[petsc-users] Segmentation violation

Tue Oct 30 12:42:57 CDT 2018

   Can you run the code on the "failing" machine using valgrind? https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind

  Barry

> On Oct 30, 2018, at 12:10 PM, Santiago Andres Triana via petsc-users <petsc-users at mcs.anl.gov> wrote:
> 
> Hi petsc-users,
> 
> I am solving a generalized eigenvalue problem using ex7 in $SLEPC_DIR/src/eps/examples/tutorials/. I provide the A and B matrices.
> The program runs fine, with correct solutions on 12-core node and also on a mac laptop.
> 
> However, on a 16-core workstation running Debian testing (fresh install) and also a fresh install of petsc and slepc I get the following error:
> 
>  $ mpiexec -n 2 ./ex7 -f1 A.petsc -f2 B.petsc -st_type sinvert -eps_nev 4 -eps_target -2e-3+1.01i
> 
> Generalized eigenproblem stored in file.
> 
>  Reading COMPLEX matrices from binary files...
> [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: [1] MatFactorNumeric_MUMPS line 1205 /home/spin2/petsc-3.10.2/src/mat/impls/aij/mpi/mumps/mumps.c
> [1]PETSC ERROR: [1] MatLUFactorNumeric line 3054 /home/spin2/petsc-3.10.2/src/mat/interface/matrix.c
> [1]PETSC ERROR: [1] PCSetUp_LU line 59 /home/spin2/petsc-3.10.2/src/ksp/pc/impls/factor/lu/lu.c
> [1]PETSC ERROR: [1] PCSetUp line 894 /home/spin2/petsc-3.10.2/src/ksp/pc/interface/precon.c
> [1]PETSC ERROR: [1] KSPSetUp line 304 /home/spin2/petsc-3.10.2/src/ksp/ksp/interface/itfunc.c
> [1]PETSC ERROR: [1] STSetUp_Sinvert line 96 /home/spin2/slepc-3.10.1/src/sys/classes/st/impls/sinvert/sinvert.c
> [1]PETSC ERROR: [1] STSetUp line 233 /home/spin2/slepc-3.10.1/src/sys/classes/st/interface/stsolve.c
> [1]PETSC ERROR: [1] EPSSetUp line 104 /home/spin2/slepc-3.10.1/src/eps/interface/epssetup.c
> [1]PETSC ERROR: [1] EPSSolve line 129 /home/spin2/slepc-3.10.1/src/eps/interface/epssolve.c
> [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 3.10.2, Oct, 09, 2018 
> [1]PETSC ERROR: ./ex7 on a arch-linux2-c-opt named wobble-wkst-as by spin2 Tue Oct 30 17:40:51 2018
> [1]PETSC ERROR: Configure options --download-mpich -with-scalar-type=complex --download-mumps --download-parmetis --download-metis --download-scalapack --download-fblaslapack --with-debugging=1 --download-superlu_dist --download-ptscotch
> [1]PETSC ERROR: #1 User provided function() line 0 in  unknown file
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1
> 
> 
> 
> the expected output is the following (on a compute node running petsc-3.9.2 and also on a mac laptop running petsc-3.10.2):
> 
> $ mpiexec -n 2 ./ex7 -f1 A.petsc -f2 B.petsc -st_type sinvert -eps_nev 4 -eps_target -2e-3+1.01i
> 
> Generalized eigenproblem stored in file.
> 
>  Reading COMPLEX matrices from binary files...
>  Number of iterations of the method: 2
>  Number of linear iterations of the method: 27
>  Solution method: krylovschur
> 
>  Number of requested eigenvalues: 4
>  Stopping condition: tol=1e-08, maxit=63157
>  Linear eigensolve converged (4 eigenpairs) due to CONVERGED_TOL; iterations 2
>  ---------------------- --------------------
>             k             ||Ax-kBx||/||kx||
>  ---------------------- --------------------
>   -0.002806+1.009827i       2.00821e-19
>   -0.002980+1.008417i       8.08359e-17
>   -0.002676+1.011755i       9.49342e-18
>   -0.003201+1.007367i       1.50869e-16
>  ---------------------- --------------------
> 
> 
> Just in case, the matrices can be downloaded from here if any one wants to give them a try
> https://www.dropbox.com/s/ejpa9owkv8tjnwi/A.petsc?dl=0
> https://www.dropbox.com/s/urjtxaezl0cv3om/B.petsc?dl=0
> 
> 
> I tried different petsc/slepc versions to no avail, including an OS reinstall. So any help would be highly appreciated. Thanks in advance!
> 
> Santiago