[petsc-users] Valgrind unhandled instruction

Wed May 21 16:48:51 CDT 2014

Hello

With petsc-dev I get the following error with my own code and also with 
ex56 as shown below. Both run fine otherwise. This is with Valgrind 3.7 
(in Debian stable).

Is this a PETSc or Valgrind issue?

T

stali at i5:~/petsc-dev/src/ksp/ksp/examples/tutorials$ valgrind ./ex56 -ne 
9 -alpha 1.e-3 -pc_type gamg -pc_gamg_type agg -pc_gamg_agg_nsmooths 1 
-pc_gamg_coarse_eq_limit 10 -pc_gamg_reuse_interpolation true 
-two_solves -ksp_monitor_short -use_mat_nearnullspace
==16123== Memcheck, a memory error detector
==16123== Copyright (C) 2002-2011, and GNU GPL'd, by Julian Seward et al.
==16123== Using Valgrind-3.7.0 and LibVEX; rerun with -h for copyright info
==16123== Command: ./ex56 -ne 9 -alpha 1.e-3 -pc_type gamg -pc_gamg_type 
agg -pc_gamg_agg_nsmooths 1 -pc_gamg_coarse_eq_limit 10 
-pc_gamg_reuse_interpolation true -two_solves -ksp_monitor_short 
-use_mat_nearnullspace
==16123==
vex x86->IR: unhandled instruction bytes: 0x66 0xF 0x38 0x39
==16123== valgrind: Unrecognised instruction at address 0x4228928.
==16123==    at 0x4228928: ISCreateGeneral_Private (in 
/home/stali/petsc-dev/arch-linux2-c-debug/lib/libpetsc.so.3.04.4)
==16123==    by 0x4228D54: ISGeneralSetIndices_General (in 
/home/stali/petsc-dev/arch-linux2-c-debug/lib/libpetsc.so.3.04.4)
==16123==    by 0x4229504: ISGeneralSetIndices (in 
/home/stali/petsc-dev/arch-linux2-c-debug/lib/libpetsc.so.3.04.4)
==16123==    by 0x422976F: ISCreateGeneral (in 
/home/stali/petsc-dev/arch-linux2-c-debug/lib/libpetsc.so.3.04.4)
==16123==    by 0x4A94CAA: PCGAMGCoarsen_AGG (in 
/home/stali/petsc-dev/arch-linux2-c-debug/lib/libpetsc.so.3.04.4)
==16123==    by 0x4A84FD6: PCSetUp_GAMG (in 
/home/stali/petsc-dev/arch-linux2-c-debug/lib/libpetsc.so.3.04.4)
==16123==    by 0x49E8163: PCSetUp (in 
/home/stali/petsc-dev/arch-linux2-c-debug/lib/libpetsc.so.3.04.4)
==16123==    by 0x4AE6023: KSPSetUp (in 
/home/stali/petsc-dev/arch-linux2-c-debug/lib/libpetsc.so.3.04.4)
==16123==    by 0x804C7D6: main (in 
/home/stali/petsc-dev/src/ksp/ksp/examples/tutorials/ex56)
==16123== Your program just tried to execute an instruction that Valgrind
==16123== did not recognise.  There are two possible reasons for this.
==16123== 1. Your program has a bug and erroneously jumped to a non-code
==16123==    location.  If you are running Memcheck and you just saw a
==16123==    warning about a bad jump, it's probably your program's fault.
==16123== 2. The instruction is legitimate but Valgrind doesn't handle it,
==16123==    i.e. it's Valgrind's fault.  If you think this is the case or
==16123==    you are not sure, please let us know and we'll try to fix it.
==16123== Either way, Valgrind will now raise a SIGILL signal which will
==16123== probably kill your program.
[0]PETSC ERROR: 
------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 4 Illegal instruction: Likely due 
to memory corruption
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see 
http://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] ISCreateGeneral_Private line 575 
/home/stali/petsc-dev/src/vec/is/is/impls/general/general.c
[0]PETSC ERROR: [0] ISGeneralSetIndices_General line 674 
/home/stali/petsc-dev/src/vec/is/is/impls/general/general.c
[0]PETSC ERROR: [0] ISGeneralSetIndices line 662 
/home/stali/petsc-dev/src/vec/is/is/impls/general/general.c
[0]PETSC ERROR: [0] ISCreateGeneral line 631 
/home/stali/petsc-dev/src/vec/is/is/impls/general/general.c
[0]PETSC ERROR: [0] PCGAMGCoarsen_AGG line 976 
/home/stali/petsc-dev/src/ksp/pc/impls/gamg/agg.c
[0]PETSC ERROR: [0] PCSetUp_GAMG line 487 
/home/stali/petsc-dev/src/ksp/pc/impls/gamg/gamg.c
[0]PETSC ERROR: [0] KSPSetUp line 219 
/home/stali/petsc-dev/src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: --------------------- Error Message 
--------------------------------------------------------------
[0]PETSC ERROR: Signal received
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html 
for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.4.4-4344-ge0d8a6f  
GIT Date: 2014-05-21 16:02:44 -0500
[0]PETSC ERROR: ./ex56 on a arch-linux2-c-debug named i5 by stali Wed 
May 21 16:41:07 2014
[0]PETSC ERROR: Configure options --with-fc=gfortran --with-cc=gcc 
--download-mpich --with-metis=1 --download-metis=1 --COPTFLAGS="-O3 
-march=native" --FOPTFLAGS="-O3 -march=native" --with-shared-libraries 
--with-debugging=1
[0]PETSC ERROR: #1 User provided function() line 0 in  unknown file
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
==16123==
==16123== HEAP SUMMARY:
==16123==     in use at exit: 4,627,684 bytes in 1,188 blocks
==16123==   total heap usage: 1,649 allocs, 461 frees, 6,073,192 bytes 
allocated
==16123==
==16123== LEAK SUMMARY:
==16123==    definitely lost: 0 bytes in 0 blocks
==16123==    indirectly lost: 0 bytes in 0 blocks
==16123==      possibly lost: 0 bytes in 0 blocks
==16123==    still reachable: 4,627,684 bytes in 1,188 blocks
==16123==         suppressed: 0 bytes in 0 blocks
==16123== Rerun with --leak-check=full to see details of leaked memory
==16123==
==16123== For counts of detected and suppressed errors, rerun with: -v
==16123== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 61 from 8)