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 <[email protected]> wrote: > On Fri, Sep 15, 2017 at 7:00 AM, Afrah Najib <[email protected]> > 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/ >
