[petsc-users] Stiff ODEs

[Katy Ghantous]

it is already on 'master' upon doing git checkout master.



On Thu, Dec 5, 2013 at 2:35 PM, Matthew Knepley <knepley at gmail.com> wrote:

> On Thu, Dec 5, 2013 at 7:21 AM, Katy Ghantous <katyghantous at gmail.com>wrote:
>>
>> 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.
>>>
>>
> It looks like you have corrupt source. Did you alter the source in any
> way. I assume you got it from
> git, so you can do 'git checkout master'.
>
> If you think it should be correct,  send src/ksp/ksp/impls/gmres/makefile
> and src/ksp/ksp/impls/gmres/dgmres/makefile.
>
>    Matt
>
>
>>   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
>>>
>>
>>
>
>
> --
> 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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