[petsc-users] Retireve eigenvectors from a paralell job/ Spectrum slicing in order to solve big eigenvalue problem

[Jan Grießer]

I am aware that SLEPc is not supposed to calculate all eigenvalues and
eigenvectors, my problem is simply that i want for a physical large enough
system all of them before i can make the transition to go to the smallest
ones.
Competitiveness is of secondary importance at the moment.
But ihave a problem connected with spectrum slicing. I followed the
instructions in the manual of Chap. 3.4.5 Spectrum Slicing and converted
them to the python package.
But now i get the following error. It appears to me that it is not able to
find the ksp object, but i actually do not know why this is the case.
aceback (most recent call last):
  File "Eigensolver_spectrum_slicing.py", line 216, in <module>
    solve_eigensystem(DynMatrix_nn, Unity_nn, D_nn.shape,
opt_dict.LowLimit, opt_dict.UpperLimit)
  File "Eigensolver_spectrum_slicing.py", line 121, in solve_eigensystem
    E.setUp()
  File "SLEPc/EPS.pyx", line 1099, in slepc4py.SLEPc.EPS.setUp
petsc4py.PETSc.Error: error code 92
[14] EPSSetUp() line 165 in
/tmp/pip-install-golhudw7/slepc/src/eps/interface/epssetup.c
[14] EPSSetUp_KrylovSchur() line 146 in
/tmp/pip-install-golhudw7/slepc/src/eps/impls/krylov/krylovschur/krylovschur.c
[14] EPSSetUp_KrylovSchur_Slice() line 410 in
/tmp/pip-install-golhudw7/slepc/src/eps/impls/krylov/krylovschur/ks-slice.c
[14] EPSSliceGetEPS() line 300 in
/tmp/pip-install-golhudw7/slepc/src/eps/impls/krylov/krylovschur/ks-slice.c
[14] EPSSetUp() line 165 in
/tmp/pip-install-golhudw7/slepc/src/eps/interface/epssetup.c
[14] EPSSetUp_KrylovSchur() line 146 in
/tmp/pip-install-golhudw7/slepc/src/eps/impls/krylov/krylovschur/krylovschur.c
[14] EPSSetUp_KrylovSchur_Slice() line 461 in
/tmp/pip-install-golhudw7/slepc/src/eps/impls/krylov/krylovschur/ks-slice.c
[14] EPSSliceGetInertia() line 331 in
/tmp/pip-install-golhudw7/slepc/src/eps/impls/krylov/krylovschur/ks-slice.c
[14] STSetUp() line 271 in
/tmp/pip-install-golhudw7/slepc/src/sys/classes/st/interface/stsolve.c
[14] STSetUp_Sinvert() line 132 in
/tmp/pip-install-golhudw7/slepc/src/sys/classes/st/impls/sinvert/sinvert.c
[14] KSPSetUp() line 381 in
/tmp/pip-install-xmiaat2t/petsc/src/ksp/ksp/interface/itfunc.c
[14] PCSetUp() line 923 in
/tmp/pip-install-xmiaat2t/petsc/src/ksp/pc/interface/precon.c
[14] PCSetUp_Cholesky() line 86 in
/tmp/pip-install-xmiaat2t/petsc/src/ksp/pc/impls/factor/cholesky/cholesky.c
[14] MatGetFactor() line 4318 in
/tmp/pip-install-xmiaat2t/petsc/src/mat/interface/matrix.c
[14] See http://www.mcs.anl.gov/petsc/documentation/linearsolvertable.html
for possible LU and Cholesky solvers
[14] Could not locate a solver package. Perhaps you must ./configure with
--download-<package>

The code i used to solve the problem is

Am Fr., 14. Sep. 2018 um 18:34 Uhr schrieb Matthew Knepley <
knepley at gmail.com>:

> On Fri, Sep 14, 2018 at 12:19 PM Jose E. Roman <jroman at dsic.upv.es> wrote:
>
>> El 14 sept 2018, a las 17:45, Jan Grießer <griesser.jan at googlemail.com>
>> escribió:
>>
>> Hey there,
>> first i want to say thanks to Satish and Matt for helping with with my
>> last problem with the mpi compilation. I have two questions related to
>> solving a big, hermitian, standard eigenvalue problem using SLEPc4py.,
>> compiled with Intel MKL and Intel MPI. - I am using slepc4py with mpi
>> and run it with around -n 20 cores at the moment and how i wanted to ask if
>> there is an easy way to retrieve the eigenvectors? When i run my code
>> and print for i in range(nconv):
>> for i in range(nconv): val = E.getEigenpair(i, vr, vi) Print(vr.getArray
>> ())
>> i get the parts of the eigenvectors according to the partition of the
>> matrix. Is there any easy way to put them together in an array and write
>> them to file ? (I am struggling a little bit with the building them in the
>> correct order)
>>
>>
>> You need VecScatterCreateToZero. There must be an equivalent in python.
>>
>
> An alternative to this which you should consider, because it is simpler,
> is to write the vector to a file
> using some format that PETSc understands, Then you just need
> vr.view(viewer) for a viewer like
> the binary viewer or some ASCII format you like.
>
>   Thanks,
>
>     Matt
>
>> - I need to solve eigenvalue problems up to a dimension of 100000 degrees
>> of freedom and i need all eigenvalues and eigenvectors. I think solving
>> all eigenvalues in one process is far too much and i thought about if it is
>> possible to apply the spectrum slicing described in Chap. 3.4.5. Due to the
>> nature of my problem, i am able to simulate smaller systems of 10000 DOF
>> and extract the biggest eigenvalue, which will be the same for larger
>> systems sizes. Is this in general possible since i have a standard HEP
>> problem or is there a better and faster possibility to do this?
>>
>>
>> In general, SLEPc is not intended for computing the whole spectrum. You
>> can try with spectrum slicing but this will be competitive if computing
>> just a percentage of eigenvalues, 50% say.
>>
>> Jose
>>
>>
>> Thank you very much!
>>
>>
>
> --
> 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/>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20180917/25699d09/attachment.html>