Ok, thank you. So for AMS there is the option to use PCHYPRESetEdgeConstantVectors. Is there any example somewhere of how this function is supposed to be used? Also, it is possible to set the pc type to hypre inside the code? e.g. PCSetType(pc, <HYPRE>)
-Ari ----- Original Message ----- From: "Satish Balay" <[email protected]> To: "Ari Rappaport" <[email protected]> Cc: "petsc-dev" <[email protected]> Sent: Wednesday, August 17, 2016 1:11:43 PM Subject: Re: [petsc-dev] Algebraic Multigrid balay@asterix /home/balay/petsc/src/ksp/ksp/examples/tutorials (master=) $ ./ex2 -pc_type hypre -h |grep pc_hypre_type -pc_hypre_type <boomeramg> (choose one of) pilut parasails boomeramg ams (PCHYPRESetType) Satish On Wed, 17 Aug 2016, Ari Rappaport wrote: > Hi again, > I am having a problem with the database option -pc_hypre_set_type ams along > with -pc_type hypre. When I run my simulation I get the message "Option left: > name:-pc_hypre_set_type value: ams". > > -Ari > > ----- Original Message ----- > From: "Satish Balay" <[email protected]> > To: "petsc-dev" <[email protected]> > Cc: "Ari Rappaport" <[email protected]> > Sent: Tuesday, August 16, 2016 3:31:16 PM > Subject: Re: [petsc-dev] Algebraic Multigrid > > Or - not use '--with-fc=0'. For some reason '-lm' is getting pulled in via > gfortran - not gcc [on this machine] > > I've pushed the following fix - to maint/3.7 > > https://bitbucket.org/petsc/petsc/commits/2d90af56370c3153360ed340bfa06d4e662fceff > > Satish > > On Tue, 16 Aug 2016, Satish Balay wrote: > > > >> > > /home/mantis/petsc/petsc-3.6.4/linux-gnu/externalpackages/hypre-2.10.0b-p4/src/utilities/exchange_data.c:205: > > undefined reference to `ceil' > > << > > > > Try adding configure flag: LIBS=-lm > > > > BTW: > > > > >>>>>>> > > Working directory: /home/mantis/petsc/petsc-3.6.4 > > > > Executing: mpicc -show > > stdout: gcc -fPIC -g3 -I/home/mantis/petsc/petsc-3.7.2/linux-gnu/include > > -L/home/mantis/petsc/petsc-3.7.2/linux-gnu/lib -Wl,-rpath > > -Wl,/home/mantis/petsc/petsc-3.7.2/linux-gnu/lib -Wl,--enable-new-dtags > > -lmpi > > <<<<<<< > > > > Mixing petsc versions might cause issues.. > > > > Satish > > > > On Tue, 16 Aug 2016, Ari Rappaport wrote: > > > > > Hi Barry, > > > Sorry for the late reply. Here is my configure.log file. I am assuming > > > you meant the configure.log in the petsc-3.6.4 home directory. > > > > > > -Ari > > > > > > ----- Original Message ----- > > > From: "Barry Smith" <[email protected]> > > > To: "Ari Rappaport" <[email protected]> > > > Cc: "Mark Adams" <[email protected]>, "For users of the development version > > > of PETSc" <[email protected]> > > > Sent: Thursday, August 11, 2016 3:59:47 PM > > > Subject: Re: [petsc-dev] Algebraic Multigrid > > > > > > > > > > On Aug 11, 2016, at 4:42 PM, Ari Rappaport <[email protected]> wrote: > > > > > > > > Hi Guys, > > > > So the algebraic multigrid works great for a Poisson equation. However, > > > > it's choking on our Maxwell's Equations solver which is a form of > > > > curl/curl if I'm not mistaken. > > > > > > Maxwell's equations are tricky for multigrid. hypre has a solver > > > specific for Maxwell's equation, you need to check it out; note this is > > > not just running with hypre boomerAMG. If you run boomerAMG directly with > > > Maxwell's you will not get satisfactory results. > > > > > > > I was going to give hypre AMS a try, but I'm having trouble installing > > > > it. I'm getting the error "Downloaded hypre could not be used". > > > > > > Send configure.log > > > > > > > > > > I'm using Ubuntu 14.04 if that makes a difference. Also, is > > > > non-algebraic multigrid a reasonable choice for Maxwell's Equations? > > > > > > Even with geometric multigrid Maxwell's equations are nontrivial; you > > > will need to do some literature search to determine how to handle the > > > restriction/interpolation and smoothing to work well for Maxwell. > > > > > > Barry > > > > > > > > > > > Thanks, > > > > Ari > > > > > > > > ----- Original Message ----- > > > > From: "Barry Smith" <[email protected]> > > > > To: "Ari Rappaport" <[email protected]> > > > > Cc: "Mark Adams" <[email protected]>, "For users of the development > > > > version of PETSc" <[email protected]> > > > > Sent: Wednesday, August 