I attached the complete output.
I used 2 processors for this run. I wanted to use only one to have a
cleaner output but I could not because of this error:
[0]PCSetData_AGG bs=1 MM=32768
[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Arguments are incompatible!
[0]PETSC ERROR: MatMatMult requires A, mpiaij, to be compatible with B,
seqaij!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.3.0, Patch 3, Wed Aug 29
11:26:24 CDT 2012
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: ./hit on a named nid15343 by Unknown Wed May 29
18:15:24 2013
[0]PETSC ERROR: Libraries linked from
[0]PETSC ERROR: Configure run at
[0]PETSC ERROR: Configure options
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: MatMatMult() line 8614 in src/mat/interface/matrix.c
[0]PETSC ERROR: PCGAMGOptprol_AGG() line 1358 in src/ksp/pc/impls/gamg/agg.c
[0]PETSC ERROR: PCSetUp_GAMG() line 673 in src/ksp/pc/impls/gamg/gamg.c
[0]PETSC ERROR: PCSetUp() line 832 in src/ksp/pc/interface/precon.c
[0]PETSC ERROR: KSPSetUp() line 278 in src/ksp/ksp/interface/itfunc.c
hit: gamg.c:568: PCSetUp_GAMG: Assertion `pc->setupcalled' failed.
On 05/29/2013 02:29 PM, Matthew Knepley wrote:
On Wed, May 29, 2013 at 5:25 PM, Michele Rosso <[email protected]
<mailto:[email protected]>> wrote:
Hi,
I proceeded as Matt suggested. I am running without nullspace
(Dirichlet's BCs) with the following options:
-pc_type gamg -pc_mg_cycle_type v -pc_gamg_agg_nsmooths 1
-mg_coarse_sub_pc_factor_shift_type NONZERO -ksp_view -options_left
The results are fine and the run finishes. The output of -ksp_view
does not say anything about the coarse solver being shifted.
In fact the option -mg_coarse_sub_pc_factor_shift_type NONZERO is
not used:
Please show us the COMPLETE output.
Thanks,
Matt
#PETSc Option Table entries:
-ksp_view
-mg_coarse_sub_pc_factor_shift_type NONZERO
-options_left
-pc_gamg_agg_nsmooths 1
-pc_mg_cycle_type v
-pc_type gamg
#End of PETSc Option Table entries
There is one unused database option. It is:
Option left: name:-mg_coarse_sub_pc_factor_shift_type value: NONZERO
Michele
On 05/24/2013 03:20 PM, Matthew Knepley wrote:
On Fri, May 24, 2013 at 5:18 PM, Michele Rosso <[email protected]
<mailto:[email protected]>> wrote:
Using
-pc_type gamg -pc_mg_cycle_type v -pc_gamg_agg_nsmooths 1
-mg_coarse_sub_pc_factor_shift_type NONZERO -option_left
-ksp_view
This is what debugging is about. We are not running your problem.
How could this be debugged?
1) Run the problem w/o a null space so that it finishes
2) Look at the output for -ksp_view
3) Does the coarse solver say that it is shifted?
4) Are there options which were unused?
Matt
still produces the same error:
[0]PCSetData_AGG bs=1 MM=131072
[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Detected zero pivot in LU factorization:
see
http://www.mcs.anl.gov/petsc/documentation/faq.html#ZeroPivot!
