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From: Robert Blake <rob.3@gm...>  20140103 12:22:32

As someone who is also working on this code, the problem is not uninitialized memory. Valgrind reports a clean bill of health. On 01/02/2014 09:45 PM, Derek Gaston wrote: > This is almost definitely not a libMesh problem. It sounds like an > uninitialized variable. I recommend running your application using > valgrind ( http://valgrind.org ) . Use a debug (dbg) build of your > application and valgrind will point you right to the problem. > > Derek > > > On Thu, Jan 2, 2014 at 7:30 PM, Dafang Wang <dafang.wang@...> wrote: > >> Hi, >> >> My libmesh progam, which uses SNES to solve a nonlinear equation, had different >> convergence behavior when running on a linux desktop and on a cluster machine. >> >> All other running conditions were double checked to be identical: It was the same program >> running as a single thread on both machines. Both machines were using Libmesh 0.9.2.2. >> >> My program was solving a simple elastic model with good numerical/physical behavior. (The >> model consists of a 5*5*5 cubic mesh with a total of ~600 degress of freedom.) For the >> nonlinear solve, I was using the Newton method and line search (the >> default settings in Petsc SNES). >> >> The Newton method took 5 iterations to converge on my desktop (Ubutun 12.04), whereas it >> took 114 iterations to converge on the cluster. Moreover, both machines generated >> identical results in the first 2 Newton iterations, then they diverged >> from the 3rd iteration. >> >> I am wondering if such difference is common for Libmesh/Petsc programs running on >> different machines. Does anyone have similar experience of running programs on different >> clusters? >> >> Thanks, >> Dafang >>  >> Dafang Wang, Ph.D. >> Postdoctoral Fellow >> Institute of Computational Medicine >> Hackerman Hall, Room 218 >> Johns Hopkins University, Baltimore, 21218 >> http://lagniappe.icm.jhu.edu/~dwang/ >> >> >>  >> 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 15day FREE TRIAL of AppDynamics >> Pro! >> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk >> _______________________________________________ >> Libmeshusers mailing list >> Libmeshusers@... >> https://lists.sourceforge.net/lists/listinfo/libmeshusers >> >  > 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 15day FREE TRIAL of AppDynamics Pro! > http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk > _______________________________________________ > Libmeshusers mailing list > Libmeshusers@... > https://lists.sourceforge.net/lists/listinfo/libmeshusers 
From: Dafang Wang <dafang.wang@jh...>  20140103 06:41:29

Hi Jed, Below are the output details. (Results were obtained with snes_converged_reason, snes_monitor. The ksp_converged_reason ended up with seg fault, so was not included. It should not be the key problem though. ) Output from the desktop (good convergence rate): total constitutive equations = ngauss = 1000 EquationSystems n_systems()=1 System #0, "Elasticity" Type "NonlinearImplicit" Variables={ "ux" "uy" "uz" } Finite Element Types="LAGRANGE" Approximation Orders="FIRST" n_dofs()=648 n_local_dofs()=648 n_constrained_dofs()=108 n_local_constrained_dofs()=108 n_vectors()=1 n_matrices()=1 DofMap Sparsity Average OnProcessor Bandwidth <= 56.8889 Average OffProcessor Bandwidth <= 0 Maximum OnProcessor Bandwidth <= 81 Maximum OffProcessor Bandwidth <= 0 DofMap Constraints Number of DoF Constraints = 108 Average DoF Constraint Length= 0 *** Warning, This code is deprecated, and likely to be removed in future library versions! src/mesh/boundary_info.C, line 752, compiled Oct 29 2013 at 08:06:16 *** NL step 0, residual_2 = 1.440000e+00 0 SNES Function norm 1.440000000000e+00 