[CIG-SHORT] Change in dt means new Jacobian

[Matthew Knepley]

On Sun, Sep 16, 2012 at 1:36 PM, Birendra jha <bjha7333 at yahoo.com> wrote:

> Hi Matt
>
> Attached is the gdb backtrace of the crash when I use LU preconditioner.
>

This crashes in the Nested Dissection routine. I have only ever seen this
in matrices missing
some rows. Are you sure that this problem has no faults turned on? If so,
please send the
cfg files and meshes so I can reproduce the problem here.

  Thanks

     Matt


> Thanks
> Birendra
>
> --- On *Fri, 9/14/12, Matthew Knepley <knepley at mcs.anl.gov>* wrote:
>
>
> From: Matthew Knepley <knepley at mcs.anl.gov>
> Subject: Re: [CIG-SHORT] Change in dt means new Jacobian
> To: "Birendra jha" <bjha7333 at yahoo.com>
> Cc: "Brad Aagaard" <baagaard at usgs.gov>, cig-short at geodynamics.org
> Date: Friday, September 14, 2012, 6:40 PM
>
>
> On Fri, Sep 14, 2012 at 1:53 AM, Birendra jha <bjha7333 at yahoo.com<http://mc/compose?to=bjha7333@yahoo.com>
> > wrote:
>
> Dear developers
>
> I simplified my problem setup to see if no. of KSP iterations goes down.
> There are 46552 nodes, 42525 hex elements in a box.  In this very simple
> setup, both ASM and ML preconditioner takes ~90 iterations for convergence.
> Attached are the cfg files and stdout from LU and ML preconditioners. ASM
> stdout is not attached.
>
>
> Something in your setup is causing the problem to be nearly or actually
> singular. Its either bad elements in
> the mesh, or an inconsistent boundary condition I think.
>
>
> Why does the run with LU crash? I just used following 2 lines to use LU:
> [pylithapp.petsc]
> pc_type = lu
> Is it incorrect?
>
>
> This is interesting. Can you run in the debugger --petsc.start_in_debugger
> and get a stack trace?
>
>   Thanks,
>
>      Matt
>
>
> For both ASM and ML, the solution looks correct in Paraview. It's just the
> time taken in integrating residual that I would like to reduce.
>
> Another question: when Pylith is running on a single multicore machine,
> can it use OpenMPI instead of MPI (I am assuming it's using MPI by default)?
>
> Thanks and regards
> Birendra
>
> --- On Tue, 9/4/12, Brad Aagaard <baagaard at usgs.gov<http://mc/compose?to=baagaard@usgs.gov>>
> wrote:
>
> > From: Brad Aagaard <baagaard at usgs.gov<http://mc/compose?to=baagaard@usgs.gov>
> >
> > Subject: Re: Change in dt means new Jacobian
> > To: "Birendra jha" <bjha7333 at yahoo.com<http://mc/compose?to=bjha7333@yahoo.com>
> >
> > Cc: cig-short at geodynamics.org<http://mc/compose?to=cig-short@geodynamics.org>
> > Date: Tuesday, September 4, 2012, 7:59 PM
> > On 09/03/2012 08:54 PM, Birendra jha
> > wrote:
> > > 3. How do I utilize multiple cores on a single machine?
> > Sorry if this
> > > question is already answered somewhere. I found
> > instructions on
> > > running parallel using a batch system but don't know
> > how to run on 1
> > > node and use multiple cores. Does this require
> > re-building Pylith?
> >
> > To run in parallel all you have to do is add the command
> > line argument --nodes=NUM_CORES. You do not need to
> > rebuild.
> >
> > > 4. For HDF5 output, is it correct that the I have to
> > wait until
> > > finish to get the xmf file which is needed to load h5
> > files in
> > > Paraview? Manual says "This file is written when PyLith
> > closes the
> > > HDF5 file at the end of the simulation".
> >
> > The Xdmf file is written when PyLith closes the HDF5 file at
> > the end of a simulation. There is a python script included
> > with PyLith called pylith_genxdmf that will generate the
> > Xdmf file given an HDF5 file. This is handy if a simulation
> > did not finish or you add additional fields to an existing
> > HDF5 file. Generating the Xdmf file in the middle of a
> > simulation can work but it is risky because the HDF5 file
> > can get corrupted if multiple processes try to access the
> > file simultaneously.
> >
> >   pylith_genxdmf --file=HDF5_FILE
> >
> > Brad
> >
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>
>
>
> --
> 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
>
>


-- 
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
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