[petsc-users] Stiff ODEs

[Matthew Knepley]

On Thu, Dec 5, 2013 at 7:38 AM, Katy Ghantous <katyghantous at gmail.com>wrote:

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

This makes no sense. The makefiles appear correct, and the gmres makefile
has the dgmres
directory, but no record of it building in that directory is in the
makefile.

Jed, how could #requiresscalar be failing?

   Matt


> 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
>>
>
>


-- 
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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