Ok, last output was from simulated multicores, in an actual cluster the
errors are of the kind:
[valera@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 <[email protected]>
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 <[email protected]> wrote:
>
>>
>> > On Sep 26, 2016, at 5:07 PM, Manuel Valera <[email protected]>
>> 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 <[email protected]>
>> 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 <[email protected]>
>> 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 <[email protected]>
>> 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 <[email protected]>
>> 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/d
>> ocumentation/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>
>>
>>
>
1.000000
2.000000
4.000000
3.000000
2.000000
1.000000
3.000000
4.000000
4.000000
3.000000
1.000000
2.000000
3.000000
4.000000
2.000000
1.000000
PROGRAM solvelinearmgpetsc
IMPLICIT NONE
!PETSc Implementation, include files:
!Created by Manuel Valera 6/10/16:
#include <petsc/finclude/petscsys.h> !core PETSc
#include <petsc/finclude/petscvec.h> !vectors
#include <petsc/finclude/petscvec.h90> !special vectors f90 functions
#include <petsc/finclude/petscmat.h> !matrixes
#include <petsc/finclude/petscis.h> !index sets
#include <petsc/finclude/petscviewer.h> !viewers
#include <petsc/finclude/petscpc.h> !preconditioners
#include <petsc/finclude/petscksp.h> !Krylov subspaces (Solver)
! Local Variables: matrix dimensions for Seamount Testcase (97x61x38)
!INTEGER, parameter :: nbnodos = 213120, nnz = 3934732
! Matrix dimension for Angie Testing case
!INTEGER, parameter :: nbnodos = 36, nnz = 394
! Tiny testcase 3x3x2
INTEGER, parameter :: nbnodos = 4, nnz = 16
DOUBLE PRECISION :: ui,uj,uk
DOUBLE PRECISION :: vi,vj,vk
DOUBLE PRECISION :: wi,wj,wk
DOUBLE PRECISION :: const,maxdiff
DOUBLE PRECISION, DIMENSION(nbnodos) :: Rhs
DOUBLE PRECISION, DIMENSION(nbnodos) :: sol,sol2,soldiff
INTEGER :: i,j,k,l
real (kind(0d0)) :: tolp,norm2
integer :: iter,iprint
INTEGER :: ierr0,ierrm
! PETSc IMPLEMENTATION, Variables:
PC :: pc,mg
KSP :: ksp
Vec :: xp,bp,up,x,y,work
Mat :: Ap,pmat
MatNullSpace :: nullsp
PetscErrorCode :: ierr
PetscInt :: nbdp,nnzp,ii,nel,its,spa
PetscReal :: norm,tol
PetscScalar :: negone,one
PetscScalar, pointer :: soln(:)
PetscScalar, pointer :: rpia(:)
PetscInt, allocatable :: iapi(:),japi(:),ind(:)
PetscScalar, allocatable :: app(:)
PetscScalar :: rpi
PetscViewer :: viewer
KSPConvergedReason :: reason
PetscMPIInt :: rankl, sizel
PetscLogDouble :: ti,tf,tt
!TODO: IMPORTANT ALL USER-DEFINED ROUTINES SHOULD BE DECLARED AS EXTERNAL
!external SampleShellPCSetUp,SampleShellPCApply
!common /mypcs/ jacobi,mg,work
!PC jacobi,mg
!Vec work
!Testing AGMG reading from a file.
