SNES Problem
Nils Erik Svangård
nilserik at gmail.com
Fri Mar 3 02:47:26 CST 2006
Hello again,
> Is it just not compiling because PETSC_ERR_ARG_DOMAIN is not
> defined? Or does it still not work even when you have put the number in?
> What is the error? Or did you get it all working with SNES?
>
It is not compiling because PETSC_ERR_ARG_DOMAIN is not defined:
error on line 585 of SNESG3D2.F: data type is undefined for variable
PETSC_ERR_ARG_DOMAIN
I tried putting a number in, then it compiles but complains while
linking that the Push() and Pop() functions is not defined. I made a
workaround by adding a variable in a common block and setting it
before returning from a non physical value in the FormFunction. Now I
can compile and when there is a non-physical value it returns and
resumes with a smaller timestep.
SNES still give non physical values which are hard to add checks for
in the program (e.g sqrt(RO(L)-RO(L+1))).
Did I understand correctly that SNES does a linesearch and probably
goes for a solution which isnt the one I looking for? Does SNES use
the linesearch algorithm when I use -snes_mf (which I use)?
> It may work automatically with TS; you would just set TS with a
> smaller timestep and call TSSolve again?
>
OK, I'll add a check and put TSSolve in a while loop.
My SNESSolve loop looks like this right now:
call VecCreateSeq(PETSC_COMM_SELF,N,x,ierr)
call VecDuplicate(x,r,ierr)
call VecDuplicate(x,xb,ierr)
call SNESCreate(PETSC_COMM_SELF,snes,ierr)
call SNESSetFunction(snes,r,FormFunction,PETSC_NULL_OBJECT,ierr)
call SNESSetFromOptions(snes,ierr)
call FormInitialGuess(x,ierr)
call VecCopy(x,xb,ierr)
write(6,*)zero,dt,tmax,i1000
step=0
timestep=dt
bang=0
C While loop
10 if (step .le. 100) then
C call PetscExceptionPush(87,ierr)
C call PetscExceptionPush(PETSC_ERR_ARG_DOMAIN,ierr)
call SNESSolve(snes,PETSC_NULL_OBJECT,x,ierr)
ierr=bang
C call PetscExceptionPop(87,ierr2)
IF ( ierr .EQ. 87) THEN
timestep=timestep/2
call VecCopy(xb,x,ierr)
write(6,*) "No physical solution, trying",
. " with smaller timestep: ",timestep
bang=0
ELSE
call SNESGetConvergedReason(snes,reason,ierr)
IF ( reason .LT. 0 ) THEN
timestep=timestep/2
call VecCopy(xb,x,ierr)
write(6,*)"Solution diverged, trying with",
. " smaller timestep: ",timestep
ELSE
timestep=dt
step=step+1
call VecCopy(x,xb,ierr)
write(6,*) "Solve success, going for step: ",step
write(6,*) "Reason: ",reason," ierr: ",ierr
reason=0
ierr=0
ENDIF
ENDIF
goto 10
endif
C End While loop
And the check in the FormFunction:
if (ET(L) .LT. 0) then
ierr = 87
bang = 87
C SETERRQ(87,"Non physical value!",ierr)
return
elseif ( RO(L) .LT. 0 ) then
ierr = 87
bang = 87
return
endif
/nisse
> Barry
>
> I'm adding a petscerror.h for Fortran that includes these values
> Sorry I forgot we hadn't given them for Fortran.
