[petsc-users] PDSLin 2.0.0 example memory corruption error
Matthew Knepley
knepley at gmail.com
Fri Sep 15 07:01:06 CDT 2017
On Fri, Sep 15, 2017 at 7:00 AM, Afrah Najib <afrah.nacib at gmail.com> wrote:
> Hi,
> I am trying to run the examples of PDSLin 2.0.0[http://portal.nersc.gov/
> project/sparse/pdslin/]
>
> but I got the following error:
>
This is not a PETSc error. PETSc is just catching the signal. I think you
have to contact
the PDSLin developers.
Thanks,
Matt
> :~/pdslin_2.0.0/examples$ mpiexec -n 8 ./dtest input matrices/U.dat
> input->num_doms = 4
> Preconditioner parameters:
> input->nproc_dcomp = 4
> input->nproc_schur = 4
> input->free_local = PDSLin_NO
> input->dcomp_type = SCOTCH
> input->diag_tau = 0.000000e+00
> input->tau_sub = 0.000000e+00
> input->drop_tau0 = 1.000000e-02
> input->drop_tau2 = 0.000000e+00
> input->drop_tau1 = 1.000000e-03
> input->drop_tau3 = 0.000000e+00
> input->ilu_lvl = -1
> input->equil_dom = 0 (no equil or row perm).
> input->perm_dom = 0
> input->mat_type = UNSYMMETRIC
> input->mat_pattern = UNSYMMETRIC
> input->blk_size = 1
> input->equil_schur = 5
> input->relax_factor = 3.000000e-01
> input->pperm_schur = PDSLin_YES
> input->psymb_schur = PDSLin_YES
> input->dom_solver = SLU_DIST
> Schur solution parameters:
> input->inner_outer = PDSLin_NO
> input->outer_tol = 1.000000e-12
> input->outer_max = 50
> input->schur_itrs = PDSLin_NO
> input->exact_schur = PDSLin_NO
> input->direct_schur = PDSLin_NO
> input->explicit_restart = PDSLin_NO
> input->inner_max = 500
> input->inner_restart = 60
> input->inner_tol = 1.000000e-12
> input->inner_solver = PDSLin_FGMRES
> ==== dtest(): reading in matrix from matrices/U.dat
> took 1.785858e-01 seconds to read matrix.
>
> **********************************************************************
>
>
> ==== dtest: factorizing the matrix.
> PARMETIS ERROR: Poor initial vertex distribution. Processor 2 has no
> vertices assigned to it!
> PARMETIS ERROR: Poor initial vertex distribution. Processor 3 has no
> vertices assigned to it!
> [0]PETSC ERROR: ------------------------------
> ------------------------------------------
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [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: 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
> ------------------------------------
> [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: is given.
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Signal received
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.7.6, Apr, 24, 2017
> [0]PETSC ERROR: ./dtest on a arch-linux2-c-debug named afrah-pc by afrah
> Fri Sep 15 13:53:42 2017
> [0]PETSC ERROR: Configure options PETSC_DIR=/home/afrah/PETSc-library2/petsc-3.7.6
> PETSC_ARCH=arch-linux2-c-debug prefix=/home/afrah/PETSc-library2/petsc-3.7.6/source
> --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 --download-blacs
> --download-scalapack=1 --download-mumps=1 --with-valgrind=1
> --with-valgrind-dir="[/usr/local/bin]"
> [0]PETSC ERROR: #1 User provided function() line 0 in unknown file
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> [1]PETSC ERROR: ------------------------------
> ------------------------------------------
> [1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [1]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
> [1]PETSC ERROR: likely location of problem given in stack below
> [1]PETSC ERROR: --------------------- Stack Frames
> ------------------------------------
> [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
> [1]PETSC ERROR: is given.
