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From: Roy Stogner <roystgnr@ic...>  20140108 23:24:59

On Wed, 8 Jan 2014, John Peterson wrote: > Yep... someone will correct me but I think the *only* thing DNDEBUG does is compile out asserts? Effectively that's all it does, however: Grep for "NDEBUG" and you'll see a bunch of preprocessor tests. Some of our asserts require extra precomputation before the asserted statement, and we generally wrap that in "#ifndef NDEBUG" to avoid unnecessary computations in optimized code and overzealous warnings from compilers and static checkers.  Roy 
From: John Peterson <jwpeterson@gm...>  20140108 22:58:06

On Wed, Jan 8, 2014 at 3:42 PM, Kirk, Benjamin (JSCEG311) < benjamin.kirk@...> wrote: > > > On Jan 8, 2014, at 4:28 PM, "Roy Stogner" <roystgnr@...> > wrote: > > > > > > I can't imagine where, though. We just don't have a lot of places > > where there's a significant difference between normal and NDEBUG code > > paths. > > Does your user code make any calls to e.g. libmesh_assert(...); ? > > That's the only thing I could think of, a predicate inside an assert that > is incorrectly constructed and is perhaps an assignment or something > instead of just a check. > Yep... someone will correct me but I think the *only* thing DNDEBUG does is compile out asserts?  John 
From: Kirk, Benjamin (JSCEG311) <benjamin.kirk@na...>  20140108 22:43:03

> On Jan 8, 2014, at 4:28 PM, "Roy Stogner" <roystgnr@...> wrote: > > > I can't imagine where, though. We just don't have a lot of places > where there's a significant difference between normal and NDEBUG code > paths. Does your user code make any calls to e.g. libmesh_assert(...); ? That's the only thing I could think of, a predicate inside an assert that is incorrectly constructed and is perhaps an assignment or something instead of just a check. Ben 
From: Roy Stogner <roystgnr@ic...>  20140108 22:28:12

On Wed, 8 Jan 2014, Dafang Wang wrote: > I figured out the cause of the problem: DNDEBUG in CXXFLAGS. With this flag > on, the program returned bad convergence results both on my desktop and on > the cluster. Without this flag, both machines yielded good results. So this > problem is not to the intel compiler on the cluster. This is pretty astonishing. Can you get the bad convergence results with DNDEBUG applied to libMesh alone? If so then we've probably got a bug worth looking into somewhere. I can't imagine where, though. We just don't have a lot of places where there's a significant difference between normal and NDEBUG code paths.  Roy 
From: Dafang Wang <dafang.wang@jh...>  20140108 22:20:29

Hi Roy (and Jed), I figured out the cause of the problem: DNDEBUG in CXXFLAGS. With this flag on, the program returned bad convergence results both on my desktop and on the cluster. Without this flag, both machines yielded good results. So this problem is not to the intel compiler on the cluster. Adding "O2 fpmodel precise" and turning on "snes_linesearchmonitor", as you suggested, changed the convergence behavior slightly but not fundamentally. The intel compiler version I am using is "Compiler/11.0/083/". It is a quite old version. Many thanks to both of you for your helpful advice. Cheers, Dafang On 01/08/2014 03:57 PM, Roy Stogner wrote: > > On Wed, 8 Jan 2014, Dafang Wang wrote: > >> Thanks for your prompt reply. Did you mean turning O2 "on" or >> "off"? I got bad results when turning it on. > > I mean using "O2 fpmodel precise". IIRC that often gets icpc to > turn off its inexactinfloatingpoint optimizations without forcing > it to turn off any optimizations which don't change the final code > output. > > No guarantees, though. I dug into the compiler configuration files > > https://github.com/manufacturedsolutions/MASA/blob/master/m4/common/ax_cxx_minopt.m4 > > > from the manufactured solutions code where we encountered these > problems, to see which options we'd ended up needing, and it looks > like we eventually gave up on any optimizations at all when we > demanded maximum accuracy there. >  > Roy  Dafang Wang, Ph.D Postdoctoral Fellow Institute of Computational Medicine Department of Biomedical Engineering Johns Hopkins University Hackerman Hall Room 218 Baltimore, MD, 21218 
From: Roy Stogner <roystgnr@ic...>  20140108 20:57:34

