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

Mon Sep 17 03:41:30 CDT 2018

def solve_eigensystem(DynMatrix_nn, Unity_nn, Dimension, LowerLimit,
UpperLimit):
# Create the EPS solver
E = SLEPc.EPS().create()

# Create the preconditioner and set it to Cholesky
pc = PETSc.PC().create()
pc.setType(pc.Type.CHOLESKY)

# Create the KSP object
ksp = PETSc.KSP().create()
ksp.setType(ksp.Type.PREONLY)
ksp.setPC(pc)

# Set up the spectral transformations
st = SLEPc.ST().create()
st.setType("sinvert")
st.setKSP(ksp)
# Setup spectral transformation
E.setST(st)
# Eigenvalues should be real, therefore we start to order them from the
smallest real value |l.real|
E.setWhichEigenpairs(E.Which.ALL)
# Set the interval of spectrum slicing
E.setInterval(LowerLimit, UpperLimit)
# Since the dynamical matrix is symmetric and real it is hermitian. Use
GHEP for the spectrum slicing. Operatormatrix B is just a unit matrix
E.setProblemType(SLEPc.EPS.ProblemType.GHEP)
# Use the Krylov Schur method to solve the eigenvalue problem
E.setType(E.Type.KRYLOVSCHUR)
# Partition the Krylov schnur problem in npart procceses
E.setKrylovSchurPartitions(10)
# Set the convergence criterion to relative to the eigenvalue and the
maximal number of iterations
E.setConvergenceTest(E.Conv.REL)
E.setTolerances(tol = 1e-7, max_it = 1000)
# Set the matrix in order to solve
E.setOperators(DynMatrix_nn, Unity_nn)
# Sets EPS options from the options database.
E.setFromOptions()
# Sets up all the internal data structures necessary for the execution of
the eigensolver.
E.setUp()

# Solve eigenvalue problem
startClock = time.clock()
startTime = time.time()
E.solve()

Has maybe one of you any idea why this happens and where the problem is ?

Am Mo., 17. Sep. 2018 um 10:40 Uhr schrieb Jan Grießer <
griesser.jan at googlemail.com>:

> 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/>
>>
>
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