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Today's Topics:
1. Re: Error using MUMPS to solve large linear system (Xiaoye S. Li)
2. Preconditioning in matrix-free methods (Konstantinos Kontzialis)
3. Re: From 1D to 3D problem ? Unstructured mesh ? (Aron Roland)
4. Re: Preconditioning in matrix-free methods (Jed Brown)
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Message: 1
Date: Mon, 24 Feb 2014 12:58:57 -0800
From: "Xiaoye S. Li" <[email protected]>
To: Hong Zhang <[email protected]>
Cc: "[email protected]" <[email protected]>
Subject: Re: [petsc-users] Error using MUMPS to solve large linear
system
Message-ID:
<cafvbobwxmpqauq+wonebm5ahxbusi9d+bysjhfzrsoofxyf...@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Samar:
If you include the error message while crashing using superlu_dist, I
probably know the reason. (better yet, include the printout before the
crash. )
Sherry
On Mon, Feb 24, 2014 at 9:56 AM, Hong Zhang <[email protected]> wrote:
Samar :
There are limitations for direct solvers.
Do not expect any solver can be used on arbitrarily large problems.
Since superlu_dist also crashes, direct solvers may not be able to work on
your application.
This is why I suggest to increase size incrementally.
You may have to experiment other type of solvers.
Hong
Hi Hong and Jed,
Many thanks for replying. It would indeed be nice if the error messages
from MUMPS were less cryptic!
1) I have tried smaller matrices although given how my problem is set
up a jump is difficult to avoid. But a good idea
that I will try.
2) I did try various ordering but not the one you suggested.
3) Tracing the error through the MUMPS code suggest a rather abrupt
termination of the program (there should be more
error messages if, for example, memory was a problem). I therefore
thought it might be an interface problem rather than
one with mumps and turned to the petsc-users group first.
4) I've tried superlu_dist but it also crashes (also unclear as to why)
at which point I decided to try mumps. The fact that both
crash would again indicate a common (memory?) problem.
I'll try a few more things before asking the MUMPS developers.
Thanks again for your help!
Samar
On Feb 24, 2014, at 11:47 AM, Hong Zhang <[email protected]> wrote:
Samar:
The crash occurs in
...
[161]PETSC ERROR: Error in external library!
[161]PETSC ERROR: Error reported by MUMPS in numerical factorization
phase: INFO(1)=-1, INFO(2)=48
for very large matrix, likely memory problem as you suspected.
I would suggest
1. run problems with increased sizes (not jump from a small one to a very
large one) and observe memory usage using
'-ksp_view'.
I see you use '-mat_mumps_icntl_14 1000', i.e., percentage of
estimated workspace increase. Is it too large?
Anyway, this input should not cause the crash, I guess.
2. experimenting with different matrix ordering -mat_mumps_icntl_7 <> (I
usually use sequential ordering 2)
I see you use parallel ordering -mat_mumps_icntl_29 2.
3. send bug report to mumps developers for their suggestion.
4. try other direct solvers, e.g., superlu_dist.
...
etc etc. The above error I can tell has something to do with processor
48 (INFO(2)) and so forth but not the previous one.
The full output enabled with -mat_mumps_icntl_4 3 looks as in the
attached file. Any hints as to what could be giving this
error would be very much appreciated.
I do not know how to interpret this output file. mumps developer would
give you better suggestion on it.
I would appreciate to learn as well :-)
Hong
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Message: 2
Date: Mon, 24 Feb 2014 22:10:11 +0000 (UTC)
From: Konstantinos Kontzialis <[email protected]>
To: [email protected]
Subject: [petsc-users] Preconditioning in matrix-free methods
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Message: 3
Date: Mon, 24 Feb 2014 23:30:29 +0100
From: Aron Roland <[email protected]>
To: Christophe Ortiz <[email protected]>, Jed Brown
<[email protected]>
Cc: [email protected], Mathieu Dutour <[email protected]>,
Thomas Huxhorn <[email protected]>
Subject: Re: [petsc-users] From 1D to 3D problem ? Unstructured mesh ?
Message-ID: <[email protected]>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
Hi,
I can provide u some nice package to generate unstructured meshes. There
are many institutions using it now. We have also used PETSC to solve
some nonlinera hyperbolic problem on 2d on unstructured meshes and it
works quite ok even if the scaling still not what it should be but well
these are other issues ...
