[petsc-users] Regarding printing to standard output. and possible mistake in the code comments in PetscBinaryWrite.m
Gaurish Telang
gaurish108 at gmail.com
Mon Jan 17 18:36:19 CST 2011
Thank you that seems to have worked! Just to confirm, I have posted the
output at the end of this message. I hope this is the way the generic output
should look like.
I have still have a few questions though.
(1)
So all I need to do, is to specify the location of the correct executable
mpiexec which is $PETSC_DIR/$PETSC_ARCH/bin/mpiexec
while running the program, right?
The contents of my $PETSC_DIR/$PETSC_ARCH/bin are
gaurish108 at gaurish108-laptop:~/Desktop/ResearchMeetings/SUPERPETS/petsc-3.1-p5/linux-gnu-c-debug/bin$
ls
mpicc mpich2version mpiexec mpif77 mpif90 parkill
(2)
Do I need to make any changes in the makefiles of the PETSc programs that I
have written? And hence recompile my codes by using the "new" mpiexec
I mean, since $PETSC_DIR/$PETSC_ARCH/bin/ also contains mpicc (as seen
above), I want to be sure that the correct mpicc is being used during
execution.
(3) Should I run the mpd daemon before using mpiexec??? On the MPICH2 that I
had installed prior to my PETSc it required me type "mpd &"
before program execution.
But it seems for my PETSc mpiexec I don;t need mpd. But should I type it in
?? I mean I am not sure if this affects program performance
Sincere thanks,
Gaurish
gaurish108 at gaurish108-laptop:~/Desktop/ResearchMeetings/SUPERPETS/petsc-3.1-p5/src/ksp/ksp/examples/tutorials$
$PETSC_DIR/$PETSC_ARCH/bin/mpiexec -n 2 ./ex23 -info
[0] PetscInitialize(): PETSc successfully started: number of processors = 2
[1] PetscInitialize(): PETSc successfully started: number of processors = 2
[1] PetscGetHostName(): Rejecting domainname, likely is NIS
gaurish108-laptop.(none)
[1] PetscInitialize(): Running on machine: gaurish108-laptop
[0] PetscGetHostName(): Rejecting domainname, likely is NIS
gaurish108-laptop.(none)
[0] PetscInitialize(): Running on machine: gaurish108-laptop
[0] PetscCommDuplicate(): Duplicating a communicator 1140850688 -2080374784
max tags = 2147483647
[1] PetscCommDuplicate(): Duplicating a communicator 1140850688 -2080374784
max tags = 2147483647
[1] PetscCommDuplicate(): returning tag 2147483647
[0] PetscCommDuplicate(): returning tag 2147483647
[0] PetscCommDuplicate(): returning tag 2147483642
[1] PetscCommDuplicate(): returning tag 2147483642
[0] PetscCommDuplicate(): returning tag 2147483637
[1] PetscCommDuplicate(): returning tag 2147483637
[0] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
-2080374784
[1] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
-2080374784
[0] PetscCommDuplicate(): returning tag 2147483632
[1] PetscCommDuplicate(): returning tag 2147483632
[0] MatSetUpPreallocation(): Warning not preallocating matrix storage
[0] PetscCommDuplicate(): Duplicating a communicator 1140850689 -2080374783
max tags = 2147483647
[0] PetscCommDuplicate(): returning tag 2147483647
[1] PetscCommDuplicate(): Duplicating a communicator 1140850689 -2080374783
max tags = 2147483647
[1] PetscCommDuplicate(): returning tag 2147483647
[0] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
-2080374783
[0] PetscCommDuplicate(): returning tag 2147483646
[1] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
-2080374783
[1] PetscCommDuplicate(): returning tag 2147483646
[0] MatStashScatterBegin_Private(): No of messages: 0
[0] MatAssemblyBegin_MPIAIJ(): Stash has 0 entries, uses 0 mallocs.
[0] MatAssemblyEnd_SeqAIJ(): Matrix size: 5 X 5; storage space: 12
unneeded,13 used
[0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
[0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 3
[1] MatAssemblyBegin_MPIAIJ(): Stash has 0 entries, uses 0 mallocs.
