[petsc-users] HYPRE AMS - Segmentation Violation with discrete gradient

Fri Jan 21 08:50:17 CST 2022

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? 

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20220121/6fe02c6d/attachment.html>