So hydra begins automatically while using mpiexec right? Meaning I don't have to manually enter in "hydra &" at the terminal??
Thanks, gaurish On Mon, Jan 17, 2011 at 7:36 PM, Gaurish Telang <gaurish108 at gmail.com>wrote: > 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 >>> %: >>> .. >>> .. >>> .. >>> .. >>> .. >>> .. >>> . >>> . >>> . >>> >>> >>> >>> >>> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20110117/ca09470f/attachment-0001.htm>
