[petsc-users] Use block Jacobi preconditioner with SNES
Ali Reza Khaz'ali
arkhazali at cc.iut.ac.ir
Wed Aug 29 14:08:41 CDT 2018
Thanks again,
> You might want to use a memory profiler to see if you have important
> leaks. See comment below about destroying objects and PETSc memory
> logging.
That's a very good suggestion. I'll do it.
> This matrix takes just a little over 100 MB (only about 35 MB of which
> is needed). If this code is using a lot more memory than that, you
> should use a memory profiler to find out where (e.g., some data
> structures in your code).
The memory usage was high for the previous (and wrong) one with
bjacobi/ilu. My code with vpbjacobi preconditioner only requires 150K,
which as you stated, most of it is not required by PETSc.
> All of your time is in function and Jacobian evaluation.
> The entire linear solve is less than 50 milliseconds.
Thanks for your comment. You are right. The Jacobian construction
involves about 40K lines of code, and a lot of phase equilibrium
calculations, which are very time intensive.
> It looks like you have forgotten to destroy all of your objects. If you
> clean up after yourself, you'll also see the totaly memory used by each
> of the PETSc classes that you use.
That is because of PetscLogView was placed before the destroy functions.
I moved it after them, and here is the new log: (additionally, this is
the log of one time step only, so all of the objects won't be destroyed
before all time steps have been finished)
SNES Object: 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=3
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: vpbjacobi
linear system matrix = precond matrix:
Mat Object: 1 MPI processes
type: seqaij
rows=108000, cols=108000
total: nonzeros=2868000, allocated nonzeros=8640000
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 23:33:39 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): 1.190e+02 1.000 1.190e+02
Objects: 3.600e+01 1.000 3.600e+01
Flop: 2.867e+07 1.000 2.867e+07 2.867e+07
Flop/sec: 2.408e+05 1.000 2.408e+05 2.408e+05
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: 1.1905e+02 100.0% 2.8668e+07 100.0% 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
PetscBarrier 1 1.0 2.1382e-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
BuildTwoSidedF 2 1.0 4.2337e-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
SNESSolve 1 1.0 1.0010e+02 1.0 2.87e+07 1.0 0.0e+00 0.0e+00
0.0e+00 84100 0 0 0 84100 0 0 0 0
SNESFunctionEval 2 1.0 5.2605e+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
SNESJacobianEval 1 1.0 9.4788e+01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00
0.0e+00 80 0 0 0 0 80 0 0 0 0 0
SNESLineSearch 1 1.0 2.6283e+00 1.0 6.82e+06 1.0 0.0e+00 0.0e+00
0.0e+00 2 24 0 0 0 2 24 0 0 0 3
VecDot 1 1.0 1.8261e-04 1.0 2.16e+05 1.0 0.0e+00 0.0e+00
0.0e+00 0 1 0 0 0 0 1 0 0 0 1183
VecMDot 3 1.0 8.1381e-04 1.0 1.30e+06 1.0 0.0e+00 0.0e+00
0.0e+00 0 5 0 0 0 0 5 0 0 0 1592
VecNorm 7 1.0 6.5849e-03 1.0 1.51e+06 1.0 0.0e+00 0.0e+00
0.0e+00 0 5 0 0 0 0 5 0 0 0 230
VecScale 4 1.0 1.6208e-04 1.0 4.32e+05 1.0 0.0e+00 0.0e+00
0.0e+00 0 2 0 0 0 0 2 0 0 0 2665
VecCopy 3 1.0 4.4561e-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
VecSet 2 1.0 1.4369e-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
VecAXPY 1 1.0 1.5823e-04 1.0 2.16e+05 1.0 0.0e+00 0.0e+00
0.0e+00 0 1 0 0 0 0 1 0 0 0 1365
VecWAXPY 1 1.0 1.9501e-04 1.0 1.08e+05 1.0 0.0e+00 0.0e+00
0.0e+00 0 0 0 0 0 0 0 0 0 0 554
VecMAXPY 4 1.0 7.7190e-04 1.0 1.94e+06 1.0 0.0e+00 0.0e+00
0.0e+00 0 7 0 0 0 0 7 0 0 0 2518
VecAssemblyBegin 2 1.0 7.9970e-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
VecAssemblyEnd 2 1.0 1.2402e-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 2.8567e-04 1.0 4.32e+05 1.0 0.0e+00 0.0e+00
0.0e+00 0 2 0 0 0 0 2 0 0 0 1512
VecReduceComm 1 1.0 5.1318e-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 4 1.0 4.6357e-04 1.0 1.30e+06 1.0 0.0e+00 0.0e+00
0.0e+00 0 5 0 0 0 0 5 0 0 0 2796
MatMult 4 1.0 1.6927e-02 1.0 2.25e+07 1.0 0.0e+00 0.0e+00
0.0e+00 0 79 0 0 0 0 79 0 0 0 1330
MatAssemblyBegin 2 1.0 8.5529e-07 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
MatAssemblyEnd 2 1.0 2.4032e-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
MatZeroEntries 1 1.0 2.8857e-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
MatView 1 1.0 3.3998e-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
KSPSetUp 1 1.0 1.2325e-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
KSPSolve 1 1.0 3.7389e-02 1.0 2.16e+07 1.0 0.0e+00 0.0e+00
0.0e+00 0 75 0 0 0 0 75 0 0 0 579
KSPGMRESOrthog 3 1.0 1.3552e-03 1.0 2.59e+06 1.0 0.0e+00 0.0e+00
0.0e+00 0 9 0 0 0 0 9 0 0 0 1913
PCSetUp 1 1.0 1.4842e-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
PCApply 4 1.0 3.1607e-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
------------------------------------------------------------------------------------------------------------------------
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 1 1372 0.
DMSNES 1 1 672 0.
SNESLineSearch 1 1 1000 0.
Vector 20 20 17313120 0.
Matrix 1 1 105843212 0.
Distributed Mesh 2 2 9504 0.
Star Forest Graph 4 4 3200 0.
Discrete System 2 2 1856 0.
Krylov Solver 1 1 18416 0.
DMKSP interface 1 1 656 0.
Preconditioner 1 1 832 0.
Viewer 1 0 0 0.
========================================================================================================================
Average time to get PetscTime(): 0.
#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
-----------------------------------------
Many thanks
Ali
>
>> ========================================================================================================================
>> Average time to get PetscTime(): 8.55292e-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 10:29 PM, Jed Brown wrote:
>>> 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);
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>> --
>> Ali Reza Khaz’ali
>> Assistant Professor of Petroleum Engineering,
>> Department of Chemical Engineering
>> Isfahan University of Technology
>> Isfahan, Iran
--
Ali Reza Khaz’ali
Assistant Professor of Petroleum Engineering,
Department of Chemical Engineering
Isfahan University of Technology
Isfahan, Iran
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