>
> On Thu, 2 Mar 2006, Nils Erik Svangård wrote:
>
> > Hi again,
> > I realised that my implementation was a bit flawed so I have rewritten
> > it again, the push and pop() functions dont seem to work, and they are
> > keeping me from compiling the program, this is the main timestep loop:
> >
> > call VecCreateSeq(PETSC_COMM_SELF,N,x,ierr)
> > call VecDuplicate(x,r,ierr)
> > call VecDuplicate(x,xb,ierr)
> > call SNESCreate(PETSC_COMM_SELF,snes,ierr)
> > call SNESSetFunction(snes,r,FormFunction,PETSC_NULL_OBJECT,ierr)
> > call SNESSetFromOptions(snes,ierr)
> > call FormInitialGuess(x,ierr)
> > call VecCopy(x,xb,ierr)
> > write(6,*)zero,dt,tmax,i1000
> > step=0
> > timestep=dt
> > C While loop
> > 10 if (step .le. 100) then
> > call PetscExceptionPush(87,ierr)
> > call SNESSolve(snes,PETSC_NULL_OBJECT,x,ierr)
> > call PetscExceptionPop(87,ierr2)
> >
> > call SNESGetConvergedReason(snes,reason,ierr)
> > IF ( reason .LT. 0 ) THEN
> > timestep=timestep/2
> > VecCopy(xb,x,ierr)
> > write(6,*)"Solution diverged, trying with",
> > . " smaller timestep: ",timestep
> > ELSE
> > IF ( ierr .EQ. 87) THEN
> > timestep=timestep/2
> > VecCopy(xb,x,ierr)
> > write(6,*) "No physical solution, trying",
> > . " with smaller timestep: ",timestep
> > ELSE
> > timestep=dt
> > step=step+1
> > VecCopy(x,xb,ierr)
> > write(6,*) "Solve success, going for step: ",step
> > ENDIF
> > ENDIF
> > goto 10
> > endif
> > C End While loop
> >
> > And in my Formfunction I have added the following check:
> > if (ET(L) .LT. 0) then
> > ierr = 87
> > return
> > endif
> >
> > PETSC_ERR_ARG_DOMAIN didnt work: error on line 6500 of SNESG3D2.F:
> > data type is undefined for variable PETSC_ERR_ARG_DOMAIN
> > Even thought I had petsc.h included.
> >
> > Can I do this check when I use TS also? I have the sameproblem with
> > the values being negative when using TS.
> >
> >
> > /nisse
> >
> >
> > On 2/27/06, Barry Smith <bsmith at mcs.anl.gov> wrote:
> >>
> >> SNES works by computing p = -approxinv(J)*F(uold) and
> >> then does a line search on unew = uold + lambda*p to get the
> >> new u. First it uses a test value of 1 for lambda so it
> >> tries to compute F(uold + p). It is possible that uold + p
> >> has some "non-physical" values in it. There are two ways
> >> you can try handling it:
> >>
> >> 1) Before doing the linesearch SNES calls a "precheck" function,
> >> that can change the step if it decides there is a problem
> >> with the step (like it is too long). You can provide your
> >> own precheck function with SNESLineSearchSetPreCheck() it could,
> >> for example, shrink the Newton direction to make it remain physical.
> >>
> >> or 2) when your form function detects an illegal value it calls
> >> SETERRQ(PETSC_ERR_ARG_DOMAIN,"Nonphysical function input"); Note:
> >> this is before it takes the square root of the negative number,
> >> so check the number and call the error before calling SETERRQ().
> >> (If using Fortran then simply set ierr = PETSC_ERR_ARG_DOMAIN and
> >> then immediately return). Then replace your call to SNESSolve with
> >> ierr = PetscExceptionTry1(SNESSolve(snes,b,x),PETSC_ERR_ARG_DOMAIN);
> >> if (PetscExceptionCaught(ierr,PETSC_ERR_ARG_DOMAIN)) {
> >> /* this means your function found a non-physical value so
> >> cut your time-step and continue through the loop again. */
> >> Put code to do this here.
> >> }
> >> If using fortran then do
> >> call PetscExceptionPush(PETSC_ERR_ARG_DOMAIN,ierr)
> >> call SNESSolve(snes,b,x,ierr)
> >> call PetscExceptionPop(PETSC_ERR_ARG_DOMAIN,anotherierr)
> >> if (ierr == PETSC_ERR_ARG_DOMAIN) then
> >> non-physical value so cut the time-step and try again
> >> else ! everything is normal so take the next time-step
> >>
> >> Barry
> >>
> >> The Fortran interface may be missing PetscExceptionPush() and Pop()
> >> if so let us know and we'll provide the patch.
> >>
> >> On Mon, 27 Feb 2006, Nils Erik Svangård wrote:
> >>
> >>> Hi all,
> >>>
> >>> I have problems solving some CFD problems using SNES and my custom
> >>> back-euler. I have 7 equations that I want to solve.