DOUBLE PRECISION,allocatable :: a(:)
integer,allocatable :: ja(:),ia(:)
allocate(a(nnz), stat=ierr)
allocate(ja(nnz), stat=ierr)
allocate(ia(nbnodos+1), stat=ierr)
! open(15,file='iac.txt', status='old')
! open(15,file='row_ptr.dat', status='old') !smalltestcase
open(15,file='ias.txt', status='old') !tinytestcase
read(15,*) ia
close(15,status='KEEP')
! open(16,file='jac.txt', status='old')
! open(16,file='Col_id.dat', status='old') !smalltestcase
open(16,file='jas.txt', status='old') !tinytestcase
read(16,*) ja
close(16,status='KEEP')
! open(17,file='ac.txt', status='old')
! open(17,file='Acsr.dat', status='old') !smalltestcase
open(17,file='as.txt', status='old') !tinytestcase
read(17,*) a
close(17,status='KEEP')
! open(18,file='rhsc.txt', status='old')
! open(18,file='rhs.dat', status='old') !smalltestcase
open(18,file='rhss.txt', status='old') !tinytestcase
read(18,*) Rhs
close(18,status='KEEP')
!PETSc IMPLEMENTATION, MAT-VEC Population:
!by Manuel Valera, June 2016.
call MPI_Init(ierrm)
call MPI_Comm_Rank(MPI_COMM_WORLD,rankl,ierrm)
call MPI_Comm_split(MPI_COMM_WORLD,1,0,PETSC_COMM_WORLD,ierrm)
call PetscInitialize(PETSC_NULL_CHARACTER,ierr)
call PetscTime(ti,ierr)
call MPI_Comm_rank(PETSC_COMM_WORLD, rankl, ierr)
call MPI_Comm_size(PETSC_COMM_WORLD, sizel, ierr)
!Adapted from Chris Paolini examples:
! 1.- SETUP VECTORS-
! Create vectors. Note that we form 1 vector from scratch and
! then duplicate to form b.
! Prepare PETSc integers:
nbdp = nbnodos !matrix dimension
nnzp = nnz !nonzero entries in each matrix row
allocate(iapi(nbdp+1), stat=ierr)
allocate(japi(nnzp), stat=ierr)
allocate(app(nnzp), stat=ierr)
allocate(ind(nnzp), stat=ierr)
allocate(soln(nbdp), stat=ierr)
call VecCreate(PETSC_COMM_WORLD,xp,ierr)
call VecSetSizes(xp,PETSC_DECIDE,nbdp,ierr) ! Size of xp - nbnodos
!VecSetSizes(Vec v, PetscInt n, PetscInt N)
call VecSetFromOptions(xp,ierr)
call VecDuplicate(xp,bp,ierr) ! duplicate xp (soln vector) into bp(RHS),both have same length
call VecDuplicate(xp,up,ierr) ! up = exact solution
call VecDuplicate(xp,work,ierr) ! some other vector
call VecDuplicate(xp,y,ierr) ! some other vector
CHKERRQ(ierr)
! 1.2.- SET VECTORS VALUES:
call VecSet(xp,0.0D0,ierr) !initializing SOLN to zeros
call VecAssemblyBegin(xp,ierr) ; call VecAssemblyEnd(xp,ierr)
call VecSet(up,1.0D0,ierr) !initializing exact soln to ones
call VecAssemblyBegin(up,ierr) ; call VecAssemblyEnd(up,ierr)
call VecAssemblyBegin(work,ierr) ; call VecAssemblyEnd(work,ierr)
call VecAssemblyBegin(y,ierr) ; call VecAssemblyEnd(y,ierr)
