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 (??) > > > xxy113 at psu.edu > > > > > > > > > > > > > > Xuan YU (??) > xxy113 at psu.edu > > > >
