Dear All, After analyzing both of the matrices (A and B) in matlab as John suggested, I found my B matrix had an empty row (as pointed out in the error message). Position of the row is related to the size of the mesh and type of element:
using QUAD8: 2x2 mesh --- B has an empty row at 18 from 21 dif: 3 3x3 mesh --- B has an empty row at 34 from 40 dif: 6 4x4 mesh --- B has an empty row at 56 from 65 dif: 9 5x5 mesh --- B has an empty row at 84 from 96 dif: 12 using QUAD9 Quad9 2x2 mesh --- B.m has an empty row at 21 from 25 dif: 4 3x3 mesh --- B.m has an empty row at 31 from 49 dif: 8 .. I must be forgetting to add something when imposing the PBCs, If anyone sees it please let me know. Thank you Peter On Fri, Jan 25, 2013 at 4:48 AM, Nachiket Gokhale <[email protected]>wrote: > You might want to try using MUMPS for LU factorization. It is robust. > Petsc and SlepC make using it very easy. > > > > > On Jan 24, 2013, at 10:12 PM, David Knezevic <[email protected]> > wrote: > > > Hi Peter, > > > > You're using SLEPc, right? Have you tried using the LAPACK eigensolver > > via SLEPc (this tends to be very robust, but it treats the matrices as > > dense so only works for small problems). To do this, use the command > > line option: > > > > -eps_type lapack > > > > David > > > > > > > > On 01/24/2013 03:29 PM, Peter Zajac wrote: > >> Hi Roy, > >> > >> after constraining the matrices I get the correct eigenvalues and > >> wavefunctions -- thank you for helping me solve the problem. > >> > >> There is one last thing I wanted to ask. When I run the code now (with > the > >> constrains), despite obtaining the correct results I get the following > >> error message: > >> > >> [0]PETSC ERROR: --------------------- Error Message > >> ------------------------------------ > >> [0]PETSC ERROR: Detected zero pivot in LU factorization: > >> see http://www.mcs.anl.gov/petsc/documentation/faq.html#ZeroPivot! > >> [0]PETSC ERROR: Empty row in matrix: row in original ordering 1223 in > >> permuted ordering 20! > >> [0]PETSC ERROR: > >> ------------------------------------------------------------------------ > >> [0]PETSC ERROR: Petsc Release Version 3.3.0, Patch 3, Wed Aug 29 > 11:26:24 > >> CDT 2012 > >> [0]PETSC ERROR: See docs/changes/index.html for recent updates. > >> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > >> [0]PETSC ERROR: See docs/index.html for manual pages. > >> [0]PETSC ERROR: > >> ------------------------------------------------------------------------ > >> [0]PETSC ERROR: ./femvib on a arch-linu named peter-VirtualBox by peter > Thu > >> Jan 24 09:25:57 2013 > >> [0]PETSC ERROR: Libraries linked from > >> /home/peter/petsc-3.3-p3/arch-linux2-c-debug/lib > >> [0]PETSC ERROR: Configure run at Fri Nov 23 19:14:06 2012 > >> [0]PETSC ERROR: Configure options --download-f2cblaslapack=1 > >> [0]PETSC ERROR: > >> ------------------------------------------------------------------------ > >> [0]PETSC ERROR: MatLUFactorSymbolic_SeqAIJ() line 334 in > >> src/mat/impls/aij/seq/aijfact.c > >> [0]PETSC ERROR: MatLUFactorSymbolic() line 2750 in > >> src/mat/interface/matrix.c > >> [0]PETSC ERROR: PCSetUp_LU() line 135 in src/ksp/pc/impls/factor/lu/lu.c > >> [0]PETSC ERROR: PCSetUp() line 832 in src/ksp/pc/interface/precon.c > >> [0]PETSC ERROR: KSPSetUp() line 278 in src/ksp/ksp/interface/itfunc.c > >> [0]PETSC ERROR: PCSetUp_Redundant() line 176 in > >> src/ksp/pc/impls/redundant/redundant.c > >> [0]PETSC ERROR: PCSetUp() line 832 in src/ksp/pc/interface/precon.c > >> [0]PETSC ERROR: KSPSetUp() line 278 in src/ksp/ksp/interface/itfunc.c > >> [0]PETSC ERROR: STSetUp_Shift() line 94 in src/st/impls/shift/shift.c > >> [0]PETSC ERROR: STSetUp() line 280 in src/st/interface/stsolve.c > >> [0]PETSC ERROR: EPSSetUp() line 204 in src/eps/interface/setup.c > >> [0]PETSC ERROR: EPSSolve() line 109 in src/eps/interface/solve.c > >> [0]PETSC ERROR: SlepcAbs() line 486 in > >> "unknowndirectory/"src/solvers/slepc_eigen_solver.C > >> application called MPI_Abort(comm=0x84000000, 71) - process 0 > >> > >> According to the PETSC documentation zero pivot does not always mean the > >> matrix is singular and since I am getting the correct results I am > ignoring > >> the error. Could my ignorance in this case cause a serious problem in > the > >> future I should be aware of? > >> > >> thank you again > >> > >> best > >> > >> Peter Zajac > >> Computational Science Research Center > >> San Diego > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> On Wed, Jan 23, 2013 at 11:33 AM, Roy Stogner <[email protected] > >wrote: > >> > >>> On Wed, 23 Jan 2013, Peter Zajac wrote: > >>> > >>> I am not applying the constraint matrices inside the assemble_mass() > >>>> function. How exactly should I do that? > >>>> > >>> See the constrain_element_* calls in the example codes. They're > >>> usually important in the context of hanging node constraints, but the > >>> periodic boundary constraints work the same way. (and any > >>> DirichletBoundaries work nearly the same way, if you're currently > >>> using penalty Dirichlet BCs and want to switch) > >>> --- > >>> Roy > >>> > >> > ------------------------------------------------------------------------------ > >> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, > >> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current > >> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft > >> MVPs and experts. ON SALE this month only -- learn more at: > >> http://p.sf.net/sfu/learnnow-d2d > >> _______________________________________________ > >> Libmesh-users mailing list > >> [email protected] > >> https://lists.sourceforge.net/lists/listinfo/libmesh-users > > > > > > > ------------------------------------------------------------------------------ > > Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, > > MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current > > with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft > > MVPs and experts. ON SALE this month only -- learn more at: > > http://p.sf.net/sfu/learnnow-d2d > > _______________________________________________ > > Libmesh-users mailing list > > [email protected] > > https://lists.sourceforge.net/lists/listinfo/libmesh-users > > > ------------------------------------------------------------------------------ > Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, > MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current > with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft > MVPs and experts. ON SALE this month only -- learn more at: > http://p.sf.net/sfu/learnnow-d2d > _______________________________________________ > Libmesh-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/libmesh-users > ------------------------------------------------------------------------------ Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d _______________________________________________ Libmesh-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/libmesh-users
