Hi,
After re-installing petsc with Hypre should I recompile libmesh as well?
Otherwise here are the detailed outputs (JFNK, LU, and -ksp_rtol 1e-4):
> ./example-opt -ksp_monitor -snes_view -snes_linesearch_type basic
> -snes_mf_operator
> Mesh Information:
> mesh_dimension()=3
> spatial_dimension()=3
> n_nodes()=66
> n_local_nodes()=66
> n_elem()=20
> n_local_elem()=20
> n_active_elem()=20
> n_subdomains()=1
> n_partitions()=1
> n_processors()=1
> n_threads()=1
> processor_id()=0
>
> EquationSystems
> n_systems()=1
> System #0, "StVen"
> Type "NonlinearImplicit"
> Variables={ "u" "v" "z" }
> Finite Element Types="LAGRANGE"
> Approximation Orders="FIRST"
> n_dofs()=198
> n_local_dofs()=198
> n_constrained_dofs()=18
> n_local_constrained_dofs()=18
> n_vectors()=1
> n_matrices()=1
> DofMap Sparsity
> Average On-Processor Bandwidth <= 39.4545
> Average Off-Processor Bandwidth <= 0
> Maximum On-Processor Bandwidth <= 54
> Maximum Off-Processor Bandwidth <= 0
> DofMap Constraints
> Number of DoF Constraints = 18
> Average DoF Constraint Length= 0
>
> NL step 0, |residual|_2 = 3.464102e-05
> 0 KSP Residual norm 3.212616421517e-03
> 1 KSP Residual norm 1.120398546137e-03
> 2 KSP Residual norm 9.967109207349e-04
> 3 KSP Residual norm 8.458532905819e-04
> 4 KSP Residual norm 7.728810753960e-04
> 5 KSP Residual norm 6.732172142339e-04
> 6 KSP Residual norm 6.576344248200e-04
> 7 KSP Residual norm 6.402094443503e-04
> 8 KSP Residual norm 6.385715679145e-04
> 9 KSP Residual norm 6.174418902540e-04
> 10 KSP Residual norm 6.152538108126e-04
> 11 KSP Residual norm 5.648590825480e-04
> 12 KSP Residual norm 4.481934208276e-04
> 13 KSP Residual norm 3.306530303084e-04
> 14 KSP Residual norm 2.690188849592e-04
> 15 KSP Residual norm 2.386473964271e-04
> 16 KSP Residual norm 2.141977103061e-04
> 17 KSP Residual norm 2.102327000179e-04
> 18 KSP Residual norm 2.078228954218e-04
> 19 KSP Residual norm 2.067071644725e-04
> 20 KSP Residual norm 1.615255528200e-04
> 21 KSP Residual norm 1.540580333282e-04
> 22 KSP Residual norm 1.276535406372e-04
> 23 KSP Residual norm 8.957902207289e-05
> 24 KSP Residual norm 1.443181175234e-05
> 25 KSP Residual norm 2.250542927482e-06
> 26 KSP Residual norm 2.917199065518e-07
> 27 KSP Residual norm 5.868687294700e-08
> 28 KSP Residual norm 8.654056711463e-09
> NL step 1, |residual|_2 = 2.417677e-04
> 0 KSP Residual norm 1.333298301871e-03
> 1 KSP Residual norm 3.805511680517e-04
> 2 KSP Residual norm 2.446787831803e-04
> 3 KSP Residual norm 1.681749772700e-04
> 4 KSP Residual norm 7.788563572601e-05
> 5 KSP Residual norm 1.464482225979e-05
> 6 KSP Residual norm 5.794628981655e-06
> 7 KSP Residual norm 5.031264536697e-06
> 8 KSP Residual norm 4.237830295237e-06
> 9 KSP Residual norm 2.682645862853e-06
> 10 KSP Residual norm 2.375434440801e-06
> 11 KSP Residual norm 2.250452181271e-06
> 12 KSP Residual norm 2.156206443150e-06
> 13 KSP Residual norm 2.095121298242e-06
> 14 KSP Residual norm 1.980586518083e-06
> 15 KSP Residual norm 1.827706054190e-06
> 16 KSP Residual norm 1.742266192586e-06
> 17 KSP Residual norm 1.538312528876e-06
> 18 KSP Residual norm 1.199164155173e-06
> 19 KSP Residual norm 8.927456022436e-07
> 20 KSP Residual norm 8.540488238927e-07
> 21 KSP Residual norm 7.218672557993e-07
> 22 KSP Residual norm 6.020750075600e-07
> 23 KSP Residual norm 5.956106102175e-07
> 24 KSP Residual norm 5.933201825052e-07
> 25 KSP Residual norm 5.278644490862e-07
> 26 KSP Residual norm 2.779283164872e-07
> 27 KSP Residual norm 6.009106355990e-08
> 28 KSP Residual norm 8.312066698183e-09
