# SNES Problem

Barry Smith bsmith at mcs.anl.gov
Mon Mar 20 07:41:48 CST 2006

```   Nisse,

Yes. You need to make sure that all the entries computed
in your FormFunction() are correctly F_i(x) for 0 <= i < globalvectorlength!!
The "zeros" will destroy the Newton convergence since the Jacobian
will be singular, plus if the "zeros" are actually random "garbage"
because the memory has not be initialized that will really screw
things up.

Barry

On Mon, 20 Mar 2006, Nils Erik Svangård wrote:

> Hi again,
> I thought that I would comment on the diff from last being 0.90 all
> the time. That is because a error in calculation (by me).
>
> do IMESH=1,NMESH
>     NMPL=NMP(IMESH)
>     NIL = NI(IMESH)
>     NJL = NJ(IMESH)
>     NKL = NK(IMESH)
>       do K=1,NKL-1
>         do J=1,NJL-1
>           do I=1,NIL-1
>              L=I+NIL*(J-1)+NIL*NJL*(K-1)+NMPL
>              count=count+1
>              DRO(L)=magic()
>           end do
>         end do
>      end do
>  end do
>
> count after a run is 8019 and L is 8899, so the vector containg the
> solution also have a couple of zeros in the middle, could this effect
> the SNES solver?
>
> /nisse
>
>
> On 3/20/06, Nils Erik Svangård <nilserik at gmail.com> wrote:
>> Hi,
>> The timestep doesnt change dramaticly just before the values get
>> strange. The term diff from last is:
>> a=new_value(L)/old_value(L)+a
>> Diff from last=a/L
>> To me it seems as something petsc does supplies strange values.
>> The output berfore crashing:
>>
>>
>>  Iterering:   667.000
>>  H2T
>>  Timestep:   1.000000000000000E-007
>>  H1T
>>  Diff from last:   0.901112485562141
>>  AUXVR
>>  ROMIN,ROMAX=   1.22541  1.22657
>>  UMIN ,UMAX =  -4.016098E-02  0.278343
>>  VMIN ,VMAX =  -1.853829E-03  3.289763E-02
>>  WMIN ,WMAX =  -1.852430E-03  1.855088E-03
>>  PMIN ,PMAX =   101283.  101416.
>>  QMIN ,QMAX =   0.815285  0.816229
>>  EMIN ,EMAX =   4.07643  4.08175
>>  V3
>>  Hello CONV4
>>  RUS:   12.2556
>>  V4
>>  DIFF3
>>  F3
>>  Iterering:   668.000
>>  H2T
>>  Timestep:   1.000000000000000E-007
>>  H1T
>>  Diff from last:   0.901112485562141
>>  AUXVR
>>  ROMIN,ROMAX=   1.22541  1.22657
>>  UMIN ,UMAX =  -4.016098E-02  0.278343
>>  VMIN ,VMAX =  -1.853829E-03  3.289763E-02
>>  WMIN ,WMAX =  -1.852430E-03  1.855088E-03
>>  PMIN ,PMAX =   101283.  101416.
>>  QMIN ,QMAX =   0.815285  0.816229
>>  EMIN ,EMAX =   4.07643  4.08175
>>  V3
>>  Hello CONV4
>>  RUS:   12.2556
>>  V4
>>  DIFF3
>>  F3
>>  Iterering:   669.000
>>  H2T
>>  Timestep:   1.000000000000000E-007
>>  H1T
>>  Diff from last:   1.785767662774350E-006
>>  AUXVR
>> --------------------------------------------------------------------------
>> Petsc Release Version 2.3.0, Patch 32, April, 26, 2005
>> See docs/changes/index.html for recent updates.
>> See docs/faq.html for hints about trouble shooting.
>> See docs/index.html for manual pages.
