[petsc-users] Use block Jacobi preconditioner with SNES
Jed Brown
jed at jedbrown.org
Wed Aug 29 12:59:40 CDT 2018
This is bjacobi/lu, not vpbjacobi.
How are you measuring memory usage? See a couple inline comments below.
Ali Reza Khaz'ali <arkhazali at cc.iut.ac.ir> writes:
> I noticed that I forgot to include the log for 10x10x5 system. Here it is:
>
>
> 1 MPI processes
> type: newtonls
> maximum iterations=2000, maximum function evaluations=2000
> tolerances: relative=0.0001, absolute=1e-05, solution=1e-05
> total number of linear solver iterations=1
> total number of function evaluations=2
> norm schedule ALWAYS
> SNESLineSearch Object: 1 MPI processes
> type: bt
> interpolation: cubic
> alpha=1.000000e-04
> maxstep=1.000000e+08, minlambda=1.000000e-12
> tolerances: relative=1.000000e-08, absolute=1.000000e-15,
> lambda=1.000000e-08
> maximum iterations=40
> KSP Object: 1 MPI processes
> type: gmres
> restart=30, using Classical (unmodified) Gram-Schmidt
> Orthogonalization with no iterative refinement
> happy breakdown tolerance 1e-30
> maximum iterations=5000, initial guess is zero
> tolerances: relative=1e-05, absolute=1e-06, divergence=10000.
> left preconditioning
> using PRECONDITIONED norm type for convergence test
> PC Object: 1 MPI processes
> type: bjacobi
> number of blocks = 1
> 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: lu
> out-of-place factorization
> tolerance for zero pivot 2.22045e-14
> matrix ordering: nd
> factor fill ratio given 0., needed 0.
> Factored matrix follows:
> Mat Object: 1 MPI processes
> type: mkl_pardiso
> rows=6000, cols=6000
> package used to perform factorization: mkl_pardiso
> total: nonzeros=150000, allocated nonzeros=150000
> total number of mallocs used during MatSetValues calls =0
> MKL_PARDISO run parameters:
> MKL_PARDISO phase: 33
> MKL_PARDISO iparm[1]: 1
> MKL_PARDISO iparm[2]: 2
> MKL_PARDISO iparm[3]: 2
> MKL_PARDISO iparm[4]: 0
> MKL_PARDISO iparm[5]: 0
> MKL_PARDISO iparm[6]: 0
> MKL_PARDISO iparm[7]: 0
> MKL_PARDISO iparm[8]: 0
> MKL_PARDISO iparm[9]: 0
> MKL_PARDISO iparm[10]: 13
> MKL_PARDISO iparm[11]: 1
> MKL_PARDISO iparm[12]: 0
> MKL_PARDISO iparm[13]: 1
> MKL_PARDISO iparm[14]: 0
> MKL_PARDISO iparm[15]: 11228
> MKL_PARDISO iparm[16]: 7563
> MKL_PARDISO iparm[17]: 37035
> MKL_PARDISO iparm[18]: 4204238
> MKL_PARDISO iparm[19]: 2659
> MKL_PARDISO iparm[20]: 0
> MKL_PARDISO iparm[21]: 0
> MKL_PARDISO iparm[22]: 0
> MKL_PARDISO iparm[23]: 0
> MKL_PARDISO iparm[24]: 0
> MKL_PARDISO iparm[25]: 0
> MKL_PARDISO iparm[26]: 0
> MKL_PARDISO iparm[27]: 0
> MKL_PARDISO iparm[28]: 0
> MKL_PARDISO iparm[29]: 0
> MKL_PARDISO iparm[30]: 0
> MKL_PARDISO iparm[31]: 0
> MKL_PARDISO iparm[32]: 0
> MKL_PARDISO iparm[33]: 0
> MKL_PARDISO iparm[34]: -1
> MKL_PARDISO iparm[35]: 1
> MKL_PARDISO iparm[36]: 0
> MKL_PARDISO iparm[37]: 0
> MKL_PARDISO iparm[38]: 0
> MKL_PARDISO iparm[39]: 0
> MKL_PARDISO iparm[40]: 0
> MKL_PARDISO iparm[41]: 0
> MKL_PARDISO iparm[42]: 0
> MKL_PARDISO iparm[43]: 0
> MKL_PARDISO iparm[44]: 0
> MKL_PARDISO iparm[45]: 0
> MKL_PARDISO iparm[46]: 0
> MKL_PARDISO iparm[47]: 0
> MKL_PARDISO iparm[48]: 0
> MKL_PARDISO iparm[49]: 0
> MKL_PARDISO iparm[50]: 0
> MKL_PARDISO iparm[51]: 0
> MKL_PARDISO iparm[52]: 0
