Segfault with psmp

Ondrej Marsalek ondrej.... at gmail.com
Thu Jan 6 14:04:59 CET 2011


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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