Re: [deal.II] Re: How to use Trilinos instead of Petsc in step-40

[Wolfgang Bangerth]

On 10/21/2016 04:01 PM, Hamed Babaei wrote:


Please look at the pdf file attached. Thanks


I'm not overly familiar with the nomenclature of large-displacement 
elasticity. But the matrix you compute does at least not look *obviously* 
symmetric to me.


If I see this right, you compute the integral

 \int_K   symm(grad phi_i * F_inv)
* Jc
*  symm(grad phi_j * F_inv)
+ similar terms with tau

Here, Jc seems like a symmetric tensor. Are you sure it's positive definite? 
For tau, is it symmetric? If tau is not symmetric, then your matrix is not 
going to be symmetric.


Best
 W.

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Re: [deal.II] Re: How to use Trilinos instead of Petsc in step-40

[Hamed Babaei]

Dear Daniel,

Please look at the pdf file attached. Thanks

On Friday, October 21, 2016 at 4:51:22 PM UTC-5, Daniel Arndt wrote:
>
> Hamed,
>
> At least I can't open your file in a way to clearly see what your 
> bilinearform is, but could just guess from the implementation. Can you 
> either write it here (using LaTeX or similar) or upload the file as pdf 
> again?
>
> Best,
> Daniel
>

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Bilinearform.pdf
Description: Adobe PDF document

Re: [deal.II] Re: How to use Trilinos instead of Petsc in step-40

[Daniel Arndt]

Hamed,

At least I can't open your file in a way to clearly see what your 
bilinearform is, but could just guess from the implementation. Can you 
either write it here (using LaTeX or similar) or upload the file as pdf 
again?

Best,
Daniel

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Re: [deal.II] Re: How to use Trilinos instead of Petsc in step-40

[Hamed Babaei]

Dear Wolfgang,

In attach you shall find the bilinear form and the assemble part of the 
code as well.

Thanks,

On Friday, October 21, 2016 at 11:14:52 AM UTC-5, Wolfgang Bangerth wrote:
>
>
> > On Thursday, October 20, 2016 at 9:48:55 PM UTC-5, Wolfgang Bangerth 
> wrote: 
> > 
> > What is the norm of the first right hand side? You now set the 
> tolerance in 
> > 
> > the first iteration to a fixed value of 1e-16, but how does this 
> compare to 
> > the previous value of 1e-12*system_rhs.l2_norm()? 
> > 
> > 
> > The system_rhs.l2_norm() before the first call to CGSolverat in the zero 
> time 
> > step was 1.82492e-09, so that the 1e-12*system_rhs.l2_norm() became in 
> the 
> > order of 1e-21 by which CGSOlver didn't converge. 
>
> OK. I have no suggestion, though, why one or the other would lead to 
> convergence or non-convergence of CG. 
>
>
> > That still seems wrong to me. As I mentioned in a previous email, 
> you 
> > ought to 
> > make sure that the matrix you build is the matrix you *want* to 
> build. 
> > 
> > 
> > I was wondering how to make sure the matrix I built is what I meant. 
>
> You need to compare properties of your bilinear form with those of your 
> matrix. For example, if your bilinear form is symmetric, then your matrix 
> is 
> as well -- and that is something you can test. If your bilinear form is 
> positive definite, then your matrix needs to be as well and as a 
> consequence 
> CG needs to converge. If CG does not seem to converge but your bilinear 
> form 
> is s.p.d., you know you have a bug in your matrix assembly. If CG 
> converges on 
> one processor but not on two for the same problem, then you know you have 
> a 
> bug in the parallel matrix assembly. Etc. 
>
> Since you haven't stated your bilinear form or the problem you are 
> solving, I 
> can't tell you whether the matrix is supposed to be s.p.d. 
>
> Best 
>   W. 
>
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>
>

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Bilinearform.docx
Description: MS-Word 2007 document

Re: [deal.II] Re: How to use Trilinos instead of Petsc in step-40

[Hamed Babaei]

Dear Wolfgang,

On Thursday, October 20, 2016 at 9:48:55 PM UTC-5, Wolfgang Bangerth wrote:
>
> What is the norm of the first right hand side? You now set the tolerance 
> in 
>
the first iteration to a fixed value of 1e-16, but how does this compare to 
> the previous value of 1e-12*system_rhs.l2_norm()? 
>

The system_rhs.l2_norm() before the first call to CGSolverat in the zero 
time step was 1.82492e-09, so that the 1e-12*system_rhs.l2_norm() became in 
the order of 1e-21 by which CGSOlver didn't converge.

