What function are you using to compute jacobian? Perhaps you are missing MatAssembly() calls in that function?
Or reordering the code as follows should work - but the correct location for MatAssembly() calls are in the routine you are using for assembling the jacobian. Satish >>>>>>>>> ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,N,N,10,PETSC_NULL,&J);CHKERRQ(ierr); ierr = SNESComputeJacobian(ts_snes,CV_Y,&J,&J,&flag);CHKERRQ(ierr); ierr = MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);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); <<<<<< On Wed, 7 Jul 2010, Xuan YU wrote: > Sorry, this is the complete one: > > [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ > [0]PETSC ERROR: Object is in wrong state! > [0]PETSC ERROR: Not for unassembled matrix! > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Petsc Development HG revision: > fdc7be12de37b8a400b6e561de9850bcc7e79f4f HG Date: Fri Jul 02 21:17:36 2010 > -0500 > [0]PETSC ERROR: See docs/changes/index.html for recent updates. > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [0]PETSC ERROR: See docs/index.html for manual pages. > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: ./pihm on a arch-linu named lionxi.rcc.psu.edu by xxy113 Wed > Jul 7 14:32:11 2010 > [0]PETSC ERROR: Libraries linked from > /gpfs/home/xxy113/soft/petsc-dev/arch-linux-gnu-c-debug/lib > [0]PETSC ERROR: Configure run at Sun Jul 4 14:09:16 2010 > [0]PETSC ERROR: Configure options --download-f-blas-lapack=1 > --download-mpich=1 > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: MatGetColoring() line 491 in src/mat/color/color.c > [0]PETSC ERROR: VecRestoreArrayPrivate3() line 201 in /work/petsc/pihm.c > > On Jul 7, 2010, at 2:28 PM, Satish Balay wrote: > > > > > 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 (???@) > > > > > > > > xxy113 at psu.edu > > > > > > > > > > > > > > > > > > > > > > > > > > > > Xuan YU (???@) > > > > > > > > xxy113 at psu.edu > > > > > > > > > > > > > > > > > > > > > > > > > > > > Xuan YU (???@) > > > > xxy113 at psu.edu > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Xuan YU (???@) > xxy113 at psu.edu > > > >
