On Thu, Dec 5, 2013 at 7:21 AM, Katy Ghantous <[email protected]>wrote: > > On Thu, Dec 5, 2013 at 12:40 PM, Matthew Knepley <[email protected]>wrote: > >> 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. >> > 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 <[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 >> > > -- 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