>
> That still seems wrong to me. As I mentioned in a previous email, you 
> ought to 
> make sure that the matrix you build is the matrix you *want* to build. 
>
 
I was wondering how to make sure the matrix I built is what I meant. 
In addition, Bruno already mentioned sometimes PreconditionerAMG has 
problem with non-positive definite System_matrices. 

Thanks  

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Re: [deal.II] Re: How to use Trilinos instead of Petsc in step-40

[Wolfgang Bangerth]

On 10/19/2016 05:55 PM, Hamed Babaei wrote:

Although the problem has been resolved by this trick but I don't know why I
need to consider different convergence criteria for CG solver in the first
newton iteration.


What is the norm of the first right hand side? You now set the tolerance in 
the first iteration to a fixed value of 1e-16, but how does this compare to 
the previous value of 1e-12*system_rhs.l2_norm()?




In addition, the CG solver still doesn't converge with PreconditionAMG but it
works with PreconditionJacobi.


That still seems wrong to me. As I mentioned in a previous email, you ought to 
make sure that the matrix you build is the matrix you *want* to build.


Best
 W.


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   www: http://www.math.colostate.edu/~bangerth/

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Re: [deal.II] Re: How to use Trilinos instead of Petsc in step-40

[Hamed Babaei]

Hi all,

I just made some changes in the second parameter of SolverControl in the 
following way which apparently resolved the problem:

my problem is nonlinear so I solve it by newton method. It seems that in 
the first Newton-Rophson iteration the CG solver can not converge if the 
tolerance for success of CG iterations is considered 
"1e-12*system_rhs.l2_norm()" 
but It converges with a smaller number like 10e-16. what I did to 
solver_control follows:

double tol ;
 if (newton_rophson_itteration_number==0)
   tol = 1e-16;
else
tol =1e-12*system_rhs.l2_norm();
 
SolverControl solver_control (dof_handler.n_dofs(), tol);

and the following is system_rhs.l2_norm (newton residual) for the first 
time step:

newton iteration   system_rhs.l2_normnumber of CG iterations
0 1.82492e-09 97
1 7.71201e-07 185
2 2.1306e-07   207
3 6.89427e-08 199
4 3.16879e-09 198
5 8.83219e-12 201
6 9.55033e-17 202

As you can see in the first newton iteration residual increases then starts 
to decrease till convergence criteria is satisfied. 
Although the problem has been resolved by this trick but I don't know why I 
need to consider different convergence criteria for CG solver in the first 
newton iteration.

In addition, the CG solver still doesn't converge with PreconditionAMG but 
it works with PreconditionJacobi. 

Thanks,

On Wednesday, October 19, 2016 at 11:01:05 AM UTC-5, Bruno Turcksin wrote:
>
> 2016-10-19 11:51 GMT-04:00 Hamed Babaei : 
>
> > I need to compute the determinant of system_matrix to check if its 
> positive 
> > or negative so that I know my system_matrix is positive definite or not. 
> That's what I thought. You don't need to know the determinant to do 
> that, you can check the sign of the eigenvalues. If all the 
> eigenvalues are positive, the matrix is positive definite. You can 
> either use a separate routine to compute the eigenvalues (see step-36 
> dealii.org/8.4.1/doxygen/deal.II/step_36.html) or you can get an 
> estimate of the eigenvalues when you are using GMRES (see 
>
> http://dealii.org/8.4.1/doxygen/deal.II/classSolverGMRES.html#a7b12c13beeb2d307f244e4dd48c06859)
>  
>
>
> Best, 
>
> Bruno 
>

