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 <[email protected]> wrote: > Katy Ghantous <[email protected]> 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. >