>> -----------------------------------------------------------------------
>> ./withrk on a linux-gnu named sethnx004.vac.com by yy26539 Mon Mar 20
>> 10:17:33 2006
>> Configure run at Thu Oct 13 08:23:56 2005
>> Configure options --with-cc=gcc --with-fc="f77 -N109"
>> -----------------------------------------------------------------------
>> [0]PETSC ERROR: Caught signal number 8 FPE: Floating Point
>> Exception,probably divide by zero
>> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>> [0]PETSC ERROR: likely location of problem given in stack below
>> [0]PETSC ERROR: --------------- Stack Frames ---------------
>> [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
>> [0]PETSC ERROR:       INSTEAD the line number of the start of the function
>> [0]PETSC ERROR:       is given.
>> [0]PETSC ERROR: [0] SNESComputeFunction line 788 src/snes/interface/snes.c
>> [0]PETSC ERROR: [0] MatMult_MFFD line 235 src/snes/mf/snesmfj.c
>> [0]PETSC ERROR: [0] MatMult line 1368 src/mat/interface/matrix.c
>> [0]PETSC ERROR: [0] SNESLSCheckLocalMin_Private line 19 src/snes/impls/ls/ls.c
>> [0]PETSC ERROR: [0] SNESSolve line 1656 src/snes/interface/snes.c
>> [0]PETSC ERROR: --------------------------------------------
>> [0]PETSC ERROR: User provided function() line 0 in unknown directory
>> unknown file
>> [0]PETSC ERROR:  !
>> aborting job:
>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>>
>>
>> /nisse
>>
>> On 3/18/06, Nils Erik Svangård <nilserik at gmail.com> wrote:
>>> On 3/18/06, Barry Smith <bsmith at mcs.anl.gov> wrote:
>>>>
>>>>    So you are saying that TS is feeding "reasonable" input
>>>> for a while? That basically matches (in scale) the values feed in
>>>> from the old rk code? Then SUDDENLY? it inputs values with a very
>>>> different size?
>>>
>>> Yes.
>>>
>>>> Does the TS time-step size? also change dramatically at
>>>> that point?
>>>>
>>>
>>> No, I dont think so. However I'm not 100% sure what the timestep
>>> hasent changed dramatically for the last iteration when it crashes
>>> (but 95% sure). I can check that on monday.
>>>
>>> /nisse
>>>
>>>>     Barry
>>>>
>>>>
>>>> On Sat, 18 Mar 2006, Nils Erik Svangård wrote:
>>>>
>>>>> On 3/17/06, Barry Smith <bsmith at mcs.anl.gov> wrote:
>>>>>>
>>>>>>    Based on my understanding. This is correct.
>>>>>
>>>>> I was almost hoping I had missed something fundamental.
>>>>>
>>>>>>
>>>>>>    Suggest you run a TINY problem with your "old" code
>>>>>> and the TS (and or SNES one). Print out everything. The
>>>>>> current solution the result from calling Get_DRO() and
>>>>>> compare the runs, when and why do they change? This will
>>>>>> help understand what is going on.
>>>>>
>>>>> Well, Get_DRO() is exactly the same in the old and new code, and they
>>>>> start with the same initial values. Get_DRO() is not producing strange
>>>>> values, it is crashing because it get strange values fed into it.
>>>>>
>>>>> A normal run for the formfunction f(in,out) in TS would look something
>>>>> like this if printed:
>>>>> in=25560         <- Start value
>>>>> out=0.0001     <-  du/dt
>>>>> in=25560         <- Value fed into formfunction after some TS magic
>>>>> out=0.0001      <- du/dt
>>>>> ...                      <- (a couple iterations)
>>>>> in=25451          <- Input value after a couple of iterations
>>>>> out=0.0001      <- du/dt
>>>>> in=0.23151       <- Value fed into formfunction decided by TS
>>>>> Petscerror divide by zero...
>>>>>
>>>>> The problem seems to be that TS decides that the input values to
>>>>> formfunction should be (in this case) 0.23151 which makes Get_DRO()
>>>>> crash because of  for example sqrt(in-1).
>>>>>
>>>>> I have no idea how to fix this. The values from Get_DRO() in TS match
>>>>> the values when running the old rk code.
