On Wed, Nov 11, 2015 at 12:24 PM, David Knezevic <david.kneze...@akselos.com > wrote:
> On Tue, Nov 10, 2015 at 10:28 PM, David Knezevic < > david.kneze...@akselos.com> wrote: > >> On Tue, Nov 10, 2015 at 10:24 PM, Matthew Knepley <knep...@gmail.com> >> wrote: >> >>> On Tue, Nov 10, 2015 at 9:21 PM, David Knezevic < >>> david.kneze...@akselos.com> wrote: >>> >>>> On Tue, Nov 10, 2015 at 10:00 PM, Matthew Knepley <knep...@gmail.com> >>>> wrote: >>>> >>>>> On Tue, Nov 10, 2015 at 8:39 PM, David Knezevic < >>>>> david.kneze...@akselos.com> wrote: >>>>> >>>>>> I'm looking into using GAMG, so I wanted to start with a simple 3D >>>>>> elasticity problem. When I first tried this, I got the following "zero >>>>>> pivot" error: >>>>>> >>>>>> >>>>>> ----------------------------------------------------------------------- >>>>>> >>>>>> [0]PETSC ERROR: Zero pivot in LU factorization: >>>>>> http://www.mcs.anl.gov/petsc/documentation/faq.html#zeropivot >>>>>> [0]PETSC ERROR: Zero pivot, row 3 >>>>>> [0]PETSC ERROR: See >>>>>> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble >>>>>> shooting. >>>>>> [0]PETSC ERROR: Petsc Release Version 3.6.1, Jul, 22, 2015 >>>>>> [0]PETSC ERROR: >>>>>> /home/dknez/akselos-dev/scrbe/build/bin/fe_solver-opt_real on a >>>>>> arch-linux2-c-opt named david-Lenovo by dknez Tue Nov 10 21:26:39 2015 >>>>>> [0]PETSC ERROR: Configure options --with-shared-libraries=1 >>>>>> --with-debugging=0 --download-suitesparse --download-parmetis >>>>>> --download-blacs >>>>>> --with-blas-lapack-dir=/opt/intel/system_studio_2015.2.050/mkl >>>>>> --CXXFLAGS=-Wl,--no-as-needed --download-scalapack --download-mumps >>>>>> --download-metis --download-superlu_dist >>>>>> --prefix=/home/dknez/software/libmesh_install/opt_real/petsc >>>>>> --download-hypre --download-ml >>>>>> [0]PETSC ERROR: #1 PetscKernel_A_gets_inverse_A_5() line 48 in >>>>>> /home/dknez/software/petsc-3.6.1/src/mat/impls/baij/seq/dgefa5.c >>>>>> [0]PETSC ERROR: #2 MatSOR_SeqAIJ_Inode() line 2808 in >>>>>> /home/dknez/software/petsc-3.6.1/src/mat/impls/aij/seq/inode.c >>>>>> [0]PETSC ERROR: #3 MatSOR() line 3697 in >>>>>> /home/dknez/software/petsc-3.6.1/src/mat/interface/matrix.c >>>>>> [0]PETSC ERROR: #4 PCApply_SOR() line 37 in >>>>>> /home/dknez/software/petsc-3.6.1/src/ksp/pc/impls/sor/sor.c >>>>>> [0]PETSC ERROR: #5 PCApply() line 482 in >>>>>> /home/dknez/software/petsc-3.6.1/src/ksp/pc/interface/precon.c >>>>>> [0]PETSC ERROR: #6 KSP_PCApply() line 242 in >>>>>> /home/dknez/software/petsc-3.6.1/include/petsc/private/kspimpl.h >>>>>> [0]PETSC ERROR: #7 KSPInitialResidual() line 63 in >>>>>> /home/dknez/software/petsc-3.6.1/src/ksp/ksp/interface/itres.c >>>>>> [0]PETSC ERROR: #8 KSPSolve_GMRES() line 235 in >>>>>> /home/dknez/software/petsc-3.6.1/src/ksp/ksp/impls/gmres/gmres.c >>>>>> [0]PETSC ERROR: #9 KSPSolve() line 604 in >>>>>> /home/dknez/software/petsc-3.6.1/src/ksp/ksp/interface/itfunc.c >>>>>> [0]PETSC ERROR: #10 KSPSolve_Chebyshev() line 381 in >>>>>> /home/dknez/software/petsc-3.6.1/src/ksp/ksp/impls/cheby/cheby.c >>>>>> [0]PETSC ERROR: #11 KSPSolve() line 604 in >>>>>> /home/dknez/software/petsc-3.6.1/src/ksp/ksp/interface/itfunc.c >>>>>> [0]PETSC ERROR: #12 PCMGMCycle_Private() line 19 in >>>>>> /home/dknez/software/petsc-3.6.1/src/ksp/pc/impls/mg/mg.c >>>>>> [0]PETSC ERROR: #13 PCMGMCycle_Private() line 48 in >>>>>> /home/dknez/software/petsc-3.6.1/src/ksp/pc/impls/mg/mg.c >>>>>> [0]PETSC ERROR: #14 PCApply_MG() line 338 in >>>>>> /home/dknez/software/petsc-3.6.1/src/ksp/pc/impls/mg/mg.c >>>>>> [0]PETSC ERROR: #15 PCApply() line 482 in >>>>>> /home/dknez/software/petsc-3.6.1/src/ksp/pc/interface/precon.c >>>>>> [0]PETSC ERROR: #16 KSP_PCApply() line 242 in >>>>>> /home/dknez/software/petsc-3.6.1/include/petsc/private/kspimpl.h >>>>>> [0]PETSC ERROR: #17 KSPSolve_CG() line 139 in >>>>>> /home/dknez/software/petsc-3.6.1/src/ksp/ksp/impls/cg/cg.c >>>>>> [0]PETSC ERROR: #18 KSPSolve() line 604 in >>>>>> /home/dknez/software/petsc-3.6.1/src/ksp/ksp/interface/itfunc.c >>>>>> >>>>>> >>>>>> ----------------------------------------------------------------------- >>>>>> >>>>>> I saw that there was a thread about this in September (subject: "gamg >>>>>> and zero pivots"), and that the fix is to use "-mg_levels_pc_type >>>>>> jacobi." When I do that, the solve succeeds (I pasted the -ksp_view at >>>>>> the >>>>>> end of this email). >>>>>> >>>>>> So I have two questions about this: >>>>>> >>>>>> 1. Is it surprising that I hit this issue for a 3D elasticity >>>>>> problem? Note that matrix assembly was done in libMesh, I can look into >>>>>> the >>>>>> structure of the assembled matrix more carefully, if needed. Also, note >>>>>> that I can solve this problem with direct solvers just fine. >>>>>> >>>>> >>>>> Yes, this seems like a bug, but it could be some strange BC thing I do >>>>> not understand. >>>>> >>>> >>>> >>>> OK, I can look into the matrix in more detail. I agree that it should >>>> have a non-zero diagonal, so I'll have a look at what's happening with >>>> that. >>>> >>>> >>>> >>>> >>>>> Naively, the elastic element matrix has a nonzero diagonal. I see that >>>>> you are doing LU >>>>> of size 5. That seems strange for 3D elasticity. Am I missing >>>>> something? I would expect >>>>> block size 3. >>>>> >>>> >>>> >>>> I'm not sure what is causing the LU of size 5. Is there a setting to >>>> control that? >>>> >>>> Regarding the block size: I set the vector and matrix block size to 3 >>>> via VecSetBlockSize and MatSetBlockSize. I also >>>> used MatNullSpaceCreateRigidBody on a vector with block size of 3, and set >>>> the matrix's near nullspace using that. >>>> >>> >>> Can you run this same example with -mat_no_inode? I think it may be a >>> strange blocking that is causing this. >>> >> >> >> That works. The -ksp_view output is below. >> > > > I just wanted to follow up on this. I had a more careful look at the > matrix, and confirmed that there are no zero entries on the diagonal (as > expected for elasticity). The matrix is from one of libMesh's example > problems: a simple cantilever model using HEX8 elements. > > Do you have any further thoughts about what might cause the "strange > blocking" that you referred to? If there's something non-standard that > libMesh is doing with the blocks, I'd be interested to look into that. I > can send over the matrix if that would be helpful. > > Thanks, > David > > P.S. I was previously calling VecSetBlockSize and MatSetBlockSize to set the block size to 3. When I don't do that, I no longer need to call -mat_no_inodes. I've pasted the -ksp_view output below. Does it look like that's working OK? ---------------------------------------------------------- KSP Object: 1 MPI processes type: cg maximum iterations=5000 tolerances: relative=1e-12, absolute=1e-50, divergence=10000 left preconditioning using nonzero initial guess using PRECONDITIONED norm type for convergence test PC Object: 1 MPI processes type: gamg MG: type is MULTIPLICATIVE, levels=6 cycles=v Cycles per PCApply=1 Using Galerkin computed coarse grid matrices GAMG specific options Threshold for dropping small values from graph 0 AGG specific options Symmetric graph false Coarse grid solver -- level ------------------------------- KSP Object: (mg_coarse_) 1 MPI processes type: gmres GMRES: restart=30, using Classical (unmodified) Gram-Schmidt Orthogonalization with no iterative refinement GMRES: happy breakdown tolerance 1e-30 maximum iterations=1, initial guess is zero tolerances: relative=1e-05, absolute=1e-50, divergence=10000 left preconditioning using NONE norm type for convergence test PC Object: (mg_coarse_) 1 MPI processes type: bjacobi block Jacobi: number of blocks = 1 Local solve is same for all blocks, in the following KSP and PC objects: KSP Object: (mg_coarse_sub_) 1 MPI processes type: preonly maximum iterations=1, initial guess is zero tolerances: relative=1e-05, absolute=1e-50, divergence=10000 left preconditioning using NONE norm type for convergence test PC Object: (mg_coarse_sub_) 1 MPI processes type: lu LU: out-of-place factorization tolerance for zero pivot 2.22045e-14 using diagonal shift on blocks to prevent zero pivot [INBLOCKS] matrix ordering: nd factor fill ratio given 5, needed 1.03941 Factored matrix follows: Mat Object: 1 MPI processes type: seqaij rows=47, cols=47 package used to perform factorization: petsc total: nonzeros=211, allocated nonzeros=211 total number of mallocs used during MatSetValues calls =0 not using I-node routines linear system matrix = precond matrix: Mat Object: 1 MPI processes type: seqaij rows=47, cols=47 total: nonzeros=203, allocated nonzeros=203 total number of mallocs used during MatSetValues calls =0 not using I-node routines linear system matrix = precond matrix: Mat Object: 1 MPI processes type: seqaij rows=47, cols=47 total: nonzeros=203, allocated nonzeros=203 total number of mallocs used during MatSetValues calls =0 not using I-node routines Down solver (pre-smoother) on level 1 ------------------------------- KSP Object: (mg_levels_1_) 1 MPI processes type: chebyshev Chebyshev: eigenvalue estimates: min = 0.0998481, max = 1.09833 Chebyshev: eigenvalues estimated using gmres with translations [0 0.1; 0 1.1] KSP Object: (mg_levels_1_esteig_) 1 MPI processes type: gmres GMRES: restart=30, using Classical (unmodified) Gram-Schmidt Orthogonalization with no iterative refinement GMRES: happy breakdown tolerance 1e-30 maximum iterations=10, initial guess is zero tolerances: relative=1e-05, absolute=1e-50, divergence=10000 left preconditioning using NONE norm type for convergence test maximum iterations=2 tolerances: relative=1e-05, absolute=1e-50, divergence=10000 left preconditioning using nonzero initial guess using NONE norm type for convergence test PC Object: (mg_levels_1_) 1 MPI processes type: sor SOR: type = local_symmetric, iterations = 1, local iterations = 1, omega = 1 linear system matrix = precond matrix: Mat Object: 1 MPI processes type: seqaij rows=67, cols=67 total: nonzeros=373, allocated nonzeros=373 total number of mallocs used during MatSetValues calls =0 not using I-node routines Up solver (post-smoother) same as down solver (pre-smoother) Down solver (pre-smoother) on level 2 ------------------------------- KSP Object: (mg_levels_2_) 1 MPI processes type: chebyshev Chebyshev: eigenvalue estimates: min = 0.0997389, max = 1.09713 Chebyshev: eigenvalues estimated using gmres with translations [0 0.1; 0 1.1] KSP Object: (mg_levels_2_esteig_) 1 MPI processes type: gmres GMRES: restart=30, using Classical (unmodified) Gram-Schmidt Orthogonalization with no iterative refinement GMRES: happy breakdown tolerance 1e-30 maximum iterations=10, initial guess is zero tolerances: relative=1e-05, absolute=1e-50, divergence=10000 left preconditioning using NONE norm type for convergence test maximum iterations=2 tolerances: relative=1e-05, absolute=1e-50, divergence=10000 left preconditioning using nonzero initial guess using NONE norm type for convergence test PC Object: (mg_levels_2_) 1 MPI processes type: sor SOR: type = local_symmetric, iterations = 1, local iterations = 1, omega = 1 linear system matrix = precond matrix: Mat Object: 1 MPI processes type: seqaij rows=129, cols=129 total: nonzeros=1029, allocated nonzeros=1029 total number of mallocs used during MatSetValues calls =0 not using I-node routines Up solver (post-smoother) same as down solver (pre-smoother) Down solver (pre-smoother) on level 3 ------------------------------- KSP Object: (mg_levels_3_) 1 MPI processes type: chebyshev Chebyshev: eigenvalue estimates: min = 0.0997179, max = 1.0969 Chebyshev: eigenvalues estimated using