[1] MatAssemblyEnd_SeqAIJ(): Matrix size: 5 X 5; storage space: 12
unneeded,13 used
[1] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
[1] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 3
[1] Mat_CheckInode(): Found 5 nodes out of 5 rows. Not using Inode routines
[0] Mat_CheckInode(): Found 5 nodes out of 5 rows. Not using Inode routines
[0] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
-2080374783
[0] PetscCommDuplicate(): returning tag 2147483645
[0] MatSetUpMultiply_MPIAIJ(): Using block index set to define scatter
[1] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
-2080374783
[1] PetscCommDuplicate(): returning tag 2147483645
[1] PetscCommDuplicate(): returning tag 2147483628
[0] PetscCommDuplicate(): returning tag 2147483628
[0] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
-2080374783
[0] PetscCommDuplicate(): returning tag 2147483644
[0] PetscCommDuplicate(): returning tag 2147483627
[1] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
-2080374783
[1] PetscCommDuplicate(): returning tag 2147483644
[1] PetscCommDuplicate(): returning tag 2147483627
[1] PetscCommDuplicate(): returning tag 2147483622
[0] PetscCommDuplicate(): returning tag 2147483622
[0] VecScatterCreateCommon_PtoS(): Using blocksize 1 scatter
[0] VecScatterCreate(): General case: MPI to Seq
[0] MatAssemblyEnd_SeqAIJ(): Matrix size: 5 X 1; storage space: 9 unneeded,1
used
[0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
[0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 1
[0] Mat_CheckCompressedRow(): Found the ratio (num_zerorows
4)/(num_localrows 5) > 0.6. Use CompressedRow routines.
[0] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
-2080374784
[1] MatAssemblyEnd_SeqAIJ(): Matrix size: 5 X 1; storage space: 9 unneeded,1
used
[1] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
[1] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 1
[1] Mat_CheckCompressedRow(): Found the ratio (num_zerorows
4)/(num_localrows 5) > 0.6. Use CompressedRow routines.
[1] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
-2080374784
[1] PetscCommDuplicate(): returning tag 2147483618
[0] PetscCommDuplicate(): returning tag 2147483618
[0] PetscCommDuplicate(): returning tag 2147483617
[1] PetscCommDuplicate(): returning tag 2147483617
[1] PetscCommDuplicate(): returning tag 2147483616
[0] PetscCommDuplicate(): returning tag 2147483616
[0] PetscCommDuplicate(): returning tag 2147483611
[1] PetscCommDuplicate(): returning tag 2147483611
[1] PetscCommDuplicate(): returning tag 2147483606
[0] PetscCommDuplicate(): returning tag 2147483606
[0] PetscCommDuplicate(): returning tag 2147483601
[1] PetscCommDuplicate(): returning tag 2147483601
[1] PetscCommDuplicate(): returning tag 2147483596
[0] PetscCommDuplicate(): returning tag 2147483596
[0] PCSetUp(): Setting up new PC
[1] PetscCommDuplicate(): returning tag 2147483591
[0] PetscCommDuplicate(): returning tag 2147483591
[0] PetscCommDuplicate(): returning tag 2147483586
[1] PetscCommDuplicate(): returning tag 2147483586
[0] PetscCommDuplicate(): returning tag 2147483581
[1] PetscCommDuplicate(): returning tag 2147483581
[0] PetscCommDuplicate(): returning tag 2147483576
[1] PetscCommDuplicate(): returning tag 2147483576
[0] PetscCommDuplicate(): returning tag 2147483571
[1] PetscCommDuplicate(): returning tag 2147483571
[1] PetscCommDuplicate(): returning tag 2147483566
[0] PetscCommDuplicate(): returning tag 2147483566
[0] PetscCommDuplicate(): returning tag 2147483561
[1] PetscCommDuplicate(): returning tag 2147483561
[0] PetscCommDuplicate(): returning tag 2147483556
[0] PetscCommDuplicate(): returning tag 2147483551
[0] PetscCommDuplicate(): returning tag 2147483546
[0] PetscCommDuplicate(): returning tag 2147483541
[0] KSPDefaultConverged(): Linear solver has converged. Residual norm
5.11279e-16 is less than relative tolerance 1e-07 times initial right hand
side norm 0.707107 at iteration 5
