TS failed due to diverged_step_rejected
My code uses TS to solve a set of multi-fluid MHD equations. The jacobian is provided with function F(t, u, u'). Both linear and nonlinear solvers converge but snes repeats itself until gets "TSStep has failed due to diverged_step_rejected." Is it because I used TSStep rather than TSSolve? I have checked the condition number. The condition number with pc_type asm is about 1 (without precondition it is about 4x10^4). The maximum ratio of off-diagonal jacobian element over diagonal element is about 21. Could you help me to identify what is going wrong? Thank you very much! Jiannan --------------------------------------------------------------------------------------------------- Run command with options mpiexec -n $1 ./iditm3d -ts_type arkimex -snes_tyep ngmres -ksp_type gmres -pc_type asm \ -ts_rtol 1.0e-4 -ts_atol 1.0e-4 -snes_monitor -snes_rtol 1.0e-4 -snes_atol 1.0e-4 \ -snes_converged_reason The output message is Start time advancing ... 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 11:59:43 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583
Can you please run with also the options -ts_monitor -ts_adapt_monitor ? The output is confusing because it prints that the Nonlinear solve has converged but then TSStep has failed due to DIVERGED_STEP_REJECTED which seems contradictory
On Feb 17, 2023, at 12:09 PM, Tu, Jiannan <[email protected]> wrote:
My code uses TS to solve a set of multi-fluid MHD equations. The jacobian is provided with function F(t, u, u'). Both linear and nonlinear solvers converge but snes repeats itself until gets "TSStep has failed due to diverged_step_rejected."
Is it because I used TSStep rather than TSSolve? I have checked the condition number. The condition number with pc_type asm is about 1 (without precondition it is about 4x10^4). The maximum ratio of off-diagonal jacobian element over diagonal element is about 21.
Could you help me to identify what is going wrong?
Thank you very much!
Jiannan
--------------------------------------------------------------------------------------------------- Run command with options
mpiexec -n $1 ./iditm3d -ts_type arkimex -snes_tyep ngmres -ksp_type gmres -pc_type asm \ -ts_rtol 1.0e-4 -ts_atol 1.0e-4 -snes_monitor -snes_rtol 1.0e-4 -snes_atol 1.0e-4 \ -snes_converged_reason
The output message is
Start time advancing ... 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 11:59:43 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583
These are what I got with the options you suggested. Thank you, Jiannan ------------------------------------------------------------------------------- 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 2.189e-02 dt=4.374e-03 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-03 dt=4.374e-04 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-04 dt=4.374e-05 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-05 dt=4.374e-06 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-06 dt=4.374e-07 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-07 dt=4.374e-08 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-08 dt=4.374e-09 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-09 dt=4.374e-10 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-10 dt=4.374e-11 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-11 dt=4.374e-12 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-12 dt=4.374e-13 wlte= 91.4 wltea= -1 wlter= -1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 14:54:22 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 12:58 PM To: Tu, Jiannan<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. Can you please run with also the options -ts_monitor -ts_adapt_monitor ? The output is confusing because it prints that the Nonlinear solve has converged but then TSStep has failed due to DIVERGED_STEP_REJECTED which seems contradictory On Feb 17, 2023, at 12:09 PM, Tu, Jiannan <[email protected]> wrote: My code uses TS to solve a set of multi-fluid MHD equations. The jacobian is provided with function F(t, u, u'). Both linear and nonlinear solvers converge but snes repeats itself until gets "TSStep has failed due to diverged_step_rejected." Is it because I used TSStep rather than TSSolve? I have checked the condition number. The condition number with pc_type asm is about 1 (without precondition it is about 4x10^4). The maximum ratio of off-diagonal jacobian element over diagonal element is about 21. Could you help me to identify what is going wrong? Thank you very much! Jiannan --------------------------------------------------------------------------------------------------- Run command with options mpiexec -n $1 ./iditm3d -ts_type arkimex -snes_tyep ngmres -ksp_type gmres -pc_type asm \ -ts_rtol 1.0e-4 -ts_atol 1.0e-4 -snes_monitor -snes_rtol 1.0e-4 -snes_atol 1.0e-4 \ -snes_converged_reason The output message is Start time advancing ... 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7C3e6f11605fab43c95c2408db11108a7a%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122534984142994%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=k0lAvbqtvRt6nMClf1e7MUT3LKU9B3ir2uek9OiRVSk%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 11:59:43 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583
I am not sure what TS you are using, but the estimate of the local truncation error is 91.4, and does not seem to change when you make the step smaller, so something is off. You can shut off the adaptivity using -ts_adapt_type none Thanks, Matt On Fri, Feb 17, 2023 at 3:01 PM Tu, Jiannan <[email protected]> wrote:
These are what I got with the options you suggested.
Thank you,
Jiannan
-------------------------------------------------------------------------------
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 1.673091274668e-03
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 8.715428433630e-02
1 SNES Function norm 4.995727626692e-04
2 SNES Function norm 5.498018152230e-08
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2
0 SNES Function norm 3.237461568254e-01
1 SNES Function norm 7.988531005091e-04
2 SNES Function norm 1.280948196292e-07
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2
TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 2.189e-02 dt=4.374e-03 wlte= 91.4 wltea= -1 wlter= -1
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 4.881903203545e-04
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 7.562592690785e-02
1 SNES Function norm 1.143078818923e-04
2 SNES Function norm 9.834547907735e-09
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2
0 SNES Function norm 2.683968949758e-01
1 SNES Function norm 1.838028436639e-04
2 SNES Function norm 9.470813523140e-09
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2
TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-03 dt=4.374e-04 wlte= 91.4 wltea= -1 wlter= -1
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 1.821562431175e-04
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 1.005443458812e-01
1 SNES Function norm 3.633336946661e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 1.515368382715e-01
1 SNES Function norm 3.389298316830e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-04 dt=4.374e-05 wlte= 91.4 wltea= -1 wlter= -1
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 4.541003359206e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 1.713800906043e-01
1 SNES Function norm 1.179958172167e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 2.020265094117e-01
1 SNES Function norm 1.513971290464e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-05 dt=4.374e-06 wlte= 91.4 wltea= -1 wlter= -1
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 6.090269704320e-06
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 2.136603895703e-01
1 SNES Function norm 1.877474016012e-06
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 3.127812462507e-01
1 SNES Function norm 2.713146825704e-06
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-06 dt=4.374e-07 wlte= 91.4 wltea= -1 wlter= -1
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 2.793512213059e-06
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 2.205196267430e-01
1 SNES Function norm 2.572653773308e-06
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 3.260057361977e-01
1 SNES Function norm 2.705816087598e-06
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-07 dt=4.374e-08 wlte= 91.4 wltea= -1 wlter= -1
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 2.764855860446e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 2.212505522844e-01
1 SNES Function norm 2.958996472386e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 3.273222034162e-01
1 SNES Function norm 2.994512887620e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-08 dt=4.374e-09 wlte= 91.4 wltea= -1 wlter= -1
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 3.317240589134e-04
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 2.213246532918e-01
1 SNES Function norm 2.799468604767e-04
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
0 SNES Function norm 3.274570888397e-01
1 SNES Function norm 3.066048050994e-04
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-09 dt=4.374e-10 wlte= 91.4 wltea= -1 wlter= -1
0 SNES Function norm 2.274473072189e+03
1 SNES Function norm 2.653507278572e-03
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 2.213869585841e-01
1 SNES Function norm 2.177156902895e-03
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
0 SNES Function norm 3.275136370365e-01
1 SNES Function norm 1.962849131557e-03
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-10 dt=4.374e-11 wlte= 91.4 wltea= -1 wlter= -1
0 SNES Function norm 2.274473072218e+03
1 SNES Function norm 5.664907315679e-03
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 2.223208399368e-01
1 SNES Function norm 5.688863091415e-03
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
0 SNES Function norm 3.287121218919e-01
1 SNES Function norm 4.085338521320e-03
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-11 dt=4.374e-12 wlte= 91.4 wltea= -1 wlter= -1
0 SNES Function norm 2.274473071968e+03
1 SNES Function norm 4.694691905235e-04
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 2.211786508657e-01
1 SNES Function norm 1.503497433939e-04
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
0 SNES Function norm 3.272667798977e-01
1 SNES Function norm 2.176132327279e-04
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-12 dt=4.374e-13 wlte= 91.4 wltea= -1 wlter= -1
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR:
[0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022
[0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 14:54:22 2023
[0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1
[0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583
*From: *Barry Smith <[email protected]> *Sent: *Friday, February 17, 2023 12:58 PM *To: *Tu, Jiannan <[email protected]> *Cc: *petsc-users <[email protected]> *Subject: *Re: [petsc-users] TS failed due to diverged_step_rejected
*CAUTION:* This email was sent from outside the UMass Lowell network.
Can you please run with also the options -ts_monitor -ts_adapt_monitor ?
The output is confusing because it prints that the Nonlinear solve has converged but then TSStep has failed due to DIVERGED_STEP_REJECTED which seems contradictory
On Feb 17, 2023, at 12:09 PM, Tu, Jiannan <[email protected]> wrote:
My code uses TS to solve a set of multi-fluid MHD equations. The jacobian is provided with function F(t, u, u'). Both linear and nonlinear solvers converge but snes repeats itself until gets "TSStep has failed due to diverged_step_rejected."
Is it because I used TSStep rather than TSSolve? I have checked the condition number. The condition number with pc_type asm is about 1 (without precondition it is about 4x10^4). The maximum ratio of off-diagonal jacobian element over diagonal element is about 21.
Could you help me to identify what is going wrong?
Thank you very much!
Jiannan
---------------------------------------------------------------------------------------------------
Run command with options
mpiexec -n $1 ./iditm3d -ts_type arkimex -snes_tyep ngmres -ksp_type gmres -pc_type asm \
-ts_rtol 1.0e-4 -ts_atol 1.0e-4 -snes_monitor -snes_rtol 1.0e-4 -snes_atol 1.0e-4 \
-snes_converged_reason
The output message is
Start time advancing ...
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 1.673091274668e-03
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 8.715428433630e-02
1 SNES Function norm 4.995727626692e-04
2 SNES Function norm 5.498018152230e-08
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2
0 SNES Function norm 3.237461568254e-01
1 SNES Function norm 7.988531005091e-04
2 SNES Function norm 1.280948196292e-07
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 4.881903203545e-04
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 7.562592690785e-02
1 SNES Function norm 1.143078818923e-04
2 SNES Function norm 9.834547907735e-09
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2
0 SNES Function norm 2.683968949758e-01
1 SNES Function norm 1.838028436639e-04
2 SNES Function norm 9.470813523140e-09
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 1.821562431175e-04
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 1.005443458812e-01
1 SNES Function norm 3.633336946661e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 1.515368382715e-01
1 SNES Function norm 3.389298316830e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 4.541003359206e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 1.713800906043e-01
1 SNES Function norm 1.179958172167e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 2.020265094117e-01
1 SNES Function norm 1.513971290464e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 6.090269704320e-06
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 2.136603895703e-01
1 SNES Function norm 1.877474016012e-06
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 3.127812462507e-01
1 SNES Function norm 2.713146825704e-06
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 2.793512213059e-06
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 2.205196267430e-01
1 SNES Function norm 2.572653773308e-06
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 3.260057361977e-01
1 SNES Function norm 2.705816087598e-06
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 2.764855860446e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 2.212505522844e-01
1 SNES Function norm 2.958996472386e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 3.273222034162e-01
1 SNES Function norm 2.994512887620e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 3.317240589134e-04
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 2.213246532918e-01
1 SNES Function norm 2.799468604767e-04
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
0 SNES Function norm 3.274570888397e-01
1 SNES Function norm 3.066048050994e-04
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
0 SNES Function norm 2.274473072189e+03
1 SNES Function norm 2.653507278572e-03
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 2.213869585841e-01
1 SNES Function norm 2.177156902895e-03
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
0 SNES Function norm 3.275136370365e-01
1 SNES Function norm 1.962849131557e-03
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
0 SNES Function norm 2.274473072218e+03
1 SNES Function norm 5.664907315679e-03
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 2.223208399368e-01
1 SNES Function norm 5.688863091415e-03
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
0 SNES Function norm 3.287121218919e-01
1 SNES Function norm 4.085338521320e-03
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
0 SNES Function norm 2.274473071968e+03
1 SNES Function norm 4.694691905235e-04
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 2.211786508657e-01
1 SNES Function norm 1.503497433939e-04
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
0 SNES Function norm 3.272667798977e-01
1 SNES Function norm 2.176132327279e-04
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR:
[0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED
[0]PETSC ERROR: See https://petsc.org/release/faq/ <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7C3e6f11605fab43c95c2408db11108a7a%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122534984142994%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=k0lAvbqtvRt6nMClf1e7MUT3LKU9B3ir2uek9OiRVSk%3D&reserved=0> for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022
[0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 11:59:43 2023
[0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1
[0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583
-- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
The ts_type arkimex is used. There is right hand-side function RHSFunction set by TSSetRHSFunction() and also stiff function set by TSSetIFunction(). With adaptivity shut off, TS can finish its first time step after the 3rd “Nonlinear solve converged due to …”. The solution gives negative electron and neutral temperatures at the bottom boundary. I need to fix the negative temperatures and see how the code works. BTW, what is this ts_adapt? Is it by default on? Thank you, Jiannan From: Matthew Knepley<mailto:[email protected]> Sent: Friday, February 17, 2023 3:15 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. I am not sure what TS you are using, but the estimate of the local truncation error is 91.4, and does not seem to change when you make the step smaller, so something is off. You can shut off the adaptivity using -ts_adapt_type none Thanks, Matt On Fri, Feb 17, 2023 at 3:01 PM Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: These are what I got with the options you suggested. Thank you, Jiannan ------------------------------------------------------------------------------- 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 2.189e-02 dt=4.374e-03 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-03 dt=4.374e-04 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-04 dt=4.374e-05 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-05 dt=4.374e-06 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-06 dt=4.374e-07 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-07 dt=4.374e-08 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-08 dt=4.374e-09 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-09 dt=4.374e-10 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-10 dt=4.374e-11 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-11 dt=4.374e-12 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-12 dt=4.374e-13 wlte= 91.4 wltea= -1 wlter= -1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7C22c17ae3c57841a2318a08db1123b692%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122617338217328%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8eFv1wG%2FSeP0lMGNMTKt582ERpT%2FBSE5wKSIecQlPkU%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 14:54:22 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 12:58 PM To: Tu, Jiannan<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. Can you please run with also the options -ts_monitor -ts_adapt_monitor ? The output is confusing because it prints that the Nonlinear solve has converged but then TSStep has failed due to DIVERGED_STEP_REJECTED which seems contradictory On Feb 17, 2023, at 12:09 PM, Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: My code uses TS to solve a set of multi-fluid MHD equations. The jacobian is provided with function F(t, u, u'). Both linear and nonlinear solvers converge but snes repeats itself until gets "TSStep has failed due to diverged_step_rejected." Is it because I used TSStep rather than TSSolve? I have checked the condition number. The condition number with pc_type asm is about 1 (without precondition it is about 4x10^4). The maximum ratio of off-diagonal jacobian element over diagonal element is about 21. Could you help me to identify what is going wrong? Thank you very much! Jiannan --------------------------------------------------------------------------------------------------- Run command with options mpiexec -n $1 ./iditm3d -ts_type arkimex -snes_tyep ngmres -ksp_type gmres -pc_type asm \ -ts_rtol 1.0e-4 -ts_atol 1.0e-4 -snes_monitor -snes_rtol 1.0e-4 -snes_atol 1.0e-4 \ -snes_converged_reason The output message is Start time advancing ... 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7C22c17ae3c57841a2318a08db1123b692%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122617338217328%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8eFv1wG%2FSeP0lMGNMTKt582ERpT%2FBSE5wKSIecQlPkU%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 11:59:43 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.cse.buffalo.edu%2F~knepley%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7C22c17ae3c57841a2318a08db1123b692%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122617338217328%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=SxBlKPP1FyoO5Vkz66viMmC5kmX1MHG8XTQYKSZTiIo%3D&reserved=0>
On Fri, Feb 17, 2023 at 3:32 PM Tu, Jiannan <[email protected]> wrote:
The ts_type arkimex is used. There is right hand-side function RHSFunction set by TSSetRHSFunction() and also stiff function set by TSSetIFunction().
With adaptivity shut off, TS can finish its first time step after the 3rd “Nonlinear solve converged due to …”. The solution gives negative electron and neutral temperatures at the bottom boundary. I need to fix the negative temperatures and see how the code works.
BTW, what is this ts_adapt? Is it by default on?
It is a controller for adaptive timestepping. It is on by default, but I suspect that you step into an unphysical regime, which makes its estimates unreliable. Thanks, Matt
Thank you,
Jiannan
*From: *Matthew Knepley <[email protected]> *Sent: *Friday, February 17, 2023 3:15 PM *To: *Tu, Jiannan <[email protected]> *Cc: *Barry Smith <[email protected]>; petsc-users <[email protected]> *Subject: *Re: [petsc-users] TS failed due to diverged_step_rejected
*CAUTION:* This email was sent from outside the UMass Lowell network.
I am not sure what TS you are using, but the estimate of the local truncation error is 91.4, and does not seem
to change when you make the step smaller, so something is off. You can shut off the adaptivity using
-ts_adapt_type none
Thanks,
Matt
On Fri, Feb 17, 2023 at 3:01 PM Tu, Jiannan <[email protected]> wrote:
These are what I got with the options you suggested.
Thank you,
Jiannan
-------------------------------------------------------------------------------
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 1.673091274668e-03
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 8.715428433630e-02
1 SNES Function norm 4.995727626692e-04
2 SNES Function norm 5.498018152230e-08
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2
0 SNES Function norm 3.237461568254e-01
1 SNES Function norm 7.988531005091e-04
2 SNES Function norm 1.280948196292e-07
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2
TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 2.189e-02 dt=4.374e-03 wlte= 91.4 wltea= -1 wlter= -1
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 4.881903203545e-04
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 7.562592690785e-02
1 SNES Function norm 1.143078818923e-04
2 SNES Function norm 9.834547907735e-09
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2
0 SNES Function norm 2.683968949758e-01
1 SNES Function norm 1.838028436639e-04
2 SNES Function norm 9.470813523140e-09
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2
TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-03 dt=4.374e-04 wlte= 91.4 wltea= -1 wlter= -1
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 1.821562431175e-04
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 1.005443458812e-01
1 SNES Function norm 3.633336946661e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 1.515368382715e-01
1 SNES Function norm 3.389298316830e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-04 dt=4.374e-05 wlte= 91.4 wltea= -1 wlter= -1
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 4.541003359206e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 1.713800906043e-01
1 SNES Function norm 1.179958172167e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 2.020265094117e-01
1 SNES Function norm 1.513971290464e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-05 dt=4.374e-06 wlte= 91.4 wltea= -1 wlter= -1
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 6.090269704320e-06
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 2.136603895703e-01
1 SNES Function norm 1.877474016012e-06
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 3.127812462507e-01
1 SNES Function norm 2.713146825704e-06
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-06 dt=4.374e-07 wlte= 91.4 wltea= -1 wlter= -1
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 2.793512213059e-06
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 2.205196267430e-01
1 SNES Function norm 2.572653773308e-06
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 3.260057361977e-01
1 SNES Function norm 2.705816087598e-06
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-07 dt=4.374e-08 wlte= 91.4 wltea= -1 wlter= -1
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 2.764855860446e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 2.212505522844e-01
1 SNES Function norm 2.958996472386e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 3.273222034162e-01
1 SNES Function norm 2.994512887620e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-08 dt=4.374e-09 wlte= 91.4 wltea= -1 wlter= -1
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 3.317240589134e-04
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 2.213246532918e-01
1 SNES Function norm 2.799468604767e-04
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
0 SNES Function norm 3.274570888397e-01
1 SNES Function norm 3.066048050994e-04
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-09 dt=4.374e-10 wlte= 91.4 wltea= -1 wlter= -1
0 SNES Function norm 2.274473072189e+03
1 SNES Function norm 2.653507278572e-03
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 2.213869585841e-01
1 SNES Function norm 2.177156902895e-03
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
0 SNES Function norm 3.275136370365e-01
1 SNES Function norm 1.962849131557e-03
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-10 dt=4.374e-11 wlte= 91.4 wltea= -1 wlter= -1
0 SNES Function norm 2.274473072218e+03
1 SNES Function norm 5.664907315679e-03
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 2.223208399368e-01
1 SNES Function norm 5.688863091415e-03
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
0 SNES Function norm 3.287121218919e-01
1 SNES Function norm 4.085338521320e-03
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-11 dt=4.374e-12 wlte= 91.4 wltea= -1 wlter= -1
0 SNES Function norm 2.274473071968e+03
1 SNES Function norm 4.694691905235e-04
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 2.211786508657e-01
1 SNES Function norm 1.503497433939e-04
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
0 SNES Function norm 3.272667798977e-01
1 SNES Function norm 2.176132327279e-04
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-12 dt=4.374e-13 wlte= 91.4 wltea= -1 wlter= -1
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR:
[0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED
[0]PETSC ERROR: See https://petsc.org/release/faq/ <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7C22c17ae3c57841a2318a08db1123b692%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122617338217328%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8eFv1wG%2FSeP0lMGNMTKt582ERpT%2FBSE5wKSIecQlPkU%3D&reserved=0> for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022
[0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 14:54:22 2023
[0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1
[0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583
*From: *Barry Smith <[email protected]> *Sent: *Friday, February 17, 2023 12:58 PM *To: *Tu, Jiannan <[email protected]> *Cc: *petsc-users <[email protected]> *Subject: *Re: [petsc-users] TS failed due to diverged_step_rejected
*CAUTION:* This email was sent from outside the UMass Lowell network.