> MKL_PARDISO iparm[53]: 0
> MKL_PARDISO iparm[54]: 0
> MKL_PARDISO iparm[55]: 0
> MKL_PARDISO iparm[56]: 0
> MKL_PARDISO iparm[57]: -1
> MKL_PARDISO iparm[58]: 0
> MKL_PARDISO iparm[59]: 0
> MKL_PARDISO iparm[60]: 0
> MKL_PARDISO iparm[61]: 11228
> MKL_PARDISO iparm[62]: 7868
> MKL_PARDISO iparm[63]: 3629
> MKL_PARDISO iparm[64]: 0
> MKL_PARDISO maxfct: 1
> MKL_PARDISO mnum: 1
> MKL_PARDISO mtype: 11
> MKL_PARDISO n: 6000
> MKL_PARDISO nrhs: 1
> MKL_PARDISO msglvl: 0
> linear system matrix = precond matrix:
> Mat Object: 1 MPI processes
> type: seqaij
> rows=6000, cols=6000
> total: nonzeros=150000, allocated nonzeros=480000
> total number of mallocs used during MatSetValues calls =0
> not using I-node routines
> linear system matrix = precond matrix:
> Mat Object: 1 MPI processes
> type: seqaij
> rows=6000, cols=6000
> total: nonzeros=150000, allocated nonzeros=480000
Note that you preallocated more than necessary here.
> total number of mallocs used during MatSetValues calls =0
> not using I-node routines
> ************************************************************************************************************************
> *** WIDEN YOUR WINDOW TO 120 CHARACTERS. Use 'enscript -r
> -fCourier9' to print this document ***
> ************************************************************************************************************************
>
> ---------------------------------------------- PETSc Performance
> Summary: ----------------------------------------------
>
> E:\Documents\Visual Studio 2015\Projects\compsim\x64\Release\compsim.exe
> on a named ALIREZA-PC with 1 processor, by AliReza Wed Aug 29 22:12:30 2018
> Using Petsc Development GIT revision: v3.9.3-1238-g434eb0c8b5 GIT Date:
> 2018-08-28 19:19:26 -0500
>
> Max Max/Min Avg Total
> Time (sec): 3.373e+01 1.000 3.373e+01
> Objects: 3.300e+01 1.000 3.300e+01
> Flop: 7.500e+05 1.000 7.500e+05 7.500e+05
> Flop/sec: 2.224e+04 1.000 2.224e+04 2.224e+04
> MPI Messages: 0.000e+00 0.000 0.000e+00 0.000e+00
> MPI Message Lengths: 0.000e+00 0.000 0.000e+00 0.000e+00
> MPI Reductions: 0.000e+00 0.000
>
> Flop counting convention: 1 flop = 1 real number operation of type
> (multiply/divide/add/subtract)
> e.g., VecAXPY() for real vectors of length
> N --> 2N flop
> and VecAXPY() for complex vectors of length
> N --> 8N flop
>
> Summary of Stages: ----- Time ------ ----- Flop ------ --- Messages
> --- -- Message Lengths -- -- Reductions --
> Avg %Total Avg %Total Count
> %Total Avg %Total Count %Total
> 0: Main Stage: 3.3730e+01 100.0% 7.5000e+05 100.0% 0.000e+00
> 0.0% 0.000e+00 0.0% 0.000e+00 0.0%
>
> ------------------------------------------------------------------------------------------------------------------------
> See the 'Profiling' chapter of the users' manual for details on
> interpreting output.
> Phase summary info:
> Count: number of times phase was executed
> Time and Flop: Max - maximum over all processors
> Ratio - ratio of maximum to minimum over all processors
> Mess: number of messages sent
> AvgLen: average message length (bytes)
> Reduct: number of global reductions
> Global: entire computation
> Stage: stages of a computation. Set stages with PetscLogStagePush()
> and PetscLogStagePop().
