[petsc-users] Segmentation violation
Santiago Andres Triana
repepo at gmail.com
Wed Oct 31 04:05:31 CDT 2018
Hi Hong,
You can find the matrices here:
https://www.dropbox.com/s/ejpa9owkv8tjnwi/A.petsc?dl=0
https://www.dropbox.com/s/urjtxaezl0cv3om/B.petsc?dl=0
Changing the target value leads to the same error. What is strange is that
this works without a problem on two other machines. But in my main
workstation (the one I use for developing and testing) it fails :(
Thanks so much for your help!
Santiago
On Wed, Oct 31, 2018 at 2:48 AM Zhang, Hong <hzhang at mcs.anl.gov> wrote:
> Santiago,
> The shift '-eps_target -2e-3+1.01i' is very close to the eigenvalues. What
> happens if you pick a target little away from your eigenvalues?
> I suspect mumps encounters a zero pivot during numerical factorization.
> There are options to handle it, but I need matrices A and B to investigate.
> I am not sure if the problem comes from memory bug.
> Anyway, I'm cc'ing mumps developers here.
>
> Hong
>
> On Tue, Oct 30, 2018 at 8:09 PM Smith, Barry F. via petsc-users <
> petsc-users at mcs.anl.gov> wrote:
>
>>
>> Yeah this doesn't look good for MUMPS but isn't for sure the problem
>> either.
>>
>> The valgrind output should be sent to the MUMPS developers.
>>
>> Hong,
>>
>> Can you send this to the MUMPS developers and see what they say?
>>
>> Thanks
>>
>> Barry
>>
>>
>> > On Oct 30, 2018, at 2:04 PM, Santiago Andres Triana <repepo at gmail.com>
>> wrote:
>> >
>> > This is the output of
>> > mpiexec -n 2 valgrind --tool=memcheck -q --num-callers=20
>> --log-file=valgrind.log.%p ./ex7 -malloc off -f1 A.petsc -f2 B.petsc
>> -eps_nev 4 -eps_target -2e-3+1.01i -st_type sinvert
>> >
>> > 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 19:42:18 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
>> >
>> >
>> >
>> > and one of the two valgrind logs (the other was empty):
>> >
>> > ==63004== Use of uninitialised value of size 8
>> > ==63004== at 0x694F8FF: zmumps_redistribution_
>> (zfac_distrib_distentry.F:367)
>> > ==63004== by 0x68E1266: zmumps_fac_driver_ (zfac_driver.F:1777)
>> > ==63004== by 0x6869F63: zmumps_ (zmumps_driver.F:1686)
>> > ==63004== by 0x6861B64: zmumps_f77_ (zmumps_f77.F:267)
>> > ==63004== by 0x685FB43: zmumps_c (mumps_c.c:417)
>> > ==63004== by 0x5B741CD: MatFactorNumeric_MUMPS (mumps.c:1227)
>> > ==63004== by 0x53C3DDB: MatLUFactorNumeric (matrix.c:3065)
>> > ==63004== by 0x626E652: PCSetUp_LU (lu.c:131)
>> > ==63004== by 0x6387B8D: PCSetUp (precon.c:932)
>> > ==63004== by 0x649CD41: KSPSetUp (itfunc.c:391)
>> > ==63004== by 0x4A0E3F7: STSetUp_Sinvert (sinvert.c:132)
>> > ==63004== by 0x4A4033F: STSetUp (stsolve.c:271)
>> > ==63004== by 0x4B586FB: EPSSetUp (epssetup.c:263)
>> > ==63004== by 0x4B5D43A: EPSSolve (epssolve.c:135)
>> > ==63004== by 0x10B6FD: main (ex7.c:134)
>> > ==63004==
>> > ==63004== Invalid read of size 4
>> > ==63004== at 0x694F8FF: zmumps_redistribution_
>> (zfac_distrib_distentry.F:367)
>> > ==63004== by 0x68E1266: zmumps_fac_driver_ (zfac_driver.F:1777)
>> > ==63004== by 0x6869F63: zmumps_ (zmumps_driver.F:1686)
>> > ==63004== by 0x6861B64: zmumps_f77_ (zmumps_f77.F:267)
>> > ==63004== by 0x685FB43: zmumps_c (mumps_c.c:417)
>> > ==63004== by 0x5B741CD: MatFactorNumeric_MUMPS (mumps.c:1227)
>> > ==63004== by 0x53C3DDB: MatLUFactorNumeric (matrix.c:3065)
>> > ==63004== by 0x626E652: PCSetUp_LU (lu.c:131)
>> > ==63004== by 0x6387B8D: PCSetUp (precon.c:932)
>> > ==63004== by 0x649CD41: KSPSetUp (itfunc.c:391)
>> > ==63004== by 0x4A0E3F7: STSetUp_Sinvert (sinvert.c:132)
>> > ==63004== by 0x4A4033F: STSetUp (stsolve.c:271)
>> > ==63004== by 0x4B586FB: EPSSetUp (epssetup.c:263)
>> > ==63004== by 0x4B5D43A: EPSSolve (epssolve.c:135)
>> > ==63004== by 0x10B6FD: main (ex7.c:134)
>> > ==63004== Address 0xe5ffda3101296ca0 is not stack'd, malloc'd or
>> (recently) free'd
>> > ==63004==
>> >
>> >
>> > Hope it gives enough info. Thanks!
>> >
>> >
>> >
>> > On Tue, Oct 30, 2018 at 6:50 PM Smith, Barry F. <bsmith at mcs.anl.gov>
>> wrote:
>> >
>> > 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
>> >
>>
>>
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