On Tue, Nov 10, 2015 at 10:24 PM, Matthew Knepley <[email protected]> wrote:
> On Tue, Nov 10, 2015 at 9:21 PM, David Knezevic < > [email protected]> wrote: > >> On Tue, Nov 10, 2015 at 10:00 PM, Matthew Knepley <[email protected]> >> wrote: >> >>> On Tue, Nov 10, 2015 at 8:39 PM, David Knezevic < >>> [email protected]> 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. Thanks, David 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=5 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 Factored matrix follows: Mat Object: 1 MPI processes type: seqaij rows=30, cols=30, bs=6 package used to perform factorization: petsc total: nonzeros=540, allocated nonzeros=540 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=30, cols=30, bs=6 total: nonzeros=540, allocated nonzeros=540 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=30, cols=30, bs=6 total: nonzeros=540, allocated nonzeros=540 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 = -1.79769e+307, max = -inf 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=72, cols=72, bs=6 total: nonzeros=1728, allocated nonzeros=1728 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 = -1.79769e+307, max = -inf 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=174, cols=174, bs=6 total: nonzeros=5796, allocated nonzeros=5796 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 = -1.79769e+307, max = -inf 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=828, cols=828, bs=6 total: nonzeros=44496, allocated nonzeros=44496 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 = 0.0998367, max = 1.0982 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=2676, cols=2676, bs=3 total: nonzeros=94014, allocated nonzeros=94014 total number of mallocs used during MatSetValues calls =0 has attached near null space not using I-node routines Up solver (post-smoother) same as down solver (pre-smoother) linear system matrix = precond matrix: Mat Object: () 1 MPI processes type: seqaij rows=2676, cols=2676, bs=3 total: nonzeros=94014, allocated nonzeros=94014 total number of mallocs used during MatSetValues calls =0 has attached near null space not using I-node routines