> %T - percent time in this phase %F - percent flop in this
> phase
> %M - percent messages in this phase %L - percent message
> lengths in this phase
> %R - percent reductions in this phase
> Total Mflop/s: 10e-6 * (sum of flop over all processors)/(max time
> over all processors)
> ------------------------------------------------------------------------------------------------------------------------
> Event Count Time (sec)
> Flop --- Global --- --- Stage ---- Total
> Max Ratio Max Ratio Max Ratio Mess AvgLen
> Reduct %T %F %M %L %R %T %F %M %L %R Mflop/s
> ------------------------------------------------------------------------------------------------------------------------
>
> --- Event Stage 0: Main Stage
>
> BuildTwoSidedF 2 1.0 7.9003e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
> SNESSolve 1 1.0 7.3396e+00 1.0 7.50e+05 1.0 0.0e+00 0.0e+00
> 0.0e+00 22100 0 0 0 22100 0 0 0 0
> SNESFunctionEval 2 1.0 3.8894e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
> SNESJacobianEval 1 1.0 5.1611e+00 1.0 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 15 0 0 0 0 15 0 0 0 0 0
Most of the time here is spent in your code computing the Jacobian, not
in the solver.
> SNESLineSearch 1 1.0 1.7655e-02 1.0 3.60e+05 1.0 0.0e+00 0.0e+00
> 0.0e+00 0 48 0 0 0 0 48 0 0 0 20
> VecDot 1 1.0 1.1546e-05 1.0 1.20e+04 1.0 0.0e+00 0.0e+00
> 0.0e+00 0 2 0 0 0 0 2 0 0 0 1039
> VecMDot 1 1.0 2.3093e-05 1.0 1.20e+04 1.0 0.0e+00 0.0e+00
> 0.0e+00 0 2 0 0 0 0 2 0 0 0 520
> VecNorm 5 1.0 4.9769e-01 1.0 6.00e+04 1.0 0.0e+00 0.0e+00
> 0.0e+00 1 8 0 0 0 1 8 0 0 0 0
> VecScale 2 1.0 9.3291e-03 1.0 1.20e+04 1.0 0.0e+00 0.0e+00
> 0.0e+00 0 2 0 0 0 0 2 0 0 0 1
> VecCopy 3 1.0 2.3093e-05 1.0 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
> VecSet 4 1.0 1.5395e-05 1.0 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
> VecAXPY 1 1.0 2.5734e-02 1.0 1.20e+04 1.0 0.0e+00 0.0e+00
> 0.0e+00 0 2 0 0 0 0 2 0 0 0 0
> VecWAXPY 1 1.0 1.3257e-05 1.0 6.00e+03 1.0 0.0e+00 0.0e+00
> 0.0e+00 0 1 0 0 0 0 1 0 0 0 453
> VecMAXPY 2 1.0 2.3521e-05 1.0 2.40e+04 1.0 0.0e+00 0.0e+00
> 0.0e+00 0 3 0 0 0 0 3 0 0 0 1020
> VecAssemblyBegin 2 1.0 7.9040e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
> VecAssemblyEnd 2 1.0 1.7961e-05 1.0 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
> VecReduceArith 2 1.0 9.8359e-06 1.0 2.40e+04 1.0 0.0e+00 0.0e+00
> 0.0e+00 0 3 0 0 0 0 3 0 0 0 2440
> VecReduceComm 1 1.0 4.7041e-06 1.0 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
> VecNormalize 2 1.0 9.3552e-03 1.0 3.60e+04 1.0 0.0e+00 0.0e+00
> 0.0e+00 0 5 0 0 0 0 5 0 0 0 4
> MatMult 2 1.0 4.4860e-04 1.0 5.88e+05 1.0 0.0e+00 0.0e+00
> 0.0e+00 0 78 0 0 0 0 78 0 0 0 1311
> MatSolve 2 1.0 1.7876e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 1 0 0 0 0 1 0 0 0 0 0
> MatLUFactorSym 1 1.0 7.6157e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 2 0 0 0 0 2 0 0 0 0 0
> MatLUFactorNum 1 1.0 6.5977e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 2 0 0 0 0 2 0 0 0 0 0
> MatAssemblyBegin 2 1.0 0.0000e+00 0.0 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
> MatAssemblyEnd 2 1.0 1.2962e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