[0] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
-2080374784
[0] PetscCommDuplicate(): returning tag 2147483536
KSP Object:
type: gmres
GMRES: restart=30, using Classical (unmodified) Gram-Schmidt
Orthogonalization with no iterative refinement
GMRES: happy breakdown tolerance 1e-30
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-07, absolute=1e-50, divergence=10000
left preconditioning
using PRECONDITIONED norm type for convergence test
PC Object:
type: jacobi
linear system matrix = precond matrix:
Matrix Object:
type=mpiaij, rows=10, cols=10
tot[1] PetscCommDuplicate(): returning tag 2147483556
[1] PetscCommDuplicate(): returning tag 2147483551
[1] PetscCommDuplicate(): returning tag 2147483546
[1] PetscCommDuplicate(): returning tag 2147483541
[1] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
-2080374784
[1] PetscCommDuplicate(): returning tag 2147483536
[1] Petsc_DelComm(): Deleting PETSc communicator imbedded in a user MPI_Comm
1140850689
[1] PetscCommDestroy(): Deleting PETSc MPI_Comm -2080374783
[1] Petsc_DelCounter(): Deleting counter data in an MPI_Comm -2080374783
[1] Petsc_DelComm(): Deleting PETSc communicator imbedded in a user MPI_Comm
-2080374783
al: nonzeros=28, allocated nonzeros=70
not using I-node (on process 0) routines
Norm of error < 1.e-12, Iterations 5
[0] Petsc_DelComm(): Deleting PETSc communicator imbedded in a user MPI_Comm
1140850689
[0] PetscCommDestroy(): Deleting PETSc MPI_Comm -2080374783
[0] Petsc_DelCounter(): Deleting counter data in an MPI_Comm -2080374783
[0] Petsc_DelComm(): Deleting PETSc communicator imbedded in a user MPI_Comm
-2080374783
[0] PetscFinalize(): PetscFinalize() called
[1] PetscFinalize(): PetscFinalize() called
[1] PetscCommDuplicate(): returning tag 2147483535
[1] Petsc_DelViewer(): Deleting viewer data in an MPI_Comm -2080374784
[1] Petsc_DelComm(): Deleting PETSc communicator imbedded in a user MPI_Comm
1140850688
[1] PetscCommDestroy(): Deleting PETSc MPI_Comm -2080374784
[0] PetscCommDuplicate(): returning tag 2147483535
[0] Petsc_DelViewer(): Deleting viewer data in an MPI_Comm -2080374784
[0] Petsc_DelComm(): Deleting PETSc communicator imbedded in a user MPI_Comm
1140850688
[0] PetscCommDestroy(): Deleting PETSc MPI_Comm -2080374784
[0] Petsc_DelCounter(): Deleting counter data in an MPI_Comm -2080374784
[0] Petsc_DelComm(): Deleting PETSc communicator imbedded in a user MPI_Comm
-2080374784
[0] Petsc_DelViewer(): Deleting viewer data in an MPI_Comm -2080374784
[1] Petsc_DelCounter(): Deleting counter data in an MPI_Comm -2080374784
[1] Petsc_DelComm(): Deleting PETSc communicator imbedded in a user MPI_Comm
-2080374784
[1] Petsc_DelViewer(): Deleting viewer data in an MPI_Comm -2080374784
gaurish108 at gaurish108-laptop:~/Desktop/ResearchMeetings/SUPERPETS/petsc-3.1-p5/src/ksp/ksp/examples/tutorials$
gaurish108 at gaurish108-laptop:~/Desktop/ResearchMeetings/SUPERPETS/petsc-3.1-p5/src/ksp/ksp/examples/tutorials$
gaurish108 at gaurish108-laptop:~/Desktop/ResearchMeetings/SUPERPETS/petsc-3.1-p5/src/ksp/ksp/examples/tutorials$
gaurish108 at gaurish108-laptop:~/Desktop/ResearchMeetings/SUPERPETS/petsc-3.1-p5/src/ksp/ksp/examples/tutorials$
gaurish108 at gaurish108-laptop:~/Desktop/ResearchMeetings/SUPERPETS/petsc-3.1-p5/src/ksp/ksp/examples/tutorials$
gaurish108 at gaurish108-laptop:~/Desktop/ResearchMeetings/SUPERPETS/petsc-3.1-p5/src/ksp/ksp/examples/tutorials$
clear
gaurish108 at gaurish108-laptop:~/Desktop/ResearchMeetings/SUPERPETS/petsc-3.1-p5/src/ksp/ksp/examples/tutorials$
$PETSC_DIR/$PETSC_ARCH/bin/mpich2version -n 2 ./ex23 -info
Unrecognized argument -n
gaurish108 at gaurish108-laptop:~/Desktop/ResearchMeetings/SUPERPETS/petsc-3.1-p5/src/ksp/ksp/examples/tutorials$
$PETSC_DIR/$PETSC_ARCH/bin/mpiexec -n 2 ./ex23 -info
[0] PetscInitialize(): PETSc successfully started: number of processors = 2
[1] PetscInitialize(): PETSc successfully started: number of processors = 2
[0] PetscGetHostName(): Rejecting domainname, likely is NIS