Can you please run with also the options -ts_monitor -ts_adapt_monitor ?
The output is confusing because it prints that the Nonlinear solve has converged but then TSStep has failed due to DIVERGED_STEP_REJECTED which seems contradictory
On Feb 17, 2023, at 12:09 PM, Tu, Jiannan <[email protected]> wrote:
My code uses TS to solve a set of multi-fluid MHD equations. The jacobian is provided with function F(t, u, u'). Both linear and nonlinear solvers converge but snes repeats itself until gets "TSStep has failed due to diverged_step_rejected."
Is it because I used TSStep rather than TSSolve? I have checked the condition number. The condition number with pc_type asm is about 1 (without precondition it is about 4x10^4). The maximum ratio of off-diagonal jacobian element over diagonal element is about 21.
Could you help me to identify what is going wrong?
Thank you very much!
Jiannan
---------------------------------------------------------------------------------------------------
Run command with options
mpiexec -n $1 ./iditm3d -ts_type arkimex -snes_tyep ngmres -ksp_type gmres -pc_type asm \
-ts_rtol 1.0e-4 -ts_atol 1.0e-4 -snes_monitor -snes_rtol 1.0e-4 -snes_atol 1.0e-4 \
-snes_converged_reason
The output message is
Start time advancing ...
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 1.673091274668e-03
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 8.715428433630e-02
1 SNES Function norm 4.995727626692e-04
2 SNES Function norm 5.498018152230e-08
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2
0 SNES Function norm 3.237461568254e-01
1 SNES Function norm 7.988531005091e-04
2 SNES Function norm 1.280948196292e-07
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 4.881903203545e-04
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 7.562592690785e-02
1 SNES Function norm 1.143078818923e-04
2 SNES Function norm 9.834547907735e-09
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2
0 SNES Function norm 2.683968949758e-01
1 SNES Function norm 1.838028436639e-04
2 SNES Function norm 9.470813523140e-09
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 1.821562431175e-04
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 1.005443458812e-01
1 SNES Function norm 3.633336946661e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 1.515368382715e-01
1 SNES Function norm 3.389298316830e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 4.541003359206e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 1.713800906043e-01
1 SNES Function norm 1.179958172167e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 2.020265094117e-01
1 SNES Function norm 1.513971290464e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 6.090269704320e-06
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 2.136603895703e-01
1 SNES Function norm 1.877474016012e-06
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 3.127812462507e-01
1 SNES Function norm 2.713146825704e-06
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 2.793512213059e-06
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 2.205196267430e-01
1 SNES Function norm 2.572653773308e-06
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 3.260057361977e-01
1 SNES Function norm 2.705816087598e-06
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 2.764855860446e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 2.212505522844e-01
1 SNES Function norm 2.958996472386e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 3.273222034162e-01
1 SNES Function norm 2.994512887620e-05
Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1
0 SNES Function norm 2.274473072186e+03
1 SNES Function norm 3.317240589134e-04
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 2.213246532918e-01
1 SNES Function norm 2.799468604767e-04
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
0 SNES Function norm 3.274570888397e-01
1 SNES Function norm 3.066048050994e-04
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
0 SNES Function norm 2.274473072189e+03
1 SNES Function norm 2.653507278572e-03
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 2.213869585841e-01
1 SNES Function norm 2.177156902895e-03
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
0 SNES Function norm 3.275136370365e-01
1 SNES Function norm 1.962849131557e-03
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
0 SNES Function norm 2.274473072218e+03
1 SNES Function norm 5.664907315679e-03
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 2.223208399368e-01
1 SNES Function norm 5.688863091415e-03
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
0 SNES Function norm 3.287121218919e-01
1 SNES Function norm 4.085338521320e-03
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
0 SNES Function norm 2.274473071968e+03
1 SNES Function norm 4.694691905235e-04
Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1
0 SNES Function norm 2.211786508657e-01
1 SNES Function norm 1.503497433939e-04
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
0 SNES Function norm 3.272667798977e-01
1 SNES Function norm 2.176132327279e-04
Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR:
[0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED
[0]PETSC ERROR: See https://petsc.org/release/faq/ <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7C22c17ae3c57841a2318a08db1123b692%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122617338217328%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8eFv1wG%2FSeP0lMGNMTKt582ERpT%2FBSE5wKSIecQlPkU%3D&reserved=0> for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022
[0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 11:59:43 2023
[0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1
[0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583
--
What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener
https://www.cse.buffalo.edu/~knepley/ <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.cse.buffalo.edu%2F~knepley%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7C22c17ae3c57841a2318a08db1123b692%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122617338217328%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=SxBlKPP1FyoO5Vkz66viMmC5kmX1MHG8XTQYKSZTiIo%3D&reserved=0>
-- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
It’s possible. I’m checking the rhs and stiff equations. Thank you, Jiannan From: Matthew Knepley<mailto:[email protected]> Sent: Friday, February 17, 2023 3:39 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. On Fri, Feb 17, 2023 at 3:32 PM Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: The ts_type arkimex is used. There is right hand-side function RHSFunction set by TSSetRHSFunction() and also stiff function set by TSSetIFunction(). With adaptivity shut off, TS can finish its first time step after the 3rd “Nonlinear solve converged due to …”. The solution gives negative electron and neutral temperatures at the bottom boundary. I need to fix the negative temperatures and see how the code works. BTW, what is this ts_adapt? Is it by default on? It is a controller for adaptive timestepping. It is on by default, but I suspect that you step into an unphysical regime, which makes its estimates unreliable. Thanks, Matt Thank you, Jiannan From: Matthew Knepley<mailto:[email protected]> Sent: Friday, February 17, 2023 3:15 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. I am not sure what TS you are using, but the estimate of the local truncation error is 91.4, and does not seem to change when you make the step smaller, so something is off. You can shut off the adaptivity using -ts_adapt_type none Thanks, Matt On Fri, Feb 17, 2023 at 3:01 PM Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: These are what I got with the options you suggested. Thank you, Jiannan ------------------------------------------------------------------------------- 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 2.189e-02 dt=4.374e-03 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-03 dt=4.374e-04 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-04 dt=4.374e-05 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-05 dt=4.374e-06 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-06 dt=4.374e-07 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-07 dt=4.374e-08 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-08 dt=4.374e-09 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-09 dt=4.374e-10 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-10 dt=4.374e-11 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-11 dt=4.374e-12 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-12 dt=4.374e-13 wlte= 91.4 wltea= -1 wlter= -1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7C01ad28026b614c9c427a08db11270481%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122631541429844%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=QUFvFMlmq8xNOLR4T%2Fz5K1bbZ45%2FY0%2Fic2dSJm%2BihpU%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 14:54:22 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 12:58 PM To: Tu, Jiannan<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. Can you please run with also the options -ts_monitor -ts_adapt_monitor ? The output is confusing because it prints that the Nonlinear solve has converged but then TSStep has failed due to DIVERGED_STEP_REJECTED which seems contradictory On Feb 17, 2023, at 12:09 PM, Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: My code uses TS to solve a set of multi-fluid MHD equations. The jacobian is provided with function F(t, u, u'). Both linear and nonlinear solvers converge but snes repeats itself until gets "TSStep has failed due to diverged_step_rejected." Is it because I used TSStep rather than TSSolve? I have checked the condition number. The condition number with pc_type asm is about 1 (without precondition it is about 4x10^4). The maximum ratio of off-diagonal jacobian element over diagonal element is about 21. Could you help me to identify what is going wrong? Thank you very much! Jiannan --------------------------------------------------------------------------------------------------- Run command with options mpiexec -n $1 ./iditm3d -ts_type arkimex -snes_tyep ngmres -ksp_type gmres -pc_type asm \ -ts_rtol 1.0e-4 -ts_atol 1.0e-4 -snes_monitor -snes_rtol 1.0e-4 -snes_atol 1.0e-4 \ -snes_converged_reason The output message is Start time advancing ... 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7C01ad28026b614c9c427a08db11270481%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122631541429844%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=QUFvFMlmq8xNOLR4T%2Fz5K1bbZ45%2FY0%2Fic2dSJm%2BihpU%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 11:59:43 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.cse.buffalo.edu%2F~knepley%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7C01ad28026b614c9c427a08db11270481%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122631541429844%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=I89Ouhn3jiKbz%2FuQzFSq6pKN47sba2rXpJN4JrBc1iQ%3D&reserved=0> -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.cse.buffalo.edu%2F~knepley%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7C01ad28026b614c9c427a08db11270481%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122631541429844%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=I89Ouhn3jiKbz%2FuQzFSq6pKN47sba2rXpJN4JrBc1iQ%3D&reserved=0>
On Feb 17, 2023, at 3:32 PM, Tu, Jiannan <[email protected]> wrote:
The ts_type arkimex is used. There is right hand-side function RHSFunction set by TSSetRHSFunction() and also stiff function set by TSSetIFunction().
With adaptivity shut off, TS can finish its first time step after the 3rd “Nonlinear solve converged due to …”. The solution gives negative electron and neutral temperatures at the bottom boundary. I need to fix the negative temperatures and see how the code works.
BTW, what is this ts_adapt? Is it by default on?
It is default for some of the TSTypes (in particular, the better ones). It adapts the timestep to ensure some local error estimate is below a certain tolerance. As Matt notes normally as it tries smaller and smaller time steps the local error estimate would get smaller and smaller; this is not happening here, hence the error. Have you tried with the argument -ts_arkimex_fully_implicit ? I am not an expert but my guess is something is "odd" about your functions, either the RHSFunction or the Function or both. Do you have a hierarchy of models for your problem? Could you try runs with fewer terms in your functions, that may be producing the difficulties? If you can determine what triggers the problem with the local error estimators, that might help the experts in ODE solution (not me) determine what could be going wrong. Barry
Thank you, Jiannan
From: Matthew Knepley <mailto:[email protected]> Sent: Friday, February 17, 2023 3:15 PM To: Tu, Jiannan <mailto:[email protected]> Cc: Barry Smith <mailto:[email protected]>; petsc-users <mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected
CAUTION: This email was sent from outside the UMass Lowell network.
I am not sure what TS you are using, but the estimate of the local truncation error is 91.4, and does not seem to change when you make the step smaller, so something is off. You can shut off the adaptivity using
-ts_adapt_type none
Thanks,
Matt
On Fri, Feb 17, 2023 at 3:01 PM Tu, Jiannan <[email protected] <mailto:[email protected]>> wrote: These are what I got with the options you suggested.
Thank you, Jiannan
------------------------------------------------------------------------------- 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 2.189e-02 dt=4.374e-03 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-03 dt=4.374e-04 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-04 dt=4.374e-05 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-05 dt=4.374e-06 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-06 dt=4.374e-07 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-07 dt=4.374e-08 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-08 dt=4.374e-09 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-09 dt=4.374e-10 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-10 dt=4.374e-11 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-11 dt=4.374e-12 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-12 dt=4.374e-13 wlte= 91.4 wltea= -1 wlter= -1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/ <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7C22c17ae3c57841a2318a08db1123b692%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122617338217328%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8eFv1wG%2FSeP0lMGNMTKt582ERpT%2FBSE5wKSIecQlPkU%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 14:54:22 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583
From: Barry Smith <mailto:[email protected]> Sent: Friday, February 17, 2023 12:58 PM To: Tu, Jiannan <mailto:[email protected]> Cc: petsc-users <mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected
CAUTION: This email was sent from outside the UMass Lowell network.
Can you please run with also the options -ts_monitor -ts_adapt_monitor ?
The output is confusing because it prints that the Nonlinear solve has converged but then TSStep has failed due to DIVERGED_STEP_REJECTED which seems contradictory
On Feb 17, 2023, at 12:09 PM, Tu, Jiannan <[email protected] <mailto:[email protected]>> wrote:
My code uses TS to solve a set of multi-fluid MHD equations. The jacobian is provided with function F(t, u, u'). Both linear and nonlinear solvers converge but snes repeats itself until gets "TSStep has failed due to diverged_step_rejected."
Is it because I used TSStep rather than TSSolve? I have checked the condition number. The condition number with pc_type asm is about 1 (without precondition it is about 4x10^4). The maximum ratio of off-diagonal jacobian element over diagonal element is about 21.
Could you help me to identify what is going wrong?
Thank you very much!
Jiannan
--------------------------------------------------------------------------------------------------- Run command with options
mpiexec -n $1 ./iditm3d -ts_type arkimex -snes_tyep ngmres -ksp_type gmres -pc_type asm \ -ts_rtol 1.0e-4 -ts_atol 1.0e-4 -snes_monitor -snes_rtol 1.0e-4 -snes_atol 1.0e-4 \ -snes_converged_reason
The output message is
Start time advancing ... 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/ <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7C22c17ae3c57841a2318a08db1123b692%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122617338217328%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8eFv1wG%2FSeP0lMGNMTKt582ERpT%2FBSE5wKSIecQlPkU%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 11:59:43 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583
-- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener
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I need to find out what causes negative temperature first. Following is the message with adaptivity turned off. The G(u) gives right-hand equation for electron temperature at bottom boundary. The F(u, u’) function is F(u, u’) = X = G(u) and the jacobian element is d F(u, u’) / dX =1. The solution from TSStep is checked for positivity of densities and temperatures.
From the message below, it is seen that G(u) > 0 (I added output of right-hand equation for electron temperature). The solution for electron temperature X should be X * jacobian element = G(u) > 0 since jacobian element = 1. I don’t understand why it becomes negative. Is my understanding of TS formula incorrect?
Thank you, Jiannan ---------------------------------- G(u) = 1.86534e-07 0 SNES Function norm 2.274473072183e+03 1 SNES Function norm 8.641749325070e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 G(u) = 1.86534e-07 0 SNES Function norm 8.716501970511e-02 1 SNES Function norm 2.213263548813e-04 2 SNES Function norm 2.779985176426e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 0 SNES Function norm 3.177195995186e-01 1 SNES Function norm 3.607702491344e-04 2 SNES Function norm 4.345809629121e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 TSAdapt none arkimex 0:3 step 0 accepted t=42960 + 2.189e-02 dt=2.189e-02 electron temperature = -3.6757e-15 at (i, j, k) = (0, 1, 0) From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 3:45 PM To: Tu, Jiannan<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Emil Constantinescu<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. On Feb 17, 2023, at 3:32 PM, Tu, Jiannan <[email protected]> wrote: The ts_type arkimex is used. There is right hand-side function RHSFunction set by TSSetRHSFunction() and also stiff function set by TSSetIFunction(). With adaptivity shut off, TS can finish its first time step after the 3rd “Nonlinear solve converged due to …”. The solution gives negative electron and neutral temperatures at the bottom boundary. I need to fix the negative temperatures and see how the code works. BTW, what is this ts_adapt? Is it by default on? It is default for some of the TSTypes (in particular, the better ones). It adapts the timestep to ensure some local error estimate is below a certain tolerance. As Matt notes normally as it tries smaller and smaller time steps the local error estimate would get smaller and smaller; this is not happening here, hence the error. Have you tried with the argument -ts_arkimex_fully_implicit ? I am not an expert but my guess is something is "odd" about your functions, either the RHSFunction or the Function or both. Do you have a hierarchy of models for your problem? Could you try runs with fewer terms in your functions, that may be producing the difficulties? If you can determine what triggers the problem with the local error estimators, that might help the experts in ODE solution (not me) determine what could be going wrong. Barry Thank you, Jiannan From: Matthew Knepley<mailto:[email protected]> Sent: Friday, February 17, 2023 3:15 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. I am not sure what TS you are using, but the estimate of the local truncation error is 91.4, and does not seem to change when you make the step smaller, so something is off. You can shut off the adaptivity using -ts_adapt_type none Thanks, Matt On Fri, Feb 17, 2023 at 3:01 PM Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: These are what I got with the options you suggested. Thank you, Jiannan ------------------------------------------------------------------------------- 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 2.189e-02 dt=4.374e-03 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-03 dt=4.374e-04 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-04 dt=4.374e-05 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-05 dt=4.374e-06 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-06 dt=4.374e-07 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-07 dt=4.374e-08 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-08 dt=4.374e-09 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-09 dt=4.374e-10 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-10 dt=4.374e-11 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-11 dt=4.374e-12 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-12 dt=4.374e-13 wlte= 91.4 wltea= -1 wlter= -1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Cd6de787a4fc942f0159708db1127f6c4%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122635595464947%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=M7B%2FUuBCftN%2BKwfQYhDocIr5WFpJPn%2BHJVjt%2BmRoU3k%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 14:54:22 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 12:58 PM To: Tu, Jiannan<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. Can you please run with also the options -ts_monitor -ts_adapt_monitor ? The output is confusing because it prints that the Nonlinear solve has converged but then TSStep has failed due to DIVERGED_STEP_REJECTED which seems contradictory On Feb 17, 2023, at 12:09 PM, Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: My code uses TS to solve a set of multi-fluid MHD equations. The jacobian is provided with function F(t, u, u'). Both linear and nonlinear solvers converge but snes repeats itself until gets "TSStep has failed due to diverged_step_rejected." Is it because I used TSStep rather than TSSolve? I have checked the condition number. The condition number with pc_type asm is about 1 (without precondition it is about 4x10^4). The maximum ratio of off-diagonal jacobian element over diagonal element is about 21. Could you help me to identify what is going wrong? Thank you very much! Jiannan --------------------------------------------------------------------------------------------------- Run command with options mpiexec -n $1 ./iditm3d -ts_type arkimex -snes_tyep ngmres -ksp_type gmres -pc_type asm \ -ts_rtol 1.0e-4 -ts_atol 1.0e-4 -snes_monitor -snes_rtol 1.0e-4 -snes_atol 1.0e-4 \ -snes_converged_reason The output message is Start time advancing ... 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Cd6de787a4fc942f0159708db1127f6c4%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122635595464947%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=M7B%2FUuBCftN%2BKwfQYhDocIr5WFpJPn%2BHJVjt%2BmRoU3k%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 11:59:43 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.cse.buffalo.edu%2F~knepley%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Cd6de787a4fc942f0159708db1127f6c4%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122635595464947%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=S5hErS8YFvtxln1LR%2FdZxBEqNxonH28eUraClfSrx4Q%3D&reserved=0>
On Feb 17, 2023, at 6:19 PM, Tu, Jiannan <[email protected]> wrote: I need to find out what causes negative temperature first. Following is the message with adaptivity turned off. The G(u) gives right-hand equation for electron temperature at bottom boundary. The F(u, u’) function is F(u, u’) = X = G(u) and the jacobian element is d F(u, u’) / dX =1. This looks strange. Can you elaborate a bit on your partitioned ODE? For example, how are your F(u,udot) (IFunction) and G(u) (RHSFunction) defined? A good IMEX example can be found at ts/tutorial/advection-diffusion-reaction/ex5.c (and reaction_diffusion.c). Hong (Mr.) The solution from TSStep is checked for positivity of densities and temperatures. From the message below, it is seen that G(u) > 0 (I added output of right-hand equation for electron temperature). The solution for electron temperature X should be X * jacobian element = G(u) > 0 since jacobian element = 1. I don’t understand why it becomes negative. Is my understanding of TS formula incorrect? Thank you, Jiannan ---------------------------------- G(u) = 1.86534e-07 0 SNES Function norm 2.274473072183e+03 1 SNES Function norm 8.641749325070e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 G(u) = 1.86534e-07 0 SNES Function norm 8.716501970511e-02 1 SNES Function norm 2.213263548813e-04 2 SNES Function norm 2.779985176426e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 0 SNES Function norm 3.177195995186e-01 1 SNES Function norm 3.607702491344e-04 2 SNES Function norm 4.345809629121e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 TSAdapt none arkimex 0:3 step 0 accepted t=42960 + 2.189e-02 dt=2.189e-02 electron temperature = -3.6757e-15 at (i, j, k) = (0, 1, 0) From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 3:45 PM To: Tu, Jiannan<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Emil Constantinescu<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. On Feb 17, 2023, at 3:32 PM, Tu, Jiannan <[email protected]> wrote: The ts_type arkimex is used. There is right hand-side function RHSFunction set by TSSetRHSFunction() and also stiff function set by TSSetIFunction(). With adaptivity shut off, TS can finish its first time step after the 3rd “Nonlinear solve converged due to …”. The solution gives negative electron and neutral temperatures at the bottom boundary. I need to fix the negative temperatures and see how the code works. BTW, what is this ts_adapt? Is it by default on? It is default for some of the TSTypes (in particular, the better ones). It adapts the timestep to ensure some local error estimate is below a certain tolerance. As Matt notes normally as it tries smaller and smaller time steps the local error estimate would get smaller and smaller; this is not happening here, hence the error. Have you tried with the argument -ts_arkimex_fully_implicit ? I am not an expert but my guess is something is "odd" about your functions, either the RHSFunction or the Function or both. Do you have a hierarchy of models for your problem? Could you try runs with fewer terms in your functions, that may be producing the difficulties? If you can determine what triggers the problem with the local error estimators, that might help the experts in ODE solution (not me) determine what could be going wrong. Barry Thank you, Jiannan From: Matthew Knepley<mailto:[email protected]> Sent: Friday, February 17, 2023 3:15 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. I am not sure what TS you are using, but the estimate of the local truncation error is 91.4, and does not seem to change when you make the step smaller, so something is off. You can shut off the adaptivity using -ts_adapt_type none Thanks, Matt On Fri, Feb 17, 2023 at 3:01 PM Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: These are what I got with the options you suggested. Thank you, Jiannan ------------------------------------------------------------------------------- 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 2.189e-02 dt=4.374e-03 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-03 dt=4.374e-04 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-04 dt=4.374e-05 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-05 dt=4.374e-06 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-06 dt=4.374e-07 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-07 dt=4.374e-08 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-08 dt=4.374e-09 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-09 dt=4.374e-10 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-10 dt=4.374e-11 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-11 dt=4.374e-12 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-12 dt=4.374e-13 wlte= 91.4 wltea= -1 wlter= -1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Cd6de787a4fc942f0159708db1127f6c4%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122635595464947%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=M7B%2FUuBCftN%2BKwfQYhDocIr5WFpJPn%2BHJVjt%2BmRoU3k%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 14:54:22 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 12:58 PM To: Tu, Jiannan<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. Can you please run with also the options -ts_monitor -ts_adapt_monitor ? The output is confusing because it prints that the Nonlinear solve has converged but then TSStep has failed due to DIVERGED_STEP_REJECTED which seems contradictory On Feb 17, 2023, at 12:09 PM, Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: My code uses TS to solve a set of multi-fluid MHD equations. The jacobian is provided with function F(t, u, u'). Both linear and nonlinear solvers converge but snes repeats itself until gets "TSStep has failed due to diverged_step_rejected." Is it because I used TSStep rather than TSSolve? I have checked the condition number. The condition number with pc_type asm is about 1 (without precondition it is about 4x10^4). The maximum ratio of off-diagonal jacobian element over diagonal element is about 21. Could you help me to identify what is going wrong? Thank you very much! Jiannan --------------------------------------------------------------------------------------------------- Run command with options mpiexec -n $1 ./iditm3d -ts_type arkimex -snes_tyep ngmres -ksp_type gmres -pc_type asm \ -ts_rtol 1.0e-4 -ts_atol 1.0e-4 -snes_monitor -snes_rtol 1.0e-4 -snes_atol 1.0e-4 \ -snes_converged_reason The output message is Start time advancing ... 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Cd6de787a4fc942f0159708db1127f6c4%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122635595464947%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=M7B%2FUuBCftN%2BKwfQYhDocIr5WFpJPn%2BHJVjt%2BmRoU3k%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 11:59:43 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.cse.buffalo.edu%2F~knepley%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Cd6de787a4fc942f0159708db1127f6c4%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122635595464947%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=S5hErS8YFvtxln1LR%2FdZxBEqNxonH28eUraClfSrx4Q%3D&reserved=0>
The RHS function at the bottom boundary is determined by the boundary condition, which is the second order derivative = 0, i.e. G(u) = 2*X[i=1] – X[i=2]. Then in IFunction, F(u, udot) = X[i=0]. Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Friday, February 17, 2023 11:54 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected You don't often get email from [email protected]. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> CAUTION: This email was sent from outside the UMass Lowell network. On Feb 17, 2023, at 6:19 PM, Tu, Jiannan <[email protected]> wrote: I need to find out what causes negative temperature first. Following is the message with adaptivity turned off. The G(u) gives right-hand equation for electron temperature at bottom boundary. The F(u, u’) function is F(u, u’) = X = G(u) and the jacobian element is d F(u, u’) / dX =1. This looks strange. Can you elaborate a bit on your partitioned ODE? For example, how are your F(u,udot) (IFunction) and G(u) (RHSFunction) defined? A good IMEX example can be found at ts/tutorial/advection-diffusion-reaction/ex5.c (and reaction_diffusion.c). Hong (Mr.) The solution from TSStep is checked for positivity of densities and temperatures.
