[petsc-users] my code runs too slow

[Matthew Knepley]

You have to assemble

  a) after setting values

  b) before using the matrix

Please consult the user examples where this is done correctly and the manual
section which explains the assembly process.

    Matt

On Wed, Jul 7, 2010 at 8:13 PM, Xuan YU <xxy113 at psu.edu> wrote:

>
> On Jul 7, 2010, at 2:06 PM, Satish Balay wrote:
>
> On Wed, 7 Jul 2010, Xuan YU wrote:
>
> ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,N,N,10,PETSC_NULL,&J);CHKERRQ(ierr);
>
>
> ierr = MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
>
> ierr = MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
>
>
> This assembly removes the unused space here. Since no values are
> inserted - it squezes out all of the allocated space. Perhaps you just
> need to remove these 2 calls as the actual matrix is assembled further
> down the code.
>
>
> I removed these 2
> But got Error Message
>
> [0]PETSC ERROR: Object is in wrong state!
> [0]PETSC ERROR: Not for unassembled matrix!
>
>
>
>
>
> Satish
>
> ierr = SNESComputeJacobian(ts_snes,CV_Y,&J,&J,&flag);CHKERRQ(ierr);
>
> ierr = MatGetColoring(J,MATCOLORINGSL,&iscoloring);CHKERRQ(ierr);
>
> ierr = MatFDColoringCreate(J,iscoloring,&matfdcoloring);CHKERRQ(ierr);
>
> ierr = MatFDColoringSetFunction(matfdcoloring,(PetscErrorCode
>
> (*)(void))f,(void*)&appctx);CHKERRQ(ierr);
>
> ierr = MatFDColoringSetFromOptions(matfdcoloring);CHKERRQ(ierr);
>
> ierr =
> TSSetRHSJacobian(ts,J,J,TSDefaultComputeJacobianColor,matfdcoloring);
>
>
> These are the Jacobian related codes.
>
>
>
>
>
> On Jul 7, 2010, at 1:51 PM, Satish Balay wrote:
>
>
> total: nonzeros=1830
>
> mallocs used during MatSetValues calls =1830
>
>
> Looks like you are zero-ing out the non-zero structure - before
>
> assembling the matrix.
>
>
> Are you calling MatZeroRows() or MatZeroEntries() or something else -
>
> before assembling the matrix?
>
>
> Satish
>
>
> On Wed, 7 Jul 2010, Xuan YU wrote:
>
>
> I made a change: ierr =
>
> MatCreateSeqAIJ(PETSC_COMM_SELF,N,N,5,PETSC_NULL,&J);CHKERRQ(ierr);
>
>
> Time of the code did not change much, and got the info:
>
> Matrix Object:
>
>     type=seqaij, rows=1830, cols=1830
>
>     total: nonzeros=1830, allocated nonzeros=36600
>
>     total number of mallocs used during MatSetValues calls =1830
>
>       not using I-node routines
>
>
>
>
> On Jul 7, 2010, at 12:51 PM, Satish Balay wrote:
>
>
>   total: nonzeros=1830, allocated nonzeros=29280
>
>   total number of mallocs used during MatSetValues calls =1830
>
>
> There is something wrong with your preallocation or matrix
>
> assembly. You should see zero mallocs for efficient assembly.
>
>
>
> http://www.mcs.anl.gov/petsc/petsc-as/documentation/faq.html#efficient-assembly
>
>
> satish
>
>
>
> On Wed, 7 Jul 2010, Xuan YU wrote:
>
>
> Hi,
>
>
> I finite difference Jacobian approximation for my TS model. The size
>
> of
>
> the
>
> vector is 1830. I got the following info with(-ts_view):
>
>
> type: beuler
>
> maximum steps=50
>
> maximum time=50
>
> total number of nonlinear solver iterations=647
>
> total number of linear solver iterations=647
>
> SNES Object:
>
> type: ls
>
> line search variant: SNESLineSearchCubic
>
> alpha=0.0001, maxstep=1e+08, minlambda=1e-12
>
> maximum iterations=50, maximum function evaluations=10000
>
> tolerances: relative=1e-08, absolute=1e-50, solution=1e-08
>
> total number of linear solver iterations=50
>
> total number of function evaluations=51
>
> KSP Object:
>
> type: gmres
>
>   GMRES: restart=30, using Classical (unmodified) Gram-Schmidt
>
> Orthogonalization with no iterative refinement
>
>   GMRES: happy breakdown tolerance 1e-30
>
> maximum iterations=10000, initial guess is zero
>
> tolerances:  relative=1e-05, absolute=1e-50, divergence=10000
>
> left preconditioning
>
> using PRECONDITIONED norm type for convergence test
>
> PC Object:
>
> type: ilu
>
>   ILU: out-of-place factorization
>
>   0 levels of fill
>
>   tolerance for zero pivot 1e-12
>
>   using diagonal shift to prevent zero pivot
>
>   matrix ordering: natural
>
>   factor fill ratio given 1, needed 1
>
>     Factored matrix follows:
>
>       Matrix Object:
>
>         type=seqaij, rows=1830, cols=1830
>
>         package used to perform factorization: petsc
>
>         total: nonzeros=1830, allocated nonzeros=1830
>
>         total number of mallocs used during MatSetValues calls =0
>
>           not using I-node routines
>
> linear system matrix = precond matrix:
>
> Matrix Object:
>
>   type=seqaij, rows=1830, cols=1830
>
>   total: nonzeros=1830, allocated nonzeros=29280
>
>   total number of mallocs used during MatSetValues calls =1830
>
>     not using I-node routines
>
>
>
> 50 output time step takes me 11.877s. So I guess there is something
>
> not
>
> appropriate with my Jacobian Matrix. Could you please tell me how to
>
> speed
>
> up
>
> my code?
>
>
> Thanks!
>
>
> Xuan YU
>
> xxy113 at psu.edu
>
>
>
>
>
>
>
>
> Xuan YU (俞烜)
>
> xxy113 at psu.edu
>
>
>
>
>
>
> Xuan YU (俞烜)
>
> xxy113 at psu.edu
>
>
>
>
>
>
> Xuan YU (俞烜)
> xxy113 at psu.edu
>
>
>
>
>


-- 
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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