[0]PETSC ERROR: Zero pivot row 280 value 6.56964e-17
tolerance 2.22045e-14!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.3.0, Patch 3, Wed Aug
29 11:26:24 CDT 2012
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble
shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: ./hit on a named nid15363 by Unknown Fri May
24 17:06:50 2013
[0]PETSC ERROR: Libraries linked from
[0]PETSC ERROR: Configure run at
[0]PETSC ERROR: Configure options
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: MatPivotCheck_none() line 583 in
src/mat/impls/aij/seq//ptmp/skelly/petsc/3.3.03/cray_interlagos_build/real/src/include/petsc-private/matimpl.h
[0]PETSC ERROR: MatPivotCheck() line 602 in
src/mat/impls/aij/seq//ptmp/skelly/petsc/3.3.03/cray_interlagos_build/real/src/include/petsc-private/matimpl.h
[0]PETSC ERROR: MatLUFactorNumeric_SeqAIJ() line 585 in
src/mat/impls/aij/seq/aijfact.c
[0]PETSC ERROR: MatLUFactorNumeric() line 2803 in
src/mat/interface/matrix.c
[0]PETSC ERROR: PCSetUp_LU() line 160 in
src/ksp/pc/impls/factor/lu/lu.c
[0]PETSC ERROR: PCSetUp() line 832 in
src/ksp/pc/interface/precon.c
[0]PETSC ERROR: KSPSetUp() line 278 in
src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: PCSetUpOnBlocks_BJacobi_Singleblock() line
715 in src/ksp/pc/impls/bjacobi/bjacobi.c
[0]PETSC ERROR: PCSetUpOnBlocks() line 865 in
src/ksp/pc/interface/precon.c
[0]PETSC ERROR: KSPSetUpOnBlocks() line 154 in
src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: KSPSolve() line 403 in
src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: PCSetUpOnBlocks_BJacobi_Singleblock() line
715 in src/ksp/pc/impls/bjacobi/bjacobi.c
[0]PETSC ERROR: PCSetUpOnBlocks() line 865 in
src/ksp/pc/interface/precon.c
[0]PETSC ERROR: KSPSetUpOnBlocks() line 154 in
src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: KSPSolve() line 403 in
src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: PCMGMCycle_Private() line 20 in
src/ksp/pc/impls/mg/mg.c
[0]PETSC ERROR: PCMGMCycle_Private() line 49 in
src/ksp/pc/impls/mg/mg.c
[0]PETSC ERROR: PCMGMCycle_Private() line 49 in
src/ksp/pc/impls/mg/mg.c
[0]PETSC ERROR: PCMGMCycle_Private() line 49 in
src/ksp/pc/impls/mg/mg.c
[0]PETSC ERROR: PCApply_MG() line 326 in src/ksp/pc/impls/mg/mg.c
[0]PETSC ERROR: PCApply() line 384 in
src/ksp/pc/interface/precon.c
[0]PETSC ERROR: KSPSolve_CG() line 139 in
src/ksp/ksp/impls/cg/cg.c
[0]PETSC ERROR: KSPSolve() line 446 in
src/ksp/ksp/interface/itfunc.c
On 05/24/2013 02:51 PM, Jed Brown wrote:
Michele Rosso<[email protected]> <mailto:[email protected]> writes:
With petsc-3.4 (which you should upgrade to), use
-mg_coarse_sub_pc_factor_shift_type NONZERO
Actually, use this with petsc-3.3 also (and please upgrade to
petsc-3.4).
The option you were passing was not being used.
--
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
[0]PCSetData_AGG bs=1 MM=16384
KSP Object: 2 MPI processes
type: cg
maximum iterations=10000
tolerances: relative=1e-14, absolute=1e-50, divergence=10000
left preconditioning
using nonzero initial guess
using PRECONDITIONED norm type for convergence test
PC Object: 2 MPI processes
type: gamg
MG: type is MULTIPLICATIVE, levels=3 cycles=v
Cycles per PCApply=1
Using Galerkin computed coarse grid matrices
Coarse grid solver -- level -------------------------------
KSP Object: (mg_coarse_) 2 MPI processes
type: gmres
GMRES: restart=30, using Classical (unmodified) Gram-Schmidt
Orthogonalization with no iterative refinement
GMRES: happy breakdown tolerance 1e-30
maximum iterations=1, initial guess is zero
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using NONE norm type for convergence test
PC Object: (mg_coarse_) 2 MPI processes
type: bjacobi
block Jacobi: number of blocks = 2
Local solve info for each block is in the following KSP and PC objects:
[0] number of local blocks = 1, first local block number = 0
[0] local block number 0
KSP Object: KSP Object: (mg_coarse_sub_)
