[petsc-users] my code runs too slow

[Satish Balay]

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.

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
> 
> 
> 
>