> >>>
> >>> First my FormFunction copies the values from the Vec that SNES uses to
> >>> the variables that my code use:
> >>>
> >>> RO(L)=xx(1,L)
> >>> RU(L)=xx(2,L)
> >>> RV(L)=xx(3,L)
> >>> RW(L)=xx(4,L)
> >>> ET(L)=xx(5,L)
> >>> RQ(L)= xx(6,L)
> >>> REPS(L)=xx(7,L)
> >>>
> >>> Here I also print the values of ET(2) for debugging:
> >>>
> >>> write(6,*)"ET(2) = xx(5,2) : ",ET(2)," = ",xx(5,2)
> >>>
> >>> Then I get the fluxes by calling custom functions
> >>>
> >>> call AUXVR
> >>> call VGRAD
> >>> call FLUX
> >>> call KESRC
> >>>
> >>> Then I perform back-euler save the new value to so that I can use it
> >>> in the next iterationi (TSF(L) is Time step function, which is set by
> >>> hand and is the same for all L):
> >>>
> >>> ff(1,L) = RO(L)-OLD(1,L)-TSF(L)*DRO(L)
> >>> ff(2,L) = RU(L)-OLD(2,L)-TSF(L)*DRU(L)
> >>> ff(3,L) = RV(L)-OLD(3,L)-TSF(L)*DRV(L)
> >>> ff(4,L) = RW(L)-OLD(4,L)-TSF(L)*DRW(L)
> >>> ff(5,L) = ET(L)-OLD(5,L)-TSF(L)*DET(L)
> >>> ff(6,L) = RQ(L)-OLD(6,L)-TSF(L)*DRQ(L)
> >>> ff(7,L) = REPS(L)-OLD(7,L)-TSF(L)*DREPS(L)
> >>>
> >>> And save the new value of RO-REPS to use in the next iteration of back-euler:
> >>>
> >>> OLD(1,L)=RO(L)
> >>> OLD(2,L)=RU(L)
> >>> OLD(3,L)=RV(L)
> >>> OLD(4,L)=RW(L)
> >>> OLD(5,L)=ET(L)
> >>> OLD(6,L)=RQ(L)
> >>> OLD(7,L)=REPS(L)
> >>>
> >>> Here I print the values of L=2 as above for debugging:
> >>>
> >>> write(6,*)ff(5,2)," = ",ET(2),"-",OLD(5,2),"-",TSF(2),"*",DET(2)
> >>>
> >>>
> >>>
> >>> The program exit abnormaly after 33 runs of the FormFunction. The
> >>> cause of this is that AUXVR tries to perform sqrt(ET(2)) when ET(2) is
> >>> negative, ET is the total energy and should never be negative. It
> >>> seems that all of a sudden the PETSc SNES solver decides to supply the
> >>> FormFunction with a negative ET value. I need help understanding why
> >>> and how to fix it (if it is fixable).
> >>>
> >>> Here is the output of:
> >>> write(6,*)"ET(2) = xx(5,2) : ",ET(2)," = ",xx(5,2)
> >>> Which is in the beginning of my FormFunction.
> >>> And:
> >>> write(6,*)ff(5,2)," = ",ET(2),"-",OLD(5,2),"-",TSF(2),"*",DET(2)
> >>> Which is in the end of my Formfunction.
> >>>
> >>> 1. ET(2) = xx(5,2) : 253250. = 253250.000000000
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.4126563437192 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.941266E+08
> >>> 2. ET(2) = xx(5,2) : 253250. = 253250.000010259
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.4126563437192 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.941266E+08
> >>> 3. ET(2) = xx(5,2) : 253250. = 253249.999999988
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.4132419437260 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.941324E+08
> >>> 4. ET(2) = xx(5,2) : 253250. = 253250.000048432
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.4126563437192 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.941266E+08
> >>> 5. ET(2) = xx(5,2) : 253250. = 253249.999999872
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.4177283437784 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.941773E+08
> >>> 6. ET(2) = xx(5,2) : 253250. = 253250.000071113
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.4126563437192 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.941266E+08
> >>> 7. ET(2) = xx(5,2) : 253250. = 253249.999980115
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.4453347441010 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.944533E+08
> >>> 8. ET(2) = xx(5,2) : 253250. = 253250.000037298
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.4082723436679 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.940827E+08
> >>> 9. ET(2) = xx(5,2) : 253250. = 253249.999942706
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.4082723436679 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.940827E+08
> >>> 10. ET(2) = xx(5,2) : 253250. = 253249.999948703
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.4126563437192 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.941266E+08
> >>> 11. ET(2) = xx(5,2) : 253250. = 253250.000007808
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.7283811474088 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.972838E+08
> >>> 12. ET(2) = xx(5,2) : 253250. = 253250.000018146
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.4126563437192 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.941266E+08
> >>> 13. ET(2) = xx(5,2) : 253250. = 253250.000001865
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 28.3742819315846 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.837428E+08
> >>> 14. ET(2) = xx(5,2) : 253250. = 253249.999997296
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.4126563437192 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.941266E+08
> >>> 15. ET(2) = xx(5,2) : 253250. = 253250.000000049
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 30.6548963582361 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -3.065490E+08
> >>> 16. ET(2) = xx(5,2) : 253250. = 253250.000022870