> NL step 2, |residual|_2 = 6.140305e-08
> 0 KSP Residual norm 4.390107230670e-07
> 1 KSP Residual norm 1.138843333125e-07
> 2 KSP Residual norm 6.427890600369e-08
> 3 KSP Residual norm 4.348970873891e-08
> 4 KSP Residual norm 2.561129926398e-08
> 5 KSP Residual norm 5.759441641679e-09
> 6 KSP Residual norm 2.701120082990e-09
> 7 KSP Residual norm 2.417238064221e-09
> 8 KSP Residual norm 2.135376110595e-09
> 9 KSP Residual norm 1.466188791935e-09
> 10 KSP Residual norm 1.357982217314e-09
> 11 KSP Residual norm 1.301823008121e-09
> 12 KSP Residual norm 1.251207827778e-09
> 13 KSP Residual norm 1.204174220396e-09
> 14 KSP Residual norm 1.144205363644e-09
> 15 KSP Residual norm 1.012225508386e-09
> 16 KSP Residual norm 9.533558540986e-10
> 17 KSP Residual norm 7.230784655660e-10
> 18 KSP Residual norm 5.085255142266e-10
> 19 KSP Residual norm 3.699847452492e-10
> 20 KSP Residual norm 3.594140312284e-10
> 21 KSP Residual norm 3.309231358833e-10
> 22 KSP Residual norm 2.860867684103e-10
> 23 KSP Residual norm 2.771853680698e-10
> 24 KSP Residual norm 2.694125344509e-10
> 25 KSP Residual norm 2.563090739856e-10
> 26 KSP Residual norm 1.544862362579e-10
> 27 KSP Residual norm 3.311660568011e-11
> 28 KSP Residual norm 3.523137533760e-12
> NL step 3, |residual|_2 = 5.398475e-13
> 0 KSP Residual norm 3.527919605631e-12
> 1 KSP Residual norm 1.035019989012e-12
> 2 KSP Residual norm 6.009753897451e-13
> 3 KSP Residual norm 4.354234754168e-13
> 4 KSP Residual norm 3.700520049204e-13
> 5 KSP Residual norm 1.460949780703e-13
> 6 KSP Residual norm 1.215630756367e-13
> 7 KSP Residual norm 1.062246593852e-13
> 8 KSP Residual norm 1.035560212385e-13
> 9 KSP Residual norm 1.017999906257e-13
> 10 KSP Residual norm 9.708750446312e-14
> 11 KSP Residual norm 8.902194111738e-14
> 12 KSP Residual norm 8.732231468356e-14
> 13 KSP Residual norm 8.612874746485e-14
> 14 KSP Residual norm 6.378879032596e-14
> 15 KSP Residual norm 4.844926458163e-14
> 16 KSP Residual norm 4.284448730212e-14
> 17 KSP Residual norm 3.156887391113e-14
> 18 KSP Residual norm 2.894109138972e-14
> 19 KSP Residual norm 2.675644914103e-14
> 20 KSP Residual norm 2.671536420686e-14
> 21 KSP Residual norm 2.387772122441e-14
> 22 KSP Residual norm 2.385094486768e-14
> 23 KSP Residual norm 2.219324945722e-14
> 24 KSP Residual norm 1.908246749210e-14
> 25 KSP Residual norm 1.099315364082e-14
> 26 KSP Residual norm 3.272321755177e-15
> 27 KSP Residual norm 5.083777840482e-16
> 28 KSP Residual norm 8.109062749581e-17
> 29 KSP Residual norm 9.301844195943e-18
> NL step 4, |residual|_2 = 9.259267e-18
> SNES Object: 1 MPI processes
> type: newtonls
> maximum iterations=50, maximum function evaluations=10000
> tolerances: relative=1e-08, absolute=1e-35, solution=1e-08
> total number of linear solver iterations=113
> total number of function evaluations=118
> SNESLineSearch Object: 1 MPI processes
> type: basic
> maxstep=1.000000e+08, minlambda=1.000000e-12
> tolerances: relative=1.000000e-08, absolute=1.000000e-15,
> lambda=1.000000e-08
> maximum iterations=40
> KSP Object: 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=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: 1 MPI processes
> type: ilu
> ILU: out-of-place factorization
> 0 levels of fill
> tolerance for zero pivot 2.22045e-14
> using diagonal shift on blocks to prevent zero pivot [INBLOCKS]
> matrix ordering: natural
> factor fill ratio given 1, needed 1
> Factored matrix follows:
> Matrix Object: 1 MPI processes
> type: seqaij
> rows=198, cols=198
> package used to perform factorization: petsc
