[petsc-users] Retireve eigenvectors from a paralell job/ Spectrum slicing in order to solve big eigenvalue problem
Jan Grießer
griesser.jan at googlemail.com
Mon Sep 17 03:50:57 CDT 2018
Is this relly necessary, because in the last sentences of the chapter it
states that:
An additional benefit of multi-communicator support is that it enables
parallel spectrum slicing runs without the need to install a parallel
direct solver (MUMPS). The following commandline example uses sequential
linear solves in 4 partitions, one process each:
Therefore i assumed that it is not necessary to compile PETsc4py with an
external solver e.g. MUMPS
Am Mo., 17. Sep. 2018 um 10:47 Uhr schrieb Jose E. Roman <jroman at dsic.upv.es
>:
> You need a parallel direct solver such as MUMPS. This is explained in
> section 3.4.5.
> Jose
>
>
> > El 17 sept 2018, a las 10:41, Jan Grießer <griesser.jan at googlemail.com>
> escribió:
> >
> > 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/
>
>
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