On Wed, 8 Jan 2014, Dafang Wang wrote: > Thanks for your prompt reply. Did you mean turning O2 "on" or "off"? I got > bad results when turning it on. I mean using "O2 fpmodel precise". IIRC that often gets icpc to turn off its inexactinfloatingpoint optimizations without forcing it to turn off any optimizations which don't change the final code output. No guarantees, though. I dug into the compiler configuration files https://github.com/manufacturedsolutions/MASA/blob/master/m4/common/ax_cxx_minopt.m4 from the manufactured solutions code where we encountered these problems, to see which options we'd ended up needing, and it looks like we eventually gave up on any optimizations at all when we demanded maximum accuracy there.  Roy 
From: Roy Stogner <roystgnr@ic...>  20140108 20:49:40

On Wed, 8 Jan 2014, Dafang Wang wrote: > When running the libmesh (and Petsc) in the debug mode (flag= g), > both the desktop and the cluster returned the same convergence > results. However, when running libmesh in the RelWithDebugInfo mode > (flag= O2), the desktop yielded good convergence whereas the > cluster yielded bad convergence. > > The cluster uses a specific Intel compiler which is different from the > desktop. Turning off O2 can really hurt, but you might be able to get away with enabling most of Intel's optimizations while still not ruining your results: try adding "fpmodel precise" ?  Roy 
From: Dafang Wang <dafang.wang@jh...>  20140108 20:33:10

Hi Jed (and others), Here is an update of my previous problem about SNES convergence difference on different machines: The convergence difference seems to be due to the different compilation modes of Petsc. When running the libmesh (and Petsc) in the debug mode (flag= g), both the desktop and the cluster returned the same convergence results. However, when running libmesh in the RelWithDebugInfo mode (flag= O2), the desktop yielded good convergence whereas the cluster yielded bad convergence. The cluster uses a specific Intel compiler which is different from the desktop. In response to Jed's previous questions: 1. No worry for the seg fault problem, which has been resolved. 2. The initial state for the nonlinear system was an allzero solution vector. This problem seems to be relevant to Petsc rather than Libmesh. Any comments would be appreciated. I can provide further details about my simulation if needed. Below are the convergence results obtained with the flags "pc_type lu ksp_monitor ksp_converged_reason snes_monitor snes_converged_reason ".  Debug mode (same results on both machines): Desktop machine: NL step 0, residual_2 = 1.440000e+00 0 SNES Function norm 1.440000000000e+00 0 KSP Residual norm 4.021760102139e+00 1 KSP Residual norm 1.040484538968e14 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 1, residual_2 = 5.960576e01 1 SNES Function norm 5.960575795099e01 0 KSP Residual norm 4.727634711341e01 1 KSP Residual norm 1.169178369623e14 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 2, residual_2 = 3.745537e02 2 SNES Function norm 3.745536863104e02 0 KSP Residual norm 5.571738493521e02 1 KSP Residual norm 4.222606354657e16 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 3, residual_2 = 7.370172e04 3 SNES Function norm 7.370171737019e04 0 KSP Residual norm 6.418014965935e04 1 KSP Residual norm 2.132391208383e18 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 4, residual_2 = 1.433233e07 4 SNES Function norm 1.433233447799e07 0 KSP Residual norm 5.038509414466e07 1 KSP Residual norm 1.948639405146e21 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 5, residual_2 = 3.440465e13 5 SNES Function norm 3.440465235277e13 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 5 Mechanics system solved at nonlinear iteration 5 , final nonlinear residual norm: 3.440465e13, converge reason= 3 Cluster: NL step 0, residual_2 = 1.440000e+00 0 SNES Function norm 1.440000000000e+00 0 KSP Residual norm 4.021760102139e+00 1 KSP Residual norm 2.379314305795e14 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 1, residual_2 = 5.960576e01 1 SNES Function norm 5.960575795099e01 0 KSP Residual norm 4.727634711341e01 1 KSP Residual norm 7.976234556294e15 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 2, residual_2 = 3.745537e02 2 SNES Function norm 3.745536863104e02 0 KSP Residual norm 5.571738493521e02 1 KSP Residual norm 2.844838895371e16 