gaurish108-laptop.(none)
[0] PetscInitialize(): Running on machine: gaurish108-laptop
[1] PetscGetHostName(): Rejecting domainname, likely is NIS
gaurish108-laptop.(none)
[1] PetscInitialize(): Running on machine: gaurish108-laptop
[0] PetscCommDuplicate(): Duplicating a communicator 1140850688 -2080374784
max tags = 2147483647
[1] PetscCommDuplicate(): Duplicating a communicator 1140850688 -2080374784
max tags = 2147483647
[1] PetscCommDuplicate(): returning tag 2147483647
[0] PetscCommDuplicate(): returning tag 2147483647
[0] PetscCommDuplicate(): returning tag 2147483642
[0] PetscCommDuplicate(): returning tag 2147483637
[1] PetscCommDuplicate(): returning tag 2147483642
[1] PetscCommDuplicate(): returning tag 2147483637
[0] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
-2080374784
[1] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
-2080374784
[1] PetscCommDuplicate(): returning tag 2147483632
[0] PetscCommDuplicate(): returning tag 2147483632
[0] MatSetUpPreallocation(): Warning not preallocating matrix storage
[0] PetscCommDuplicate(): Duplicating a communicator 1140850689 -2080374783
max tags = 2147483647
[0] PetscCommDuplicate(): returning tag 2147483647
[0] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
-2080374783
[0] PetscCommDuplicate(): returning tag 2147483646
[1] PetscCommDuplicate(): Duplicating a communicator 1140850689 -2080374783
max tags = 2147483647
[1] PetscCommDuplicate(): returning tag 2147483647
[1] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
-2080374783
[1] PetscCommDuplicate(): returning tag 2147483646
[0] MatStashScatterBegin_Private(): No of messages: 0
[0] MatAssemblyBegin_MPIAIJ(): Stash has 0 entries, uses 0 mallocs.
[0] MatAssemblyEnd_SeqAIJ(): Matrix size: 5 X 5; storage space: 12
unneeded,13 used
[0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
[0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 3
[0] Mat_CheckInode(): Found 5 nodes out of 5 rows. Not using Inode routines
[0] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
-2080374783
[0] PetscCommDuplicate(): returning tag 2147483645
[0] MatSetUpMultiply_MPIAIJ(): Using block index set to define scatter
[0] PetscCommDuplicate(): returning tag 2147483628
[0] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
-2080374783
[0] PetscCommDuplicate(): returning tag 2147483644
[0] PetscCommDuplicate(): returning tag 2147483627
[0] PetscCommDuplicate(): returning tag 2147483622
[1] MatAssemblyBegin_MPIAIJ(): Stash has 0 entries, uses 0 mallocs.
[1] MatAssemblyEnd_SeqAIJ(): Matrix size: 5 X 5; storage space: 12
unneeded,13 used
[1] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
[1] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 3
[1] Mat_CheckInode(): Found 5 nodes out of 5 rows. Not using Inode routines
[1] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
-2080374783
[1] PetscCommDuplicate(): returning tag 2147483645
[1] PetscCommDuplicate(): returning tag 2147483628
[1] PetscCommDuplicate(): Using internal PETSc communicator 1140850689
-2080374783
[1] PetscCommDuplicate(): returning tag 2147483644
[1] PetscCommDuplicate(): returning tag 2147483627
[1] PetscCommDuplicate(): returning tag 2147483622
[0] VecScatterCreateCommon_PtoS(): Using blocksize 1 scatter
[0] VecScatterCreate(): General case: MPI to Seq
[0] MatAssemblyEnd_SeqAIJ(): Matrix size: 5 X 1; storage space: 9 unneeded,1
used
[0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
[0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 1
[0] Mat_CheckCompressedRow(): Found the ratio (num_zerorows
4)/(num_localrows 5) > 0.6. Use CompressedRow routines.
[1] MatAssemblyEnd_SeqAIJ(): Matrix size: 5 X 1; storage space: 9 unneeded,1
used
[1] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
[1] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 1
[1] Mat_CheckCompressedRow(): Found the ratio (num_zerorows
4)/(num_localrows 5) > 0.6. Use CompressedRow routines.