> MatGetRowIJ 1 1.0 1.1534e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
> MatGetOrdering 1 1.0 5.1809e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
> MatZeroEntries 1 1.0 1.1298e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
> MatView 3 1.0 3.8344e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 1 0 0 0 0 1 0 0 0 0 0
> KSPSetUp 2 1.0 3.2843e-04 1.0 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
> KSPSolve 1 1.0 1.6414e+00 1.0 3.78e+05 1.0 0.0e+00 0.0e+00
> 0.0e+00 5 50 0 0 0 5 50 0 0 0 0
> KSPGMRESOrthog 1 1.0 5.9015e-05 1.0 2.40e+04 1.0 0.0e+00 0.0e+00
> 0.0e+00 0 3 0 0 0 0 3 0 0 0 407
> PCSetUp 2 1.0 1.4267e+00 1.0 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 4 0 0 0 0 4 0 0 0 0 0
> PCSetUpOnBlocks 1 1.0 1.4266e+00 1.0 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 4 0 0 0 0 4 0 0 0 0 0
> PCApply 2 1.0 1.7882e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 1 0 0 0 0 1 0 0 0 0 0
> ------------------------------------------------------------------------------------------------------------------------
>
> Memory usage is given in bytes:
>
> Object Type Creations Destructions Memory Descendants' Mem.
> Reports information only for process 0.
>
> --- Event Stage 0: Main Stage
>
> SNES 1 0 0 0.
> DMSNES 1 0 0 0.
> SNESLineSearch 1 0 0 0.
> Vector 12 0 0 0.
> Matrix 2 0 0 0.
> Distributed Mesh 2 0 0 0.
> Index Set 2 0 0 0.
> Star Forest Graph 4 0 0 0.
> Discrete System 2 0 0 0.
> Krylov Solver 2 0 0 0.
> DMKSP interface 1 0 0 0.
> Preconditioner 2 0 0 0.
> Viewer 1 0 0 0.
> ========================================================================================================================
> Average time to get PetscTime(): 4.27647e-08
> #PETSc Option Table entries:
> -ksp_atol 1e-6
> -ksp_rtol 1e-5
> -snes_rtol 1e-4
> -sub_ksp_type preonly
> -sub_pc_factor_mat_solver_type mkl_pardiso
> -sub_pc_type lu
> #End of PETSc Option Table entries
> Compiled without FORTRAN kernels
> Compiled with full precision matrices (default)
> sizeof(short) 2 sizeof(int) 4 sizeof(long) 4 sizeof(void*) 8
> sizeof(PetscScalar) 8 sizeof(PetscInt) 4
> Configure options: --prefix=/home/alireza/PetscGit
> --with-mkl_pardiso-dir=/cygdrive/E/Program_Files_x86/IntelSWTools/compilers_and_libraries/windows/mkl
> --with-hypre-incl
> ude=/cygdrive/E/hypre-2.11.2/Builds/Bins/include
> --with-hypre-lib=/cygdrive/E/hypre-2.11.2/Builds/Bins/lib/HYPRE.lib
> --with-ml-include=/cygdrive/E/Trilinos-master/Bins/in
> clude --with-ml-lib=/cygdrive/E/Trilinos-master/Bins/lib/ml.lib
> ظ€ôwith-openmp --with-cc="win32fe icl" --with-fc="win32fe ifort"
> --with-mpi-include=/cygdrive/E/Program_Fi
> les_x86/IntelSWTools/compilers_and_libraries/windows/mpi/intel64/include
> --with-mpi-lib=/cygdrive/E/Program_Files_x86/IntelSWTools/compilers_and_libraries/windows/mpi/int
> el64/lib/impi.lib
> --with-mpi-mpiexec=/cygdrive/E/Program_Files_x86/IntelSWTools/compilers_and_libraries/windows/mpi/intel64/bin/mpiexec.exe
> --with-debugging=0 --with-blas
> -lib=/cygdrive/E/Program_Files_x86/IntelSWTools/compilers_and_libraries/windows/mkl/lib/intel64_win/mkl_rt.lib
> --with-lapack-lib=/cygdrive/E/Program_Files_x86/IntelSWTool