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 3, residual_2 = 7.370172e04 3 SNES Function norm 7.370171737018e04 0 KSP Residual norm 6.418014965934e04 1 KSP Residual norm 4.308781214538e18 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 4, residual_2 = 1.433233e07 4 SNES Function norm 1.433233452409e07 0 KSP Residual norm 5.038509410375e07 1 KSP Residual norm 2.281704035369e21 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 5, residual_2 = 3.436775e13 5 SNES Function norm 3.436774565070e13 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 5 Mechanics system solved at nonlinear iteration 5 , final nonlinear residual norm: 3.436775e13, converge reason= 3  RelWIthDebugInfo mode (O2), different convergence behavior Desktop (good convergence, also same as the debug mode): NL step 0, residual_2 = 1.440000e+00 0 SNES Function norm 1.440000000000e+00 0 KSP Residual norm 4.021760102139e+00 1 KSP Residual norm 1.040484538968e14 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 1, residual_2 = 5.960576e01 1 SNES Function norm 5.960575795099e01 0 KSP Residual norm 4.727634711341e01 1 KSP Residual norm 1.169178369623e14 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 2, residual_2 = 3.745537e02 2 SNES Function norm 3.745536863104e02 0 KSP Residual norm 5.571738493521e02 1 KSP Residual norm 4.222606354657e16 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 3, residual_2 = 7.370172e04 3 SNES Function norm 7.370171737019e04 0 KSP Residual norm 6.418014965935e04 1 KSP Residual norm 2.132391208383e18 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 4, residual_2 = 1.433233e07 4 SNES Function norm 1.433233447799e07 0 KSP Residual norm 5.038509414466e07 1 KSP Residual norm 1.948639405146e21 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 5, residual_2 = 3.440465e13 5 SNES Function norm 3.440465235277e13 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 5 Mechanics system solved at nonlinear iteration 5 , final nonlinear residual norm: 3.440465e13, converge reason= 3 Cluster (poor convergence, different from the debug mode): NL step 0, residual_2 = 1.440000e+00 0 SNES Function norm 1.440000000000e+00 0 KSP Residual norm 4.021760102139e+00 1 KSP Residual norm 2.222981076063e14 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 1, residual_2 = 5.960576e01 1 SNES Function norm 5.960575795099e01 0 KSP Residual norm 5.724516760789e01 1 KSP Residual norm 4.044030898145e14 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 2, residual_2 = 1.482067e01 2 SNES Function norm 1.482067440081e01 0 KSP Residual norm 1.899198487299e01 1 KSP Residual norm 2.132006073251e15 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 3, residual_2 = 7.270703e02 3 SNES Function norm 7.270702856431e02 0 KSP Residual norm 3.483657684658e02 1 KSP Residual norm 3.286054408774e16 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 4, residual_2 = 3.049751e03 4 SNES Function norm 3.049750785313e03 0 KSP Residual norm 4.812920494029e03 1 KSP Residual norm 5.700508014744e16 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 5, residual_2 = 4.513461e04 5 SNES Function norm 4.513461421076e04 0 KSP Residual norm 1.209655693065e03 1 KSP Residual norm 4.945249451450e16 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 6, residual_2 = 1.793522e04 6 SNES Function norm 1.793521679461e04 0 KSP Residual norm 7.011178005420e04 1 KSP Residual norm 8.758630689120e17 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 7, residual_2 = 9.131320e05 7 SNES Function norm 9.131320113186e05 0 KSP Residual norm 3.544244645037e04 1 KSP Residual norm 1.540261136238e16 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 8, residual_2 = 4.648251e05 8 SNES Function norm 4.648251104473e05 0 KSP Residual norm 2.790752923777e04 1 KSP Residual norm 1.079811215541e16 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 9, residual_2 = 2.515710e05 9 SNES Function norm 2.515709920202e05 0 KSP Residual norm 1.355995795589e02 1 KSP Residual norm 1.111094748172e16 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 10, residual_2 = 2.351012e05 10 SNES Function norm 2.351012455292e05 0 KSP Residual norm 4.715035865139e03 1 KSP Residual norm 5.621155808935e17 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 11, residual_2 = 2.248736e05 11 SNES Function norm 2.248736326877e05 0 KSP