>>>>>
>>>>> /nisse
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>>
>>>>>>     Barry
>>>>>>
>>>>>>
>>>>>> On Fri, 17 Mar 2006, Nils Erik Svangård wrote:
>>>>>>
>>>>>>> Ok, I managed to compile and link rk.c to my fortran program, I forgot
>>>>>>> that in C you need a ;  in the end of every statement. (stupid mistake
>>>>>>> ;) )
>>>>>>>
>>>>>>> I have just added one line to see if it works.
>>>>>>>
>>>>>>>  /* computing new dt */
>>>>>>>     dt = dt * dt_fac;
>>>>>>>
>>>>>>>     /* Start Nisse stuff */
>>>>>>>        ierr = PetscPrintf(PETSC_COMM_WORLD,"Nisse prints dt: %f\n",dt);
>>>>>>>     /* End nisse stuff */
>>>>>>>
>>>>>>>
>>>>>>>     if(ts->ptime+dt > ts->max_time){
>>>>>>>        dt = ts->max_time - ts->ptime;
>>>>>>>     }
>>>>>>>
>>>>>>> I just try to print the current timestep, however this is never
>>>>>>> printed. And I'm not really sure that it is the timestep that is
>>>>>>> causing the problems.
>>>>>>>
>>>>>>> I have used call TSGetTimeStep(ts,timestep,ierr) to monitor what
>>>>>>> timestep TS uses and it seem ok. However after the first iteration of
>>>>>>> FormFunction everything seems ok, but in start of the second iteration
>>>>>>> all values are really strange.
>>>>>>>
>>>>>>> I see the same thing when using SNES and my back euler implementation,
>>>>>>> it iterate many more times however, but all of a sudden the all "in"
>>>>>>> values are in the range 0.2-0.7 (for all 7 equations) and my code
>>>>>>> bombs because of the strange values.
>>>>>>>
>>>>>>> When using TS and  running with  -snes_mf -ts_type beuler -ksp_rtol
>>>>>>> 1.e-10 this is what printed just before producing strange values:
>>>>>>> KSP Object:
>>>>>>>  type: gmres
>>>>>>>    GMRES: restart=30, using Classical (unmodified) Gram-Schmidt
>>>>>>> Orthogonalization with no iterative refinement
>>>>>>>    GMRES: happy breakdown tolerance 1e-30
>>>>>>>  maximum iterations=10000, initial guess is zero
>>>>>>>  tolerances:  relative=1e-10, absolute=1e-50, divergence=10000
>>>>>>>  left preconditioning
>>>>>>> PC Object:
>>>>>>>  type: none
>>>>>>>  linear system matrix = precond matrix:
>>>>>>>  Matrix Object:
>>>>>>>    type=mffd, rows=70000, cols=70000
>>>>>>>        SNES matrix-free approximation:
>>>>>>>          err=1e-07 (relative error in function evaluation)
>>>>>>>          Using wp compute h routine
>>>>>>>          Computes normA
>>>>>>>
>>>>>>>
>>>>>>> And just to make sure that I havent misunderstood how SNES and TS work:
>>>>>>> If the original 3-stage RK uses (my numbering):
>>>>>>> 1.  RO0(L)=RO(L)
>>>>>>>     Get_DRO(RO(L))
>>>>>>>     RO(L)=RO0(L)+CFL*DRO(L)
>>>>>>> 2.  RO0(L)=.5*(RO0(L)+RO(L))
>>>>>>>     Get_DRO(RO(L))
>>>>>>>     RO(L)=RO0(L)+.5*CFL*DRO(L)
>>>>>>> 3.  Get_DRO(RO(L))
>>>>>>>     RO(L)=RO0(L)+.5*CFL*DRO(L)
>>>>>>>
>>>>>>> Then this should be in TS which should return du/dt which is DRO:
>>>>>>>      RO(L)=xx(1,L)
>>>>>>>      Get_DRO(RO(L))
>>>>>>>      ff(1,L) = DRO(L)
>>>>>>>
>>>>>>> And in SNES with back euler:
>>>>>>>      (Old RO from previous iteration ORO(L)
>>>>>>>      RO(L)=xx(1,L)
>>>>>>>      Get_DRO(RO(L))
>>>>>>>      ff(1,L)= RO(L)-OLD(1,L)-TSF(L)*DRO(L)
>>>>>>>
>>>>>>>
>>>>>>> This became a long mail, I hope this shows if I missed something vital.
