[petsc-users] Solve KSP in parallel.
Manuel Valera
mvalera at mail.sdsu.edu
Sat Oct 1 11:11:51 CDT 2016
I'm comparing with the ones vector as in many examples from petsc docs, so
this may be because i hadn't set up the output to a single processor, but i
get the following output for 1,2,4 processors:
n=1
TrivSoln loaded, size: 213120 / 213120
RHS loaded, size: 213120 / 213120
* Norm: 7.21632103486563610E-011*
Its: 101
Total time: 5.0112988948822021
n=2
TrivSoln loaded, size: 213120 / 213120
TrivSoln loaded, size: 213120 / 213120
RHS loaded, size: 213120 / 213120
RHS loaded, size: 213120 / 213120
* Norm: 1.09862436488003634E-007*
Its: 101
Norm: 1.09862436488003634E-007
Its: 101
Total time: 2.9765341281890869
Total time: 2.9770300388336182
n=4
TrivSoln loaded, size: 213120 / 213120
TrivSoln loaded, size: 213120 / 213120
TrivSoln loaded, size: 213120 / 213120
TrivSoln loaded, size: 213120 / 213120
RHS loaded, size: 213120 / 213120
RHS loaded, size: 213120 / 213120
RHS loaded, size: 213120 / 213120
RHS loaded, size: 213120 / 213120
* Norm: 1.72790692829407788E-005*
Its: 101
Norm: 1.72790692829407788E-005
Its: 101
Norm: 1.72790692829407788E-005
Its: 101
Norm: 1.72790692829407788E-005
Its: 101
Total time: 1.8007240295410156
Total time: 1.8008360862731934
Total time: 1.8008909225463867
Total time: 1.8009200096130371
That is the error norm from the ones vector, im attaching the script again.
On Sat, Oct 1, 2016 at 8:59 AM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>
> > On Sep 30, 2016, at 9:13 PM, Manuel Valera <mvalera at mail.sdsu.edu>
> wrote:
> >
> > Hi Barry and all,
> >
> > I was successful on creating the parallel version to solve my big
> system, it is scaling accordingly, but i noticed the error norm increasing
> too, i don't know if this is because the output is duplicated or if its
> really increasing. Is this expected ?
>
> What do you mean by error norm? Do you have an exact solution you are
> comparing to? If so, you should scale the norm arising from this by
> 1/sqrt(nx*ny) where nx and ny are the number of grid points in the x and y
> direction. This scaling makes the norm correspond to the L2 norm of the
> error which is what you want to measure.
>
> With this new scaling you can do convergence studies, for example
> refine the grid once how much does the error norm reduce, refine the grid
> again and you should see a similar reduction in the error norm.
>
>
> Barry
>
> >
> > Thanks
> >
> > On Tue, Sep 27, 2016 at 4:07 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
> >
> > Yes, always use the binary file
> >
> > > On Sep 27, 2016, at 3:13 PM, Manuel Valera <mvalera at mail.sdsu.edu>
> wrote:
> > >
> > > Barry, thanks for your insight,
> > >
> > > This standalone script must be translated into a much bigger model,
> which uses AIJ matrices to define the laplacian in the form of the 3 usual
> arrays, the ascii files in the script take the place of the arrays which
> are passed to the solving routine in the model.
> > >
> > > So, can i use the approach you mention to create the MPIAIJ from the
> petsc binary file ? would this be a better solution than reading the three
> arrays directly? In the model, even the smallest matrix is 10^5x10^5
> elements
> > >
> > > Thanks.
> > >
> > >
> > > On Tue, Sep 27, 2016 at 12:53 PM, Barry Smith <bsmith at mcs.anl.gov>
> wrote:
> > >
> > > Are you loading a matrix from an ASCII file? If so don't do that.
> You should write a simple sequential PETSc program that reads in the ASCII
> file and saves the matrix as a PETSc binary file with MatView(). Then write
> your parallel code that reads in the binary file with MatLoad() and solves
> the system. You can read in the right hand side from ASCII and save it in
> the binary file also. Trying to read an ASCII file in parallel and set it
> into a PETSc parallel matrix is just a totally thankless task that is
> unnecessary.