From the message below, it is seen that G(u) > 0 (I added output of right-hand equation for electron temperature). The solution for electron temperature X should be X * jacobian element = G(u) > 0 since jacobian element = 1. I don’t understand why it becomes negative. Is my understanding of TS formula incorrect?
Thank you, Jiannan ---------------------------------- G(u) = 1.86534e-07 0 SNES Function norm 2.274473072183e+03 1 SNES Function norm 8.641749325070e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 G(u) = 1.86534e-07 0 SNES Function norm 8.716501970511e-02 1 SNES Function norm 2.213263548813e-04 2 SNES Function norm 2.779985176426e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 0 SNES Function norm 3.177195995186e-01 1 SNES Function norm 3.607702491344e-04 2 SNES Function norm 4.345809629121e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 TSAdapt none arkimex 0:3 step 0 accepted t=42960 + 2.189e-02 dt=2.189e-02 electron temperature = -3.6757e-15 at (i, j, k) = (0, 1, 0) From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 3:45 PM To: Tu, Jiannan<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Emil Constantinescu<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. On Feb 17, 2023, at 3:32 PM, Tu, Jiannan <[email protected]> wrote: The ts_type arkimex is used. There is right hand-side function RHSFunction set by TSSetRHSFunction() and also stiff function set by TSSetIFunction(). With adaptivity shut off, TS can finish its first time step after the 3rd “Nonlinear solve converged due to …”. The solution gives negative electron and neutral temperatures at the bottom boundary. I need to fix the negative temperatures and see how the code works. BTW, what is this ts_adapt? Is it by default on? It is default for some of the TSTypes (in particular, the better ones). It adapts the timestep to ensure some local error estimate is below a certain tolerance. As Matt notes normally as it tries smaller and smaller time steps the local error estimate would get smaller and smaller; this is not happening here, hence the error. Have you tried with the argument -ts_arkimex_fully_implicit ? I am not an expert but my guess is something is "odd" about your functions, either the RHSFunction or the Function or both. Do you have a hierarchy of models for your problem? Could you try runs with fewer terms in your functions, that may be producing the difficulties? If you can determine what triggers the problem with the local error estimators, that might help the experts in ODE solution (not me) determine what could be going wrong. Barry Thank you, Jiannan From: Matthew Knepley<mailto:[email protected]> Sent: Friday, February 17, 2023 3:15 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. I am not sure what TS you are using, but the estimate of the local truncation error is 91.4, and does not seem to change when you make the step smaller, so something is off. You can shut off the adaptivity using -ts_adapt_type none Thanks, Matt On Fri, Feb 17, 2023 at 3:01 PM Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: These are what I got with the options you suggested. Thank you, Jiannan ------------------------------------------------------------------------------- 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 2.189e-02 dt=4.374e-03 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-03 dt=4.374e-04 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-04 dt=4.374e-05 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-05 dt=4.374e-06 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-06 dt=4.374e-07 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-07 dt=4.374e-08 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-08 dt=4.374e-09 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-09 dt=4.374e-10 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-10 dt=4.374e-11 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-11 dt=4.374e-12 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-12 dt=4.374e-13 wlte= 91.4 wltea= -1 wlter= -1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Cd30dea44e9f14a4b2a8508db116c42d2%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122928922283739%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=RpYfp48Sy5%2BJjChLqv0sNo9pcs3zwcWhWcJoPr3xiZQ%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 14:54:22 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 12:58 PM To: Tu, Jiannan<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. Can you please run with also the options -ts_monitor -ts_adapt_monitor ? The output is confusing because it prints that the Nonlinear solve has converged but then TSStep has failed due to DIVERGED_STEP_REJECTED which seems contradictory On Feb 17, 2023, at 12:09 PM, Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: My code uses TS to solve a set of multi-fluid MHD equations. The jacobian is provided with function F(t, u, u'). Both linear and nonlinear solvers converge but snes repeats itself until gets "TSStep has failed due to diverged_step_rejected." Is it because I used TSStep rather than TSSolve? I have checked the condition number. The condition number with pc_type asm is about 1 (without precondition it is about 4x10^4). The maximum ratio of off-diagonal jacobian element over diagonal element is about 21. Could you help me to identify what is going wrong? Thank you very much! Jiannan --------------------------------------------------------------------------------------------------- Run command with options mpiexec -n $1 ./iditm3d -ts_type arkimex -snes_tyep ngmres -ksp_type gmres -pc_type asm \ -ts_rtol 1.0e-4 -ts_atol 1.0e-4 -snes_monitor -snes_rtol 1.0e-4 -snes_atol 1.0e-4 \ -snes_converged_reason The output message is Start time advancing ... 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Cd30dea44e9f14a4b2a8508db116c42d2%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122928922283739%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=RpYfp48Sy5%2BJjChLqv0sNo9pcs3zwcWhWcJoPr3xiZQ%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 11:59:43 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.cse.buffalo.edu%2F~knepley%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Cd30dea44e9f14a4b2a8508db116c42d2%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122928922283739%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=lh%2Fjd1XAOe5JnmmY5adNKx3t7apOL%2ByGA6HcVeI2CAU%3D&reserved=0>
On Feb 18, 2023, at 8:44 AM, Tu, Jiannan <[email protected]> wrote: The RHS function at the bottom boundary is determined by the boundary condition, which is the second order derivative = 0, i.e. G(u) = 2*X[i=1] – X[i=2]. Then in IFunction, F(u, udot) = X[i=0]. This might be the problem. Your F(u, udot) is missing udot according to your description. Take a simple ODE udot = f(u) + g(u) for example. One way to partition this ODE is to define F = udot - f(u) as the IFunction and G = g(u) as the RHSFunction. Hong (Mr.) Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Friday, February 17, 2023 11:54 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected You don't often get email from [email protected]<mailto:[email protected]>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> CAUTION: This email was sent from outside the UMass Lowell network. On Feb 17, 2023, at 6:19 PM, Tu, Jiannan <[email protected]> wrote: I need to find out what causes negative temperature first. Following is the message with adaptivity turned off. The G(u) gives right-hand equation for electron temperature at bottom boundary. The F(u, u’) function is F(u, u’) = X = G(u) and the jacobian element is d F(u, u’) / dX =1. This looks strange. Can you elaborate a bit on your partitioned ODE? For example, how are your F(u,udot) (IFunction) and G(u) (RHSFunction) defined? A good IMEX example can be found at ts/tutorial/advection-diffusion-reaction/ex5.c (and reaction_diffusion.c). Hong (Mr.) The solution from TSStep is checked for positivity of densities and temperatures. From the message below, it is seen that G(u) > 0 (I added output of right-hand equation for electron temperature). The solution for electron temperature X should be X * jacobian element = G(u) > 0 since jacobian element = 1. I don’t understand why it becomes negative. Is my understanding of TS formula incorrect? Thank you, Jiannan ---------------------------------- G(u) = 1.86534e-07 0 SNES Function norm 2.274473072183e+03 1 SNES Function norm 8.641749325070e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 G(u) = 1.86534e-07 0 SNES Function norm 8.716501970511e-02 1 SNES Function norm 2.213263548813e-04 2 SNES Function norm 2.779985176426e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 0 SNES Function norm 3.177195995186e-01 1 SNES Function norm 3.607702491344e-04 2 SNES Function norm 4.345809629121e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 TSAdapt none arkimex 0:3 step 0 accepted t=42960 + 2.189e-02 dt=2.189e-02 electron temperature = -3.6757e-15 at (i, j, k) = (0, 1, 0) From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 3:45 PM To: Tu, Jiannan<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Emil Constantinescu<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. On Feb 17, 2023, at 3:32 PM, Tu, Jiannan <[email protected]> wrote: The ts_type arkimex is used. There is right hand-side function RHSFunction set by TSSetRHSFunction() and also stiff function set by TSSetIFunction(). With adaptivity shut off, TS can finish its first time step after the 3rd “Nonlinear solve converged due to …”. The solution gives negative electron and neutral temperatures at the bottom boundary. I need to fix the negative temperatures and see how the code works. BTW, what is this ts_adapt? Is it by default on? It is default for some of the TSTypes (in particular, the better ones). It adapts the timestep to ensure some local error estimate is below a certain tolerance. As Matt notes normally as it tries smaller and smaller time steps the local error estimate would get smaller and smaller; this is not happening here, hence the error. Have you tried with the argument -ts_arkimex_fully_implicit ? I am not an expert but my guess is something is "odd" about your functions, either the RHSFunction or the Function or both. Do you have a hierarchy of models for your problem? Could you try runs with fewer terms in your functions, that may be producing the difficulties? If you can determine what triggers the problem with the local error estimators, that might help the experts in ODE solution (not me) determine what could be going wrong. Barry Thank you, Jiannan From: Matthew Knepley<mailto:[email protected]> Sent: Friday, February 17, 2023 3:15 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. I am not sure what TS you are using, but the estimate of the local truncation error is 91.4, and does not seem to change when you make the step smaller, so something is off. You can shut off the adaptivity using -ts_adapt_type none Thanks, Matt On Fri, Feb 17, 2023 at 3:01 PM Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: These are what I got with the options you suggested. Thank you, Jiannan ------------------------------------------------------------------------------- 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 2.189e-02 dt=4.374e-03 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-03 dt=4.374e-04 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-04 dt=4.374e-05 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-05 dt=4.374e-06 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-06 dt=4.374e-07 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-07 dt=4.374e-08 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-08 dt=4.374e-09 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-09 dt=4.374e-10 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-10 dt=4.374e-11 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-11 dt=4.374e-12 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-12 dt=4.374e-13 wlte= 91.4 wltea= -1 wlter= -1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Cd30dea44e9f14a4b2a8508db116c42d2%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122928922283739%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=RpYfp48Sy5%2BJjChLqv0sNo9pcs3zwcWhWcJoPr3xiZQ%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 14:54:22 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 12:58 PM To: Tu, Jiannan<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. Can you please run with also the options -ts_monitor -ts_adapt_monitor ? The output is confusing because it prints that the Nonlinear solve has converged but then TSStep has failed due to DIVERGED_STEP_REJECTED which seems contradictory On Feb 17, 2023, at 12:09 PM, Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: My code uses TS to solve a set of multi-fluid MHD equations. The jacobian is provided with function F(t, u, u'). Both linear and nonlinear solvers converge but snes repeats itself until gets "TSStep has failed due to diverged_step_rejected." Is it because I used TSStep rather than TSSolve? I have checked the condition number. The condition number with pc_type asm is about 1 (without precondition it is about 4x10^4). The maximum ratio of off-diagonal jacobian element over diagonal element is about 21. Could you help me to identify what is going wrong? Thank you very much! Jiannan --------------------------------------------------------------------------------------------------- Run command with options mpiexec -n $1 ./iditm3d -ts_type arkimex -snes_tyep ngmres -ksp_type gmres -pc_type asm \ -ts_rtol 1.0e-4 -ts_atol 1.0e-4 -snes_monitor -snes_rtol 1.0e-4 -snes_atol 1.0e-4 \ -snes_converged_reason The output message is Start time advancing ... 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Cd30dea44e9f14a4b2a8508db116c42d2%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122928922283739%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=RpYfp48Sy5%2BJjChLqv0sNo9pcs3zwcWhWcJoPr3xiZQ%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 11:59:43 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.cse.buffalo.edu%2F~knepley%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Cd30dea44e9f14a4b2a8508db116c42d2%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638122928922283739%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=lh%2Fjd1XAOe5JnmmY5adNKx3t7apOL%2ByGA6HcVeI2CAU%3D&reserved=0>
Thanks for the instruction. This is the boundary condition and there is no udot in the equation. I think this is the way to define IFunction at the boundary. Maybe I’m wrong? Or is there some way to introduce udot into the specification of the equation at the boundary from the aspect of the implementation for TS? Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Saturday, February 18, 2023 12:40 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected You don't often get email from [email protected]. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> CAUTION: This email was sent from outside the UMass Lowell network. On Feb 18, 2023, at 8:44 AM, Tu, Jiannan <[email protected]> wrote: The RHS function at the bottom boundary is determined by the boundary condition, which is the second order derivative = 0, i.e. G(u) = 2*X[i=1] – X[i=2]. Then in IFunction, F(u, udot) = X[i=0]. This might be the problem. Your F(u, udot) is missing udot according to your description. Take a simple ODE udot = f(u) + g(u) for example. One way to partition this ODE is to define F = udot - f(u) as the IFunction and G = g(u) as the RHSFunction. Hong (Mr.) Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Friday, February 17, 2023 11:54 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected You don't often get email from [email protected]<mailto:[email protected]>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> CAUTION: This email was sent from outside the UMass Lowell network. On Feb 17, 2023, at 6:19 PM, Tu, Jiannan <[email protected]> wrote: I need to find out what causes negative temperature first. Following is the message with adaptivity turned off. The G(u) gives right-hand equation for electron temperature at bottom boundary. The F(u, u’) function is F(u, u’) = X = G(u) and the jacobian element is d F(u, u’) / dX =1. This looks strange. Can you elaborate a bit on your partitioned ODE? For example, how are your F(u,udot) (IFunction) and G(u) (RHSFunction) defined? A good IMEX example can be found at ts/tutorial/advection-diffusion-reaction/ex5.c (and reaction_diffusion.c). Hong (Mr.) The solution from TSStep is checked for positivity of densities and temperatures.
From the message below, it is seen that G(u) > 0 (I added output of right-hand equation for electron temperature). The solution for electron temperature X should be X * jacobian element = G(u) > 0 since jacobian element = 1. I don’t understand why it becomes negative. Is my understanding of TS formula incorrect?
