[petsc-users] PDSLin 2.0.0 example memory corruption error
Xiaoye S. Li
xsli at lbl.gov
Sun Sep 17 19:42:26 CDT 2017
This looks like error from ParMETIS -- some processes do not have initial
vertices.
Which version of PerMETIS are you using?
There may be error in the way you run the test:
$ mpiexec -n 8 ./dtest input matrices/U.dat
Try to remove "input" in the command line.
Can also try using smaller number of processes, e.g.:
$ mpiexec -n 2 ./dtest matrices/U.dat
Sherry Li
On Fri, Sep 15, 2017 at 5:01 AM, Matthew Knepley <knepley at gmail.com> wrote:
> 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/d
>> ocumentation/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/d
>> ocumentation/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/d
>> ocumentation/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/d
>> ocumentation/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/d
>> ocumentation/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/d
>> ocumentation/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/d
>> ocumentation/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/d
>> ocumentation/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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