> > >
> > > Barry
> > >
> > > > On Sep 26, 2016, at 6:40 PM, Manuel Valera <mvalera at mail.sdsu.edu>
> wrote:
> > > >
> > > > Ok, last output was from simulated multicores, in an actual cluster
> the errors are of the kind:
> > > >
> > > > [valera at cinci CSRMatrix]$ petsc -n 2 ./solvelinearmgPETSc
> > > > TrivSoln loaded, size: 4 / 4
> > > > TrivSoln loaded, size: 4 / 4
> > > > RHS loaded, size: 4 / 4
> > > > RHS loaded, size: 4 / 4
> > > > [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > > > [0]PETSC ERROR: Argument out of range
> > > > [0]PETSC ERROR: Comm must be of size 1
> > > > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/
> documentation/faq.html for trouble shooting.
> > > > [0]PETSC ERROR: Petsc Release Version 3.7.2, Jun, 05, 2016
> > > > [0]PETSC ERROR: ./solvelinearmgPETSc
>
>
> P on a
> arch-linux2-c-debug named cinci by valera Mon Sep 26 16:39:02 2016
> > > > [0]PETSC ERROR: [1]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > > > [1]PETSC ERROR: Argument out of range
> > > > [1]PETSC ERROR: Comm must be of size 1
> > > > [1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/
> documentation/faq.html for trouble shooting.
> > > > [1]PETSC ERROR: Petsc Release Version 3.7.2, Jun, 05, 2016
> > > > [1]PETSC ERROR: ./solvelinearmgPETSc
>
>
> P on a
> arch-linux2-c-debug named cinci by valera Mon Sep 26 16:39:02 2016
> > > > [1]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
> --with-fc=gfortran --download-fblaslapack=1 --download-mpich
> > > > [1]PETSC ERROR: #1 MatCreate_SeqAIJ() line 3958 in
> /home/valera/petsc-3.7.2/src/mat/impls/aij/seq/aij.c
> > > > [1]PETSC ERROR: #2 MatSetType() line 94 in
> /home/valera/petsc-3.7.2/src/mat/interface/matreg.c
> > > > [1]PETSC ERROR: #3 MatCreateSeqAIJWithArrays() line 4300 in
> /home/valera/petsc-3.7.2/src/mat/impls/aij/seq/aij.c
> > > > local size: 2
> > > > local size: 2
> > > > Configure options --with-cc=gcc --with-cxx=g++ --with-fc=gfortran
> --download-fblaslapack=1 --download-mpich
> > > > [0]PETSC ERROR: #1 MatCreate_SeqAIJ() line 3958 in
> /home/valera/petsc-3.7.2/src/mat/impls/aij/seq/aij.c
> > > > [0]PETSC ERROR: #2 MatSetType() line 94 in
> /home/valera/petsc-3.7.2/src/mat/interface/matreg.c
> > > > [0]PETSC ERROR: #3 MatCreateSeqAIJWithArrays() line 4300 in
> /home/valera/petsc-3.7.2/src/mat/impls/aij/seq/aij.c
> > > > [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > > > [1]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > > > [1]PETSC ERROR: [0]PETSC ERROR: Nonconforming object sizes
> > > > [0]PETSC ERROR: Sum of local lengths 8 does not equal global length
> 4, my local length 4
> > > > likely a call to VecSetSizes() or MatSetSizes() is wrong.
> > > > See http://www.mcs.anl.gov/petsc/documentation/faq.html#split
> > > > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/
> documentation/faq.html for trouble shooting.
> > > > Nonconforming object sizes
> > > > [1]PETSC ERROR: Sum of local lengths 8 does not equal global length
> 4, my local length 4
> > > > likely a call to VecSetSizes() or MatSetSizes() is wrong.
> > > > See http://www.mcs.anl.gov/petsc/documentation/faq.html#split
> > > > [1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/
> documentation/faq.html for trouble shooting.