Residual norm 3.557797254429e03 1 KSP Residual norm 3.341418332138e17 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 12, residual_2 = 2.128736e05 12 SNES Function norm 2.128735852036e05 0 KSP Residual norm 7.703099954589e03 1 KSP Residual norm 1.154597763933e16 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 13, residual_2 = 2.048972e05 13 SNES Function norm 2.048971947471e05 0 KSP Residual norm 2.679644378167e03 1 KSP Residual norm 8.909261104450e17 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 14, residual_2 = 1.965486e05 14 SNES Function norm 1.965485620055e05 0 KSP Residual norm 1.479045966367e02 1 KSP Residual norm 5.645787321175e17 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 15, residual_2 = 1.737326e05 15 SNES Function norm 1.737325739134e05 0 KSP Residual norm 5.144625209331e03 1 KSP Residual norm 8.043824552860e17 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 16, residual_2 = 1.680721e05 16 SNES Function norm 1.680721071217e05 0 KSP Residual norm 1.409004856850e03 1 KSP Residual norm 1.055045286656e17 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 17, residual_2 = 1.505455e05 17 SNES Function norm 1.505455093030e05 0 KSP Residual norm 7.771120407446e03 1 KSP Residual norm 5.978364642141e17 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 18, residual_2 = 1.413325e05 18 SNES Function norm 1.413324859093e05 0 KSP Residual norm 2.703906031576e03 1 KSP Residual norm 3.156540186874e17 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 19, residual_2 = 1.349265e05 19 SNES Function norm 1.349264959991e05 0 KSP Residual norm 2.604619849008e03 1 KSP Residual norm 4.556754801716e17 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 20, residual_2 = 1.288406e05 20 SNES Function norm 1.288406277123e05 0 KSP Residual norm 2.408639307512e03 1 KSP Residual norm 1.574105435806e17 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 21, residual_2 = 1.228811e05 21 SNES Function norm 1.228810775661e05 0 KSP Residual norm 2.592267975097e03 1 KSP Residual norm 4.275624728417e17 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 22, residual_2 = 1.177481e05 22 SNES Function norm 1.177481128032e05 0 KSP Residual norm 1.447675648634e03 1 KSP Residual norm 1.769626897387e17 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 23, residual_2 = 1.115206e05 23 SNES Function norm 1.115206302877e05 0 KSP Residual norm 7.987558615343e03 1 KSP Residual norm 3.471776844754e17 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 24, residual_2 = 9.968437e06 24 SNES Function norm 9.968436832047e06 0 KSP Residual norm 2.779729958997e03 1 KSP Residual norm 2.539893189750e17 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 25, residual_2 = 9.631119e06 25 SNES Function norm 9.631119115197e06 0 KSP Residual norm 4.793844577865e04 1 KSP Residual norm 1.642814961535e18 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 26, residual_2 = 7.658449e06 26 SNES Function norm 7.658449202595e06 0 KSP Residual norm 5.463625248925e03 1 KSP Residual norm 4.389074959683e17 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 27, residual_2 = 6.852486e06 27 SNES Function norm 6.852485650682e06 0 KSP Residual norm 1.901774052606e03 1 KSP Residual norm 1.166130675804e17 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 28, residual_2 = 6.620653e06 28 SNES Function norm 6.620653139738e06 0 KSP Residual norm 3.141182445840e04 1 KSP Residual norm 6.065443405558e18 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 29, residual_2 = 5.171843e06 29 SNES Function norm 5.171843144827e06 0 KSP Residual norm 3.871258196172e03 1 KSP Residual norm 1.951195061396e17 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 30, residual_2 = 4.576905e06 30 SNES Function norm 4.576905178809e06 0 KSP Residual norm 1.347692935990e03 1 KSP Residual norm 1.446770176793e17 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 31, residual_2 = 4.427166e06 31 SNES Function norm 4.427166013787e06 0 KSP Residual norm 3.574992580610e04 1 KSP Residual norm 7.908091467650e18 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 32, residual_2 = 3.950633e06 32 SNES Function norm 3.950633118913e06 0 KSP Residual norm 1.970680556721e03 1 KSP Residual norm 1.088685998265e17 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 33, residual_2 = 3.721235e06 33 SNES