> s/compilers_and_libraries/windows/mkl/lib/intel64_win/mkl_rt.lib
> -CFLAGS="-O2 -MT -wd4996 -Qopenmp" -CXXFLAGS="-O2 -MT -wd4996 -Qopenmp"
> -FFLAGS="-MT -O2 -Qopenmp"
> -----------------------------------------
> Libraries compiled on 2018-08-29 08:35:21 on AliReza-PC
> Machine characteristics: CYGWIN_NT-6.1-2.10.0-0.325-5-3-x86_64-64bit
> Using PETSc directory: /home/alireza/PetscGit
> Using PETSc arch:
> -----------------------------------------
>
> Using C compiler: /home/alireza/PETSc/lib/petsc/bin/win32fe/win32fe icl
> -O2 -MT -wd4996 -Qopenmp
> Using Fortran compiler:
> /home/alireza/PETSc/lib/petsc/bin/win32fe/win32fe ifort -MT -O2 -Qopenmp
> -fpp
> -----------------------------------------
>
> Using include paths: -I/home/alireza/PetscGit/include
> -I/cygdrive/E/Program_Files_x86/IntelSWTools/compilers_and_libraries/windows/mkl/include
> -I/cygdrive/E/hypre-2.11.2/
> Builds/Bins/include -I/cygdrive/E/Trilinos-master/Bins/include
> -I/cygdrive/E/Program_Files_x86/IntelSWTools/compilers_and_libraries/windows/mpi/intel64/include
> -----------------------------------------
>
> Using C linker: /home/alireza/PETSc/lib/petsc/bin/win32fe/win32fe icl
> Using Fortran linker: /home/alireza/PETSc/lib/petsc/bin/win32fe/win32fe
> ifort
> Using libraries: -L/home/alireza/PetscGit/lib
> -L/home/alireza/PetscGit/lib -lpetsc
> /cygdrive/E/hypre-2.11.2/Builds/Bins/lib/HYPRE.lib
> /cygdrive/E/Trilinos-master/Bins/lib
> /ml.lib
> /cygdrive/E/Program_Files_x86/IntelSWTools/compilers_and_libraries/windows/mkl/lib/intel64_win/mkl_rt.lib
> /cygdrive/E/Program_Files_x86/IntelSWTools/compilers_and
> _libraries/windows/mkl/lib/intel64_win/mkl_rt.lib
> /cygdrive/E/Program_Files_x86/IntelSWTools/compilers_and_libraries/windows/mpi/intel64/lib/impi.lib
> Gdi32.lib User32.lib
> Advapi32.lib Kernel32.lib Ws2_32.lib
> -----------------------------------------
>
>
>
> On 8/29/2018 7:40 PM, Smith, Barry F. wrote:
>> You need to add the line
>>
>> ierr = MatSetVariableBlockSizes(J,3,lens);CHKERRQ(ierr);
>>
>> with the number of blocks replacing 3 and the sizes of each block in lens
>>
>> Barry
>>
>>
>>> On Aug 29, 2018, at 4:27 AM, Ali Reza Khaz'ali <arkhazali at cc.iut.ac.ir> wrote:
>>>
>>> Barry,
>>>
>>> Thanks a lot for your efforts. Using PCVPBJACOBI causes SNESSolve to throw the following error (the code and the system being simulated is the same, just PCBJACOBI changed to PCVPBJACOBI):
>>>
>>>
>>> [0]PETSC ERROR: --------------------- Error Message ---------------------------------------
>>> -----------------------
>>> [0]PETSC ERROR: Nonconforming object sizes
>>> [0]PETSC ERROR: Total blocksizes 0 doesn't match number matrix rows 108000
>>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
>>> [0]PETSC ERROR: Petsc Development GIT revision: v3.9.3-1238-g434eb0c8b5 GIT Date: 2018-08-28 19:19:26 -0500
>>> [0]PETSC ERROR: E:\Documents\Visual Studio 2015\Projects\compsim\x64\Release\compsim.exe on a named ALIREZA-PC by AliReza Wed Aug 29 13:46:38 2018
>>> [0]PETSC ERROR: Configure options --prefix=/home/alireza/PetscGit --with-mkl_pardiso-dir=/cygdrive/E/Program_Files_x86/IntelSWTools/compilers_and_libraries/windows/mkl --