> > > > [0]PETSC ERROR: Petsc Release Version 3.7.2, Jun, 05, 2016
> > > > [0]PETSC ERROR: ./solvelinearmgPETSc
>
>
> P on a
> arch-linux2-c-debug named cinci by valera Mon Sep 26 16:39:02 2016
> > > > [1]PETSC ERROR: Petsc Release Version 3.7.2, Jun, 05, 2016
> > > > [1]PETSC ERROR: ./solvelinearmgPETSc
>
>
> P on a
> arch-linux2-c-debug named cinci by valera Mon Sep 26 16:39:02 2016
> > > > [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
> --with-fc=gfortran --download-fblaslapack=1 --download-mpich
> > > > [0]PETSC ERROR: #4 PetscSplitOwnership() line 93 in
> /home/valera/petsc-3.7.2/src/sys/utils/psplit.c
> > > > [1]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
> --with-fc=gfortran --download-fblaslapack=1 --download-mpich
> > > > [1]PETSC ERROR: #4 PetscSplitOwnership() line 93 in
> /home/valera/petsc-3.7.2/src/sys/utils/psplit.c
> > > > [0]PETSC ERROR: #5 PetscLayoutSetUp() line 143 in
> /home/valera/petsc-3.7.2/src/vec/is/utils/pmap.c
> > > > [0]PETSC ERROR: #6 MatMPIAIJSetPreallocation_MPIAIJ() line 2768 in
> /home/valera/petsc-3.7.2/src/mat/impls/aij/mpi/mpiaij.c
> > > > [1]PETSC ERROR: #5 PetscLayoutSetUp() line 143 in
> /home/valera/petsc-3.7.2/src/vec/is/utils/pmap.c
> > > > [1]PETSC ERROR: [0]PETSC ERROR: #7 MatMPIAIJSetPreallocation() line
> 3505 in /home/valera/petsc-3.7.2/src/mat/impls/aij/mpi/mpiaij.c
> > > > #6 MatMPIAIJSetPreallocation_MPIAIJ() line 2768 in
> /home/valera/petsc-3.7.2/src/mat/impls/aij/mpi/mpiaij.c
> > > > [1]PETSC ERROR: [0]PETSC ERROR: #8 MatSetUp_MPIAIJ() line 2153 in
> /home/valera/petsc-3.7.2/src/mat/impls/aij/mpi/mpiaij.c
> > > > #7 MatMPIAIJSetPreallocation() line 3505 in
> /home/valera/petsc-3.7.2/src/mat/impls/aij/mpi/mpiaij.c
> > > > [1]PETSC ERROR: #8 MatSetUp_MPIAIJ() line 2153 in
> /home/valera/petsc-3.7.2/src/mat/impls/aij/mpi/mpiaij.c
> > > > [0]PETSC ERROR: #9 MatSetUp() line 739 in
> /home/valera/petsc-3.7.2/src/mat/interface/matrix.c
> > > > [1]PETSC ERROR: #9 MatSetUp() line 739 in
> /home/valera/petsc-3.7.2/src/mat/interface/matrix.c
> > > > [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > > > [0]PETSC ERROR: Object is in wrong state
> > > > [0]PETSC ERROR: Must call MatXXXSetPreallocation() or MatSetUp() on
> argument 1 "mat" before MatSetNearNullSpace()
> > > > [0]PETSC ERROR: [1]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > > > [1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/
> documentation/faq.html for trouble shooting.
> > > > [0]PETSC ERROR: Petsc Release Version 3.7.2, Jun, 05, 2016
> > > > [0]PETSC ERROR: ./solvelinearmgPETSc
>
>
> P on a
> arch-linux2-c-debug named cinci by valera Mon Sep 26 16:39:02 2016
> > > > Object is in wrong state
> > > > [1]PETSC ERROR: Must call MatXXXSetPreallocation() or MatSetUp() on
> argument 1 "mat" before MatSetNearNullSpace()
> > > > [1]PETSC ERROR: [0]PETSC ERROR: Configure options --with-cc=gcc
> --with-cxx=g++ --with-fc=gfortran --download-fblaslapack=1 --download-mpich
> > > > [0]PETSC ERROR: #10 MatSetNearNullSpace() line 8195 in
> /home/valera/petsc-3.7.2/src/mat/interface/matrix.c
> > > > See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
> shooting.
