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 <[email protected]> > 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 > <[email protected]>: > 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 > <[email protected]>: > On Fri, Sep 14, 2018 at 12:19 PM Jose E. Roman <[email protected]> wrote: > El 14 sept 2018, a las 17:45, Jan Grießer <[email protected]> > 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/