10, 2016 2:02:10 PM > > > > Subject: Re: [petsc-dev] Algebraic Multigrid > > > > > > > > > > > >> On Aug 10, 2016, at 2:52 PM, Ari Rappaport <[email protected]> wrote: > > > >> > > > >> Hi Mark, > > > >> There was indeed a bug on our end. Now that we fixed it everything is > > > >> working correctly even in parallel. I have one question still though. > > > >> Is there a way to get the mg_levels_pc_type jacobi option > > > >> set in the code without passing it as an argument to PetscInitialize? > > > >> I'm using PCGAMGSetType(pc, PCJACOBI) but it doesn't seem to be > > > >> working. > > > > > > > > You can call PetscOptionsSetValue("-<appropriate > > > > prefix>_mg_levels_pc_type","jacobi") in the code anywhere before your > > > > code creates the SNES or KSP object you are using. This is equivalent > > > > to putting it on the command line. > > > > > > > > Barry > > > > > > > >> > > > >> > > > >> -Ari > > > >> > > > >> ----- Original Message ----- > > > >> From: "Mark Adams" <[email protected]> > > > >> To: "Ari Rappaport" <[email protected]> > > > >> Cc: "For users of the development version of PETSc" > > > >> <[email protected]> > > > >> Sent: Wednesday, July 27, 2016 7:24:24 PM > > > >> Subject: Re: [petsc-dev] Algebraic Multigrid > > > >> > > > >> There is clearly something very wrong with your code. I would suggest > > > >> starting with an example code for instance > > > >> KSP/examples/tutorial/ex56.c and incrementally add your operator to > > > >> get something that is working. > > > >> > > > >> > > > >> Also if you have multiple degrees of freedom per vertex, for instance > > > >> elasticity, then you want to set the block size of the matrix > > > >> accordingly. > > > >> > > > >> On Wednesday, July 27, 2016, Ari Rappaport < [email protected] > wrote: > > > >> > > > >> > > > >> Hi Mark, > > > >> We added the Jacobi line and it appears to accept that flag now. > > > >> However, we are getting all zeros for the solution vector. And PETSc > > > >> is claiming to have converged in 7 iterations to the relative > > > >> tolerance. > > > >> > > > >> -Ari > > > >> > > > >> ----- Original Message ----- > > > >> From: "Mark Adams" < [email protected] > > > > >> To: "Ari Rappaport" < [email protected] >, "For users of the > > > >> development version of PETSc" < [email protected] > > > > >> Sent: Wednesday, July 27, 2016 3:26:03 PM > > > >> Subject: Re: [petsc-dev] Algebraic Multigrid > > > >> > > > >> > > > >> Please keep this on the Petsc list. > > > >> > > > >> We seem to have lost Jacobi smoother again. I'm suspecting that you're > > > >> some funny character in your line with Jacobi that is Confusing the > > > >> parser. Get back to the old file with the two two Jacobi entries and > > > >> delete the other line and get Jacobi in the KSP view output. There > > > >> should be no SOR in the output. > > > >> > > > >> > > > >> On Wednesday, July 27, 2016, Ari Rappaport < [email protected] > wrote: > > > >> > > > >> > > > >> Hi Mark, > > > >> I added all these new things. The PCAMG is now ending very quickly but > > > >> the residual is unreasonably large by about 10 orders of magnitude. I > > > >> noticed the line "Linear solve did not converge due to > > > >> DIVERGED_INDEFINITE_PC iterations 2" in the output, could this be > > > >> causing the problem? It only appears to be going for 2 iterations now. > > > >> > > > >> -Ari > > > >> > > > >> ----- Original Message ----- > > > >> From: "Mark Adams" < [email protected] > > > > >> To: "Ari Rappaport" < [email protected] > > > > >> Cc: "For users of the development version of PETSc" < > > > >> [email protected] > > > > >> Sent: Tuesday, July 26, 2016 5:07:34 PM > > > >> Subject: Re: [petsc-dev] Algebraic Multigrid > > > >> > > > >> > > > >> Ari, I would also check that your operator is not messed up in > > > >> parallel. The solver is looking pretty solid. > > > >> > > > >> > > > >> Also, you can configure PETSc with hypre and use '-pc_type hypre'. If > > > >> hypre is also good in serial but hosed on multi-proc then it is most > > > >> probably your operator. > > > >> > > > >> > > > >> > > > >> > > > >> On Tue, Jul 26, 2016 at 6:58 PM, Mark Adams < [email protected] > wrote: > > > >> > > > >> > > > >> > > > >> So remove