> > > > [1]PETSC ERROR: Petsc Release Version 3.7.2, Jun, 05, 2016
> > > > [1]PETSC ERROR: ./solvelinearmgPETSc
>
>
> P on a
> arch-linux2-c-debug named cinci by valera Mon Sep 26 16:39:02 2016
> > > > [1]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
> --with-fc=gfortran --download-fblaslapack=1 --download-mpich
> > > > [1]PETSC ERROR: #10 MatSetNearNullSpace() line 8195 in
> /home/valera/petsc-3.7.2/src/mat/interface/matrix.c
> > > > [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > > > [0]PETSC ERROR: Object is in wrong state
> > > > [1]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > > > [0]PETSC ERROR: Must call MatXXXSetPreallocation() or MatSetUp() on
> argument 1 "mat" before MatAssemblyBegin()
> > > > [0]PETSC ERROR: [1]PETSC ERROR: Object is in wrong state
> > > > [1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/
> documentation/faq.html for trouble shooting.
> > > > [0]PETSC ERROR: Petsc Release Version 3.7.2, Jun, 05, 2016
> > > > [0]PETSC ERROR: Must call MatXXXSetPreallocation() or MatSetUp() on
> argument 1 "mat" before MatAssemblyBegin()
> > > > [1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/
> documentation/faq.html for trouble shooting.
> > > > [1]PETSC ERROR: ./solvelinearmgPETSc
>
>
> P on a
> arch-linux2-c-debug named cinci by valera Mon Sep 26 16:39:02 2016
> > > > [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
> --with-fc=gfortran --download-fblaslapack=1 --download-mpich
> > > > [0]PETSC ERROR: Petsc Release Version 3.7.2, Jun, 05, 2016
> > > > [1]PETSC ERROR: ./solvelinearmgPETSc
>
>
> P on a
> arch-linux2-c-debug named cinci by valera Mon Sep 26 16:39:02 2016
> > > > [1]PETSC ERROR: #11 MatAssemblyBegin() line 5093 in
> /home/valera/petsc-3.7.2/src/mat/interface/matrix.c
> > > > Configure options --with-cc=gcc --with-cxx=g++ --with-fc=gfortran
> --download-fblaslapack=1 --download-mpich
> > > > [1]PETSC ERROR: #11 MatAssemblyBegin() line 5093 in
> /home/valera/petsc-3.7.2/src/mat/interface/matrix.c
> > > > [0]PETSC ERROR: ------------------------------
> ------------------------------------------
> > > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation
> Violation, probably memory access out of range
> > > > [1]PETSC ERROR: ------------------------------
> ------------------------------------------
> > > > [1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation
> Violation, probably memory access out of range
> > > > [1]PETSC ERROR: [0]PETSC ERROR: Try option -start_in_debugger or
> -on_error_attach_debugger
> > > > [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/
> documentation/faq.html#valgrind
> > > > [0]PETSC ERROR: Try option -start_in_debugger or
> -on_error_attach_debugger
> > > > [1]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/
> documentation/faq.html#valgrind
> > > > [1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple
> Mac OS X to find memory corruption errors
> > > > or try http://valgrind.org on GNU/linux and Apple Mac OS X to find
> memory corruption errors
> > > > [0]PETSC ERROR: likely location of problem given in stack below
> > > > [0]PETSC ERROR: --------------------- Stack Frames
> ------------------------------------
> > > > [1]PETSC ERROR: likely location of problem given in stack below
> > > > [1]PETSC ERROR: --------------------- Stack Frames
> ------------------------------------
> > > > [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not
> available,
> > > > [0]PETSC ERROR: INSTEAD the line number of the start of the
> function
> > > > [0]PETSC ERROR: [1]PETSC ERROR: Note: The EXACT line numbers in the
> stack are not available,
> > > > [1]PETSC ERROR: INSTEAD the line number of the start of the
> function
> > > > is given.
