[petsc-users] Segmentation violation

Tue Oct 30 12:10:59 CDT 2018

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
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