[petsc-users] my code runs too slow

[Satish Balay]

> > ierr = SNESComputeJacobian(ts_snes,CV_Y,&J,&J,&flag);CHKERRQ(ierr);

Perhaps there is a function thats set to compute jacobinan thats not
assembling the matrix properly?

Also - please dont' truncate error messages - when you send
them. Incomplete info is not useful.

Satish

On Wed, 7 Jul 2010, Matthew Knepley wrote:

> 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
> >
> >
> >
> >
> >
> 
> 
>