<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Thu, Dec 5, 2013 at 7:38 AM, Katy Ghantous <span dir="ltr"><<a href="mailto:katyghantous@gmail.com" target="_blank">katyghantous@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>it is already on 'master' upon doing git checkout master.</div></div></blockquote><div><br>
</div><div>This makes no sense. The makefiles appear correct, and the gmres makefile has the dgmres</div><div>directory, but no record of it building in that directory is in the makefile.</div><div><br></div><div>Jed, how could #requiresscalar be failing?</div>
<div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="gmail_extra"><div class="gmail_quote">On Thu, Dec 5, 2013 at 2:35 PM, Matthew Knepley <span dir="ltr"><<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div>On Thu, Dec 5, 2013 at 7:21 AM, Katy Ghantous <span dir="ltr"><<a href="mailto:katyghantous@gmail.com" target="_blank">katyghantous@gmail.com</a>></span> wrote:<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="gmail_extra"><div class="gmail_quote">On Thu, Dec 5, 2013 at 12:40 PM, Matthew Knepley <span dir="ltr"><<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div>On Thu, Dec 5, 2013 at 5:25 AM, Katy Ghantous <span dir="ltr"><<a href="mailto:katyghantous@gmail.com" target="_blank">katyghantous@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">thank you! <br>i used master from petsc-dev on mac and have TSRK working now. <br><br>i am using an explicit scheme since its a set of coupled nonlinear equations:<div>
<br><div>dφ<sub>n</sub>/d t = a<sub>n</sub> φ<sub>n-2</sub>φ<sub>n-1</sub> - b<sub>n</sub> φ<sub>n-1</sub>φ<sub>n+1</sub> + c<sub>n</sub> φ<sub>n+1</sub>φ<sub>n+2</sub></div>
<div> </div><div>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.<br></div></div></div></blockquote><div><br></div></div><div>It is.</div><div><div>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><div><div></div><div>But i need petsc on linux too, and testing to verify installation (same options on configure as mac expect arch) gave an error:<br>
<br></div><div><br></div><div>/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<br>
/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 <br>
/home/katy/petsc/linux-gnu-cxx-debug/lib/libpetsc.so: undefined reference to `SNESDefaultMatrixFreeCreate2(_p_SNES*, _p_Vec*, _p_Mat**)'<br>/home/katy/petsc/linux-gnu-cxx-debug/lib/libpetsc.so: undefined reference to `KSPCreate_DGMRES'<br>
/home/katy/petsc/linux-gnu-cxx-debug/lib/libpetsc.so: undefined reference to `PCCreate_TFS'</div></div></div></blockquote><div><br></div></div><div>Send make.log.</div></div></div></div></blockquote></div></div></blockquote>
<div><br></div></div><div>It looks like you have corrupt source. Did you alter the source in any way. I assume you got it from</div><div>git, so you can do 'git checkout master'.</div><div><br></div><div>If you think it should be correct, send src/ksp/ksp/impls/gmres/makefile and src/ksp/ksp/impls/gmres/dgmres/makefile.</div>
<div><br></div><div> Matt</div><div><div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div> Matt</div><div><div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="gmail_extra"><div class="gmail_quote">On Tue, Dec 3, 2013 at 6:13 PM, Jed Brown <span dir="ltr"><<a href="mailto:jedbrown@mcs.anl.gov" target="_blank">jedbrown@mcs.anl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>Katy Ghantous <<a href="mailto:katyghantous@gmail.com" target="_blank">katyghantous@gmail.com</a>> writes:<br>
<br>
> Hi,<br>
> I have just started with Petsc and have very elementary equations.<br>
> I am trying to solve a set of stiff ODEs explicitly.<br>
<br>
</div>If your ODEs are stiff, why are you trying to use an explicit method?<br>
(A common definition of "stiff" is that explicit methods do not work<br>
well.)<br>
<div><br>
> They are very stiff and was hoping to use TSRK with variable time<br>
> steps, but it is throwing a segmentation fault<br>
<br>
</div>Always show the full error message. Please also use 'master' from<br>
petsc-dev, because TSRK was overhauled recently to be consistent with<br>
the other integrators (and adding a bunch of new functionality).<br>
<br>
<a href="https://bitbucket.org/petsc/petsc/wiki/" target="_blank">https://bitbucket.org/petsc/petsc/wiki/</a><br>
<div><br>
> otherwise non existent with Euler or TSSSP. 1. should i look into the<br>
> TSRK error or is it something with the new version of Petsc? 2. i<br>
> read somewhere (but cant find the source again) that TSSSP is not<br>
> recommended for stiff equations (even with the rk solvers set as the<br>
> type).<br>
<br>
</div>Yes, TSSSP is for non-stiff problems that require "strong stability"<br>
(like controlling total variation or positivity in transport-dominated<br>
applications).<br>
<div><br>
> Is that correct? if so, what would be most optimized to solve stiff<br>
> odes explicitly.<br>
<br>
</div>Stiff ODEs should be solved *implicitly*.<br>
<div><br>
> 3. If it is not correct and TSSSP is useful for stiff equations, how<br>
> can i run it with variable time steps, since with TSStep it is taking<br>
> equal time steps which is the time step that i am specifying as an<br>
> initial time step TSSetInitialTimeStep.<br>
<br>
</div>TSSSP does not have an adaptive controller. A user can set a post-check<br>
function that adapts the time step based on a custom stability function<br>
(e.g., CFL criteria).<br>
<br>
TSROSW and TSARKIMEX are IMEX methods that can handle stiff problems.<br>
They have adaptive error estimators and the like.<br>
</blockquote></div><br></div>
</blockquote></div></div></div><span><font color="#888888"><br><br clear="all"><span class="HOEnZb"><font color="#888888"><span><font color="#888888"><div><br></div>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener
</font></span></font></span></font></span></div></div><span class="HOEnZb"><font color="#888888">
</font></span></blockquote></div><span class="HOEnZb"><font color="#888888"><br></font></span></div><span class="HOEnZb"><font color="#888888">
</font></span></blockquote></div></div></div><span class="HOEnZb"><font color="#888888"><div><div><br><br clear="all"><div><br></div>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener
</div></div></font></span></div></div>
</blockquote></div><br></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener
</div></div>