> [1]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [1]PETSC ERROR: Signal received
> [1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [1]PETSC ERROR: Petsc Release Version 3.7.6, Apr, 24, 2017
> [1]PETSC ERROR: ./dtest on a arch-linux2-c-debug named afrah-pc by afrah
> Fri Sep 15 13:53:42 2017
> [1]PETSC ERROR: Configure options PETSC_DIR=/home/afrah/PETSc-library2/petsc-3.7.6
> PETSC_ARCH=arch-linux2-c-debug prefix=/home/afrah/PETSc-library2/petsc-3.7.6/source
> --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 --download-blacs
> --download-scalapack=1 --download-mumps=1 --with-valgrind=1
> --with-valgrind-dir="[/usr/local/bin]"
> [1]PETSC ERROR: #1 User provided function() line 0 in unknown file
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1
> [2]PETSC ERROR: ------------------------------
> ------------------------------------------
> [2]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [2]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [2]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/
> documentation/faq.html#valgrind
> [2]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
> X to find memory corruption errors
> [2]PETSC ERROR: likely location of problem given in stack below
> [2]PETSC ERROR: --------------------- Stack Frames
> ------------------------------------
> [2]PETSC ERROR: Note: The EXACT line numbers in the stack are not
> available,
> [2]PETSC ERROR: INSTEAD the line number of the start of the function
> [2]PETSC ERROR: is given.
> [2]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [2]PETSC ERROR: Signal received
> [2]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [2]PETSC ERROR: Petsc Release Version 3.7.6, Apr, 24, 2017
> [2]PETSC ERROR: ./dtest on a arch-linux2-c-debug named afrah-pc by afrah
> Fri Sep 15 13:53:42 2017
> [2]PETSC ERROR: Configure options PETSC_DIR=/home/afrah/PETSc-library2/petsc-3.7.6
> PETSC_ARCH=arch-linux2-c-debug prefix=/home/afrah/PETSc-library2/petsc-3.7.6/source
> --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 --download-blacs
> --download-scalapack=1 --download-mumps=1 --with-valgrind=1
> --with-valgrind-dir="[/usr/local/bin]"
> [2]PETSC ERROR: #1 User provided function() line 0 in unknown file
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 2
> [3]PETSC ERROR: ------------------------------
> ------------------------------------------
> [3]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [3]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [3]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/
> documentation/faq.html#valgrind
> [3]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
> X to find memory corruption errors
> [3]PETSC ERROR: likely location of problem given in stack below
> [3]PETSC ERROR: --------------------- Stack Frames
> ------------------------------------
> [3]PETSC ERROR: Note: The EXACT line numbers in the stack are not
> available,
> [3]PETSC ERROR: INSTEAD the line number of the start of the function
> [3]PETSC ERROR: is given.
> [3]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [3]PETSC ERROR: Signal received
> [3]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [3]PETSC ERROR: Petsc Release Version 3.7.6, Apr, 24, 2017
> [3]PETSC ERROR: ./dtest on a arch-linux2-c-debug named afrah-pc by afrah
> Fri Sep 15 13:53:42 2017
> [3]PETSC ERROR: Configure options PETSC_DIR=/home/afrah/PETSc-library2/petsc-3.7.6
> PETSC_ARCH=arch-linux2-c-debug prefix=/home/afrah/PETSc-library2/petsc-3.7.6/source
> --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 --download-blacs
> --download-scalapack=1 --download-mumps=1 --with-valgrind=1
> --with-valgrind-dir="[/usr/local/bin]"
> [3]PETSC ERROR: #1 User provided function() line 0 in unknown file
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 3
> [4]PETSC ERROR: ------------------------------
> ------------------------------------------
> [4]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [4]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [4]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/
> documentation/faq.html#valgrind
> [4]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
> X to find memory corruption errors
> [4]PETSC ERROR: likely location of problem given in stack below
> [4]PETSC ERROR: --------------------- Stack Frames
> ------------------------------------
> [4]PETSC ERROR: Note: The EXACT line numbers in the stack are not
> available,
> [4]PETSC ERROR: INSTEAD the line number of the start of the function
> [4]PETSC ERROR: is given.
> [4]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [4]PETSC ERROR: Signal received
> [4]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [4]PETSC ERROR: Petsc Release Version 3.7.6, Apr, 24, 2017
> [4]PETSC ERROR: ./dtest on a arch-linux2-c-debug named afrah-pc by afrah
> Fri Sep 15 13:53:42 2017
> [4]PETSC ERROR: Configure options PETSC_DIR=/home/afrah/PETSc-library2/petsc-3.7.6
> PETSC_ARCH=arch-linux2-c-debug prefix=/home/afrah/PETSc-library2/petsc-3.7.6/source
> --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 --download-blacs
> --download-scalapack=1 --download-mumps=1 --with-valgrind=1
> --with-valgrind-dir="[/usr/local/bin]"
> [4]PETSC ERROR: #1 User provided function() line 0 in unknown file
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 4
> [5]PETSC ERROR: ------------------------------
> ------------------------------------------
> [5]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [5]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [5]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/
> documentation/faq.html#valgrind
> [5]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
> X to find memory corruption errors
> [5]PETSC ERROR: likely location of problem given in stack below
> [5]PETSC ERROR: --------------------- Stack Frames
> ------------------------------------
> [5]PETSC ERROR: Note: The EXACT line numbers in the stack are not
> available,
> [5]PETSC ERROR: INSTEAD the line number of the start of the function
> [5]PETSC ERROR: is given.