> > > > [0]PETSC ERROR: [0] MatAssemblyEnd line 5185
> /home/valera/petsc-3.7.2/src/mat/interface/matrix.c
> > > > [0]PETSC ERROR: [1]PETSC ERROR: is given.
> > > > [1]PETSC ERROR: [1] MatAssemblyEnd line 5185
> /home/valera/petsc-3.7.2/src/mat/interface/matrix.c
> > > > [0] MatAssemblyBegin line 5090 /home/valera/petsc-3.7.2/src/
> mat/interface/matrix.c
> > > > [0]PETSC ERROR: [0] MatSetNearNullSpace line 8191
> /home/valera/petsc-3.7.2/src/mat/interface/matrix.c
> > > > [0]PETSC ERROR: [1]PETSC ERROR: [1] MatAssemblyBegin line 5090
> /home/valera/petsc-3.7.2/src/mat/interface/matrix.c
> > > > [1]PETSC ERROR: [0] PetscSplitOwnership line 80
> /home/valera/petsc-3.7.2/src/sys/utils/psplit.c
> > > > [0]PETSC ERROR: [0] PetscLayoutSetUp line 129
> /home/valera/petsc-3.7.2/src/vec/is/utils/pmap.c
> > > > [0]PETSC ERROR: [0] MatMPIAIJSetPreallocation_MPIAIJ line 2767
> /home/valera/petsc-3.7.2/src/mat/impls/aij/mpi/mpiaij.c
> > > > [1] MatSetNearNullSpace line 8191 /home/valera/petsc-3.7.2/src/
> mat/interface/matrix.c
> > > > [1]PETSC ERROR: [1] PetscSplitOwnership line 80
> /home/valera/petsc-3.7.2/src/sys/utils/psplit.c
> > > > [1]PETSC ERROR: [0]PETSC ERROR: [0] MatMPIAIJSetPreallocation line
> 3502 /home/valera/petsc-3.7.2/src/mat/impls/aij/mpi/mpiaij.c
> > > > [0]PETSC ERROR: [0] MatSetUp_MPIAIJ line 2152
> /home/valera/petsc-3.7.2/src/mat/impls/aij/mpi/mpiaij.c
> > > > [1] PetscLayoutSetUp line 129 /home/valera/petsc-3.7.2/src/
> vec/is/utils/pmap.c
> > > > [1]PETSC ERROR: [1] MatMPIAIJSetPreallocation_MPIAIJ line 2767
> /home/valera/petsc-3.7.2/src/mat/impls/aij/mpi/mpiaij.c
> > > > [0]PETSC ERROR: [0] MatSetUp line 727 /home/valera/petsc-3.7.2/src/
> mat/interface/matrix.c
> > > > [0]PETSC ERROR: [0] MatCreate_SeqAIJ line 3956
> /home/valera/petsc-3.7.2/src/mat/impls/aij/seq/aij.c
> > > > [1]PETSC ERROR: [1] MatMPIAIJSetPreallocation line 3502
> /home/valera/petsc-3.7.2/src/mat/impls/aij/mpi/mpiaij.c
> > > > [1]PETSC ERROR: [1] MatSetUp_MPIAIJ line 2152
> /home/valera/petsc-3.7.2/src/mat/impls/aij/mpi/mpiaij.c
> > > > [0]PETSC ERROR: [0] MatSetType line 44 /home/valera/petsc-3.7.2/src/
> mat/interface/matreg.c
> > > > [0]PETSC ERROR: [0] MatCreateSeqAIJWithArrays line 4295
> /home/valera/petsc-3.7.2/src/mat/impls/aij/seq/aij.c
> > > > [1]PETSC ERROR: [1] MatSetUp line 727 /home/valera/petsc-3.7.2/src/
> mat/interface/matrix.c
> > > > [1]PETSC ERROR: [1] MatCreate_SeqAIJ line 3956
> /home/valera/petsc-3.7.2/src/mat/impls/aij/seq/aij.c
> > > > [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > > > [0]PETSC ERROR: Signal received
> > > > [1]PETSC ERROR: [1] MatSetType line 44 /home/valera/petsc-3.7.2/src/
> mat/interface/matreg.c
> > > > [1]PETSC ERROR: [1] MatCreateSeqAIJWithArrays line 4295
> /home/valera/petsc-3.7.2/src/mat/impls/aij/seq/aij.c
> > > > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/
> documentation/faq.html for trouble shooting.