NL step 1, residual_2 = 5.960479e01 1 SNES Function norm 5.960478586457e01 NL step 2, residual_2 = 3.745465e02 2 SNES Function norm 3.745464932748e02 NL step 3, residual_2 = 7.372288e04 3 SNES Function norm 7.372287735879e04 NL step 4, residual_2 = 1.426607e07 4 SNES Function norm 1.426607123296e07 NL step 5, residual_2 = 4.472564e12 5 SNES Function norm 4.472564229796e12 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 5 Mechanics system solved at nonlinear iteration 5 , final nonlinear residual norm: 4.472564e12, converge reason= 3  Output from the cluster (poor convergence rate): total constitutive equations = ngauss = 1000 EquationSystems n_systems()=1 System #0, "Elasticity" Type "NonlinearImplicit" Variables={ "ux" "uy" "uz" } Finite Element Types="LAGRANGE" Approximation Orders="FIRST" n_dofs()=648 n_local_dofs()=648 n_constrained_dofs()=108 n_local_constrained_dofs()=108 n_vectors()=1 n_matrices()=1 DofMap Sparsity Average OnProcessor Bandwidth <= 56.8889 Average OffProcessor Bandwidth <= 0 Maximum OnProcessor Bandwidth <= 81 Maximum OffProcessor Bandwidth <= 0 DofMap Constraints Number of DoF Constraints = 108 Average DoF Constraint Length= 0 *** Warning, This code is deprecated, and likely to be removed in future library versions! src/mesh/boundary_info.C, line 752, compiled Dec 19 2013 at 15:59:31 *** NL step 0, residual_2 = 1.440000e+00 0 SNES Function norm 1.440000000000e+00 NL step 1, residual_2 = 5.960479e01 1 SNES Function norm 5.960478586457e01 NL step 2, residual_2 = 1.481775e01 2 SNES Function norm 1.481775334529e01 NL step 3, residual_2 = 7.269557e02 3 SNES Function norm 7.269556782845e02 NL step 4, residual_2 = 3.051185e03 4 SNES Function norm 3.051184607506e03 NL step 5, residual_2 = 2.572549e03 5 SNES Function norm 2.572548835065e03 NL step 6, residual_2 = 2.207251e03 6 SNES Function norm 2.207251245116e03 NL step 7, residual_2 = 2.131013e03 7 SNES Function norm 2.131012652111e03 NL step 8, residual_2 = 2.054042e03 8 SNES Function norm 2.054041562027e03 NL step 9, residual_2 = 1.981749e03 9 SNES Function norm 1.981749134719e03 NL step 10, residual_2 = 1.829931e03 10 SNES Function norm 1.829930870093e03 NL step 11, residual_2 = 1.732368e03 11 SNES Function norm 1.732367614052e03 NL step 12, residual_2 = 1.661435e03 12 SNES Function norm 1.661435082740e03 NL step 13, residual_2 = 1.550510e03 13 SNES Function norm 1.550509928763e03 NL step 14, residual_2 = 1.498905e03 14 SNES Function norm 1.498904724330e03 NL step 15, residual_2 = 1.451520e03 15 SNES Function norm 1.451520028630e03 NL step 16, residual_2 = 1.415582e03 16 SNES Function norm 1.415581852666e03 NL step 17, residual_2 = 1.314334e03 17 SNES Function norm 1.314334358891e03 NL step 18, residual_2 = 1.274014e03 18 SNES Function norm 1.274013709112e03 NL step 19, residual_2 = 1.774630e04 19 SNES Function norm 1.774630063354e04 NL step 20, residual_2 = 1.525944e04 20 SNES Function norm 1.525944094760e04 NL step 21, residual_2 = 1.477031e04 21 SNES Function norm 1.477031246669e04 NL step 22, residual_2 = 1.453195e04 22 SNES Function norm 1.453195226456e04 NL step 23, residual_2 = 1.302904e04 23 SNES Function norm 1.302904239436e04 NL step 24, residual_2 = 1.264238e04 24 SNES Function norm 1.264238361159e04 NL step 25, residual_2 = 1.135667e04 25 SNES Function norm 1.135667030231e04 NL step 26, residual_2 = 1.070810e04 26 SNES Function norm 1.070810206898e04 NL step 27, residual_2 = 1.036418e04 27 SNES Function norm 1.036417750251e04 NL step 28, residual_2 = 1.004803e04 28 SNES Function norm 1.004803143137e04 NL step 29, residual_2 = 9.154985e05 29 SNES Function norm 9.154985324734e05 NL step 30, residual_2 = 8.900270e05 30 SNES Function norm 8.900270443665e05 NL step 31, residual_2 = 6.523513e05 31 SNES Function norm 6.523513427832e05 