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Re: [deal.II] Re: How to use Trilinos instead of Petsc in step-40

[Bruno Turcksin]

2016-10-19 11:51 GMT-04:00 Hamed Babaei :
> I need to compute the determinant of system_matrix to check if its positive
> or negative so that I know my system_matrix is positive definite or not.
That's what I thought. You don't need to know the determinant to do
that, you can check the sign of the eigenvalues. If all the
eigenvalues are positive, the matrix is positive definite. You can
either use a separate routine to compute the eigenvalues (see step-36
dealii.org/8.4.1/doxygen/deal.II/step_36.html) or you can get an
estimate of the eigenvalues when you are using GMRES (see
http://dealii.org/8.4.1/doxygen/deal.II/classSolverGMRES.html#a7b12c13beeb2d307f244e4dd48c06859)

Best,

Bruno

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Re: [deal.II] Re: How to use Trilinos instead of Petsc in step-40

[Hamed Babaei]

I need to compute the determinant of system_matrix to check if its positive 
or negative so that I know my system_matrix is positive definite or not.

On Wednesday, October 19, 2016 at 10:38:09 AM UTC-5, Bruno Turcksin wrote:
>
> Hamed,
>
> On Wednesday, October 19, 2016 at 10:25:37 AM UTC-4, Hamed Babaei wrote:It 
> seems that I've been choosing wrong solver for my problem. Since my problem 
> has some sort of instability in its nature, 
>>
>> although my system_matrix is symmetric, it is not necessarily positive 
>> definite. So I have two questions: 
>> First, Is there any function in Dealii or Petsc to compute the 
>> determinant of system_matrix. I have used a determinant function for 3*3 
>> matrices and it doesn't work for higher dimensions.
>>
> Why do you need this?
>  
>
>> Second, which solver and preconditioner can be used for symmetric but 
>> non-positive definite system_matrix.
>>
> For the solver, you can use GMRES, BiCGSTAB, or MinRES. For the 
> preconditioner, you can use ILU, SSOR, or algebraic multigrid (AMG). 
> Sometimes AMG have difficulties with non-s.p.d. matrices though.
>
> Best,
>
> Bruno 
>

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Re: [deal.II] Re: How to use Trilinos instead of Petsc in step-40

[Hamed Babaei]

Hi everyone,

Thank you all for your incredible guides.
It seems that I've been choosing wrong solver for my problem. Since my 
problem has some sort of instability in its nature, 
although my system_matrix is symmetric, it is not necessarily positive 
definite. So I have two questions: 
First, Is there any function in Dealii or Petsc to compute the determinant 
of system_matrix. I have used a determinant function for 3*3 matrices and 
it doesn't work for higher dimensions.
Second, which solver and preconditioner can be used for symmetric but 
non-positive definite system_matrix.

Thanks


On Tuesday, October 18, 2016 at 9:49:03 AM UTC-5, Wolfgang Bangerth wrote:
>
> > which solvers do you think I can examin and see if they can be used 
> > instead of SolverCG? 
>
> That's the wrong question. If you know that the matrix you have *should 
> be* 
> symmetric and positive definite, but the CG solver does not converge, then 
> you 
> need to debug why the matrix *is not* s.p.d. Using a different solver 
> might 
> allow you to solve the linear system, but since the linear system is 
> apparently not the correct one, the solution will also not be correct. 
>
> Best 
>   W. 
>
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>
>

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Re: [deal.II] Re: How to use Trilinos instead of Petsc in step-40

[Wolfgang Bangerth]

which solvers do you think I can examin and see if they can be used
instead of SolverCG?


That's the wrong question. If you know that the matrix you have *should be* 
symmetric and positive definite, but the CG solver does not converge, then you 
need to debug why the matrix *is not* s.p.d. Using a different solver might 
allow you to solve the linear system, but since the linear system is 
apparently not the correct one, the solution will also not be correct.


Best
 W.


