[petsc-users] Stiff ODEs

[Katy Ghantous]

thank you!
i used master from petsc-dev on mac and have TSRK working now.

i am using an explicit scheme since its a set of coupled nonlinear
equations:

dφn/d t = an φn-2φn-1 - bn φn-1φn+1 + cn φn+1φn+2

where n can go up to 24 or so.. I didnt think it is possible to solve it
implicitly. and TSRK works for it now.

But i need petsc on linux too, and testing to verify installation (same
options on configure as mac expect arch) gave an error:


/home/katy/petsc/linux-gnu-cxx-debug/bin/mpicxx -o ex19.o -c -Wall
-Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g -O0  -fPIC
-I/home/katy/petsc/include
-I/home/katy/petsc/linux-gnu-cxx-debug/include    `pwd`/ex19.c
/home/katy/petsc/linux-gnu-cxx-debug/bin/mpicxx -Wall -Wwrite-strings
-Wno-strict-aliasing -Wno-unknown-pragmas -g -O0  -o ex19  ex19.o
-Wl,-rpath,/home/katy/petsc/linux-gnu-cxx-debug/lib
-L/home/katy/petsc/linux-gnu-cxx-debug/lib  -lpetsc
-Wl,-rpath,/home/katy/petsc/linux-gnu-cxx-debug/lib -lf2clapack -lf2cblas
-lm -lpthread -lm -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.6
-L/usr/lib/gcc/x86_64-linux-gnu/4.6 -Wl,-rpath,/usr/lib/x86_64-linux-gnu
-L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu
-L/lib/x86_64-linux-gnu -lmpichcxx -lstdc++ -ldl -lmpich -lopa -lmpl -lrt
-lpthread -lgcc_s -ldl
/home/katy/petsc/linux-gnu-cxx-debug/lib/libpetsc.so: undefined reference
to `SNESDefaultMatrixFreeCreate2(_p_SNES*, _p_Vec*, _p_Mat**)'
/home/katy/petsc/linux-gnu-cxx-debug/lib/libpetsc.so: undefined reference
to `KSPCreate_DGMRES'
/home/katy/petsc/linux-gnu-cxx-debug/lib/libpetsc.so: undefined reference
to `PCCreate_TFS'




On Tue, Dec 3, 2013 at 6:13 PM, Jed Brown <jedbrown at mcs.anl.gov> wrote:

> Katy Ghantous <katyghantous at gmail.com> writes:
>
> > Hi,
> > I have just started with Petsc and have very elementary equations.
> > I am trying to solve a set of stiff ODEs explicitly.
>
> If your ODEs are stiff, why are you trying to use an explicit method?
> (A common definition of "stiff" is that explicit methods do not work
> well.)
>
> > They are very stiff and was hoping to use TSRK with variable time
> > steps, but it is throwing a segmentation fault
>
> Always show the full error message.  Please also use 'master' from
> petsc-dev, because TSRK was overhauled recently to be consistent with
> the other integrators (and adding a bunch of new functionality).
>
>   https://bitbucket.org/petsc/petsc/wiki/
>
> > otherwise non existent with Euler or TSSSP.  1. should i look into the
> > TSRK error or is it something with the new version of Petsc?  2. i
> > read somewhere (but cant find the source again) that TSSSP is not
> > recommended for stiff equations (even with the rk solvers set as the
> > type).
>
> Yes, TSSSP is for non-stiff problems that require "strong stability"
> (like controlling total variation or positivity in transport-dominated
> applications).
>
> > Is that correct? if so, what would be most optimized to solve stiff
> > odes explicitly.
>
> Stiff ODEs should be solved *implicitly*.
>
> > 3. If it is not correct and TSSSP is useful for stiff equations, how
> > can i run it with variable time steps, since with TSStep it is taking
> > equal time steps which is the time step that i am specifying as an
> > initial time step TSSetInitialTimeStep.
>
> TSSSP does not have an adaptive controller.  A user can set a post-check
> function that adapts the time step based on a custom stability function
> (e.g., CFL criteria).
>
> TSROSW and TSARKIMEX are IMEX methods that can handle stiff problems.
> They have adaptive error estimators and the like.
>
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