one of the -mg_levels_pc_type jacobi and add > > > >> -mg_coarse_ksp_type preonly, then verify that this works on one proc > > > >> and then try two procs. > > > >> > > > >> > > > >> > > > >> > > > >> On Tue, Jul 26, 2016 at 6:56 PM, Mark Adams < [email protected] > wrote: > > > >> > > > >> > > > >> > > > >> Oh, actually this worked. You have this ...pc_type jacobi in there > > > >> twice, so one of them was "unused". > > > >> > > > >> > > > >> Try this with 2 processors now. > > > >> > > > >> > > > >> > > > >> > > > >> On Tue, Jul 26, 2016 at 6:42 PM, Mark Adams < [email protected] > wrote: > > > >> > > > >> > > > >> > > > >> > > > >> > > > >> > > > >> > > > >> On Tue, Jul 26, 2016 at 6:24 PM, Ari Rappaport < [email protected] > > > > >> wrote: > > > >> > > > >> > > > >> So I commented out the line PCSetType(pc, PCGAMG). The line > > > >> KSPSetFromOptions(ksp) was already in the code at the end of our > > > >> initialization routine. I also added .petscrc to the working dir. Here > > > >> is the current output. It seems as if Option left: > > > >> name:-mg_levels_pc_type jacobi (no value) is still present in the > > > >> output..I dunno. > > > >> > > > >> > > > >> > > > >> Yea, I dunno either. If you use -help you will get printout of the > > > >> available options. If you do this you will see stuff like > > > >> -mg_levels_1_ ... you can also see this in the ksp_view. There is a > > > >> shortcut that lets you _not_ put "_1" in. Try putting this in for each > > > >> level like so: > > > >> > > > >> > > > >> > > > >> -mg_levels_1_pc_type jacobi > > > >> > > > >> -mg_levels_2_pc_type jacobi > > > >> -mg_levels_3_pc_type jacobi > > > >> > > > >> > > > >> > > > >> I also notice that the coarse grid ksp is GMRES. This is our fault. It > > > >> should be preonly. Add: > > > >> > > > >> > > > >> -mg_coarse_ksp_type preonly > > > >> > > > >> > > > >> > > > >> > > > >> > > > >> > > > >> > > > >> > > > >> > > > >> > > > >> > > > >> > > > >> > > > >> > > > >> > > > >> > > > >> > > > >> > > > >> -Ari > > > >> > > > >> ----- Original Message ----- > > > >> From: "Mark Adams" < [email protected] > > > > >> To: "Ari Rappaport" < [email protected] >, "For users of the > > > >> development version of PETSc" < [email protected] > > > > >> Sent: Tuesday, July 26, 2016 4:03:03 PM > > > >> Subject: Re: [petsc-dev] Algebraic Multigrid > > > >> > > > >> > > > >> > > > >> > > > >> At the end of this you have: > > > >> > > > >> > > > >> > > > >> #PETSc Option Table entries: > > > >> -ksp_view > > > >> -mg_levels_pc_type jacobi > > > >> -options_left > > > >> #End of PETSc Option Table entries > > > >> There is one unused database option. It is: > > > >> Option left: name:-mg_levels_pc_type jacobi (no value) > > > >> > > > >> > > > >> So this jacobi parameter is not being used. > > > >> > > > >> > > > >> Do you call KPSSetFromOptions? Do you set solver parameters in the > > > >> code? Like PCGAMG? > > > >> > > > >> > > > >> You should not set anything in the code, it just confuses things at > > > >> this point. Use KSPSetFromOptions(). You can hardwire stuff before > > > >> this call, this just lets you set the defaults, but you should always > > > >> call this last to let command line parameters override the defaults. > > > >> > > > >> > > > >> You can put this in a .petscrc file in the working directory and try > > > >> again. > > > >> > > > >> > > > >> > > > >> -ksp_type cg > > > >> -ksp_max_it 50 > > > >> > > > >> -ksp_rtol 1.e-6 > > > >> -ksp_converged_reason > > > >> -pc_type gamg > > > >> -pc_gamg_type agg > > > >> -pc_gamg_agg_nsmooths 1 > > > >> -pc_gamg_coarse_eq_limit 10 > > > >> -pc_gamg_reuse_interpolation true > > > >> -pc_gamg_square_graph 1 > > > >> -pc_gamg_threshold -0.05 > > > >> -mg_levels_ksp_max_it 2 > > > >> -mg_levels_ksp_type chebyshev > > > >> -mg_levels_esteig_ksp_type cg > > > >> -mg_levels_esteig_ksp_max_it 10 > > > >> -mg_levels_ksp_chebyshev_esteig 0,.05,0,1.05 > > > >> -mg_levels_pc_type jacobi > > > >> -pc_hypre_type boomeramg > > > >> -pc_hypre_boomeramg_no_CF > > > >> -pc_hypre_boomeramg_agg_nl 1 > > > >> -pc_hypre_boomeramg_coarsen_type HMIS > > > >> -pc_hypre_boomeramg_interp_type ext+i > > > >> > > > >> > > > >> > > > >> > > > >> > > > > > > > > > > > > > > > >