>>>>>>> /nisse
>>>>>>> On 3/16/06, Nils Erik Svangård <nilserik at gmail.com> wrote:
>>>>>>>> Barry,
>>>>>>>> the problem is making the objectfile, but I'll try again when I have
>>>>>>>> the code. I will check the makefile for the c-examples.
>>>>>>>> /nisse
>>>>>>>>
>>>>>>>> On 3/16/06, Barry Smith <bsmith at mcs.anl.gov> wrote:
>>>>>>>>>
>>>>>>>>>    Nisse,
>>>>>>>>>
>>>>>>>>>      Just list it in your makefile with all your other object
>>>>>>>>> files (that come from Fortran). Send the output if this fails.
>>>>>>>>>
>>>>>>>>>     Barry
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Thu, 16 Mar 2006, Nils Erik Svangård wrote:
>>>>>>>>>
>>>>>>>>>> I havent managed to get rk.c compiled with changes. how do I compile
>>>>>>>>>> it in my working directory to get a object file. I just realised that
>>>>>>>>>> I probably forgot to link it against \$TSLIB but should I need to that
>>>>>>>>>> fortran and the c code?
>>>>>>>>>> Or what am I doing wrong (I not that good with C++ and linking).
>>>>>>>>>> /nisse
>>>>>>>>>>
>>>>>>>>>> On 3/15/06, Barry Smith <bsmith at mcs.anl.gov> wrote:
>>>>>>>>>>>
>>>>>>>>>>>    Both
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Wed, 15 Mar 2006, Nils Erik Svangård wrote:
>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>    Sorry, I forgot. Is the linear solver converging? If not, then that
>>>>>>>>>>>>> is the problem? Use a tolerance like -ksp_rtol 1.e-10 and see if the
>>>>>>>>>>>>> nonlinear solver converges.
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> I'll try that when I have access to the code. I havent checked if the
>>>>>>>>>>>> linear solver converges is thera a -kspmonitor or -kspconvergedreason
>>>>>>>>>>>> I should use?
>>>>>>>>>>>>
>>>>>>>>>>>> /nisse
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Nils-Erik Svangård
>>>>>>>>>> E-Mail: nilserik at gmail.com
>>>>>>>>>> MSN: schweingaard at hotmail.com
>>>>>>>>>> Skype: schweingaard
>>>>>>>>>> Mobil: +46-(0)70-3612178
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Nils-Erik Svangård
>>>>>>>> E-Mail: nilserik at gmail.com
>>>>>>>> MSN: schweingaard at hotmail.com
>>>>>>>> Skype: schweingaard
>>>>>>>> Mobil: +46-(0)70-3612178
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Nils-Erik Svangård
>>>>>>> E-Mail: nilserik at gmail.com
>>>>>>> MSN: schweingaard at hotmail.com
>>>>>>> Skype: schweingaard
>>>>>>> Mobil: +46-(0)70-3612178
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Nils-Erik Svangård
>>>>> E-Mail: nilserik at gmail.com
>>>>> MSN: schweingaard at hotmail.com
>>>>> Skype: schweingaard
>>>>> Mobil: +46-(0)70-3612178
>>>>>
>>>>>
>>>>
>>>
>>>
>>> --
>>> Nils-Erik Svangård
>>> E-Mail: nilserik at gmail.com
>>> MSN: schweingaard at hotmail.com
>>> Skype: schweingaard
>>> Mobil: +46-(0)70-3612178
>>>
>>
>>
>> --
>> Nils-Erik Svangård
>> E-Mail: nilserik at gmail.com
>> MSN: schweingaard at hotmail.com
>> Skype: schweingaard
>> Mobil: +46-(0)70-3612178
>>
>
>
> --
> Nils-Erik Svangård
> E-Mail: nilserik at gmail.com
> MSN: schweingaard at hotmail.com
> Skype: schweingaard
> Mobil: +46-(0)70-3612178
>
>
```