gmres with translations [0 0.1; 0 1.1] KSP Object: (mg_levels_3_esteig_) 1 MPI processes type: gmres GMRES: restart=30, using Classical (unmodified) Gram-Schmidt Orthogonalization with no iterative refinement GMRES: happy breakdown tolerance 1e-30 maximum iterations=10, initial guess is zero tolerances: relative=1e-05, absolute=1e-50, divergence=10000 left preconditioning using NONE norm type for convergence test maximum iterations=2 tolerances: relative=1e-05, absolute=1e-50, divergence=10000 left preconditioning using nonzero initial guess using NONE norm type for convergence test PC Object: (mg_levels_3_) 1 MPI processes type: sor SOR: type = local_symmetric, iterations = 1, local iterations = 1, omega = 1 linear system matrix = precond matrix: Mat Object: 1 MPI processes type: seqaij rows=372, cols=372 total: nonzeros=4116, allocated nonzeros=4116 total number of mallocs used during MatSetValues calls =0 not using I-node routines Up solver (post-smoother) same as down solver (pre-smoother) Down solver (pre-smoother) on level 4 ------------------------------- KSP Object: (mg_levels_4_) 1 MPI processes type: chebyshev Chebyshev: eigenvalue estimates: min = 0.0995012, max = 1.09451 Chebyshev: eigenvalues estimated using gmres with translations [0 0.1; 0 1.1] KSP Object: (mg_levels_4_esteig_) 1 MPI processes type: gmres GMRES: restart=30, using Classical (unmodified) Gram-Schmidt Orthogonalization with no iterative refinement GMRES: happy breakdown tolerance 1e-30 maximum iterations=10, initial guess is zero tolerances: relative=1e-05, absolute=1e-50, divergence=10000 left preconditioning using NONE norm type for convergence test maximum iterations=2 tolerances: relative=1e-05, absolute=1e-50, divergence=10000 left preconditioning using nonzero initial guess using NONE norm type for convergence test PC Object: (mg_levels_4_) 1 MPI processes type: sor SOR: type = local_symmetric, iterations = 1, local iterations = 1, omega = 1 linear system matrix = precond matrix: Mat Object: 1 MPI processes type: seqaij rows=1816, cols=1816 total: nonzeros=26636, allocated nonzeros=26636 total number of mallocs used during MatSetValues calls =0 not using I-node routines Up solver (post-smoother) same as down solver (pre-smoother) Down solver (pre-smoother) on level 5 ------------------------------- KSP Object: (mg_levels_5_) 1 MPI processes type: chebyshev Chebyshev: eigenvalue estimates: min = 0.0994721, max = 1.09419 Chebyshev: eigenvalues estimated using gmres with translations [0 0.1; 0 1.1] KSP Object: (mg_levels_5_esteig_) 1 MPI processes type: gmres GMRES: restart=30, using Classical (unmodified) Gram-Schmidt Orthogonalization with no iterative refinement GMRES: happy breakdown tolerance 1e-30 maximum iterations=10, initial guess is zero tolerances: relative=1e-05, absolute=1e-50, divergence=10000 left preconditioning using NONE norm type for convergence test maximum iterations=2 tolerances: relative=1e-05, absolute=1e-50, divergence=10000 left preconditioning using nonzero initial guess using NONE norm type for convergence test PC Object: (mg_levels_5_) 1 MPI processes type: sor SOR: type = local_symmetric, iterations = 1, local iterations = 1, omega = 1 linear system matrix = precond matrix: Mat Object: () 1 MPI processes type: seqaij rows=55473, cols=55473 total: nonzeros=4.08484e+06, allocated nonzeros=4.08484e+06 total number of mallocs used during MatSetValues calls =0 has attached near null space using I-node routines: found 18491 nodes, limit used is 5 Up solver (post-smoother) same as down solver (pre-smoother) linear system matrix = precond matrix: Mat Object: () 1 MPI processes type: seqaij rows=55473, cols=55473 total: nonzeros=4.08484e+06, allocated nonzeros=4.08484e+06 total number of mallocs used during MatSetValues calls =0 has attached near null space using I-node routines: found 18491 nodes, limit used is 5