[petsc-users] my code runs too slow
Satish Balay
balay at mcs.anl.gov
Wed Jul 7 13:36:58 CDT 2010
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 (ÓáŸ@)
> > > >
> > > > xxy113 at psu.edu
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > Xuan YU (ÓáŸ@)
> > > >
> > > > xxy113 at psu.edu
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > Xuan YU (ÓáŸ@)
> > > > xxy113 at psu.edu
> > > >
> > > >
> > > >
> > > >
> > > >
> > >
> > >
> > >
>
> Xuan YU (ÓáŸ@)
> xxy113 at psu.edu
>
>
>
>
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