[petsc-users] eps_target malloc issue

[jifeng zhao]

Hello Hong,

There is no problem. You can add the following description:

"The matrices come from Jifeng Zhao, Northwestern University,
zhaojf06 at gmail.com. The stiffness and mass matrices arise from a extended
finite element model to predict phononic band gap of a three-dimensional
two-phase composite with periodic SCC crystal structure. In addition,
periodic boundary conditions are applied on the primary unit cell by
employing Bloch wave analysis."

----------------------------

In addition, do want to let you know that I tried the runtime command you
gave me using PETSC/3.4.4 (3.5 is not ready yet for me), it failed to
converge.

PETSC ERROR: !
PETSC ERROR: KSP did not converge (reason=DIVERGED_ITS)*!*

*I also tried to different preconditioners:*
minres/bjacobi/ icc
minres/bjacobi/ asm
minres/bjacobi/ gamg

All of them failed by the same error. I can try to increase the maximum
iteration number to remove this error message, but it will converge very
slow for sure.

Since I am already using -aij command, I am not sure if these slow
convergence performance will disappear if I upgrade to PETSC/3.5. Is there
anything else I can try on?

Thank you so much,
Jifeng Zhao


On Mon, Aug 4, 2014 at 11:18 PM, hong at aspiritech.org <hong at aspiritech.org>
wrote:

> jifeng :
> >
> > I just want to check with you if there is any updates on why the code
> > crashes under -sbaij?
>
> It is a bug in petsc. I've fixed it in the brach hzhang/mataxpy-bugfix:
> https://bitbucket.org/petsc/petsc/branch/hzhang/mataxpy-bugfix
>
> which will be merged to 'next' branch for tests, then patch to petsc-3.5.
> You can use this branch if you like.
>
> Again, I like to add your matrices into petsc matrix collection.
> Can you give me a short sentence describing your matrices, e.g.,
> "The following matrices come from Rick Dean, Arco E&P Technology,
> rhd at arco.com.  They arise from multiphase flow modeling of oil
> reservoirs,..."
>
> Thanks,
> Hong
>
>
> >
> > At the meanwhile, unfortunately PETSC-3.5 hasn't been installed on my
> server
> > due to some technical problems. I hope technicians can get it done as
> soon
> > as possible. I will update you when I have any new results. Thanks so
> much.
> >
> > Best regards,
> > Jifeng
> >
> >
> > On Wed, Jul 30, 2014 at 2:53 PM, jifeng zhao
> > <jifengzhao2015 at u.northwestern.edu> wrote:
> >>
> >> Hello Hong,
> >>
> >> Thanks a lot. The result makes sense, but I think I will need higher
> >> accuracy (smaller tolerance). I will take a try myself at the meanwhile.
> >>
> >> Best regards,
> >> Jifeng Zhao
> >>
> >>
> >> On Wed, Jul 30, 2014 at 1:16 PM, hong at aspiritech.org <
> hong at aspiritech.org>
> >> wrote:
> >>>
> >>> Jifeng,
> >>> Using petsc-3.5 and slepc-3.5 (maint branch), I tested your matrices
> >>>
> >>> mpiexec -n 32 ./ex7 -f1 $data/zhao/petsc_stiff20.dat -f2
> >>> $data/zhao/petsc_mass20.dat -mat_view ascii::ascii_info -mat_type aij
> >>> -eps_gen_hermitian -eps_type krylovschur -eps_target -0.1 -st_ksp_type
> >>> minres -st_pc_type bjacobi -st_sub_pc_type icc -st_ksp_rtol 1.e-2
> >>> -eps_tol 1.e-2 -eps_nev 40 -st_type sinvert -log_summary |& tee
> >>> log.mat20.ex7.np32.tol-2
> >>>
> >>> The output is attached.
> >>>
> >>> When using '-mat_type sbaij', I got same error as reported, which
> >>> might be a bug in our libraries. I'll investigate it.
> >>> Switching to '-mat_type aij' works (I'm not sure if the computed
> >>> eigenvalues are meaningful though), but the linear solver
> >>> minres/bjacobi/icc converges very slow, takes around 500 - 1000 linear
> >>> iterations for each eps iteration. You may experiment with stronger
> >>> pc_type, e.g., '-pc_type asm' etc.
> >>>
> >>> I'll let you know why sbaij crashes.
> >>>
> >>> Hong
> >>>
> >>> On Mon, Jul 28, 2014 at 4:52 PM, Jose E. Roman <jroman at dsic.upv.es>
> >>> wrote:
> >>> >
> >>> > El 28/07/2014, a las 23:48, jifeng zhao escribió:
> >>> >
> >>> >> Hi Barry,
> >>> >>
> >>> >> Thanks for the reply. I see. I am still testing it and looking for
> the
> >>> >> bug.
> >>> >>
> >>> >> It is pretty weird that the error appears, since the code I am
> running
> >>> >> is ex7 and I didn't change anything.
> >>> >>
> >>> >> My matrices are assembled in binary files separately. As I explained
> >>> >> earlier, I have a series of matrices to solve, each of them have
> the same
> >>> >> patterns but with different values. The way I assembly the matrix
> has proven
> >>> >> to be correct for all the other cases. Only for this one, when the
> matrix
> >>> >> has an zero eigenvalue, ex7 failed to solve it.
> >>> >>
> >>> >> In fact, I don't understand why this "Out of range" error could
> >>> >> possibly appear? 1. my matrices have the correct parrellel lay up.
> 2. In
> >>> >> ex7, I am not explicitly accessing to any elements at all! All I
> did is
> >>> >> EPSSolve();
> >>> >>
> >>> >> Any ideas?
> >>> >>
> >>> >> Best regards,
> >>> >> Jifeng Zhao
> >>> >>
> >>> >
> >>> > Tomorrow we will release slepc-3.5. I would suggest trying with the
> new
> >>> > version. If the problem persist we can help to track down the
> problem.
> >>> >
> >>> > Jose
> >>> >
> >>
> >>
> >>
> >>
> >> --
> >> Jifeng Zhao
> >> PhD candidate at Northwestern University, US
> >> Theoretical and Applied Mechanics Program
> >
> >
> >
> >
> > --
> > Jifeng Zhao
> > PhD candidate at Northwestern University, US
> > Theoretical and Applied Mechanics Program
>



-- 
Jifeng Zhao
PhD candidate at Northwestern University, US
Theoretical and Applied Mechanics Program
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