[petsc-users] Zero pivot in LU factorisation
Toby
T.W.Searle at sms.ed.ac.uk
Thu Jul 25 06:46:12 CDT 2013
Ok, it looks like the -st_pc_factor_shift_type option is now being used,
thanks. Unfortunately it hasn't fixed the problem.
if I use the NONZERO type and a shift amount, the shift amount option is
not recognised and I still get the zero pivot error. If I use the
POSITIVE_DEFINITE type I also get the pivot error. Output is below
Thanks,
Toby
tobymac:SLEPC toby$ mpiexec ./ex7 -f1
LHS-N7-M40-Re0.0-b0.1-Wi5.0-amp0.02.petsc -f2
RHS-N7-M40-Re0.0-b0.1-Wi5.0-amp0.02.petsc -st_pc_type lu
-st_pc_factor_shift_type NONZERO -st_pc_shift_type_amount 1
Generalized eigenproblem stored in file.
Reading COMPLEX matrices from binary files...
[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: Empty row in matrix: row in original ordering 2395 in
permuted ordering 3600!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.3.0, Patch 5, Sat Dec 1
15:10:41 CST 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: ./ex7 on a arch-darw named tobymac by toby Thu Jul 25
12:41:57 2013
[0]PETSC ERROR: Libraries linked from /opt/local/lib
[0]PETSC ERROR: Configure run at Tue Jul 23 15:11:27 2013
[0]PETSC ERROR: Configure options --prefix=/opt/local
--with-valgrind-dir=/opt/local --with-shared-libraries
--with-scalar-type=complex --with-clanguage=C++
--with-superlu-dir=/opt/local --with-blacs-dir=/opt/local
--with-scalapack-dir=/opt/local --with-mumps-dir=/opt/local
--with-metis-dir=/opt/local --with-parmetis-dir=/opt/local
--COPTFLAGS=-O2 --CXXOPTFLAGS=-O2 --FOPTFLAGS=-O2
--LDFLAGS=-L/opt/local/lib --CFLAGS="-O2 -mtune=native" --CXXFLAGS="-O2
-mtune=native"
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: MatLUFactorSymbolic_SeqAIJ() line 334 in
/opt/local/var/macports/build/_Users_toby_MyPorts_scienceports_math_petsc/petsc/work/petsc-3.3-p5/src/mat/impls/aij/seq/aijfact.c
[0]PETSC ERROR: MatLUFactorSymbolic() line 2750 in
/opt/local/var/macports/build/_Users_toby_MyPorts_scienceports_math_petsc/petsc/work/petsc-3.3-p5/src/mat/interface/matrix.c
[0]PETSC ERROR: PCSetUp_LU() line 135 in
/opt/local/var/macports/build/_Users_toby_MyPorts_scienceports_math_petsc/petsc/work/petsc-3.3-p5/src/ksp/pc/impls/factor/lu/lu.c
[0]PETSC ERROR: PCSetUp() line 832 in
/opt/local/var/macports/build/_Users_toby_MyPorts_scienceports_math_petsc/petsc/work/petsc-3.3-p5/src/ksp/pc/interface/precon.c
[0]PETSC ERROR: KSPSetUp() line 278 in
/opt/local/var/macports/build/_Users_toby_MyPorts_scienceports_math_petsc/petsc/work/petsc-3.3-p5/src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: STSetUp_Shift() line 94 in src/st/impls/shift/shift.c
[0]PETSC ERROR: STSetUp() line 280 in src/st/interface/stsolve.c
[0]PETSC ERROR: EPSSetUp() line 204 in src/eps/interface/setup.c
[0]PETSC ERROR: EPSSolve() line 109 in src/eps/interface/solve.c
Number of iterations of the method: 0
Number of linear iterations of the method: 0
Number of requested eigenvalues: 1
Stopping condition: tol=1e-08, maxit=750
Number of converged approximate eigenpairs: 0
WARNING! There are options you set that were not used!
WARNING! could be spelling mistake, etc!
Option left: name:-st_pc_shift_type_amount value: 1
mpiexec ./ex7 -f1 LHS-N7-M40-Re0.0-b0.1-Wi5.0-amp0.02.petsc -f2
RHS-N7-M40-Re0.0-b0.1-Wi5.0-amp0.02.petsc -st_pc_type lu
-st_pc_factor_shift_type POSITIVE_DEFINITE
Generalized eigenproblem stored in file.
Reading COMPLEX matrices from binary files...