> > > > [0]PETSC ERROR: Petsc Release Version 3.7.2, Jun, 05, 2016
> > > > [0]PETSC ERROR: [1]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > > > [1]PETSC ERROR: ./solvelinearmgPETSc
>
>
> P on a
> arch-linux2-c-debug named cinci by valera Mon Sep 26 16:39:02 2016
> > > > [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
> --with-fc=gfortran --download-fblaslapack=1 --download-mpich
> > > > [0]PETSC ERROR: Signal received
> > > > [1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/
> documentation/faq.html for trouble shooting.
> > > > [1]PETSC ERROR: #12 User provided function() line 0 in unknown file
> > > > Petsc Release Version 3.7.2, Jun, 05, 2016
> > > > [1]PETSC ERROR: ./solvelinearmgPETSc
>
>
> P on a
> arch-linux2-c-debug named cinci by valera Mon Sep 26 16:39:02 2016
> > > > [1]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
> --with-fc=gfortran --download-fblaslapack=1 --download-mpich
> > > > [1]PETSC ERROR: #12 User provided function() line 0 in unknown file
> > > > application called MPI_Abort(comm=0x84000004, 59) - process 0
> > > > [cli_0]: aborting job:
> > > > application called MPI_Abort(comm=0x84000004, 59) - process 0
> > > > application called MPI_Abort(comm=0x84000002, 59) - process 1
> > > > [cli_1]: aborting job:
> > > > application called MPI_Abort(comm=0x84000002, 59) - process 1
> > > >
> > > > ============================================================
> =======================
> > > > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> > > > = PID 10266 RUNNING AT cinci
> > > > = EXIT CODE: 59
> > > > = CLEANING UP REMAINING PROCESSES
> > > > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
> > > > ============================================================
> =======================
> > > >
> > > >
> > > > On Mon, Sep 26, 2016 at 3:51 PM, Manuel Valera <
> mvalera at mail.sdsu.edu> wrote:
> > > > Ok, i created a tiny testcase just for this,
> > > >
> > > > The output from n# calls are as follows:
> > > >
> > > > n1:
> > > > Mat Object: 1 MPI processes
> > > > type: mpiaij
> > > > row 0: (0, 1.) (1, 2.) (2, 4.) (3, 3.)
> > > > row 1: (0, 2.) (1, 1.) (2, 3.) (3, 4.)
> > > > row 2: (0, 4.) (1, 3.) (2, 1.) (3, 2.)
> > > > row 3: (0, 3.) (1, 4.) (2, 2.) (3, 1.)
> > > >
> > > > n2:
> > > > Mat Object: 2 MPI processes
> > > > type: mpiaij
> > > > row 0: (0, 1.) (1, 2.) (2, 4.) (3, 3.)
> > > > row 1: (0, 2.) (1, 1.) (2, 3.) (3, 4.)
> > > > row 2: (0, 1.) (1, 2.) (2, 4.) (3, 3.)
> > > > row 3: (0, 2.) (1, 1.) (2, 3.) (3, 4.)
> > > >
> > > > n4:
> > > > Mat Object: 4 MPI processes
> > > > type: mpiaij
> > > > row 0: (0, 1.) (1, 2.) (2, 4.) (3, 3.)
> > > > row 1: (0, 1.) (1, 2.) (2, 4.) (3, 3.)
> > > > row 2: (0, 1.) (1, 2.) (2, 4.) (3, 3.)
> > > > row 3: (0, 1.) (1, 2.) (2, 4.) (3, 3.)
> > > >
> > > >
> > > >
> > > > It really gets messed, no idea what's happening.
