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>
