it is already on 'master' upon doing git checkout master.
On Thu, Dec 5, 2013 at 2:35 PM, Matthew Knepley <[email protected]> wrote: > 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 >
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