[petsc-users] Retireve eigenvectors from a paralell job/ Spectrum slicing in order to solve big eigenvalue problem
Jan Grießer
griesser.jan at googlemail.com
Tue Sep 18 02:26:23 CDT 2018
Now it works. Thank you very much!
Am Mo., 17. Sep. 2018 um 10:54 Uhr schrieb Jose E. Roman <jroman at dsic.upv.es
>:
> For this you have to set a number of partitions equal to the number of MPI
> processes. If you get this error it is because these values are different.
> Jose
>
>
> > El 17 sept 2018, a las 10:50, Jan Grießer <griesser.jan at googlemail.com>
> escribió:
> >
> > 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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