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[Václav Šmilauer <eudoxos@xxxxxxxx>]

Ok, I found the cause by compiling without optimization:

#4  <signal handler called>
#5  0x00007f4ec5c0e800 in std::_List_base<boost::shared_ptr<Archive>, std::allocator<boost::shared_ptr<Archive> > >::_M_clear (this=0x7fffcde8adb8) at /usr/include/c++/4.4/bits/list.tcc:72
#6  0x00007f4ec5be0af1 in ~_List_base (this=0x7fffcde8adb8, __in_chrg=<value optimized out>) at /usr/include/c++/4.4/bits/stl_list.h:360
#7  0x00007f4ec5bbbb08 in ~list (this=0x7fffcde8adb8, __in_chrg=<value optimized out>) at /usr/include/c++/4.4/bits/stl_list.h:418
#8  0x00007f4ec5bbbc0b in ~Serializable (this=0x7fffcde8adb0, __in_chrg=<value optimized out>) at /home/vaclav/yade/build-trunk-dbg/include/yade-trunk/yade/lib-serialization/Serializable.hpp:261
#9  0x00007f4ec5bb2ad8 in ~Shape (this=0x7fffcde8adb0, __in_chrg=<value optimized out>) at /home/vaclav/yade/trunk/core/Shape.cpp:2
#10 0x00007f4eb614c6e2 in ~Sphere (this=0x7fffcde8adb0, __in_chrg=<value optimized out>) at pkg/common/DataClass/Shape/Sphere.cpp:13
#11 0x00007f4ea43ea258 in InsertGenerator3D::seedParticles (this=0x327bee0, vol=0x313daa0, ntable=0x313dbb0, gid=0, tag=0) at ../src/InsertGenerator3D.cc:200
[...]

Now relevant part of code at InsertGenerator3D.cc is

     Sphere S(Vec3(px,py,pz),r);
     /* stuff that is not important */
     // line 200 is here
}

It means that the crash happens (line 200) when scope is being left.
Destructor for the S object (of type Sphere) is called. But:

  #10 0x00007f4eb614c6e2 in ~Sphere (this=0x7fffcde8adb0,
__in_chrg=<value optimized out>) at
pkg/common/DataClass/Shape/Sphere.cpp:13

Dtor of _yade's_ Sphere is called instead, leading obviously to crash!

There seems to be no way to avoid that, as we have to load libs with
RTLD_GLOBAL (see py/__init__.py.in for comment on that); that also means
that even if new module (gengeo) is loaded, already existing symbol for
~Sphere will be used.

Proper solution would be to put all yade classes inside yade::
namespace, avoiding the clash. It works if done for Sphere only (hack).
I will commit that soon.

-- 
genCylLSM.py calls a crash
https://bugs.launchpad.net/bugs/528509
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Status in Yet Another Dynamic Engine: New

Bug description:
It seems, that the function packer.generatePacking () calls a crash.

.....
InsertGenerator3D::seedParticles
bbx: -25 -25 -25 - 25 25 225
SIGSEGV/SIGABRT handler called; gdb batch file is `/tmp/yade-7ZdmxQ/tmp-0'
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[Thread debugging using libthread_db enabled]
[New Thread 0x7fe71a8e4910 (LWP 30782)]
[New Thread 0x7fe71c1c4910 (LWP 30781)]
[New Thread 0x7fe71c9c5910 (LWP 30780)]
0x00007fe73308db4d in __libc_waitpid (pid=30783, stat_loc=<value optimized out>, 
    options=0) at ../sysdeps/unix/sysv/linux/waitpid.c:41
41	../sysdeps/unix/sysv/linux/waitpid.c: No such file or directory.
	in ../sysdeps/unix/sysv/linux/waitpid.c
No symbol "info" in current context.

Thread 4 (Thread 0x7fe71c9c5910 (LWP 30780)):
#0  sem_wait () at ../nptl/sysdeps/unix/sysv/linux/x86_64/sem_wait.S:85
#1  0x00000000004cd598 in PyThread_acquire_lock (lock=0x23f3710, waitflag=128) at ../Python/thread_pthread.h:349
#2  0x000000000049c85a in PyEval_AcquireThread (tstate=0x2b41c50) at ../Python/ceval.c:253
#3  0x00000000004d0bdc in t_bootstrap (boot_raw=0x2a86e20) at ../Modules/threadmodule.c:424
#4  0x00007fe733c01a04 in start_thread (arg=<value optimized out>) at pthread_create.c:300
#5  0x00007fe7330c980d in clone () at ../sysdeps/unix/sysv/linux/x86_64/clone.S:112
#6  0x0000000000000000 in ?? ()