--

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Re: [deal.II] Re: How to use Trilinos instead of Petsc in step-40

[Daniel Arndt]

Hamed,

which solvers do you think I can examin and see if they can be used instead 
> of SolverCG?
>

Running with the deal.II CG solver gives me


An error occurred in line <424> of file 
 in function
void 
PhaseField::Material_Compressible_Neo_Hook_Three_Field::update_material_data(const
 
dealii::Tensor<2, dim, double>&, const dealii::Tensor<2, dim, double>&, 
double, double, double, double, double) [with int dim = 3]
The violated condition was: 
det_F > 0

so there seem to be some more problems... 
Is everything working as expected with a direct solver (like 
SparseDirectUMFPACK)?

Best,
Daniel 

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Re: [deal.II] Re: How to use Trilinos instead of Petsc in step-40

[Daniel Arndt]

Hamed,

running your code with a Trilinos installation alone fails for me in line 
1617 with

An error occurred in line <279> of file 
 in function
void dealii::TrilinosWrappers::SolverBase::do_solve(const 
dealii::TrilinosWrappers::PreconditionBase&)
The violated condition was:
false
Additional information:
AztecOO::Iterate error code -2: numerical breakdown

and the same for no preconditioner. The same holds for PETSc. It seems that 
you should review if this matrix is assembled correctly and that CG is 
appropriate, i.e. is this matrix symmetric and positive definite?

I can't reproduce your error

"PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, 
probably memory access out of range"

running with a developer version.

Best,
Daniel


Am Montag, 17. Oktober 2016 04:47:32 UTC+2 schrieb Wolfgang Bangerth:
>
> On 10/16/2016 03:46 PM, Hamed Babaei wrote: 
> > Another point I need to mention is that I had the same problem when as 
> my 
> > first try of parallelization, I paralleled a much simpler code, the 
> step-25, 
> > based on the step-40 . 
> > I received the same Segmentation Violation error from Petsc. At that 
> time, I 
> > replaced PreconditionerAMG with PreconditionerJacobi and the problem 
> resolved. 
>
> This does not help right now, but as a general rule, it is far simpler to 
> debug things when you have a small, simple program that when you have a 
> large, 
> complicated one. In your case, you had a problem you didn't understand, 
> and 
> you chose to address it in a way that papered over it, rather than 
> properly 
> fixed it based on an understanding of what is going on. It is a truism 
> that 
> this sort of issue will come back at some time. 
>
> In other words, if you have a problem, debug it until you understand what 
> the 
> problem is, and then fix it the right way. Don't paper over it. 
>
> Best 
>   W. 
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>
>

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Re: [deal.II] Re: How to use Trilinos instead of Petsc in step-40

[Wolfgang Bangerth]

On 10/16/2016 03:46 PM, Hamed Babaei wrote:

Another point I need to mention is that I had the same problem when as my
first try of parallelization, I paralleled a much simpler code, the step-25,
based on the step-40 .
I received the same Segmentation Violation error from Petsc. At that time, I
replaced PreconditionerAMG with PreconditionerJacobi and the problem resolved.


This does not help right now, but as a general rule, it is far simpler to 
debug things when you have a small, simple program that when you have a large, 
complicated one. In your case, you had a problem you didn't understand, and 
you chose to address it in a way that papered over it, rather than properly 
fixed it based on an understanding of what is going on. It is a truism that 
this sort of issue will come back at some time.


In other words, if you have a problem, debug it until you understand what the 
problem is, and then fix it the right way. Don't paper over it.


Best
 W.

--

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   www: http://www.math.colostate.edu/~bangerth/

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[deal.II] Re: How to use Trilinos instead of Petsc in step-40

[Hamed Babaei]

Another point I need to mention is that I had the same problem when as my 
first try of parallelization, I paralleled a much simpler code, the 
step-25, based on the step-40 . 
I received the same Segmentation Violation error from Petsc. At that time, 
I replaced PreconditionerAMG with PreconditionerJacobi and the problem 
resolved. 

However, Now even using PreconditionerJacobi can not remedy the issue even 
if it works for very few initial value and boundary conditions.