NL step 32, residual_2 = 5.196890e05 32 SNES Function norm 5.196889874832e05 NL step 33, residual_2 = 4.962914e05 33 SNES Function norm 4.962914434970e05 NL step 34, residual_2 = 4.802445e05 34 SNES Function norm 4.802445335167e05 NL step 35, residual_2 = 4.660265e05 35 SNES Function norm 4.660265300997e05 NL step 36, residual_2 = 4.560508e05 36 SNES Function norm 4.560508074305e05 NL step 37, residual_2 = 4.176890e05 37 SNES Function norm 4.176889934246e05 NL step 38, residual_2 = 4.065922e05 38 SNES Function norm 4.065922035297e05 NL step 39, residual_2 = 2.819062e05 39 SNES Function norm 2.819062187692e05 NL step 40, residual_2 = 1.229634e05 40 SNES Function norm 1.229633591270e05 NL step 41, residual_2 = 8.466334e06 41 SNES Function norm 8.466333505983e06 NL step 42, residual_2 = 7.785196e06 42 SNES Function norm 7.785196405201e06 NL step 43, residual_2 = 7.517116e06 43 SNES Function norm 7.517115760778e06 NL step 44, residual_2 = 5.517172e06 44 SNES Function norm 5.517171865105e06 NL step 45, residual_2 = 4.627790e06 45 SNES Function norm 4.627789977237e06 NL step 46, residual_2 = 4.457517e06 46 SNES Function norm 4.457517058356e06 NL step 47, residual_2 = 4.393732e06 47 SNES Function norm 4.393732353601e06 NL step 48, residual_2 = 3.879515e06 48 SNES Function norm 3.879515135247e06 NL step 49, residual_2 = 3.763677e06 49 SNES Function norm 3.763677330091e06 NL step 50, residual_2 = 3.500036e06 50 SNES Function norm 3.500036191831e06 NL step 51, residual_2 = 3.256444e06 51 SNES Function norm 3.256444300502e06 NL step 52, residual_2 = 3.147962e06 52 SNES Function norm 3.147962249732e06 NL step 53, residual_2 = 2.860652e06 53 SNES Function norm 2.860652455813e06 NL step 54, residual_2 = 2.724702e06 54 SNES Function norm 2.724702170315e06 NL step 55, residual_2 = 2.619289e06 55 SNES Function norm 2.619289101215e06 NL step 56, residual_2 = 2.531273e06 56 SNES Function norm 2.531273013757e06 NL step 57, residual_2 = 2.229636e06 57 SNES Function norm 2.229636056679e06 NL step 58, residual_2 = 2.073304e06 58 SNES Function norm 2.073303801469e06 NL step 59, residual_2 = 2.003962e06 59 SNES Function norm 2.003961608610e06 NL step 60, residual_2 = 1.846291e06 60 SNES Function norm 1.846291365509e06 NL step 61, residual_2 = 1.752788e06 61 SNES Function norm 1.752788290496e06 NL step 62, residual_2 = 1.687328e06 62 SNES Function norm 1.687327986194e06 NL step 63, residual_2 = 1.633939e06 63 SNES Function norm 1.633938540202e06 NL step 64, residual_2 = 1.546997e06 64 SNES Function norm 1.546997405760e06 NL step 65, residual_2 = 1.436955e06 65 SNES Function norm 1.436954500901e06 NL step 66, residual_2 = 1.394765e06 66 SNES Function norm 1.394765119799e06 NL step 67, residual_2 = 1.177653e06 67 SNES Function norm 1.177652615109e06 NL step 68, residual_2 = 1.056466e06 68 SNES Function norm 1.056465738701e06 NL step 69, residual_2 = 1.029155e06 69 SNES Function norm 1.029154936896e06 NL step 70, residual_2 = 9.585998e07 70 SNES Function norm 9.585998143404e07 NL step 71, residual_2 = 9.124501e07 71 SNES Function norm 9.124500896542e07 NL step 72, residual_2 = 8.813674e07 72 SNES Function norm 8.813674410684e07 NL step 73, residual_2 = 8.557197e07 73 SNES Function norm 8.557196934474e07 NL step 74, residual_2 = 8.266958e07 74 SNES Function norm 8.266957904914e07 NL step 75, residual_2 = 7.628019e07 75 SNES Function norm 7.628018815310e07 NL step 76, residual_2 = 7.427199e07 76 SNES Function norm 7.427198948047e07 NL step 77, residual_2 = 2.892657e07 77 SNES Function norm 2.892656631445e07 NL step 78, residual_2 = 2.110709e07 78 SNES Function norm 2.110709381321e07 NL step 79, residual_2 = 1.971659e07 79 SNES Function norm 1.971659429523e07 NL step 80, residual_2 = 1.894502e07 80 SNES Function norm 1.894501578413e07 