(mg_coarse_sub_) 1 MPI processes
1 MPI processes
type: preonly
type: preonly
maximum iterations=10000, initial guess is zero
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
left preconditioning
using NONE norm type for convergence test
using NONE norm type for convergence test
PC Object:PC Object:
(mg_coarse_sub_)(mg_coarse_sub_) 1 MPI processes
1 MPI processes
type: lu
type: lu
LU: out-of-place factorization
LU: out-of-place factorization
tolerance for zero pivot 2.22045e-14
tolerance for zero pivot 2.22045e-14
matrix ordering: nd
matrix ordering: nd
factor fill ratio given 5, needed 1.07862
factor fill ratio given 5, needed 0
Factored matrix follows:
Factored matrix follows:
Matrix Object:Matrix Object:
1 MPI processes
1 MPI processes
type: seqaij
type: seqaij
rows=61, cols=61
rows=0, cols=0
package used to perform factorization: petsc
package used to perform factorization: petsc
total: nonzeros=3677, allocated
nonzeros=3677
total: nonzeros=1, allocated nonzeros=1
total number of mallocs used during
MatSetValues calls =0
total number of mallocs used during MatSetValues calls =0
not using I-node routines
not using I-node routines
linear system matrix = precond matrix:
linear system matrix = precond matrix:
Matrix Object:Matrix Object: 1 MPI
processes
1 MPI processes
type: seqaij
type: seqaij
rows=61, cols=61
rows=0, cols=0
total: nonzeros=3409, allocated nonzeros=3409
total: nonzeros=0, allocated nonzeros=0
total number of mallocs used during MatSetValues calls
=0
total number of mallocs used during MatSetValues calls =0
not using I-node routines
not using I-node routines
- - - - - - - - - - - - - - - - - -
[1] number of local blocks = 1, first local block number = 1
[1] local block number 0
- - - - - - - - - - - - - - - - - -
linear system matrix = precond matrix:
Matrix Object: 2 MPI processes
type: mpiaij
rows=61, cols=61
total: nonzeros=3409, allocated nonzeros=3409
total number of mallocs used during MatSetValues calls =0
not using I-node (on process 0) routines
Down solver (pre-smoother) on level 1 -------------------------------
KSP Object: (mg_levels_1_) 2 MPI processes
type: chebyshev
Chebyshev: eigenvalue estimates: min = 0.0266892, max = 1.42507
maximum iterations=2
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using nonzero initial guess
using NONE norm type for convergence test
PC Object: (mg_levels_1_) 2 MPI processes
type: jacobi
linear system matrix = precond matrix:
Matrix Object: 2 MPI processes
type: mpiaij
rows=3102, cols=3102
total: nonzeros=108330, allocated nonzeros=108330
total number of mallocs used during MatSetValues calls =0
not using I-node (on process 0) routines
Up solver (post-smoother) same as down solver (pre-smoother)
Down solver (pre-smoother) on level 2 -------------------------------
KSP Object: (mg_levels_2_) 2 MPI processes
type: chebyshev
Chebyshev: eigenvalue estimates: min = 0.182939, max = 2.0291
maximum iterations=2
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using nonzero initial guess
using NONE norm type for convergence test
PC Object: (mg_levels_2_) 2 MPI processes
type: jacobi
linear system matrix = precond matrix:
Matrix Object: 2 MPI processes
type: mpiaij
rows=32768, cols=32768
total: nonzeros=229376, allocated nonzeros=229376
total number of mallocs used during MatSetValues calls =0
Up solver (post-smoother) same as down solver (pre-smoother)
linear system matrix = precond matrix:
Matrix Object: 2 MPI processes
type: mpiaij
rows=32768, cols=32768
total: nonzeros=229376, allocated nonzeros=229376
total number of mallocs used during MatSetValues calls =0
#PETSc Option Table entries:
-ksp_view
-mg_coarse_sub_pc_factor_shift_type NONZERO
-options_left
-pc_gamg_agg_nsmooths 1
-pc_mg_cycle_type v
-pc_type gamg
#End of PETSc Option Table entries
There is one unused database option. It is:
Option left: name:-mg_coarse_sub_pc_factor_shift_type value: NONZERO