>>> with-hypre-include=/cygdrive/E/hypre-2.11.2/Builds/Bins/include --with-hypre-lib=/cygdrive/E/hypre-2.11.2/Builds/Bins/lib/HYPRE.lib --with-ml-include=/cygdrive/E/Trilinos
>>> -master/Bins/include --with-ml-lib=/cygdrive/E/Trilinos-master/Bins/lib/ml.lib ظ€ôwith-openmp --with-cc="win32fe icl" --with-fc="win32fe ifort" --with-mpi-include=/cygdri
>>> ve/E/Program_Files_x86/IntelSWTools/compilers_and_libraries/windows/mpi/intel64/include --with-mpi-lib=/cygdrive/E/Program_Files_x86/IntelSWTools/compilers_and_libraries/
>>> windows/mpi/intel64/lib/impi.lib --with-mpi-mpiexec=/cygdrive/E/Program_Files_x86/IntelSWTools/compilers_and_libraries/windows/mpi/intel64/bin/mpiexec.exe --with-debuggin
>>> g=0 --with-blas-lib=/cygdrive/E/Program_Files_x86/IntelSWTools/compilers_and_libraries/windows/mkl/lib/intel64_win/mkl_rt.lib --with-lapack-lib=/cygdrive/E/Program_Files_
>>> x86/IntelSWTools/compilers_and_libraries/windows/mkl/lib/intel64_win/mkl_rt.lib -CFLAGS="-O2 -MT -wd4996 -Qopenmp" -CXXFLAGS="-O2 -MT -wd4996 -Qopenmp" -FFLAGS="-MT -O2 -
>>> Qopenmp"
>>> [0]PETSC ERROR: #1 MatInvertVariableBlockDiagonal_SeqAIJ() line 1569 in E:\cygwin64\home\alireza\PETSc\src\mat\impls\aij\seq\aij.c
>>> [0]PETSC ERROR: #2 MatInvertVariableBlockDiagonal() line 10482 in E:\cygwin64\home\alireza\PETSc\src\mat\interface\matrix.c
>>> [0]PETSC ERROR: #3 PCSetUp_VPBJacobi() line 120 in E:\cygwin64\home\alireza\PETSc\src\ksp\pc\impls\vpbjacobi\vpbjacobi.c
>>> [0]PETSC ERROR: #4 PCSetUp() line 932 in E:\cygwin64\home\alireza\PETSc\src\ksp\pc\interface\precon.c
>>> [0]PETSC ERROR: #5 KSPSetUp() line 381 in E:\cygwin64\home\alireza\PETSc\src\ksp\ksp\interface\itfunc.c
>>> [0]PETSC ERROR: #6 KSPSolve() line 612 in E:\cygwin64\home\alireza\PETSc\src\ksp\ksp\interface\itfunc.c
>>> [0]PETSC ERROR: #7 SNESSolve_NEWTONLS() line 224 in E:\cygwin64\home\alireza\PETSc\src\snes\impls\ls\ls.c
>>> [0]PETSC ERROR: #8 SNESSolve() line 4355 in E:\cygwin64\home\alireza\PETSc\src\snes\interface\snes.c
>>>
>>> Many thanks,
>>> Ali
>>>
>>> On 8/29/2018 2:24 AM, Smith, Barry F. wrote:
>>>> Ali,
>>>>
>>>> In the branch barry/feature-PCVPBJACOBI (see src/snes/examples/tutorials/ex5.c) I have implemented PCVPBJACOBI that is a point block Jacobi with variable size blocks. It has very little testing.
>>>>
>>>> Could you please try your code with it; you should see very very similar convergence history with this branch and the previous approach you used (the only numerical difference between the two approaches is that this one uses a dense LU factorization for each small block while the previous used a sparse factorization). This new one should also be slightly faster in the KSPSolve().
>>>>
>>>> Thanks
>>>>
>>>> Barry
>>>>
>>>>
>>>>
>>>>
>>>>> On Aug 27, 2018, at 4:04 PM, Jed Brown <jed at jedbrown.org> wrote:
>>>>>
>>>>> "Smith, Barry F." <bsmith at mcs.anl.gov> writes:
>>>>>
>>>>>> I have added new functionality within SNES to allow one to do as you desire in the branch barry/feature-snessetkspsetupcallback. Please see src/snes/examples/tests/ex3.c
>>>>> Note that this example is block Jacobi with O(1) sparse blocks per
>>>>> process, not variable-sized point-block Jacobi which I think is what Ali
>>>>> had in mind.