> total: nonzeros=7812, allocated nonzeros=7812
> total number of mallocs used during MatSetValues calls =0
> using I-node routines: found 66 nodes, limit used is 5
> linear system matrix followed by preconditioner matrix:
> Matrix Object: 1 MPI processes
> type: mffd
> rows=198, cols=198
> Matrix-free approximation:
> err=1.49012e-08 (relative error in function evaluation)
> Using wp compute h routine
> Does not compute normU
> Matrix Object: () 1 MPI processes
> type: seqaij
> rows=198, cols=198
> total: nonzeros=7812, allocated nonzeros=7812
> total number of mallocs used during MatSetValues calls =0
> using I-node routines: found 66 nodes, limit used is 5
> StVen system solved at nonlinear iteration 4 , final nonlinear residual norm:
> 9.259267e-18
> ./example-opt -ksp_monitor -snes_view -snes_linesearch_type basic -pc_type lu
> NL step 0, |residual|_2 = 3.464102e-05
> 0 KSP Residual norm 2.935224615808e-01
> 1 KSP Residual norm 1.520331233634e-14
> NL step 1, |residual|_2 = 2.417676e-04
> 0 KSP Residual norm 2.278956475389e-03
> 1 KSP Residual norm 2.012171403392e-16
> NL step 2, |residual|_2 = 6.144363e-08
> 0 KSP Residual norm 7.461774437599e-07
> 1 KSP Residual norm 7.509596943461e-21
> NL step 3, |residual|_2 = 8.023655e-15
> SNES Object: 1 MPI processes
> type: newtonls
> maximum iterations=50, maximum function evaluations=10000
> tolerances: relative=1e-08, absolute=1e-35, solution=1e-08
> total number of linear solver iterations=3
> total number of function evaluations=4
> SNESLineSearch Object: 1 MPI processes
> type: basic
> maxstep=1.000000e+08, minlambda=1.000000e-12
> tolerances: relative=1.000000e-08, absolute=1.000000e-15,
> lambda=1.000000e-08
> maximum iterations=40
> KSP Object: 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=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: 1 MPI processes
> type: lu
> LU: out-of-place factorization
> tolerance for zero pivot 2.22045e-14
> matrix ordering: nd
> factor fill ratio given 5, needed 1.46083
> Factored matrix follows:
> Matrix Object: 1 MPI processes
> type: seqaij
> rows=198, cols=198
> package used to perform factorization: petsc
> total: nonzeros=11412, allocated nonzeros=11412
> total number of mallocs used during MatSetValues calls =0
> using I-node routines: found 60 nodes, limit used is 5
> linear system matrix = precond matrix:
> Matrix Object: () 1 MPI processes
> type: seqaij
> rows=198, cols=198
> total: nonzeros=7812, allocated nonzeros=7812
> total number of mallocs used during MatSetValues calls =0
> using I-node routines: found 66 nodes, limit used is 5
> StVen system solved at nonlinear iteration 3 , final nonlinear residual norm:
> 8.023655e-15
> ./example-opt -ksp_monitor -snes_view -snes_linesearch_type basic -ksp_rtol
> 1e-4
> NL step 0, |residual|_2 = 3.464102e-05
> 0 KSP Residual norm 3.212616421517e-03
> 1 KSP Residual norm 1.120398547109e-03
> 2 KSP Residual norm 9.967109218543e-04
> 3 KSP Residual norm 8.458532936948e-04
> 4 KSP Residual norm 7.728810766578e-04
> 5 KSP Residual norm 6.732172176276e-04
> 6 KSP Residual norm 6.576344282958e-04
> 7 KSP Residual norm 6.402094485036e-04
> 8 KSP Residual norm 6.385715720308e-04
> 9 KSP Residual norm 6.174418951196e-04
> 10 KSP Residual norm 6.152538158701e-04
> 11 KSP Residual norm 5.648590869377e-04
> 12 KSP Residual norm 4.481934266021e-04
> 13 KSP Residual norm 3.306530506113e-04
> 14 KSP Residual norm 2.690188953869e-04
> 15 KSP Residual norm 2.386474000359e-04
> 16 KSP Residual norm 2.141977071264e-04
