(Putting this back on the list) I see. My commands for the parallel ilu might be out of date. Does anyone know the current syntax ?
Thanks. On Thu, May 29, 2014 at 7:28 PM, walter kou <[email protected]> wrote: > Yes, > in serial, I put "pc_type ilu" or just put "pc_type lu", the residual is > small. > > In parallel, I will put "-sub_pc_type ilu", the residual is still big. > > > On Thu, May 29, 2014 at 6:26 PM, Vikram Garg <[email protected]> > wrote: > >> So it works in serial, but not in parallel ? >> >> >> On Thu, May 29, 2014 at 7:25 PM, walter kou <[email protected]> >> wrote: >> >>> -sub_pc_type ilu: >>> >>> The residual is big. >>> >>> 250 KSP Residual norm 1.289444373237e-05 % max 3.713155970657e+05 min >>> 2.280681360715e-03 max/min 1.628090637568e+08 >>> >>> Linear solver converged at step: 25, final residual: 1.28944e-05 >>> >>> >>> On Thu, May 29, 2014 at 6:21 PM, Vikram Garg <[email protected]> >>> wrote: >>> >>>> Right, I dont remember the syntax for ilu in parallel, but I believe it >>>> is >>>> >>>> -sub_pc_type ilu >>>> >>>> Try that. >>>> >>>> >>>> On Thu, May 29, 2014 at 7:18 PM, walter kou <[email protected]> >>>> wrote: >>>> >>>>> The above is mpiexec -np 2, >>>>> Running with single processor is OK. >>>>> >>>>> 249 KSP Residual norm 4.369357920020e-19 % max 5.529938049388e+01 min >>>>> 3.238293945443e-16 max/min 1.707670193797e+17 >>>>> 250 KSP Residual norm 4.369357920020e-19 % max 5.530031976618e+01 min >>>>> 5.037092721368e-16 max/min 1.097861858520e+17 >>>>> >>>>> Linear solver converged at step: 29, final residual: 4.36936e-19 >>>>> >>>>> >>>>> On Thu, May 29, 2014 at 6:15 PM, walter kou <[email protected]> >>>>> wrote: >>>>> >>>>>> It seems I do not have PETSc ILU: >>>>>> >>>>>> [0]PETSC ERROR: --------------------- Error Message >>>>>> ------------------------------------ >>>>>> [0]PETSC ERROR: No support for this operation for this object type! >>>>>> [0]PETSC ERROR: Matrix format mpiaij does not have a built-in PETSc >>>>>> >>>>>> >>>>>> On Thu, May 29, 2014 at 6:11 PM, Vikram Garg <[email protected] >>>>>> > wrote: >>>>>> >>>>>>> That looks good. So it most likely a linear solver settings issue. >>>>>>> Try these options: >>>>>>> >>>>>>> -ksp_monitor_singular_value -ksp_gmres_modifiedgramschmidt >>>>>>> -ksp_gmres_restart 500 -pc_type ilu -pc_factor_levels 4 >>>>>>> >>>>>>> >>>>>>> On Thu, May 29, 2014 at 7:10 PM, walter kou <[email protected]> >>>>>>> wrote: >>>>>>> >>>>>>>> I can only try single processor : -pc_type lu >>>>>>>> The residual is good. >>>>>>>> >>>>>>>> Linear solver converged at step: 53, final residual: 4.67731e-30 >>>>>>>> begin solve: iteration #54 >>>>>>>> >>>>>>>> Linear solver converged at step: 54, final residual: 1.35495e-30 >>>>>>>> begin solve: iteration #55 >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Thu, May 29, 2014 at 6:07 PM, Vikram Garg < >>>>>>>> [email protected]> wrote: >>>>>>>> >>>>>>>>> I see. What happens with LU ? >>>>>>>>> >>>>>>>>> >>>>>>>>> On Thu, May 29, 2014 at 7:06 PM, walter kou <[email protected] >>>>>>>>> > wrote: >>>>>>>>> >>>>>>>>>> tried -ksp_gmres_restart 5000, with residual as below >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Linear solver converged at step: 53, final residual: 1.5531e-05 >>>>>>>>>> begin solve: iteration #54 >>>>>>>>>> >>>>>>>>>> Linear solver converged at step: 54, final residual: 1.55013e-05 >>>>>>>>>> begin solve: iteration #55 >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Thu, May 29, 2014 at 6:01 PM, Vikram Garg < >>>>>>>>>> [email protected]> wrote: >>>>>>>>>> >>>>>>>>>>> Try using a higher number of restart steps, say 500, >>>>>>>>>>> >>>>>>>>>>> -ksp_gmres_restart 500 >>>>>>>>>>> >>>>>>>>>>> Thanks. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Thu, May 29, 2014 at 7:00 PM, walter kou < >>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>> >>>>>>>>>>>> output from the -ksp_monitor_singular_value ? >>>>>>>>>>>> >>>>>>>>>>>> 250 KSP Residual norm 8.867989901517e-05 % max >>>>>>>>>>>> 1.372837955534e+05 min 1.502965355599e+01 max/min >>>>>>>>>>>> 9.134195611495e+03 >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On Thu, May 29, 2014 at 5:54 PM, Vikram Garg < >>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Try the following solver options: >>>>>>>>>>>>> >>>>>>>>>>>>> -pc_type lu -pc_factor_mat_solver_package superlu >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> What was the output from the -ksp_monitor_singular_value ? >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks. >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On Thu, May 29, 2014 at 6:52 PM, walter kou < >>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Vikram, >>>>>>>>>>>>>> >>>>>>>>>>>>>> How to try using just lu or super lu? I am pretty ignorant in >>>>>>>>>>>>>> playing with proper ksp options in the command line. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Could you point out any introductory materials on this? >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks so much. >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Wed, May 28, 2014 at 11:54 AM, Vikram Garg < >>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hey Walter, >>>>>>>>>>>>>>> Have you tried using just lu or super >>>>>>>>>>>>>>> lu ? You might also want to check and see whats the output for >>>>>>>>>>>>>>> -ksp_monitor_singular_value and increase the gmres restart >>>>>>>>>>>>>>> steps. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thanks. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Mon, May 26, 2014 at 1:57 PM, walter kou < >>>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi all, >>>>>>>>>>>>>>>> I ran a larger case: with elements = 200, and found for >>>>>>>>>>>>>>>> each calculation in >>>>>>>>>>>>>>>> the iteration, system.final_linear_residual() is about 0.5%. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> 1) Is the system.final_linear_residual() r = b -A X* (X* >>>>>>>>>>>>>>>> is the solution) >>>>>>>>>>>>>>>> ? right? >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> 2) It seems final residual is too big, and the equation is >>>>>>>>>>>>>>>> not solved well >>>>>>>>>>>>>>>> (here |b| is about 1e-4). Does anyone have suggestion in >>>>>>>>>>>>>>>> playing with >>>>>>>>>>>>>>>> solvers of Ax=b? >>>>>>>>>>>>>>>> Here my case is on nonlinear elasticity, and A is almost >>>>>>>>>>>>>>>> symmetrical >>>>>>>>>>>>>>>> positive definite (only components influenced by boundary >>>>>>>>>>>>>>>> conditions will >>>>>>>>>>>>>>>> break the symmetry). >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Also, following the suggestion of Paul, I use -ksp_view and >>>>>>>>>>>>>>>> find my solver >>>>>>>>>>>>>>>> information is as below: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> KSP Object: 4 MPI processes >>>>>>>>>>>>>>>> type: gmres >>>>>>>>>>>>>>>> GMRES: restart=30, using Classical (unmodified) >>>>>>>>>>>>>>>> Gram-Schmidt >>>>>>>>>>>>>>>> Orthogonalization with no iterative refinement >>>>>>>>>>>>>>>> GMRES: happy breakdown tolerance 1e-30 >>>>>>>>>>>>>>>> maximum iterations=250 >>>>>>>>>>>>>>>> tolerances: relative=1e-08, absolute=1e-50, >>>>>>>>>>>>>>>> divergence=10000 >>>>>>>>>>>>>>>> left preconditioning >>>>>>>>>>>>>>>> using nonzero initial guess >>>>>>>>>>>>>>>> using PRECONDITIONED norm type for convergence test >>>>>>>>>>>>>>>> PC Object: 4 MPI processes >>>>>>>>>>>>>>>> type: bjacobi >>>>>>>>>>>>>>>> block Jacobi: number of blocks = 4 >>>>>>>>>>>>>>>> Local solve is same for all blocks, in the following >>>>>>>>>>>>>>>> KSP and PC objects: >>>>>>>>>>>>>>>> KSP Object: (sub_) 1 MPI processes >>>>>>>>>>>>>>>> type: preonly >>>>>>>>>>>>>>>> maximum iterations=10000, initial guess is zero >>>>>>>>>>>>>>>> tolerances: relative=1e-05, absolute=1e-50, >>>>>>>>>>>>>>>> divergence=10000 >>>>>>>>>>>>>>>> left preconditioning >>>>>>>>>>>>>>>> using NONE norm type for convergence test >>>>>>>>>>>>>>>> PC Object: (sub_) 1 MPI processes >>>>>>>>>>>>>>>> type: ilu >>>>>>>>>>>>>>>> ILU: out-of-place factorization >>>>>>>>>>>>>>>> 0 levels of fill >>>>>>>>>>>>>>>> tolerance for zero pivot 2.22045e-14 >>>>>>>>>>>>>>>> using diagonal shift to prevent zero pivot >>>>>>>>>>>>>>>> matrix ordering: natural >>>>>>>>>>>>>>>> factor fill ratio given 1, needed 1 >>>>>>>>>>>>>>>> Factored matrix follows: >>>>>>>>>>>>>>>> Matrix Object: 1 MPI processes >>>>>>>>>>>>>>>> type: seqaij >>>>>>>>>>>>>>>> rows=324, cols=324 >>>>>>>>>>>>>>>> package used to perform factorization: petsc >>>>>>>>>>>>>>>> total: nonzeros=16128, allocated nonzeros=16128 >>>>>>>>>>>>>>>> total number of mallocs used during >>>>>>>>>>>>>>>> MatSetValues calls =0 >>>>>>>>>>>>>>>> not using I-node routines >>>>>>>>>>>>>>>> linear system matrix = precond matrix: >>>>>>>>>>>>>>>> Matrix Object: () 1 MPI processes >>>>>>>>>>>>>>>> type: seqaij >>>>>>>>>>>>>>>> rows=324, cols=324 >>>>>>>>>>>>>>>> total: nonzeros=16128, allocated nonzeros=19215 >>>>>>>>>>>>>>>> total number of mallocs used during MatSetValues >>>>>>>>>>>>>>>> calls =0 >>>>>>>>>>>>>>>> not using I-node routines >>>>>>>>>>>>>>>> linear system matrix = precond matrix: >>>>>>>>>>>>>>>> Matrix Object: () 4 MPI processes >>>>>>>>>>>>>>>> type: mpiaij >>>>>>>>>>>>>>>> rows=990, cols=990 >>>>>>>>>>>>>>>> total: nonzeros=58590, allocated nonzeros=64512 >>>>>>>>>>>>>>>> total number of mallocs used during MatSetValues calls >>>>>>>>>>>>>>>> =0 >>>>>>>>>>>>>>>> not using I-node (on process 0) routines >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> /********************************************************* >>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Walter >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Thu, May 22, 2014 at 12:18 PM, Paul T. Bauman < >>>>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>> > On Thu, May 22, 2014 at 12:11 PM, walter kou < >>>>>>>>>>>>>>>> [email protected]>wrote: >>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>> >> OK, but libMesh calls a library, defaulting to PETSc if >>>>>>>>>>>>>>>> it's installed. >>>>>>>>>>>>>>>> >> Which library are you using? >>>>>>>>>>>>>>>> >> >>>>>>>>>>>>>>>> >> PETSc-3.3 >>>>>>>>>>>>>>>> >> >>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>> > I recommend checking out the PETSc documentation ( >>>>>>>>>>>>>>>> > http://www.mcs.anl.gov/petsc/petsc-as/documentation/) >>>>>>>>>>>>>>>> and tutorials. But >>>>>>>>>>>>>>>> > you'll want to start with -ksp_view to get the parameters >>>>>>>>>>>>>>>> PETSc is using. >>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ------------------------------------------------------------------------------ >>>>>>>>>>>>>>>> The best possible search technologies are now affordable >>>>>>>>>>>>>>>> for all companies. >>>>>>>>>>>>>>>> Download your FREE open source Enterprise Search Engine >>>>>>>>>>>>>>>> today! >>>>>>>>>>>>>>>> Our experts will assist you in its installation for $59/mo, >>>>>>>>>>>>>>>> no commitment. >>>>>>>>>>>>>>>> Test it for FREE on our Cloud platform anytime! >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=145328191&iu=/4140/ostg.clktrk >>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>> Libmesh-users mailing list >>>>>>>>>>>>>>>> [email protected] >>>>>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/libmesh-users >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>> Vikram Garg >>>>>>>>>>>>>>> Postdoctoral Associate >>>>>>>>>>>>>>> Center for Computational Engineering >>>>>>>>>>>>>>> Massachusetts Institute of Technology >>>>>>>>>>>>>>> http://web.mit.edu/vikramvg/www/ >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> http://www.runforindia.org/runners/vikramg >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> -- >>>>>>>>>>>>> Vikram Garg >>>>>>>>>>>>> Postdoctoral Associate >>>>>>>>>>>>> Center for Computational Engineering >>>>>>>>>>>>> Massachusetts Institute of Technology >>>>>>>>>>>>> http://web.mit.edu/vikramvg/www/ >>>>>>>>>>>>> >>>>>>>>>>>>> http://www.runforindia.org/runners/vikramg >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> Vikram Garg >>>>>>>>>>> Postdoctoral Associate >>>>>>>>>>> Center for Computational Engineering >>>>>>>>>>> Massachusetts Institute of Technology >>>>>>>>>>> http://web.mit.edu/vikramvg/www/ >>>>>>>>>>> >>>>>>>>>>> http://www.runforindia.org/runners/vikramg >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Vikram Garg >>>>>>>>> Postdoctoral Associate >>>>>>>>> Center for Computational Engineering >>>>>>>>> Massachusetts Institute of Technology >>>>>>>>> http://web.mit.edu/vikramvg/www/ >>>>>>>>> >>>>>>>>> http://www.runforindia.org/runners/vikramg >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Vikram Garg >>>>>>> Postdoctoral Associate >>>>>>> Center for Computational Engineering >>>>>>> Massachusetts Institute of Technology >>>>>>> http://web.mit.edu/vikramvg/www/ >>>>>>> >>>>>>> http://www.runforindia.org/runners/vikramg >>>>>>> >>>>>> >>>>>> >>>>> >>>> >>>> >>>> -- >>>> Vikram Garg >>>> Postdoctoral Associate >>>> Center for Computational Engineering >>>> Massachusetts Institute of Technology >>>> http://web.mit.edu/vikramvg/www/ >>>> >>>> http://www.runforindia.org/runners/vikramg >>>> >>> >>> >> >> >> -- >> Vikram Garg >> Postdoctoral Associate >> Center for Computational Engineering >> Massachusetts Institute of Technology >> http://web.mit.edu/vikramvg/www/ >> >> http://www.runforindia.org/runners/vikramg >> > > -- Vikram Garg Postdoctoral Associate Center for Computational Engineering Massachusetts Institute of Technology http://web.mit.edu/vikramvg/www/ http://www.runforindia.org/runners/vikramg ------------------------------------------------------------------------------ Time is money. 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