>>>>>
>>>>>> Please let us know if it works for you and if you have any questions or problems.
>>>>>>
>>>>>> Barry
>>>>>>
>>>>>> Note that it has to be handled by a callback called from within the SNES solver because that is the first time the matrix exists in a form that the block sizes may be set.
>>>>>>
>>>>>> Sorry for the runaround with so many emails.
>>>>>>
>>>>>>
>>>>>>> On Aug 24, 2018, at 3:48 PM, Ali Reza Khaz'ali <arkhazali at cc.iut.ac.ir> wrote:
>>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I am trying to use block Jacobi preconditioner in SNES (SNESNEWTONLS). However, PCBJacobiGetSubKSP function returns an error stating "Object is in wrong state, Must call KSPSetUp() or PCSetUp() first". When I add KSPSetUp, I got and error from them as: "Must call DMShellSetGlobalVector() or DMShellSetCreateGlobalVector()", and if PCSetUp is added, "Object is in wrong state, Matrix must be set first" error is printed.
>>>>>>>
>>>>>>> Below is a part of my code. It is run serially. Any help is much appreciated.
>>>>>>>
>>>>>>> ierr = SNESGetKSP(snes, &Petsc_ksp);
>>>>>>> CHKERRQ(ierr);
>>>>>>> ierr = KSPGetPC(Petsc_ksp, &Petsc_pc);
>>>>>>> CHKERRQ(ierr);
>>>>>>> ierr = KSPSetTolerances(Petsc_ksp, 1.e-3, 1e-3, PETSC_DEFAULT, 20000);
>>>>>>> CHKERRQ(ierr);
>>>>>>> ierr = SNESSetTolerances(snes, 1e-1, 1e-1, 1e-1, 2000, 2000);
>>>>>>> CHKERRQ(ierr);
>>>>>>> ierr = SNESSetType(snes, SNESNEWTONLS);
>>>>>>> CHKERRQ(ierr);
>>>>>>> ierr = KSPSetType(Petsc_ksp, KSPGMRES);
>>>>>>> CHKERRQ(ierr);
>>>>>>> ierr = PCSetType(Petsc_pc, PCBJACOBI);
>>>>>>> CHKERRQ(ierr);
>>>>>>> ierr = PCSetType(Petsc_pc, PCBJACOBI);
>>>>>>> CHKERRQ(ierr);
>>>>>>> ierr = PCBJacobiSetTotalBlocks(Petsc_pc, 2*Nx*Ny*Nz, SadeqSize);
>>>>>>> CHKERRQ(ierr);
>>>>>>>
>>>>>>> SNESSetUp(snes);
>>>>>>> CHKERRQ(ierr);
>>>>>>> ierr = PCBJacobiGetSubKSP(Petsc_pc, &nLocal, &Firstly, &subKSP);
>>>>>>> CHKERRQ(ierr);
>>>>>>>
>>>>>>> for (i = 0; i < nLocal; i++) {
>>>>>>> ierr = KSPGetPC(subKSP[i], &SubPc);
>>>>>>> CHKERRQ(ierr);
>>>>>>> ierr = PCSetType(SubPc, PCLU);
>>>>>>> CHKERRQ(ierr);
>>>>>>> ierr = PCFactorSetMatSolverPackage(SubPc, "mkl_pardiso");
>>>>>>> CHKERRQ(ierr);
>>>>>>> ierr = KSPSetType(subKSP[i], KSPPREONLY);
>>>>>>> CHKERRQ(ierr);
>>>>>>> ierr = KSPSetTolerances(subKSP[i], 1.e-6, PETSC_DEFAULT, PETSC_DEFAULT, PETSC_DEFAULT);
>>>>>>> CHKERRQ(ierr);
>>>>>>> }
>>>>>>> ierr = SNESSolve(snes, NULL, Petsc_X);
>>>>>>> CHKERRQ(ierr);
>>>>>>>
>>>>>>>
>>>>>>>
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