Thank you, Jiannan ---------------------------------- G(u) = 1.86534e-07 0 SNES Function norm 2.274473072183e+03 1 SNES Function norm 8.641749325070e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 G(u) = 1.86534e-07 0 SNES Function norm 8.716501970511e-02 1 SNES Function norm 2.213263548813e-04 2 SNES Function norm 2.779985176426e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 0 SNES Function norm 3.177195995186e-01 1 SNES Function norm 3.607702491344e-04 2 SNES Function norm 4.345809629121e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 TSAdapt none arkimex 0:3 step 0 accepted t=42960 + 2.189e-02 dt=2.189e-02 electron temperature = -3.6757e-15 at (i, j, k) = (0, 1, 0) From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 3:45 PM To: Tu, Jiannan<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Emil Constantinescu<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. On Feb 17, 2023, at 3:32 PM, Tu, Jiannan <[email protected]> wrote: The ts_type arkimex is used. There is right hand-side function RHSFunction set by TSSetRHSFunction() and also stiff function set by TSSetIFunction(). With adaptivity shut off, TS can finish its first time step after the 3rd “Nonlinear solve converged due to …”. The solution gives negative electron and neutral temperatures at the bottom boundary. I need to fix the negative temperatures and see how the code works. BTW, what is this ts_adapt? Is it by default on? It is default for some of the TSTypes (in particular, the better ones). It adapts the timestep to ensure some local error estimate is below a certain tolerance. As Matt notes normally as it tries smaller and smaller time steps the local error estimate would get smaller and smaller; this is not happening here, hence the error. Have you tried with the argument -ts_arkimex_fully_implicit ? I am not an expert but my guess is something is "odd" about your functions, either the RHSFunction or the Function or both. Do you have a hierarchy of models for your problem? Could you try runs with fewer terms in your functions, that may be producing the difficulties? If you can determine what triggers the problem with the local error estimators, that might help the experts in ODE solution (not me) determine what could be going wrong. Barry Thank you, Jiannan From: Matthew Knepley<mailto:[email protected]> Sent: Friday, February 17, 2023 3:15 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. I am not sure what TS you are using, but the estimate of the local truncation error is 91.4, and does not seem to change when you make the step smaller, so something is off. You can shut off the adaptivity using -ts_adapt_type none Thanks, Matt On Fri, Feb 17, 2023 at 3:01 PM Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: These are what I got with the options you suggested. Thank you, Jiannan ------------------------------------------------------------------------------- 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 2.189e-02 dt=4.374e-03 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-03 dt=4.374e-04 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-04 dt=4.374e-05 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-05 dt=4.374e-06 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-06 dt=4.374e-07 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-07 dt=4.374e-08 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-08 dt=4.374e-09 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-09 dt=4.374e-10 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-10 dt=4.374e-11 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-11 dt=4.374e-12 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-12 dt=4.374e-13 wlte= 91.4 wltea= -1 wlter= -1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7C683af8c0511e4499d31308db11d72edb%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638123388160203530%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=WX7OoIK9oSACKQMSj95fkJ8VilF3QvPVRNw30kyZwB0%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 14:54:22 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 12:58 PM To: Tu, Jiannan<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. Can you please run with also the options -ts_monitor -ts_adapt_monitor ? The output is confusing because it prints that the Nonlinear solve has converged but then TSStep has failed due to DIVERGED_STEP_REJECTED which seems contradictory On Feb 17, 2023, at 12:09 PM, Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: My code uses TS to solve a set of multi-fluid MHD equations. The jacobian is provided with function F(t, u, u'). Both linear and nonlinear solvers converge but snes repeats itself until gets "TSStep has failed due to diverged_step_rejected." Is it because I used TSStep rather than TSSolve? I have checked the condition number. The condition number with pc_type asm is about 1 (without precondition it is about 4x10^4). The maximum ratio of off-diagonal jacobian element over diagonal element is about 21. Could you help me to identify what is going wrong? Thank you very much! Jiannan --------------------------------------------------------------------------------------------------- Run command with options mpiexec -n $1 ./iditm3d -ts_type arkimex -snes_tyep ngmres -ksp_type gmres -pc_type asm \ -ts_rtol 1.0e-4 -ts_atol 1.0e-4 -snes_monitor -snes_rtol 1.0e-4 -snes_atol 1.0e-4 \ -snes_converged_reason The output message is Start time advancing ... 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7C683af8c0511e4499d31308db11d72edb%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638123388160203530%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=WX7OoIK9oSACKQMSj95fkJ8VilF3QvPVRNw30kyZwB0%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 11:59:43 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.cse.buffalo.edu%2F~knepley%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7C683af8c0511e4499d31308db11d72edb%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638123388160203530%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=RwNvX0Wqg7tkKs%2BIYG1svHVyEgXae1JAbwouhjZdLrE%3D&reserved=0>
It is fine to drop udot for the boundary points, but you need to keep udot for all the other points. In addition, which boundary condition do you use in IFunction? The way you are treating the boundary points actually leads to a system of differential-algebraic equations, which could be difficult to solve with the ARKIMEX solver. Can you try to exclude the boundary points from the computational domain so that you will have just a system of ODEs? Hong (Mr.) On Feb 18, 2023, at 4:28 PM, Tu, Jiannan <[email protected]> wrote: Thanks for the instruction. This is the boundary condition and there is no udot in the equation. I think this is the way to define IFunction at the boundary. Maybe I’m wrong? Or is there some way to introduce udot into the specification of the equation at the boundary from the aspect of the implementation for TS? Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Saturday, February 18, 2023 12:40 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected You don't often get email from [email protected]<mailto:[email protected]>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> CAUTION: This email was sent from outside the UMass Lowell network. On Feb 18, 2023, at 8:44 AM, Tu, Jiannan <[email protected]> wrote: The RHS function at the bottom boundary is determined by the boundary condition, which is the second order derivative = 0, i.e. G(u) = 2*X[i=1] – X[i=2]. Then in IFunction, F(u, udot) = X[i=0]. This might be the problem. Your F(u, udot) is missing udot according to your description. Take a simple ODE udot = f(u) + g(u) for example. One way to partition this ODE is to define F = udot - f(u) as the IFunction and G = g(u) as the RHSFunction. Hong (Mr.) Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Friday, February 17, 2023 11:54 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected You don't often get email from [email protected]<mailto:[email protected]>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> CAUTION: This email was sent from outside the UMass Lowell network. On Feb 17, 2023, at 6:19 PM, Tu, Jiannan <[email protected]> wrote: I need to find out what causes negative temperature first. Following is the message with adaptivity turned off. The G(u) gives right-hand equation for electron temperature at bottom boundary. The F(u, u’) function is F(u, u’) = X = G(u) and the jacobian element is d F(u, u’) / dX =1. This looks strange. Can you elaborate a bit on your partitioned ODE? For example, how are your F(u,udot) (IFunction) and G(u) (RHSFunction) defined? A good IMEX example can be found at ts/tutorial/advection-diffusion-reaction/ex5.c (and reaction_diffusion.c). Hong (Mr.) The solution from TSStep is checked for positivity of densities and temperatures. From the message below, it is seen that G(u) > 0 (I added output of right-hand equation for electron temperature). The solution for electron temperature X should be X * jacobian element = G(u) > 0 since jacobian element = 1. I don’t understand why it becomes negative. Is my understanding of TS formula incorrect? Thank you, Jiannan ---------------------------------- G(u) = 1.86534e-07 0 SNES Function norm 2.274473072183e+03 1 SNES Function norm 8.641749325070e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 G(u) = 1.86534e-07 0 SNES Function norm 8.716501970511e-02 1 SNES Function norm 2.213263548813e-04 2 SNES Function norm 2.779985176426e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 0 SNES Function norm 3.177195995186e-01 1 SNES Function norm 3.607702491344e-04 2 SNES Function norm 4.345809629121e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 TSAdapt none arkimex 0:3 step 0 accepted t=42960 + 2.189e-02 dt=2.189e-02 electron temperature = -3.6757e-15 at (i, j, k) = (0, 1, 0) From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 3:45 PM To: Tu, Jiannan<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Emil Constantinescu<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. On Feb 17, 2023, at 3:32 PM, Tu, Jiannan <[email protected]> wrote: The ts_type arkimex is used. There is right hand-side function RHSFunction set by TSSetRHSFunction() and also stiff function set by TSSetIFunction(). With adaptivity shut off, TS can finish its first time step after the 3rd “Nonlinear solve converged due to …”. The solution gives negative electron and neutral temperatures at the bottom boundary. I need to fix the negative temperatures and see how the code works. BTW, what is this ts_adapt? Is it by default on? It is default for some of the TSTypes (in particular, the better ones). It adapts the timestep to ensure some local error estimate is below a certain tolerance. As Matt notes normally as it tries smaller and smaller time steps the local error estimate would get smaller and smaller; this is not happening here, hence the error. Have you tried with the argument -ts_arkimex_fully_implicit ? I am not an expert but my guess is something is "odd" about your functions, either the RHSFunction or the Function or both. Do you have a hierarchy of models for your problem? Could you try runs with fewer terms in your functions, that may be producing the difficulties? If you can determine what triggers the problem with the local error estimators, that might help the experts in ODE solution (not me) determine what could be going wrong. Barry Thank you, Jiannan From: Matthew Knepley<mailto:[email protected]> Sent: Friday, February 17, 2023 3:15 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. I am not sure what TS you are using, but the estimate of the local truncation error is 91.4, and does not seem to change when you make the step smaller, so something is off. You can shut off the adaptivity using -ts_adapt_type none Thanks, Matt On Fri, Feb 17, 2023 at 3:01 PM Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: These are what I got with the options you suggested. Thank you, Jiannan ------------------------------------------------------------------------------- 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 2.189e-02 dt=4.374e-03 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-03 dt=4.374e-04 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-04 dt=4.374e-05 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-05 dt=4.374e-06 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-06 dt=4.374e-07 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-07 dt=4.374e-08 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-08 dt=4.374e-09 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-09 dt=4.374e-10 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-10 dt=4.374e-11 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-11 dt=4.374e-12 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-12 dt=4.374e-13 wlte= 91.4 wltea= -1 wlter= -1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7C683af8c0511e4499d31308db11d72edb%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638123388160203530%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=WX7OoIK9oSACKQMSj95fkJ8VilF3QvPVRNw30kyZwB0%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 14:54:22 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 12:58 PM To: Tu, Jiannan<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. Can you please run with also the options -ts_monitor -ts_adapt_monitor ? The output is confusing because it prints that the Nonlinear solve has converged but then TSStep has failed due to DIVERGED_STEP_REJECTED which seems contradictory On Feb 17, 2023, at 12:09 PM, Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: My code uses TS to solve a set of multi-fluid MHD equations. The jacobian is provided with function F(t, u, u'). Both linear and nonlinear solvers converge but snes repeats itself until gets "TSStep has failed due to diverged_step_rejected." Is it because I used TSStep rather than TSSolve? I have checked the condition number. The condition number with pc_type asm is about 1 (without precondition it is about 4x10^4). The maximum ratio of off-diagonal jacobian element over diagonal element is about 21. Could you help me to identify what is going wrong? Thank you very much! Jiannan --------------------------------------------------------------------------------------------------- Run command with options mpiexec -n $1 ./iditm3d -ts_type arkimex -snes_tyep ngmres -ksp_type gmres -pc_type asm \ -ts_rtol 1.0e-4 -ts_atol 1.0e-4 -snes_monitor -snes_rtol 1.0e-4 -snes_atol 1.0e-4 \ -snes_converged_reason The output message is Start time advancing ... 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7C683af8c0511e4499d31308db11d72edb%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638123388160203530%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=WX7OoIK9oSACKQMSj95fkJ8VilF3QvPVRNw30kyZwB0%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 11:59:43 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.cse.buffalo.edu%2F~knepley%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7C683af8c0511e4499d31308db11d72edb%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638123388160203530%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=RwNvX0Wqg7tkKs%2BIYG1svHVyEgXae1JAbwouhjZdLrE%3D&reserved=0>
It is the second order derivative of, say electron temperature = 0 at the boundary. I am not sure how I can exclude the boundary points because the values of unknowns must be specified at the boundary. Are there any other solvers, e.g., CN, good to solve the equation system? Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Sunday, February 19, 2023 4:48 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. It is fine to drop udot for the boundary points, but you need to keep udot for all the other points. In addition, which boundary condition do you use in IFunction? The way you are treating the boundary points actually leads to a system of differential-algebraic equations, which could be difficult to solve with the ARKIMEX solver. Can you try to exclude the boundary points from the computational domain so that you will have just a system of ODEs? Hong (Mr.) On Feb 18, 2023, at 4:28 PM, Tu, Jiannan <[email protected]> wrote: Thanks for the instruction. This is the boundary condition and there is no udot in the equation. I think this is the way to define IFunction at the boundary. Maybe I’m wrong? Or is there some way to introduce udot into the specification of the equation at the boundary from the aspect of the implementation for TS? Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Saturday, February 18, 2023 12:40 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected You don't often get email from [email protected]<mailto:[email protected]>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> CAUTION: This email was sent from outside the UMass Lowell network. On Feb 18, 2023, at 8:44 AM, Tu, Jiannan <[email protected]> wrote: The RHS function at the bottom boundary is determined by the boundary condition, which is the second order derivative = 0, i.e. G(u) = 2*X[i=1] – X[i=2]. Then in IFunction, F(u, udot) = X[i=0]. This might be the problem. Your F(u, udot) is missing udot according to your description. Take a simple ODE udot = f(u) + g(u) for example. One way to partition this ODE is to define F = udot - f(u) as the IFunction and G = g(u) as the RHSFunction. Hong (Mr.) Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Friday, February 17, 2023 11:54 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected You don't often get email from [email protected]<mailto:[email protected]>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> CAUTION: This email was sent from outside the UMass Lowell network. On Feb 17, 2023, at 6:19 PM, Tu, Jiannan <[email protected]> wrote: I need to find out what causes negative temperature first. Following is the message with adaptivity turned off. The G(u) gives right-hand equation for electron temperature at bottom boundary. The F(u, u’) function is F(u, u’) = X = G(u) and the jacobian element is d F(u, u’) / dX =1. This looks strange. Can you elaborate a bit on your partitioned ODE? For example, how are your F(u,udot) (IFunction) and G(u) (RHSFunction) defined? A good IMEX example can be found at ts/tutorial/advection-diffusion-reaction/ex5.c (and reaction_diffusion.c). Hong (Mr.) The solution from TSStep is checked for positivity of densities and temperatures.
From the message below, it is seen that G(u) > 0 (I added output of right-hand equation for electron temperature). The solution for electron temperature X should be X * jacobian element = G(u) > 0 since jacobian element = 1. I don’t understand why it becomes negative. Is my understanding of TS formula incorrect?
Thank you, Jiannan ---------------------------------- G(u) = 1.86534e-07 0 SNES Function norm 2.274473072183e+03 1 SNES Function norm 8.641749325070e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 G(u) = 1.86534e-07 0 SNES Function norm 8.716501970511e-02 1 SNES Function norm 2.213263548813e-04 2 SNES Function norm 2.779985176426e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 0 SNES Function norm 3.177195995186e-01 1 SNES Function norm 3.607702491344e-04 2 SNES Function norm 4.345809629121e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 TSAdapt none arkimex 0:3 step 0 accepted t=42960 + 2.189e-02 dt=2.189e-02 electron temperature = -3.6757e-15 at (i, j, k) = (0, 1, 0) From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 3:45 PM To: Tu, Jiannan<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Emil Constantinescu<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. On Feb 17, 2023, at 3:32 PM, Tu, Jiannan <[email protected]> wrote: The ts_type arkimex is used. There is right hand-side function RHSFunction set by TSSetRHSFunction() and also stiff function set by TSSetIFunction(). With adaptivity shut off, TS can finish its first time step after the 3rd “Nonlinear solve converged due to …”. The solution gives negative electron and neutral temperatures at the bottom boundary. I need to fix the negative temperatures and see how the code works. BTW, what is this ts_adapt? Is it by default on? It is default for some of the TSTypes (in particular, the better ones). It adapts the timestep to ensure some local error estimate is below a certain tolerance. As Matt notes normally as it tries smaller and smaller time steps the local error estimate would get smaller and smaller; this is not happening here, hence the error. Have you tried with the argument -ts_arkimex_fully_implicit ? I am not an expert but my guess is something is "odd" about your functions, either the RHSFunction or the Function or both. Do you have a hierarchy of models for your problem? Could you try runs with fewer terms in your functions, that may be producing the difficulties? If you can determine what triggers the problem with the local error estimators, that might help the experts in ODE solution (not me) determine what could be going wrong. Barry Thank you, Jiannan From: Matthew Knepley<mailto:[email protected]> Sent: Friday, February 17, 2023 3:15 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. I am not sure what TS you are using, but the estimate of the local truncation error is 91.4, and does not seem to change when you make the step smaller, so something is off. You can shut off the adaptivity using -ts_adapt_type none Thanks, Matt On Fri, Feb 17, 2023 at 3:01 PM Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: These are what I got with the options you suggested. Thank you, Jiannan ------------------------------------------------------------------------------- 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 2.189e-02 dt=4.374e-03 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-03 dt=4.374e-04 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-04 dt=4.374e-05 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-05 dt=4.374e-06 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-06 dt=4.374e-07 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-07 dt=4.374e-08 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-08 dt=4.374e-09 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-09 dt=4.374e-10 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-10 dt=4.374e-11 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-11 dt=4.374e-12 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-12 dt=4.374e-13 wlte= 91.4 wltea= -1 wlter= -1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Cfd42b18d0d094df8fc7508db12c30720%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638124401123944894%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=pU5RPkMt3KWGce%2BBxVx81YqWg4BJWUmyaReHk6IzHMo%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 14:54:22 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 12:58 PM To: Tu, Jiannan<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. Can you please run with also the options -ts_monitor -ts_adapt_monitor ? The output is confusing because it prints that the Nonlinear solve has converged but then TSStep has failed due to DIVERGED_STEP_REJECTED which seems contradictory On Feb 17, 2023, at 12:09 PM, Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: My code uses TS to solve a set of multi-fluid MHD equations. The jacobian is provided with function F(t, u, u'). Both linear and nonlinear solvers converge but snes repeats itself until gets "TSStep has failed due to diverged_step_rejected." Is it because I used TSStep rather than TSSolve? I have checked the condition number. The condition number with pc_type asm is about 1 (without precondition it is about 4x10^4). The maximum ratio of off-diagonal jacobian element over diagonal element is about 21. Could you help me to identify what is going wrong? Thank you very much! Jiannan --------------------------------------------------------------------------------------------------- Run command with options mpiexec -n $1 ./iditm3d -ts_type arkimex -snes_tyep ngmres -ksp_type gmres -pc_type asm \ -ts_rtol 1.0e-4 -ts_atol 1.0e-4 -snes_monitor -snes_rtol 1.0e-4 -snes_atol 1.0e-4 \ -snes_converged_reason The output message is Start time advancing ... 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Cfd42b18d0d094df8fc7508db12c30720%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638124401123944894%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=pU5RPkMt3KWGce%2BBxVx81YqWg4BJWUmyaReHk6IzHMo%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 11:59:43 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.cse.buffalo.edu%2F~knepley%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Cfd42b18d0d094df8fc7508db12c30720%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638124401123944894%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=wdJRbHevYI7gENtlvxd8T5KcO%2BOuE%2FC1jhQG2SibXQ4%3D&reserved=0>
