[petsc-users] BCs for a EPS solver

Tue Feb 18 03:51:36 CST 2020

You put alpha on the diagonal of A and beta on the diagonal of B to get an eigenvalue lambda=alpha/beta. If you set beta=0 then lambda=Inf. The choice depends on where your wanted eigenvalues are and how you are solving the eigenproblem. The choice of lambda=Inf suggested by Jeremy avoids inserting eigenvalues that may interfere with the problem's eigenvalues, but this is good for shift-and-invert, not for the case where you solve linear systems with B.

Anyway, this kind of manipulation may have an impact on convergence of the eigensolver or on conditioning of the linear solves. A possibly better approach is just to get rid of the BC unknowns by creating smaller A, B matrices, e.g. with MatGetSubMatrix().

Jose

> El 18 feb 2020, a las 0:41, Matthew Knepley <knepley at gmail.com> escribió:
> 
> On Mon, Feb 17, 2020 at 4:33 PM Emmanuel Ayala <juaneah at gmail.com <mailto:juaneah at gmail.com>> wrote:
> Hi,
> 
> Thank you for the clarification, now I understand what means change those values, and I tried to do that.
> 
> But if I put the row i to the identity in A, and zero in B, the solver crash:
> 
> So if you need to factor B, maybe reverse it?
> 
>   Thanks,
> 
>     Matt
>  
> [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> [0]PETSC ERROR: Error in external library
> [1]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> [1]PETSC ERROR: Error in external library
> [1]PETSC ERROR: Error reported by MUMPS in numerical factorization phase: INFOG(1)=-10, INFO(2)=0
> 
> [1]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html <https://www.mcs.anl.gov/petsc/documentation/faq.html> for trouble shooting.
> [1]PETSC ERROR: Petsc Release Version 3.12.3, Jan, 03, 2020 
> [1]PETSC ERROR: [2]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> [2]PETSC ERROR: Error in external library
> [2]PETSC ERROR: Error reported by MUMPS in numerical factorization phase: INFOG(1)=-10, INFO(2)=0
> 
> [2]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html <https://www.mcs.anl.gov/petsc/documentation/faq.html> for trouble shooting.
> [2]PETSC ERROR: Petsc Release Version 3.12.3, Jan, 03, 2020 
> [2]PETSC ERROR: ./comp on a arch-linux-c-opt-O2-mumps named ayala by ayala Mon Feb 17 15:28:01 2020
> [3]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> [3]PETSC ERROR: Error in external library
> [3]PETSC ERROR: Error reported by MUMPS in numerical factorization phase: INFOG(1)=-10, INFO(2)=0
> 
> [3]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html <https://www.mcs.anl.gov/petsc/documentation/faq.html> for trouble shooting.
> [3]PETSC ERROR: Petsc Release Version 3.12.3, Jan, 03, 2020 
> [3]PETSC ERROR: ./comp on a arch-linux-c-opt-O2-mumps named ayala by ayala Mon Feb 17 15:28:01 2020
> [3]PETSC ERROR: Configure options --with-debugging=0 COPTFLAGS="-O2 -march=native -mtune=native" CXXOPTFLAGS="-O2 -march=native -mtune=native" FOPTFLAGS="-O2 -march=native -mtune=native" --download-mpich --download-mumps --download-scalapack --download-parmetis --download-metis --download-superlu_dist --download-cmake --download-fblaslapack=1 --with-cxx-dialect=C++11
> [3]PETSC ERROR: #1 MatFactorNumeric_MUMPS() line 1365 in /home/ayala/Documents/PETSc/petsc-3.12.3/src/mat/impls/aij/mpi/mumps/mumps.c
> [0]PETSC ERROR: Error reported by MUMPS in numerical factorization phase: INFOG(1)=-10, INFO(2)=33
> 
> [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html <https://www.mcs.anl.gov/petsc/documentation/faq.html> for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.12.3, Jan, 03, 2020 