> > > >
> > > >
> > > >
> > > >
> > > > On Mon, Sep 26, 2016 at 3:12 PM, Barry Smith <bsmith at mcs.anl.gov>
> wrote:
> > > >
> > > > > On Sep 26, 2016, at 5:07 PM, Manuel Valera <mvalera at mail.sdsu.edu>
> wrote:
> > > > >
> > > > > Ok i was using a big matrix before, from a smaller testcase i got
> the output and effectively, it looks like is not well read at all, results
> are attached for DRAW viewer, output is too big to use STDOUT even in the
> small testcase. n# is the number of processors requested.
> > > >
> > > > You need to construct a very small test case so you can determine
> why the values do not end up where you expect them. There is no way around
> it.
> > > > >
> > > > > is there a way to create the matrix in one node and the distribute
> it as needed on the rest ? maybe that would work.
> > > >
> > > > No the is not scalable. You become limited by the memory of the
> one node.
> > > >
> > > > >
> > > > > Thanks
> > > > >
> > > > > On Mon, Sep 26, 2016 at 2:40 PM, Barry Smith <bsmith at mcs.anl.gov>
> wrote:
> > > > >
> > > > > How large is the matrix? It will take a very long time if the
> matrix is large. Debug with a very small matrix.
> > > > >
> > > > > Barry
> > > > >
> > > > > > On Sep 26, 2016, at 4:34 PM, Manuel Valera <
> mvalera at mail.sdsu.edu> wrote:
> > > > > >
> > > > > > Indeed there is something wrong with that call, it hangs out
> indefinitely showing only:
> > > > > >
> > > > > > Mat Object: 1 MPI processes
> > > > > > type: mpiaij
> > > > > >
> > > > > > It draws my attention that this program works for 1 processor
> but not more, but it doesnt show anything for that viewer in either case.
> > > > > >
> > > > > > Thanks for the insight on the redundant calls, this is not very
> clear on documentation, which calls are included in others.
> > > > > >
> > > > > >
> > > > > >
> > > > > > On Mon, Sep 26, 2016 at 2:02 PM, Barry Smith <bsmith at mcs.anl.gov>
> wrote:
> > > > > >
> > > > > > The call to MatCreateMPIAIJWithArrays() is likely
> interpreting the values you pass in different than you expect.
> > > > > >
> > > > > > Put a call to MatView(Ap,PETSC_VIEWER_STDOUT_WORLD,ierr)
> after the MatCreateMPIAIJWithArray() to see what PETSc thinks the matrix is.
> > > > > >
> > > > > >
> > > > > > > On Sep 26, 2016, at 3:42 PM, Manuel Valera <
> mvalera at mail.sdsu.edu> wrote:
> > > > > > >
> > > > > > > Hello,
> > > > > > >
> > > > > > > I'm working on solve a linear system in parallel, following
> ex12 of the ksp tutorial i don't see major complication on doing so, so for
> a working linear system solver with PCJACOBI and KSPGCR i did only the
> following changes:
> > > > > > >
> > > > > > > call MatCreate(PETSC_COMM_WORLD,Ap,ierr)
> > > > > > > ! call MatSetType(Ap,MATSEQAIJ,ierr)
> > > > > > > call MatSetType(Ap,MATMPIAIJ,ierr) !paralellization
> > > > > > >
> > > > > > > call MatSetSizes(Ap,PETSC_DECIDE,
> PETSC_DECIDE,nbdp,nbdp,ierr);
> > > > > > >
> > > > > > > ! call MatSeqAIJSetPreallocationCSR(Ap,iapi,japi,app,ierr)
> > > > > > > call MatSetFromOptions(Ap,ierr)
> > > > > >
> > > > > > Note that none of the lines above are needed (or do
> anything) because the MatCreateMPIAIJWithArrays() creates the matrix from
> scratch itself.