If you have to include the boundary points, I would suggest starting from a fully implicit solver such as CN or BEuler with a finite-difference approximated Jacobian. When this works for a small scale setting, you can build up more functionalities such as IMEX and analytical Jacobians and extend the problem to a larger scale. But the udot issue needs to be fixed in the first place. Hong (Mr.) On Feb 19, 2023, at 9:23 PM, Tu, Jiannan <[email protected]> wrote: It is the second order derivative of, say electron temperature = 0 at the boundary. I am not sure how I can exclude the boundary points because the values of unknowns must be specified at the boundary. Are there any other solvers, e.g., CN, good to solve the equation system? Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Sunday, February 19, 2023 4:48 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. It is fine to drop udot for the boundary points, but you need to keep udot for all the other points. In addition, which boundary condition do you use in IFunction? The way you are treating the boundary points actually leads to a system of differential-algebraic equations, which could be difficult to solve with the ARKIMEX solver. Can you try to exclude the boundary points from the computational domain so that you will have just a system of ODEs? Hong (Mr.) On Feb 18, 2023, at 4:28 PM, Tu, Jiannan <[email protected]> wrote: Thanks for the instruction. This is the boundary condition and there is no udot in the equation. I think this is the way to define IFunction at the boundary. Maybe I’m wrong? Or is there some way to introduce udot into the specification of the equation at the boundary from the aspect of the implementation for TS? Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Saturday, February 18, 2023 12:40 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected You don't often get email from [email protected]<mailto:[email protected]>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> CAUTION: This email was sent from outside the UMass Lowell network. On Feb 18, 2023, at 8:44 AM, Tu, Jiannan <[email protected]> wrote: The RHS function at the bottom boundary is determined by the boundary condition, which is the second order derivative = 0, i.e. G(u) = 2*X[i=1] – X[i=2]. Then in IFunction, F(u, udot) = X[i=0]. This might be the problem. Your F(u, udot) is missing udot according to your description. Take a simple ODE udot = f(u) + g(u) for example. One way to partition this ODE is to define F = udot - f(u) as the IFunction and G = g(u) as the RHSFunction. Hong (Mr.) Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Friday, February 17, 2023 11:54 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected You don't often get email from [email protected]<mailto:[email protected]>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> CAUTION: This email was sent from outside the UMass Lowell network. On Feb 17, 2023, at 6:19 PM, Tu, Jiannan <[email protected]> wrote: I need to find out what causes negative temperature first. Following is the message with adaptivity turned off. The G(u) gives right-hand equation for electron temperature at bottom boundary. The F(u, u’) function is F(u, u’) = X = G(u) and the jacobian element is d F(u, u’) / dX =1. This looks strange. Can you elaborate a bit on your partitioned ODE? For example, how are your F(u,udot) (IFunction) and G(u) (RHSFunction) defined? A good IMEX example can be found at ts/tutorial/advection-diffusion-reaction/ex5.c (and reaction_diffusion.c). Hong (Mr.) The solution from TSStep is checked for positivity of densities and temperatures. From the message below, it is seen that G(u) > 0 (I added output of right-hand equation for electron temperature). The solution for electron temperature X should be X * jacobian element = G(u) > 0 since jacobian element = 1. I don’t understand why it becomes negative. Is my understanding of TS formula incorrect? Thank you, Jiannan ---------------------------------- G(u) = 1.86534e-07 0 SNES Function norm 2.274473072183e+03 1 SNES Function norm 8.641749325070e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 G(u) = 1.86534e-07 0 SNES Function norm 8.716501970511e-02 1 SNES Function norm 2.213263548813e-04 2 SNES Function norm 2.779985176426e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 0 SNES Function norm 3.177195995186e-01 1 SNES Function norm 3.607702491344e-04 2 SNES Function norm 4.345809629121e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 TSAdapt none arkimex 0:3 step 0 accepted t=42960 + 2.189e-02 dt=2.189e-02 electron temperature = -3.6757e-15 at (i, j, k) = (0, 1, 0) From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 3:45 PM To: Tu, Jiannan<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Emil Constantinescu<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. On Feb 17, 2023, at 3:32 PM, Tu, Jiannan <[email protected]> wrote: The ts_type arkimex is used. There is right hand-side function RHSFunction set by TSSetRHSFunction() and also stiff function set by TSSetIFunction(). With adaptivity shut off, TS can finish its first time step after the 3rd “Nonlinear solve converged due to …”. The solution gives negative electron and neutral temperatures at the bottom boundary. I need to fix the negative temperatures and see how the code works. BTW, what is this ts_adapt? Is it by default on? It is default for some of the TSTypes (in particular, the better ones). It adapts the timestep to ensure some local error estimate is below a certain tolerance. As Matt notes normally as it tries smaller and smaller time steps the local error estimate would get smaller and smaller; this is not happening here, hence the error. Have you tried with the argument -ts_arkimex_fully_implicit ? I am not an expert but my guess is something is "odd" about your functions, either the RHSFunction or the Function or both. Do you have a hierarchy of models for your problem? Could you try runs with fewer terms in your functions, that may be producing the difficulties? If you can determine what triggers the problem with the local error estimators, that might help the experts in ODE solution (not me) determine what could be going wrong. Barry Thank you, Jiannan From: Matthew Knepley<mailto:[email protected]> Sent: Friday, February 17, 2023 3:15 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. I am not sure what TS you are using, but the estimate of the local truncation error is 91.4, and does not seem to change when you make the step smaller, so something is off. You can shut off the adaptivity using -ts_adapt_type none Thanks, Matt On Fri, Feb 17, 2023 at 3:01 PM Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: These are what I got with the options you suggested. Thank you, Jiannan ------------------------------------------------------------------------------- 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 2.189e-02 dt=4.374e-03 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-03 dt=4.374e-04 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-04 dt=4.374e-05 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-05 dt=4.374e-06 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-06 dt=4.374e-07 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-07 dt=4.374e-08 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-08 dt=4.374e-09 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-09 dt=4.374e-10 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-10 dt=4.374e-11 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-11 dt=4.374e-12 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-12 dt=4.374e-13 wlte= 91.4 wltea= -1 wlter= -1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Cfd42b18d0d094df8fc7508db12c30720%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638124401123944894%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=pU5RPkMt3KWGce%2BBxVx81YqWg4BJWUmyaReHk6IzHMo%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 14:54:22 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 12:58 PM To: Tu, Jiannan<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. Can you please run with also the options -ts_monitor -ts_adapt_monitor ? The output is confusing because it prints that the Nonlinear solve has converged but then TSStep has failed due to DIVERGED_STEP_REJECTED which seems contradictory On Feb 17, 2023, at 12:09 PM, Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: My code uses TS to solve a set of multi-fluid MHD equations. The jacobian is provided with function F(t, u, u'). Both linear and nonlinear solvers converge but snes repeats itself until gets "TSStep has failed due to diverged_step_rejected." Is it because I used TSStep rather than TSSolve? I have checked the condition number. The condition number with pc_type asm is about 1 (without precondition it is about 4x10^4). The maximum ratio of off-diagonal jacobian element over diagonal element is about 21. Could you help me to identify what is going wrong? Thank you very much! Jiannan --------------------------------------------------------------------------------------------------- Run command with options mpiexec -n $1 ./iditm3d -ts_type arkimex -snes_tyep ngmres -ksp_type gmres -pc_type asm \ -ts_rtol 1.0e-4 -ts_atol 1.0e-4 -snes_monitor -snes_rtol 1.0e-4 -snes_atol 1.0e-4 \ -snes_converged_reason The output message is Start time advancing ... 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Cfd42b18d0d094df8fc7508db12c30720%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638124401123944894%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=pU5RPkMt3KWGce%2BBxVx81YqWg4BJWUmyaReHk6IzHMo%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 11:59:43 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.cse.buffalo.edu%2F~knepley%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Cfd42b18d0d094df8fc7508db12c30720%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638124401123944894%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=wdJRbHevYI7gENtlvxd8T5KcO%2BOuE%2FC1jhQG2SibXQ4%3D&reserved=0>
Thanks for the suggestion. I’ll try CN and other implicit solvers and see how they works. Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Monday, February 20, 2023 11:07 AM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. If you have to include the boundary points, I would suggest starting from a fully implicit solver such as CN or BEuler with a finite-difference approximated Jacobian. When this works for a small scale setting, you can build up more functionalities such as IMEX and analytical Jacobians and extend the problem to a larger scale. But the udot issue needs to be fixed in the first place. Hong (Mr.) On Feb 19, 2023, at 9:23 PM, Tu, Jiannan <[email protected]> wrote: It is the second order derivative of, say electron temperature = 0 at the boundary. I am not sure how I can exclude the boundary points because the values of unknowns must be specified at the boundary. Are there any other solvers, e.g., CN, good to solve the equation system? Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Sunday, February 19, 2023 4:48 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. It is fine to drop udot for the boundary points, but you need to keep udot for all the other points. In addition, which boundary condition do you use in IFunction? The way you are treating the boundary points actually leads to a system of differential-algebraic equations, which could be difficult to solve with the ARKIMEX solver. Can you try to exclude the boundary points from the computational domain so that you will have just a system of ODEs? Hong (Mr.) On Feb 18, 2023, at 4:28 PM, Tu, Jiannan <[email protected]> wrote: Thanks for the instruction. This is the boundary condition and there is no udot in the equation. I think this is the way to define IFunction at the boundary. Maybe I’m wrong? Or is there some way to introduce udot into the specification of the equation at the boundary from the aspect of the implementation for TS? Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Saturday, February 18, 2023 12:40 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected You don't often get email from [email protected]<mailto:[email protected]>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> CAUTION: This email was sent from outside the UMass Lowell network. On Feb 18, 2023, at 8:44 AM, Tu, Jiannan <[email protected]> wrote: The RHS function at the bottom boundary is determined by the boundary condition, which is the second order derivative = 0, i.e. G(u) = 2*X[i=1] – X[i=2]. Then in IFunction, F(u, udot) = X[i=0]. This might be the problem. Your F(u, udot) is missing udot according to your description. Take a simple ODE udot = f(u) + g(u) for example. One way to partition this ODE is to define F = udot - f(u) as the IFunction and G = g(u) as the RHSFunction. Hong (Mr.) Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Friday, February 17, 2023 11:54 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected You don't often get email from [email protected]<mailto:[email protected]>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> CAUTION: This email was sent from outside the UMass Lowell network. On Feb 17, 2023, at 6:19 PM, Tu, Jiannan <[email protected]> wrote: I need to find out what causes negative temperature first. Following is the message with adaptivity turned off. The G(u) gives right-hand equation for electron temperature at bottom boundary. The F(u, u’) function is F(u, u’) = X = G(u) and the jacobian element is d F(u, u’) / dX =1. This looks strange. Can you elaborate a bit on your partitioned ODE? For example, how are your F(u,udot) (IFunction) and G(u) (RHSFunction) defined? A good IMEX example can be found at ts/tutorial/advection-diffusion-reaction/ex5.c (and reaction_diffusion.c). Hong (Mr.) The solution from TSStep is checked for positivity of densities and temperatures.
From the message below, it is seen that G(u) > 0 (I added output of right-hand equation for electron temperature). The solution for electron temperature X should be X * jacobian element = G(u) > 0 since jacobian element = 1. I don’t understand why it becomes negative. Is my understanding of TS formula incorrect?
Thank you, Jiannan ---------------------------------- G(u) = 1.86534e-07 0 SNES Function norm 2.274473072183e+03 1 SNES Function norm 8.641749325070e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 G(u) = 1.86534e-07 0 SNES Function norm 8.716501970511e-02 1 SNES Function norm 2.213263548813e-04 2 SNES Function norm 2.779985176426e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 0 SNES Function norm 3.177195995186e-01 1 SNES Function norm 3.607702491344e-04 2 SNES Function norm 4.345809629121e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 TSAdapt none arkimex 0:3 step 0 accepted t=42960 + 2.189e-02 dt=2.189e-02 electron temperature = -3.6757e-15 at (i, j, k) = (0, 1, 0) From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 3:45 PM To: Tu, Jiannan<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Emil Constantinescu<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. On Feb 17, 2023, at 3:32 PM, Tu, Jiannan <[email protected]> wrote: The ts_type arkimex is used. There is right hand-side function RHSFunction set by TSSetRHSFunction() and also stiff function set by TSSetIFunction(). With adaptivity shut off, TS can finish its first time step after the 3rd “Nonlinear solve converged due to …”. The solution gives negative electron and neutral temperatures at the bottom boundary. I need to fix the negative temperatures and see how the code works. BTW, what is this ts_adapt? Is it by default on? It is default for some of the TSTypes (in particular, the better ones). It adapts the timestep to ensure some local error estimate is below a certain tolerance. As Matt notes normally as it tries smaller and smaller time steps the local error estimate would get smaller and smaller; this is not happening here, hence the error. Have you tried with the argument -ts_arkimex_fully_implicit ? I am not an expert but my guess is something is "odd" about your functions, either the RHSFunction or the Function or both. Do you have a hierarchy of models for your problem? Could you try runs with fewer terms in your functions, that may be producing the difficulties? If you can determine what triggers the problem with the local error estimators, that might help the experts in ODE solution (not me) determine what could be going wrong. Barry Thank you, Jiannan From: Matthew Knepley<mailto:[email protected]> Sent: Friday, February 17, 2023 3:15 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. I am not sure what TS you are using, but the estimate of the local truncation error is 91.4, and does not seem to change when you make the step smaller, so something is off. You can shut off the adaptivity using -ts_adapt_type none Thanks, Matt On Fri, Feb 17, 2023 at 3:01 PM Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: These are what I got with the options you suggested. Thank you, Jiannan ------------------------------------------------------------------------------- 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 2.189e-02 dt=4.374e-03 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-03 dt=4.374e-04 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-04 dt=4.374e-05 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-05 dt=4.374e-06 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-06 dt=4.374e-07 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-07 dt=4.374e-08 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-08 dt=4.374e-09 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-09 dt=4.374e-10 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-10 dt=4.374e-11 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-11 dt=4.374e-12 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-12 dt=4.374e-13 wlte= 91.4 wltea= -1 wlter= -1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Ce26f36670ab44d9403b508db135c90da%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638125060538031187%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=vmlHEXtZIOA4oNOi7ZK1xBK%2BL0Cz52XVoJLrqJL06sw%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 14:54:22 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 12:58 PM To: Tu, Jiannan<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. Can you please run with also the options -ts_monitor -ts_adapt_monitor ? The output is confusing because it prints that the Nonlinear solve has converged but then TSStep has failed due to DIVERGED_STEP_REJECTED which seems contradictory On Feb 17, 2023, at 12:09 PM, Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: My code uses TS to solve a set of multi-fluid MHD equations. The jacobian is provided with function F(t, u, u'). Both linear and nonlinear solvers converge but snes repeats itself until gets "TSStep has failed due to diverged_step_rejected." Is it because I used TSStep rather than TSSolve? I have checked the condition number. The condition number with pc_type asm is about 1 (without precondition it is about 4x10^4). The maximum ratio of off-diagonal jacobian element over diagonal element is about 21. Could you help me to identify what is going wrong? Thank you very much! Jiannan --------------------------------------------------------------------------------------------------- Run command with options mpiexec -n $1 ./iditm3d -ts_type arkimex -snes_tyep ngmres -ksp_type gmres -pc_type asm \ -ts_rtol 1.0e-4 -ts_atol 1.0e-4 -snes_monitor -snes_rtol 1.0e-4 -snes_atol 1.0e-4 \ -snes_converged_reason The output message is Start time advancing ... 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Ce26f36670ab44d9403b508db135c90da%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638125060538031187%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=vmlHEXtZIOA4oNOi7ZK1xBK%2BL0Cz52XVoJLrqJL06sw%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 11:59:43 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.cse.buffalo.edu%2F~knepley%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Ce26f36670ab44d9403b508db135c90da%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638125060538187398%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=NNlNDia1%2BSjeZvLng2bo83b1V%2BBClTEp5bz2JkuwYm0%3D&reserved=0>
CN or BEular doesn’t work. They produce negative densities at the lower boundary even RHS functions are positive. So for TS, all equations must include udot? Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Monday, February 20, 2023 11:07 AM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. If you have to include the boundary points, I would suggest starting from a fully implicit solver such as CN or BEuler with a finite-difference approximated Jacobian. When this works for a small scale setting, you can build up more functionalities such as IMEX and analytical Jacobians and extend the problem to a larger scale. But the udot issue needs to be fixed in the first place. Hong (Mr.) On Feb 19, 2023, at 9:23 PM, Tu, Jiannan <[email protected]> wrote: It is the second order derivative of, say electron temperature = 0 at the boundary. I am not sure how I can exclude the boundary points because the values of unknowns must be specified at the boundary. Are there any other solvers, e.g., CN, good to solve the equation system? Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Sunday, February 19, 2023 4:48 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. It is fine to drop udot for the boundary points, but you need to keep udot for all the other points. In addition, which boundary condition do you use in IFunction? The way you are treating the boundary points actually leads to a system of differential-algebraic equations, which could be difficult to solve with the ARKIMEX solver. Can you try to exclude the boundary points from the computational domain so that you will have just a system of ODEs? Hong (Mr.) On Feb 18, 2023, at 4:28 PM, Tu, Jiannan <[email protected]> wrote: Thanks for the instruction. This is the boundary condition and there is no udot in the equation. I think this is the way to define IFunction at the boundary. Maybe I’m wrong? Or is there some way to introduce udot into the specification of the equation at the boundary from the aspect of the implementation for TS? Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Saturday, February 18, 2023 12:40 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected You don't often get email from [email protected]<mailto:[email protected]>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> CAUTION: This email was sent from outside the UMass Lowell network. On Feb 18, 2023, at 8:44 AM, Tu, Jiannan <[email protected]> wrote: The RHS function at the bottom boundary is determined by the boundary condition, which is the second order derivative = 0, i.e. G(u) = 2*X[i=1] – X[i=2]. Then in IFunction, F(u, udot) = X[i=0]. This might be the problem. Your F(u, udot) is missing udot according to your description. Take a simple ODE udot = f(u) + g(u) for example. One way to partition this ODE is to define F = udot - f(u) as the IFunction and G = g(u) as the RHSFunction. Hong (Mr.) Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Friday, February 17, 2023 11:54 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected You don't often get email from [email protected]<mailto:[email protected]>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> CAUTION: This email was sent from outside the UMass Lowell network. On Feb 17, 2023, at 6:19 PM, Tu, Jiannan <[email protected]> wrote: I need to find out what causes negative temperature first. Following is the message with adaptivity turned off. The G(u) gives right-hand equation for electron temperature at bottom boundary. The F(u, u’) function is F(u, u’) = X = G(u) and the jacobian element is d F(u, u’) / dX =1. This looks strange. Can you elaborate a bit on your partitioned ODE? For example, how are your F(u,udot) (IFunction) and G(u) (RHSFunction) defined? A good IMEX example can be found at ts/tutorial/advection-diffusion-reaction/ex5.c (and reaction_diffusion.c). Hong (Mr.) The solution from TSStep is checked for positivity of densities and temperatures.
From the message below, it is seen that G(u) > 0 (I added output of right-hand equation for electron temperature). The solution for electron temperature X should be X * jacobian element = G(u) > 0 since jacobian element = 1. I don’t understand why it becomes negative. Is my understanding of TS formula incorrect?