> [0]PETSC ERROR: ./comp on a arch-linux-c-opt-O2-mumps named ayala by ayala Mon Feb 17 15:28:01 2020
> [0]PETSC ERROR: Configure options --with-debugging=0 COPTFLAGS="-O2 -march=native -mtune=native" CXXOPTFLAGS="-O2 -march=native -mtune=native" FOPTFLAGS="-O2 -march=native -mtune=native" --download-mpich --download-mumps --download-scalapack --download-parmetis --download-metis --download-superlu_dist --download-cmake --download-fblaslapack=1 --with-cxx-dialect=C++11
> [0]PETSC ERROR: #1 MatFactorNumeric_MUMPS() line 1365 in /home/ayala/Documents/PETSc/petsc-3.12.3/src/mat/impls/aij/mpi/mumps/mumps.c
> ./comp on a arch-linux-c-opt-O2-mumps named ayala by ayala Mon Feb 17 15:28:01 2020
> [1]PETSC ERROR: Configure options --with-debugging=0 COPTFLAGS="-O2 -march=native -mtune=native" CXXOPTFLAGS="-O2 -march=native -mtune=native" FOPTFLAGS="-O2 -march=native -mtune=native" --download-mpich --download-mumps --download-scalapack --download-parmetis --download-metis --download-superlu_dist --download-cmake --download-fblaslapack=1 --with-cxx-dialect=C++11
> [1]PETSC ERROR: #1 MatFactorNumeric_MUMPS() line 1365 in /home/ayala/Documents/PETSc/petsc-3.12.3/src/mat/impls/aij/mpi/mumps/mumps.c
> [1]PETSC ERROR: #2 MatLUFactorNumeric() line 3057 in /home/ayala/Documents/PETSc/petsc-3.12.3/src/mat/interface/matrix.c
> [2]PETSC ERROR: Configure options --with-debugging=0 COPTFLAGS="-O2 -march=native -mtune=native" CXXOPTFLAGS="-O2 -march=native -mtune=native" FOPTFLAGS="-O2 -march=native -mtune=native" --download-mpich --download-mumps --download-scalapack --download-parmetis --download-metis --download-superlu_dist --download-cmake --download-fblaslapack=1 --with-cxx-dialect=C++11
> [2]PETSC ERROR: #1 MatFactorNumeric_MUMPS() line 1365 in /home/ayala/Documents/PETSc/petsc-3.12.3/src/mat/impls/aij/mpi/mumps/mumps.c
> [2]PETSC ERROR: #2 MatLUFactorNumeric() line 3057 in /home/ayala/Documents/PETSc/petsc-3.12.3/src/mat/interface/matrix.c
> [2]PETSC ERROR: [3]PETSC ERROR: #2 MatLUFactorNumeric() line 3057 in /home/ayala/Documents/PETSc/petsc-3.12.3/src/mat/interface/matrix.c
> [3]PETSC ERROR: #3 PCSetUp_LU() line 126 in /home/ayala/Documents/PETSc/petsc-3.12.3/src/ksp/pc/impls/factor/lu/lu.c
> [3]PETSC ERROR: #4 PCSetUp() line 894 in /home/ayala/Documents/PETSc/petsc-3.12.3/src/ksp/pc/interface/precon.c
> [0]PETSC ERROR: #2 MatLUFactorNumeric() line 3057 in /home/ayala/Documents/PETSc/petsc-3.12.3/src/mat/interface/matrix.c
> [0]PETSC ERROR: #3 PCSetUp_LU() line 126 in /home/ayala/Documents/PETSc/petsc-3.12.3/src/ksp/pc/impls/factor/lu/lu.c
> [0]PETSC ERROR: [1]PETSC ERROR: #3 PCSetUp_LU() line 126 in /home/ayala/Documents/PETSc/petsc-3.12.3/src/ksp/pc/impls/factor/lu/lu.c
> [1]PETSC ERROR: #4 PCSetUp() line 894 in /home/ayala/Documents/PETSc/petsc-3.12.3/src/ksp/pc/interface/precon.c
> [1]PETSC ERROR: #3 PCSetUp_LU() line 126 in /home/ayala/Documents/PETSc/petsc-3.12.3/src/ksp/pc/impls/factor/lu/lu.c
> [2]PETSC ERROR: #4 PCSetUp() line 894 in /home/ayala/Documents/PETSc/petsc-3.12.3/src/ksp/pc/interface/precon.c
> [2]PETSC ERROR: #5 KSPSetUp() line 376 in /home/ayala/Documents/PETSc/petsc-3.12.3/src/ksp/ksp/interface/itfunc.c
> [3]PETSC ERROR: #5 KSPSetUp() line 376 in /home/ayala/Documents/PETSc/petsc-3.12.3/src/ksp/ksp/interface/itfunc.c
> [3]PETSC ERROR: #6 STSetUp_Shift() line 120 in /home/ayala/Documents/SLEPc/slepc-3.12.2/src/sys/classes/st/impls/shift/shift.c