[1] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
-2080374784
[1] PetscCommDuplicate(): returning tag 2147483618
[0] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
-2080374784
[0] PetscCommDuplicate(): returning tag 2147483618
[0] PetscCommDuplicate(): returning tag 2147483617
[0] PetscCommDuplicate(): returning tag 2147483616
[1] PetscCommDuplicate(): returning tag 2147483617
[1] PetscCommDuplicate(): returning tag 2147483616
[1] PetscCommDuplicate(): returning tag 2147483611
[1] PetscCommDuplicate(): returning tag 2147483606
[0] PetscCommDuplicate(): returning tag 2147483611
[0] PetscCommDuplicate(): returning tag 2147483606
[0] PetscCommDuplicate(): returning tag 2147483601
[0] PetscCommDuplicate(): returning tag 2147483596
[0] PCSetUp(): Setting up new PC
[1] PetscCommDuplicate(): returning tag 2147483601
[1] PetscCommDuplicate(): returning tag 2147483596
[1] PetscCommDuplicate(): returning tag 2147483591
[0] PetscCommDuplicate(): returning tag 2147483591
[0] PetscCommDuplicate(): returning tag 2147483586
[0] PetscCommDuplicate(): returning tag 2147483581
[0] PetscCommDuplicate(): returning tag 2147483576
[1] PetscCommDuplicate(): returning tag 2147483586
[1] PetscCommDuplicate(): returning tag 2147483581
[1] PetscCommDuplicate(): returning tag 2147483576
[1] PetscCommDuplicate(): returning tag 2147483571
[0] PetscCommDuplicate(): returning tag 2147483571
[0] PetscCommDuplicate(): returning tag 2147483566
[0] PetscCommDuplicate(): returning tag 2147483561
[1] PetscCommDuplicate(): returning tag 2147483566
[1] PetscCommDuplicate(): returning tag 2147483561
[1] PetscCommDuplicate(): returning tag 2147483556
[0] PetscCommDuplicate(): returning tag 2147483556
[0] PetscCommDuplicate(): returning tag 2147483551
[1] PetscCommDuplicate(): returning tag 2147483551
[1] PetscCommDuplicate(): returning tag 2147483546
[0] PetscCommDuplicate(): returning tag 2147483546
[0] PetscCommDuplicate(): returning tag 2147483541
[1] PetscCommDuplicate(): returning tag 2147483541
[0] KSPDefaultConverged(): Linear solver has converged. Residual norm
5.11279e-16 is less than relative tolerance 1e-07 times initial right hand
side norm 0.707107 at iteration 5
[0] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
-2080374784
[1] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
-2080374784
[0] PetscCommDuplicate(): returning tag 2147483536
KSP Object:
type: gmres
GMRES: restart=30, using Classical (unmodified) Gram-Schmidt
Orthogonalization with no iterative refinement
GMRES: happy breakdown tolerance 1e-30
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-07, absolute=1e-50, divergence=10000
left preconditioning
using PRECONDITIONED norm type for convergence test
PC Object:
type: jacobi
linear system matrix = precond matrix:
Matrix Object:
type=mpiaij, rows=10, cols=10
[1] PetscCommDuplicate(): returning tag 2147483536
total: nonzeros=28, allocated nonzeros=70
not using I-node (on process 0) routines
Norm of error < 1.e-12, Iterations 5
[0] Petsc_DelComm(): Deleting PETSc communicator imbedded in a user MPI_Comm
1140850689
[0] PetscCommDestroy(): Deleting PETSc MPI_Comm -2080374783
[0] Petsc_DelCounter(): Deleting counter data in an MPI_Comm -2080374783
[0] Petsc_DelComm(): Deleting PETSc communicator imbedded in a user MPI_Comm
-2080374783
[0] PetscFinalize(): PetscFinalize() called
[1] Petsc_DelComm(): Deleting PETSc communicator imbedded in a user MPI_Comm
1140850689
[1] PetscCommDestroy(): Deleting PETSc MPI_Comm -2080374783
[1] Petsc_DelCounter(): Deleting counter data in an MPI_Comm -2080374783
[1] Petsc_DelComm(): Deleting PETSc communicator imbedded in a user MPI_Comm
-2080374783
[1] PetscFinalize(): PetscFinalize() called
[1] PetscCommDuplicate(): returning tag 2147483535
[1] Petsc_DelViewer(): Deleting viewer data in an MPI_Comm -2080374784
[1] Petsc_DelComm(): Deleting PETSc communicator imbedded in a user MPI_Comm
1140850688
[1] PetscCommDestroy(): Deleting PETSc MPI_Comm -2080374784
[1] Petsc_DelCounter(): Deleting counter data in an MPI_Comm -2080374784
[1] Petsc_DelComm(): Deleting PETSc communicator imbedded in a user MPI_Comm
-2080374784
[1] Petsc_DelViewer(): Deleting viewer data in an MPI_Comm -2080374784
[0] PetscCommDuplicate(): returning tag 2147483535
[0] Petsc_DelViewer(): Deleting viewer data in an MPI_Comm -2080374784
[0] Petsc_DelComm(): Deleting PETSc communicator imbedded in a user MPI_Comm
1140850688
[0] PetscCommDestroy(): Deleting PETSc MPI_Comm -2080374784
[0] Petsc_DelCounter(): Deleting counter data in an MPI_Comm -2080374784
[0] Petsc_DelComm(): Deleting PETSc communicator imbedded in a user MPI_Comm
-2080374784
[0] Petsc_DelViewer(): Deleting viewer data in an MPI_Comm -2080374784
gaurish108 at gaurish108-laptop:~/Desktop/ResearchMeetings/SUPERPETS/petsc-3.1-p5/src/ksp/ksp/examples/tutorials$
On Mon, Jan 17, 2011 at 6:20 PM, Gaurish Telang <gaurish108 at gmail.com>wrote:
> This is what I get on running mpiexec -n 2 ./ex23 -info
>
> Also, using mpirun in place of mpiexec and using the -info option I get
> the exact same output you see below.