On Sunday, October 16, 2016 at 10:39:49 AM UTC-5, Daniel Arndt wrote:
>
> In case there is an error with Trilinos, what is it?
>
> Am Sonntag, 16. Oktober 2016 17:27:26 UTC+2 schrieb Daniel Arndt:
>>
>> Hamed,
>>
>>
> It still works with Petsc and Trilinos is not implemented at all. I 
> appreciate it if you could let me know what changes should be made in 
> step-40 to make it work with Trilinos.
>
 What exactly, do you mean by that? So you have both PETSc and Trilinos 
>> installed and step-40 works. Are you saying that PETSc objects are used 
>> even if you use 
>> "using namespace ::LinearAlgebraTrilinos;" ? How did you find out?
>>
>> Best,
>> Daniel
>>
>

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[deal.II] Re: How to use Trilinos instead of Petsc in step-40

[Hamed Babaei]

Hi Jean-Paul,

I have installed latest version of Dealii (8.4.1) and all of its library 
dependencies (Petsc, P4est, Trilinos,...) all together via Candi ( the bash 
script installer tool) https://github.com/koecher/candi. 

Thanks

On Saturday, October 15, 2016 at 12:25:44 AM UTC-5, Jean-Paul Pelteret 
wrote:
>
> Hi Hamad,
>
> Can you please tell us which version of deal.II you are using, and provide 
> us with the installation logs?
>
> Regards,
> J-P
>
> On Friday, October 14, 2016 at 11:51:09 PM UTC+2, Hamed Babaei wrote:
>>
>> Hi friends,
>>
>> I want to use Trilinos instead of Petsc in my parallel code which is 
>> based on step-40. I guess some changes should be made in the following 
>> lines of the include files part:
>>
>> namespace LA
>> {
>> #if defined(DEAL_II_WITH_PETSC) && !(defined(DEAL_II_WITH_TRILINOS) && 
>> defined(FORCE_USE_OF_TRILINOS))
>> using namespace ::LinearAlgebraPETSc 
>> 
>> ;
>> # define USE_PETSC_LA
>> #elif defined(DEAL_II_WITH_TRILINOS)
>> using namespace ::LinearAlgebraTrilinos 
>> 
>> ;
>> #else
>> # error DEAL_II_WITH_PETSC or DEAL_II_WITH_TRILINOS required
>> #endif
>> }
>>
>> My problem is even if I replace the above lines with the following:
>>
>> namespace LA
>> {
>> using namespace ::LinearAlgebraTrilinos 
>> 
>> ;
>> }
>>
>> It still works with Petsc and Trilinos is not implemented at all. I 
>> appreciate it if you could let me know what changes should be made in 
>> step-40 to make it work with Trilinos.
>>
>> Thanks,
>> Hamed
>>
>

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[deal.II] Re: How to use Trilinos instead of Petsc in step-40

[Jean-Paul Pelteret]

Hi Hamad,

Can you please tell us which version of deal.II you are using, and provide 
us with the installation logs?

Regards,
J-P

On Friday, October 14, 2016 at 11:51:09 PM UTC+2, Hamed Babaei wrote:
>
> Hi friends,
>
> I want to use Trilinos instead of Petsc in my parallel code which is based 
> on step-40. I guess some changes should be made in the following lines of 
> the include files part:
>
> namespace LA
> {
> #if defined(DEAL_II_WITH_PETSC) && !(defined(DEAL_II_WITH_TRILINOS) && 
> defined(FORCE_USE_OF_TRILINOS))
> using namespace ::LinearAlgebraPETSc 
> 
> ;
> # define USE_PETSC_LA
> #elif defined(DEAL_II_WITH_TRILINOS)
> using namespace ::LinearAlgebraTrilinos 
> 
> ;
> #else
> # error DEAL_II_WITH_PETSC or DEAL_II_WITH_TRILINOS required
> #endif
> }
>
> My problem is even if I replace the above lines with the following:
>
> namespace LA
> {
> using namespace ::LinearAlgebraTrilinos 
> 
> ;
> }
>
> It still works with Petsc and Trilinos is not implemented at all. I 
> appreciate it if you could let me know what changes should be made in 
> step-40 to make it work with Trilinos.
>
> Thanks,
> Hamed
>

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