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.4126563437192 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.941266E+08
> >>> 17. ET(2) = xx(5,2) : 253250. = 253249.999999716
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.5326051451209 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.953260E+08
> >>> 18. ET(2) = xx(5,2) : 253250. = 253250.000074328
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.4165187437643 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.941652E+08
> >>> 19. ET(2) = xx(5,2) : 253250. = 253250.000049809
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.4085059436707 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.940851E+08
> >>> 20. ET(2) = xx(5,2) : 253250. = 253250.000019253
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.4126563437192 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.941266E+08
> >>> 21. ET(2) = xx(5,2) : 253250. = 253250.000000189
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.8851075492403 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.988511E+08
> >>> 22. ET(2) = xx(5,2) : 253250. = 253249.999997897
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.4085059436707 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.940851E+08
> >>> 23. ET(2) = xx(5,2) : 253250. = 253249.999975142
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.3961539435263 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.939615E+08
> >>> 24. ET(2) = xx(5,2) : 253250. = 253250.000018324
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.4085059436707 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.940851E+08
> >>> 25. ET(2) = xx(5,2) : 253250. = 253249.999987073
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.4165187437643 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.941652E+08
> >>> 26. ET(2) = xx(5,2) : 253250. = 253249.999980982
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.4165187437643 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.941652E+08
> >>> 27. ET(2) = xx(5,2) : 253250. = 253249.999994645
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.4126563437192 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.941266E+08
> >>> 28. ET(2) = xx(5,2) : 253250. = 253249.999962364
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.4165187437643 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.941652E+08
> >>> 29. ET(2) = xx(5,2) : 253250. = 253249.999999921
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.4126563437192 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.941266E+08
> >>> 30. ET(2) = xx(5,2) : 253250. = 253250.000000058
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 28.4019971319085 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.840200E+08
> >>> 31. ET(2) = xx(5,2) : 253250. = 253250.000040348
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.4085059436707 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.940851E+08
> >>> 32. ET(2) = xx(5,2) : 253250. = 253250.000005245
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.4126563437192 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.941266E+08
> >>> 33. ET(2) = xx(5,2) : 253250. = 253250.000005245
> >>> ff(5,2) = ET(2)-OLD(5,2)-TSF(2)*DET(2) : 29.4126563437192 =
> >>> 253250. - 253250.000000000 - 1.000000E-07 * -2.941266E+08
> >>> 34. ET(2) = xx(5,2) : -848141. = -848141.388090847
> >>> --------------------------------------------------------------------------
> >>> 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.
> >>> -----------------------------------------------------------------------
> >>> ./SNESG3D2 on a linux-gnu named sethnx004.vac.com by yy26539 Mon Feb
> >>> 27 14:21:13 2006
> >>> Libraries linked from /home/yy26539/work/NISSE/petsc-2.3.0/lib/linux-gnu
> >>> Configure run at Thu Oct 13 08:23:56 2005
> >>> Configure options --with-cc=gcc --with-fc="f77 -N109"
> >>> --download-mpich=1 --download-mpich-pm=gforker
> >>> --download-f-blas-lapack=1 --with-shared=0
> >>> -----------------------------------------------------------------------
> >>> [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] SNES user function line 0 unknownunknown
> >>> [0]PETSC ERROR: [0] SNESComputeFunction line 788 src/snes/interface/snes.c
> >>> [0]PETSC ERROR: [0] SNESLineSearchCubic line 514 src/snes/impls/ls/ls.c
> >>> [0]PETSC ERROR: --------------------------------------------
> >>> [0]PETSC ERROR: User provided function() line 0 in unknown directory
> >>> unknown file
> >>> [0]PETSC ERROR: Signal received!
> >>> [0]PETSC ERROR: !
> >>>
> >>>
> >>> Suggestions and tips are very welcome!
> >>> /nisse
> >>>
> >>>
> >>> --
> >>> Nils-Erik Svang�rd
> >>> MSN: schweingaard at hotmail.com
> >>> Skype: schweingaard
> >>>
> >>>
> >>
> >
> >
> > --
> > Nils-Erik Svangård
> > MSN: schweingaard at hotmail.com
> > Skype: schweingaard
> >
> >
>
--
Nils-Erik Svangård
E-Mail: nilserik at gmail.com
MSN: schweingaard at hotmail.com
Skype: schweingaard
Mobil: +46-(0)70-3612178
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