Function norm 3.721234938692e06 0 KSP Residual norm 6.861687491055e04 1 KSP Residual norm 1.953135470491e17 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 34, residual_2 = 3.547135e06 34 SNES Function norm 3.547134826276e06 0 KSP Residual norm 7.856677852322e04 1 KSP Residual norm 1.330652439994e17 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 35, residual_2 = 3.404737e06 35 SNES Function norm 3.404737346554e06 0 KSP Residual norm 3.073815582292e04 1 KSP Residual norm 1.603901159353e17 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 36, residual_2 = 3.075132e06 36 SNES Function norm 3.075131676655e06 0 KSP Residual norm 1.694745606692e03 1 KSP Residual norm 1.791266224670e17 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 37, residual_2 = 2.866068e06 37 SNES Function norm 2.866068373248e06 0 KSP Residual norm 5.901013004031e04 1 KSP Residual norm 3.927275386298e18 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 38, residual_2 = 2.743693e06 38 SNES Function norm 2.743693466503e06 0 KSP Residual norm 3.838214494089e04 1 KSP Residual norm 9.894588963925e18 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 39, residual_2 = 2.673055e06 39 SNES Function norm 2.673055265273e06 0 KSP Residual norm 2.117297982903e03 1 KSP Residual norm 9.292131679050e18 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 40, residual_2 = 2.331440e06 40 SNES Function norm 2.331439782776e06 0 KSP Residual norm 7.371907291326e04 1 KSP Residual norm 8.470282280236e18 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 41, residual_2 = 2.256311e06 41 SNES Function norm 2.256310976814e06 0 KSP Residual norm 2.567895446571e04 1 KSP Residual norm 6.852266839368e18 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 42, residual_2 = 2.105991e06 42 SNES Function norm 2.105991050251e06 0 KSP Residual norm 1.416238836146e03 1 KSP Residual norm 1.550853158673e17 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 43, residual_2 = 1.906527e06 43 SNES Function norm 1.906526750558e06 0 KSP Residual norm 4.931289500004e04 1 KSP Residual norm 5.290867863556e18 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 44, residual_2 = 1.838924e06 44 SNES Function norm 1.838923996912e06 0 KSP Residual norm 1.405762049962e05 1 KSP Residual norm 4.585529421262e18 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 45, residual_2 = 1.058048e06 45 SNES Function norm 1.058047908625e06 0 KSP Residual norm 7.729636904681e04 1 KSP Residual norm 4.133047612862e18 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 46, residual_2 = 9.417074e07 46 SNES Function norm 9.417073985418e07 0 KSP Residual norm 2.691875835493e04 1 KSP Residual norm 1.023461541301e18 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 47, residual_2 = 9.104019e07 47 SNES Function norm 9.104018687209e07 0 KSP Residual norm 5.848764695778e05 1 KSP Residual norm 3.731574398649e18 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 48, residual_2 = 7.821364e07 48 SNES Function norm 7.821364289332e07 0 KSP Residual norm 4.227277266633e04 1 KSP Residual norm 4.822287553611e18 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 49, residual_2 = 7.306530e07 49 SNES Function norm 7.306529623165e07 0 KSP Residual norm 1.472269887921e04 1 KSP Residual norm 3.360940671559e18 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 50, residual_2 = 6.989741e07 50 SNES Function norm 6.989741368342e07 0 KSP Residual norm 1.079610402578e04 1 KSP Residual norm 6.085658602505e19 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 51, residual_2 = 6.986050e07 51 SNES Function norm 6.986049538262e07 0 KSP Residual norm 5.955220857101e04 1 KSP Residual norm 5.588488888499e18 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 52, residual_2 = 5.960243e07 52 SNES Function norm 5.960242923830e07 0 KSP Residual norm 2.073824147391e04 1 KSP Residual norm 5.058556742009e18 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 53, residual_2 = 5.746872e07 53 SNES Function norm 5.746872331107e07 0 KSP Residual norm 7.224510981546e05 1 KSP Residual norm 9.534294596381e19 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 54, residual_2 = 5.467005e07 54 SNES Function norm 5.467005265595e07 0 KSP Residual norm 3.984467805183e04 1 KSP Residual norm 1.600986090410e18 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 