[petsc-users] my code runs too slow

[Satish Balay]

> 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
> 
> 
> 
>