Actually - those look really good. What preconditioner are you using now? If you're happy with the speed I would stop there...
But - yes, after recompiling PETSc you would want to recompile libMesh... Derek On Tue, Dec 10, 2013 at 8:58 AM, Lorenzo Zanon <[email protected]>wrote: > 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 >> >> >> ------------------------------------------------------------------------------ >> Sponsored by Intel(R) XDK >> Develop, test and display web and hybrid apps with a single code base. >> Download it for free now! >> >> http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk >> _______________________________________________ >> Libmesh-users mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/libmesh-users >> > > > > -- > 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 > ----------------------- > Phone: 630-252-1229 > Fax: 630-252-5986 > > > ------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk _______________________________________________ Libmesh-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/libmesh-users