55, residual_2 = 4.868459e07 55 SNES Function norm 4.868459415833e07 0 KSP Residual norm 1.387564478005e04 1 KSP Residual norm 9.383394994032e19 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 56, residual_2 = 4.706315e07 56 SNES Function norm 4.706315384417e07 0 KSP Residual norm 2.944560147317e05 1 KSP Residual norm 6.638072600237e19 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 57, residual_2 = 4.016471e07 57 SNES Function norm 4.016470859394e07 0 KSP Residual norm 2.238135265392e04 1 KSP Residual norm 1.576103980007e18 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 58, residual_2 = 3.738898e07 58 SNES Function norm 3.738897675506e07 0 KSP Residual norm 7.794670768988e05 1 KSP Residual norm 5.237500072288e19 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 59, residual_2 = 3.581483e07 59 SNES Function norm 3.581482680037e07 0 KSP Residual norm 4.670929752150e05 1 KSP Residual norm 1.147265035210e18 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 60, residual_2 = 3.433438e07 60 SNES Function norm 3.433437845239e07 0 KSP Residual norm 2.576227607006e04 1 KSP Residual norm 2.498690560261e18 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 61, residual_2 = 3.037047e07 61 SNES Function norm 3.037046887097e07 0 KSP Residual norm 8.971382982151e05 1 KSP Residual norm 3.992428337482e19 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 62, residual_2 = 2.938123e07 62 SNES Function norm 2.938123021372e07 0 KSP Residual norm 2.434251616706e05 1 KSP Residual norm 6.288305083577e19 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 63, residual_2 = 2.629026e07 63 SNES Function norm 2.629025543286e07 0 KSP Residual norm 1.341713156961e04 1 KSP Residual norm 9.005362267699e19 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 64, residual_2 = 2.470770e07 64 SNES Function norm 2.470769796053e07 0 KSP Residual norm 4.672848087816e05 1 KSP Residual norm 5.806073812076e19 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 65, residual_2 = 2.357535e07 65 SNES Function norm 2.357534534358e07 0 KSP Residual norm 4.758611162337e05 1 KSP Residual norm 2.479409167491e19 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 66, residual_2 = 2.255490e07 66 SNES Function norm 2.255489784177e07 0 KSP Residual norm 3.455253521731e05 1 KSP Residual norm 1.848686476485e18 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 67, residual_2 = 2.249190e07 67 SNES Function norm 2.249189779176e07 0 KSP Residual norm 1.905971621337e04 1 KSP Residual norm 1.693538835814e18 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 68, residual_2 = 1.922701e07 68 SNES Function norm 1.922701107315e07 0 KSP Residual norm 6.637113796734e05 1 KSP Residual norm 5.714211105785e19 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 69, residual_2 = 1.854509e07 69 SNES Function norm 1.854508680080e07 0 KSP Residual norm 2.312103836137e05 1 KSP Residual norm 9.855648245687e20 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 70, residual_2 = 1.761273e07 70 SNES Function norm 1.761273273016e07 0 KSP Residual norm 1.275181139415e04 1 KSP Residual norm 4.506070339430e19 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 71, residual_2 = 1.570743e07 71 SNES Function norm 1.570743326797e07 0 KSP Residual norm 4.440640194736e05 1 KSP Residual norm 5.422068035420e19 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 72, residual_2 = 1.518161e07 72 SNES Function norm 1.518161153491e07 0 KSP Residual norm 8.797907000209e06 1 KSP Residual norm 2.075176146890e19 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 73, residual_2 = 1.268831e07 73 SNES Function norm 1.268830968047e07 0 KSP Residual norm 7.705514125563e05 1 KSP Residual norm 1.017793788404e18 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 74, residual_2 = 1.167839e07 74 SNES Function norm 1.167838585279e07 0 KSP Residual norm 2.683450054484e05 1 KSP Residual norm 5.132689633111e19 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 75, residual_2 = 1.122477e07 75 SNES Function norm 1.122477442296e07 0 KSP Residual norm 7.409290455259e06 1 KSP Residual norm 3.645143742976e19 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 76, residual_2 = 9.706797e08 76 SNES Function norm 9.706796620796e08 0 KSP Residual norm 5.082292041698e05 1 KSP Residual norm 3.544425465304e19 