On Mon, Oct 2, 2017 at 10:43 AM, Wenbo Zhao <zhaowenbo.n...@gmail.com> wrote:
> Mark, > > Thanks for your reply. > > On Mon, Oct 2, 2017 at 9:51 PM, Mark Adams <mfad...@lbl.gov> wrote: > >> Please send the output with -st_ksp_view and -st_ksp_monitor and we can >> start to debug it. >> >> Test 1 with nonsmooth and preonly is OK > zhaowenbo@ubuntu:~/test_slepc/SPARK/spark$ make NCORE=1 runkr_nonsmooth > mpirun -n 1 ./step-41 \ > -st_ksp_type gmres -st_ksp_view -st_ksp_monitor \ > -st_pc_type gamg -st_pc_gamg_type agg -st_pc_gamg_agg_nsmooths 0 \ > -st_ksp_view -mata AMAT.dat -matb BMAT.dat \ > -st_mg_coarse_ksp_type preonly -st_mg_coarse_ksp_monitor \ > -eps_nev 1 -eps_ncv 10 -eps_monitor -log_view > log_nonsmooth 2>&1 > > Test 2 smooth and preonly is not OK > zhaowenbo@ubuntu:~/test_slepc/SPARK/spark$ make NCORE=1 runkr_smooth > mpirun -n 1 ./step-41 \ > -st_ksp_type gmres -st_ksp_view -st_ksp_monitor \ > -st_pc_type gamg -st_pc_gamg_type agg -st_pc_gamg_agg_nsmooths 1 \ > -st_ksp_view -mata AMAT.dat -matb BMAT.dat \ > -st_mg_coarse_ksp_type preonly -st_mg_coarse_ksp_monitor \ > -eps_nev 1 -eps_ncv 10 -eps_monitor -log_view > log_smooth 2>&1 > makefile:43: recipe for target 'runkr_smooth' failed > make: *** [runkr_smooth] Error 91 > > Test 3 nonsmooth and gmres is not OK > zhaowenbo@ubuntu:~/test_slepc/SPARK/spark$ make NCORE=1 runkr_gmres > mpirun -n 1 ./step-41 \ > -st_ksp_type gmres -st_ksp_view -st_ksp_monitor \ > -st_pc_type gamg -st_pc_gamg_type agg -st_pc_gamg_agg_nsmooths 0 \ > -st_ksp_view -mata AMAT.dat -matb BMAT.dat \ > -st_mg_coarse_ksp_type gmres -st_mg_coarse_ksp_monitor > -st_mg_coarse_ksp_rtol 1.0e-6 \ > DO NOT DO THIS. Please send the output where you do NOTHING to the coarse solver. Thanks, Matt > -eps_nev 1 -eps_ncv 10 -eps_monitor -log_view > log_gmres 2>&1 > makefile:59: recipe for target 'runkr_gmres' failed > make: *** [runkr_gmres] Error 91 > > log-files is attached. > > > You mentioned that B is not symmetric. I assume it is elliptic >> (diffusion). Where does the asymmetry come from? >> >> > It is a two-group diffusion equations, where group denotes neutron enegry > discretisation. > Matrix B consists of neutron diffusion/leakage term, removal term and > minus neutron scatter source term between different energies, when matrix A > denotes neutron fission source. > > Diffusion term(Laplace operator) is elliptic and symmetric. Removal term > is diagonal only. However scatter term is asymmetry since scatter term from > high energy to low energy is far greater than the term from low to high. > > > Wenbo > > >> On Mon, Oct 2, 2017 at 9:39 AM, Wenbo Zhao <zhaowenbo.n...@gmail.com> >> wrote: >> >>> Matt, >>> Thanks for your reply. >>> For the defalt option doesnt work firstly( -st_ksp_type gmres >>> -st_pc_type gamg -st_pc_gamg_type agg -st_pc_gamg_agg_nsmooths 1), I tried >>> to test those options. >>> >>> Wenbo >>> >>> On Mon, Oct 2, 2017 at 9:08 PM, Matthew Knepley <knep...@gmail.com> >>> wrote: >>> >>>> On Mon, Oct 2, 2017 at 8:30 AM, Wenbo Zhao <zhaowenbo.n...@gmail.com> >>>> wrote: >>>> >>>>> Matt >>>>> >>>>> Because I am not clear about what will happen using 'preonly' for >>>>> large scale problem. >>>>> >>>> >>>> The size of the problem has nothing to do with 'preonly'. All it means >>>> is to apply a preconditioner without a Krylov solver. >>>> >>>> >>>>> It seems to use a direct solver from below, >>>>> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/ >>>>> KSP/KSPPREONLY.html >>>>> >>>> >>>> However, I still cannot understand why you would change the default? >>>> >>>> Matt >>>> >>>> >>>>> >>>>> Thanks! >>>>> Wenbo >>>>> >>>>> On Mon, Oct 2, 2017 at 5:09 PM, Matthew Knepley <knep...@gmail.com> >>>>> wrote: >>>>> >>>>>> On Sun, Oct 1, 2017 at 9:53 PM, Wenbo Zhao <zhaowenbo.n...