On Mon, Oct 2, 2017 at 11:06 AM, Wenbo Zhao <zhaowenbo.n...@gmail.com> wrote:
> Matt, > Thanks Wenbo. > Test 1 nonsmooth > 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 \ > -mata AMAT.dat -matb BMAT.dat \ > -eps_nev 1 -eps_ncv 10 -eps_monitor -log_view > log_nonsmooth 2>&1 > > Test 2 smooth > 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 \ > -mata AMAT.dat -matb BMAT.dat \ > -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 > > Mark, the solve is not failing, its the construction of the interpolator I think. Check out this stack [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [0]PETSC ERROR: KSPSolve has not converged [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.8.0, unknown [0]PETSC ERROR: ./step-41 on a arch-linux2-c-debug named ubuntu by zhaowenbo Mon Oct 2 08:00:58 2017 [0]PETSC ERROR: Configure options --with-mpi=1 --with-shared-libraries=1 --with-64-bit-indices=1 --with-debugging=1 [0]PETSC ERROR: #1 KSPSolve() line 855 in /home/zhaowenbo/research/petsc/petsc_git/src/ksp/ksp/interface/itfunc.c [0]PETSC ERROR: #2 PCGAMGOptProlongator_AGG() line 1186 in /home/zhaowenbo/research/petsc/petsc_git/src/ksp/pc/impls/gamg/agg.c [0]PETSC ERROR: #3 PCSetUp_GAMG() line 528 in /home/zhaowenbo/research/petsc/petsc_git/src/ksp/pc/impls/gamg/gamg.c [0]PETSC ERROR: #4 PCSetUp() line 924 in /home/zhaowenbo/research/petsc/petsc_git/src/ksp/pc/interface/precon.c [0]PETSC ERROR: #5 KSPSetUp() line 378 in /home/zhaowenbo/research/petsc/petsc_git/src/ksp/ksp/interface/itfunc.c [0]PETSC ERROR: #6 STSetUp_Shift() line 129 in /home/zhaowenbo/research/slepc/slepc_git/src/sys/classes/st/impls/shift/shift.c [0]PETSC ERROR: #7 STSetUp() line 281 in /home/zhaowenbo/research/slepc/slepc_git/src/sys/classes/st/interface/stsolve.c [0]PETSC ERROR: #8 EPSSetUp() line 273 in /home/zhaowenbo/research/slepc/slepc_git/src/eps/interface/epssetup.c [0]PETSC ERROR: #9 solve_diffusion_3d() line 1029 in src/diffu.c [0]PETSC ERROR: #10 main() line 25 in src/main.c [0]PETSC ERROR: PETSc Option Table entries: [0]PETSC ERROR: -eps_monitor [0]PETSC ERROR: -eps_ncv 10 [0]PETSC ERROR: -eps_nev 1 [0]PETSC ERROR: -log_view [0]PETSC ERROR: -mata AMAT.dat [0]PETSC ERROR: -matb BMAT.dat [0]PETSC ERROR: -st_ksp_monitor [0]PETSC ERROR: -st_ksp_type gmres [0]PETSC ERROR: -st_ksp_view [0]PETSC ERROR: -st_pc_gamg_agg_nsmooths 1 [0]PETSC ERROR: -st_pc_gamg_type agg [0]PETSC ERROR: -st_pc_type gamg [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-ma...@mcs.anl.gov---------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 91. Thanks, Matt > Thanks, > > Wenbo > > On Mon, Oct 2, 2017 at 10:48 PM, Matthew Knepley <knep...@gmail.com> > wrote: > >> 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/> >> > > -- 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/>
