I suggest you check the code is valgrind clean. See the petsc FAQ page for details of how to do this.
Thanks, Dave On Sun, 8 Jan 2017 at 04:57, Mark Adams <mfad...@lbl.gov> wrote: > This error seems to be coming from the computation of the extreme > eigenvalues of the matrix for smoothing in smoothed aggregation. > > Are you getting good solutions with hypre? This error looks like it might > just be the first place where a messed up matrix fails in GAMG. > > On Sat, Jan 7, 2017 at 10:23 PM, Matthew Knepley <knep...@gmail.com> > wrote: > > On Sat, Jan 7, 2017 at 7:38 PM, Manuel Valera <mval...@mail.sdsu.edu> > wrote: > > Ok great, i tried those command line args and this is the result: > > when i use -pc_type gamg: > > [1]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > > > [1]PETSC ERROR: Petsc has generated inconsistent data > > > [1]PETSC ERROR: Have un-symmetric graph (apparently). Use > '-pc_gamg_sym_graph true' to symetrize the graph or '-pc_gamg_threshold > -1.0' if the matrix is structurally symmetric. > > > [1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > > > [1]PETSC ERROR: Petsc Release Version 3.7.4, unknown > > > [1]PETSC ERROR: ./ucmsMR on a arch-linux2-c-debug named ocean by valera > Sat Jan 7 17:35:05 2017 > > > [1]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ > --with-fc=gfortran --download-fblaslapack --download-mpich --download-hdf5 > --download-netcdf --download-hypre --download-metis --download-parmetis > --download-trillinos > > > [1]PETSC ERROR: #1 smoothAggs() line 462 in > /usr/dataC/home/valera/petsc/src/ksp/pc/impls/gamg/agg.c > > > [1]PETSC ERROR: #2 PCGAMGCoarsen_AGG() line 998 in > /usr/dataC/home/valera/petsc/src/ksp/pc/impls/gamg/agg.c > > > [1]PETSC ERROR: #3 PCSetUp_GAMG() line 571 in > /usr/dataC/home/valera/petsc/src/ksp/pc/impls/gamg/gamg.c > > > [1]PETSC ERROR: #4 PCSetUp() line 968 in > /usr/dataC/home/valera/petsc/src/ksp/pc/interface/precon.c > > > [1]PETSC ERROR: #5 KSPSetUp() line 390 in > /usr/dataC/home/valera/petsc/src/ksp/ksp/interface/itfunc.c > > > application called MPI_Abort(comm=0x84000002, 77) - process 1 > > > when i use -pc_type gamg and -pc_gamg_sym_graph true: > > > Do everything Barry said. > > However, I would like to track down this error. It could be a bug in our > code. However, it appears to happen in the call > to LAPACK, so it could also be a problem with that library on your > machine. Could you run this case in the debugger > and give the stack trace? > > Thanks, > > Matt > > > ------------------------------------------------------------------------ > > > [0]PETSC ERROR: Caught signal number 8 FPE: Floating Point > Exception,probably divide by zero > > > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > > [0]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind > > > [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS > X to find memory corruption errors > > > [1]PETSC ERROR: > ------------------------------------------------------------------------ > > [1]PETSC ERROR: --------------------- Stack Frames > ------------------------------------ > > > [1]PETSC ERROR: Note: The EXACT line numbers in the stack are not > available, > > > [1]PETSC ERROR: INSTEAD the line number of the start of the function > > > [1]PETSC ERROR: is given. > > > [1]PETSC ERROR: [1] LAPACKgesvd line 42 > /usr/dataC/home/valera/petsc/src/ksp/ksp/impls/gmres/gmreig.c > > > [1]PETSC ERROR: [1] KSPComputeExtremeSingularValues_GMRES line 24 > /usr/dataC/home/valera/petsc/src/ksp/ksp/impls/gmres/gmreig.c > > > [1]PETSC ERROR: [1] KSPComputeExtremeSingularValues line 51 > /usr/dataC/home/valera/petsc/src/ksp/ksp/interface/itfunc.c > > > [1]PETSC ERROR: [1] PCGAMGOptProlongator_AGG line 1187 > /usr/dataC/home/valera/petsc/src/ksp/pc/impls/gamg/agg.c > > > [1]PETSC ERROR: [1] PCSetUp_GAMG line 472 > /usr/dataC/home/valera/petsc/src/ksp/pc/impls/gamg/gamg.c > > > [1]PETSC ERROR: [1] PCSetUp line 930 > /usr/dataC/home/valera/petsc/src/ksp/pc/interface/precon.c > > > [1]PETSC ERROR: [1] KSPSetUp line 305 > /usr/dataC/home/valera/petsc/src/ksp/ksp/interface/itfunc.c > > > [0] PCGAMGOptProlongator_AGG line 1187 > /usr/dataC/home/valera/petsc/src/ksp/pc/impls/gamg/agg.c > > > [0]PETSC ERROR: [0] PCSetUp_GAMG line 472 > /usr/dataC/home/valera/petsc/src/ksp/pc/impls/gamg/gamg.c > > > [0]PETSC ERROR: [0] PCSetUp line 930 > /usr/dataC/home/valera/petsc/src/ksp/pc/interface/precon.c > > > [0]PETSC ERROR: [0] KSPSetUp line 305 > /usr/dataC/home/valera/petsc/src/ksp/ksp/interface/itfunc.c > > > [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > > > when i use -pc_type hypre it actually shows something different on > -ksp_view : > > > KSP Object: 2 MPI processes > > type: gcr > > GCR: restart = 30 > > GCR: restarts performed = 37 > > maximum iterations=10000, initial guess is zero > > tolerances: relative=1e-14, absolute=1e-50, divergence=10000. > > right preconditioning > > using UNPRECONDITIONED norm type for convergence test > > PC Object: 2 MPI processes > > type: hypre > > HYPRE BoomerAMG preconditioning > > HYPRE BoomerAMG: Cycle type V > > HYPRE BoomerAMG: Maximum number of levels 25 > > HYPRE BoomerAMG: Maximum number of iterations PER hypre call 1 > > HYPRE BoomerAMG: Convergence tolerance PER hypre call 0. > > HYPRE BoomerAMG: Threshold for strong coupling 0.25 > > HYPRE BoomerAMG: Interpolation truncation factor 0. > > HYPRE BoomerAMG: Interpolation: max elements per row 0 > > HYPRE BoomerAMG: Number of levels of aggressive coarsening 0 > > HYPRE BoomerAMG: Number of paths for aggressive coarsening 1 > > HYPRE BoomerAMG: Maximum row sums 0.9 > > HYPRE BoomerAMG: Sweeps down 1 > > HYPRE BoomerAMG: Sweeps up 1 > > HYPRE BoomerAMG: Sweeps on coarse 1 > > HYPRE BoomerAMG: Relax down symmetric-SOR/Jacobi > > HYPRE BoomerAMG: Relax up symmetric-SOR/Jacobi > > HYPRE BoomerAMG: Relax on coarse Gaussian-elimination > > HYPRE BoomerAMG: Relax weight (all) 1. > > HYPRE BoomerAMG: Outer relax weight (all) 1. > > HYPRE BoomerAMG: Using CF-relaxation > > HYPRE BoomerAMG: Not using more complex smoothers. > > HYPRE BoomerAMG: Measure type local > > HYPRE BoomerAMG: Coarsen type Falgout > > HYPRE BoomerAMG: Interpolation type classical > > HYPRE BoomerAMG: Using nodal coarsening (with > HYPRE_BOOMERAMGSetNodal() 1 > > HYPRE BoomerAMG: HYPRE_BoomerAMGSetInterpVecVariant() 1 > > linear system matrix = precond matrix: > > Mat Object: 2 MPI processes > > type: mpiaij > > rows=200000, cols=200000 > > total: nonzeros=3373340, allocated nonzeros=3373340 > > total number of mallocs used during MatSetValues calls =0 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > not using I-node (on process 0) routines > > > > but still the timing is terrible. > > > > > > On Sat, Jan 7, 2017 at 5:28 PM, Jed Brown <j...@jedbrown.org> wrote: > > Manuel Valera <mval...@mail.sdsu.edu> writes: > > > > > > > Awesome Matt and Jed, > > > > > > > > The GCR is used because the matrix is not invertible and because this was > > > > the algorithm that the previous library used, > > > > > > > > The Preconditioned im aiming to use is multigrid, i thought i configured > > > > the hypre-boomerAmg solver for this, but i agree in that it doesn't show > in > > > > the log anywhere, how can i be sure is being used ? i sent -ksp_view log > > > > before in this thread > > > > > > Did you run with -pc_type hypre? > > > > > > > I had a problem with the matrix block sizes so i couldn't make the petsc > > > > native multigrid solver to work, > > > > > > What block sizes? If the only variable is pressure, the block size > > > would be 1 (default). > > > > > > > This is a nonhidrostatic pressure solver, it is an elliptic problem so > > > > multigrid is a must, > > > > > > Yes, multigrid should work well. > > > > > > > > > -- > 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 > > > > > > > > -- > *The secret to doing good research is always be a little underemployed. > You waste years by not being able to waste hours* -- Amos Tversky > > >