[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: Empty row in matrix: row in original ordering 2395 in
permuted ordering 3600!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.3.0, Patch 5, Sat Dec 1
15:10:41 CST 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: ./ex7 on a arch-darw named tobymac by toby Thu Jul 25
12:40:20 2013
[0]PETSC ERROR: Libraries linked from /opt/local/lib
[0]PETSC ERROR: Configure run at Tue Jul 23 15:11:27 2013
[0]PETSC ERROR: Configure options --prefix=/opt/local
--with-valgrind-dir=/opt/local --with-shared-libraries
--with-scalar-type=complex --with-clanguage=C++
--with-superlu-dir=/opt/local --with-blacs-dir=/opt/local
--with-scalapack-dir=/opt/local --with-mumps-dir=/opt/local
--with-metis-dir=/opt/local --with-parmetis-dir=/opt/local
--COPTFLAGS=-O2 --CXXOPTFLAGS=-O2 --FOPTFLAGS=-O2
--LDFLAGS=-L/opt/local/lib --CFLAGS="-O2 -mtune=native" --CXXFLAGS="-O2
-mtune=native"
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: MatLUFactorSymbolic_SeqAIJ() line 334 in
/opt/local/var/macports/build/_Users_toby_MyPorts_scienceports_math_petsc/petsc/work/petsc-3.3-p5/src/mat/impls/aij/seq/aijfact.c
[0]PETSC ERROR: MatLUFactorSymbolic() line 2750 in
/opt/local/var/macports/build/_Users_toby_MyPorts_scienceports_math_petsc/petsc/work/petsc-3.3-p5/src/mat/interface/matrix.c
[0]PETSC ERROR: PCSetUp_LU() line 135 in
/opt/local/var/macports/build/_Users_toby_MyPorts_scienceports_math_petsc/petsc/work/petsc-3.3-p5/src/ksp/pc/impls/factor/lu/lu.c
[0]PETSC ERROR: PCSetUp() line 832 in
/opt/local/var/macports/build/_Users_toby_MyPorts_scienceports_math_petsc/petsc/work/petsc-3.3-p5/src/ksp/pc/interface/precon.c
[0]PETSC ERROR: KSPSetUp() line 278 in
/opt/local/var/macports/build/_Users_toby_MyPorts_scienceports_math_petsc/petsc/work/petsc-3.3-p5/src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: STSetUp_Shift() line 94 in src/st/impls/shift/shift.c
[0]PETSC ERROR: STSetUp() line 280 in src/st/interface/stsolve.c
[0]PETSC ERROR: EPSSetUp() line 204 in src/eps/interface/setup.c
[0]PETSC ERROR: EPSSolve() line 109 in src/eps/interface/solve.c
Number of iterations of the method: 0
Number of linear iterations of the method: 0
Number of requested eigenvalues: 1
Stopping condition: tol=1e-08, maxit=750
Number of converged approximate eigenpairs: 0
On 25/07/2013 12:34, Jose E. Roman wrote:
> El 25/07/2013, a las 13:30, Toby escribió:
>
>> Hi Matt,
>>
>> Thanks for the speedy reply. I tried using the options you suggested:
>>
>> mpiexec ./ex7 -f1 LHS-N7-M40-Re0.0-b0.1-Wi5.0-amp0.02.petsc -f2 RHS-N7-M40-Re0.0-b0.1-Wi5.0-amp0.02.petsc -st_pc_factor_shift_type NONZERO -st_pc_shift_type_amount 1
>>
>> But I still get the warnings:
>> Option left: name:-st_pc_factor_shift_type value: NONZERO
>> Option left: name:-st_pc_shift_type_amount value: 1
> By default, ST is using PCREDUNDANT. In order to use the above options you must change it to e.g. PCLU.
> That is, add -st_pc_type lu
>
> Jose
>
>
>> I have tried it with just the -st_pc_type jacobi and -st_ksp_view. This gives me some eigenvalues, but I don't believe them (they do not appear on the spectrum which I solve using LAPACK where all eigenvalues have a real part less than 0). The output was very large, but consists of repetitions of this:
>>
>> mpiexec ./ex7 -f1 LHS-N7-M40-Re0.0-b0.1-Wi5.0-amp0.02.petsc -f2 RHS-N7-M40-Re0.0-b0.1-Wi5.0-amp0.02.petsc -st_pc_type jacobi -st_ksp_view
>>
>> Generalized eigenproblem stored in file.
>>
>> Reading COMPLEX matrices from binary files...
>> KSP Object:(st_) 1 MPI processes
>> type: preonly
>> maximum iterations=10000, initial guess is zero
>> tolerances: relative=1e-08, absolute=1e-50, divergence=10000
>> left preconditioning
>> using NONE norm type for convergence test
>> PC Object:(st_) 1 MPI processes
>> type: jacobi
>> linear system matrix = precond matrix:
>> Matrix Object: 1 MPI processes
>> type: seqaij
>> rows=6000, cols=6000
>> total: nonzeros=3600, allocated nonzeros=3600
>> total number of mallocs used during MatSetValues calls =0
>> using I-node routines: found 4080 nodes, limit used is 5
>>
>> ...
>>
>> Number of iterations of the method: 189
>> Number of linear iterations of the method: 1520
>> Number of requested eigenvalues: 1
>> Stopping condition: tol=1e-08, maxit=750
>> Number of converged approximate eigenpairs: 2
>>
>> k ||Ax-kBx||/||kx||
>> ----------------- ------------------
>> 1388.774454+0.001823 i 0.751726
>> 1388.774441+0.001820 i 0.912665
>>
>>
>> Thanks again,
>> Toby
>
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