@gmail.com> >>>>>> wrote: >>>>>> >>>>>>> Matt, >>>>>>> Thanks for your reply. >>>>>>> It DOES make no sense for this problem. >>>>>>> But I am not clear about the 'preonly' option. Which solver is used >>>>>>> in preonly? I wonder if 'preonly' is suitable for large scale problem >>>>>>> such >>>>>>> as 400,000,000 unknowns. >>>>>>> So I tried 'gmres' option and found these error messages. >>>>>>> >>>>>> >>>>>> I mean, why are you setting this at all. Just do not set the coarse >>>>>> solver. The default should work fine. >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Matt >>>>>> >>>>>> >>>>>>> Could you give me some suggestions? >>>>>>> >>>>>>> Thanks. >>>>>>> >>>>>>> Wenbo >>>>>>> >>>>>>> >>>>>>> On Mon, Oct 2, 2017 at 12:34 AM, Matthew Knepley <knep...@gmail.com> >>>>>>> wrote: >>>>>>> >>>>>>>> On Sun, Oct 1, 2017 at 6:49 AM, Wenbo Zhao < >>>>>>>> zhaowenbo.n...@gmail.com> wrote: >>>>>>>> >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> I met some questions when I use PETSC/SLEPC to solve two-group >>>>>>>>> neutron diffusion equations with finite difference method. The grid is >>>>>>>>> 3*3*3, when DOF on each points is 2. So the matrix size is 54*54. >>>>>>>>> It is generalized eigenvalue problem Ax=\lamda Bx, where B is >>>>>>>>> diagonally dominant matrix but not symmetry. >>>>>>>>> EPS is set as below, >>>>>>>>> ierr = EPSSetProblemType(eps,EPS_GNHEP);CHKERRQ(ierr);¬ >>>>>>>>> ierr = EPSSetWhichEigenpairs(eps,EPS_ >>>>>>>>> LARGEST_REAL);CHKERRQ(ierr);¬ >>>>>>>>> >>>>>>>>> Krylovschur is used as eps sovler. GAMG is used as PC. >>>>>>>>> I tried agg_nsmooths and mg_coarse_ksp_type. Only non-smooths and >>>>>>>>> preonly is OK. >>>>>>>>> >>>>>>>> >>>>>>>> Why are you setting the coarse solver. This makes no sense. >>>>>>>> >>>>>>>> Thanks, >>>>>>>> >>>>>>>> Matt >>>>>>>> >>>>>>>> >>>>>>>>> >>>>>>>>> Test 1 >>>>>>>>> $ make NCORE=1 runkr_nonsmooth >>>>>>>>> mpirun -n 1 ./step-41 \ >>>>>>>>> -st_ksp_type gmres \ >>>>>>>>> -st_pc_type gamg -st_pc_gamg_type agg -st_pc_gamg_agg_nsmooths >>>>>>>>> 0 \ >>>>>>>>> -st_ksp_view -mata AMAT.dat -matb BMAT.dat \ >>>>>>>>> -st_mg_coarse_ksp_type preonly -st_mg_coarse_ksp_monitor \ >>>>>>>>> -eps_nev 1 -eps_ncv 10 -eps_monitor -log_view > log_nonsmooth >>>>>>>>> 2>&1 >>>>>>>>> >>>>>>>>> Test 2 >>>>>>>>> $ make NCORE=1 runkr_smooth >>>>>>>>> mpirun -n 1 ./step-41 \ >>>>>>>>> -st_ksp_type gmres \ >>>>>>>>> -st_pc_type gamg -st_pc_gamg_type agg -st_pc_gamg_agg_nsmooths >>>>>>>>> 1 \ >>>>>>>>> -st_ksp_view -mata AMAT.dat -matb BMAT.dat \ >>>>>>>>> -st_mg_coarse_ksp_type preonly -st_mg_coarse_ksp_monitor \ >>>>>>>>> -eps_nev 1 -eps_ncv 10 -eps_monitor -log_view > log_smooth 2>&1 >>>>>>>>> makefile:43: recipe for target 'runkr_smooth' failed >>>>>>>>> make: *** [runkr_smooth] Error 91 >>>>>>>>> >>>>>>>>> Test 3 >>>>>>>>> $ make NCORE=1 runkr_gmres >>>>>>>>> mpirun -n 1 ./step-41 \ >>>>>>>>> -st_ksp_type gmres \ >>>>>>>>> -st_pc_type gamg -st_pc_gamg_type agg -st_pc_gamg_agg_nsmooths >>>>>>>>> 0 \ >>>>>>>>> -st_ksp_view -mata AMAT.dat -matb BMAT.dat \ >>>>>>>>> -st_mg_coarse_ksp_type gmres -st_mg_coarse_ksp_monitor >>>>>>>>> -st_mg_coarse_ksp_rtol 1.0e-6 \ >>>>>>>>> -eps_nev 1 -eps_ncv 10 -eps_monitor -log_view > log_gmres 2>&1 >>>>>>>>> makefile:59: recipe for target 'runkr_gmres' failed >>>>>>>>> make: *** [runkr_gmres] Error 91 >>>>>>>>> >>>>>>>>> Log files were attched. >>>>>>>>> The matrix file were also attched as AMAT.dat and BMAT.dat. >>>>>>>>> >>>>>>>>> Is it correct? Or something wrong with my code or commad-line? >>>>>>>>> >>>>>>>>> Thanks! >>>>>>>>> >>>>>>>>> Wenbo >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> 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/ >>>>>>>> <http://www.caam.rice.edu/%7Emk51/> >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> 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/ >>>>>> <http://www.caam.rice.edu/%7Emk51/> >>>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>>> 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/ >>>> <http://www.caam.rice.edu/%7Emk51/> >>>> >>> >>> >> > -- 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/ <http://www.caam.rice.edu/~mk51/>