't crash under Windows
> > > > only by luck.
> > > >
> > > > The call stack if the folowing:
> > > > [C] MatSeqAIJSetPreallocation_SeqAIJ, FP=7fffb4513880
> > > > [C] MatCreateSeqAIJ, FP=7fffb4513900
> > > > [C] matcreateseqaij_, FP=7fffb4513960
> > > > [F90] MODELING_MOD`modeling, FP=7fffb4517740
> > > >
> > > > As far as I understand after debugging the problem is
> > > > that nnz in MatSeqAIJSetPreallocation isn't 0 and I go
> > > > through this code:
> > > > if (nnz) {
> > > > for (i=0; i<B->rmap->n; i++) {
> > > > if (nnz[i] < 0)
> > > > SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"nnz cannot be less
> > > > than 0: local row %d value %d",i,nnz[i]);
> > > > if (nnz[i] > B->cmap->n)
> > > > SETERRQ3(PETSC_ERR_ARG_OUTOFRANGE,"nnz cannot be greater
> > > > than row length: local row %d value %d rowlength %
> > > > d",i,nnz[i],B->cmap->n);
> > > > }
> > > > }
> > > >
> > > > But why is nnz nonzero? I passed PETSC_NULL. It seems
> > > > like macros CHKFORTRANNULLINTEGER in matcreateseqaij_
> > > > should set it to zero, but it doesn't.
> > > >
> > > >
> > > >
> > > > Thanks.
> > > >
> > > > On 06.03.2011 16:49, Jed Brown wrote:
> > > >
> > > >
> > > > >
> > > > > On Sun, Mar 6, 2011 at 07:39, Alexander Grayver
> > > > <agrayver at gfz-potsdam.de> wrote:
> > > > >>
> > > > >> Hello,
> > > > >...
> > > >
> > > >
> >
> >
> >
> >
> >
> > --
> > What most experimenters take for granted before they begin their
> > experiments is infinitely more interesting than any results to which
> > their experiments lead.
> > -- Norbert Wiener
>
--
------------------------------------
Ethan Coon
Post-Doctoral Researcher
Applied Mathematics - T-5
Los Alamos National Laboratory
505-665-8289
http://www.ldeo.columbia.edu/~ecoon/
------------------------------------
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