>
> As far as the MPI implmentation I am using, I have OpenMPI and MPICH
> installed on my laptop.
>
> While installing PETSc there were some external packages required. In the
> external packages folder I can see the following softwares:
>
> fblaslapack-3.1.1 mpich2-1.0.8 ParMetis-dev-p3 SuperLU_DIST_2.4-hg-v2
>
> Possibly it is this mpich2 that should be used??
> Please let me know what I should do. I am quite new to PETSc.
>
> gaurish108 at gaurish108-laptop:~/Desktop/ResearchMeetings/SUPERPETS/petsc-3.1-p5/src/ksp/ksp/examples/tutorials$
> mpiexec -n 2 ./ex23 -info
> [0] PetscInitialize(): PETSc successfully started: number of processors = 1
> [0] PetscGetHostName(): Rejecting domainname, likely is NIS
> gaurish108-laptop.(none)
> [0] PetscInitialize(): Running on machine: gaurish108-laptop
> [0] PetscCommDuplicate(): Duplicating a communicator 1140850688 -2080374784
> max tags = 2147483647
> [0] PetscCommDuplicate(): returning tag 2147483647
> [0] PetscCommDuplicate(): returning tag 2147483646
> [0] PetscCommDuplicate(): returning tag 2147483645
> [0] PetscInitialize(): PETSc successfully started: number of processors = 1
> [0] PetscGetHostName(): Rejecting domainname, likely is NIS
> gaurish108-laptop.(none)
> [0] PetscInitialize(): Running on machine: gaurish108-laptop
> [0] PetscCommDuplicate(): Duplicating a communicator 1140850688 -2080374784
> max tags = 2147483647
> [0] PetscCommDuplicate(): returning tag 2147483647
> [0] PetscCommDuplicate(): returning tag 2147483646
> [0] PetscCommDuplicate(): returning tag 2147483645
> [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
> -2080374784
> [0] PetscCommDuplicate(): returning tag 2147483644
> [0] MatSetUpPreallocation(): Warning not preallocating matrix storage
> [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 10 X 10; storage space: 22
> unneeded,28 used
> [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
> [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 3
> [0] Mat_CheckInode(): Found 10 nodes out of 10 rows. Not using Inode
> routines
> [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
> -2080374784
> [0] PetscCommDuplicate(): returning tag 2147483643
> [0] PetscCommDuplicate(): returning tag 2147483642
> [0] PetscCommDuplicate(): returning tag 2147483641
> [0] PetscCommDuplicate(): returning tag 2147483640
> [0] PetscCommDuplicate(): returning tag 2147483639
> [0] PetscCommDuplicate(): returning tag 2147483638
> [0] PetscCommDuplicate(): returning tag 2147483637
> [0] PCSetUp(): Setting up new PC
> [0] PetscCommDuplicate(): returning tag 2147483636
> [0] PetscCommDuplicate(): returning tag 2147483635
> [0] PetscCommDuplicate(): returning tag 2147483634
> [0] PetscCommDuplicate(): returning tag 2147483633
> [0] PetscCommDuplicate(): returning tag 2147483632
> [0] PetscCommDuplicate(): returning tag 2147483631
> [0] PetscCommDuplicate(): returning tag 2147483630
> [0] PetscCommDuplicate(): returning tag 2147483629
> [0] PetscCommDuplicate(): returning tag 2147483628
> [0] PetscCommDuplicate(): returning tag 2147483627
> [0] PetscCommDuplicate(): returning tag 2147483626
> [0] KSPDefaultConverged(): Linear solver has converged. Residual norm
> 4.50879e-16 is less than relative tolerance 1e-07 times initial right hand
> side norm 0.707107 at iteration 5
> [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
> -2080374784
> [0] PetscCommDuplicate(): returning tag 2147483625
>
> KSP Object:
> type: gmres
> GMRES: restart=30, using Classical (unmodified) Gram-Schmidt
> Orthogonalization with no iterative refinement
> GMRES: happy breakdown tolerance 1e-30
> maximum iterations=10000, initial guess is zero
> tolerances: relative=1e-07, absolute=1e-50, divergence=10000
> left preconditioning
> using PRECONDITIONED norm type for convergence test
> PC Object:
> type: jacobi
> linear system matrix = precond matrix:
> Matrix Object:
> type=seqaij, rows=10, cols=10