> 17 KSP Residual norm 2.102326932511e-04
> 18 KSP Residual norm 2.078228882501e-04
> 19 KSP Residual norm 2.067071553192e-04
> 20 KSP Residual norm 1.615255475939e-04
> 21 KSP Residual norm 1.540580334921e-04
> 22 KSP Residual norm 1.276535440255e-04
> 23 KSP Residual norm 8.957903046652e-05
> 24 KSP Residual norm 1.443181315137e-05
> 25 KSP Residual norm 2.250543102652e-06
> 26 KSP Residual norm 2.917198939738e-07
> NL step 1, |residual|_2 = 2.417591e-04
> 0 KSP Residual norm 1.333235985406e-03
> 1 KSP Residual norm 3.805281509852e-04
> 2 KSP Residual norm 2.446722664627e-04
> 3 KSP Residual norm 1.681792936293e-04
> 4 KSP Residual norm 7.787501844281e-05
> 5 KSP Residual norm 1.465542127151e-05
> 6 KSP Residual norm 5.801751298083e-06
> 7 KSP Residual norm 5.035187876534e-06
> 8 KSP Residual norm 4.243969045328e-06
> 9 KSP Residual norm 2.680601029765e-06
> 10 KSP Residual norm 2.377737099944e-06
> 11 KSP Residual norm 2.256889739176e-06
> 12 KSP Residual norm 2.166393508350e-06
> 13 KSP Residual norm 2.105104317769e-06
> 14 KSP Residual norm 1.986592043870e-06
> 15 KSP Residual norm 1.828530134293e-06
> 16 KSP Residual norm 1.740656911937e-06
> 17 KSP Residual norm 1.530055724199e-06
> 18 KSP Residual norm 1.188818442952e-06
> 19 KSP Residual norm 8.844867349262e-07
> 20 KSP Residual norm 8.457155647014e-07
> 21 KSP Residual norm 7.160503850340e-07
> 22 KSP Residual norm 5.986449996924e-07
> 23 KSP Residual norm 5.922449520540e-07
> 24 KSP Residual norm 5.898790177982e-07
> 25 KSP Residual norm 5.230405076245e-07
> 26 KSP Residual norm 2.745262903799e-07
> 27 KSP Residual norm 5.996929540573e-08
> NL step 2, |residual|_2 = 6.148539e-08
> 0 KSP Residual norm 4.438065916788e-07
> 1 KSP Residual norm 1.102546762523e-07
> 2 KSP Residual norm 6.101658503721e-08
> 3 KSP Residual norm 3.892043542473e-08
> 4 KSP Residual norm 2.545607584015e-08
> 5 KSP Residual norm 9.185586325846e-09
> 6 KSP Residual norm 8.120407917835e-09
> 7 KSP Residual norm 7.332797232974e-09
> 8 KSP Residual norm 6.897524298169e-09
> 9 KSP Residual norm 6.721797058447e-09
> 10 KSP Residual norm 6.081332952767e-09
> 11 KSP Residual norm 5.925983333102e-09
> 12 KSP Residual norm 5.763399321322e-09
> 13 KSP Residual norm 5.658798569415e-09
> 14 KSP Residual norm 4.380899459878e-09
> 15 KSP Residual norm 2.987907429703e-09
> 16 KSP Residual norm 2.602849823313e-09
> 17 KSP Residual norm 2.007859106166e-09
> 18 KSP Residual norm 1.774356855215e-09
> 19 KSP Residual norm 1.661785774521e-09
> 20 KSP Residual norm 1.643287316539e-09
> 21 KSP Residual norm 1.623622276146e-09
> 22 KSP Residual norm 1.418446600745e-09
> 23 KSP Residual norm 9.304700213186e-10
> 24 KSP Residual norm 7.851391468968e-10
> 25 KSP Residual norm 6.782990472312e-10
> 26 KSP Residual norm 2.542603600685e-10
> 27 KSP Residual norm 4.401858002395e-11
> NL step 3, |residual|_2 = 6.398663e-12
> 0 KSP Residual norm 4.401758090986e-11
> 1 KSP Residual norm 2.391541512835e-11
> 2 KSP Residual norm 1.514835448920e-11
> 3 KSP Residual norm 1.411430736978e-11
> 4 KSP Residual norm 1.082077200496e-11
> 5 KSP Residual norm 9.816569497836e-12
> 6 KSP Residual norm 9.370398483665e-12
> 7 KSP Residual norm 9.349907985279e-12
> 8 KSP Residual norm 8.045346126569e-12
> 9 KSP Residual norm 8.045331126452e-12
> 10 KSP Residual norm 7.579815591644e-12
> 11 KSP Residual norm 7.284737582076e-12
> 12 KSP Residual norm 6.783775150066e-12
> 13 KSP Residual norm 4.639846079482e-12
> 14 KSP Residual norm 3.135294994089e-12
> 15 KSP Residual norm 1.805256047778e-12
> 16 KSP Residual norm 1.520281278758e-12