> > > > > >
> > > > > > Barry
> > > > > >
> > > > > > > ! call MatCreateSeqAIJWithArrays(PETSC_COMM_WORLD,nbdp,nbdp,
> iapi,japi,app,Ap,ierr)
> > > > > > > call MatCreateMPIAIJWithArrays(PETSC_COMM_WORLD,floor(real(
> nbdp)/sizel),PETSC_DECIDE,nbdp,nbdp,iapi,japi,app,Ap,ierr)
> > > > > > >
> > > > > > >
> > > > > > > I grayed out the changes from sequential implementation.
> > > > > > >
> > > > > > > So, it does not complain at runtime until it reaches
> KSPSolve(), with the following error:
> > > > > > >
> > > > > > >
> > > > > > > [1]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > > > > > > [1]PETSC ERROR: Object is in wrong state
> > > > > > > [1]PETSC ERROR: Matrix is missing diagonal entry 0
> > > > > > > [1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/
> documentation/faq.html for trouble shooting.
> > > > > > > [1]PETSC ERROR: Petsc Release Version 3.7.3, unknown
> > > > > > > [1]PETSC ERROR: ./solvelinearmgPETSc
>
>
> � � on a
> arch-linux2-c-debug named valera-HP-xw4600-Workstation by valera Mon Sep 26
> 13:35:15 2016
> > > > > > > [1]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
> --with-fc=gfortran --download-fblaslapack=1 --download-mpich=1
> --download-ml=1
> > > > > > > [1]PETSC ERROR: #1 MatILUFactorSymbolic_SeqAIJ() line 1733 in
> /home/valera/v5PETSc/petsc/petsc/src/mat/impls/aij/seq/aijfact.c
> > > > > > > [1]PETSC ERROR: #2 MatILUFactorSymbolic() line 6579 in
> /home/valera/v5PETSc/petsc/petsc/src/mat/interface/matrix.c
> > > > > > > [1]PETSC ERROR: #3 PCSetUp_ILU() line 212 in
> /home/valera/v5PETSc/petsc/petsc/src/ksp/pc/impls/factor/ilu/ilu.c
> > > > > > > [1]PETSC ERROR: #4 PCSetUp() line 968 in
> /home/valera/v5PETSc/petsc/petsc/src/ksp/pc/interface/precon.c
> > > > > > > [1]PETSC ERROR: #5 KSPSetUp() line 390 in
> /home/valera/v5PETSc/petsc/petsc/src/ksp/ksp/interface/itfunc.c
> > > > > > > [1]PETSC ERROR: #6 PCSetUpOnBlocks_BJacobi_Singleblock() line
> 650 in /home/valera/v5PETSc/petsc/petsc/src/ksp/pc/impls/bjacobi/bjacobi.c
> > > > > > > [1]PETSC ERROR: #7 PCSetUpOnBlocks() line 1001 in
> /home/valera/v5PETSc/petsc/petsc/src/ksp/pc/interface/precon.c
> > > > > > > [1]PETSC ERROR: #8 KSPSetUpOnBlocks() line 220 in
> /home/valera/v5PETSc/petsc/petsc/src/ksp/ksp/interface/itfunc.c
> > > > > > > [1]PETSC ERROR: #9 KSPSolve() line 600 in
> /home/valera/v5PETSc/petsc/petsc/src/ksp/ksp/interface/itfunc.c
> > > > > > > At line 333 of file solvelinearmgPETSc.f90
> > > > > > > Fortran runtime error: Array bound mismatch for dimension 1 of
> array 'sol' (213120/106560)
> > > > > > >
> > > > > > >
> > > > > > > This code works for -n 1 cores, but it gives this error when
> using more than one core.
> > > > > > >
> > > > > > > What am i missing?
> > > > > > >
> > > > > > > Regards,
> > > > > > >
> > > > > > > Manuel.
> > > > > > >
> > > > > > > <solvelinearmgPETSc.f90>
> > > > > >
> > > > > >
> > > > >
> > > > >
> > > > > <n4.png><n2.png><n1.png>
> > > >
> > > >
> > > >
> > > > <rhss.txt><solvelinearmgPETSc.f90><as.txt><ias.txt><jas.txt>
> > >
> > >
> >
> >
>
>
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