Thank you, Jiannan ---------------------------------- G(u) = 1.86534e-07 0 SNES Function norm 2.274473072183e+03 1 SNES Function norm 8.641749325070e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 G(u) = 1.86534e-07 0 SNES Function norm 8.716501970511e-02 1 SNES Function norm 2.213263548813e-04 2 SNES Function norm 2.779985176426e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 0 SNES Function norm 3.177195995186e-01 1 SNES Function norm 3.607702491344e-04 2 SNES Function norm 4.345809629121e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 TSAdapt none arkimex 0:3 step 0 accepted t=42960 + 2.189e-02 dt=2.189e-02 electron temperature = -3.6757e-15 at (i, j, k) = (0, 1, 0) From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 3:45 PM To: Tu, Jiannan<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Emil Constantinescu<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. On Feb 17, 2023, at 3:32 PM, Tu, Jiannan <[email protected]> wrote: The ts_type arkimex is used. There is right hand-side function RHSFunction set by TSSetRHSFunction() and also stiff function set by TSSetIFunction(). With adaptivity shut off, TS can finish its first time step after the 3rd “Nonlinear solve converged due to …”. The solution gives negative electron and neutral temperatures at the bottom boundary. I need to fix the negative temperatures and see how the code works. BTW, what is this ts_adapt? Is it by default on? It is default for some of the TSTypes (in particular, the better ones). It adapts the timestep to ensure some local error estimate is below a certain tolerance. As Matt notes normally as it tries smaller and smaller time steps the local error estimate would get smaller and smaller; this is not happening here, hence the error. Have you tried with the argument -ts_arkimex_fully_implicit ? I am not an expert but my guess is something is "odd" about your functions, either the RHSFunction or the Function or both. Do you have a hierarchy of models for your problem? Could you try runs with fewer terms in your functions, that may be producing the difficulties? If you can determine what triggers the problem with the local error estimators, that might help the experts in ODE solution (not me) determine what could be going wrong. Barry Thank you, Jiannan From: Matthew Knepley<mailto:[email protected]> Sent: Friday, February 17, 2023 3:15 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. I am not sure what TS you are using, but the estimate of the local truncation error is 91.4, and does not seem to change when you make the step smaller, so something is off. You can shut off the adaptivity using -ts_adapt_type none Thanks, Matt On Fri, Feb 17, 2023 at 3:01 PM Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: These are what I got with the options you suggested. Thank you, Jiannan ------------------------------------------------------------------------------- 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 2.189e-02 dt=4.374e-03 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-03 dt=4.374e-04 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-04 dt=4.374e-05 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-05 dt=4.374e-06 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-06 dt=4.374e-07 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-07 dt=4.374e-08 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-08 dt=4.374e-09 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-09 dt=4.374e-10 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-10 dt=4.374e-11 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-11 dt=4.374e-12 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-12 dt=4.374e-13 wlte= 91.4 wltea= -1 wlter= -1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Ce26f36670ab44d9403b508db135c90da%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638125060538031187%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=vmlHEXtZIOA4oNOi7ZK1xBK%2BL0Cz52XVoJLrqJL06sw%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 14:54:22 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 12:58 PM To: Tu, Jiannan<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. Can you please run with also the options -ts_monitor -ts_adapt_monitor ? The output is confusing because it prints that the Nonlinear solve has converged but then TSStep has failed due to DIVERGED_STEP_REJECTED which seems contradictory On Feb 17, 2023, at 12:09 PM, Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: My code uses TS to solve a set of multi-fluid MHD equations. The jacobian is provided with function F(t, u, u'). Both linear and nonlinear solvers converge but snes repeats itself until gets "TSStep has failed due to diverged_step_rejected." Is it because I used TSStep rather than TSSolve? I have checked the condition number. The condition number with pc_type asm is about 1 (without precondition it is about 4x10^4). The maximum ratio of off-diagonal jacobian element over diagonal element is about 21. Could you help me to identify what is going wrong? Thank you very much! Jiannan --------------------------------------------------------------------------------------------------- Run command with options mpiexec -n $1 ./iditm3d -ts_type arkimex -snes_tyep ngmres -ksp_type gmres -pc_type asm \ -ts_rtol 1.0e-4 -ts_atol 1.0e-4 -snes_monitor -snes_rtol 1.0e-4 -snes_atol 1.0e-4 \ -snes_converged_reason The output message is Start time advancing ... 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See 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[0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 11:59:43 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.cse.buffalo.edu%2F~knepley%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Ce26f36670ab44d9403b508db135c90da%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638125060538187398%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=NNlNDia1%2BSjeZvLng2bo83b1V%2BBClTEp5bz2JkuwYm0%3D&reserved=0>
On Feb 21, 2023, at 8:54 PM, Tu, Jiannan <[email protected]> wrote: CN or BEular doesn’t work. They produce negative densities at the lower boundary even RHS functions are positive. So for TS, all equations must include udot? You have algebraic constraints only for the boundary points. For all the other points, you must have udot in IFunction. I recommend you to take a look at the example src/ts/tutorials/ex25.c Hong (Mr.) Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Monday, February 20, 2023 11:07 AM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. If you have to include the boundary points, I would suggest starting from a fully implicit solver such as CN or BEuler with a finite-difference approximated Jacobian. When this works for a small scale setting, you can build up more functionalities such as IMEX and analytical Jacobians and extend the problem to a larger scale. But the udot issue needs to be fixed in the first place. Hong (Mr.) On Feb 19, 2023, at 9:23 PM, Tu, Jiannan <[email protected]> wrote: It is the second order derivative of, say electron temperature = 0 at the boundary. I am not sure how I can exclude the boundary points because the values of unknowns must be specified at the boundary. Are there any other solvers, e.g., CN, good to solve the equation system? Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Sunday, February 19, 2023 4:48 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. It is fine to drop udot for the boundary points, but you need to keep udot for all the other points. In addition, which boundary condition do you use in IFunction? The way you are treating the boundary points actually leads to a system of differential-algebraic equations, which could be difficult to solve with the ARKIMEX solver. Can you try to exclude the boundary points from the computational domain so that you will have just a system of ODEs? Hong (Mr.) On Feb 18, 2023, at 4:28 PM, Tu, Jiannan <[email protected]> wrote: Thanks for the instruction. This is the boundary condition and there is no udot in the equation. I think this is the way to define IFunction at the boundary. Maybe I’m wrong? Or is there some way to introduce udot into the specification of the equation at the boundary from the aspect of the implementation for TS? Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Saturday, February 18, 2023 12:40 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected You don't often get email from [email protected]<mailto:[email protected]>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> CAUTION: This email was sent from outside the UMass Lowell network. On Feb 18, 2023, at 8:44 AM, Tu, Jiannan <[email protected]> wrote: The RHS function at the bottom boundary is determined by the boundary condition, which is the second order derivative = 0, i.e. G(u) = 2*X[i=1] – X[i=2]. Then in IFunction, F(u, udot) = X[i=0]. This might be the problem. Your F(u, udot) is missing udot according to your description. Take a simple ODE udot = f(u) + g(u) for example. One way to partition this ODE is to define F = udot - f(u) as the IFunction and G = g(u) as the RHSFunction. Hong (Mr.) Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Friday, February 17, 2023 11:54 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected You don't often get email from [email protected]<mailto:[email protected]>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> CAUTION: This email was sent from outside the UMass Lowell network. On Feb 17, 2023, at 6:19 PM, Tu, Jiannan <[email protected]> wrote: I need to find out what causes negative temperature first. Following is the message with adaptivity turned off. The G(u) gives right-hand equation for electron temperature at bottom boundary. The F(u, u’) function is F(u, u’) = X = G(u) and the jacobian element is d F(u, u’) / dX =1. This looks strange. Can you elaborate a bit on your partitioned ODE? For example, how are your F(u,udot) (IFunction) and G(u) (RHSFunction) defined? A good IMEX example can be found at ts/tutorial/advection-diffusion-reaction/ex5.c (and reaction_diffusion.c). Hong (Mr.) The solution from TSStep is checked for positivity of densities and temperatures. From the message below, it is seen that G(u) > 0 (I added output of right-hand equation for electron temperature). The solution for electron temperature X should be X * jacobian element = G(u) > 0 since jacobian element = 1. I don’t understand why it becomes negative. Is my understanding of TS formula incorrect? Thank you, Jiannan ---------------------------------- G(u) = 1.86534e-07 0 SNES Function norm 2.274473072183e+03 1 SNES Function norm 8.641749325070e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 G(u) = 1.86534e-07 0 SNES Function norm 8.716501970511e-02 1 SNES Function norm 2.213263548813e-04 2 SNES Function norm 2.779985176426e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 0 SNES Function norm 3.177195995186e-01 1 SNES Function norm 3.607702491344e-04 2 SNES Function norm 4.345809629121e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 TSAdapt none arkimex 0:3 step 0 accepted t=42960 + 2.189e-02 dt=2.189e-02 electron temperature = -3.6757e-15 at (i, j, k) = (0, 1, 0) From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 3:45 PM To: Tu, Jiannan<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Emil Constantinescu<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. On Feb 17, 2023, at 3:32 PM, Tu, Jiannan <[email protected]> wrote: The ts_type arkimex is used. There is right hand-side function RHSFunction set by TSSetRHSFunction() and also stiff function set by TSSetIFunction(). With adaptivity shut off, TS can finish its first time step after the 3rd “Nonlinear solve converged due to …”. The solution gives negative electron and neutral temperatures at the bottom boundary. I need to fix the negative temperatures and see how the code works. BTW, what is this ts_adapt? Is it by default on? It is default for some of the TSTypes (in particular, the better ones). It adapts the timestep to ensure some local error estimate is below a certain tolerance. As Matt notes normally as it tries smaller and smaller time steps the local error estimate would get smaller and smaller; this is not happening here, hence the error. Have you tried with the argument -ts_arkimex_fully_implicit ? I am not an expert but my guess is something is "odd" about your functions, either the RHSFunction or the Function or both. Do you have a hierarchy of models for your problem? Could you try runs with fewer terms in your functions, that may be producing the difficulties? If you can determine what triggers the problem with the local error estimators, that might help the experts in ODE solution (not me) determine what could be going wrong. Barry Thank you, Jiannan From: Matthew Knepley<mailto:[email protected]> Sent: Friday, February 17, 2023 3:15 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. I am not sure what TS you are using, but the estimate of the local truncation error is 91.4, and does not seem to change when you make the step smaller, so something is off. You can shut off the adaptivity using -ts_adapt_type none Thanks, Matt On Fri, Feb 17, 2023 at 3:01 PM Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: These are what I got with the options you suggested. Thank you, Jiannan ------------------------------------------------------------------------------- 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 2.189e-02 dt=4.374e-03 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-03 dt=4.374e-04 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-04 dt=4.374e-05 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-05 dt=4.374e-06 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-06 dt=4.374e-07 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-07 dt=4.374e-08 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-08 dt=4.374e-09 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-09 dt=4.374e-10 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-10 dt=4.374e-11 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-11 dt=4.374e-12 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-12 dt=4.374e-13 wlte= 91.4 wltea= -1 wlter= -1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Ce26f36670ab44d9403b508db135c90da%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638125060538031187%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=vmlHEXtZIOA4oNOi7ZK1xBK%2BL0Cz52XVoJLrqJL06sw%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 14:54:22 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 12:58 PM To: Tu, Jiannan<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. Can you please run with also the options -ts_monitor -ts_adapt_monitor ? The output is confusing because it prints that the Nonlinear solve has converged but then TSStep has failed due to DIVERGED_STEP_REJECTED which seems contradictory On Feb 17, 2023, at 12:09 PM, Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: My code uses TS to solve a set of multi-fluid MHD equations. The jacobian is provided with function F(t, u, u'). Both linear and nonlinear solvers converge but snes repeats itself until gets "TSStep has failed due to diverged_step_rejected." Is it because I used TSStep rather than TSSolve? I have checked the condition number. The condition number with pc_type asm is about 1 (without precondition it is about 4x10^4). The maximum ratio of off-diagonal jacobian element over diagonal element is about 21. Could you help me to identify what is going wrong? Thank you very much! Jiannan --------------------------------------------------------------------------------------------------- Run command with options mpiexec -n $1 ./iditm3d -ts_type arkimex -snes_tyep ngmres -ksp_type gmres -pc_type asm \ -ts_rtol 1.0e-4 -ts_atol 1.0e-4 -snes_monitor -snes_rtol 1.0e-4 -snes_atol 1.0e-4 \ -snes_converged_reason The output message is Start time advancing ... 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpetsc.org%2Frelease%2Ffaq%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Ce26f36670ab44d9403b508db135c90da%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638125060538031187%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=vmlHEXtZIOA4oNOi7ZK1xBK%2BL0Cz52XVoJLrqJL06sw%3D&reserved=0> for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 11:59:43 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.cse.buffalo.edu%2F~knepley%2F&data=05%7C01%7CJiannan_Tu%40uml.edu%7Ce26f36670ab44d9403b508db135c90da%7C4c25b8a617f746f983f054734ab81fb1%7C0%7C0%7C638125060538187398%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=NNlNDia1%2BSjeZvLng2bo83b1V%2BBClTEp5bz2JkuwYm0%3D&reserved=0>
I am using PETSC SNES to solve a nonlinear equation system resulted from discretization of partial differential equations. When I use Valgrind to check my program, there are lots of errors of ‘Unconditional jump or move depends on uninitialised value(s)’ produced. The errors occur in the function routine set by SNESSetFunction(snes, NULL, formfunctions, ¶ms). Even using only one MPI process such errors occur. It seems solution vector X is not initialized through SNESSolve(). But if the formfunctions() is called directly from main(), there are no errors. I really don’t understand why. Could you please help me identify what is going wrong? Thank you very much, Jiannan ------------------------------------------------- The error message is like the following example Conditional jump or move depends on uninitialised value(s) ==866758== at 0xA19178C: sqrt (w_sqrt_compat.c:31) ==866758== by 0x4EA9E4C: VecNorm_Seq (bvec2.c:227) ==866758== by 0x4F705C8: VecNorm (rvector.c:228) ==866758== by 0x65D5B16: SNESSolve_NEWTONLS (ls.c:179) ==866758== by 0x673093F: SNESSolve (snes.c:4809) ==866758== by 0x12F607: main (iditm3d.cpp:138) ==866758== Uninitialised value was created by a stack allocation ==866758== at 0x11AC36: functions(Field***, Field***, Field***, int, int, int, int, int, int, AppCtx*, Field***) (formfunctions.cpp:16) functions() is called within the formfunctions(). The code snippet using SNES solver is int formfunctions(SNES, Vec, Vec, void *ctx); int jacobian(SNES, Vec, Mat, Mat, void *ctx); DMDACreate3d(MPI_COMM_WORLD,DM_BOUNDARY_GHOSTED,DM_BOUNDARY_GHOSTED,DM_BOUNDARY_PERIODIC, DMDA_STENCIL_STAR,a1,a2,a3,PETSC_DECIDE,PETSC_DECIDE,1,a4,2,NULL,NULL,NULL,&da); DMSetFromOptions(da); DMSetUp(da); DMCreateGlobalVector(da, &X); VecDuplicate(X, ¶ms.U); VecDuplicate(X, ¶ms.Xn); /* set up grids and related geometric parameters. Set up initial solution vector X */ if (initialize(da, X, ¶ms) < 0) exit(-1); SNES snes; SNESCreate(MPI_COMM_WORLD, &snes); SNESSetType(snes, SNESNEWTONLS); SNESSetFromOptions(snes); SNESSetDM(snes, da); SNESSetFunction(snes, NULL, formfunctions, ¶ms); KSP ksp; SNESGetKSP(snes, &ksp); KSPSetType(ksp, KSPFGMRES); KSPSetFromOptions(ksp); PC pc; KSPGetPC(ksp, &pc); PCSetType(pc, PCJACOBI); PCSetFromOptions(pc); Mat A; DMSetMatrixPreallocateOnly(da, PETSC_FALSE); DMSetMatType(da, MATMPIAIJ); DMDASetBlockFills(da, dfill, ofill); DMCreateMatrix(da, &A); SNESSetJacobian(snes, A, A, jacobian, ¶ms); SNESSetSolution(snes, X); //set initial guess of the solution SNESSolve(snes, PETSC_NULL, X); //iterative solver to find the solution From: Zhang, Hong<mailto:[email protected]> Sent: Tuesday, February 21, 2023 11:21 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. On Feb 21, 2023, at 8:54 PM, Tu, Jiannan <[email protected]> wrote: CN or BEular doesn’t work. They produce negative densities at the lower boundary even RHS functions are positive. So for TS, all equations must include udot? You have algebraic constraints only for the boundary points. For all the other points, you must have udot in IFunction. I recommend you to take a look at the example src/ts/tutorials/ex25.c Hong (Mr.) Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Monday, February 20, 2023 11:07 AM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. If you have to include the boundary points, I would suggest starting from a fully implicit solver such as CN or BEuler with a finite-difference approximated Jacobian. When this works for a small scale setting, you can build up more functionalities such as IMEX and analytical Jacobians and extend the problem to a larger scale. But the udot issue needs to be fixed in the first place. Hong (Mr.) On Feb 19, 2023, at 9:23 PM, Tu, Jiannan <[email protected]> wrote: It is the second order derivative of, say electron temperature = 0 at the boundary. I am not sure how I can exclude the boundary points because the values of unknowns must be specified at the boundary. Are there any other solvers, e.g., CN, good to solve the equation system? Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Sunday, February 19, 2023 4:48 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. It is fine to drop udot for the boundary points, but you need to keep udot for all the other points. In addition, which boundary condition do you use in IFunction? The way you are treating the boundary points actually leads to a system of differential-algebraic equations, which could be difficult to solve with the ARKIMEX solver. Can you try to exclude the boundary points from the computational domain so that you will have just a system of ODEs? Hong (Mr.) On Feb 18, 2023, at 4:28 PM, Tu, Jiannan <[email protected]> wrote: Thanks for the instruction. This is the boundary condition and there is no udot in the equation. I think this is the way to define IFunction at the boundary. Maybe I’m wrong? Or is there some way to introduce udot into the specification of the equation at the boundary from the aspect of the implementation for TS? Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Saturday, February 18, 2023 12:40 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected You don't often get email from [email protected]<mailto:[email protected]>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> CAUTION: This email was sent from outside the UMass Lowell network. On Feb 18, 2023, at 8:44 AM, Tu, Jiannan <[email protected]> wrote: The RHS function at the bottom boundary is determined by the boundary condition, which is the second order derivative = 0, i.e. G(u) = 2*X[i=1] – X[i=2]. Then in IFunction, F(u, udot) = X[i=0]. This might be the problem. Your F(u, udot) is missing udot according to your description. Take a simple ODE udot = f(u) + g(u) for example. One way to partition this ODE is to define F = udot - f(u) as the IFunction and G = g(u) as the RHSFunction. Hong (Mr.) Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Friday, February 17, 2023 11:54 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected You don't often get email from [email protected]<mailto:[email protected]>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> CAUTION: This email was sent from outside the UMass Lowell network. On Feb 17, 2023, at 6:19 PM, Tu, Jiannan <[email protected]> wrote: I need to find out what causes negative temperature first. Following is the message with adaptivity turned off. The G(u) gives right-hand equation for electron temperature at bottom boundary. The F(u, u’) function is F(u, u’) = X = G(u) and the jacobian element is d F(u, u’) / dX =1. This looks strange. Can you elaborate a bit on your partitioned ODE? For example, how are your F(u,udot) (IFunction) and G(u) (RHSFunction) defined? A good IMEX example can be found at ts/tutorial/advection-diffusion-reaction/ex5.c (and reaction_diffusion.c). Hong (Mr.) The solution from TSStep is checked for positivity of densities and temperatures.
From the message below, it is seen that G(u) > 0 (I added output of right-hand equation for electron temperature). The solution for electron temperature X should be X * jacobian element = G(u) > 0 since jacobian element = 1. I don’t understand why it becomes negative. Is my understanding of TS formula incorrect?
Thank you, Jiannan ---------------------------------- G(u) = 1.86534e-07 0 SNES Function norm 2.274473072183e+03 1 SNES Function norm 8.641749325070e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 G(u) = 1.86534e-07 0 SNES Function norm 8.716501970511e-02 1 SNES Function norm 2.213263548813e-04 2 SNES Function norm 2.779985176426e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 0 SNES Function norm 3.177195995186e-01 1 SNES Function norm 3.607702491344e-04 2 SNES Function norm 4.345809629121e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 TSAdapt none arkimex 0:3 step 0 accepted t=42960 + 2.189e-02 dt=2.189e-02 electron temperature = -3.6757e-15 at (i, j, k) = (0, 1, 0) From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 3:45 PM To: Tu, Jiannan<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Emil Constantinescu<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. On Feb 17, 2023, at 3:32 PM, Tu, Jiannan <[email protected]> wrote: The ts_type arkimex is used. There is right hand-side function RHSFunction set by TSSetRHSFunction() and also stiff function set by TSSetIFunction(). With adaptivity shut off, TS can finish its first time step after the 3rd “Nonlinear solve converged due to …”. The solution gives negative electron and neutral temperatures at the bottom boundary. I need to fix the negative temperatures and see how the code works. BTW, what is this ts_adapt? Is it by default on? It is default for some of the TSTypes (in particular, the better ones). It adapts the timestep to ensure some local error estimate is below a certain tolerance. As Matt notes normally as it tries smaller and smaller time steps the local error estimate would get smaller and smaller; this is not happening here, hence the error. Have you tried with the argument -ts_arkimex_fully_implicit ? I am not an expert but my guess is something is "odd" about your functions, either the RHSFunction or the Function or both. Do you have a hierarchy of models for your problem? Could you try runs with fewer terms in your functions, that may be producing the difficulties? If you can determine what triggers the problem with the local error estimators, that might help the experts in ODE solution (not me) determine what could be going wrong. Barry Thank you, Jiannan From: Matthew Knepley<mailto:[email protected]> Sent: Friday, February 17, 2023 3:15 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. I am not sure what TS you are using, but the estimate of the local truncation error is 91.4, and does not seem to change when you make the step smaller, so something is off. You can shut off the adaptivity using -ts_adapt_type none Thanks, Matt On Fri, Feb 17, 2023 at 3:01 PM Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: These are what I got with the options you suggested. Thank you, Jiannan ------------------------------------------------------------------------------- 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 2.189e-02 dt=4.374e-03 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-03 dt=4.374e-04 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-04 dt=4.374e-05 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-05 dt=4.374e-06 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-06 dt=4.374e-07 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-07 dt=4.374e-08 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-08 dt=4.374e-09 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-09 dt=4.374e-10 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-10 dt=4.374e-11 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-11 dt=4.374e-12 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-12 dt=4.374e-13 wlte= 91.4 wltea= -1 wlter= -1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 14:54:22 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 12:58 PM To: Tu, Jiannan<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. Can you please run with also the options -ts_monitor -ts_adapt_monitor ? The output is confusing because it prints that the Nonlinear solve has converged but then TSStep has failed due to DIVERGED_STEP_REJECTED which seems contradictory On Feb 17, 2023, at 12:09 PM, Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: My code uses TS to solve a set of multi-fluid MHD equations. The jacobian is provided with function F(t, u, u'). Both linear and nonlinear solvers converge but snes repeats itself until gets "TSStep has failed due to diverged_step_rejected." Is it because I used TSStep rather than TSSolve? I have checked the condition number. The condition number with pc_type asm is about 1 (without precondition it is about 4x10^4). The maximum ratio of off-diagonal jacobian element over diagonal element is about 21. Could you help me to identify what is going wrong? Thank you very much! Jiannan --------------------------------------------------------------------------------------------------- Run command with options mpiexec -n $1 ./iditm3d -ts_type arkimex -snes_tyep ngmres -ksp_type gmres -pc_type asm \ -ts_rtol 1.0e-4 -ts_atol 1.0e-4 -snes_monitor -snes_rtol 1.0e-4 -snes_atol 1.0e-4 \ -snes_converged_reason The output message is Start time advancing ... 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 11:59:43 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/<http://www.cse.buffalo.edu/~knepley/>
It would have been best to send formfunctions.cpp: since that is where the problem is. Likely you have a local variable (hence the message "stack-allocation") in that function that is not initialized but that you use to fill up the function array values. Valgrind does not detect all uses of unitialized memory, it only detects them when they would change a flow direction in the code, like in an if () test. This is why the problem pops up in the VecNorm() and not if you just call your function from main(). There are compiler options to detect the use of used declared variables that are not initialized which might help you find the problem at compile time. Barry
On May 9, 2023, at 10:59 PM, Tu, Jiannan <[email protected]> wrote:
I am using PETSC SNES to solve a nonlinear equation system resulted from discretization of partial differential equations. When I use Valgrind to check my program, there are lots of errors of ‘Unconditional jump or move depends on uninitialised value(s)’ produced. The errors occur in the function routine set by SNESSetFunction(snes, NULL, formfunctions, ¶ms). Even using only one MPI process such errors occur. It seems solution vector X is not initialized through SNESSolve(). But if the formfunctions() is called directly from main(), there are no errors. I really don’t understand why. Could you please help me identify what is going wrong?
