[petsc-users] Stiff ODEs

[Katy Ghantous]

On Thu, Dec 5, 2013 at 12:40 PM, Matthew Knepley <knepley at gmail.com> wrote:

> On Thu, Dec 5, 2013 at 5:25 AM, Katy Ghantous <katyghantous at gmail.com>wrote:
>
>> 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.
>>
>
> It is.
>
>
>> 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'
>>
>
> Send make.log.
>
>   Matt
>
>
>> 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.
>>>
>>
>>
>
>
> --
> 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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