call VecGetSize(xp,nel,ierr)
print*, "TrivSoln loaded, size: ", nel, "/",nbdp
! call VecGetArrayF90(xp,soln,ierr)
! sol = soln
! call VecRestoreArrayF90(xp,soln,ierr)
! print*, "XP EYE maxval:", MAXVAL(sol)
! print*, "XP EYE minval:", MINVAL(sol)
! Load RHS:
! call VecSet(bp,5.0D0,ierr) !making Rhs something else (all 5's)
do i=0,nbdp-1,1
ind(i+1) = i
enddo
call VecSetValues(bp,nbdp,ind,Rhs,INSERT_VALUES,ierr) !feeding whole RHS in one call
call VecAssemblyBegin(bp,ierr) ; call VecAssemblyEnd(bp,ierr) !rhs
! call VecView(bp,PETSC_VIEWER_STDOUT_WORLD,ierr) ! RHS looks OK
call VecGetSize(bp,nel,ierr)
print*, "RHS loaded, size: ", nel, "/",nbdp
! allocate(rpia(nbdp),stat=ierr)
! call VecGetArrayF90(bp,rpia,ierr)
! print*, "RHS maxvalue:", MAXVAL(rpia) !a way to look if rhs is changing
! call VecRestoreArrayF90(bp,rpia,ierr)
! deallocate(rpia,stat=ierr)
!!! Converting CSR arrays into PETSc
iapi = ia
japi = ja
app = a
!Reordering CSR Matrix to Sorted-CSR
do i=1,nbdp,1
spa = iapi(i+1)-iapi(i)
select case (i)
case(1)
call PetscSortIntWithScalarArray(spa,japi(i),app(i),ierr); !1st row case
case default
call PetscSortIntWithScalarArray(spa,japi(iapi(i)+1),app(iapi(i)+1),ierr); !other rows case
end select
enddo
! 2.- SETUP MATRIXES:
! Create matrix from CSR arrays directly:
!Recommended Paradigm:
! call MatCreate(PETSC_COMM_WORLD,Ap,ierr)
! call MatSetType(Ap,MATSEQAIJ,ierr) !in parallel, type changes. check.
! call MatSetType(Ap,MATMPIAIJ,ierr) !paralellization
! call MatSetSizes(Ap,PETSC_DECIDE,PETSC_DECIDE,nbdp,nbdp,ierr);
! call MatSetBlockSize(Ap,3,ierr) ! NEEDED ? 3 == Freedom degrees *** for pcgamg
! call MatSeqAIJSetPreallocationCSR(Ap,iapi,japi,app,ierr)
! call MatSetFromOptions(Ap,ierr)
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)
print*, "local size:", floor(real(nbdp)/sizel)
! call exit()
! 2.1.- ASSEMBLE MATRIX:
! Setup Matrix:
call MatSetUp(Ap,ierr)
call MatNullSpaceCreate(PETSC_COMM_WORLD,PETSC_TRUE,0,0,nullsp,ierr); !NO IDEA ABOUT THIS. TODO
call MatSetNearNullSpace(Ap,nullsp,ierr) ! NEEDED ? ***for pcgamg
call MatNullSpaceDestroy(nullsp,ierr);
CHKERRQ(ierr)
call MatAssemblyBegin(Ap,MAT_FINAL_ASSEMBLY,ierr)
call MatAssemblyEnd(Ap,MAT_FINAL_ASSEMBLY,ierr)
!Matrix viewer (off diagonals not shown ?)
call MatView(Ap,PETSC_VIEWER_STDOUT_WORLD,ierr) !prints everything to stdout
! call MatView(Ap,PETSC_VIEWER_DRAW_WORLD,ierr) !shows image
! call sleep(3)
call exit()
!!!! Creating A*eye=RHS
call MatMult(Ap,up,bp,ierr) !Ap*up=bp
!!!