NL step 81, residual_2 = 1.811535e07 81 SNES Function norm 1.811534729574e07 NL step 82, residual_2 = 1.619090e07 82 SNES Function norm 1.619090109708e07 NL step 83, residual_2 = 1.568687e07 83 SNES Function norm 1.568686804349e07 NL step 84, residual_2 = 1.366121e07 84 SNES Function norm 1.366120654786e07 NL step 85, residual_2 = 1.276916e07 85 SNES Function norm 1.276915915061e07 NL step 86, residual_2 = 1.223932e07 86 SNES Function norm 1.223931884127e07 NL step 87, residual_2 = 1.163863e07 87 SNES Function norm 1.163863154650e07 NL step 88, residual_2 = 1.121774e07 88 SNES Function norm 1.121774061403e07 NL step 89, residual_2 = 1.079065e07 89 SNES Function norm 1.079065066402e07 NL step 90, residual_2 = 9.627717e08 90 SNES Function norm 9.627717396832e08 NL step 91, residual_2 = 9.338040e08 91 SNES Function norm 9.338040321284e08 NL step 92, residual_2 = 8.395781e08 92 SNES Function norm 8.395780687987e08 NL step 93, residual_2 = 7.972458e08 93 SNES Function norm 7.972458335224e08 NL step 94, residual_2 = 7.599603e08 94 SNES Function norm 7.599603469718e08 NL step 95, residual_2 = 7.371015e08 95 SNES Function norm 7.371015086782e08 NL step 96, residual_2 = 6.365861e08 96 SNES Function norm 6.365860767062e08 NL step 97, residual_2 = 5.893407e08 97 SNES Function norm 5.893407486421e08 NL step 98, residual_2 = 5.673266e08 98 SNES Function norm 5.673265571740e08 NL step 99, residual_2 = 5.195474e08 99 SNES Function norm 5.195473569965e08 NL step 100, residual_2 = 4.885457e08 100 SNES Function norm 4.885457271896e08 NL step 101, residual_2 = 4.685175e08 101 SNES Function norm 4.685175202156e08 NL step 102, residual_2 = 4.505639e08 102 SNES Function norm 4.505639250964e08 NL step 103, residual_2 = 4.324372e08 103 SNES Function norm 4.324372186040e08 NL step 104, residual_2 = 4.150867e08 104 SNES Function norm 4.150867469968e08 NL step 105, residual_2 = 4.006847e08 105 SNES Function norm 4.006846993522e08 NL step 106, residual_2 = 2.916694e08 106 SNES Function norm 2.916693756766e08 NL step 107, residual_2 = 2.374078e08 107 SNES Function norm 2.374078268250e08 NL step 108, residual_2 = 2.272917e08 108 SNES Function norm 2.272917460537e08 NL step 109, residual_2 = 2.173385e08 109 SNES Function norm 2.173385018336e08 NL step 110, residual_2 = 2.114292e08 110 SNES Function norm 2.114291507081e08 NL step 111, residual_2 = 2.040838e08 111 SNES Function norm 2.040838239152e08 NL step 112, residual_2 = 1.864519e08 112 SNES Function norm 1.864518544055e08 NL step 113, residual_2 = 1.805016e08 113 SNES Function norm 1.805015962441e08 NL step 114, residual_2 = 1.024459e08 114 SNES Function norm 1.024458891160e08 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 114 Mechanics system solved at nonlinear iteration 114 , final nonlinear residual norm: 1.024459e08, converge reason= 3 Thanks, Dafang On 1/2/2014 9:33 PM, Jed Brown wrote: > Dafang Wang <dafang.wang@...> writes: > >> Hi, >> >> My libmesh progam, which uses SNES to solve a nonlinear equation, had different >> convergence behavior when running on a linux desktop and on a cluster machine. >> >> All other running conditions were double checked to be identical: It was the same program >> running as a single thread on both machines. Both machines were using Libmesh 0.9.2.2. >> >> My program was solving a simple elastic model with good numerical/physical behavior. (The >> model consists of a 5*5*5 cubic mesh with a total of ~600 degress of freedom.) For the >> nonlinear solve, I was using the Newton method and line search (the default settings in >> Petsc SNES). >> >> The Newton method took 5 iterations to converge on my desktop (Ubutun 12.04), whereas it >> took 114 iterations to converge on the cluster. Moreover, both machines generated >> identical results in the first 2 Newton iterations, then they diverged from the 3rd >> iteration. > Please send the output of ksp_converged_reason > ksp_monitor_true_residual snes_monitor snes_converged_reason > snes_view for both cases.  Dafang Wang, Ph.D. Postdoctoral Fellow Institute of Computational Medicine Hackerman Hall, Room 218 Johns Hopkins University, Baltimore, 21218 http://lagniappe.icm.jhu.edu/~dwang/ 