> 17 KSP Residual norm 1.308568574591e-12
> 18 KSP Residual norm 1.230713382323e-12
> 19 KSP Residual norm 1.226915989003e-12
> 20 KSP Residual norm 1.216457811750e-12
> 21 KSP Residual norm 1.121219956880e-12
> 22 KSP Residual norm 1.108526048419e-12
> 23 KSP Residual norm 1.058254737633e-12
> 24 KSP Residual norm 5.776165288887e-13
> 25 KSP Residual norm 1.430593479447e-13
> 26 KSP Residual norm 3.256387223302e-14
> 27 KSP Residual norm 5.110458721876e-15
> 28 KSP Residual norm 9.573578653622e-16
> NL step 4, |residual|_2 = 1.376115e-16
> SNES Object: 1 MPI processes
> type: newtonls
> maximum iterations=50, maximum function evaluations=10000
> tolerances: relative=1e-08, absolute=1e-35, solution=1e-08
> total number of linear solver iterations=108
> total number of function evaluations=5
> SNESLineSearch Object: 1 MPI processes
> type: basic
> maxstep=1.000000e+08, minlambda=1.000000e-12
> tolerances: relative=1.000000e-08, absolute=1.000000e-15,
> lambda=1.000000e-08
> maximum iterations=40
> KSP Object: 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=10000, initial guess is zero
> tolerances: relative=0.0001, absolute=1e-50, divergence=10000
> left preconditioning
> using PRECONDITIONED norm type for convergence test
> PC Object: 1 MPI processes
> type: ilu
> ILU: out-of-place factorization
> 0 levels of fill
> tolerance for zero pivot 2.22045e-14
> using diagonal shift on blocks to prevent zero pivot [INBLOCKS]
> matrix ordering: natural
> factor fill ratio given 1, needed 1
> Factored matrix follows:
> Matrix Object: 1 MPI processes
> type: seqaij
> rows=198, cols=198
> package used to perform factorization: petsc
> total: nonzeros=7812, allocated nonzeros=7812
> total number of mallocs used during MatSetValues calls =0
> using I-node routines: found 66 nodes, limit used is 5
> linear system matrix = precond matrix:
> Matrix Object: () 1 MPI processes
> type: seqaij
> rows=198, cols=198
> total: nonzeros=7812, allocated nonzeros=7812
> total number of mallocs used during MatSetValues calls =0
> using I-node routines: found 66 nodes, limit used is 5
> StVen system solved at nonlinear iteration 4 , final nonlinear residual norm:
> 1.376115e-16
On Dec 9, 2013, at 11:03 PM, Dmitry Karpeyev wrote:
> Please, include -snes_view so that we can see exactly what solver options are
> being used.
> Dmitry.
>
>
> On Mon, Dec 9, 2013 at 12:48 PM, John Peterson <[email protected]> wrote:
> > On Mon, Dec 9, 2013 at 11:31 AM, Lorenzo Zanon
> > <[email protected]>wrote:
> >
> >> I get faster convergence with e.g. -snes_linesearch_type basic -ksp_rtol
> >> 1e-4:
> >>
> >> NL step 0, |residual|_2 = 3.464102e-05
> >> NL step 1, |residual|_2 = 2.417540e-04
> >> NL step 2, |residual|_2 = 6.174706e-08
> >> NL step 3, |residual|_2 = 3.577768e-12
> >> NL step 4, |residual|_2 = 7.687278e-17
> >> StVen system solved at nonlinear iteration 4 , final nonlinear residual
> >> norm: 7.687278e-17
>
> Your ksp_rtol might be hurting your convergence a bit near the root...
>
> Have you tried -snes_ksp_ew? There are several EW-specific options
> within you can play with as well:
>
> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/SNES/SNESSetFromOptions.html
>
> --
> John
>
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>
> --
> Dmitry Karpeev
> Mathematics and Computer Science
> Argonne National Laboratory
> Argonne, Illinois, USA
> and
> Computation Institute
> University of Chicago
> 5735 S. Ellis Avenue
> Chicago, IL 60637
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