[petsc-users] eigensolution error with slepc
Manav Bhatia
bhatiamanav at gmail.com
Mon Apr 4 11:23:33 CDT 2016
Thanks, Jose!
I am currently running 3.6.2, and will update to 3.6.3.
Is there a recommended strategy to automatically switch from GHEP to GNHEP for some subset of problems? Or should I choose to run all my eigenprobelms with GNHEP?
Regards,
Manav
> On Apr 4, 2016, at 11:18 AM, Jose E. Roman <jroman at dsic.upv.es> wrote:
>
>>
>> El 4 abr 2016, a las 18:06, Manav Bhatia <bhatiamanav at gmail.com> escribió:
>>
>> Hi Jose,
>>
>> I also read these matrices into matlab and found the eigenvalues as
>>
>>>> A = PetscBinaryRead('A.petsc’);
>>>> B = PetscBinaryRead(‘B.petsc’);
>>>> [v,d] = eigs(A,B)
>> (*** got a lot of output about poor-conditioning ***)
>>>> diag(d)
>>
>> ans =
>>
>> 1.0e-05 *
>>
>> -0.2219
>> 0.0229
>> 0.0229
>> 0.0025
>> 0.0019
>> 0.0014
>>
>>>> So, one of these is turning out to be negative, but I am still getting numbers.
>>
>>
>>
>> Using these matrices with ex7 produces an error:
>>
>> Dhcp-90-243:T_400_V_0 manav$ /Users/manav/Documents/codes/numerical_lib/slepc/slepc-3.6.2/src/eps/examples/tutorials/ex7 -f1 A.petsc -f2 B.petsc -eps_gen_hermitian -eps_view -eps_nev 1
>>
>> Generalized eigenproblem stored in file.
>>
>> Reading REAL matrices from binary files...
>> [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
>> [0]PETSC ERROR: Error in external library
>> [0]PETSC ERROR: Error in Lapack xSTEQR 15
>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
>> [0]PETSC ERROR: Petsc Release Version 3.6.3, Dec, 03, 2015
>> [0]PETSC ERROR: /Users/manav/Documents/codes/numerical_lib/slepc/slepc-3.6.2/src/eps/examples/tutorials/ex7 on a arch-darwin-cxx-opt named ws243-49.walker.dynamic.msstate.edu by manav Mon Apr 4 11:05:30 2016
>> [0]PETSC ERROR: Configure options --prefix=/Users/manav/Documents/codes/numerical_lib/petsc/petsc-3.6.3/../ --CC=mpicc --CXX=mpicxx --FC=mpif90 --with-clanguage=c++ --with-fortran=0 --with-mpiexec=/opt/local/bin/mpiexec --with-shared-libraries=1 --with-x=1 --with-x-dir=/opt/X11 --with-debugging=0 --with-lapack-lib=/usr/lib/liblapack.dylib --with-blas-lib=/usr/lib/libblas.dylib --download-superlu=yes --download-superlu_dist=yes --download-suitesparse=yes --download-mumps=yes --download-scalapack=yes --download-parmetis=yes --download-parmetis-shared=1 --download-metis=yes --download-metis-shared=1 --download-hypre=yes --download-hypre-shared=1 --download-ml=yes --download-ml-shared=1 --download-sundials=yes --download-sundials-shared=1
>> [0]PETSC ERROR: #1 DSSolve_HEP_QR() line 495 in /Users/manav/Documents/codes/numerical_lib/slepc/slepc-3.6.2/src/sys/classes/ds/impls/hep/dshep.c
>> [0]PETSC ERROR: #2 DSSolve() line 543 in /Users/manav/Documents/codes/numerical_lib/slepc/slepc-3.6.2/src/sys/classes/ds/interface/dsops.c
>> [0]PETSC ERROR: #3 EPSSolve_KrylovSchur_Symm() line 68 in /Users/manav/Documents/codes/numerical_lib/slepc/slepc-3.6.2/src/eps/impls/krylov/krylovschur/ks-symm.c
>> [0]PETSC ERROR: #4 EPSSolve() line 101 in /Users/manav/Documents/codes/numerical_lib/slepc/slepc-3.6.2/src/eps/interface/epssolve.c
>> [0]PETSC ERROR: #5 main() line 147 in /Users/manav/Documents/codes/numerical_lib/slepc/slepc-3.6.2/src/eps/examples/tutorials/ex7.c
>> [0]PETSC ERROR: PETSc Option Table entries:
>> [0]PETSC ERROR: -eps_gen_hermitian
>> [0]PETSC ERROR: -eps_nev 1
>> [0]PETSC ERROR: -eps_view
>> [0]PETSC ERROR: -f1 A.petsc
>> [0]PETSC ERROR: -f2 B.petsc
>> [0]PETSC ERROR: -matload_block_size 1
>> [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov----------
>> --------------------------------------------------------------------------
>> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>> with errorcode 76.
>>
>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>> You may or may not see output from other processes, depending on
>> exactly when Open MPI kills them.
>> --------------------------------------------------------------------------
>>
>
> The problem is that now K is indefinite. The check for indefinite B-matrix was not done correctly. This is fixed in 3.6.3, where you should get a more informative error:
>
> [0]PETSC ERROR: The inner product is not well defined: indefinite matrix
>
> When considered as a non-symmetric problem, the solver returns reasonable output:
>
> $ ./ex7 -f1 ~/tmp/bhatia/A.petsc -f2 ~/tmp/bhatia/B.petsc
>
> Generalized eigenproblem stored in file.
>
> Reading REAL matrices from binary files...
> Number of iterations of the method: 1
> Number of linear iterations of the method: 16
> Solution method: krylovschur
>
> Number of requested eigenvalues: 1
> Stopping condition: tol=1e-08, maxit=768
> Linear eigensolve converged (6 eigenpairs) due to CONVERGED_TOL; iterations 1
> ---------------------- --------------------
> k ||Ax-kBx||/||kx||
> ---------------------- --------------------
> -22.185956 8.66397e-08
> 2.291422 1.32466e-07
> 2.291422 1.55081e-07
> 0.252494 8.88997e-05
> 0.192453 0.000780395
> 0.141618 0.00113141
> ---------------------- --------------------
>
> The large residuals are due to bad scaling/conditioning of your matrices. You can also try the symmetric-indefinite solver, but this is not recommended since it is not numerically stable.
>
> $ ./ex7 -f1 ~/tmp/bhatia/A.petsc -f2 ~/tmp/bhatia/B.petsc -eps_gen_indefinite
>
> Generalized eigenproblem stored in file.
>
> Reading REAL matrices from binary files...
> Number of iterations of the method: 1
> Number of linear iterations of the method: 17
> Solution method: krylovschur
>
> Number of requested eigenvalues: 1
> Stopping condition: tol=1e-08, maxit=768
> Linear eigensolve converged (6 eigenpairs) due to CONVERGED_TOL; iterations 1
> ---------------------- --------------------
> k ||Ax-kBx||/||kx||
> ---------------------- --------------------
> -22.185956 7.08858e-09
> 2.291422 5.87577e-09
> 2.291422 6.39304e-09
> 0.252494 1.7497e-07
> 0.192453 1.63916e-06
> 0.141618 1.75568e-06
> ---------------------- --------------------
>
>
> Jose
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20160404/0f3d0d56/attachment-0001.html>
More information about the petsc-users
mailing list