On Thu, Dec 5, 2013 at 5:25 AM, Katy Ghantous <[email protected]>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 <[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. >> > > -- 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
