[petsc-users] PDSLin 2.0.0 example memory corruption error
Afrah Najib
afrah.nacib at gmail.com
Fri Sep 15 06:00:36 CDT 2017
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:
:~/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
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