Cheers
Aron
On 02/24/2014 09:04 AM, Christophe Ortiz wrote:
On Sat, Feb 22, 2014 at 2:33 AM, Jed Brown <[email protected]
<mailto:[email protected]>> wrote:
Christophe Ortiz <[email protected]
<mailto:[email protected]>> writes:
> Hi all,
>
> Recently I have implemented a 1D problem of coupled diffusion
equations
> using PETSc. I did it using finite differences for diffusion
terms and
> F(t,U,U_t) = 0. It works pretty well with ARKIMEX3. I get a nice
timestep
> variation and all boundary conditions work well.
>
> Now I would like to move to 3D problems to simulate the
diffusion and
> interaction of species in a "real material". By real material I
mean a
> material made of subregions with internal surfaces where species
could
> recombine (means Dirichlet). These subregions are distributed in a
> complicated manner, ie not cartesian. A good picture of this
would be a
> polycrystal (see attachment to get an idea). Each crystal has a
different
> orientation and the boundary between two small crystals forms an
internal
> surface.
>
> I have several questions on how to implement this:
>
> 1) Since, the problem will not be solved in a cartesian mesh,
should I use
> unstructured meshes ? If so, how can this unstructured mesh can be
> generated ( I have no experience with unstructured meshes. I
always work in
> 1D).
Are you intending to mesh the boundaries of the crystals? Will you be
dynamically remeshing? (That is very complicated and expensive in
3D.)
What formulation will you be using for grain boundary evolution?
No, in principle I will not consider the evolution of grains.
Therefore, no dynamic remershing (in principle).
What I want is just the evolution of diffusing and reacting species
inside the ensemble of grains, including their interaction with the
grain boundaries (trapping, segregation, ...).
I think you should check out phase field models, such as the
publication
below.
I never used phase-field models. According to what I read, it can
model many phnomena but in particular it substitutes a boundary
condition at an interface by a PDE for the evolution of an auxiliary
field (Wikipedia). In this sense, maybe it could be interesting since
I want to simulate the evolution of species inside grains with many
internal grain boundaries.
But I don't know if to treat a grain boundary as a infinitely sharp
interface or as a thin but finite piece of material with different
properties for species (diffusion coeff for instance).
Perhaps check out the paper below. The framework (MOOSE) used
for this publication should be released open source on github next
week
(check https://github.com/idaholab/). I don't know if Marmot, the
phase-field component, will be open source any time soon, but they are
typically happy to collaborate. MOOSE uses PETSc for solvers, but
provides a higher level interface.
@article{tonks2012object,
title={An object-oriented finite element framework for
multiphysics phase field simulations},
author={Tonks, M.R. and Gaston, D. and Millett, P.C. and Andrs,
D. and Talbot, P.},
journal={Computational Materials Science},
volume={51},
number={1},
pages={20--29},
year={2012},
publisher={Elsevier}
}
Sorry, I could not download the article. We don't have access. Crisis
in Spain :-( !
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Message: 4
Date: Mon, 24 Feb 2014 18:18:36 -0700
From: Jed Brown <[email protected]>
To: Konstantinos Kontzialis <[email protected]>,
[email protected]
Subject: Re: [petsc-users] Preconditioning in matrix-free methods
Message-ID: <[email protected]>
Content-Type: text/plain; charset="us-ascii"
Konstantinos Kontzialis <[email protected]> writes:
Dear all,
I am trying to use preconditioning in SNES within a matrix free conext. I use
petsc 3.3 and whenever I use the option
-snes_mf_operator I get the following error:
-snes_mf_operator means to use the matrix you assemble for
preconditioning, but apply the true Jacobian using matrix-free finite
differencing. It is normally used when the function you pass to
TSSetIJacobian() only approximates the true Jacobian, typically by
using a lower-order discretization or by discarding some terms.
Must call DMShellSetMatrix() or DMShellSetCreateMatrix()
I code the following:
call TSCreate (petsc_comm_world, ts_mhd, ierpetsc)
c
call TSSetProblemType (ts_mhd, TS_NONLINEAR, ierpetsc)
c
call TSSetIFunction ( ts_mhd, res_mhd, residual_mag,
@ PETSC_NULL_OBJECT, ierpetsc )
c
call TSSetSolution( ts_mhd, Bmagnetic_pet, ierpetsc )
c
call TSSetMaxSNESFailures ( ts_mhd, -1, ierpetsc)
c
call TSGetSNES (ts_mhd, snes_mhd, ierpetsc )
call MatCreateSNESMF ( snes_mhd, J_mf, ierpetsc )
c
call SNESSetJacobian ( snes_mhd, J_mf, M_mhd,
@ SNESDefaultComputeJacobianColor, fdcoloring,
@ ierpetsc )
Has anyone any suggestions on what to do?
Kostas
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