[petsc-users] HYPRE AMS - Segmentation Violation with discrete gradient
Matthew Knepley
knepley at gmail.com
Mon Jan 24 16:02:07 CST 2022
On Mon, Jan 24, 2022 at 4:42 PM Matthew Knepley <knepley at gmail.com> wrote:
> Okay, I can run your example and get an error. I am looking at it. Not
> sure if it is us or Hypre yet.
>
This is failing inside Hypre. It appears that the A_diag offset array does
not match the matrix. Are you giving Hypre
a rectangular matrix? If so, it appears that the code cannot handle it and
accidentally indexes out of the array.
Thanks,
Matt
> Thanks,
>
> Matt
>
> On Mon, Jan 24, 2022 at 12:39 PM Nicolas Alejandro Barnafi <
> nicolas.barnafi at unimi.it> wrote:
>
>> Please let me know if you were able to run the example (or anyone else).
>> Thanks for the help.
>> Kind regards
>>
>> Il 21/01/22 18:05, *"Nicolas Alejandro Barnafi" * <
>> nicolas.barnafi at unimi.it> ha scritto:
>>
>> Thank you Matt, I have trimmed down ex10 (a lot) to do as required, and
>> it indeed reproduces the error.
>> You may find it attached and it can be reproduced with
>> ./ex10 -fA Amat -fP Pmat -fG Gmat -ksp_type gmres -pc_type hypre
>> -pc_hypre_type ams
>>
>> Thank you!
>>
>> Il 21/01/22 16:35, *Matthew Knepley * <knepley at gmail.com> ha scritto:
>>
>> On Fri, Jan 21, 2022 at 9:50 AM Nicolas Alejandro Barnafi <
>> nicolas.barnafi at unimi.it> wrote:
>>
>>> Dear community,
>>>
>>> I'm giving the discrete gradient to a PC object (sub PC of a fieldsplit)
>>> but HYPRE internally gives a segmentation violation error. The matrix has
>>> been adequately set, as I have added it to the program output for
>>> inspection. Has this happened to anyone?
>>>
>>
>> Is there a chance of sending us something that we can run? Alternatively,
>> can you run
>>
>> https://gitlab.com/petsc/petsc/-/blob/main/src/ksp/ksp/tutorials/ex10.c
>>
>> loading your matrix and giving options to select Hypre? Then we can do
>> the same thing here with your matrix.
>>
>> Thanks,
>>
>> Matt
>>
>> I have attached the error below together with the discrete gradient, in
>>> case you see something I am missing.
>>>
>>> The code is currently running in serial, so I don't expect
>>> communication/partitioning to be an issue (although it could be in the
>>> future).
>>>
>>> Thanks in advance,
>>> Nicolas
>>>
>>>
>>> ------------------------------ PETSc output
>>> ------------------------------------
>>>
>>> Mat Object: 1 MPI processes
>>> type: seqaij
>>> -1.00000e+00 1.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
>>> 0.00000e+00 0.00000e+00 0.00000e+00
>>> 1.00000e+00 0.00000e+00 -1.00000e+00 0.00000e+00 0.00000e+00
>>> 0.00000e+00 0.00000e+00 0.00000e+00
>>> -1.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 1.00000e+00
>>> 0.00000e+00 0.00000e+00 0.00000e+00
>>> 0.00000e+00 -1.00000e+00 0.00000e+00 1.00000e+00 0.00000e+00
>>> 0.00000e+00 0.00000e+00 0.00000e+00
>>> 0.00000e+00 1.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
>>> -1.00000e+00 0.00000e+00 0.00000e+00
>>> 0.00000e+00 0.00000e+00 1.00000e+00 -1.00000e+00 0.00000e+00
>>> 0.00000e+00 0.00000e+00 0.00000e+00
>>> 0.00000e+00 0.00000e+00 1.00000e+00 0.00000e+00 0.00000e+00
>>> 0.00000e+00 -1.00000e+00 0.00000e+00
>>> 0.00000e+00 0.00000e+00 0.00000e+00 -1.00000e+00 0.00000e+00
>>> 0.00000e+00 0.00000e+00 1.00000e+00
>>> 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 1.00000e+00
