Segfault with psmp

Ondrej Marsalek ondrej.... at gmail.com
Tue Jan 11 14:25:23 CET 2011


I have simplified the problem further by doing a ssmp build. The arch
file can be found here:

http://marge.uochb.cas.cz/~marsalek/tmp/Linux-x86-64-intel.psmp

And the problem persists as described, regardless of the number of
OpenMP threads.

Any ideas how to get this working?

Thanks,
Ondrej


On Thu, Jan 6, 2011 at 14:04, Ondrej Marsalek <ondrej.... at gmail.com> wrote:
> Dear all,
>
> I get a segfault with a psmp build of cp2k trunk. The corresponding
> popt works. The problem occurs even when run as a single process and
> with OMP_NUM_THREADS=1. This is what it looks like to gdb:
>
> ==========
> ...
>  Spin 1
>
>  Number of electrons:                                                         17
>  Number of occupied orbitals:                                                 17
>  Number of molecular orbitals:                                                17
>
>  Spin 2
>
>  Number of electrons:                                                         16
>  Number of occupied orbitals:                                                 16
>  Number of molecular orbitals:                                                16
>
>  Number of orbital functions:                                                169
>  Number of independent orbital functions:                                    169
>
>  Extrapolation method: initial_guess
>
> Program received signal SIGSEGV, Segmentation fault.
> [Switching to Thread 0x7fffef887700 (LWP 23493)]
> __libc_free (mem=0x2020202000000001) at malloc.c:3709
> 3709    malloc.c: No such file or directory.
>        in malloc.c
> (gdb) backtrace
> #0  __libc_free (mem=0x2020202000000001) at malloc.c:3709
> #1  0x000000000257a6ec in for_deallocate ()
> #2  0x00000000016d413b in
> QS_COLLOCATE_DENSITY::L_qs_collocate_density_mp_calculate_rho_elec__917__par_region0_2_110
> ()
>    at /home/andy/build/cp2k/cp2k/makefiles/../src/qs_collocate_density.F:1163
> #3  0x0000000002634763 in L_kmp_invoke_pass_parms ()
> #4  0x00007fffffff53fc in ?? ()
> #5  0x00007fffffff53c4 in ?? ()
> #6  0x00007fffffff5380 in ?? ()
> ...
> ==========
>
> The CPU is a Core i7. The arch file and the input that triggers the
> segfault (almost immediately after start) are here:
>
> http://marge.uochb.cas.cz/~marsalek/tmp/W3-H3O-min-global.tar.gz
> http://marge.uochb.cas.cz/~marsalek/tmp/Linux-x86-64-intel.psmp
>
> The versions used for the build are:
> cp2k trunk checked out today
> OpenMPI 1.5
> Intel Compiler 11.1.073 and corresponding MKL
>
> I understand that this might be difficult or impossible to reproduce,
> but would be grateful for any suggestions as for how to try to resolve
> this.
>
> Thanks,
> Ondrej
>



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