Thank you very much,
Jiannan
------------------------------------------------- The error message is like the following example
Conditional jump or move depends on uninitialised value(s) ==866758== at 0xA19178C: sqrt (w_sqrt_compat.c:31) ==866758== by 0x4EA9E4C: VecNorm_Seq (bvec2.c:227) ==866758== by 0x4F705C8: VecNorm (rvector.c:228) ==866758== by 0x65D5B16: SNESSolve_NEWTONLS (ls.c:179) ==866758== by 0x673093F: SNESSolve (snes.c:4809) ==866758== by 0x12F607: main (iditm3d.cpp:138) ==866758== Uninitialised value was created by a stack allocation ==866758== at 0x11AC36: functions(Field***, Field***, Field***, int, int, int, int, int, int, AppCtx*, Field***) (formfunctions.cpp:16)
functions() is called within the formfunctions(). The code snippet using SNES solver is
int formfunctions(SNES, Vec, Vec, void *ctx); int jacobian(SNES, Vec, Mat, Mat, void *ctx);
DMDACreate3d(MPI_COMM_WORLD,DM_BOUNDARY_GHOSTED,DM_BOUNDARY_GHOSTED,DM_BOUNDARY_PERIODIC, DMDA_STENCIL_STAR,a1,a2,a3,PETSC_DECIDE,PETSC_DECIDE,1,a4,2,NULL,NULL,NULL,&da);
DMSetFromOptions(da); DMSetUp(da);
DMCreateGlobalVector(da, &X); VecDuplicate(X, ¶ms.U); VecDuplicate(X, ¶ms.Xn);
/* set up grids and related geometric parameters. Set up initial solution vector X */ if (initialize(da, X, ¶ms) < 0) exit(-1);
SNES snes; SNESCreate(MPI_COMM_WORLD, &snes); SNESSetType(snes, SNESNEWTONLS); SNESSetFromOptions(snes); SNESSetDM(snes, da); SNESSetFunction(snes, NULL, formfunctions, ¶ms);
KSP ksp; SNESGetKSP(snes, &ksp); KSPSetType(ksp, KSPFGMRES); KSPSetFromOptions(ksp);
PC pc; KSPGetPC(ksp, &pc); PCSetType(pc, PCJACOBI); PCSetFromOptions(pc);
Mat A; DMSetMatrixPreallocateOnly(da, PETSC_FALSE); DMSetMatType(da, MATMPIAIJ); DMDASetBlockFills(da, dfill, ofill); DMCreateMatrix(da, &A);
SNESSetJacobian(snes, A, A, jacobian, ¶ms);
SNESSetSolution(snes, X); //set initial guess of the solution SNESSolve(snes, PETSC_NULL, X); //iterative solver to find the solution
From: Zhang, Hong <mailto:[email protected]> Sent: Tuesday, February 21, 2023 11:21 PM To: Tu, Jiannan <mailto:[email protected]> Cc: Barry Smith <mailto:[email protected]>; Hong Zhang <mailto:[email protected]>; Constantinescu, Emil M. <mailto:[email protected]>; petsc-users <mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected
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On Feb 21, 2023, at 8:54 PM, Tu, Jiannan <[email protected] <mailto:[email protected]>> wrote:
CN or BEular doesn’t work. They produce negative densities at the lower boundary even RHS functions are positive. So for TS, all equations must include udot?
You have algebraic constraints only for the boundary points. For all the other points, you must have udot in IFunction. I recommend you to take a look at the example src/ts/tutorials/ex25.c
Hong (Mr.)
Thank you, Jiannan
From: Zhang, Hong <mailto:[email protected]> Sent: Monday, February 20, 2023 11:07 AM To: Tu, Jiannan <mailto:[email protected]> Cc: Barry Smith <mailto:[email protected]>; Hong Zhang <mailto:[email protected]>; Constantinescu, Emil M. <mailto:[email protected]>; petsc-users <mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected
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If you have to include the boundary points, I would suggest starting from a fully implicit solver such as CN or BEuler with a finite-difference approximated Jacobian. When this works for a small scale setting, you can build up more functionalities such as IMEX and analytical Jacobians and extend the problem to a larger scale. But the udot issue needs to be fixed in the first place.
Hong (Mr.)
On Feb 19, 2023, at 9:23 PM, Tu, Jiannan <[email protected] <mailto:[email protected]>> wrote:
It is the second order derivative of, say electron temperature = 0 at the boundary.
I am not sure how I can exclude the boundary points because the values of unknowns must be specified at the boundary. Are there any other solvers, e.g., CN, good to solve the equation system?
Thank you, Jiannan
From: Zhang, Hong <mailto:[email protected]> Sent: Sunday, February 19, 2023 4:48 PM To: Tu, Jiannan <mailto:[email protected]> Cc: Barry Smith <mailto:[email protected]>; Hong Zhang <mailto:[email protected]>; Constantinescu, Emil M. <mailto:[email protected]>; petsc-users <mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected
CAUTION: This email was sent from outside the UMass Lowell network.
It is fine to drop udot for the boundary points, but you need to keep udot for all the other points.
In addition, which boundary condition do you use in IFunction? The way you are treating the boundary points actually leads to a system of differential-algebraic equations, which could be difficult to solve with the ARKIMEX solver. Can you try to exclude the boundary points from the computational domain so that you will have just a system of ODEs?
Hong (Mr.)
On Feb 18, 2023, at 4:28 PM, Tu, Jiannan <[email protected] <mailto:[email protected]>> wrote:
Thanks for the instruction. This is the boundary condition and there is no udot in the equation. I think this is the way to define IFunction at the boundary. Maybe I’m wrong? Or is there some way to introduce udot into the specification of the equation at the boundary from the aspect of the implementation for TS?
Thank you, Jiannan
From: Zhang, Hong <mailto:[email protected]> Sent: Saturday, February 18, 2023 12:40 PM To: Tu, Jiannan <mailto:[email protected]> Cc: Barry Smith <mailto:[email protected]>; Hong Zhang <mailto:[email protected]>; Constantinescu, Emil M. <mailto:[email protected]>; petsc-users <mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected
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On Feb 18, 2023, at 8:44 AM, Tu, Jiannan <[email protected] <mailto:[email protected]>> wrote:
The RHS function at the bottom boundary is determined by the boundary condition, which is the second order derivative = 0, i.e. G(u) = 2*X[i=1] – X[i=2]. Then in IFunction, F(u, udot) = X[i=0].
This might be the problem. Your F(u, udot) is missing udot according to your description. Take a simple ODE udot = f(u) + g(u) for example. One way to partition this ODE is to define F = udot - f(u) as the IFunction and G = g(u) as the RHSFunction.
Hong (Mr.)
Thank you, Jiannan
From: Zhang, Hong <mailto:[email protected]> Sent: Friday, February 17, 2023 11:54 PM To: Tu, Jiannan <mailto:[email protected]> Cc: Barry Smith <mailto:[email protected]>; Hong Zhang <mailto:[email protected]>; Constantinescu, Emil M. <mailto:[email protected]>; petsc-users <mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected
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On Feb 17, 2023, at 6:19 PM, Tu, Jiannan <[email protected] <mailto:[email protected]>> wrote:
I need to find out what causes negative temperature first. Following is the message with adaptivity turned off. The G(u) gives right-hand equation for electron temperature at bottom boundary. The F(u, u’) function is F(u, u’) = X = G(u) and the jacobian element is d F(u, u’) / dX =1.
This looks strange. Can you elaborate a bit on your partitioned ODE? For example, how are your F(u,udot) (IFunction) and G(u) (RHSFunction) defined?
A good IMEX example can be found at ts/tutorial/advection-diffusion-reaction/ex5.c (and reaction_diffusion.c).
Hong (Mr.)
The solution from TSStep is checked for positivity of densities and temperatures.
From the message below, it is seen that G(u) > 0 (I added output of right-hand equation for electron temperature). The solution for electron temperature X should be X * jacobian element = G(u) > 0 since jacobian element = 1. I don’t understand why it becomes negative. Is my understanding of TS formula incorrect?
Thank you, Jiannan
---------------------------------- G(u) = 1.86534e-07 0 SNES Function norm 2.274473072183e+03 1 SNES Function norm 8.641749325070e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 G(u) = 1.86534e-07 0 SNES Function norm 8.716501970511e-02 1 SNES Function norm 2.213263548813e-04 2 SNES Function norm 2.779985176426e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 0 SNES Function norm 3.177195995186e-01 1 SNES Function norm 3.607702491344e-04 2 SNES Function norm 4.345809629121e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 TSAdapt none arkimex 0:3 step 0 accepted t=42960 + 2.189e-02 dt=2.189e-02 electron temperature = -3.6757e-15 at (i, j, k) = (0, 1, 0)
From: Barry Smith <mailto:[email protected]> Sent: Friday, February 17, 2023 3:45 PM To: Tu, Jiannan <mailto:[email protected]>; Hong Zhang <mailto:[email protected]>; Emil Constantinescu <mailto:[email protected]> Cc: petsc-users <mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected
CAUTION: This email was sent from outside the UMass Lowell network.
On Feb 17, 2023, at 3:32 PM, Tu, Jiannan <[email protected] <mailto:[email protected]>> wrote:
The ts_type arkimex is used. There is right hand-side function RHSFunction set by TSSetRHSFunction() and also stiff function set by TSSetIFunction().
With adaptivity shut off, TS can finish its first time step after the 3rd “Nonlinear solve converged due to …”. The solution gives negative electron and neutral temperatures at the bottom boundary. I need to fix the negative temperatures and see how the code works.
BTW, what is this ts_adapt? Is it by default on?
It is default for some of the TSTypes (in particular, the better ones). It adapts the timestep to ensure some local error estimate is below a certain tolerance. As Matt notes normally as it tries smaller and smaller time steps the local error estimate would get smaller and smaller; this is not happening here, hence the error.
Have you tried with the argument -ts_arkimex_fully_implicit ?
I am not an expert but my guess is something is "odd" about your functions, either the RHSFunction or the Function or both. Do you have a hierarchy of models for your problem? Could you try runs with fewer terms in your functions, that may be producing the difficulties? If you can determine what triggers the problem with the local error estimators, that might help the experts in ODE solution (not me) determine what could be going wrong.
Barry
Thank you, Jiannan
From: Matthew Knepley <mailto:[email protected]> Sent: Friday, February 17, 2023 3:15 PM To: Tu, Jiannan <mailto:[email protected]> Cc: Barry Smith <mailto:[email protected]>; petsc-users <mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected
CAUTION: This email was sent from outside the UMass Lowell network.
I am not sure what TS you are using, but the estimate of the local truncation error is 91.4, and does not seem to change when you make the step smaller, so something is off. You can shut off the adaptivity using
-ts_adapt_type none
Thanks,
Matt
On Fri, Feb 17, 2023 at 3:01 PM Tu, Jiannan <[email protected] <mailto:[email protected]>> wrote: These are what I got with the options you suggested.
Thank you, Jiannan
------------------------------------------------------------------------------- 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 2.189e-02 dt=4.374e-03 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-03 dt=4.374e-04 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-04 dt=4.374e-05 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-05 dt=4.374e-06 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-06 dt=4.374e-07 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-07 dt=4.374e-08 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-08 dt=4.374e-09 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-09 dt=4.374e-10 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-10 dt=4.374e-11 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-11 dt=4.374e-12 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-12 dt=4.374e-13 wlte= 91.4 wltea= -1 wlter= -1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 14:54:22 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583
From: Barry Smith <mailto:[email protected]> Sent: Friday, February 17, 2023 12:58 PM To: Tu, Jiannan <mailto:[email protected]> Cc: petsc-users <mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected
CAUTION: This email was sent from outside the UMass Lowell network.
Can you please run with also the options -ts_monitor -ts_adapt_monitor ?
The output is confusing because it prints that the Nonlinear solve has converged but then TSStep has failed due to DIVERGED_STEP_REJECTED which seems contradictory
On Feb 17, 2023, at 12:09 PM, Tu, Jiannan <[email protected] <mailto:[email protected]>> wrote:
My code uses TS to solve a set of multi-fluid MHD equations. The jacobian is provided with function F(t, u, u'). Both linear and nonlinear solvers converge but snes repeats itself until gets "TSStep has failed due to diverged_step_rejected."
Is it because I used TSStep rather than TSSolve? I have checked the condition number. The condition number with pc_type asm is about 1 (without precondition it is about 4x10^4). The maximum ratio of off-diagonal jacobian element over diagonal element is about 21.
Could you help me to identify what is going wrong?
Thank you very much!
Jiannan
--------------------------------------------------------------------------------------------------- Run command with options
mpiexec -n $1 ./iditm3d -ts_type arkimex -snes_tyep ngmres -ksp_type gmres -pc_type asm \ -ts_rtol 1.0e-4 -ts_atol 1.0e-4 -snes_monitor -snes_rtol 1.0e-4 -snes_atol 1.0e-4 \ -snes_converged_reason
The output message is
Start time advancing ... 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 11:59:43 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583
-- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener
https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
Hi Barry, Thank you for your advice. I didn't send the function because it is a little bit long. The function is attached. Your reply reminds me I should need also to check all the other local variables besides vector X (which the error messages give me the impression the array from the vector X is the cause). I'll see what gcc complier options I should use to detect the use of declared variables that are not initialized. Jiannan ________________________________ From: Barry Smith <[email protected]> Sent: Tuesday, May 9, 2023 11:16 PM To: Tu, Jiannan <[email protected]> Cc: [email protected] <[email protected]>; Zhang, Hong <[email protected]> Subject: Re: [petsc-users]Unconditional jump or move depends on uninitialised value(s) CAUTION: This email was sent from outside the UMass Lowell network. It would have been best to send formfunctions.cpp: since that is where the problem is. Likely you have a local variable (hence the message "stack-allocation") in that function that is not initialized but that you use to fill up the function array values. Valgrind does not detect all uses of unitialized memory, it only detects them when they would change a flow direction in the code, like in an if () test. This is why the problem pops up in the VecNorm() and not if you just call your function from main(). There are compiler options to detect the use of used declared variables that are not initialized which might help you find the problem at compile time. Barry On May 9, 2023, at 10:59 PM, Tu, Jiannan <[email protected]> wrote: I am using PETSC SNES to solve a nonlinear equation system resulted from discretization of partial differential equations. When I use Valgrind to check my program, there are lots of errors of ‘Unconditional jump or move depends on uninitialised value(s)’ produced. The errors occur in the function routine set by SNESSetFunction(snes, NULL, formfunctions, ¶ms). Even using only one MPI process such errors occur. It seems solution vector X is not initialized through SNESSolve(). But if the formfunctions() is called directly from main(), there are no errors. I really don’t understand why. Could you please help me identify what is going wrong? Thank you very much, Jiannan ------------------------------------------------- The error message is like the following example Conditional jump or move depends on uninitialised value(s) ==866758== at 0xA19178C: sqrt (w_sqrt_compat.c:31) ==866758== by 0x4EA9E4C: VecNorm_Seq (bvec2.c:227) ==866758== by 0x4F705C8: VecNorm (rvector.c:228) ==866758== by 0x65D5B16: SNESSolve_NEWTONLS (ls.c:179) ==866758== by 0x673093F: SNESSolve (snes.c:4809) ==866758== by 0x12F607: main (iditm3d.cpp:138) ==866758== Uninitialised value was created by a stack allocation ==866758== at 0x11AC36: functions(Field***, Field***, Field***, int, int, int, int, int, int, AppCtx*, Field***) (formfunctions.cpp:16) functions() is called within the formfunctions(). The code snippet using SNES solver is int formfunctions(SNES, Vec, Vec, void *ctx); int jacobian(SNES, Vec, Mat, Mat, void *ctx); DMDACreate3d(MPI_COMM_WORLD,DM_BOUNDARY_GHOSTED,DM_BOUNDARY_GHOSTED,DM_BOUNDARY_PERIODIC, DMDA_STENCIL_STAR,a1,a2,a3,PETSC_DECIDE,PETSC_DECIDE,1,a4,2,NULL,NULL,NULL,&da); DMSetFromOptions(da); DMSetUp(da); DMCreateGlobalVector(da, &X); VecDuplicate(X, ¶ms.U); VecDuplicate(X, ¶ms.Xn); /* set up grids and related geometric parameters. Set up initial solution vector X */ if (initialize(da, X, ¶ms) < 0) exit(-1); SNES snes; SNESCreate(MPI_COMM_WORLD, &snes); SNESSetType(snes, SNESNEWTONLS); SNESSetFromOptions(snes); SNESSetDM(snes, da); SNESSetFunction(snes, NULL, formfunctions, ¶ms); KSP ksp; SNESGetKSP(snes, &ksp); KSPSetType(ksp, KSPFGMRES); KSPSetFromOptions(ksp); PC pc; KSPGetPC(ksp, &pc); PCSetType(pc, PCJACOBI); PCSetFromOptions(pc); Mat A; DMSetMatrixPreallocateOnly(da, PETSC_FALSE); DMSetMatType(da, MATMPIAIJ); DMDASetBlockFills(da, dfill, ofill); DMCreateMatrix(da, &A); SNESSetJacobian(snes, A, A, jacobian, ¶ms); SNESSetSolution(snes, X); //set initial guess of the solution SNESSolve(snes, PETSC_NULL, X); //iterative solver to find the solution From: Zhang, Hong<mailto:[email protected]> Sent: Tuesday, February 21, 2023 11:21 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. On Feb 21, 2023, at 8:54 PM, Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: CN or BEular doesn’t work. They produce negative densities at the lower boundary even RHS functions are positive. So for TS, all equations must include udot? You have algebraic constraints only for the boundary points. For all the other points, you must have udot in IFunction. I recommend you to take a look at the example src/ts/tutorials/ex25.c Hong (Mr.) Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Monday, February 20, 2023 11:07 AM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. If you have to include the boundary points, I would suggest starting from a fully implicit solver such as CN or BEuler with a finite-difference approximated Jacobian. When this works for a small scale setting, you can build up more functionalities such as IMEX and analytical Jacobians and extend the problem to a larger scale. But the udot issue needs to be fixed in the first place. Hong (Mr.) On Feb 19, 2023, at 9:23 PM, Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: It is the second order derivative of, say electron temperature = 0 at the boundary. I am not sure how I can exclude the boundary points because the values of unknowns must be specified at the boundary. Are there any other solvers, e.g., CN, good to solve the equation system? Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Sunday, February 19, 2023 4:48 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. It is fine to drop udot for the boundary points, but you need to keep udot for all the other points. In addition, which boundary condition do you use in IFunction? The way you are treating the boundary points actually leads to a system of differential-algebraic equations, which could be difficult to solve with the ARKIMEX solver. Can you try to exclude the boundary points from the computational domain so that you will have just a system of ODEs? Hong (Mr.) On Feb 18, 2023, at 4:28 PM, Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: Thanks for the instruction. This is the boundary condition and there is no udot in the equation. I think this is the way to define IFunction at the boundary. Maybe I’m wrong? Or is there some way to introduce udot into the specification of the equation at the boundary from the aspect of the implementation for TS? Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Saturday, February 18, 2023 12:40 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected You don't often get email from [email protected]<mailto:[email protected]>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> CAUTION: This email was sent from outside the UMass Lowell network. On Feb 18, 2023, at 8:44 AM, Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: The RHS function at the bottom boundary is determined by the boundary condition, which is the second order derivative = 0, i.e. G(u) = 2*X[i=1] – X[i=2]. Then in IFunction, F(u, udot) = X[i=0]. This might be the problem. Your F(u, udot) is missing udot according to your description. Take a simple ODE udot = f(u) + g(u) for example. One way to partition this ODE is to define F = udot - f(u) as the IFunction and G = g(u) as the RHSFunction. Hong (Mr.) Thank you, Jiannan From: Zhang, Hong<mailto:[email protected]> Sent: Friday, February 17, 2023 11:54 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Constantinescu, Emil M.<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected You don't often get email from [email protected]<mailto:[email protected]>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> CAUTION: This email was sent from outside the UMass Lowell network. On Feb 17, 2023, at 6:19 PM, Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: I need to find out what causes negative temperature first. Following is the message with adaptivity turned off. The G(u) gives right-hand equation for electron temperature at bottom boundary. The F(u, u’) function is F(u, u’) = X = G(u) and the jacobian element is d F(u, u’) / dX =1. This looks strange. Can you elaborate a bit on your partitioned ODE? For example, how are your F(u,udot) (IFunction) and G(u) (RHSFunction) defined? A good IMEX example can be found at ts/tutorial/advection-diffusion-reaction/ex5.c (and reaction_diffusion.c). Hong (Mr.) The solution from TSStep is checked for positivity of densities and temperatures.
From the message below, it is seen that G(u) > 0 (I added output of right-hand equation for electron temperature). The solution for electron temperature X should be X * jacobian element = G(u) > 0 since jacobian element = 1. I don’t understand why it becomes negative. Is my understanding of TS formula incorrect?