> #4 PCSetUp() line 894 in /home/ayala/Documents/PETSc/petsc-3.12.3/src/ksp/pc/interface/precon.c
> [0]PETSC ERROR: #5 KSPSetUp() line 376 in /home/ayala/Documents/PETSc/petsc-3.12.3/src/ksp/ksp/interface/itfunc.c
> [0]PETSC ERROR: #6 STSetUp_Shift() line 120 in /home/ayala/Documents/SLEPc/slepc-3.12.2/src/sys/classes/st/impls/shift/shift.c
> [0]PETSC ERROR: #5 KSPSetUp() line 376 in /home/ayala/Documents/PETSc/petsc-3.12.3/src/ksp/ksp/interface/itfunc.c
> [1]PETSC ERROR: #6 STSetUp_Shift() line 120 in /home/ayala/Documents/SLEPc/slepc-3.12.2/src/sys/classes/st/impls/shift/shift.c
> [1]PETSC ERROR: #7 STSetUp() line 271 in /home/ayala/Documents/SLEPc/slepc-3.12.2/src/sys/classes/st/interface/stsolve.c
> [1]PETSC ERROR: #8 EPSSetUp() line 273 in /home/ayala/Documents/SLEPc/slepc-3.12.2/src/eps/interface/epssetup.c
> [2]PETSC ERROR: #6 STSetUp_Shift() line 120 in /home/ayala/Documents/SLEPc/slepc-3.12.2/src/sys/classes/st/impls/shift/shift.c
> [2]PETSC ERROR: #7 STSetUp() line 271 in /home/ayala/Documents/SLEPc/slepc-3.12.2/src/sys/classes/st/interface/stsolve.c
> [2]PETSC ERROR: #8 EPSSetUp() line 273 in /home/ayala/Documents/SLEPc/slepc-3.12.2/src/eps/interface/epssetup.c
> [2]PETSC ERROR: #9 FourBar_NaturalPulsation() line 3937 in /home/ayala/Nextcloud/cpp_projects/2020-02-13-muboto-balancing-v17-mma/Multibody.cc
> 
> El lun., 17 de feb. de 2020 a la(s) 13:20, Matthew Knepley (knepley at gmail.com <mailto:knepley at gmail.com>) escribió:
> On Mon, Feb 17, 2020 at 1:59 PM Emmanuel Ayala <juaneah at gmail.com <mailto:juaneah at gmail.com>> wrote:
> Hi, thanks for the quick answer.
> 
> I just did it, and it does not work. My problem is GNHEP and I use the default solver (Krylov-Schur). Moreover I run the code with the options: -st_ksp_type preonly -st_pc_type lu -st_pc_factor_mat_solver_type mumps
> 
> I guess a better question is: What do you expect to work?
> 
> For a linear solve,
> 
>   A x = b
> 
> if a row i is 0 except for a one on the diagonal, then I get
> 
>   x_i = b_i
> 
> so hopefully you put the correct boundary value in b_i. For the generalized eigenproblem
> 
>   A x = \lambda B x
> 
> if you set row i to the identity in A, and zero in B, we get
> 
>   x_i = 0
> 
> and you must put the boundary values into x after you have finished the solve. Is this what you did?
> 
>   Thanks,
> 
>      Matt
>  
> Any other suggestions?
> Kind regards.
> 
> El lun., 17 de feb. de 2020 a la(s) 12:39, Jeremy Theler (jeremy at seamplex.com <mailto:jeremy at seamplex.com>) escribió:
> The usual trick is to set ones in one matrix and zeros in the other
> one.
> 
> 
> On Mon, 2020-02-17 at 12:35 -0600, Emmanuel Ayala wrote:
> > Hi everyone,
> > 
> > I have an eigenvalue problem where I need to apply BCs to the
> > stiffness and mass matrix. 
> > 
> > Usually, for KSP solver, it is enough to set to zero the rows and
> > columns related to the boundary conditions. I used to apply it with
> > MatZeroRowsColumns, with a 1s on the diagonal. Then the solver works
> > well.
> > 
> > There is something similar to KSP for EPS solver ? 
> > 
> > I already used MatZeroRowsColumns (for EPS solver), with a 1s on the
> > diagonal, and I got wrong result.
> > 
> > Kind regards.
> > 
> > 
> > 
> > 
> 
> 
> 
> -- 
> 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
> 
> https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
> 
> 
> -- 
> 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
> 
> https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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