[petsc-users] killed 9 signal after upgrade from petsc 3.9.4 to 3.12.2

[Matthew Knepley]

On Mon, Dec 23, 2019 at 3:14 PM Santiago Andres Triana <repepo at gmail.com>
wrote:

> Dear all,
>
> After upgrading to petsc 3.12.2 my solver program crashes consistently.
> Before the upgrade I was using petsc 3.9.4 with no problems.
>
> My application deals with a complex-valued, generalized eigenvalue
> problem. The matrices involved are relatively large, typically 2 to 10 Gb
> in size, which is no problem for petsc 3.9.4.
>

Are you sure that your indices do not exceed 4B? If so, you need to
configure using

  --with-64-bit-indices

Also, it would be nice if you ran with the debugger so we can get a stack
trace for the SEGV.

  Thanks,

    Matt


> However, after the upgrade I can only obtain solutions when the matrices
> are small, the solver crashes when the matrices' size exceed about 1.5 Gb:
>
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the
> batch system) has told this process to end
> [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: configure using --with-debugging=yes, recompile, link, and
> run
> [0]PETSC ERROR: to get more information on the crash.
>
> and so on for each cpu.
>
>
> I tried using valgrind and this is the typical output:
>
> ==2874== Conditional jump or move depends on uninitialised value(s)
> ==2874==    at 0x4018178: index (in /lib64/ld-2.22.so)
> ==2874==    by 0x400752D: expand_dynamic_string_token (in /lib64/
> ld-2.22.so)
> ==2874==    by 0x4008009: _dl_map_object (in /lib64/ld-2.22.so)
> ==2874==    by 0x40013E4: map_doit (in /lib64/ld-2.22.so)
> ==2874==    by 0x400EA53: _dl_catch_error (in /lib64/ld-2.22.so)
> ==2874==    by 0x4000ABE: do_preload (in /lib64/ld-2.22.so)
> ==2874==    by 0x4000EC0: handle_ld_preload (in /lib64/ld-2.22.so)
> ==2874==    by 0x40034F0: dl_main (in /lib64/ld-2.22.so)
> ==2874==    by 0x4016274: _dl_sysdep_start (in /lib64/ld-2.22.so)
> ==2874==    by 0x4004A99: _dl_start (in /lib64/ld-2.22.so)
> ==2874==    by 0x40011F7: ??? (in /lib64/ld-2.22.so)
> ==2874==    by 0x12: ???
> ==2874==
>
>
> These are my configuration options. Identical for both petsc 3.9.4 and
> 3.12.2:
>
> ./configure --with-scalar-type=complex --download-mumps
> --download-parmetis --download-metis --download-scalapack=1
> --download-fblaslapack=1 --with-debugging=0 --download-superlu_dist=1
> --download-ptscotch=1 CXXOPTFLAGS='-O3 -march=native' FOPTFLAGS='-O3
> -march=native' COPTFLAGS='-O3 -march=native'
>
>
> Thanks in advance for any comments or ideas!
>
> Cheers,
> Santiago
>


-- 
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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