! 4.- PETSc IMPLEMENTATION, ACTUAL SOLVER:
!/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
! Create the linear solver and set various options
! - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
! /*
! Create linear solver context
! */
call KSPCreate(PETSC_COMM_WORLD,ksp,ierr) ! Solver (linear, for nonlinear must use SNES)
call KSPSetOperators(ksp,Ap,Ap,ierr)
call KSPGetPC(ksp,pc,ierr)
tol = 1.e-5
call KSPSetTolerances(ksp,tol,PETSC_DEFAULT_REAL,PETSC_DEFAULT_REAL,PETSC_DEFAULT_INTEGER,ierr)
!Create PC
call PCGetOperators(pc,Ap,pmat,ierr)
call PCCreate(PETSC_COMM_WORLD,mg,ierr)
call PCSetType(mg,PCJACOBI,ierr)
call PCSetOperators(mg,Ap,pmat,ierr)
call PCSetUp(mg,ierr)
! call PCGetOperators(pc,PETSC_NULL_OBJECT,pmat,ierr)
! call PCCreate(PETSC_COMM_WORLD,mg,ierr)
! call PCSetType(mg,PCGAMG,ierr)
! call PCSetOperators(mg,pmat,pmat,ierr)
! call PCSetUp(mg,ierr)
!MG options
! call PCGAMGSetNLevels(mg,3,PETSC_NULL_OBJECT,ierr)
! call PCGAMGSetNSmooths(mg,1,ierr)
! call PCGAMGSetThreshold(mg,0.0d0,ierr)
!Apply PC
call PCApply(mg,xp,work,ierr)
one = 1.0
call VecAXPY(y,one,work,ierr)
!!Calling PCs as example42KSP:
! call PCSetType(pc,PCSHELL,ierr) !PC setted as ex42 of ksp
! call PCSetType(pc,PCJACOBI,ierr) !
! call PCShellSetApply(pc,SampleShellPCApply,ierr)
! call SampleShellPCSetUp(pc,xp,ierr)
call KSPSetType(ksp,KSPGCR,ierr) !agmg uses this, basically.
call KSPSetCheckNormIteration(ksp,100,ierr) !agmg has 5000
CHKERRQ(ierr)
call KSPSetFromOptions(ksp,ierr)
CHKERRQ(ierr)
call KSPSetUp(ksp,ierr);
! call KSPSetUpOnBlocks(ksp,ierr);
CHKERRQ(ierr)
!/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
! Solve the linear system
! - - - - - - - - - - - - - - - - - - - - - - - */
call KSPSolve(ksp,bp,xp,ierr)
! call KSPMonitorTrueResidualNorm(ksp,its,norm,viewer,ierr)
call VecGetArrayF90(xp,soln,ierr)
sol = soln !Copying new solution to regular scalar array
call VecRestoreArrayF90(xp,soln,ierr)
print*, "soln maxval:", MAXVAL(sol)
print*, "soln minval:", MINVAL(sol)
!Check the error as in ex1.c from petsc manual:
negone = -1.0d0
call VecAXPY(xp,negone,up,ierr);
call VecNorm(xp,NORM_2,norm,ierr);
call KSPGetIterationNumber(ksp,its,ierr);
iter = its
norm2 = norm
print *, "Norm:", norm2
print *, "Its:", iter
!End checking error
deallocate(iapi,stat=ierr0)
IF (ierr0 /= 0) STOP "*** iapi ***"
deallocate(japi,stat=ierr0)
IF (ierr0 /= 0) STOP "*** japi ***"
! 5.- CLEAN UP OBJECTS:
call MatDestroy(Ap,ierr)
call VecDestroy(xp,ierr)
call VecDestroy(bp,ierr)
call VecDestroy(up,ierr)
call KSPDestroy(ksp,ierr)
call PCDestroy(mg,ierr)
! call PCDestroy(pc,ierr) !this gives error - weird
call VecDestroy(work,ierr)
call VecDestroy(y,ierr)
CHKERRQ(ierr)
deallocate(app,stat=ierr0)
IF (ierr0 /= 0) STOP "*** app ***"
CHKERRQ(ierr)
call PetscTime(tf,ierr)
tt = tf - ti
print*, "Total time:", tt
call PetscFinalize(ierr)
call MPI_Finalize(ierrm)
call EXIT() !abort program at this point.
END PROGRAM solvelinearmgpetsc
!Subroutines from example42 KSP-PETSc:
!/***********************************************************************/
!/* Routines for a user-defined shell preconditioner */
!/***********************************************************************/
!
! SampleShellPCSetUp - This routine sets up a user-defined
! preconditioner context.
!
! Input Parameters:
! pc - preconditioner object
! x - vector
!
! Output Parameter:
! ierr - error code (nonzero if error has been detected)
!
