[petsc-users] -log_view hangs unexpectedly // how to optimize my kspsolve
Manuel Valera
mvalera at mail.sdsu.edu
Sat Jan 7 19:38:41 CST 2017
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:
------------------------------------------------------------------------
[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 <jed at jedbrown.org> wrote:
> Manuel Valera <mvalera at 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.
>
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