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