> [5]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [5]PETSC ERROR: Signal received
> [5]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [5]PETSC ERROR: Petsc Release Version 3.7.6, Apr, 24, 2017
> [5]PETSC ERROR: ./dtest on a arch-linux2-c-debug named afrah-pc by afrah
> Fri Sep 15 13:53:42 2017
> [5]PETSC ERROR: Configure options PETSC_DIR=/home/afrah/PETSc-library2/petsc-3.7.6
> PETSC_ARCH=arch-linux2-c-debug prefix=/home/afrah/PETSc-library2/petsc-3.7.6/source
> --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 --download-blacs
> --download-scalapack=1 --download-mumps=1 --with-valgrind=1
> --with-valgrind-dir="[/usr/local/bin]"
> [5]PETSC ERROR: #1 User provided function() line 0 in unknown file
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 5
> [6]PETSC ERROR: [7]PETSC ERROR: ------------------------------
> ------------------------------------------
> [7]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [7]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [7]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/
> documentation/faq.html#valgrind
> [7]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
> X to find memory corruption errors
> [7]PETSC ERROR: likely location of problem given in stack below
> [7]PETSC ERROR: --------------------- Stack Frames
> ------------------------------------
> [7]PETSC ERROR: Note: The EXACT line numbers in the stack are not
> available,
> [7]PETSC ERROR: INSTEAD the line number of the start of the function
> [7]PETSC ERROR: is given.
> [7]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [7]PETSC ERROR: Signal received
> [7]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [7]PETSC ERROR: Petsc Release Version 3.7.6, Apr, 24, 2017
> [7]PETSC ERROR: ./dtest on a arch-linux2-c-debug named afrah-pc by afrah
> Fri Sep 15 13:53:42 2017
> [7]PETSC ERROR: Configure options PETSC_DIR=/home/afrah/PETSc-library2/petsc-3.7.6
> PETSC_ARCH=arch-linux2-c-debug prefix=/home/afrah/PETSc-library2/petsc-3.7.6/source
> --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 --download-blacs
> --download-scalapack=1 --download-mumps=1 --with-valgrind=1
> --with-valgrind-dir="[/usr/local/bin]"
> [7]PETSC ERROR: #1 User provided function() line 0 in unknown file
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 7
> ------------------------------------------------------------------------
> [6]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [6]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [6]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/
> documentation/faq.html#valgrind
> [6]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
> X to find memory corruption errors
> [6]PETSC ERROR: likely location of problem given in stack below
> [6]PETSC ERROR: --------------------- Stack Frames
> ------------------------------------
> [6]PETSC ERROR: Note: The EXACT line numbers in the stack are not
> available,
> [6]PETSC ERROR: INSTEAD the line number of the start of the function
> [6]PETSC ERROR: is given.
> [6]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [6]PETSC ERROR: Signal received
> [6]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [6]PETSC ERROR: Petsc Release Version 3.7.6, Apr, 24, 2017
> [6]PETSC ERROR: ./dtest on a arch-linux2-c-debug named afrah-pc by afrah
> Fri Sep 15 13:53:42 2017
> [6]PETSC ERROR: Configure options PETSC_DIR=/home/afrah/PETSc-library2/petsc-3.7.6
> PETSC_ARCH=arch-linux2-c-debug prefix=/home/afrah/PETSc-library2/petsc-3.7.6/source
> --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 --download-blacs
> --download-scalapack=1 --download-mumps=1 --with-valgrind=1
> --with-valgrind-dir="[/usr/local/bin]"
> [6]PETSC ERROR: #1 User provided function() line 0 in unknown file
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 6
>
> any idea
>
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
http://www.caam.rice.edu/~mk51/
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