>>> -1.00000e+00 0.00000e+00 0.00000e+00
>>> 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 -1.00000e+00
>>> 0.00000e+00 1.00000e+00 0.00000e+00
>>> 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
>>> 1.00000e+00 0.00000e+00 -1.00000e+00
>>> 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
>>> 0.00000e+00 -1.00000e+00 1.00000e+00
>>> [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
>>> https://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: [0] jac->setup line 408
>>> /home/ubuntu/petsc/src/ksp/pc/impls/hypre/hypre.c
>>> [0]PETSC ERROR: [0] PCSetUp_HYPRE line 223
>>> /home/ubuntu/petsc/src/ksp/pc/impls/hypre/hypre.c
>>> [0]PETSC ERROR: [0] PCSetUp line 971
>>> /home/ubuntu/petsc/src/ksp/pc/interface/precon.c
>>> [0]PETSC ERROR: [0] KSPSetUp line 319
>>> /home/ubuntu/petsc/src/ksp/ksp/interface/itfunc.c
>>> [0]PETSC ERROR: [0] KSPSolve_Private line 615
>>> /home/ubuntu/petsc/src/ksp/ksp/interface/itfunc.c
>>> [0]PETSC ERROR: [0] KSPSolve line 884
>>> /home/ubuntu/petsc/src/ksp/ksp/interface/itfunc.c
>>> [0]PETSC ERROR: [0] PCApply_FieldSplit line 1241
>>> /home/ubuntu/petsc/src/ksp/pc/impls/fieldsplit/fieldsplit.c
>>> [0]PETSC ERROR: [0] PCApply line 426
>>> /home/ubuntu/petsc/src/ksp/pc/interface/precon.c
>>> [0]PETSC ERROR: [0] KSP_PCApply line 281
>>> /home/ubuntu/petsc/include/petsc/private/kspimpl.h
>>> [0]PETSC ERROR: [0] KSPInitialResidual line 40
>>> /home/ubuntu/petsc/src/ksp/ksp/interface/itres.c
>>> [0]PETSC ERROR: [0] KSPSolve_GMRES line 233
>>> /home/ubuntu/petsc/src/ksp/ksp/impls/gmres/gmres.c
>>> [0]PETSC ERROR: [0] KSPSolve_Private line 615
>>> /home/ubuntu/petsc/src/ksp/ksp/interface/itfunc.c
>>> [0]PETSC ERROR: [0] KSPSolve line 884
>>> /home/ubuntu/petsc/src/ksp/ksp/interface/itfunc.c
>>> [0]PETSC ERROR: --------------------- Error Message
>>> --------------------------------------------------------------
>>> [0]PETSC ERROR: Signal received
>>> [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html
>>> for trouble shooting.
>>> [0]PETSC ERROR: Petsc Release Version 3.14.6, unknown
>>> [0]PETSC ERROR: Unknown Name on a arch-linux-c-debug named
>>> ubuntu-ThinkPad-L14-Gen-1 by ubuntu Fri Jan 21 15:37:45 2022
>>> [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
>>> --with-fc=gfortran --download-mpich --download-fblaslapack --with-mpi=1
>>> --download-superlu_dist --download-mumps --download-hypre
>>> --with-debugging=1 COPTFLAGS="-O3 -march=native -mtune=native"
>>> CXXOPTFLAGS="-O3 -march=native -mtune=native" FOPTFLAGS="-O3 -march=native
>>> -mtune=native" --download-scalapack --download-hpddm
>>> [0]PETSC ERROR: #1 User provided function() line 0 in unknown file
>>> [0]PETSC ERROR: Checking the memory for corruption.
>>> application called MPI_Abort(MPI_COMM_WORLD, 50176059) - process 0
>>> [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=50176059
>>> :
>>> system msg for write_line failure : Bad file descriptor
>>>
>>
>>
>> --
>> 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
>>
>> https://www.cse.buffalo.edu/~knepley/
>> <http://www.cse.buffalo.edu/~knepley/>
>>
>>
>
> --
> 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
>
> https://www.cse.buffalo.edu/~knepley/
> <http://www.cse.buffalo.edu/~knepley/>
>
--
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
https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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