> total: nonzeros=28, allocated nonzeros=50
> not using I-node routines
> Norm of error < 1.e-12, Iterations 5
> [0] PetscFinalize(): PetscFinalize() called
> [0] PetscCommDuplicate(): returning tag 2147483624
> [0] Petsc_DelViewer(): Deleting viewer data in an MPI_Comm -2080374784
> [0] Petsc_DelComm(): Deleting PETSc communicator imbedded in a user
> MPI_Comm 1140850688
> [0] PetscCommDestroy(): Deleting PETSc MPI_Comm -2080374784
> [0] Petsc_DelCounter(): Deleting counter data in an MPI_Comm -2080374784
> [0] Petsc_DelComm(): Deleting PETSc communicator imbedded in a user
> MPI_Comm -2080374784
> [0] Petsc_DelViewer(): Deleting viewer data in an MPI_Comm -2080374784
> [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
> -2080374784
> [0] PetscCommDuplicate(): returning tag 2147483644
> [0] MatSetUpPreallocation(): Warning not preallocating matrix storage
> [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 10 X 10; storage space: 22
> unneeded,28 used
> [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
> [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 3
> [0] Mat_CheckInode(): Found 10 nodes out of 10 rows. Not using Inode
> routines
> [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
> -2080374784
> [0] PetscCommDuplicate(): returning tag 2147483643
> [0] PetscCommDuplicate(): returning tag 2147483642
> [0] PetscCommDuplicate(): returning tag 2147483641
> [0] PetscCommDuplicate(): returning tag 2147483640
> [0] PetscCommDuplicate(): returning tag 2147483639
> [0] PetscCommDuplicate(): returning tag 2147483638
> [0] PetscCommDuplicate(): returning tag 2147483637
> [0] PCSetUp(): Setting up new PC
> [0] PetscCommDuplicate(): returning tag 2147483636
> [0] PetscCommDuplicate(): returning tag 2147483635
> [0] PetscCommDuplicate(): returning tag 2147483634
> [0] PetscCommDuplicate(): returning tag 2147483633
> [0] PetscCommDuplicate(): returning tag 2147483632
> [0] PetscCommDuplicate(): returning tag 2147483631
> [0] PetscCommDuplicate(): returning tag 2147483630
> [0] PetscCommDuplicate(): returning tag 2147483629
> [0] PetscCommDuplicate(): returning tag 2147483628
> [0] PetscCommDuplicate(): returning tag 2147483627
> [0] PetscCommDuplicate(): returning tag 2147483626
> [0] KSPDefaultConverged(): Linear solver has converged. Residual norm
> 4.50879e-16 is less than relative tolerance 1e-07 times initial right hand
> side norm 0.707107 at iteration 5
> [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
> -2080374784
> [0] PetscCommDuplicate(): returning tag 2147483625
>
> KSP Object:
> type: gmres
> GMRES: restart=30, using Classical (unmodified) Gram-Schmidt
> Orthogonalization with no iterative refinement
> GMRES: happy breakdown tolerance 1e-30
> maximum iterations=10000, initial guess is zero
> tolerances: relative=1e-07, absolute=1e-50, divergence=10000
> left preconditioning
> using PRECONDITIONED norm type for convergence test
> PC Object:
> type: jacobi
> linear system matrix = precond matrix:
> Matrix Object:
> type=seqaij, rows=10, cols=10
> total: nonzeros=28, allocated nonzeros=50
> not using I-node routines
> Norm of error < 1.e-12, Iterations 5
> [0] PetscFinalize(): PetscFinalize() called
> [0] PetscCommDuplicate(): returning tag 2147483624
> [0] Petsc_DelViewer(): Deleting viewer data in an MPI_Comm -2080374784
> [0] Petsc_DelComm(): Deleting PETSc communicator imbedded in a user
> MPI_Comm 1140850688
> [0] PetscCommDestroy(): Deleting PETSc MPI_Comm -2080374784
> [0] Petsc_DelCounter(): Deleting counter data in an MPI_Comm -2080374784
> [0] Petsc_DelComm(): Deleting PETSc communicator imbedded in a user
> MPI_Comm -2080374784
> [0] Petsc_DelViewer(): Deleting viewer data in an MPI_Comm -2080374784
>
> gaurish108 at gaurish108-laptop:~/Desktop/ResearchMeetings/SUPERPETS/petsc-3.1-p5/src/ksp/ksp/examples/tutorials$
>
>
> On Mon, Jan 17, 2011 at 5:46 PM, Gaurish Telang <gaurish108 at gmail.com>wrote:
>
>> Hi.
