It seems, that I had to enable dumping in /etc/security/limits.conf .
Running  with "ntop - u ntop" I could get a corefile in about 1 h again.

# gdb ntop core.14541
GNU gdb (GDB) 7.0.1-debian
Copyright (C) 2009 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html
>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "i486-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /usr/local/bin/ntop...done.
[New Thread 14546]
[New Thread 14547]
[New Thread 14548]
[New Thread 14551]
[New Thread 14552]
[New Thread 14553]
[New Thread 14541]
[New Thread 14543]
[New Thread 14544]
[New Thread 14549]
[New Thread 14550]

warning: Can't read pathname for load map: Eingabe-/Ausgabefehler.
Reading symbols from /usr/local/lib/libntopreport-4.0.3.so...done.
Loaded symbols for /usr/local/lib/libntopreport-4.0.3.so

[cut]

Reading symbols from /usr/local/lib/ntop/plugins/netflowPlugin.so...done.
Loaded symbols for /usr/local/lib/ntop/plugins/netflowPlugin.so
Reading symbols from /usr/local/lib/ntop/plugins/cpacketPlugin.so...done.
Loaded symbols for /usr/local/lib/ntop/plugins/cpacketPlugin.so
Reading symbols from /usr/local/lib/ntop/plugins/icmpPlugin.so...done.
Loaded symbols for /usr/local/lib/ntop/plugins/icmpPlugin.so
Reading symbols from /usr/local/lib/ntop/plugins/sflowPlugin.so...done.
Loaded symbols for /usr/local/lib/ntop/plugins/sflowPlugin.so
Reading symbols from /usr/local/lib/ntop/plugins/rrdPlugin.so...done.
Loaded symbols for /usr/local/lib/ntop/plugins/rrdPlugin.so
Reading symbols from /lib/i686/cmov/libnss_dns.so.2...(no debugging symbols
found)...done.
Loaded symbols for /lib/i686/cmov/libnss_dns.so.2
Reading symbols from /lib/i686/cmov/libresolv.so.2...(no debugging symbols
found)...done.
Loaded symbols for /lib/i686/cmov/libresolv.so.2
Reading symbols from /lib/libgcc_s.so.1...(no debugging symbols
found)...done.
Loaded symbols for /lib/libgcc_s.so.1
Core was generated by `ntop -u ntop'.
Program terminated with signal 6, Aborted.
#0  0xb76ef424 in __kernel_vsyscall ()

I am not familiar with debugging. Does this help?
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