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 77, residual_2 = 9.099011e08 77 SNES Function norm 9.099010557425e08 0 KSP Residual norm 1.769998454096e05 1 KSP Residual norm 3.363150042480e19 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 78, residual_2 = 8.692366e08 78 SNES Function norm 8.692366224026e08 0 KSP Residual norm 1.566736777879e05 1 KSP Residual norm 2.819452990843e19 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 79, residual_2 = 8.276834e08 79 SNES Function norm 8.276834291448e08 0 KSP Residual norm 1.990319801652e05 1 KSP Residual norm 1.068580372799e19 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 80, residual_2 = 7.966571e08 80 SNES Function norm 7.966570700260e08 0 KSP Residual norm 3.003444562499e06 1 KSP Residual norm 5.206872525061e19 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 81, residual_2 = 5.608802e08 81 SNES Function norm 5.608802450435e08 0 KSP Residual norm 5.211286640517e05 1 KSP Residual norm 1.336954688010e19 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 82, residual_2 = 4.633277e08 82 SNES Function norm 4.633277025854e08 0 KSP Residual norm 1.814671884668e05 1 KSP Residual norm 1.945186873110e19 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 83, residual_2 = 4.441497e08 83 SNES Function norm 4.441496884398e08 0 KSP Residual norm 6.320882672742e06 1 KSP Residual norm 6.522712340090e20 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 84, residual_2 = 4.345014e08 84 SNES Function norm 4.345013744524e08 0 KSP Residual norm 3.486532415243e05 1 KSP Residual norm 2.820388278092e19 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 85, residual_2 = 3.776562e08 85 SNES Function norm 3.776561517098e08 0 KSP Residual norm 1.214102392542e05 1 KSP Residual norm 4.637953640500e20 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 86, residual_2 = 3.652905e08 86 SNES Function norm 3.652904667916e08 0 KSP Residual norm 4.229676380623e06 1 KSP Residual norm 2.985543935183e19 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 87, residual_2 = 3.421015e08 87 SNES Function norm 3.421015322140e08 0 KSP Residual norm 2.332617444021e05 1 KSP Residual norm 1.899596182975e19 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 88, residual_2 = 3.088663e08 88 SNES Function norm 3.088662974125e08 0 KSP Residual norm 8.123061571912e06 1 KSP Residual norm 9.730785565672e20 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 89, residual_2 = 2.980237e08 89 SNES Function norm 2.980236808814e08 0 KSP Residual norm 4.955116260996e07 1 KSP Residual norm 3.777642296031e20 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 90, residual_2 = 2.461180e08 90 SNES Function norm 2.461180426859e08 0 KSP Residual norm 3.089926846929e05 1 KSP Residual norm 1.152580814246e19 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 91, residual_2 = 1.641444e08 91 SNES Function norm 1.641444000238e08 0 KSP Residual norm 1.075937296980e05 1 KSP Residual norm 9.644931034537e20 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 92, residual_2 = 1.492579e08 92 SNES Function norm 1.492578941113e08 0 KSP Residual norm 3.746844578568e06 1 KSP Residual norm 2.240329961008e20 Linear solve converged due to CONVERGED_RTOL iterations 1 NL step 93, residual_2 = 1.438360e08 93 SNES Function norm 1.438360232831e08 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 93 Mechanics system solved at nonlinear iteration 93 , final nonlinear residual norm: 1.438360e08, converge reason= 3 Thanks, Dafang On 01/03/2014 08:51 AM, Jed Brown wrote: > Dafang Wang <dafang.wang@...> writes: > >> 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. ) > It should not SEGV. Can you get a stack trace? > >> 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 *** > What is this about? > >> 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 > Can you try with low optimization? This has the look of an incorrect > Jacobian (perhaps due to bad optimization or a bad dependent library). > > What is the initial state? Can you try running with snes_mf_operator? > (And get the ksp_monitor ksp_converged_reason working; we need to know > what's happening with that solve.)  Dafang Wang, Ph.D Postdoctoral Fellow Institute of Computational Medicine Department of Biomedical Engineering Johns Hopkins University Hackerman Hall Room 218 Baltimore, MD, 21218 