From: Derek Gaston <friedmud@gm...>  20140103 02:45:59

This is almost definitely not a libMesh problem. It sounds like an uninitialized variable. I recommend running your application using valgrind ( http://valgrind.org ) . Use a debug (dbg) build of your application and valgrind will point you right to the problem. Derek On Thu, Jan 2, 2014 at 7:30 PM, Dafang Wang <dafang.wang@...> wrote: > Hi, > > My libmesh progam, which uses SNES to solve a nonlinear equation, had > different > convergence behavior when running on a linux desktop and on a cluster > machine. > > All other running conditions were double checked to be identical: It was > the same program > running as a single thread on both machines. Both machines were using > Libmesh 0.9.2.2. > > My program was solving a simple elastic model with good numerical/physical > behavior. (The > model consists of a 5*5*5 cubic mesh with a total of ~600 degress of > freedom.) For the > nonlinear solve, I was using the Newton method and line search (the > default settings in > Petsc SNES). > > The Newton method took 5 iterations to converge on my desktop (Ubutun > 12.04), whereas it > took 114 iterations to converge on the cluster. Moreover, both machines > generated > identical results in the first 2 Newton iterations, then they diverged > from the 3rd > iteration. > > I am wondering if such difference is common for Libmesh/Petsc programs > running on > different machines. Does anyone have similar experience of running > programs on different > clusters? > > Thanks, > Dafang >  > Dafang Wang, Ph.D. > Postdoctoral Fellow > Institute of Computational Medicine > Hackerman Hall, Room 218 > Johns Hopkins University, Baltimore, 21218 > http://lagniappe.icm.jhu.edu/~dwang/ > > >  > 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 15day FREE TRIAL of AppDynamics > Pro! > http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk > _______________________________________________ > Libmeshusers mailing list > Libmeshusers@... > https://lists.sourceforge.net/lists/listinfo/libmeshusers > 
From: Dafang Wang <dafang.wang@jh...>  20140103 02:30:19

Hi, My libmesh progam, which uses SNES to solve a nonlinear equation, had different convergence behavior when running on a linux desktop and on a cluster machine. All other running conditions were double checked to be identical: It was the same program running as a single thread on both machines. Both machines were using Libmesh 0.9.2.2. My program was solving a simple elastic model with good numerical/physical behavior. (The model consists of a 5*5*5 cubic mesh with a total of ~600 degress of freedom.) For the nonlinear solve, I was using the Newton method and line search (the default settings in Petsc SNES). The Newton method took 5 iterations to converge on my desktop (Ubutun 12.04), whereas it took 114 iterations to converge on the cluster. Moreover, both machines generated identical results in the first 2 Newton iterations, then they diverged from the 3rd iteration. I am wondering if such difference is common for Libmesh/Petsc programs running on different machines. Does anyone have similar experience of running programs on different clusters? Thanks, Dafang  Dafang Wang, Ph.D. Postdoctoral Fellow Institute of Computational Medicine Hackerman Hall, Room 218 Johns Hopkins University, Baltimore, 21218 http://lagniappe.icm.jhu.edu/~dwang/ 