Thank you, Jiannan ---------------------------------- G(u) = 1.86534e-07 0 SNES Function norm 2.274473072183e+03 1 SNES Function norm 8.641749325070e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 G(u) = 1.86534e-07 0 SNES Function norm 8.716501970511e-02 1 SNES Function norm 2.213263548813e-04 2 SNES Function norm 2.779985176426e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 0 SNES Function norm 3.177195995186e-01 1 SNES Function norm 3.607702491344e-04 2 SNES Function norm 4.345809629121e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 G(u) = 1.86534e-07 TSAdapt none arkimex 0:3 step 0 accepted t=42960 + 2.189e-02 dt=2.189e-02 electron temperature = -3.6757e-15 at (i, j, k) = (0, 1, 0) From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 3:45 PM To: Tu, Jiannan<mailto:[email protected]>; Hong Zhang<mailto:[email protected]>; Emil Constantinescu<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. On Feb 17, 2023, at 3:32 PM, Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: The ts_type arkimex is used. There is right hand-side function RHSFunction set by TSSetRHSFunction() and also stiff function set by TSSetIFunction(). With adaptivity shut off, TS can finish its first time step after the 3rd “Nonlinear solve converged due to …”. The solution gives negative electron and neutral temperatures at the bottom boundary. I need to fix the negative temperatures and see how the code works. BTW, what is this ts_adapt? Is it by default on? It is default for some of the TSTypes (in particular, the better ones). It adapts the timestep to ensure some local error estimate is below a certain tolerance. As Matt notes normally as it tries smaller and smaller time steps the local error estimate would get smaller and smaller; this is not happening here, hence the error. Have you tried with the argument -ts_arkimex_fully_implicit ? I am not an expert but my guess is something is "odd" about your functions, either the RHSFunction or the Function or both. Do you have a hierarchy of models for your problem? Could you try runs with fewer terms in your functions, that may be producing the difficulties? If you can determine what triggers the problem with the local error estimators, that might help the experts in ODE solution (not me) determine what could be going wrong. Barry Thank you, Jiannan From: Matthew Knepley<mailto:[email protected]> Sent: Friday, February 17, 2023 3:15 PM To: Tu, Jiannan<mailto:[email protected]> Cc: Barry Smith<mailto:[email protected]>; petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. I am not sure what TS you are using, but the estimate of the local truncation error is 91.4, and does not seem to change when you make the step smaller, so something is off. You can shut off the adaptivity using -ts_adapt_type none Thanks, Matt On Fri, Feb 17, 2023 at 3:01 PM Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: These are what I got with the options you suggested. Thank you, Jiannan ------------------------------------------------------------------------------- 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 2.189e-02 dt=4.374e-03 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-03 dt=4.374e-04 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-04 dt=4.374e-05 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-05 dt=4.374e-06 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-06 dt=4.374e-07 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-07 dt=4.374e-08 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-08 dt=4.374e-09 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-09 dt=4.374e-10 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-10 dt=4.374e-11 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-11 dt=4.374e-12 wlte= 91.4 wltea= -1 wlter= -1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 TSAdapt basic arkimex 0:3 step 0 rejected t=42960 + 4.374e-12 dt=4.374e-13 wlte= 91.4 wltea= -1 wlter= -1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 14:54:22 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 From: Barry Smith<mailto:[email protected]> Sent: Friday, February 17, 2023 12:58 PM To: Tu, Jiannan<mailto:[email protected]> Cc: petsc-users<mailto:[email protected]> Subject: Re: [petsc-users] TS failed due to diverged_step_rejected CAUTION: This email was sent from outside the UMass Lowell network. Can you please run with also the options -ts_monitor -ts_adapt_monitor ? The output is confusing because it prints that the Nonlinear solve has converged but then TSStep has failed due to DIVERGED_STEP_REJECTED which seems contradictory On Feb 17, 2023, at 12:09 PM, Tu, Jiannan <[email protected]<mailto:[email protected]>> wrote: My code uses TS to solve a set of multi-fluid MHD equations. The jacobian is provided with function F(t, u, u'). Both linear and nonlinear solvers converge but snes repeats itself until gets "TSStep has failed due to diverged_step_rejected." Is it because I used TSStep rather than TSSolve? I have checked the condition number. The condition number with pc_type asm is about 1 (without precondition it is about 4x10^4). The maximum ratio of off-diagonal jacobian element over diagonal element is about 21. Could you help me to identify what is going wrong? Thank you very much! Jiannan --------------------------------------------------------------------------------------------------- Run command with options mpiexec -n $1 ./iditm3d -ts_type arkimex -snes_tyep ngmres -ksp_type gmres -pc_type asm \ -ts_rtol 1.0e-4 -ts_atol 1.0e-4 -snes_monitor -snes_rtol 1.0e-4 -snes_atol 1.0e-4 \ -snes_converged_reason The output message is Start time advancing ... 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.673091274668e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 8.715428433630e-02 1 SNES Function norm 4.995727626692e-04 2 SNES Function norm 5.498018152230e-08 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 3.237461568254e-01 1 SNES Function norm 7.988531005091e-04 2 SNES Function norm 1.280948196292e-07 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.881903203545e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 7.562592690785e-02 1 SNES Function norm 1.143078818923e-04 2 SNES Function norm 9.834547907735e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.683968949758e-01 1 SNES Function norm 1.838028436639e-04 2 SNES Function norm 9.470813523140e-09 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 2 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 1.821562431175e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 1.005443458812e-01 1 SNES Function norm 3.633336946661e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.515368382715e-01 1 SNES Function norm 3.389298316830e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 4.541003359206e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 1.713800906043e-01 1 SNES Function norm 1.179958172167e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.020265094117e-01 1 SNES Function norm 1.513971290464e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 6.090269704320e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.136603895703e-01 1 SNES Function norm 1.877474016012e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.127812462507e-01 1 SNES Function norm 2.713146825704e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.793512213059e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.205196267430e-01 1 SNES Function norm 2.572653773308e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.260057361977e-01 1 SNES Function norm 2.705816087598e-06 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 2.764855860446e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.212505522844e-01 1 SNES Function norm 2.958996472386e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 3.273222034162e-01 1 SNES Function norm 2.994512887620e-05 Nonlinear solve converged due to CONVERGED_FNORM_ABS iterations 1 0 SNES Function norm 2.274473072186e+03 1 SNES Function norm 3.317240589134e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213246532918e-01 1 SNES Function norm 2.799468604767e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.274570888397e-01 1 SNES Function norm 3.066048050994e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072189e+03 1 SNES Function norm 2.653507278572e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.213869585841e-01 1 SNES Function norm 2.177156902895e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.275136370365e-01 1 SNES Function norm 1.962849131557e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473072218e+03 1 SNES Function norm 5.664907315679e-03 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.223208399368e-01 1 SNES Function norm 5.688863091415e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.287121218919e-01 1 SNES Function norm 4.085338521320e-03 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 2.274473071968e+03 1 SNES Function norm 4.694691905235e-04 Nonlinear solve converged due to CONVERGED_FNORM_RELATIVE iterations 1 0 SNES Function norm 2.211786508657e-01 1 SNES Function norm 1.503497433939e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 0 SNES Function norm 3.272667798977e-01 1 SNES Function norm 2.176132327279e-04 Nonlinear solve converged due to CONVERGED_SNORM_RELATIVE iterations 1 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: TSStep has failed due to DIVERGED_STEP_REJECTED [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.6, Mar 30, 2022 [0]PETSC ERROR: ./iditm3d on a named office by jtu Fri Feb 17 11:59:43 2023 [0]PETSC ERROR: Configure options --prefix=/usr/local --with-mpi-dir=/usr/local --with-fc=0 --with-openmp --with-hdf5-dir=/usr/local --download-f2cblaslapack=1 [0]PETSC ERROR: #1 TSStep() at /home/jtu/Downloads/petsc-3.16.6/src/ts/interface/ts.c:3583 -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/<http://www.cse.buffalo.edu/~knepley/>
I'll see what gcc complier options I should use to detect the use of declared variables that are not initialized
The flag you are looking for is -Wall. Please fix all the warnings that it may raise. Generally speaking, it is also much easier to ensure your variables are initialized if you restrict them to the smallest scope possible. That is, declare the variable immediately before you use it. If you only use it within a loop, then only declare it inside that loop. If you only use it in an if branch, then only declare it inside that branch. Best regards, Jacob Faibussowitsch (Jacob Fai - booss - oh - vitch)
On May 10, 2023, at 12:38, Tu, Jiannan <[email protected]> wrote:
I'll see what gcc complier options I should use to detect the use of declared variables that are not initialized
Jacob, Thank you very much. I did use -Wall compiler option. Nevertheless, declaring the variables in the smallest scope is a very good way to avoid uninitialized usage of the variables. Jiannan ________________________________ From: Jacob Faibussowitsch <[email protected]> Sent: Friday, June 9, 2023 3:55 PM To: Tu, Jiannan <[email protected]> Cc: Barry Smith <[email protected]>; [email protected] <[email protected]> Subject: Re: [petsc-users] Unconditional jump or move depends on uninitialised value(s) You don't often get email from [email protected]. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> CAUTION: This email was sent from outside the UMass Lowell network.
I'll see what gcc complier options I should use to detect the use of declared variables that are not initialized
The flag you are looking for is -Wall. Please fix all the warnings that it may raise. Generally speaking, it is also much easier to ensure your variables are initialized if you restrict them to the smallest scope possible. That is, declare the variable immediately before you use it. If you only use it within a loop, then only declare it inside that loop. If you only use it in an if branch, then only declare it inside that branch. Best regards, Jacob Faibussowitsch (Jacob Fai - booss - oh - vitch) On May 10, 2023, at 12:38, Tu, Jiannan <[email protected]> wrote: I'll see what gcc complier options I should use to detect the use of declared variables that are not initialized
To avoid warninigs about “unconditional jump or move depends on uninitialized value(s)”, I simplified my programs so that the warnings remain only through SNESSolve(). Some of them are appended below. My question is if such warnings really matter and affect the simulation results? Thank you for your kind advice. Jiannan ==1988731== Conditional jump or move depends on uninitialised value(s) ==1988731== at 0xA19178C: sqrt (w_sqrt_compat.c:31) ==1988731== by 0x4EA9E4C: VecNorm_Seq (bvec2.c:227) ==1988731== by 0x4F705C8: VecNorm (rvector.c:228) ==1988731== by 0x6678D91: SNESSolve_NEWTONTR (tr.c:300) ==1988731== by 0x673093F: SNESSolve (snes.c:4809) ==1988731== by 0x122FA7: main (iditm3d.cpp:138) ==1988731== ==1988731== Conditional jump or move depends on uninitialised value(s) ==1988731== at 0x667495C: PetscIsInfOrNanReal (petscmath.h:788) ==1988731== by 0x6678E0C: SNESSolve_NEWTONTR (tr.c:301) ==1988731== by 0x673093F: SNESSolve (snes.c:4809) ==1988731== by 0x122FA7: main (iditm3d.cpp:138) ==1988731== ==1988731== Conditional jump or move depends on uninitialised value(s) ==1988731== at 0xA347078: __printf_fp_l (printf_fp.c:387) ==1988731== by 0xA360547: printf_positional (vfprintf-internal.c:2072) ==1988731== by 0xA361DCC: __vfprintf_internal (vfprintf-internal.c:1733) ==1988731== by 0xA376F99: __vsnprintf_internal (vsnprintf.c:114) ==1988731== by 0x4A77784: PetscVSNPrintf (mprint.c:176) ==1988731== by 0x4A77EF4: PetscVFPrintfDefault (mprint.c:292) ==1988731== by 0x4BCBB92: PetscViewerASCIIPrintf (filev.c:607) ==1988731== by 0x674764B: SNESMonitorDefault (snesut.c:296) ==1988731== by 0x6728A3E: SNESMonitor (snes.c:4059) ==1988731== by 0x6679743: SNESSolve_NEWTONTR (tr.c:309) ==1988731== by 0x673093F: SNESSolve (snes.c:4809) ==1988731== by 0x122FA7: main (iditm3d.cpp:138) ==1988731== ==1988731== Conditional jump or move depends on uninitialised value(s) ==1988731== at 0xA342B34: __mpn_extract_double (dbl2mpn.c:56) ==1988731== by 0xA34738E: __printf_fp_l (printf_fp.c:387) ==1988731== by 0xA360547: printf_positional (vfprintf-internal.c:2072) ==1988731== by 0xA361DCC: __vfprintf_internal (vfprintf-internal.c:1733) ==1988731== by 0xA376F99: __vsnprintf_internal (vsnprintf.c:114) ==1988731== by 0x4A77784: PetscVSNPrintf (mprint.c:176) ==1988731== by 0x4A77EF4: PetscVFPrintfDefault (mprint.c:292) ==1988731== by 0x4BCBB92: PetscViewerASCIIPrintf (filev.c:607) ==1988731== by 0x674764B: SNESMonitorDefault (snesut.c:296) ==1988731== by 0x6728A3E: SNESMonitor (snes.c:4059) ==1988731== by 0x6679743: SNESSolve_NEWTONTR (tr.c:309) ==1988731== by 0x673093F: SNESSolve (snes.c:4809)
Yes they matter; they cannot be ignored. The most likely cause is that you did not fill in certain entries in the vector during the function evaluation routine you set with SNESSetFunction(). Another possibility is if you provided a right hand side vector to the SNES (uncommon) that not all values in that vector have been filled in. If you call VecView() inside your function evaluation routine immediately after you have finished filling the vector it may help track down which entries you missed. Barry
On Jun 9, 2023, at 3:24 PM, Tu, Jiannan <[email protected]> wrote:
To avoid warninigs about “unconditional jump or move depends on uninitialized value(s)”, I simplified my programs so that the warnings remain only through SNESSolve(). Some of them are appended below. My question is if such warnings really matter and affect the simulation results? <>
Thank you for your kind advice.
Jiannan
==1988731== Conditional jump or move depends on uninitialised value(s) ==1988731== at 0xA19178C: sqrt (w_sqrt_compat.c:31) ==1988731== by 0x4EA9E4C: VecNorm_Seq (bvec2.c:227) ==1988731== by 0x4F705C8: VecNorm (rvector.c:228) ==1988731== by 0x6678D91: SNESSolve_NEWTONTR (tr.c:300) ==1988731== by 0x673093F: SNESSolve (snes.c:4809) ==1988731== by 0x122FA7: main (iditm3d.cpp:138) ==1988731== ==1988731== Conditional jump or move depends on uninitialised value(s) ==1988731== at 0x667495C: PetscIsInfOrNanReal (petscmath.h:788) ==1988731== by 0x6678E0C: SNESSolve_NEWTONTR (tr.c:301) ==1988731== by 0x673093F: SNESSolve (snes.c:4809) ==1988731== by 0x122FA7: main (iditm3d.cpp:138) ==1988731== ==1988731== Conditional jump or move depends on uninitialised value(s) ==1988731== at 0xA347078: __printf_fp_l (printf_fp.c:387) ==1988731== by 0xA360547: printf_positional (vfprintf-internal.c:2072) ==1988731== by 0xA361DCC: __vfprintf_internal (vfprintf-internal.c:1733) ==1988731== by 0xA376F99: __vsnprintf_internal (vsnprintf.c:114) ==1988731== by 0x4A77784: PetscVSNPrintf (mprint.c:176) ==1988731== by 0x4A77EF4: PetscVFPrintfDefault (mprint.c:292) ==1988731== by 0x4BCBB92: PetscViewerASCIIPrintf (filev.c:607) ==1988731== by 0x674764B: SNESMonitorDefault (snesut.c:296) ==1988731== by 0x6728A3E: SNESMonitor (snes.c:4059) ==1988731== by 0x6679743: SNESSolve_NEWTONTR (tr.c:309) ==1988731== by 0x673093F: SNESSolve (snes.c:4809) ==1988731== by 0x122FA7: main (iditm3d.cpp:138) ==1988731== ==1988731== Conditional jump or move depends on uninitialised value(s) ==1988731== at 0xA342B34: __mpn_extract_double (dbl2mpn.c:56) ==1988731== by 0xA34738E: __printf_fp_l (printf_fp.c:387) ==1988731== by 0xA360547: printf_positional (vfprintf-internal.c:2072) ==1988731== by 0xA361DCC: __vfprintf_internal (vfprintf-internal.c:1733) ==1988731== by 0xA376F99: __vsnprintf_internal (vsnprintf.c:114) ==1988731== by 0x4A77784: PetscVSNPrintf (mprint.c:176) ==1988731== by 0x4A77EF4: PetscVFPrintfDefault (mprint.c:292) ==1988731== by 0x4BCBB92: PetscViewerASCIIPrintf (filev.c:607) ==1988731== by 0x674764B: SNESMonitorDefault (snesut.c:296) ==1988731== by 0x6728A3E: SNESMonitor (snes.c:4059) ==1988731== by 0x6679743: SNESSolve_NEWTONTR (tr.c:309) ==1988731== by 0x673093F: SNESSolve (snes.c:4809)
Barry, Thank you for the very good advice. I think all the elements have been filled but there may be some on the boundaries missed. Jiannan ________________________________ From: Barry Smith <[email protected]> Sent: Friday, June 9, 2023 3:35 PM To: Tu, Jiannan <[email protected]> Cc: [email protected] <[email protected]>; Zhang, Hong <[email protected]> Subject: Re: [petsc-users]Unconditional jump or move depends on uninitialised value(s) CAUTION: This email was sent from outside the UMass Lowell network. Yes they matter; they cannot be ignored. The most likely cause is that you did not fill in certain entries in the vector during the function evaluation routine you set with SNESSetFunction(). Another possibility is if you provided a right hand side vector to the SNES (uncommon) that not all values in that vector have been filled in. If you call VecView() inside your function evaluation routine immediately after you have finished filling the vector it may help track down which entries you missed. Barry On Jun 9, 2023, at 3:24 PM, Tu, Jiannan <[email protected]> wrote: To avoid warninigs about “unconditional jump or move depends on uninitialized value(s)”, I simplified my programs so that the warnings remain only through SNESSolve(). Some of them are appended below. My question is if such warnings really matter and affect the simulation results? Thank you for your kind advice. Jiannan ==1988731== Conditional jump or move depends on uninitialised value(s) ==1988731== at 0xA19178C: sqrt (w_sqrt_compat.c:31) ==1988731== by 0x4EA9E4C: VecNorm_Seq (bvec2.c:227) ==1988731== by 0x4F705C8: VecNorm (rvector.c:228) ==1988731== by 0x6678D91: SNESSolve_NEWTONTR (tr.c:300) ==1988731== by 0x673093F: SNESSolve (snes.c:4809) ==1988731== by 0x122FA7: main (iditm3d.cpp:138) ==1988731== ==1988731== Conditional jump or move depends on uninitialised value(s) ==1988731== at 0x667495C: PetscIsInfOrNanReal (petscmath.h:788) ==1988731== by 0x6678E0C: SNESSolve_NEWTONTR (tr.c:301) ==1988731== by 0x673093F: SNESSolve (snes.c:4809) ==1988731== by 0x122FA7: main (iditm3d.cpp:138) ==1988731== ==1988731== Conditional jump or move depends on uninitialised value(s) ==1988731== at 0xA347078: __printf_fp_l (printf_fp.c:387) ==1988731== by 0xA360547: printf_positional (vfprintf-internal.c:2072) ==1988731== by 0xA361DCC: __vfprintf_internal (vfprintf-internal.c:1733) ==1988731== by 0xA376F99: __vsnprintf_internal (vsnprintf.c:114) ==1988731== by 0x4A77784: PetscVSNPrintf (mprint.c:176) ==1988731== by 0x4A77EF4: PetscVFPrintfDefault (mprint.c:292) ==1988731== by 0x4BCBB92: PetscViewerASCIIPrintf (filev.c:607) ==1988731== by 0x674764B: SNESMonitorDefault (snesut.c:296) ==1988731== by 0x6728A3E: SNESMonitor (snes.c:4059) ==1988731== by 0x6679743: SNESSolve_NEWTONTR (tr.c:309) ==1988731== by 0x673093F: SNESSolve (snes.c:4809) ==1988731== by 0x122FA7: main (iditm3d.cpp:138) ==1988731== ==1988731== Conditional jump or move depends on uninitialised value(s) ==1988731== at 0xA342B34: __mpn_extract_double (dbl2mpn.c:56) ==1988731== by 0xA34738E: __printf_fp_l (printf_fp.c:387) ==1988731== by 0xA360547: printf_positional (vfprintf-internal.c:2072) ==1988731== by 0xA361DCC: __vfprintf_internal (vfprintf-internal.c:1733) ==1988731== by 0xA376F99: __vsnprintf_internal (vsnprintf.c:114) ==1988731== by 0x4A77784: PetscVSNPrintf (mprint.c:176) ==1988731== by 0x4A77EF4: PetscVFPrintfDefault (mprint.c:292) ==1988731== by 0x4BCBB92: PetscViewerASCIIPrintf (filev.c:607) ==1988731== by 0x674764B: SNESMonitorDefault (snesut.c:296) ==1988731== by 0x6728A3E: SNESMonitor (snes.c:4059) ==1988731== by 0x6679743: SNESSolve_NEWTONTR (tr.c:309) ==1988731== by 0x673093F: SNESSolve (snes.c:4809)
participants (5)
-
Barry Smith -
Jacob Faibussowitsch -
Matthew Knepley -
Tu, Jiannan -
Zhang, Hong