>>
>> I had two questions
>>
>> (1)
>>
>> I was curious to know why the following happens with the PETSc standard
>> output. Having created the executable 'test' when I try to run it with
>> mpiexec -n 2 ./test
>> the same output is printed to the terminal twice. If I use 3 processors,
>> then the same output is printed thrice.
>>
>> In short the number of processors = number of times the output from PETSc
>> is printed. Could this be a mistake with my PETSc installation???
>>
>> For example, consider the code in src/ksp/ksp/examples/tutorials/ex23.c
>> After creating ex23 the executable and running it with two processors gives
>> the following terminal output:
>>
>> gaurish108 at gaurish108-laptop:~/Desktop/ResearchMeetings/SUPERPETS/petsc-3.1-p5/src/ksp/ksp/examples/tutorials$
>> mpiexec -n 1 ./ex23
>> KSP Object:
>> type: gmres
>> GMRES: restart=30, using Classical (unmodified) Gram-Schmidt
>> Orthogonalization with no iterative refinement
>> GMRES: happy breakdown tolerance 1e-30
>> maximum iterations=10000, initial guess is zero
>> tolerances: relative=1e-07, absolute=1e-50, divergence=10000
>> left preconditioning
>> using PRECONDITIONED norm type for convergence test
>> PC Object:
>> type: jacobi
>> linear system matrix = precond matrix:
>> Matrix Object:
>> type=seqaij, rows=10, cols=10
>> total: nonzeros=28, allocated nonzeros=50
>> not using I-node routines
>> Norm of error < 1.e-12, Iterations 5
>> gaurish108 at gaurish108-laptop:~/Desktop/ResearchMeetings/SUPERPETS/petsc-3.1-p5/src/ksp/ksp/examples/tutorials$
>> mpiexec -n 2 ./ex23
>> KSP Object:
>> type: gmres
>> GMRES: restart=30, using Classical (unmodified) Gram-Schmidt
>> Orthogonalization with no iterative refinement
>> GMRES: happy breakdown tolerance 1e-30
>> maximum iterations=10000, initial guess is zero
>> tolerances: relative=1e-07, absolute=1e-50, divergence=10000
>> left preconditioning
>> using PRECONDITIONED norm type for convergence test
>> PC Object:
>> type: jacobi
>> linear system matrix = precond matrix:
>> Matrix Object:
>> type=seqaij, rows=10, cols=10
>> total: nonzeros=28, allocated nonzeros=50
>> not using I-node routines
>> Norm of error < 1.e-12, Iterations 5
>> KSP Object:
>> type: gmres
>> GMRES: restart=30, using Classical (unmodified) Gram-Schmidt
>> Orthogonalization with no iterative refinement
>> GMRES: happy breakdown tolerance 1e-30
>> maximum iterations=10000, initial guess is zero
>> tolerances: relative=1e-07, absolute=1e-50, divergence=10000
>> left preconditioning
>> using PRECONDITIONED norm type for convergence test
>> PC Object:
>> type: jacobi
>> linear system matrix = precond matrix:
>> Matrix Object:
>> type=seqaij, rows=10, cols=10
>> total: nonzeros=28, allocated nonzeros=50
>> not using I-node routines
>> Norm of error < 1.e-12, Iterations 5
>> gaurish108 at gaurish108-laptop:~/Desktop/ResearchMeetings/SUPERPETS/petsc-3.1-p5/src/ksp/ksp/examples/tutorials$
>>
>>
>>
>>
>> (2)
>>
>> Also I was told yesterday on the PETSC users mailing list that the MATLAB
>> m file PetscBinaryWrite.m converts a sparse matrix in MATLAB into Petsc
>> Binary format.
>> The following are the comments in the code near the heading saying
>> that it works only for square sparse matrices . But it seems to be working
>> quite well for rectangular sparse MATLAB matrices also.
>> I have tested this in conjunction with PetscBinaryRead.m also, which reads
>> in a Petsc binary file into MATLAB as a sparse matrix.
>>
>> Is there something I might have missed or some error that I might be
>> making???
>>
>> Comments in PetscBinaryWrite.m
>> "-================================================
>> % Writes in PETSc binary file sparse matrices and vectors
>> % if the array is multidimensional and dense it is saved
>> % as a one dimensional array
>> %
>> % Only works for square sparse matrices
>> %:
>> ..
>> ..
>> ..
>> ..
>> ..
>> ..
>> .
>> .
>> .
>>
>>
>>
>>
>>
>
>
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