[petsc-users] lying about nullspaces

[Matthew Knepley]

On Tue, Jan 10, 2012 at 5:28 PM, Geoffrey Irving <irving at naml.us> wrote:

> On Tue, Jan 10, 2012 at 5:52 AM, Jed Brown <jedbrown at mcs.anl.gov> wrote:
> > On Tue, Jan 10, 2012 at 00:08, Geoffrey Irving <irving at naml.us> wrote:
> >>
> >> For now, I believe I can get away with a single linear iteration.
> >
> >
> > Single linear iteration (e.g. one GMRES cycle) or single linear solve
> (e.g.
> > one Newton step)?
>
> Single linear solve (one Newton step).
>
> >> Even if I need a few, the extra cost of the first linear solve appears
> >> to be drastic.  However, it appears you're right that this isn't due
> >> to preconditioner setup.  The first solve takes over 50 times as long
> >> as the other solves:
> >>
> >>    step 1
> >>      dt = 0.00694444, time = 0
> >>      cg icc converged: iterations = 4, rtol = 0.001, error = 9.56519e-05
> >>      actual L2 residual = 1.10131e-05
> >>      max speed = 0.00728987
> >>    END step 1                                      0.6109 s
> >
> >
> > How are you measuring this time? In -log_summary, I see 0.02 seconds in
> > KSPSolve(). Maybe the time you see is because there are lots of page
> faults
> > until you get the code loaded into memory?
>
> It turns out the initial overhead was due to a bug in my computation
> of row lengths.  It's much faster with the bug fixed.  Is there a way
> to detect reallocations so as avoid this kind of error in future?  I
> looked through the seqaij code and didn't see anything obvious, and
> also couldn't find a function to compute the actual final row lengths.
>

MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_TRUE);

http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatSetOption.html

   Matt


> Thanks,
> Geoffrey
>



-- 
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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