! Notes:
! In this example, we define the shell preconditioner to be Jacobi
! method. Thus, here we create a work vector for storing the reciprocal
! of the diagonal of the preconditioner matrix; this vector is then
! used within the routine SampleShellPCApply().
!
! subroutine SampleShellPCSetUp(pc,x,ierr)
! implicit none
!#include <petsc/finclude/petscsys.h>
!#include <petsc/finclude/petscvec.h>
!#include <petsc/finclude/petscvec.h90>
!#include <petsc/finclude/petscmat.h>
!#include <petsc/finclude/petscpc.h>
!#include <petsc/finclude/petscksp.h>
! PC pc
! Vec x
! Mat pmat
! PetscErrorCode ierr
! PetscInt nl,k,finest
! DM da_list,daclist
! Mat R
! Common block to store data for user-provided preconditioner
! common /mypcs/ jacobi,mg,work
! PC jacobi,mg
! Vec work
!! adapting from example 42 of ksp - Petsc
! call PCGetOperators(pc,PETSC_NULL_OBJECT,pmat,ierr)
! call PCCreate(PETSC_COMM_WORLD,jacobi,ierr)
! call PCSetType(jacobi,PCJACOBI,ierr)
! call PCSetOperators(jacobi,pmat,pmat,ierr)
! call PCSetUp(jacobi,ierr)
! .- SOR "2nd level" Preconditioner - as Ex42-ksp
! call PCSetType(mg,PCSOR,ierr) !This was PCSOR before
! call PCSetOperators(mg,pmat,pmat,ierr)
! call PCSORSetSymmetric(mg,SOR_LOCAL_SYMMETRIC_SWEEP,ierr)
! 3.- MULTIGRID SETUP (PCGAMG): !THIS IS PCAMG = ALGEBRAIC MG (same results than MG)
! call PCGetOperators(pc,PETSC_NULL_OBJECT,pmat,ierr)
! call PCCreate(PETSC_COMM_WORLD,mg,ierr)
! call PCSetType(mg,PCGAMG,ierr)
! call PCSetOperators(mg,pmat,pmat,ierr)
! call PCGAMGSetNLevels(mg,3,PETSC_NULL_OBJECT,ierr)
! call PCGAMGSetNSmooths(mg,1,ierr)
! call PCGAMGSetThreshold(mg,0.0d0,ierr)
! call PCSetUp(mg,ierr)
! call PCApply(mg,x,y,ierr)
! call VecAXPY(y,one,x,ierr)
!!!! Endof
! call VecDuplicate(x,work,ierr)
! end
! -------------------------------------------------------------------
!
! SampleShellPCApply - This routine demonstrates the use of a
! user-provided preconditioner.
!
! Input Parameters:
! pc - preconditioner object
! x - input vector
!
! Output Parameters:
! y - preconditioned vector
! ierr - error code (nonzero if error has been detected)
!
! Notes:
! This code implements the Jacobi preconditioner plus the
! SOR preconditioner
!
! YOU CAN GET THE EXACT SAME EFFECT WITH THE PCCOMPOSITE preconditioner using
! mpiexec -n 1 ex21f -ksp_monitor -pc_type composite -pc_composite_pcs jacobi,sor -pc_composite_type additive
!
! subroutine SampleShellPCApply(pc,x,y,ierr)
! implicit none
!#include <petsc/finclude/petscsys.h>
!#include <petsc/finclude/petscvec.h>
!#include <petsc/finclude/petscpc.h>
! PC pc
! Vec x,y
! PetscErrorCode ierr
! PetscScalar one
! Common block to store data for user-provided preconditioner
! common /mypcs/ jacobi,mg,work
! PC jacobi,mg
! Vec work
! one = 1.0
! call PCApply(jacobi,x,y,ierr)
! call PCApply(mg,x,work,ierr)
! call VecAXPY(y,one,work,ierr)
! end
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